Toward Millions of File System IOPS on Low-Cost, Commodity Hardware

PubMed Central

Zheng, Da; Burns, Randal; Szalay, Alexander S.

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads. PMID:24402052

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware.

PubMed

Zheng, Da; Burns, Randal; Szalay, Alexander S

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads.

X-LUNA: Extending Free/Open Source Real Time Executive for On-Board Space Applications

NASA Astrophysics Data System (ADS)

Braga, P.; Henriques, L.; Zulianello, M.

2008-08-01

In this paper we present xLuna, a system based on the RTEMS [1] Real-Time Operating System that is able to run on demand a GNU/Linux Operating System [2] as RTEMS' lowest priority task. Linux runs in user-mode and in a different memory partition. This allows running Hard Real-Time tasks and Linux applications on the same system sharing the Hardware resources while keeping a safe isolation and the Real-Time characteristics of RTEMS. Communication between both Systems is possible through a loose coupled mechanism based on message queues. Currently only SPARC LEON2 processor with Memory Management Unit (MMU) is supported. The advantage in having two isolated systems is that non critical components are quickly developed or simply ported reducing time-to-market and budget.

MAPA: Implementation of the Standard Interchange Format and use for analyzing lattices

NASA Astrophysics Data System (ADS)

Shasharina, Svetlana G.; Cary, John R.

1997-05-01

MAPA (Modular Accelerator Physics Analysis) is an object oriented application for accelerator design and analysis with a Motif based graphical user interface. MAPA has been ported to AIX, Linux, HPUX, Solaris, and IRIX. MAPA provides an intuitive environment for accelerator study and design. The user can bring up windows for fully nonlinear analysis of accelerator lattices in any number of dimensions. The current graphical analysis methods of Lifetime plots and Surfaces of Section have been used to analyze the improved lattice designs of Wan, Cary, and Shasharina (this conference). MAPA can now read and write Standard Interchange Format (MAD) accelerator description files and it has a general graphical user interface for adding, changing, and deleting elements. MAPA's consistency checks prevent deletion of used elements and prevent creation of recursive beam lines. Plans include development of a richer set of modeling tools and the ability to invoke existing modeling codes through the MAPA interface. MAPA will be demonstrated on a Pentium 150 laptop running Linux.

HEP Computing

Science.gov Websites

Service Request Password Help New Users Back to HEP Computing Mail-Migration Procedure on Linux Mail -Migration Procedure on Windows How to Migrate a Folder to GMail using Pine U.S. Department of Energy The

Development of a portable Linux-based ECG measurement and monitoring system.

PubMed

Tan, Tan-Hsu; Chang, Ching-Su; Huang, Yung-Fa; Chen, Yung-Fu; Lee, Cheng

2011-08-01

This work presents a portable Linux-based electrocardiogram (ECG) signals measurement and monitoring system. The proposed system consists of an ECG front end and an embedded Linux platform (ELP). The ECG front end digitizes 12-lead ECG signals acquired from electrodes and then delivers them to the ELP via a universal serial bus (USB) interface for storage, signal processing, and graphic display. The proposed system can be installed anywhere (e.g., offices, homes, healthcare centers and ambulances) to allow people to self-monitor their health conditions at any time. The proposed system also enables remote diagnosis via Internet. Additionally, the system has a 7-in. interactive TFT-LCD touch screen that enables users to execute various functions, such as scaling a single-lead or multiple-lead ECG waveforms. The effectiveness of the proposed system was verified by using a commercial 12-lead ECG signal simulator and in vivo experiments. In addition to its portability, the proposed system is license-free as Linux, an open-source code, is utilized during software development. The cost-effectiveness of the system significantly enhances its practical application for personal healthcare.

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

Linux VPN Set Up | High-Performance Computing | NREL

Science.gov Websites

methods to connect to NREL's HPC systems via the HPC VPN: one using a simple command line, and a second UserID in place of the one in the example image. Connection name: hpcvpn Gateway: hpcvpn.nrel.gov User hpcvpn option as seen in the following screen shot. Screenshot image NetworkManager will present you with

A Prototype Implementation of a Time Interval File Protection System in Linux

DTIC Science & Technology

2006-09-01

when a user logs in, the /etc/ passwd file is read by the system to get the user’s home directory. The user’s login shell then changes the directory...and don. • Users can be added with the command: # useradd – m <username> • Set the password by: # passwd <username> • Make a copy of the

DOVIS: an implementation for high-throughput virtual screening using AutoDock.

PubMed

Zhang, Shuxing; Kumar, Kamal; Jiang, Xiaohui; Wallqvist, Anders; Reifman, Jaques

2008-02-27

Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Centralized Authorization Using a Direct Service, Part II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wachsmann, A

Authorization is the process of deciding if entity X is allowed to have access to resource Y. Determining the identity of X is the job of the authentication process. One task of authorization in computer networks is to define and determine which user has access to which computers in the network. On Linux, the tendency exists to create a local account for each single user who should be allowed to logon to a computer. This is typically the case because a user not only needs login privileges to a computer but also additional resources like a home directory to actuallymore » do some work. Creating a local account on every computer takes care of all this. The problem with this approach is that these local accounts can be inconsistent with each other. The same user name could have a different user ID and/or group ID on different computers. Even more problematic is when two different accounts share the same user ID and group ID on different computers: User joe on computer1 could have user ID 1234 and group ID 56 and user jane on computer2 could have the same user ID 1234 and group ID 56. This is a big security risk in case shared resources like NFS are used. These two different accounts are the same for an NFS server so that these users can wipe out each other's files. The solution to this inconsistency problem is to have only one central, authoritative data source for this kind of information and a means of providing all your computers with access to this central source. This is what a ''Directory Service'' is. The two directory services most widely used for centralizing authorization data are the Network Information Service (NIS, formerly known as Yellow Pages or YP) and Lightweight Directory Access Protocol (LDAP).« less

The Linux operating system: An introduction

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Linux is a Unix-like operating system for Intel 386/486/Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyrighted by the author, may be freely distributed. A world-wide group has collaborated in developing Linux on the Internet. Linux can run the powerful set of compilers and programming tools of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TeX, LaTeX, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs, etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, it provides an essentially cost-free path away from DOS into the world of Unix and X Windows.

The General Mission Analysis Tool (GMAT): Current Features And Adding Custom Functionality

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

The General Mission Analysis Tool (GMAT) is a software system for trajectory optimization, mission analysis, trajectory estimation, and prediction developed by NASA, the Air Force Research Lab, and private industry. GMAT's design and implementation are based on four basic principles: open source visibility for both the source code and design documentation; platform independence; modular design; and user extensibility. The system, released under the NASA Open Source Agreement, runs on Windows, Mac and Linux. User extensions, loaded at run time, have been built for optimization, trajectory visualization, force model extension, and estimation, by parties outside of GMAT's development group. The system has been used to optimize maneuvers for the Lunar Crater Observation and Sensing Satellite (LCROSS) and ARTEMIS missions and is being used for formation design and analysis for the Magnetospheric Multiscale Mission (MMS).

JAX Colony Management System (JCMS): an extensible colony and phenotype data management system.

PubMed

Donnelly, Chuck J; McFarland, Mike; Ames, Abigail; Sundberg, Beth; Springer, Dave; Blauth, Peter; Bult, Carol J

2010-04-01

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

Image Capture and Display Based on Embedded Linux

NASA Astrophysics Data System (ADS)

Weigong, Zhang; Suran, Di; Yongxiang, Zhang; Liming, Li

For the requirement of building a highly reliable communication system, SpaceWire was selected in the integrated electronic system. There was a need to test the performance of SpaceWire. As part of the testing work, the goal of this paper is to transmit image data from CMOS camera through SpaceWire and display real-time images on the graphical user interface with Qt in the embedded development platform of Linux & ARM. A point-to-point mode of transmission was chosen; the running result showed the two communication ends basically reach a consensus picture in succession. It suggests that the SpaceWire can transmit the data reliably.

Cyber Fundamental Exercises

DTIC Science & Technology

2013-03-01

the /bin, /sbin, /etc, /var/log, /home, /proc, /root, /dev, /tmp, and /lib directories • Describe the purpose of the /etc/shadow and /etc/ passwd ...UNLIMITED 19 2.6.2 /etc/ passwd and /etc/shadow The /etc/shadow file didn’t exist on early Linux distributions. Originally only root could access the...etc/ passwd file, which stored user names, user configuration information, and passwords. However, when common programs such as ls running under

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, P.; Benveniste, J.

2011-07-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

A dynamic kernel modifier for linux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minnich, R. G.

2002-09-03

Dynamic Kernel Modifier, or DKM, is a kernel module for Linux that allows user-mode programs to modify the execution of functions in the kernel without recompiling or modifying the kernel source in any way. Functions may be traced, either function entry only or function entry and exit; nullified; or replaced with some other function. For the tracing case, function execution results in the activation of a watchpoint. When the watchpoint is activated, the address of the function is logged in a FIFO buffer that is readable by external applications. The watchpoints are time-stamped with the resolution of the processor highmore » resolution timers, which on most modem processors are accurate to a single processor tick. DKM is very similar to earlier systems such as the SunOS trace device or Linux TT. Unlike these two systems, and other similar systems, DKM requires no kernel modifications. DKM allows users to do initial probing of the kernel to look for performance problems, or even to resolve potential problems by turning functions off or replacing them. DKM watchpoints are not without cost: it takes about 200 nanoseconds to make a log entry on an 800 Mhz Pentium-Ill. The overhead numbers are actually competitive with other hardware-based trace systems, although it has less 'Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration of the United States Department of Energy under contract W-7405-ENG-36. accuracy than an In-Circuit Emulator such as the American Arium. Once the user has zeroed in on a problem, other mechanisms with a higher degree of accuracy can be used.« less

Network Penetration Testing and Research

NASA Technical Reports Server (NTRS)

Murphy, Brandon F.

2013-01-01

This paper will focus the on research and testing done on penetrating a network for security purposes. This research will provide the IT security office new methods of attacks across and against a company's network as well as introduce them to new platforms and software that can be used to better assist with protecting against such attacks. Throughout this paper testing and research has been done on two different Linux based operating systems, for attacking and compromising a Windows based host computer. Backtrack 5 and BlackBuntu (Linux based penetration testing operating systems) are two different "attacker'' computers that will attempt to plant viruses and or NASA USRP - Internship Final Report exploits on a host Windows 7 operating system, as well as try to retrieve information from the host. On each Linux OS (Backtrack 5 and BlackBuntu) there is penetration testing software which provides the necessary tools to create exploits that can compromise a windows system as well as other operating systems. This paper will focus on two main methods of deploying exploits 1 onto a host computer in order to retrieve information from a compromised system. One method of deployment for an exploit that was tested is known as a "social engineering" exploit. This type of method requires interaction from unsuspecting user. With this user interaction, a deployed exploit may allow a malicious user to gain access to the unsuspecting user's computer as well as the network that such computer is connected to. Due to more advance security setting and antivirus protection and detection, this method is easily identified and defended against. The second method of exploit deployment is the method mainly focused upon within this paper. This method required extensive research on the best way to compromise a security enabled protected network. Once a network has been compromised, then any and all devices connected to such network has the potential to be compromised as well. With a compromised network, computers and devices can be penetrated through deployed exploits. This paper will illustrate the research done to test ability to penetrate a network without user interaction, in order to retrieve personal information from a targeted host.

Gaining Cyber Dominance

DTIC Science & Technology

2015-01-01

Robust team exercise and simulation • Air-gapped; isolation from production networks • “Train as you fight” scenarios • Advanced user and Internet...Security Onion • SIFT (Linux/Windows) • Kali • Rucksack • Docker • VTS 18 GCD Overview January 2015 © 2014 Carnegie Mellon University TEXN Architecture

BSD Portals for LINUX 2.0

NASA Technical Reports Server (NTRS)

McNab, A. David; woo, Alex (Technical Monitor)

1999-01-01

Portals, an experimental feature of 4.4BSD, extend the file system name space by exporting certain open () requests to a user-space daemon. A portal daemon is mounted into the file name space as if it were a standard file system. When the kernel resolves a pathname and encounters a portal mount point, the remainder of the path is passed to the portal daemon. Depending on the portal "pathname" and the daemon's configuration, some type of open (2) is performed. The resulting file descriptor is passed back to the kernel which eventually returns it to the user, to whom it appears that a "normal" open has occurred. A proxy portalfs file system is responsible for kernel interaction with the daemon. The overall effect is that the portal daemon performs an open (2) on behalf of the kernel, possibly hiding substantial complexity from the calling process. One particularly useful application is implementing a connection service that allows simple scripts to open network sockets. This paper describes the implementation of portals for LINUX 2.0.

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

NanoPack: visualizing and processing long read sequencing data.

PubMed

De Coster, Wouter; D'Hert, Svenn; Schultz, Darrin T; Cruts, Marc; Van Broeckhoven, Christine

2018-03-14

Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. wouter.decoster@molgen.vib-ua.be. Supplementary tables and figures are available at Bioinformatics online.

Real-time head movement system and embedded Linux implementation for the control of power wheelchairs.

PubMed

Nguyen, H T; King, L M; Knight, G

2004-01-01

Mobility has become very important for our quality of life. A loss of mobility due to an injury is usually accompanied by a loss of self-confidence. For many individuals, independent mobility is an important aspect of self-esteem. Head movement is a natural form of pointing and can be used to directly replace the joystick whilst still allowing for similar control. Through the use of embedded LINUX and artificial intelligence, a hands-free head movement wheelchair controller has been designed and implemented successfully. This system provides for severely disabled users an effective power wheelchair control method with improved posture, ease of use and attractiveness.

Real-time Experiment Interface for Biological Control Applications

PubMed Central

Lin, Risa J.; Bettencourt, Jonathan; White, John A.; Christini, David J.; Butera, Robert J.

2013-01-01

The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux. RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when using the Live CD). RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology. RTXI includes standard plug-ins for implementing commonly used electrophysiology protocols with synchronized stimulation, event detection, and online analysis. These and other user-contributed plug-ins can be found on the website (http://www.rtxi.org). PMID:21096883

Real Time Linux - The RTOS for Astronomy?

NASA Astrophysics Data System (ADS)

Daly, P. N.

The BoF was attended by about 30 participants and a free CD of real time Linux-based upon RedHat 5.2-was available. There was a detailed presentation on the nature of real time Linux and the variants for hard real time: New Mexico Tech's RTL and DIAPM's RTAI. Comparison tables between standard Linux and real time Linux responses to time interval generation and interrupt response latency were presented (see elsewhere in these proceedings). The present recommendations are to use RTL for UP machines running the 2.0.x kernels and RTAI for SMP machines running the 2.2.x kernel. Support, both academically and commercially, is available. Some known limitations were presented and the solutions reported e.g., debugging and hardware support. The features of RTAI (scheduler, fifos, shared memory, semaphores, message queues and RPCs) were described. Typical performance statistics were presented: Pentium-based oneshot tasks running > 30kHz, 486-based oneshot tasks running at ~ 10 kHz, periodic timer tasks running in excess of 90 kHz with average zero jitter peaking to ~ 13 mus (UP) and ~ 30 mus (SMP). Some detail on kernel module programming, including coding examples, were presented showing a typical data acquisition system generating simulated (random) data writing to a shared memory buffer and a fifo buffer to communicate between real time Linux and user space. All coding examples were complete and tested under RTAI v0.6 and the 2.2.12 kernel. Finally, arguments were raised in support of real time Linux: it's open source, free under GPL, enables rapid prototyping, has good support and the ability to have a fully functioning workstation capable of co-existing hard real time performance. The counter weight-the negatives-of lack of platforms (x86 and PowerPC only at present), lack of board support, promiscuous root access and the danger of ignorance of real time programming issues were also discussed. See ftp://orion.tuc.noao.edu/pub/pnd/rtlbof.tgz for the StarOffice overheads for this presentation.

Consed: a graphical editor for next-generation sequencing.

PubMed

Gordon, David; Green, Phil

2013-11-15

The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added. The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html dgordon@uw.edu .

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

Manipulation of volumetric patient data in a distributed virtual reality environment.

PubMed

Dech, F; Ai, Z; Silverstein, J C

2001-01-01

Due to increases in network speed and bandwidth, distributed exploration of medical data in immersive Virtual Reality (VR) environments is becoming increasingly feasible. The volumetric display of radiological data in such environments presents a unique set of challenges. The shear size and complexity of the datasets involved not only make them difficult to transmit to remote sites, but these datasets also require extensive user interaction in order to make them understandable to the investigator and manageable to the rendering hardware. A sophisticated VR user interface is required in order for the clinician to focus on the aspects of the data that will provide educational and/or diagnostic insight. We will describe a software system of data acquisition, data display, Tele-Immersion, and data manipulation that supports interactive, collaborative investigation of large radiological datasets. The hardware required in this strategy is still at the high-end of the graphics workstation market. Future software ports to Linux and NT, along with the rapid development of PC graphics cards, open the possibility for later work with Linux or NT PCs and PC clusters.

RTSPM: real-time Linux control software for scanning probe microscopy.

PubMed

Chandrasekhar, V; Mehta, M M

2013-01-01

Real time computer control is an essential feature of scanning probe microscopes, which have become important tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe data acquisition software uses digital signal processors to handle the real time data processing and control, which adds to the expense and complexity of the control software. We describe here scan control software that uses a single computer and a data acquisition card to acquire scan data. The computer runs an open-source real time Linux kernel, which permits fast acquisition and control while maintaining a responsive graphical user interface. Images from a simulated tuning-fork based microscope as well as a standard topographical sample are also presented, showing some of the capabilities of the software.

Peregrine System User Basics | High-Performance Computing | NREL

Science.gov Websites

peregrine.hpc.nrel.gov or to one of the login nodes. Example commands to access Peregrine from a Linux or Mac OS X system Code Example Create a file called hello.F90 containing the following code: program hello write(6 information by enclosing it in brackets < >. For example: $ ssh -Y

Towards Efficient Scientific Data Management Using Cloud Storage

NASA Technical Reports Server (NTRS)

He, Qiming

2013-01-01

A software prototype allows users to backup and restore data to/from both public and private cloud storage such as Amazon's S3 and NASA's Nebula. Unlike other off-the-shelf tools, this software ensures user data security in the cloud (through encryption), and minimizes users operating costs by using space- and bandwidth-efficient compression and incremental backup. Parallel data processing utilities have also been developed by using massively scalable cloud computing in conjunction with cloud storage. One of the innovations in this software is using modified open source components to work with a private cloud like NASA Nebula. Another innovation is porting the complex backup to- cloud software to embedded Linux, running on the home networking devices, in order to benefit more users.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

KNBD: A Remote Kernel Block Server for Linux

NASA Technical Reports Server (NTRS)

Becker, Jeff

1999-01-01

I am developing a prototype of a Linux remote disk block server whose purpose is to serve as a lower level component of a parallel file system. Parallel file systems are an important component of high performance supercomputers and clusters. Although supercomputer vendors such as SGI and IBM have their own custom solutions, there has been a void and hence a demand for such a system on Beowulf-type PC Clusters. Recently, the Parallel Virtual File System (PVFS) project at Clemson University has begun to address this need (1). Although their system provides much of the functionality of (and indeed was inspired by) the equivalent file systems in the commercial supercomputer market, their system is all in user-space. Migrating their 10 services to the kernel could provide a performance boost, by obviating the need for expensive system calls. Thanks to Pavel Machek, the Linux kernel has provided the network block device (2) with kernels 2.1.101 and later. You can configure this block device to redirect reads and writes to a remote machine's disk. This can be used as a building block for constructing a striped file system across several nodes.

Transitioning to Intel-based Linux Servers in the Payload Operations Integration Center

NASA Technical Reports Server (NTRS)

Guillebeau, P. L.

2004-01-01

The MSFC Payload Operations Integration Center (POIC) is the focal point for International Space Station (ISS) payload operations. The POIC contains the facilities, hardware, software and communication interface necessary to support payload operations. ISS ground system support for processing and display of real-time spacecraft and telemetry and command data has been operational for several years. The hardware components were reaching end of life and vendor costs were increasing while ISS budgets were becoming severely constrained. Therefore it has been necessary to migrate the Unix portions of our ground systems to commodity priced Intel-based Linux servers. hardware architecture including networks, data storage, and highly available resources. This paper will concentrate on the Linux migration implementation for the software portion of our ground system. The migration began with 3.5 million lines of code running on Unix platforms with separate servers for telemetry, command, Payload information management systems, web, system control, remote server interface and databases. The Intel-based system is scheduled to be available for initial operational use by August 2004 The overall migration to Intel-based Linux servers in the control center involves changes to the This paper will address the Linux migration study approach including the proof of concept, criticality of customer buy-in and importance of beginning with POSlX compliant code. It will focus on the development approach explaining the software lifecycle. Other aspects of development will be covered including phased implementation, interim milestones and metrics measurements and reporting mechanisms. This paper will also address the testing approach covering all levels of testing including development, development integration, IV&V, user beta testing and acceptance testing. Test results including performance numbers compared with Unix servers will be included. need for a smooth transition while maintaining real-time support. An important aspect of the paper will involve challenges and lessons learned. product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support. This paper will also address the deployment approach including user involvement in testing and the , This includes COTS product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support.

MCR Container Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

Charliecloud: Unprivileged containers for user-defined software stacks in HPC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priedhorsky, Reid; Randles, Timothy C.

Supercomputing centers are seeing increasing demand for user-defined software stacks (UDSS), instead of or in addition to the stack provided by the center. These UDSS support user needs such as complex dependencies or build requirements, externally required configurations, portability, and consistency. The challenge for centers is to provide these services in a usable manner while minimizing the risks: security, support burden, missing functionality, and performance. We present Charliecloud, which uses the Linux user and mount namespaces to run industry-standard Docker containers with no privileged operations or daemons on center resources. Our simple approach avoids most security risks while maintaining accessmore » to the performance and functionality already on offer, doing so in less than 500 lines of code. Charliecloud promises to bring an industry-standard UDSS user workflow to existing, minimally altered HPC resources.« less

FLY MPI-2: a parallel tree code for LSS

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Antonuccio-Delogu, V.

2006-04-01

New version program summaryProgram title: FLY 3.1 Catalogue identifier: ADSC_v2_0 Licensing provisions: yes Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSC_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 158 172 No. of bytes in distributed program, including test data, etc.: 4 719 953 Distribution format: tar.gz Programming language: Fortran 90, C Computer: Beowulf cluster, PC, MPP systems Operating system: Linux, Aix RAM: 100M words Catalogue identifier of previous version: ADSC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 155 (2003) 159 Does the new version supersede the previous version?: yes Nature of problem: FLY is a parallel collisionless N-body code for the calculation of the gravitational force Solution method: FLY is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986) Reasons for the new version: The new version of FLY is implemented by using the MPI-2 standard: the distributed version 3.1 was developed by using the MPICH2 library on a PC Linux cluster. Today the FLY performance allows us to consider the FLY code among the most powerful parallel codes for tree N-body simulations. Another important new feature regards the availability of an interface with hydrodynamical Paramesh based codes. Simulations must follow a box large enough to accurately represent the power spectrum of fluctuations on very large scales so that we may hope to compare them meaningfully with real data. The number of particles then sets the mass resolution of the simulation, which we would like to make as fine as possible. The idea to build an interface between two codes, that have different and complementary cosmological tasks, allows us to execute complex cosmological simulations with FLY, specialized for DM evolution, and a code specialized for hydrodynamical components that uses a Paramesh block structure. Summary of revisions: The parallel communication schema was totally changed. The new version adopts the MPICH2 library. Now FLY can be executed on all Unix systems having an MPI-2 standard library. The main data structure, is declared in a module procedure of FLY (fly_h.F90 routine). FLY creates the MPI Window object for one-sided communication for all the shared arrays, with a call like the following: CALL MPI_WIN_CREATE(POS, SIZE, REAL8, MPI_INFO_NULL, MPI_COMM_WORLD, WIN_POS, IERR) the following main window objects are created: win_pos, win_vel, win_acc: particles positions velocities and accelerations, win_pos_cell, win_mass_cell, win_quad, win_subp, win_grouping: cells positions, masses, quadrupole momenta, tree structure and grouping cells. Other windows are created for dynamic load balance and global counters. Restrictions: The program uses the leapfrog integrator schema, but could be changed by the user. Unusual features: FLY uses the MPI-2 standard: the MPICH2 library on Linux systems was adopted. To run this version of FLY the working directory must be shared among all the processors that execute FLY. Additional comments: Full documentation for the program is included in the distribution in the form of a README file, a User Guide and a Reference manuscript. Running time: IBM Linux Cluster 1350, 512 nodes with 2 processors for each node and 2 GB RAM for each processor, at Cineca, was adopted to make performance tests. Processor type: Intel Xeon Pentium IV 3.0 GHz and 512 KB cache (128 nodes have Nocona processors). Internal Network: Myricom LAN Card "C" Version and "D" Version. Operating System: Linux SuSE SLES 8. The code was compiled using the mpif90 compiler version 8.1 and with basic optimization options in order to have performances that could be useful compared with other generic clusters Processors

A Business Case Study of Open Source Software

DTIC Science & Technology

2001-07-01

LinuxPPC LinuxPPC www.linuxppc.com MandrakeSoft Linux -Mandrake www.linux-mandrake.com/ en / CLE Project CLE cle.linux.org.tw/CLE/e_index.shtml Red Hat... en Coyote Linux www2.vortech.net/coyte/coyte.htm MNIS www.mnis.fr Data-Portal www.data-portal.com Mr O’s Linux Emporium www.ouin.com DLX Linux www.wu...1998 1999 Year S h ip m en ts ( in m ill io n s) Source: IDC, 2000. Figure 11. Worldwide New Linux Shipments (Client and Server) 3.2.2 Market

Collaboration rules.

PubMed

Evans, Philip; Wolf, Bob

2005-01-01

Corporate leaders seeking to boost growth, learning, and innovation may find the answer in a surprising place: the Linux open-source software community. Linux is developed by an essentially volunteer, self-organizing community of thousands of programmers. Most leaders would sell their grandmothers for workforces that collaborate as efficiently, frictionlessly, and creatively as the self-styled Linux hackers. But Linux is software, and software is hardly a model for mainstream business. The authors have, nonetheless, found surprising parallels between the anarchistic, caffeinated, hirsute world of Linux hackers and the disciplined, tea-sipping, clean-cut world of Toyota engineering. Specifically, Toyota and Linux operate by rules that blend the self-organizing advantages of markets with the low transaction costs of hierarchies. In place of markets' cash and contracts and hierarchies' authority are rules about how individuals and groups work together (with rigorous discipline); how they communicate (widely and with granularity); and how leaders guide them toward a common goal (through example). Those rules, augmented by simple communication technologies and a lack of legal barriers to sharing information, create rich common knowledge, the ability to organize teams modularly, extraordinary motivation, and high levels of trust, which radically lowers transaction costs. Low transaction costs, in turn, make it profitable for organizations to perform more and smaller transactions--and so increase the pace and flexibility typical of high-performance organizations. Once the system achieves critical mass, it feeds on itself. The larger the system, the more broadly shared the knowledge, language, and work style. The greater individuals' reputational capital, the louder the applause and the stronger the motivation. The success of Linux is evidence of the power of that virtuous circle. Toyota's success is evidence that it is also powerful in conventional companies.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

PubMed

Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

2012-03-19

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

PubMed Central

2012-01-01

Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them. PMID:22429538

Wiretapping the Internet

NASA Astrophysics Data System (ADS)

Antonelli, Charles J.; Honeyman, Peter

2001-02-01

This paper describes the Advanced Packet Vault, a technology for creating such a record by collecting and securely storing all packets observed on a network, with a scalable architecture intended to support network speeds in excess of 100 Mbps. Encryption is used to preserve users' security and privacy, permitting selected traffic to be made available without revealing other traffic. The Vault implementation, based on Linux and OpenBSD, is open-source.

Improved Distance Learning Environment For Marine Forces Reserve

DTIC Science & Technology

2016-09-01

keyboard, to 20 form a desktop computer . Laptop computers share similar components but add mobility to the user. If additional desktop computers ...for stationary computing devices such as desktop PCs and laptops include the Microsoft Windows, Mac OS, and Linux families of OSs 44 (Hopkins...opportunities to all Marines. For active duty Marines, government-provided desktops and laptops (GPDLs) typically support DL T&E or learning resource

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

JESPP: Joint Experimentation on Scalable Parallel Processors Supercomputers

DTIC Science & Technology

2010-03-01

were for the relatively small market of scientific and engineering applications. Contrast this with GPUs that are designed to improve the end- user...experience in mass- market arenas such as gaming. In order to get meaningful speed-up using the GPU, it was determined that the data transfer and...Included) Conference Year Effectively using a Large GPGPU-Enhanced Linux Cluster HPCMP UGC 2009 FLOPS per Watt: Heterogeneous-Computing’s Approach

PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

PubMed

Bläßle, Alexander; Müller, Patrick

2015-03-15

We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options. PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

WAZA-ARI: computational dosimetry system for X-ray CT examinations II: development of web-based system.

PubMed

Ban, Nobuhiko; Takahashi, Fumiaki; Ono, Koji; Hasegawa, Takayuki; Yoshitake, Takayasu; Katsunuma, Yasushi; Sato, Kaoru; Endo, Akira; Kai, Michiaki

2011-07-01

A web-based dose computation system, WAZA-ARI, is being developed for patients undergoing X-ray CT examinations. The system is implemented in Java on a Linux server running Apache Tomcat. Users choose scanning options and input parameters via a web browser over the Internet. Dose coefficients, which were calculated in a Japanese adult male phantom (JM phantom) are called upon user request and are summed over the scan range specified by the user to estimate a normalised dose. Tissue doses are finally computed based on the radiographic exposure (mA s) and the pitch factor. While dose coefficients are currently available only for limited CT scanner models, the system has achieved a high degree of flexibility and scalability without the use of commercial software.

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

Scalable Unix commands for parallel processors : a high-performance implementation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

A package of Linux scripts for the parallelization of Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Badal, Andreu; Sempau, Josep

2006-09-01

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1Title of program:clonEasy Catalogue identifier:ADYD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYD_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a Unix style shell (bash), support for the Secure Shell protocol and a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1) Compilers:GNU FORTRAN g77 (Linux); g95 (Linux); Intel Fortran Compiler 7.1 (Linux) Programming language used:Linux shell (bash) script, FORTRAN 77 No. of bits in a word:32 No. of lines in distributed program, including test data, etc.:1916 No. of bytes in distributed program, including test data, etc.:18 202 Distribution format:tar.gz Nature of the physical problem:There are many situations where a Monte Carlo simulation involves a huge amount of CPU time. The parallelization of such calculations is a simple way of obtaining a relatively low statistical uncertainty using a reasonable amount of time. Method of solution:The presented collection of Linux scripts and auxiliary FORTRAN programs implement Secure Shell-based communication between a "master" computer and a set of "clones". The aim of this communication is to execute a code that performs a Monte Carlo simulation on all the clones simultaneously. The code is unique, but each clone is fed with a different set of random seeds. Hence, clonEasy effectively permits the parallelization of the calculation. Restrictions on the complexity of the program:clonEasy can only be used with programs that produce statistically independent results using the same code, but with a different sequence of random numbers. Users must choose the initialization values for the random number generator on each computer and combine the output from the different executions. A FORTRAN program to combine the final results is also provided. Typical running time:The execution time of each script largely depends on the number of computers that are used, the actions that are to be performed and, to a lesser extent, on the network connexion bandwidth. Unusual features of the program:Any computer on the Internet with a Secure Shell client/server program installed can be used as a node of a virtual computer cluster for parallel calculations with the sequential source code. The simplicity of the parallelization scheme makes the use of this package a straightforward task, which does not require installing any additional libraries. Program summary 2Title of program:seedsMLCG Catalogue identifier:ADYE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYE_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1), MS Windows (2000, XP) Compilers:GNU FORTRAN g77 (Linux and Windows); g95 (Linux); Intel Fortran Compiler 7.1 (Linux); Compaq Visual Fortran 6.1 (Windows) Programming language used:FORTRAN 77 No. of bits in a word:32 Memory required to execute with typical data:500 kilobytes No. of lines in distributed program, including test data, etc.:492 No. of bytes in distributed program, including test data, etc.:5582 Distribution format:tar.gz Nature of the physical problem:Statistically independent results from different runs of a Monte Carlo code can be obtained using uncorrelated sequences of random numbers on each execution. Multiplicative linear congruential generators (MLCG), or other generators that are based on them such as RANECU, can be adapted to produce these sequences. Method of solution:For a given MLCG, the presented program calculates initialization values that produce disjoint, consecutive sequences of pseudo-random numbers. The calculated values initiate the generator in distant positions of the random number cycle and can be used, for instance, on a parallel simulation. The values are found using the formula S=(aS)MODm, which gives the random value that will be generated after J iterations of the MLCG. Restrictions on the complexity of the program:The 32-bit length restriction for the integer variables in standard FORTRAN 77 limits the produced seeds to be separated a distance smaller than 2 31, when the distance J is expressed as an integer value. The program allows the user to input the distance as a power of 10 for the purpose of efficiently splitting the sequence of generators with a very long period. Typical running time:The execution time depends on the parameters of the used MLCG and the distance between the generated seeds. The generation of 10 6 seeds separated 10 12 units in the sequential cycle, for one of the MLCGs found in the RANECU generator, takes 3 s on a 2.4 GHz Intel Pentium 4 using the g77 compiler.

High speed real-time wavefront processing system for a solid-state laser system

NASA Astrophysics Data System (ADS)

Liu, Yuan; Yang, Ping; Chen, Shanqiu; Ma, Lifang; Xu, Bing

2008-03-01

A high speed real-time wavefront processing system for a solid-state laser beam cleanup system has been built. This system consists of a core2 Industrial PC (IPC) using Linux and real-time Linux (RT-Linux) operation system (OS), a PCI image grabber, a D/A card. More often than not, the phase aberrations of the output beam from solid-state lasers vary fast with intracavity thermal effects and environmental influence. To compensate the phase aberrations of solid-state lasers successfully, a high speed real-time wavefront processing system is presented. Compared to former systems, this system can improve the speed efficiently. In the new system, the acquisition of image data, the output of control voltage data and the implementation of reconstructor control algorithm are treated as real-time tasks in kernel-space, the display of wavefront information and man-machine conversation are treated as non real-time tasks in user-space. The parallel processing of real-time tasks in Symmetric Multi Processors (SMP) mode is the main strategy of improving the speed. In this paper, the performance and efficiency of this wavefront processing system are analyzed. The opened-loop experimental results show that the sampling frequency of this system is up to 3300Hz, and this system can well deal with phase aberrations from solid-state lasers.

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

LXtoo: an integrated live Linux distribution for the bioinformatics community.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

2012-07-19

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

PubMed

Geeleher, Paul; Morris, Dermot; Hinde, John P; Golden, Aaron

2009-06-01

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets. BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from (http://bioinf.nuigalway.ie).

BioSMACK: a linux live CD for genome-wide association analyses.

PubMed

Hong, Chang Bum; Kim, Young Jin; Moon, Sanghoon; Shin, Young-Ah; Go, Min Jin; Kim, Dong-Joon; Lee, Jong-Young; Cho, Yoon Shin

2012-01-01

Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc. go.kr/biosmack.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

PhamDB: a web-based application for building Phamerator databases.

PubMed

Lamine, James G; DeJong, Randall J; Nelesen, Serita M

2016-07-01

PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided. snelesen@calvin.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

TankSIM: A Cryogenic Tank Performance Prediction Program

NASA Technical Reports Server (NTRS)

Bolshinskiy, L. G.; Hedayat, A.; Hastings, L. J.; Moder, J. P.; Schnell, A. R.; Sutherlin, S. G.

2015-01-01

Developed for predicting the behavior of cryogenic liquids inside propellant tanks under various environmental and operating conditions. Provides a multi-node analysis of pressurization, ullage venting and thermodynamic venting systems (TVS) pressure control using axial jet or spray bar TVS. Allows user to combine several different phases for predicting the liquid behavior for the entire flight mission timeline or part of it. Is a NASA in-house code, based on FORTRAN 90-95 and Intel Visual FORTRAN compiler, but can be used on any other platform (Unix-Linux, Compaq Visual FORTRAN, etc.). The last Version 7, released on December 2014, included detailed User's Manual. Includes the use of several RefPROP subroutines for calculating fluid properties.

Semi-Automated Identification of Rocks in Images

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin; Castano, Andres; Anderson, Robert

2006-01-01

Rock Identification Toolkit Suite is a computer program that assists users in identifying and characterizing rocks shown in images returned by the Mars Explorer Rover mission. Included in the program are components for automated finding of rocks, interactive adjustments of outlines of rocks, active contouring of rocks, and automated analysis of shapes in two dimensions. The program assists users in evaluating the surface properties of rocks and soil and reports basic properties of rocks. The program requires either the Mac OS X operating system running on a G4 (or more capable) processor or a Linux operating system running on a Pentium (or more capable) processor, plus at least 128MB of random-access memory.

A Dedicated Computational Platform for Cellular Monte Carlo T-CAD Software Tools

DTIC Science & Technology

2015-07-14

computer that establishes an encrypted Virtual Private Network ( OpenVPN [44]) based on the Secure Socket Layer (SSL) paradigm. Each user is given a...security certificate for each device used to connect to the computing nodes. Stable OpenVPN clients are available for Linux, Microsoft Windows, Apple OSX...platform is granted by an encrypted connection base on the Secure Socket Layer (SSL) protocol, and implemented in the OpenVPN Virtual Personal Network

Comparative visualization of genetic and physical maps with Strudel.

PubMed

Bayer, Micha; Milne, Iain; Stephen, Gordon; Shaw, Paul; Cardle, Linda; Wright, Frank; Marshall, David

2011-05-01

Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these. Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/.

Research and Design of Embedded Wireless Meal Ordering System Based on SQLite

NASA Astrophysics Data System (ADS)

Zhang, Jihong; Chen, Xiaoquan

The paper describes features and internal architecture and developing method of SQLite. And then it gives a design and program of meal ordering system. The system realizes the information interaction among the users and embedded devices with SQLite as database system. The embedded database SQLite manages the data and achieves wireless communication by using Bluetooth. A system program based on Qt/Embedded and Linux drivers realizes the local management of environmental data.

Development of Automatic Live Linux Rebuilding System with Flexibility in Science and Engineering Education and Applying to Information Processing Education

NASA Astrophysics Data System (ADS)

Sonoda, Jun; Yamaki, Kota

We develop an automatic Live Linux rebuilding system for science and engineering education, such as information processing education, numerical analysis and so on. Our system is enable to easily and automatically rebuild a customized Live Linux from a ISO image of Ubuntu, which is one of the Linux distribution. Also, it is easily possible to install/uninstall packages and to enable/disable init daemons. When we rebuild a Live Linux CD using our system, we show number of the operations is 8, and the rebuilding time is about 33 minutes on CD version and about 50 minutes on DVD version. Moreover, we have applied the rebuilded Live Linux CD in a class of information processing education in our college. As the results of a questionnaires survey from our 43 students who used the Live Linux CD, we obtain that the our Live Linux is useful for about 80 percents of students. From these results, we conclude that our system is able to easily and automatically rebuild a useful Live Linux in short time.

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

AutoFACT: An Automatic Functional Annotation and Classification Tool

PubMed Central

Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

2005-01-01

Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

PubMed

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-11-23

Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

PubMed Central

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-01-01

Background Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from or . PMID:17123449

WOD - Weather On Demand forecasting system

NASA Astrophysics Data System (ADS)

Rognvaldsson, Olafur; Ragnarsson, Logi; Stanislawska, Karolina

2017-04-01

The backbone of the Belgingur forecasting system (called WOD - Weather On Demand) is the WRF-Chem atmospheric model, with a number of in-house customisations. Initial and boundary data are taken from the Global Forecasting System, operated by the National Oceanic and Atmospheric Administration (NOAA). Operational forecasts use cycling of a number of parameters, mainly deep soil and surface fields. This is done to minimise spin-up effects and to ensure proper book-keeping of hydrological fields such as snow accumulation and runoff, as well as the constituents of various chemical parameters. The WOD system can be used to create conventional short- to medium-range weather forecasts for any location on the globe. The WOD system can also be used for air quality purposes (e.g. dispersion forecasts from volcanic eruptions) and as a tool to provide input to other modelling systems, such as hydrological models. A wide variety of post-processing options are also available, making WOD an ideal tool for creating highly customised output that can be tailored to the specific needs of individual end-users. The most recent addition to the WOD system is an integrated verification system where forecasts can be compared to surface observations from chosen locations. Forecast visualisation, such as weather charts, meteograms, weather icons and tables, is done via number of web components that can be configured to serve the varying needs of different end-users. The WOD system itself can be installed in an automatic way on hardware running a range of Linux based OS. System upgrades can also be done in semi-automatic fashion, i.e. upgrades and/or bug-fixes can be pushed to the end-user hardware without system downtime. Importantly, the WOD system requires only rudimentary knowledge of the WRF modelling, and the Linux operating systems on behalf of the end-user, making it an ideal NWP tool in locations with limited IT infrastructure.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

Potential performance bottleneck in Linux TCP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system tomore » its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.« less

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

MYRaf: An Easy Aperture Photometry GUI for IRAF

NASA Astrophysics Data System (ADS)

Niaei, M. S.; KiliÇ, Y.; Özeren, F. F.

2015-07-01

We describe the design and development of MYRaf, a GUI (Graphical User Interface) that aims to be completely open-source under General Public License (GPL). MYRaf is an easy to use, reliable, and a fast IRAF aperture photometry GUI tool for those who are conversant with text-based software and command-line procedures in GNU/Linux OSs. MYRaf uses IRAF, PyRAF, matplotlib, ginga, alipy, and SExtractor with the general-purpose and high-level programming language Python, and uses the Qt framework.

CHROMA: consensus-based colouring of multiple alignments for publication.

PubMed

Goodstadt, L; Ponting, C P

2001-09-01

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

Learnable Models for Information Diffusion and its Associated User Behavior in Micro-blogosphere

DTIC Science & Technology

2012-08-30

According to the work of Even-Dar and Shapira (2007), we recall the definition of the ba- sic voter model on network G. In the model, each node of G...reason as follows. We started with the K distinct initial nodes and all the other nodes were neutral in the beginning. Recall that we set the average time... memory , running under Linux. Learning to predict opinion share and detect anti-majority opinionists in social networks 29 7 Conclusion Unlike the popular

PKPass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamson, Ryan M.

Password management solutions exist, but few are designed for enterprise systems administrators sharing oncall rotations. Due to the Multi-Factor Level of Assurance 4 effort, DOE is now distributing PIV cards with cryptographically signed certificate and private key pairs to administrators and other security-significant users. We utilize this public key infrastructure (PKI) to encrypt passwords for other recipients in a secure way. This is cross platform (works on OSX and Linux systems), and has already been adopted internally by the NCCS systems administration staff to replace their old password book system.

Configuring the HYSPLIT Model for National Weather Service Forecast Office and Spaceflight Meteorology Group Applications

NASA Technical Reports Server (NTRS)

Dreher, Joseph G.

2009-01-01

For expedience in delivering dispersion guidance in the diversity of operational situations, National Weather Service Melbourne (MLB) and Spaceflight Meteorology Group (SMG) are becoming increasingly reliant on the PC-based version of the HYSPLIT model run through a graphical user interface (GUI). While the GUI offers unique advantages when compared to traditional methods, it is difficult for forecasters to run and manage in an operational environment. To alleviate the difficulty in providing scheduled real-time trajectory and concentration guidance, the Applied Meteorology Unit (AMU) configured a Linux version of the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) (HYSPLIT) model that ingests the National Centers for Environmental Prediction (NCEP) guidance, such as the North American Mesoscale (NAM) and the Rapid Update Cycle (RUC) models. The AMU configured the HYSPLIT system to automatically download the NCEP model products, convert the meteorological grids into HYSPLIT binary format, run the model from several pre-selected latitude/longitude sites, and post-process the data to create output graphics. In addition, the AMU configured several software programs to convert local Weather Research and Forecast (WRF) model output into HYSPLIT format.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

Embedded systems for supporting computer accessibility.

PubMed

Mulfari, Davide; Celesti, Antonio; Fazio, Maria; Villari, Massimo; Puliafito, Antonio

2015-01-01

Nowadays, customized AT software solutions allow their users to interact with various kinds of computer systems. Such tools are generally available on personal devices (e.g., smartphones, laptops and so on) commonly used by a person with a disability. In this paper, we investigate a way of using the aforementioned AT equipments in order to access many different devices without assistive preferences. The solution takes advantage of open source hardware and its core component consists of an affordable Linux embedded system: it grabs data coming from the assistive software, which runs on the user's personal device, then, after processing, it generates native keyboard and mouse HID commands for the target computing device controlled by the end user. This process supports any operating system available on the target machine and it requires no specialized software installation; therefore the user with a disability can rely on a single assistive tool to control a wide range of computing platforms, including conventional computers and many kinds of mobile devices, which receive input commands through the USB HID protocol.

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

T-LECS: The Control Software System for MOIRCS

NASA Astrophysics Data System (ADS)

Yoshikawa, T.; Omata, K.; Konishi, M.; Ichikawa, T.; Suzuki, R.; Tokoku, C.; Katsuno, Y.; Nishimura, T.

2006-07-01

MOIRCS (Multi-Object Infrared Camera and Spectrograph) is a new instrument for the Subaru Telescope. We present the system design of the control software system for MOIRCS, named T-LECS (Tohoku University - Layered Electronic Control System). T-LECS is a PC-Linux based network distributed system. Two PCs equipped with the focal plane array system operate two HAWAII2 detectors, respectively, and another PC is used for user interfaces and a database server. Moreover, these PCs control various devices for observations distributed on a TCP/IP network. T-LECS has three interfaces; interfaces to the devices and two user interfaces. One of the user interfaces is to the integrated observation control system (Subaru Observation Software System) for observers, and another one provides the system developers the direct access to the devices of MOIRCS. In order to help the communication between these interfaces, we employ an SQL database system.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2013-10-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2014-01-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

A New Generation of Real-Time Systems in the JET Tokamak

NASA Astrophysics Data System (ADS)

Alves, Diogo; Neto, Andre C.; Valcarcel, Daniel F.; Felton, Robert; Lopez, Juan M.; Barbalace, Antonio; Boncagni, Luca; Card, Peter; De Tommasi, Gianmaria; Goodyear, Alex; Jachmich, Stefan; Lomas, Peter J.; Maviglia, Francesco; McCullen, Paul; Murari, Andrea; Rainford, Mark; Reux, Cedric; Rimini, Fernanda; Sartori, Filippo; Stephen, Adam V.; Vega, Jesus; Vitelli, Riccardo; Zabeo, Luca; Zastrow, Klaus-Dieter

2014-04-01

Recently, a new recipe for developing and deploying real-time systems has become increasingly adopted in the JET tokamak. Powered by the advent of x86 multi-core technology and the reliability of JET's well established Real-Time Data Network (RTDN) to handle all real-time I/O, an official Linux vanilla kernel has been demonstrated to be able to provide real-time performance to user-space applications that are required to meet stringent timing constraints. In particular, a careful rearrangement of the Interrupt ReQuests' (IRQs) affinities together with the kernel's CPU isolation mechanism allows one to obtain either soft or hard real-time behavior depending on the synchronization mechanism adopted. Finally, the Multithreaded Application Real-Time executor (MARTe) framework is used for building applications particularly optimised for exploring multi-core architectures. In the past year, four new systems based on this philosophy have been installed and are now part of JET's routine operation. The focus of the present work is on the configuration aspects that enable these new systems' real-time capability. Details are given about the common real-time configuration of these systems, followed by a brief description of each system together with results regarding their real-time performance. A cycle time jitter analysis of a user-space MARTe based application synchronizing over a network is also presented. The goal is to compare its deterministic performance while running on a vanilla and on a Messaging Real time Grid (MRG) Linux kernel.

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

PubMed

Abreu, Rui Mv; Froufe, Hugo Jc; Queiroz, Maria João Rp; Ferreira, Isabel Cfr

2010-10-28

Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.

A Design and Development of Multi-Purpose CCD Camera System with Thermoelectric Cooling: Software

NASA Astrophysics Data System (ADS)

Oh, S. H.; Kang, Y. W.; Byun, Y. I.

2007-12-01

We present a software which we developed for the multi-purpose CCD camera. This software can be used on the all 3 types of CCD - KAF-0401E (768×512), KAF-1602E (15367times;1024), KAF-3200E (2184×1472) made in KODAK Co.. For the efficient CCD camera control, the software is operated with two independent processes of the CCD control program and the temperature/shutter operation program. This software is designed to fully automatic operation as well as manually operation under LINUX system, and is controled by LINUX user signal procedure. We plan to use this software for all sky survey system and also night sky monitoring and sky observation. As our results, the read-out time of each CCD are about 15sec, 64sec, 134sec for KAF-0401E, KAF-1602E, KAF-3200E., because these time are limited by the data transmission speed of parallel port. For larger format CCD, the data transmission is required more high speed. we are considering this control software to one using USB port for high speed data transmission.

I/O performance evaluation of a Linux-based network-attached storage device

NASA Astrophysics Data System (ADS)

Sun, Zhaoyan; Dong, Yonggui; Wu, Jinglian; Jia, Huibo; Feng, Guanping

2002-09-01

In a Local Area Network (LAN), clients are permitted to access the files on high-density optical disks via a network server. But the quality of read service offered by the conventional server is not satisfied because of the multiple functions on the server and the overmuch caller. This paper develops a Linux-based Network-Attached Storage (NAS) server. The Operation System (OS), composed of an optimized kernel and a miniaturized file system, is stored in a flash memory. After initialization, the NAS device is connected into the LAN. The administrator and users could configure the access the server through the web page respectively. In order to enhance the quality of access, the management of buffer cache in file system is optimized. Some benchmark programs are peformed to evaluate the I/O performance of the NAS device. Since data recorded in optical disks are usually for reading accesses, our attention is focused on the reading throughput of the device. The experimental results indicate that the I/O performance of our NAS device is excellent.

Open Technologies at Athabasca University's Geospace Observatories

NASA Astrophysics Data System (ADS)

Connors, M. G.; Schofield, I. S.

2012-12-01

Athabasca University Geophysical Observatories feature two auroral observation sites situated in the subauroral zone of western Canada, separated by approximately 25 km. These sites are both on high-speed internet and ideal for observing phenomena detectable from this latitude, which include noctilucent clouds, meteors, and magnetic and optical aspects of the aurora. General aspects of use of Linux in observatory management are described, with emphasis on recent imaging projects involving control of high resolution digital SLR cameras at low cadence, and inexpensive white light analog video cameras at 30 Hz. Linux shell scripts are extensively used, with image capture controlled by gphoto2, the ivtv-utils package, x264 video coding library, and ffmpeg. Imagemagick allows processing of images in an automated fashion. Image archives and movies are created and can be correlated with magnetic data. Much of the magnetic data stream also uses GMT (Generic Mapping Tools) within shell scripts for display. Additionally, SPASE metadata are generated for most of the magnetic data, thus allowing users of our AUTUMN magnetic data repository to perform SPASE queries on the dataset. Visualization products from our twin observatories will be presented.

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

Content Documents Management

NASA Technical Reports Server (NTRS)

Muniz, R.; Hochstadt, J.; Boelke J.; Dalton, A.

2011-01-01

The Content Documents are created and managed under the System Software group with. Launch Control System (LCS) project. The System Software product group is lead by NASA Engineering Control and Data Systems branch (NEC3) at Kennedy Space Center. The team is working on creating Operating System Images (OSI) for different platforms (i.e. AIX, Linux, Solaris and Windows). Before the OSI can be created, the team must create a Content Document which provides the information of a workstation or server, with the list of all the software that is to be installed on it and also the set where the hardware belongs. This can be for example in the LDS, the ADS or the FR-l. The objective of this project is to create a User Interface Web application that can manage the information of the Content Documents, with all the correct validations and filters for administrator purposes. For this project we used one of the most excellent tools in agile development applications called Ruby on Rails. This tool helps pragmatic programmers develop Web applications with Rails framework and Ruby programming language. It is very amazing to see how a student can learn about OOP features with the Ruby language, manage the user interface with HTML and CSS, create associations and queries with gems, manage databases and run a server with MYSQL, run shell commands with command prompt and create Web frameworks with Rails. All of this in a real world project and in just fifteen weeks!

Report of AAPM Task Group 162: Software for planar image quality metrology.

PubMed

Samei, Ehsan; Ikejimba, Lynda C; Harrawood, Brian P; Rong, John; Cunningham, Ian A; Flynn, Michael J

2018-02-01

The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE). First, a methodological framework is provided to highlight the theoretical basis of the work. Then, a step-by-step guide is included to assist in proper execution of each component of the code. Lastly, an evaluation of the method is included to validate its accuracy against model-based and experimental data. The code was built using a Macintosh OSX operating system. The software package contains all the source codes to permit an experienced user to build the suite on a Linux or other *nix type system. The package further includes manuals and sample images and scripts to demonstrate use of the software for new users. The results of the code are in close alignment with theoretical expectations and published results of experimental data. The methodology and the software package offered in AAPM TG162 can be used as baseline for characterization of inherent image quality attributes of planar imaging systems. © 2017 American Association of Physicists in Medicine.

Building CHAOS: An Operating System for Livermore Linux Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

Development of an Autonomous Navigation Technology Test Vehicle

DTIC Science & Technology

2004-08-01

as an independent thread on processors using the Linux operating system. The computer hardware selected for the nodes that host the MRS threads...communications system design. Linux was chosen as the operating system for all of the single board computers used on the Mule. Linux was specifically...used for system analysis and development. The simple realization of multi-thread processing and inter-process communications in Linux made it a

Space Communications Emulation Facility

NASA Technical Reports Server (NTRS)

Hill, Chante A.

2004-01-01

Establishing space communication between ground facilities and other satellites is a painstaking task that requires many precise calculations dealing with relay time, atmospheric conditions, and satellite positions, to name a few. The Space Communications Emulation Facility (SCEF) team here at NASA is developing a facility that will approximately emulate the conditions in space that impact space communication. The emulation facility is comprised of a 32 node distributed cluster of computers; each node representing a satellite or ground station. The objective of the satellites is to observe the topography of the Earth (water, vegetation, land, and ice) and relay this information back to the ground stations. Software originally designed by the University of Kansas, labeled the Emulation Manager, controls the interaction of the satellites and ground stations, as well as handling the recording of data. The Emulation Manager is installed on a Linux Operating System, employing both Java and C++ programming codes. The emulation scenarios are written in extensible Markup Language, XML. XML documents are designed to store, carry, and exchange data. With XML documents data can be exchanged between incompatible systems, which makes it ideal for this project because Linux, MAC and Windows Operating Systems are all used. Unfortunately, XML documents cannot display data like HTML documents. Therefore, the SCEF team uses XML Schema Definition (XSD) or just schema to describe the structure of an XML document. Schemas are very important because they have the capability to validate the correctness of data, define restrictions on data, define data formats, and convert data between different data types, among other things. At this time, in order for the Emulation Manager to open and run an XML emulation scenario file, the user must first establish a link between the schema file and the directory under which the XML scenario files are saved. This procedure takes place on the command line on the Linux Operating System. Once this link has been established the Emulation manager validates all the XML files in that directory against the schema file, before the actual scenario is run. Using some very sophisticated commercial software called the Satellite Tool Kit (STK) installed on the Linux box, the Emulation Manager is able to display the data and graphics generated by the execution of a XML emulation scenario file. The Emulation Manager software is written in JAVA programming code. Since the SCEF project is in the developmental stage, the source code for this type of software is being modified to better fit the requirements of the SCEF project. Some parameters for the emulation are hard coded, set at fixed values. Members of the SCEF team are altering the code to allow the user to choose the values of these hard coded parameters by inserting a toolbar onto the preexisting GUI.

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

PubMed

Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

2018-04-15

High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

PubMed

Samoylova, Liubov; Buzmakov, Alexey; Chubar, Oleg; Sinn, Harald

2016-08-01

This article describes the WavePropaGator ( WPG ) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop ( SRW ) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

AIDE - Advanced Intrusion Detection Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Cathy L.

2013-04-28

Would you like to know when someone has dropped an undesirable executable binary on our system? What about something less malicious such as a software installation by a user? What about the user who decides to install a newer version of mod_perl or PHP on your web server without letting you know beforehand? Or even something as simple as when an undocumented config file change is made by another member of the admin group? Do you even want to know about all the changes that happen on a daily basis on your server? The purpose of an intrusion detection systemmore » (IDS) is to detect unauthorized, possibly malicious activity. The purpose of a host-based IDS, or file integrity checker, is check for unauthorized changes to key system files, binaries, libraries, and directories on the system. AIDE is an Open Source file and directory integrity checker. AIDE will let you know when a file or directory has been added, deleted, modified. It is included with the Red Hat Enterprise 6. It is available for other Linux distros. This is a case study describing the process of configuring AIDE on an out of the box RHEL6 installation. Its goal is to illustrate the thinking and the process by which a useful AIDE configuration is built.« less

Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M.

2009-09-09

SLURM is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small computer clusters. As a cluster resource manager, SLURM has three key functions. First, it allocates exclusive and/or non exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allciated nodes. Finally, it arbitrates conflicting requests for resouces by managing a queue of pending work.

AdvoCATE - User Guide

NASA Technical Reports Server (NTRS)

Denney, Ewen W.

2015-01-01

The basic vision of AdvoCATE is to automate the creation, manipulation, and management of large-scale assurance cases based on a formal theory of argument structures. Its main purposes are for creating and manipulating argument structures for safety assurance cases using the Goal Structuring Notation (GSN), and as a test bed and proof-of-concept for the formal theory of argument structures. AdvoCATE is available for Windows 7, Macintosh OSX, and Linux. Eventually, AdvoCATE will serve as a dashboard for safety related information and provide an infrastructure for safety decisions and management.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Comparative visualization of genetic and physical maps with Strudel

PubMed Central

Bayer, Micha; Milne, Iain; Stephen, Gordon; Shaw, Paul; Cardle, Linda; Wright, Frank; Marshall, David

2011-01-01

Summary: Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these. Availability and implementation: Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/. Contact: strudel@scri.ac.uk; micha.bayer@scri.ac.uk PMID:21372085

Turning a remotely controllable observatory into a fully autonomous system

NASA Astrophysics Data System (ADS)

Swindell, Scott; Johnson, Chris; Gabor, Paul; Zareba, Grzegorz; Kubánek, Petr; Prouza, Michael

2014-08-01

We describe a complex process needed to turn an existing, old, operational observatory - The Steward Observatory's 61" Kuiper Telescope - into a fully autonomous system, which observers without an observer. For this purpose, we employed RTS2,1 an open sourced, Linux based observatory control system, together with other open sourced programs and tools (GNU compilers, Python language for scripting, JQuery UI for Web user interface). This presentation provides a guide with time estimates needed for a newcomers to the field to handle such challenging tasks, as fully autonomous observatory operations.

The EPICS-based remote control system for muon beam line devices at J-PARC MUSE

NASA Astrophysics Data System (ADS)

Ito, T. U.; Nakahara, K.; Kawase, M.; Fujimori, H.; Kobayashi, Y.; Higemoto, W.; Miyake, Y.

2010-04-01

The remote control system for muon beam line devices of J-PARC MUSE has been developed with the Experimental Physics and Industrial Control System (EPICS). The EPICS input/output controller was installed in standard Linux PCs for slow control of the devices. Power supplies for 21 magnetic elements and four slit controllers for the decay-surface muon beam line in the Materials and Life Science Experimental Facility are now accessible via Ethernet from a graphical user interface which has been composed using the Motif Editor and Display Manger.

Estimating aquifer transmissivity from specific capacity using MATLAB.

PubMed

McLin, Stephen G

2005-01-01

Historically, specific capacity information has been used to calculate aquifer transmissivity when pumping test data are unavailable. This paper presents a simple computer program written in the MATLAB programming language that estimates transmissivity from specific capacity data while correcting for aquifer partial penetration and well efficiency. The program graphically plots transmissivity as a function of these factors so that the user can visually estimate their relative importance in a particular application. The program is compatible with any computer operating system running MATLAB, including Windows, Macintosh OS, Linux, and Unix. Two simple examples illustrate program usage.

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves. Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/. © The Author 2014. Published by Oxford University Press.

Multichannel Networked Phasemeter Readout and Analysis

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

Netmeter software reads a data stream from up to 250 networked phasemeters, synchronizes the data, saves the reduced data to disk (after applying a low-pass filter), and provides a Web server interface for remote control. Unlike older phasemeter software that requires a special, real-time operating system, this program can run on any general-purpose computer. It needs about five percent of the CPU (central processing unit) to process 20 channels because it adds built-in data logging and network-based GUIs (graphical user interfaces) that are implemented in Scalable Vector Graphics (SVG). Netmeter runs on Linux and Windows. It displays the instantaneous displacements measured by several phasemeters at a user-selectable rate, up to 1 kHz. The program monitors the measure and reference channel frequencies. For ease of use, levels of status in Netmeter are color coded: green for normal operation, yellow for network errors, and red for optical misalignment problems. Netmeter includes user-selectable filters up to 4 k samples, and user-selectable averaging windows (after filtering). Before filtering, the program saves raw data to disk using a burst-write technique.

Tuning Linux to meet real time requirements

NASA Astrophysics Data System (ADS)

Herbel, Richard S.; Le, Dang N.

2007-04-01

There is a desire to use Linux in military systems. Customers are requesting contractors to use open source to the maximal possible extent in contracts. Linux is probably the best operating system of choice to meet this need. It is widely used. It is free. It is royalty free, and, best of all, it is completely open source. However, there is a problem. Linux was not originally built to be a real time operating system. There are many places where interrupts can and will be blocked for an indeterminate amount of time. There have been several attempts to bridge this gap. One of them is from RTLinux, which attempts to build a microkernel underneath Linux. The microkernel will handle all interrupts and then pass it up to the Linux operating system. This does insure good interrupt latency; however, it is not free [1]. Another is RTAI, which provides a similar typed interface; however, the PowerPC platform, which is used widely in real time embedded community, was stated as "recovering" [2]. Thus this is not suited for military usage. This paper provides a method for tuning a standard Linux kernel so it can meet the real time requirement of an embedded system.

HARE: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mckie, Jim

2012-01-09

This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. Themore » HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating systems and runtime research follows; we discuss infrastructure software; and close with a description of the new NIX operating system, future work, and conclusions.« less

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

SFT: Scalable Fault Tolerance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrini, Fabrizio; Nieplocha, Jarek; Tipparaju, Vinod

2006-04-15

In this paper we will present a new technology that we are currently developing within the SFT: Scalable Fault Tolerance FastOS project which seeks to implement fault tolerance at the operating system level. Major design goals include dynamic reallocation of resources to allow continuing execution in the presence of hardware failures, very high scalability, high efficiency (low overhead), and transparency—requiring no changes to user applications. Our technology is based on a global coordination mechanism, that enforces transparent recovery lines in the system, and TICK, a lightweight, incremental checkpointing software architecture implemented as a Linux kernel module. TICK is completely user-transparentmore » and does not require any changes to user code or system libraries; it is highly responsive: an interrupt, such as a timer interrupt, can trigger a checkpoint in as little as 2.5μs; and it supports incremental and full checkpoints with minimal overhead—less than 6% with full checkpointing to disk performed as frequently as once per minute.« less

Online plasma calculator

NASA Astrophysics Data System (ADS)

Wisniewski, H.; Gourdain, P.-A.

2017-10-01

APOLLO is an online, Linux based plasma calculator. Users can input variables that correspond to their specific plasma, such as ion and electron densities, temperatures, and external magnetic fields. The system is based on a webserver where a FastCGI protocol computes key plasma parameters including frequencies, lengths, velocities, and dimensionless numbers. FastCGI was chosen to overcome security problems caused by JAVA-based plugins. The FastCGI also speeds up calculations over PHP based systems. APOLLO is built upon the WT library, which turns any web browser into a versatile, fast graphic user interface. All values with units are expressed in SI units except temperature, which is in electron-volts. SI units were chosen over cgs units because of the gradual shift to using SI units within the plasma community. APOLLO is intended to be a fast calculator that also provides the user with the proper equations used to calculate the plasma parameters. This system is intended to be used by undergraduates taking plasma courses as well as graduate students and researchers who need a quick reference calculation.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Linux thin-client conversion in a large cardiology practice: initial experience.

PubMed

Echt, Martin P; Rosen, Jordan

2004-01-01

Capital Cardiology Associates (CCA) is a single-specialty cardiology practice with offices in New York and Massachusetts. In 2003, CCA converted its IT system from a Microsoft-based network to a Linux network employing Linux thin-client technology with overall positive outcomes.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.

PubMed

Poehlman, William L; Rynge, Mats; Branton, Chris; Balamurugan, D; Feltus, Frank A

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid

PubMed Central

Poehlman, William L.; Rynge, Mats; Branton, Chris; Balamurugan, D.; Feltus, Frank A.

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID:27499617

CERNBox + EOS: end-user storage for science

NASA Astrophysics Data System (ADS)

Mascetti, L.; Gonzalez Labrador, H.; Lamanna, M.; Mościcki, JT; Peters, AJ

2015-12-01

CERNBox is a cloud synchronisation service for end-users: it allows syncing and sharing files on all major mobile and desktop platforms (Linux, Windows, MacOSX, Android, iOS) aiming to provide offline availability to any data stored in the CERN EOS infrastructure. The successful beta phase of the service confirmed the high demand in the community for an easily accessible cloud storage solution such as CERNBox. Integration of the CERNBox service with the EOS storage back-end is the next step towards providing “sync and share” capabilities for scientific and engineering use-cases. In this report we will present lessons learnt in offering the CERNBox service, key technical aspects of CERNBox/EOS integration and new, emerging usage possibilities. The latter includes the ongoing integration of “sync and share” capabilities with the LHC data analysis tools and transfer services.

Next Generation Security for the 10,240 Processor Columbia System

NASA Technical Reports Server (NTRS)

Hinke, Thomas; Kolano, Paul; Shaw, Derek; Keller, Chris; Tweton, Dave; Welch, Todd; Liu, Wen (Betty)

2005-01-01

This presentation includes a discussion of the Columbia 10,240-processor system located at the NASA Advanced Supercomputing (NAS) division at the NASA Ames Research Center which supports each of NASA's four missions: science, exploration systems, aeronautics, and space operations. It is comprised of 20 Silicon Graphics nodes, each consisting of 512 Itanium II processors. A 64 processor Columbia front-end system supports users as they prepare their jobs and then submits them to the PBS system. Columbia nodes and front-end systems use the Linux OS. Prior to SC04, the Columbia system was used to attain a processing speed of 51.87 TeraFlops, which made it number two on the Top 500 list of the world's supercomputers and the world's fastest "operational" supercomputer since it was fully engaged in supporting NASA users.

Development and Testing of a High-Speed Real-Time Kinematic Precise DGPS Positioning System Between Two Aircraft

DTIC Science & Technology

2006-09-01

work-horse for this thesis. He spent hours writing some of the more tedious code, and as much time helping me learn C++ and Linux . He was always there...compared with C++, and the need to use Linux as the operating system, the filter was coded using C++ and KDevelop [28] in SUSE LINUX Professional 9.2 [42...The driving factor for using Linux was the operating system’s ability to access the serial ports in a reliable fashion. Under the original MATLAB® and

Open discovery: An integrated live Linux platform of Bioinformatics tools.

PubMed

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Robert; Rivers, Wilmer

any single computer program for seismic data analysis will not have all the capabilities needed to study reference events, since hese detailed studies will be highly specialized. It may be necessary to develop and test new algorithms, and then these special ;odes must be integrated with existing software to use their conventional data-processing routines. We have investigated two neans of establishing communications between the legacy and new codes: CORBA and XML/SOAP Web services. We have nvestigated making new Java code communicate with a legacy C-language program, geotool, running under Linux. Both methods vere successful, but both were difficult to implement.more » C programs on UNIX/Linux are poorly supported for Web services, compared vith the Java and .NET languages and platforms. Easier-to-use middleware will be required for scientists to construct distributed applications as easily as stand-alone ones. Considerable difficulty was encountered in modifying geotool, and this problem shows he need to use component-based user interfaces instead of large C-language codes where changes to one part of the program nay introduce side effects into other parts. We have nevertheless made bug fixes and enhancements to that legacy program, but t remains difficult to expand it through communications with external software.« less

Optimizing ion channel models using a parallel genetic algorithm on graphical processors.

PubMed

Ben-Shalom, Roy; Aviv, Amit; Razon, Benjamin; Korngreen, Alon

2012-01-01

We have recently shown that we can semi-automatically constrain models of voltage-gated ion channels by combining a stochastic search algorithm with ionic currents measured using multiple voltage-clamp protocols. Although numerically successful, this approach is highly demanding computationally, with optimization on a high performance Linux cluster typically lasting several days. To solve this computational bottleneck we converted our optimization algorithm for work on a graphical processing unit (GPU) using NVIDIA's CUDA. Parallelizing the process on a Fermi graphic computing engine from NVIDIA increased the speed ∼180 times over an application running on an 80 node Linux cluster, considerably reducing simulation times. This application allows users to optimize models for ion channel kinetics on a single, inexpensive, desktop "super computer," greatly reducing the time and cost of building models relevant to neuronal physiology. We also demonstrate that the point of algorithm parallelization is crucial to its performance. We substantially reduced computing time by solving the ODEs (Ordinary Differential Equations) so as to massively reduce memory transfers to and from the GPU. This approach may be applied to speed up other data intensive applications requiring iterative solutions of ODEs. Copyright © 2012 Elsevier B.V. All rights reserved.

Data Collection with Linux in the Undergraduate Physics Lab

NASA Astrophysics Data System (ADS)

Ramey, R. Dwayne

2004-11-01

Electronic data devices such as photogates can greatly facilitate data collection in the undergraduate physics laboratory. Unfortunately, these devices have several practical drawbacks. While the photogates themselves are not particularly expensive, manufacturers of these devices have created intermediary hardware devices for data buffering and manipulation. These devices, while useful in some contexts, greatly increase the overall price of data collection and, through the use of proprietary software, limit the ability of the enduser to customize the software. As an alternative, I outline the procedure for establishing a computer-based data collection system that consists of opensource software and user constructed connections. The data collection system consists of the wiring needed to connect a data device to a computer and the software needed to collect and manipulate data. Data devices can be connected to a computer through either through the USB port or the gameport of a sound card. Software capable of collecting and manipulating the data from a photogate type device on a Linux system has been developed and will be discrussed. Results for typical undergraduate photogate based experiments will be shown, error limits and data collect rates will be discussed for both the gameport and USB connections.

MCBooster: a library for fast Monte Carlo generation of phase-space decays on massively parallel platforms.

NASA Astrophysics Data System (ADS)

Alves Júnior, A. A.; Sokoloff, M. D.

2017-10-01

MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. This contribution summarizes the main features of MCBooster. A basic description of the user interface and some examples of applications are provided, along with measurements of performance in a variety of environments

Efficient Parallel Engineering Computing on Linux Workstations

NASA Technical Reports Server (NTRS)

Lou, John Z.

2010-01-01

A C software module has been developed that creates lightweight processes (LWPs) dynamically to achieve parallel computing performance in a variety of engineering simulation and analysis applications to support NASA and DoD project tasks. The required interface between the module and the application it supports is simple, minimal and almost completely transparent to the user applications, and it can achieve nearly ideal computing speed-up on multi-CPU engineering workstations of all operating system platforms. The module can be integrated into an existing application (C, C++, Fortran and others) either as part of a compiled module or as a dynamically linked library (DLL).

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Grondona, M

2002-12-19

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

SLURM: Simplex Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Grondona, M

2003-04-22

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling, and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

77 FR 5864 - BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano Superlattice Technology, Inc.; Order of Suspension of... current and accurate information concerning the securities of BluePoint Linux Software Corp. because it...

Open discovery: An integrated live Linux platform of Bioinformatics tools

PubMed Central

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery ‐ a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. Availability The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in PMID:19238235

The Research on Linux Memory Forensics

NASA Astrophysics Data System (ADS)

Zhang, Jun; Che, ShengBing

2018-03-01

Memory forensics is a branch of computer forensics. It does not depend on the operating system API, and analyzes operating system information from binary memory data. Based on the 64-bit Linux operating system, it analyzes system process and thread information from physical memory data. Using ELF file debugging information and propose a method for locating kernel structure member variable, it can be applied to different versions of the Linux operating system. The experimental results show that the method can successfully obtain the sytem process information from physical memory data, and can be compatible with multiple versions of the Linux kernel.

Real-time data collection in Linux: a case study.

PubMed

Finney, S A

2001-05-01

Multiuser UNIX-like operating systems such as Linux are often considered unsuitable for real-time data collection because of the potential for indeterminate timing latencies resulting from preemptive scheduling. In this paper, Linux is shown to be fully adequate for precisely controlled programming with millisecond resolution or better. The Linux system calls that subserve such timing control are described and tested and then utilized in a MIDI-based program for tapping and music performance experiments. The timing of this program, including data input and output, is shown to be accurate at the millisecond level. This demonstrates that Linux, with proper programming, is suitable for real-time experiment software. In addition, the detailed description and test of both the operating system facilities and the application program itself may serve as a model for publicly documenting programming methods and software performance on other operating systems.

NASA's Climate in a Box: Desktop Supercomputing for Open Scientific Model Development

NASA Astrophysics Data System (ADS)

Wojcik, G. S.; Seablom, M. S.; Lee, T. J.; McConaughy, G. R.; Syed, R.; Oloso, A.; Kemp, E. M.; Greenseid, J.; Smith, R.

2009-12-01

NASA's High Performance Computing Portfolio in cooperation with its Modeling, Analysis, and Prediction program intends to make its climate and earth science models more accessible to a larger community. A key goal of this effort is to open the model development and validation process to the scientific community at large such that a natural selection process is enabled and results in a more efficient scientific process. One obstacle to others using NASA models is the complexity of the models and the difficulty in learning how to use them. This situation applies not only to scientists who regularly use these models but also non-typical users who may want to use the models such as scientists from different domains, policy makers, and teachers. Another obstacle to the use of these models is that access to high performance computing (HPC) accounts, from which the models are implemented, can be restrictive with long wait times in job queues and delays caused by an arduous process of obtaining an account, especially for foreign nationals. This project explores the utility of using desktop supercomputers in providing a complete ready-to-use toolkit of climate research products to investigators and on demand access to an HPC system. One objective of this work is to pre-package NASA and NOAA models so that new users will not have to spend significant time porting the models. In addition, the prepackaged toolkit will include tools, such as workflow, visualization, social networking web sites, and analysis tools, to assist users in running the models and analyzing the data. The system architecture to be developed will allow for automatic code updates for each user and an effective means with which to deal with data that are generated. We plan to investigate several desktop systems, but our work to date has focused on a Cray CX1. Currently, we are investigating the potential capabilities of several non-traditional development environments. While most NASA and NOAA models are designed for Linux operating systems (OS), the arrival of the WindowsHPC 2008 OS provides the opportunity to evaluate the use of a new platform on which to develop and port climate and earth science models. In particular, we are evaluating Microsoft's Visual Studio Integrated Developer Environment to determine its appropriateness for the climate modeling community. In the initial phases of this project, we have ported GEOS-5, WRF, GISS ModelE, and GFS to Linux on a CX1 and are in the process of porting WRF and ModelE to WindowsHPC 2008. Initial tests on the CX1 Linux OS indicate favorable comparisons in terms of performance and consistency of scientific results when compared with experiments executed on NASA high end systems. As in the past, NASA's large clusters will continue to be an important part of our objectives. We envision a seamless environment in which an investigator performs model development and testing on a desktop system and can seamlessly transfer execution to supercomputer clusters for production.

Virtual network computing: cross-platform remote display and collaboration software.

PubMed

Konerding, D E

1999-04-01

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

XOP: a multiplatform graphical user interface for synchrotron radiation spectral and optics calculations

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Dejus, Roger J.

1997-11-01

XOP (X-ray OPtics utilities) is a graphical user interface (GUI) created to execute several computer programs that calculate the basic information needed by a synchrotron beamline scientist (designer or experimentalist). Typical examples of such calculations are: insertion device (undulator or wiggler) spectral and angular distributions, mirror and multilayer reflectivities, and crystal diffraction profiles. All programs are provided to the user under a unified GUI, which greatly simplifies their execution. The XOP optics applications (especially mirror calculations) take their basic input (optical constants, compound and mixture tables) from a flexible file-oriented database, which allows the user to select data from a large number of choices and also to customize their own data sets. XOP includes many mathematical and visualization capabilities. It also permits the combination of reflectivities from several mirrors and filters, and their effect, onto a source spectrum. This feature is very useful when calculating thermal load on a series of optical elements. The XOP interface is written in the IDL (Interactive Data Language). An embedded version of XOP, which freely runs under most Unix platforms (HP, Sun, Dec, Linux, etc) and under Windows95 and NT, is available upon request.

Microprocessor-controlled, wide-range streak camera

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

poRe: an R package for the visualization and analysis of nanopore sequencing data.

PubMed

Watson, Mick; Thomson, Marian; Risse, Judith; Talbot, Richard; Santoyo-Lopez, Javier; Gharbi, Karim; Blaxter, Mark

2015-01-01

The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data. Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device. poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/. © The Author 2014. Published by Oxford University Press.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

FLASH Interface; a GUI for managing runtime parameters in FLASH simulations

NASA Astrophysics Data System (ADS)

Walker, Christopher; Tzeferacos, Petros; Weide, Klaus; Lamb, Donald; Flocke, Norbert; Feister, Scott

2017-10-01

We present FLASH Interface, a novel graphical user interface (GUI) for managing runtime parameters in simulations performed with the FLASH code. FLASH Interface supports full text search of available parameters; provides descriptions of each parameter's role and function; allows for the filtering of parameters based on categories; performs input validation; and maintains all comments and non-parameter information already present in existing parameter files. The GUI can be used to edit existing parameter files or generate new ones. FLASH Interface is open source and was implemented with the Electron framework, making it available on Mac OSX, Windows, and Linux operating systems. The new interface lowers the entry barrier for new FLASH users and provides an easy-to-use tool for experienced FLASH simulators. U.S. Department of Energy (DOE), NNSA ASC/Alliances Center for Astrophysical Thermonuclear Flashes, U.S. DOE NNSA ASC through the Argonne Institute for Computing in Science, U.S. National Science Foundation.

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems

PubMed Central

Sriyudthsak, Kansuporn; Mejia, Ramon Francisco; Arita, Masanori; Hirai, Masami Yokota

2016-01-01

PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems. PMID:27174940

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-07-08

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. The design also includes a scalable, general-purpose communication infrastructure. This paper presents a overview of the SLURM architecture and functionality.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

MMX-I: A data-processing software for multi-modal X-ray imaging and tomography

NASA Astrophysics Data System (ADS)

Bergamaschi, A.; Medjoubi, K.; Messaoudi, C.; Marco, S.; Somogyi, A.

2017-06-01

Scanning hard X-ray imaging allows simultaneous acquisition of multimodal information, including X-ray fluorescence, absorption, phase and dark-field contrasts, providing structural and chemical details of the samples. Combining these scanning techniques with the infrastructure developed for fast data acquisition at Synchrotron Soleil permits to perform multimodal imaging and tomography during routine user experiments at the Nanoscopium beamline. A main challenge of such imaging techniques is the online processing and analysis of the generated very large volume (several hundreds of Giga Bytes) multimodal data-sets. This is especially important for the wide user community foreseen at the user oriented Nanoscopium beamline (e.g. from the fields of Biology, Life Sciences, Geology, Geobiology), having no experience in such data-handling. MMX-I is a new multi-platform open-source freeware for the processing and reconstruction of scanning multi-technique X-ray imaging and tomographic datasets. The MMX-I project aims to offer, both expert users and beginners, the possibility of processing and analysing raw data, either on-site or off-site. Therefore we have developed a multi-platform (Mac, Windows and Linux 64bit) data processing tool, which is easy to install, comprehensive, intuitive, extendable and user-friendly. MMX-I is now routinely used by the Nanoscopium user community and has demonstrated its performance in treating big data.

Teaching Astronomy at Columbus State University using Small Radio Telescopes

NASA Astrophysics Data System (ADS)

Webster, Zodiac T.

2006-12-01

Astronomy is inherently fascinating to students but dark skies and good weather are not often scheduled during the school day. Radio telescopes provide an all-weather, all-day opportunity for astronomical observations. Columbus State University (CSU) has installed two “Small Radio Telescopes” for use by undergraduate students to pursue extra-curricular research in introductory astronomy. These telescopes are relatively affordable and are designed to be remotely operated through a Windows, Linux, or Macintosh environment. They are capable of diffraction-limited observations of the Sun and galactic Hydrogen in the ‘L-band’. A comprehensive website of projects suitable for high-school students and undergraduates is maintained by a group at MIT. This website ensures users are not left to explore the telescope’s abilities blindly. Students with varied interests learn about the nature of science by using an instrument that doesn’t lend itself to pretty pictures. Radio telescopes also provide a slight engineering flavor drawing in students who might not otherwise be interested in astronomy. This poster will provide a summary of installation, calibration, and future plans, and will share some observations by undergraduates at CSU.

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi.

PubMed

Sapes, Jordi; Solsona, Francesc

2016-02-06

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

PuffinPlot: A versatile, user-friendly program for paleomagnetic analysis

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Wilson, G. S.

2012-06-01

PuffinPlot is a user-friendly desktop application for analysis of paleomagnetic data, offering a unique combination of features. It runs on several operating systems, including Windows, Mac OS X, and Linux; supports both discrete and long core data; and facilitates analysis of very weakly magnetic samples. As well as interactive graphical operation, PuffinPlot offers batch analysis for large volumes of data, and a Python scripting interface for programmatic control of its features. Available data displays include demagnetization/intensity, Zijderveld, equal-area (for sample, site, and suite level demagnetization data, and for magnetic susceptibility anisotropy data), a demagnetization data table, and a natural remanent magnetization intensity histogram. Analysis types include principal component analysis, Fisherian statistics, and great-circle path intersections. The results of calculations can be exported as CSV (comma-separated value) files; graphs can be printed, and can also be saved as publication-quality vector files in SVG or PDF format. PuffinPlot is free, and the program, user manual, and fully documented source code may be downloaded from http://code.google.com/p/puffinplot/.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

LK Scripting Language

DOE Office of Scientific and Technical Information (OSTI.GOV)

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Versionmore » 3.0+ toolkit.« less

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Molmil: a molecular viewer for the PDB and beyond.

PubMed

Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

2016-01-01

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

Digital Image Correlation Engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turner, Dan; Crozier, Paul; Reu, Phil

DICe is an open source digital image correlation (DIC) tool intended for use as a module in an external application or as a standalone analysis code. It's primary capability is computing full-field displacements and strains from sequences of digital These images are typically of a material sample undergoing a materials characterization experiment, but DICe is also useful for other applications (for example, trajectory tracking). DICe is machine portable (Windows, Linux and Mac) and can be effectively deployed on a high performance computing platform. Capabilities from DICe can be invoked through a library interface, via source code integration of DICe classesmore » or through a graphical user interface.« less

Using Stellarium to cyber-observe the Great American Eclipse

NASA Astrophysics Data System (ADS)

Prim, Ellie R.; Sitar, David J.

2017-09-01

The Great American Eclipse is over. Somewhat sad, is it not? Individuals who were unable to experience the event on August 21, 2017, can now cyber-observe the eclipse with Stellarium (http://www.stellarium.org). In the authors' opinion, it is fun and has many great applications in the classroom. In addition it is open source and available for Android, iOS, and Linux users. We here at Appalachian use it in our introductory astronomy labs for specific activities such as investigating coordinate systems, discovering differences between solar and sidereal days, as well as determining why your "astrological sign" is most often not your "astronomical sign."

NREL's OpenStudio Helps Design More Efficient Buildings (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2014-07-01

The National Renewable Energy Laboratory (NREL) has created the OpenStudio software platform that makes it easier for architects and engineers to evaluate building energy efficiency measures throughout the design process. OpenStudio makes energy modeling more accessible and affordable, helping professionals to design structures with lower utility bills and less carbon emissions, resulting in a healthier environment. OpenStudio includes a user-friendly application suite that makes the U.S. Department of Energy's EnergyPlus and Radiance simulation engines easier to use for whole building energy and daylighting performance analysis. OpenStudio is freely available and runs on Windows, Mac, and Linux operating systems.

Secure Video Surveillance System Acquisition Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

2009-12-04

The SVSS Acquisition Software collects and displays video images from two cameras through a VPN, and store the images onto a collection controller. The software is configured to allow a user to enter a time window to display up to 2 1/2, hours of video review. The software collects images from the cameras at a rate of 1 image per second and automatically deletes images older than 3 hours. The software code operates in a linux environment and can be run in a virtual machine on Windows XP. The Sandia software integrates the different COTS software together to build themore » video review system.« less

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

Alcator C-Mod Digital Plasma Control System

NASA Astrophysics Data System (ADS)

Wolfe, S. M.

2005-10-01

A new digital plasma control system (DPCS) has been implemented for Alcator C-Mod. The new system was put into service at the start of the 2005 run campaign and has been in routine operation since. The system consists of two 64-input, 16-output cPCI digitizers attached to a rack-mounted single-CPU Linux server, which performs both the I/O and the computation. During initial operation, the system was set up to directly emulate the original C-Mod ``Hybrid'' MIMO linear control system. Compatibility with the previous control system allows the existing user interface software and data structures to be used with the new hardware. The control program is written in IDL and runs under standard Linux. Interrupts are disabled during the plasma pulses to achieve real-time operation. A synchronous loop is executed with a nominal cycle rate of 10 kHz. Emulation of the original linear control algorithms requires 50 μsec per iteration, with the time evenly split between I/O and computation, so rates of about 20 KHz are achievable. Reliable vertical position control has been demonstrated with cycle rates as low as 5 KHz. Additional computations, including non-linear algorithms and adaptive response, are implemented as optional procedure calls within the main real-time loop.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi

PubMed Central

Sapes, Jordi; Solsona, Francesc

2016-01-01

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux. PMID:26861340

Testing SLURM open source batch system for a Tierl/Tier2 HEP computing facility

NASA Astrophysics Data System (ADS)

Donvito, Giacinto; Salomoni, Davide; Italiano, Alessandro

2014-06-01

In this work the testing activities that were carried on to verify if the SLURM batch system could be used as the production batch system of a typical Tier1/Tier2 HEP computing center are shown. SLURM (Simple Linux Utility for Resource Management) is an Open Source batch system developed mainly by the Lawrence Livermore National Laboratory, SchedMD, Linux NetworX, Hewlett-Packard, and Groupe Bull. Testing was focused both on verifying the functionalities of the batch system and the performance that SLURM is able to offer. We first describe our initial set of requirements. Functionally, we started configuring SLURM so that it replicates all the scheduling policies already used in production in the computing centers involved in the test, i.e. INFN-Bari and the INFN-Tier1 at CNAF, Bologna. Currently, the INFN-Tier1 is using IBM LSF (Load Sharing Facility), while INFN-Bari, an LHC Tier2 for both CMS and Alice, is using Torque as resource manager and MAUI as scheduler. We show how we configured SLURM in order to enable several scheduling functionalities such as Hierarchical FairShare, Quality of Service, user-based and group-based priority, limits on the number of jobs per user/group/queue, job age scheduling, job size scheduling, and scheduling of consumable resources. We then show how different job typologies, like serial, MPI, multi-thread, whole-node and interactive jobs can be managed. Tests on the use of ACLs on queues or in general other resources are then described. A peculiar SLURM feature we also verified is triggers on event, useful to configure specific actions on each possible event in the batch system. We also tested highly available configurations for the master node. This feature is of paramount importance since a mandatory requirement in our scenarios is to have a working farm cluster even in case of hardware failure of the server(s) hosting the batch system. Among our requirements there is also the possibility to deal with pre-execution and post-execution scripts, and controlled handling of the failure of such scripts. This feature is heavily used, for example, at the INFN-Tier1 in order to check the health status of a worker node before execution of each job. Pre- and post-execution scripts are also important to let WNoDeS, the IaaS Cloud solution developed at INFN, use SLURM as its resource manager. WNoDeS has already been supporting the LSF and Torque batch systems for some time; in this work we show the work done so that WNoDeS supports SLURM as well. Finally, we show several performance tests that we carried on to verify SLURM scalability and reliability, detailing scalability tests both in terms of managed nodes and of queued jobs.

Improving Block-level Efficiency with scsi-mq

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldwell, Blake A

2015-01-01

Current generation solid-state storage devices are exposing a new bottlenecks in the SCSI and block layers of the Linux kernel, where IO throughput is limited by lock contention, inefficient interrupt handling, and poor memory locality. To address these limitations, the Linux kernel block layer underwent a major rewrite with the blk-mq project to move from a single request queue to a multi-queue model. The Linux SCSI subsystem rework to make use of this new model, known as scsi-mq, has been merged into the Linux kernel and work is underway for dm-multipath support in the upcoming Linux 4.0 kernel. These piecesmore » were necessary to make use of the multi-queue block layer in a Lustre parallel filesystem with high availability requirements. We undertook adding support of the 3.18 kernel to Lustre with scsi-mq and dm-multipath patches to evaluate the potential of these efficiency improvements. In this paper we evaluate the block-level performance of scsi-mq with backing storage hardware representative of a HPC-targerted Lustre filesystem. Our findings show that SCSI write request latency is reduced by as much as 13.6%. Additionally, when profiling the CPU usage of our prototype Lustre filesystem, we found that CPU idle time increased by a factor of 7 with Linux 3.18 and blk-mq as compared to a standard 2.6.32 Linux kernel. Our findings demonstrate increased efficiency of the multi-queue block layer even with disk-based caching storage arrays used in existing parallel filesystems.« less

Linux Kernel Co-Scheduling and Bulk Synchronous Parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2012-01-01

This paper describes a kernel scheduling algorithm that is based on coscheduling principles and that is intended for parallel applications running on 1000 cores or more. Experimental results for a Linux implementation on a Cray XT5 machine are presented. The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Evaluation of Open-Source Hard Real Time Software Packages

NASA Technical Reports Server (NTRS)

Mattei, Nicholas S.

2004-01-01

Reliable software is, at times, hard to find. No piece of software can be guaranteed to work in every situation that may arise during its use here at Glenn Research Center or in space. The job of the Software Assurance (SA) group in the Risk Management Office is to rigorously test the software in an effort to ensure it matches the contract specifications. In some cases the SA team also researches new alternatives for selected software packages. This testing and research is an integral part of the department of Safety and Mission Assurance. Real Time operation in reference to a computer system is a particular style of handing the timing and manner with which inputs and outputs are handled. A real time system executes these commands and appropriate processing within a defined timing constraint. Within this definition there are two other classifications of real time systems: hard and soft. A soft real time system is one in which if the particular timing constraints are not rigidly met there will be no critical results. On the other hand, a hard real time system is one in which if the timing constraints are not met the results could be catastrophic. An example of a soft real time system is a DVD decoder. If the particular piece of data from the input is not decoded and displayed to the screen at exactly the correct moment nothing critical will become of it, the user may not even notice it. However, a hard real time system is needed to control the timing of fuel injections or steering on the Space Shuttle; a delay of even a fraction of a second could be catastrophic in such a complex system. The current real time system employed by most NASA projects is Wind River's VxWorks operating system. This is a proprietary operating system that can be configured to work with many of NASA s needs and it provides very accurate and reliable hard real time performance. The down side is that since it is a proprietary operating system it is also costly to implement. The prospect of replacing this somewhat costly implementation is the focus of one of the SA group s current research projects. The explosion of open source software in the last ten years has led to the development of a multitude of software solutions which were once only produced by major corporations. The benefits of these open projects include faster release and bug patching cycles as well as inexpensive if not free software solutions. The main packages for hard real time solutions under Linux are Real Time Application Interface (RTAI) and two varieties of Real Time Linux (RTL), RTLFree and RTLPro. During my time here at NASA I have been testing various hard real time solutions operating as layers on the Linux Operating System. All testing is being run on an Intel SBC 2590 which is a common embedded hardware platform. The test plan was provided to me by the Software Assurance group at the start of my internship and my job has been to test the systems by developing and executing the test cases on the hardware. These tests are constructed so that the Software Assurance group can get hard test data for a comparison between the open source and proprietary implementations of hard real time solutions.

Memory Analysis of the KBeast Linux Rootkit: Investigating Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-06-01

examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills , can successfully...memory images and malware, this new series of reports will be directed at those who must analyse Linux malware-infected memory images. The skills ...disable 1287 1000 1000 /usr/lib/policykit-1-gnome/polkit-gnome-authentication- agent-1 1310 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1350

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

NASA Astrophysics Data System (ADS)

Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

2014-09-01

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571570 No. of bytes in distributed program, including test data, etc.: 120226886 Distribution format: tar.gz Programming language: Java, Fortran95. Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3. Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler. RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters. Classification: 1.3. External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization). Nature of problem: Optical properties of cosmic dust aggregates. Solution method: Java application based on Mackowski and Mischenko's Superposition T-Matrix code. Restrictions: The program is designed for single processor systems. Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Ranging from few minutes to several hours, depending on the input parameters. References: [1] http://www.jfree.org/index.html [2] https://java3d.java.net/

Linux Kernel Co-Scheduling For Bulk Synchronous Parallel Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2011-01-01

This paper describes a kernel scheduling algorithm that is based on co-scheduling principles and that is intended for parallel applications running on 1000 cores or more where inter-node scalability is key. Experimental results for a Linux implementation on a Cray XT5 machine are presented.1 The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Develop, Build, and Test a Virtual Lab to Support a Vulnerability Training System

DTIC Science & Technology

2004-09-01

docs.us.dell.com/support/edocs/systems/pe1650/ en /it/index.htm> (20 August 2004) “HOWTO: Installing Web Services with Linux /Tomcat/Apache/Struts...configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web server was configured as the external interface to...1650, dual processor, blade servers were configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

PubMed

Xia, Xuhua

2018-06-01

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

KITTEN Lightweight Kernel 0.1 Beta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pedretti, Kevin; Levenhagen, Michael; Kelly, Suzanne

2007-12-12

The Kitten Lightweight Kernel is a simplified OS (operating system) kernel that is intended to manage a compute node's hardware resources. It provides a set of mechanisms to user-level applications for utilizing hardware resources (e.g., allocating memory, creating processes, accessing the network). Kitten is much simpler than general-purpose OS kernels, such as Linux or Windows, but includes all of the esssential functionality needed to support HPC (high-performance computing) MPI, PGAS and OpenMP applications. Kitten provides unique capabilities such as physically contiguous application memory, transparent large page support, and noise-free tick-less operation, which enable HPC applications to obtain greater efficiency andmore » scalability than with general purpose OS kernels.« less

Free and open source software for the manipulation of digital images.

PubMed

Solomon, Robert W

2009-06-01

Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.

Low Cost Night Vision System for Intruder Detection

NASA Astrophysics Data System (ADS)

Ng, Liang S.; Yusoff, Wan Azhar Wan; R, Dhinesh; Sak, J. S.

2016-02-01

The growth in production of Android devices has resulted in greater functionalities as well as lower costs. This has made previously more expensive systems such as night vision affordable for more businesses and end users. We designed and implemented robust and low cost night vision systems based on red-green-blue (RGB) colour histogram for a static camera as well as a camera on an unmanned aerial vehicle (UAV), using OpenCV library on Intel compatible notebook computers, running Ubuntu Linux operating system, with less than 8GB of RAM. They were tested against human intruders under low light conditions (indoor, outdoor, night time) and were shown to have successfully detected the intruders.

GRIL: genome rearrangement and inversion locator.

PubMed

Darling, Aaron E; Mau, Bob; Blattner, Frederick R; Perna, Nicole T

2004-01-01

GRIL is a tool to automatically identify collinear regions in a set of bacterial-size genome sequences. GRIL uses three basic steps. First, regions of high sequence identity are located. Second, some of these regions are filtered based on user-specified criteria. Finally, the remaining regions of sequence identity are used to define significant collinear regions among the sequences. By locating collinear regions of sequence, GRIL provides a basis for multiple genome alignment using current alignment systems. GRIL also provides a basis for using current inversion distance tools to infer phylogeny. GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from http://asap.ahabs.wisc.edu/gril

MAX: Multiplatform Applications for XAFS

NASA Astrophysics Data System (ADS)

Alain, Michalowicz; Jacques, Moscovici; Diane, Muller-Bouvet; Karine, Provost

2009-11-01

MAX is a new EXAFS and XANES analysis package, replacing our old "EXAFS pour le Mac" software suite. The major improvement is the ability to work with strictly the same code, compiled at once for Microsoft Windows, Apple MacOSX and LINUX systems, justifying the title "Multiplatform Applications for XAFS". It is organized as four modules: ABSORBIX (X-ray absorbance and fluorescence self-absorption calculations), CHEROKEE (EXAFS and XANES data treatment), ROUNDMIDNIGHT (EXAFS modeling and fit) and CRYSTALFFREV (from crystal structures and molecular modeling to FEFF EXAFS and XANES theoretical calculations). Most features developed in "EXAFS pour le Mac" are still available, but with much improvements in the user's interface, data treatment algorithms and new functionalities.

Raven-II: an open platform for surgical robotics research.

PubMed

Hannaford, Blake; Rosen, Jacob; Friedman, Diana W; King, Hawkeye; Roan, Phillip; Cheng, Lei; Glozman, Daniel; Ma, Ji; Kosari, Sina Nia; White, Lee

2013-04-01

The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven universities have begun research using this platform. The Raven-II system has two 3-DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechanism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bauer, Gerry; et al.

The DAQ system of the CMS experiment at CERN collects data from more than 600 custom detector Front-End Drivers (FEDs). During 2013 and 2014 the CMS DAQ system will undergo a major upgrade to address the obsolescence of current hardware and the requirements posed by the upgrade of the LHC accelerator and various detector components. For a loss-less data collection from the FEDs a new FPGA based card implementing the TCP/IP protocol suite over 10Gbps Ethernet has been developed. To limit the TCP hardware implementation complexity the DAQ group developed a simplified and unidirectional but RFC 793 compliant version ofmore » the TCP protocol. This allows to use a PC with the standard Linux TCP/IP stack as a receiver. We present the challenges and protocol modifications made to TCP in order to simplify its FPGA implementation. We also describe the interaction between the simplified TCP and Linux TCP/IP stack including the performance measurements.« less

HEP Computing

Science.gov Websites

Computing Visitors who do not need a HEP linux account Visitors with laptops can use wireless network HEP linux account Step 1: Click Here for New Account Application After submitting the application, you

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Radio Astronomy Software Defined Receiver Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vacaliuc, Bogdan; Leech, Marcus; Oxley, Paul

The paper describes a Radio Astronomy Software Defined Receiver (RASDR) that is currently under development. RASDR is targeted for use by amateurs and small institutions where cost is a primary consideration. The receiver will operate from HF thru 2.8 GHz. Front-end components such as preamps, block down-converters and pre-select bandpass filters are outside the scope of this development and will be provided by the user. The receiver includes RF amplifiers and attenuators, synthesized LOs, quadrature down converters, dual 8 bit ADCs and a Signal Processor that provides firmware processing of the digital bit stream. RASDR will interface to a usermore » s PC via a USB or higher speed Ethernet LAN connection. The PC will run software that provides processing of the bit stream, a graphical user interface, as well as data analysis and storage. Software should support MAC OS, Windows and Linux platforms and will focus on such radio astronomy applications as total power measurements, pulsar detection, and spectral line studies.« less

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

Gener: a minimal programming module for chemical controllers based on DNA strand displacement

PubMed Central

Kahramanoğulları, Ozan; Cardelli, Luca

2015-01-01

Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact: ozan@cosbi.eu PMID:25957353

Healthwatch-2 System Overview

NASA Technical Reports Server (NTRS)

Barszcz, Eric; Mosher, Marianne; Huff, Edward M.

2004-01-01

Healthwatch-2 (HW-2) is a research tool designed to facilitate the development and testing of in-flight health monitoring algorithms. HW-2 software is written in C/C++ and executes on an x86-based computer running the Linux operating system. The executive module has interfaces for collecting various signal data, such as vibration, torque, tachometer, and GPS. It is designed to perform in-flight time or frequency averaging based on specifications defined in a user-supplied configuration file. Averaged data are then passed to a user-supplied algorithm written as a Matlab function. This allows researchers a convenient method for testing in-flight algorithms. In addition to its in-flight capabilities, HW-2 software is also capable of reading archived flight data and processing it as if collected in-flight. This allows algorithms to be developed and tested in the laboratory before being flown. Currently HW-2 has passed its checkout phase and is collecting data on a Bell OH-58C helicopter operated by the U.S. Army at NASA Ames Research Center.

ACS sampling system: design, implementation, and performance evaluation

NASA Astrophysics Data System (ADS)

Di Marcantonio, Paolo; Cirami, Roberto; Chiozzi, Gianluca

2004-09-01

By means of ACS (ALMA Common Software) framework we designed and implemented a sampling system which allows sampling of every Characteristic Component Property with a specific, user-defined, sustained frequency limited only by the hardware. Collected data are sent to various clients (one or more Java plotting widgets, a dedicated GUI or a COTS application) using the ACS/CORBA Notification Channel. The data transport is optimized: samples are cached locally and sent in packets with a lower and user-defined frequency to keep network load under control. Simultaneous sampling of the Properties of different Components is also possible. Together with the design and implementation issues we present the performance of the sampling system evaluated on two different platforms: on a VME based system using VxWorks RTOS (currently adopted by ALMA) and on a PC/104+ embedded platform using Red Hat 9 Linux operating system. The PC/104+ solution offers, as an alternative, a low cost PC compatible hardware environment with free and open operating system.

Gener: a minimal programming module for chemical controllers based on DNA strand displacement.

PubMed

Kahramanoğulları, Ozan; Cardelli, Luca

2015-09-01

: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research's DSD tool as well as to LaTeX. Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. ozan@cosbi.eu. © The Author 2015. Published by Oxford University Press.

World Wide Web Metaphors for Search Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

Iris: Constructing and Analyzing Spectral Energy Distributions with the Virtual Observatory

NASA Astrophysics Data System (ADS)

Laurino, O.; Budynkiewicz, J.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2014-05-01

We present Iris 2.0, the latest release of the Virtual Astronomical Observatory application for building and analyzing Spectral Energy Distributions (SEDs). With Iris, users may read in and display SEDs inspect and edit any selection of SED data, fit models to SEDs in arbitrary spectral ranges, and calculate confidence limits on best-fit parameters. SED data may be loaded into the application from VOTable and FITS files compliant with the International Virtual Observatoy Alliance interoperable data models, or retrieved directly from NED or the Italian Space Agency Science Data Center; data in non-standard formats may also be converted within the application. Users may seamlessy exchange data between Iris and other Virtual Observatoy tools using the Simple Application Messaging Protocol. Iris 2.0 also provides a tool for redshifting, interpolating, and measuring integratd fluxes, and allows simple aperture corrections for individual points and SED segments. Custom Python functions, template models and template libraries may be imported into Iris for fitting SEDs. Iris may be extended through Java plugins; users can install third-party packages, or develop their own plugin using Iris' Software Development Kit. Iris 2.0 is available for Linux and Mac OS X systems.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

The instrument control software package for the Habitable-Zone Planet Finder spectrometer

NASA Astrophysics Data System (ADS)

Bender, Chad F.; Robertson, Paul; Stefansson, Gudmundur Kari; Monson, Andrew; Anderson, Tyler; Halverson, Samuel; Hearty, Frederick; Levi, Eric; Mahadevan, Suvrath; Nelson, Matthew; Ramsey, Larry; Roy, Arpita; Schwab, Christian; Shetrone, Matthew; Terrien, Ryan

2016-08-01

We describe the Instrument Control Software (ICS) package that we have built for The Habitable-Zone Planet Finder (HPF) spectrometer. The ICS controls and monitors instrument subsystems, facilitates communication with the Hobby-Eberly Telescope facility, and provides user interfaces for observers and telescope operators. The backend is built around the asynchronous network software stack provided by the Python Twisted engine, and is linked to a suite of custom hardware communication protocols. This backend is accessed through Python-based command-line and PyQt graphical frontends. In this paper we describe several of the customized subsystem communication protocols that provide access to and help maintain the hardware systems that comprise HPF, and show how asynchronous communication benefits the numerous hardware components. We also discuss our Detector Control Subsystem, built as a set of custom Python wrappers around a C-library that provides native Linux access to the SIDECAR ASIC and Hawaii-2RG detector system used by HPF. HPF will be one of the first astronomical instruments on sky to utilize this native Linux capability through the SIDECAR Acquisition Module (SAM) electronics. The ICS we have created is very flexible, and we are adapting it for NEID, NASA's Extreme Precision Doppler Spectrometer for the WIYN telescope; we will describe this adaptation, and describe the potential for use in other astronomical instruments.

RELAP5-3D developmental assessment: Comparison of version 4.2.1i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul D.

2014-06-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.2i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

RELAP5-3D Developmental Assessment. Comparison of Version 4.3.4i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul David

2015-10-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.3i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine.

PubMed

Gómez-Martín, Cristina; Lebrón, Ricardo; Rueda, Antonio; Oliver, José L; Hackenberg, Michael

2017-01-01

High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories. Web servers are an alternative that can be used if the data is not subjected to privacy issues (what very often is an important issue with medical data). However, in any case they are less flexible than stand-alone programs limiting the number of workflows and analysis types that can be carried out.We show in this protocol how virtual machines can be used to overcome those problems and limitations. sRNAtoolboxVM is a virtual machine that can be executed on all common operating systems through virtualization programs like VirtualBox or VMware, providing the user with a high number of preinstalled programs like sRNAbench for small RNA analysis without the need to maintain additional servers and/or operating systems.

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

A General Purpose High Performance Linux Installation Infrastructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wachsmann, Alf

2002-06-17

With more and more and larger and larger Linux clusters, the question arises how to install them. This paper addresses this question by proposing a solution using only standard software components. This installation infrastructure scales well for a large number of nodes. It is also usable for installing desktop machines or diskless Linux clients, thus, is not designed for cluster installations in particular but is, nevertheless, highly performant. The infrastructure proposed uses PXE as the network boot component on the nodes. It uses DHCP and TFTP servers to get IP addresses and a bootloader to all nodes. It then usesmore » kickstart to install Red Hat Linux over NFS. We have implemented this installation infrastructure at SLAC with our given server hardware and installed a 256 node cluster in 30 minutes. This paper presents the measurements from this installation and discusses the bottlenecks in our installation.« less

Glenn Heat Transfer Simulation and Solver Graphical User Interface: Development and Testing

NASA Technical Reports Server (NTRS)

Kardamis, Joseph R.

2004-01-01

In the Tui ine Branch of the Turbomachinery and Propulsion Systems Division, researching and developing efficient turbine aerothermodynamics technologies is the main objective. Creating effective turbines for jet engines is a process which, if based purely on physical experimental testing, would be extremely expensive. It is for this reason, and also for the reasons of speed and ease, that the Turbine Branch spends a large amount of effort working with simulations of turbines. Specifically, they focus their work on two main fields: Computational Field Dynamics (CFD), and Experimental data analysis. The experimental field involves comparing experimental results to simulated results, whereas the CFD field involves running these simulations. The simulations are applied to aerodynamics and heat transfer cases, for both steady and unsteady flow conditions. By and large this work is applied to the domain of flow and heat transfer in axial turbines. The main application used to run these heat flow simulations is GlennHT. This program, recently rewritten in FORTRAN 90, allows the user to input a job file which specifies all the necessary parameters needed to simulate flow through a user-defined grid. There are several other executables used as well, ranging in application from converting grid files to and from particular formats, to merging blocks in a connectivity file, to converting connectivity files to a GlennHT compatible format. All of these executables are run from the command line in a terminal; some of them have interactive prompts where the user must specify the files to be manipulated after the program starts, while others take all of their parameters from the command line. With this amount of variation comes a good deal of commands and formats to memorize, which can cause slower and less efficient work, as users may forget how to execute a certain program, or not remember the pathnames of the files they wish to use. Two years ago, steps were made to expedite this process with a graphical user interface (GUI) that combines the functionality of all the executables along with adding some new functionality, such as residuals graphing and boundary conditions creation. Upon my beginning here at Glenn, many parts of the GUI, which was developed in Java, were nonfunctional. There were also issues with cross-platforming, as systems in the branch were transitioning from Silicon Graphics (SGI) machines to Linux machines. My goals this summer are to finish the parts of the GUI that are not yet completed, fix parts that did not work correctly, expand the functionality to include other useful features, such as grid surface highlighting, and make the system compatible with both Linux and SGI. I will also be heavily testing the system and providing sufficient documentation on how to use the GUI, as no such documentation existed previously.

mr: A C++ library for the matching and running of the Standard Model parameters

NASA Astrophysics Data System (ADS)

Kniehl, Bernd A.; Pikelner, Andrey F.; Veretin, Oleg L.

2016-09-01

We present the C++ program library mr that allows us to reliably calculate the values of the running parameters in the Standard Model at high energy scales. The initial conditions are obtained by relating the running parameters in the MS bar renormalization scheme to observables at lower energies with full two-loop precision. The evolution is then performed in accordance with the renormalization group equations with full three-loop precision. Pure QCD corrections to the matching and running are included through four loops. We also provide a Mathematica interface for this program library. Catalogue identifier: AFAI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 517613 No. of bytes in distributed program, including test data, etc.: 2358729 Distribution format: tar.gz Programming language: C++. Computer: IBM PC. Operating system: Linux, Mac OS X. RAM: 1 GB Classification: 11.1. External routines: TSIL [1], OdeInt [2], boost [3] Nature of problem: The running parameters of the Standard Model renormalized in the MS bar scheme at some high renormalization scale, which is chosen by the user, are evaluated in perturbation theory as precisely as possible in two steps. First, the initial conditions at the electroweak energy scale are evaluated from the Fermi constant GF and the pole masses of the W, Z, and Higgs bosons and the bottom and top quarks including the full two-loop threshold corrections. Second, the evolution to the high energy scale is performed by numerically solving the renormalization group evolution equations through three loops. Pure QCD corrections to the matching and running are included through four loops. Solution method: Numerical integration of analytic expressions Additional comments: Available for download from URL: http://apik.github.io/mr/. The MathLink interface is tested to work with Mathematica 7-9 and, with an additional flag, also with Mathematica 10 under Linux and with Mathematica 10 under Mac OS X. Running time: less than 1 second References: [1] S. P. Martin and D. G. Robertson, Comput. Phys. Commun. 174 (2006) 133-151 [hep-ph/0501132]. [2] K. Ahnert and M. Mulansky, AIP Conf. Proc. 1389 (2011) 1586-1589 [arxiv:1110.3397 [cs.MS

[Study for lung sound acquisition module based on ARM and Linux].

PubMed

Lu, Qiang; Li, Wenfeng; Zhang, Xixue; Li, Junmin; Liu, Longqing

2011-07-01

A acquisition module with ARM and Linux as a core was developed. This paper presents the hardware configuration and the software design. It is shown that the module can extract human lung sound reliably and effectively.

Social Tagging of Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Trajectory Optimization: OTIS 4

NASA Technical Reports Server (NTRS)

Riehl, John P.; Sjauw, Waldy K.; Falck, Robert D.; Paris, Stephen W.

2010-01-01

The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended.

Creating interactive physics simulations using the power of GeoGebra

NASA Astrophysics Data System (ADS)

Walsh, Tom

2017-05-01

I have long incorporated physics simulations in my physics teaching, and truly appreciate those who have made their simulations available to the public. I often would think of an idea for a simulation I would love to be able to use, but with no real programming background I did not know how I could make my own. That was the case until I discovered GeoGebra, which is an open source software offering "Dynamic Mathematics for Teaching and Learning." GeoGebra is freely available for non-commercial users. It is powerful, easy to learn, and versatile. There are versions for Windows, Mac, and Linux, as well as tablet and phone versions. It can also be run directly from a Chrome browser.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Glnemo2: Interactive Visualization 3D Program

NASA Astrophysics Data System (ADS)

Lambert, Jean-Charles

2011-10-01

Glnemo2 is an interactive 3D visualization program developed in C++ using the OpenGL library and Nokia QT 4.X API. It displays in 3D the particles positions of the different components of an nbody snapshot. It quickly gives a lot of information about the data (shape, density area, formation of structures such as spirals, bars, or peanuts). It allows for in/out zooms, rotations, changes of scale, translations, selection of different groups of particles and plots in different blending colors. It can color particles according to their density or temperature, play with the density threshold, trace orbits, display different time steps, take automatic screenshots to make movies, select particles using the mouse, and fly over a simulation using a given camera path. All these features are accessible from a very intuitive graphic user interface. Glnemo2 supports a wide range of input file formats (Nemo, Gadget 1 and 2, phiGrape, Ramses, list of files, realtime gyrfalcON simulation) which are automatically detected at loading time without user intervention. Glnemo2 uses a plugin mechanism to load the data, so that it is easy to add a new file reader. It's powered by a 3D engine which uses the latest OpenGL technology, such as shaders (glsl), vertex buffer object, frame buffer object, and takes in account the power of the graphic card used in order to accelerate the rendering. With a fast GPU, millions of particles can be rendered in real time. Glnemo2 runs on Linux, Windows (using minGW compiler), and MaxOSX, thanks to the QT4API.

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

Developing Online Communities with LAMP (Linux, Apache, MySQL, PHP) - the IMIA OSNI and CHIRAD Experiences.

PubMed

Murray, Peter J; Oyri, Karl

2005-01-01

Many health informatics organisations do not seem to use, on a practical basis, for the benefit of their activities and interaction with their members, the very technologies that they often promote for use within healthcare environments. In particular, many organisations seem to be slow to take up the benefits of interactive web technologies. This paper presents an introduction to some of the many free/libre and open source (FLOSS) applications currently available and using the LAMP - Linux, Apache, MySQL, PHP architecture - as a way of cheaply deploying reliable, scalable, and secure web applications. The experience of moving to applications using LAMP architecture, in particular that of the Open Source Nursing Informatics (OSNI) Working Group of the Special Interest Group in Nursing Informatics of the International Medical Informatics Association (IMIA-NI), in using PostNuke, a FLOSS Content Management System (CMS) illustrates many of the benefits of such applications. The experiences of the authors in installing and maintaining a large number of websites using FLOSS CMS to develop dynamic, interactive websites that facilitate real engagement with the members of IMIA-NI OSNI, the IMIA Open Source Working Group, and the Centre for Health Informatics Research and Development (CHIRAD), as well as other organisations, is used as the basis for discussing the potential benefits that could be realised by others within the health informatics community.

Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system

NASA Astrophysics Data System (ADS)

Meier, Konrad; Fleig, Georg; Hauth, Thomas; Janczyk, Michael; Quast, Günter; von Suchodoletz, Dirk; Wiebelt, Bernd

2016-10-01

Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications. To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare policies of the cluster. The developed thin integration layer between OpenStack and Moab can be adapted to other batch servers and virtualization systems, making the concept also applicable for other cluster operators. This contribution will report on the concept and implementation of an OpenStack-virtualized cluster used for HEP workflows. While the full cluster will be installed in spring 2016, a test-bed setup with 800 cores has been used to study the overall system performance and dedicated HEP jobs were run in a virtualized environment over many weeks. Furthermore, the dynamic integration of the virtualized worker nodes, depending on the workload at the institute's computing system, will be described.

Rcount: simple and flexible RNA-Seq read counting.

PubMed

Schmid, Marc W; Grossniklaus, Ueli

2015-02-01

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with multiple locations in the genome (multireads) or reads aligning with positions where two or more genes overlap (ambiguous reads). Rcount specifically addresses these issues. Furthermore, Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA-coding genes) or to add flanking regions. Rcount provides a fast and easy-to-use graphical user interface requiring no command line or programming skills. It is implemented in C++ using the SeqAn (www.seqan.de) and the Qt libraries (qt-project.org). Source code and 64 bit binaries for (Ubuntu) Linux, Windows (7) and MacOSX are released under the GPLv3 license and are freely available on github.com/MWSchmid/Rcount. marcschmid@gmx.ch Test data, genome annotation files, useful Python and R scripts and a step-by-step user guide (including run-time and memory usage tests) are available on github.com/MWSchmid/Rcount. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Poster — Thur Eve — 52: A Web-based Platform for Collaborative Document Management in Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kildea, J.; Joseph, A.

We describe DepDocs, a web-based platform that we have developed to manage the committee meetings, policies, procedures and other documents within our otherwise paperless radiotherapy clinic. DepDocs is essentially a document management system based on the popular Drupal content management software. For security and confidentiality, it is hosted on a linux server internal to our hospital network such that documents are never sent to the cloud or outside of the hospital firewall. We used Drupal's in-built role-based user rights management system to assign a role, and associated document editing rights, to each user. Documents are accessed for viewing using eithermore » a simple Google-like search or by generating a list of related documents from a taxonomy of categorization terms. Our system provides document revision tracking and an document review and approval mechanism for all official policies and procedures. Committee meeting schedules, agendas and minutes are maintained by committee chairs and are restricted to committee members. DepDocs has been operational within our department for over six months and has already 45 unique users and an archive of over 1000 documents, mostly policies and procedures. Documents are easily retrievable from the system using any web browser within our hospital's network.« less

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

PubMed Central

Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

Linux Incident Response Volatile Data Analysis Framework

ERIC Educational Resources Information Center

McFadden, Matthew

2013-01-01

Cyber incident response is an emphasized subject area in cybersecurity in information technology with increased need for the protection of data. Due to ongoing threats, cybersecurity imposes many challenges and requires new investigative response techniques. In this study a Linux Incident Response Framework is designed for collecting volatile data…

Onboard Flow Sensing For Downwash Detection and Avoidance On Small Quadrotor Helicopters

DTIC Science & Technology

2015-01-01

onboard computers, one for flight stabilization and a Linux computer for sensor integration and control calculations . The Linux computer runs Robot...Hirokawa, D. Kubo , S. Suzuki, J. Meguro, and T. Suzuki. Small uav for immediate hazard map generation. In AIAA Infotech@Aerospace Conf, May 2007. 8F

Cross platform development using Delphi and Kylix

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, J.L.; Nishimura, H.; Timossi, C.

2002-10-08

A cross platform component for EPICS Simple Channel Access (SCA) has been developed for the use with Delphi on Windows and Kylix on Linux. An EPICS controls GUI application developed on Windows runs on Linux by simply rebuilding it, and vice versa. This paper describes the technical details of the component.

C-mii: a tool for plant miRNA and target identification.

PubMed

Numnark, Somrak; Mhuantong, Wuttichai; Ingsriswang, Supawadee; Wichadakul, Duangdao

2012-01-01

MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.

C-mii: a tool for plant miRNA and target identification

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. Results To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. Conclusions C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms. PMID:23281648

KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.

PubMed

Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Mewes, H Werner; Küffner, Robert

2017-05-15

Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME. See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license). robert.kueffner@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.

Name-Based Address Mapping for Virtual Private Networks

NASA Astrophysics Data System (ADS)

Surányi, Péter; Shinjo, Yasushi; Kato, Kazuhiko

IPv4 private addresses are commonly used in local area networks (LANs). With the increasing popularity of virtual private networks (VPNs), it has become common that a user connects to multiple LANs at the same time. However, private address ranges for LANs frequently overlap. In such cases, existing systems do not allow the user to access the resources on all LANs at the same time. In this paper, we propose name-based address mapping for VPNs, a novel method that allows connecting to hosts through multiple VPNs at the same time, even when the address ranges of the VPNs overlap. In name-based address mapping, rather than using the IP addresses used on the LANs (the real addresses), we assign a unique virtual address to each remote host based on its domain name. The local host uses the virtual addresses to communicate with remote hosts. We have implemented name-based address mapping for layer 3 OpenVPN connections on Linux and measured its performance. The communication overhead of our system is less than 1.5% for throughput and less than 0.2ms for each name resolution.

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

PubMed Central

Kleffner, Robert; Flatten, Jeff; Leaver-Fay, Andrew; Baker, David; Siegel, Justin B.; Khatib, Firas; Cooper, Seth

2017-01-01

Abstract Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter. Availability and Implementation: Foldit Standalone is available for download at https://fold.it/standalone, under the Rosetta license, which is free for academic and non-profit users. It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux. Contact: scooper@ccs.neu.edu PMID:28481970

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

Remote Numerical Simulations of the Interaction of High Velocity Clouds with Random Magnetic Fields

NASA Astrophysics Data System (ADS)

Santillan, Alfredo; Hernandez--Cervantes, Liliana; Gonzalez--Ponce, Alejandro; Kim, Jongsoo

The numerical simulations associated with the interaction of High Velocity Clouds (HVC) with the Magnetized Galactic Interstellar Medium (ISM) are a powerful tool to describe the evolution of the interaction of these objects in our Galaxy. In this work we present a new project referred to as Theoretical Virtual i Observatories. It is oriented toward to perform numerical simulations in real time through a Web page. This is a powerful astrophysical computational tool that consists of an intuitive graphical user interface (GUI) and a database produced by numerical calculations. In this Website the user can make use of the existing numerical simulations from the database or run a new simulation introducing initial conditions such as temperatures, densities, velocities, and magnetic field intensities for both the ISM and HVC. The prototype is programmed using Linux, Apache, MySQL, and PHP (LAMP), based on the open source philosophy. All simulations were performed with the MHD code ZEUS-3D, which solves the ideal MHD equations by finite differences on a fixed Eulerian mesh. Finally, we present typical results that can be obtained with this tool.

GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.

PubMed

Caniza, Horacio; Romero, Alfonso E; Heron, Samuel; Yang, Haixuan; Devoto, Alessandra; Frasca, Marco; Mesiti, Marco; Valentini, Giorgio; Paccanaro, Alberto

2014-08-01

We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. alberto@cs.rhul.ac.uk GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines. © The Author 2014. Published by Oxford University Press.

PRISE2: software for designing sequence-selective PCR primers and probes.

PubMed

Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

2014-09-25

PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Benveniste, Jérôme; Knudsen, Per

2016-07-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. Without any doubt the development of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy, Oceanography and Solid earth studies. Accordingly, the GUT version 3 has: - An attractive and easy to use Graphic User Interface (GUI) for the toolbox, - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients, anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies. - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-04-24

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, and scheduling modules. The design also includes a scalable, general-purpose communication infrastructure. Development will take place in four phases: Phase I results in a solid infrastructure; Phase II produces a functional but limited interactive job initiation capability without use of the interconnect/switch; Phase III provides switch support and documentation; Phase IV provides job status, fault-tolerance, and job queuing and control through Livermore's Distributed Productionmore » Control System (DPCS), a meta-batch and resource management system.« less

Implementation of image transmission server system using embedded Linux

NASA Astrophysics Data System (ADS)

Park, Jong-Hyun; Jung, Yeon Sung; Nam, Boo Hee

2005-12-01

In this paper, we performed the implementation of image transmission server system using embedded system that is for the specified object and easy to install and move. Since the embedded system has lower capability than the PC, we have to reduce the quantity of calculation of the baseline JPEG image compression and transmission. We used the Redhat Linux 9.0 OS at the host PC and the target board based on embedded Linux. The image sequences are obtained from the camera attached to the FPGA (Field Programmable Gate Array) board with ALTERA cooperation chip. For effectiveness and avoiding some constraints from the vendor's own, we made the device driver using kernel module.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

PubMed

Barnett, Derek W; Garrison, Erik K; Quinlan, Aaron R; Strömberg, Michael P; Marth, Gabor T

2011-06-15

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

Sophia Daemon Version 12

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-08-09

Sophia Daemon Version 12 contains the code that is exclusively used by the ‘sophiad’ application. It runs as a service on a Linux host and analyzes network traffic obtained from libpcap and produces a network fingerprint based on hosts and channels. Sophia Daemon Version 12 can, if desired by the user, produce alerts when its fingerprint changes. Sophia Daemon Version 12 can receive data from another Sophia Daemon or raw packet data. It can output data to another Sophia Daemon Version 12, OglNet Version 12 or MySQL. Sophia Daemon Version 12 runs in a passive real-time manner that allows itmore » to be used on a SCADA network. Its network fingerprint is designed to be applicable to SCADA networks rather than general IT networks.« less

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

An Open-Source Standard T-Wave Alternans Detector for Benchmarking.

PubMed

Khaustov, A; Nemati, S; Clifford, Gd

2008-09-14

We describe an open source algorithm suite for T-Wave Alternans (TWA) detection and quantification. The software consists of Matlab implementations of the widely used Spectral Method and Modified Moving Average with libraries to read both WFDB and ASCII data under windows and Linux. The software suite can run in both batch mode and with a provided graphical user interface to aid waveform exploration. Our software suite was calibrated using an open source TWA model, described in a partner paper [1] by Clifford and Sameni. For the PhysioNet/CinC Challenge 2008 we obtained a score of 0.881 for the Spectral Method and 0.400 for the MMA method. However, our objective was not to provide the best TWA detector, but rather a basis for detailed discussion of algorithms.

Protect sensitive data with lightweight memory encryption

NASA Astrophysics Data System (ADS)

Zhou, Hongwei; Yuan, Jinhui; Xiao, Rui; Zhang, Kai; Sun, Jingyao

2018-04-01

Since current commercial processor is not able to deal with the data in the cipher text, the sensitive data have to be exposed in the memory. It leaves a window for the adversary. To protect the sensitive data, a direct idea is to encrypt the data when the processor does not access them. On the observation, we have developed a lightweight memory encryption, called LeMe, to protect the sensitive data in the application. LeMe marks the sensitive data in the memory with the page table entry, and encrypts the data in their free time. LeMe is built on the Linux with a 3.17.6 kernel, and provides four user interfaces as dynamic link library. Our evaluations show LeMe is effective to protect the sensitive data and incurs an acceptable performance overhead.

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

Mendel-GPU: haplotyping and genotype imputation on graphics processing units

PubMed Central

Chen, Gary K.; Wang, Kai; Stram, Alex H.; Sobel, Eric M.; Lange, Kenneth

2012-01-01

Motivation: In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data. Results: Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand. Availability: Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/. Contact: gary.k.chen@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22954633

ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

PubMed

Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

2016-01-01

To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

Linux Adventures on a Laptop. Computers in Small Libraries

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

78 FR 57648 - Notice of Issuance of Final Determination Concerning Video Teleconferencing Server

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... the Chinese- origin Video Board and the Filter Board, impart the essential character to the video... includes the codec; a network filter electronic circuit board (``Filter Board''); a housing case; a power... (``Linux software''). The Linux software allows the Filter Board to inspect each Ethernet packet of...

Impact of the Shodan Computer Search Engine on Internet-facing Industrial Control System Devices

DTIC Science & Technology

2014-03-27

bridge implementation. The transparent bridge is designed using a Raspberry Pi configured with Linux IPtables and bridge-utils to bridge the on board...Ethernet card and a second USB Ethernet adapter. A Raspberry Pi is a credit-card-sized single-board computer running a version of Debian Linux. There

Chicks in Charge: Andrea Baker & Amy Daniels--Airport High School Media Center, Columbia, SC

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

This article briefly discusses two librarians exploration of Linux. Andrea Baker and Amy Daniels were tired of telling their students that new technology items were not in the budget. They explored Linux, which is a program that recycles older computers, installs free operating systems and free software.

Diversifying the Department of Defense Network Enterprise with Linux

DTIC Science & Technology

2010-03-01

Cyberspace, Cyberwar, Legacy, Inventory, Acquisition, Competitive Advantage, Coalition Communications, Ubiquitous, Strategic, Centricity, Kaizen , ISO... Kaizen , ISO, Outsource CLASSIFICATION: Unclassified Historically, the United States and its closest allies have grown increasingly reliant...control through the use of continuous improvement processes ( Kaizen )34. In choosing the Linux client operating system, the move encourages open standards

Managing a Real-Time Embedded Linux Platform with Buildroot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

The One Universal Graph — a free and open graph database

NASA Astrophysics Data System (ADS)

Ng, Liang S.; Champion, Corbin

2016-02-01

Recent developments in graph database mostly are huge projects involving big organizations, big operations and big capital, as the name Big Data attests. We proposed the concept of One Universal Graph (OUG) which states that all observable and known objects and concepts (physical, conceptual or digitally represented) can be connected with only one single graph; furthermore the OUG can be implemented with a very simple text file format with free software, capable of being executed on Android or smaller devices. As such the One Universal Graph Data Exchange (GOUDEX) modules can potentially be installed on hundreds of millions of Android devices and Intel compatible computers shipped annually. Coupled with its open nature and ability to connect to existing leading search engines and databases currently in operation, GOUDEX has the potential to become the largest and a better interface for users and programmers to interact with the data on the Internet. With a Web User Interface for users to use and program in native Linux environment, Free Crowdware implemented in GOUDEX can help inexperienced users learn programming with better organized documentation for free software, and is able to manage programmer's contribution down to a single line of code or a single variable in software projects. It can become the first practically realizable “Internet brain” on which a global artificial intelligence system can be implemented. Being practically free and open, One Universal Graph can have significant applications in robotics, artificial intelligence as well as social networks.

Visualizer: 3D Gridded Data Visualization Software for Geoscience Education and Research

NASA Astrophysics Data System (ADS)

Harwood, C.; Billen, M. I.; Kreylos, O.; Jadamec, M.; Sumner, D. Y.; Kellogg, L. H.; Hamann, B.

2008-12-01

In both research and education learning is an interactive and iterative process of exploring and analyzing data or model results. However, visualization software often presents challenges on the path to learning because it assumes the user already knows the locations and types of features of interest, instead of enabling flexible and intuitive examination of results. We present examples of research and teaching using the software, Visualizer, specifically designed to create an effective and intuitive environment for interactive, scientific analysis of 3D gridded data. Visualizer runs in a range of 3D virtual reality environments (e.g., GeoWall, ImmersaDesk, or CAVE), but also provides a similar level of real-time interactivity on a desktop computer. When using Visualizer in a 3D-enabled environment, the software allows the user to interact with the data images as real objects, grabbing, rotating or walking around the data to gain insight and perspective. On the desktop, simple features, such as a set of cross-bars marking the plane of the screen, provide extra 3D spatial cues that allow the user to more quickly understand geometric relationships within the data. This platform portability allows the user to more easily integrate research results into classroom demonstrations and exercises, while the interactivity provides an engaging environment for self-directed and inquiry-based learning by students. Visualizer software is freely available for download (www.keckcaves.org) and runs on Mac OSX and Linux platforms.

The ALICE Electronic Logbook

NASA Astrophysics Data System (ADS)

Altini, V.; Carena, F.; Carena, W.; Chapeland, S.; Chibante Barroso, V.; Costa, F.; Divià, R.; Fuchs, U.; Makhlyueva, I.; Roukoutakis, F.; Schossmaier, K.; Soòs, C.; Vande Vyvre, P.; Von Haller, B.; ALICE Collaboration

2010-04-01

All major experiments need tools that provide a way to keep a record of the events and activities, both during commissioning and operations. In ALICE (A Large Ion Collider Experiment) at CERN, this task is performed by the Alice Electronic Logbook (eLogbook), a custom-made application developed and maintained by the Data-Acquisition group (DAQ). Started as a statistics repository, the eLogbook has evolved to become not only a fully functional electronic logbook, but also a massive information repository used to store the conditions and statistics of the several online systems. It's currently used by more than 600 users in 30 different countries and it plays an important role in the daily ALICE collaboration activities. This paper will describe the LAMP (Linux, Apache, MySQL and PHP) based architecture of the eLogbook, the database schema and the relevance of the information stored in the eLogbook to the different ALICE actors, not only for near real time procedures but also for long term data-mining and analysis. It will also present the web interface, including the different used technologies, the implemented security measures and the current main features. Finally it will present the roadmap for the future, including a migration to the web 2.0 paradigm, the handling of the database ever-increasing data volume and the deployment of data-mining tools.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

minimega

DOE Office of Scientific and Technical Information (OSTI.GOV)

David Fritz, John Floren

2013-08-27

Minimega is a simple emulytics platform for creating testbeds of networked devices. The platform consists of easily deployable tools to facilitate bringing up large networks of virtual machines including Windows, Linux, and Android. Minimega attempts to allow experiments to be brought up quickly with nearly no configuration. Minimega also includes tools for simple cluster management, as well as tools for creating Linux based virtual machine images.

Malware Memory Analysis of the Jynx2 Linux Rootkit (Part 1): Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2014-10-01

indication that not a single scanner was able to detect the rootkit as malicious or infected. SHA256 ...clear indication that not a single scanner was able detect it as malicious, infected or associated to the Jynx2 rootkit. SHA256

Teaching Hands-On Linux Host Computer Security

ERIC Educational Resources Information Center

Shumba, Rose

2006-01-01

In the summer of 2003, a project to augment and improve the teaching of information assurance courses was started at IUP. Thus far, ten hands-on exercises have been developed. The exercises described in this article, and presented in the appendix, are based on actions required to secure a Linux host. Publicly available resources were used to…

A PC parallel port button box provides millisecond response time accuracy under Linux.

PubMed

Stewart, Neil

2006-02-01

For psychologists, it is sometimes necessary to measure people's reaction times to the nearest millisecond. This article describes how to use the PC parallel port to receive signals from a button box to achieve millisecond response time accuracy. The workings of the parallel port, the corresponding port addresses, and a simple Linux program for controlling the port are described. A test of the speed and reliability of button box signal detection is reported. If the reader is moderately familiar with Linux, this article should provide sufficient instruction for him or her to build and test his or her own parallel port button box. This article also describes how the parallel port could be used to control an external apparatus.

Will Your Next Supercomputer Come from Costco?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farber, Rob

2007-04-15

A fun topic for April, one that is not an April fool’s joke, is that you can purchase a commodity 200+ Gflop (single-precision) Linux supercomputer for around $600 from your favorite electronic vendor. Yes, it’s true. Just walk in and ask for a Sony Playstation 3 (PS3), take it home and install Linux on it. IBM has provided an excellent tutorial for installing Linux and building applications at http://www-128.ibm.com/developerworks/power/library/pa-linuxps3-1. If you want to raise some eyebrows at work, then submit a purchase request for a Sony PS3 game console and watch the reactions as your paperwork wends its way throughmore » the procurement process.« less

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

Entering the Matrix: The Challenge of Regulating Radical Leveling Technologies

DTIC Science & Technology

2015-12-01

Source Horizon: 3D Printing,” LinuxInsider, May 28, 2014, http://www.linuxinsider.com/story/ 80519.html; Nozomi Hayase, “ Blockchain Revolution: Open...Source Democracy for the 99%,” openDemocracy UK, August 4, 2014, https://www.opendemocracy.net/ourkingdom/nozomi-hayase/ blockchain -revolution-open...8,000. The funds raised on Kickstarter: $500,000.75 A private technology watchdog, the ETC Group, notified the US Department of Agriculture about

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Linux OS Jitter Measurements at Large Node Counts using a BlueGene/L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R; Tauferner, Mr. Andrew; Inglett, Mr. Todd

2010-01-01

We present experimental results for a coordinated scheduling implementation of the Linux operating system. Results were collected on an IBM Blue Gene/L machine at scales up to 16K nodes. Our results indicate coordinated scheduling was able to provide a dramatic improvement in scaling performance for two applications characterized as bulk synchronous parallel programs.

Interactivity vs. fairness in networked linux systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Thoughmore » each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.« less

The new version 2.12 of BKG Ntrip Client (BNC)

NASA Astrophysics Data System (ADS)

Stürze, Andrea; Mervart, Leos; Weber, Georg; Rülke, Axel; Wiesensarter, Erwin; Neumaier, Peter

2016-04-01

A new version of the BKG Ntrip Client (BNC) has been released. Originally developed in cooperation of the Federal Agency for Cartography and Geodesy (BKG) and the Czech Technical University (CTU) with a focus on multi-stream real-time access to GPS observations, the software has once again been substantially extended. Promoting Open Standards as recommended by the Radio Technical Commission for Maritime Services (RTCM) remains the prime subject. Beside its Graphical User Interface (GUI), the real-time software for Windows, Linux, Mac, and Linux platforms now comes with complete Command Line Interface (CLI) and considerable post processing functionality. RINEX Version 3 file editing & Quality Check (QC) with full support of Galileo, BeiDou, and SBAS - besides GPS and GLONASS - is part of the new features. Comparison of satellite orbit/clock files in SP3 format is another fresh ability of BNC. Simultaneous multi-station Precise Point Positioning (PPP) for real-time displacement-monitoring of entire reference station networks is one more recent addition to BNC. Implemented RTCM messages for PPP (under development) comprise satellite orbit and clock corrections, code and phase observation biases, and the Vertical Total Electron Content (VTEC) of the ionosphere. The well established, mature codebase is mostly written in C++ language. Its publication under GNU GPL is thought to be well-suited for test, validation and demonstration of new approaches in precise real-time satellite navigation when IP streaming is involved. The poster highlights BNC features which are new in version 2.12 and beneficial to IAG institutions and services such as IGS/RT-IGS and to the interested public in general.

iPat: intelligent prediction and association tool for genomic research.

PubMed

Chen, Chunpeng James; Zhang, Zhiwu

2018-06-01

The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills. Non-programmers struggle to use them efficiently because of the steep learning curves and zero tolerance for data formats and mistakes when inputting keywords and parameters. To address these problems, this study developed a software package, named the Intelligent Prediction and Association Tool (iPat), with a user-friendly graphical user interface. With iPat, GWAS or GS can be performed using a pointing device to simply drag and/or click on graphical elements to specify input data files, choose input parameters and select analytical models. Models available to users include those implemented in third party CLI packages such as GAPIT, PLINK, FarmCPU, BLINK, rrBLUP and BGLR. Users can choose any data format and conduct analyses with any of these packages. File conversions are automatically conducted for specified input data and selected packages. A GWAS-assisted genomic prediction method was implemented to perform genomic prediction using any GWAS method such as FarmCPU. iPat was written in Java for adaptation to multiple operating systems including Windows, Mac and Linux. The iPat executable file, user manual, tutorials and example datasets are freely available at http://zzlab.net/iPat. zhiwu.zhang@wsu.edu.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, Per; Benveniste, Jerome

2017-04-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products.
GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information
and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced
computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations,
and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT
Install Guide. A set of a-priori data and models are made available as well. Without any doubt the development
of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for
oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming
on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy,
Oceanography and Solid earth studies.
Accordingly, the GUT version 3 has:
 - An attractive and easy to use Graphic User Interface (GUI) for the toolbox,
 - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients,
anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies.
 - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, Per; Benveniste, Jerome; Team Gut

2016-04-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products.
GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information
and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced
computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations,
and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT
Install Guide. A set of a-priori data and models are made available as well. Without any doubt the development
of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for
oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming
on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy,
Oceanography and Solid earth studies.
Accordingly, the GUT version 3 has:
 - An attractive and easy to use Graphic User Interface (GUI) for the toolbox,
 - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients,
anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies.
 - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

NASA Astrophysics Data System (ADS)

Carniel, Roberto; Di Cecca, Mauro; Jaquet, Olivier

2006-05-01

In the framework of the EU-funded project "Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard" (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

PubMed

Fidaner, Işık Barış; Cankorur-Cetinkaya, Ayca; Dikicioglu, Duygu; Kirdar, Betul; Cemgil, Ali Taylan; Oliver, Stephen G

2016-02-01

Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets. We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. This algorithm involves two components of operation. Component 1 constructs a Bayesian non-parametric model (Infinite Mixture of Piecewise Linear Sequences) and Component 2, which applies a novel clustering methodology (Two-Stage Clustering). The software can also assign biological meaning to the identified clusters using an appropriate ontology. It applies multiple hypothesis testing to report the significance of these enrichments. The algorithm has a four-phase pipeline. The application can be executed using either command-line tools or a user-friendly Graphical User Interface. The latter has been developed to address the needs of both specialist and non-specialist users. We use three diverse test cases to demonstrate the flexibility of the proposed strategy. In all cases, CLUSTERnGO not only outperformed existing algorithms in assigning unique GO term enrichments to the identified clusters, but also revealed novel insights regarding the biological systems examined, which were not uncovered in the original publications. The C++ and QT source codes, the GUI applications for Windows, OS X and Linux operating systems and user manual are freely available for download under the GNU GPL v3 license at http://www.cmpe.boun.edu.tr/content/CnG. sgo24@cam.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

al3c: high-performance software for parameter inference using Approximate Bayesian Computation.

PubMed

Stram, Alexander H; Marjoram, Paul; Chen, Gary K

2015-11-01

The development of Approximate Bayesian Computation (ABC) algorithms for parameter inference which are both computationally efficient and scalable in parallel computing environments is an important area of research. Monte Carlo rejection sampling, a fundamental component of ABC algorithms, is trivial to distribute over multiple processors but is inherently inefficient. While development of algorithms such as ABC Sequential Monte Carlo (ABC-SMC) help address the inherent inefficiencies of rejection sampling, such approaches are not as easily scaled on multiple processors. As a result, current Bayesian inference software offerings that use ABC-SMC lack the ability to scale in parallel computing environments. We present al3c, a C++ framework for implementing ABC-SMC in parallel. By requiring only that users define essential functions such as the simulation model and prior distribution function, al3c abstracts the user from both the complexities of parallel programming and the details of the ABC-SMC algorithm. By using the al3c framework, the user is able to scale the ABC-SMC algorithm in parallel computing environments for his or her specific application, with minimal programming overhead. al3c is offered as a static binary for Linux and OS-X computing environments. The user completes an XML configuration file and C++ plug-in template for the specific application, which are used by al3c to obtain the desired results. Users can download the static binaries, source code, reference documentation and examples (including those in this article) by visiting https://github.com/ahstram/al3c. astram@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

psRNATarget: a plant small RNA target analysis server (2017 release).

PubMed

Dai, Xinbin; Zhuang, Zhaohong; Zhao, Patrick Xuechun

2018-04-30

Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility. This update enhances its analytical performance by developing a new scoring schema that is capable of discovering miRNA-mRNA interactions at higher 'recall rates' without significantly increasing total prediction output. The scoring procedure is customizable for the users to search both canonical and non-canonical targets. This update also enables transmitting and analyzing 'big' data empowered by (a) the implementation of multi-threading chunked file uploading, which can be paused and resumed, using HTML5 APIs and (b) the allocation of significantly more computing nodes to its back-end Linux cluster. The updated psRNATarget server has clear, compelling and user-friendly interfaces that enhance user experiences and present data clearly and concisely. The psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/.

Microcomputer-based artificial vision support system for real-time image processing for camera-driven visual prostheses

NASA Astrophysics Data System (ADS)

Fink, Wolfgang; You, Cindy X.; Tarbell, Mark A.

2010-01-01

It is difficult to predict exactly what blind subjects with camera-driven visual prostheses (e.g., retinal implants) can perceive. Thus, it is prudent to offer them a wide variety of image processing filters and the capability to engage these filters repeatedly in any user-defined order to enhance their visual perception. To attain true portability, we employ a commercial off-the-shelf battery-powered general purpose Linux microprocessor platform to create the microcomputer-based artificial vision support system (μAVS2) for real-time image processing. Truly standalone, μAVS2 is smaller than a deck of playing cards, lightweight, fast, and equipped with USB, RS-232 and Ethernet interfaces. Image processing filters on μAVS2 operate in a user-defined linear sequential-loop fashion, resulting in vastly reduced memory and CPU requirements during execution. μAVS2 imports raw video frames from a USB or IP camera, performs image processing, and issues the processed data over an outbound Internet TCP/IP or RS-232 connection to the visual prosthesis system. Hence, μAVS2 affords users of current and future visual prostheses independent mobility and the capability to customize the visual perception generated. Additionally, μAVS2 can easily be reconfigured for other prosthetic systems. Testing of μAVS2 with actual retinal implant carriers is envisioned in the near future.

Porting and redesign of Geotool software system to Qt

NASA Astrophysics Data System (ADS)

Miljanovic Tamarit, V.; Carneiro, L.; Henson, I. H.; Tomuta, E.

2016-12-01

Geotool is a software system that allows a user to interactively display and process seismoacoustic data from International Monitoring System (IMS) station. Geotool can be used to perform a number of analysis and review tasks, including data I/O, waveform filtering, quality control, component rotation, amplitude and arrival measurement and review, array beamforming, correlation, Fourier analysis, FK analysis, event review and location, particle motion visualization, polarization analysis, instrument response convolution/deconvolution, real-time display, signal to noise measurement, spectrogram, and travel time model display. The Geotool program was originally written in C using the X11/Xt/Motif libraries for graphics. It was later ported to C++. Now the program is being ported to the Qt graphics system to be more compatible with the other software in the International Data Centre (IDC). Along with this port, a redesign of the architecture is underway to achieve a separation between user interface, control, and data model elements, in line with design patterns such as Model-View-Controller. Qt is a cross-platform application framework that will allow geotool to easily run on Linux, Mac, and Windows. The Qt environment includes modern libraries and user interfaces for standard utilities such as file and database access, printing, and inter-process communications. The Qt Widgets for Technical Applications library (QWT) provides tools for displaying standard data analysis graphics.

PandASoft: Open Source Instructional Laboratory Administration Software

NASA Astrophysics Data System (ADS)

Gay, P. L.; Braasch, P.; Synkova, Y. N.

2004-12-01

PandASoft (Physics and Astronomy Software) is software for organizing and archiving a department's teaching resources and materials. An easy to use, secure interface allows faculty and staff to explore equipment inventories, see what laboratory experiments are available, find handouts, and track what has been used in different classes in the past. Divided into five sections: classes, equipment, laboratories, links, and media, its database cross links materials, allowing users to see what labs are used with which classes, what media and equipment are used with which labs, or simply what equipment is lurking in which room. Written in PHP and MySQL, this software can be installed on any UNIX / Linux platform, including Macintosh OS X. It is designed to allow users to easily customize the headers, footers and colors to blend with existing sites - no programming experience required. While initial data input is labor intensive, the system will save time later by allowing users to quickly answer questions related to what is in inventory, where it is located, how many are in stock, and where online they can learn more. It will also provide a central location for storing PDFs of handouts, and links to applets and cool sites at other universities. PandASoft comes with over 100 links to online resources pre-installed. We would like to thank Dr. Wolfgang Rueckner and the Harvard University Science Center for providing computers and resources for this project.

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

PubMed

Ahmed, Aqeel; Smith, Richard D; Clark, Jordan J; Dunbar, James B; Carlson, Heather A

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Microcomputer-based artificial vision support system for real-time image processing for camera-driven visual prostheses.

PubMed

Fink, Wolfgang; You, Cindy X; Tarbell, Mark A

2010-01-01

It is difficult to predict exactly what blind subjects with camera-driven visual prostheses (e.g., retinal implants) can perceive. Thus, it is prudent to offer them a wide variety of image processing filters and the capability to engage these filters repeatedly in any user-defined order to enhance their visual perception. To attain true portability, we employ a commercial off-the-shelf battery-powered general purpose Linux microprocessor platform to create the microcomputer-based artificial vision support system (microAVS(2)) for real-time image processing. Truly standalone, microAVS(2) is smaller than a deck of playing cards, lightweight, fast, and equipped with USB, RS-232 and Ethernet interfaces. Image processing filters on microAVS(2) operate in a user-defined linear sequential-loop fashion, resulting in vastly reduced memory and CPU requirements during execution. MiccroAVS(2) imports raw video frames from a USB or IP camera, performs image processing, and issues the processed data over an outbound Internet TCP/IP or RS-232 connection to the visual prosthesis system. Hence, microAVS(2) affords users of current and future visual prostheses independent mobility and the capability to customize the visual perception generated. Additionally, microAVS(2) can easily be reconfigured for other prosthetic systems. Testing of microAVS(2) with actual retinal implant carriers is envisioned in the near future.

BamTools: a C++ API and toolkit for analyzing and managing BAM files

PubMed Central

Barnett, Derek W.; Garrison, Erik K.; Quinlan, Aaron R.; Strömberg, Michael P.; Marth, Gabor T.

2011-01-01

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools. Contact: barnetde@bc.edu PMID:21493652

Level 1 Processing of MODIS Direct Broadcast Data at the GSFC DAAC

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Kempler, Steven J. (Technical Monitor)

2001-01-01

The GSFC DAAC is working to test and package the MODIS Level 1 Processing software for Aqua Direct Broadcast data. This entails the same code base, but different lookup tables for Aqua and Terra. However, the most significant change is the use of ancillary attitude and ephemeris files instead of orbit/attitude information within the science data stream (as with Terra). In addition, we are working on Linux: ports of the algorithms, which could eventually enable processing on PC clusters. Finally, the GSFC DAAC is also working with the GSFC Direct Readout laboratory to ingest Level 0 data from the GSFC DB antenna into the main DAAC, enabling level 1 production in near real time in support of applications users, such as the Synergy project. The mechanism developed for this could conceivably be extended to other participating stations.

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.

PubMed

Chew, Teong Han; Joyce-Tan, Kwee Hong; Akma, Farizuwana; Shamsir, Mohd Shahir

2011-05-01

birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware. The birgHPC Live CD and relevant user guide are available for free at http://birg1.fbb.utm.my/birghpc.

A Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing (SAPE)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2009-01-01

SAPE is a Python-based multidisciplinary analysis tool for systems analysis of planetary entry, descent, and landing (EDL) for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. The purpose of SAPE is to provide a variable-fidelity capability for conceptual and preliminary analysis within the same framework. SAPE includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and structural sizing. SAPE uses the Python language-a platform-independent open-source software for integration and for the user interface. The development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE runs on Microsoft Windows and Apple Mac OS X and has been partially tested on Linux.

A user's guide to Sandia's latin hypercube sampling software : LHS UNIX library/standalone version.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Wyss, Gregory Dane

2004-07-01

This document is a reference guide for the UNIX Library/Standalone version of the Latin Hypercube Sampling Software. This software has been developed to generate Latin hypercube multivariate samples. This version runs on Linux or UNIX platforms. This manual covers the use of the LHS code in a UNIX environment, run either as a standalone program or as a callable library. The underlying code in the UNIX Library/Standalone version of LHS is almost identical to the updated Windows version of LHS released in 1998 (SAND98-0210). However, some modifications were made to customize it for a UNIX environment and as a librarymore » that is called from the DAKOTA environment. This manual covers the use of the LHS code as a library and in the standalone mode under UNIX.« less

Eternal Sunshine of the Spotless Machine: Protecting Privacy with Ephemeral Channels

PubMed Central

Dunn, Alan M.; Lee, Michael Z.; Jana, Suman; Kim, Sangman; Silberstein, Mark; Xu, Yuanzhong; Shmatikov, Vitaly; Witchel, Emmett

2014-01-01

Modern systems keep long memories. As we show in this paper, an adversary who gains access to a Linux system, even one that implements secure deallocation, can recover the contents of applications’ windows, audio buffers, and data remaining in device drivers—long after the applications have terminated. We design and implement Lacuna, a system that allows users to run programs in “private sessions.” After the session is over, all memories of its execution are erased. The key abstraction in Lacuna is an ephemeral channel, which allows the protected program to talk to peripheral devices while making it possible to delete the memories of this communication from the host. Lacuna can run unmodified applications that use graphics, sound, USB input devices, and the network, with only 20 percentage points of additional CPU utilization. PMID:24755709

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

2016-01-01

Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

Soft control of scanning probe microscope with high flexibility.

PubMed

Liu, Zhenghui; Guo, Yuzheng; Zhang, Zhaohui; Zhu, Xing

2007-01-01

Most commercial scanning probe microscopes have multiple embedded digital microprocessors and utilize complex software for system control, which is not easily obtained or modified by researchers wishing to perform novel and special applications. In this paper, we present a simple and flexible control solution that just depends on software running on a single-processor personal computer with real-time Linux operating system to carry out all the control tasks including negative feedback, tip moving, data processing and user interface. In this way, we fully exploit the potential of a personal computer in calculating and programming, enabling us to manipulate the scanning probe as required without any special digital control circuits and related technical know-how. This solution has been successfully applied to a homemade ultrahigh vacuum scanning tunneling microscope and a multiprobe scanning tunneling microscope.

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

GoView is a video-game-like software engine, written in the C and C++ computing languages, that enables real-time, three-dimensional (3D)-appearing visual representation of spacecraft and trajectories (1) from any perspective; (2) at any spatial scale from spacecraft to Solar-system dimensions; (3) in user-selectable time scales; (4) in the past, present, and/or future; (5) with varying speeds; and (6) forward or backward in time. GoView constructs an interactive 3D world by use of spacecraft-mission data from pre-existing engineering software tools. GoView can also be used to produce distributable application programs for depicting NASA orbital missions on personal computers running the Windows XP, Mac OsX, and Linux operating systems. GoView enables seamless rendering of Cartesian coordinate spaces with programmable graphics hardware, whereas prior programs for depicting spacecraft trajectories variously require non-Cartesian coordinates and/or are not compatible with programmable hardware. GoView incorporates an algorithm for nonlinear interpolation between arbitrary reference frames, whereas the prior programs are restricted to special classes of inertial and non-inertial reference frames. Finally, whereas the prior programs present complex user interfaces requiring hours of training, the GoView interface provides guidance, enabling use without any training.

Neuronify: An Educational Simulator for Neural Circuits.

PubMed

Dragly, Svenn-Arne; Hobbi Mobarhan, Milad; Våvang Solbrå, Andreas; Tennøe, Simen; Hafreager, Anders; Malthe-Sørenssen, Anders; Fyhn, Marianne; Hafting, Torkel; Einevoll, Gaute T

2017-01-01

Educational software (apps) can improve science education by providing an interactive way of learning about complicated topics that are hard to explain with text and static illustrations. However, few educational apps are available for simulation of neural networks. Here, we describe an educational app, Neuronify, allowing the user to easily create and explore neural networks in a plug-and-play simulation environment. The user can pick network elements with adjustable parameters from a menu, i.e., synaptically connected neurons modelled as integrate-and-fire neurons and various stimulators (current sources, spike generators, visual, and touch) and recording devices (voltmeter, spike detector, and loudspeaker). We aim to provide a low entry point to simulation-based neuroscience by allowing students with no programming experience to create and simulate neural networks. To facilitate the use of Neuronify in teaching, a set of premade common network motifs is provided, performing functions such as input summation, gain control by inhibition, and detection of direction of stimulus movement. Neuronify is developed in C++ and QML using the cross-platform application framework Qt and runs on smart phones (Android, iOS) and tablet computers as well personal computers (Windows, Mac, Linux).

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta.

PubMed

Kleffner, Robert; Flatten, Jeff; Leaver-Fay, Andrew; Baker, David; Siegel, Justin B; Khatib, Firas; Cooper, Seth

2017-09-01

Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter. Foldit Standalone is available for download at https://fold.it/standalone , under the Rosetta license, which is free for academic and non-profit users. It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux. scooper@ccs.neu.edu. © The Author(s) 2017. Published by Oxford University Press.

Hacking and securing the AR.Drone 2.0 quadcopter: investigations for improving the security of a toy

NASA Astrophysics Data System (ADS)

Pleban, Johann-Sebastian; Band, Ricardo; Creutzburg, Reiner

2014-02-01

In this article we describe the security problems of the Parrot AR.Drone 2.0 quadcopter. Due to the fact that it is promoted as a toy with low acquisition costs, it may end up being used by many individuals which makes it a target for harmful attacks. In addition, the videostream of the drone could be of interest for a potential attacker due to its ability of revealing confidential information. Therefore, we will perform a security threat analysis on this particular drone. We will set the focus mainly on obvious security vulnerabilities like the unencrypted Wi-Fi connection or the user management of the GNU/Linux operating system which runs on the drone. We will show how the drone can be hacked in order to hijack the AR.Drone 2.0. Our aim is to sensitize the end-user of AR.Drones by describing the security vulnerabilities and to show how the AR.Drone 2.0 could be secured from unauthorized access. We will provide instructions to secure the drones Wi-Fi connection and its operation with the official Smartphone App and third party PC software.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

PubMed

Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

2016-02-01

Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

UNIPIC code for simulations of high power microwave devices

NASA Astrophysics Data System (ADS)

Wang, Jianguo; Zhang, Dianhui; Liu, Chunliang; Li, Yongdong; Wang, Yue; Wang, Hongguang; Qiao, Hailiang; Li, Xiaoze

2009-03-01

In this paper, UNIPIC code, a new member in the family of fully electromagnetic particle-in-cell (PIC) codes for simulations of high power microwave (HPM) generation, is introduced. In the UNIPIC code, the electromagnetic fields are updated using the second-order, finite-difference time-domain (FDTD) method, and the particles are moved using the relativistic Newton-Lorentz force equation. The convolutional perfectly matched layer method is used to truncate the open boundaries of HPM devices. To model curved surfaces and avoid the time step reduction in the conformal-path FDTD method, CP weakly conditional-stable FDTD (WCS FDTD) method which combines the WCS FDTD and CP-FDTD methods, is implemented. UNIPIC is two-and-a-half dimensional, is written in the object-oriented C++ language, and can be run on a variety of platforms including WINDOWS, LINUX, and UNIX. Users can use the graphical user's interface to create the geometric structures of the simulated HPM devices, or input the old structures created before. Numerical experiments on some typical HPM devices by using the UNIPIC code are given. The results are compared to those obtained from some well-known PIC codes, which agree well with each other.

Neuronify: An Educational Simulator for Neural Circuits

PubMed Central

Hafreager, Anders; Malthe-Sørenssen, Anders; Fyhn, Marianne

2017-01-01

Abstract Educational software (apps) can improve science education by providing an interactive way of learning about complicated topics that are hard to explain with text and static illustrations. However, few educational apps are available for simulation of neural networks. Here, we describe an educational app, Neuronify, allowing the user to easily create and explore neural networks in a plug-and-play simulation environment. The user can pick network elements with adjustable parameters from a menu, i.e., synaptically connected neurons modelled as integrate-and-fire neurons and various stimulators (current sources, spike generators, visual, and touch) and recording devices (voltmeter, spike detector, and loudspeaker). We aim to provide a low entry point to simulation-based neuroscience by allowing students with no programming experience to create and simulate neural networks. To facilitate the use of Neuronify in teaching, a set of premade common network motifs is provided, performing functions such as input summation, gain control by inhibition, and detection of direction of stimulus movement. Neuronify is developed in C++ and QML using the cross-platform application framework Qt and runs on smart phones (Android, iOS) and tablet computers as well personal computers (Windows, Mac, Linux). PMID:28321440

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

Review of Enabling Technologies to Facilitate Secure Compute Customization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aderholdt, Ferrol; Caldwell, Blake A; Hicks, Susan Elaine

High performance computing environments are often used for a wide variety of workloads ranging from simulation, data transformation and analysis, and complex workflows to name just a few. These systems may process data for a variety of users, often requiring strong separation between job allocations. There are many challenges to establishing these secure enclaves within the shared infrastructure of high-performance computing (HPC) environments. The isolation mechanisms in the system software are the basic building blocks for enabling secure compute enclaves. There are a variety of approaches and the focus of this report is to review the different virtualization technologies thatmore » facilitate the creation of secure compute enclaves. The report reviews current operating system (OS) protection mechanisms and modern virtualization technologies to better understand the performance/isolation properties. We also examine the feasibility of running ``virtualized'' computing resources as non-privileged users, and providing controlled administrative permissions for standard users running within a virtualized context. Our examination includes technologies such as Linux containers (LXC [32], Docker [15]) and full virtualization (KVM [26], Xen [5]). We categorize these different approaches to virtualization into two broad groups: OS-level virtualization and system-level virtualization. The OS-level virtualization uses containers to allow a single OS kernel to be partitioned to create Virtual Environments (VE), e.g., LXC. The resources within the host's kernel are only virtualized in the sense of separate namespaces. In contrast, system-level virtualization uses hypervisors to manage multiple OS kernels and virtualize the physical resources (hardware) to create Virtual Machines (VM), e.g., Xen, KVM. This terminology of VE and VM, detailed in Section 2, is used throughout the report to distinguish between the two different approaches to providing virtualized execution environments. As part of our technology review we analyzed several current virtualization solutions to assess their vulnerabilities. This included a review of common vulnerabilities and exposures (CVEs) for Xen, KVM, LXC and Docker to gauge their susceptibility to different attacks. The complete details are provided in Section 5 on page 33. Based on this review we concluded that system-level virtualization solutions have many more vulnerabilities than OS level virtualization solutions. As such, security mechanisms like sVirt (Section 3.3) should be considered when using system-level virtualization solutions in order to protect the host against exploits. The majority of vulnerabilities related to KVM, LXC, and Docker are in specific regions of the system. Therefore, future "zero day attacks" are likely to be in the same regions, which suggests that protecting these areas can simplify the protection of the host and maintain the isolation between users. The evaluations of virtualization technologies done thus far are discussed in Section 4. This includes experiments with 'user' namespaces in VEs, which provides the ability to isolate user privileges and allow a user to run with different UIDs within the container while mapping them to non-privileged UIDs in the host. We have identified Linux namespaces as a promising mechanism to isolate shared resources, while maintaining good performance. In Section 4.1 we describe our tests with LXC as a non-root user and leveraging namespaces to control UID/GID mappings and support controlled sharing of parallel file-systems. We highlight several of these namespace capabilities in Section 6.2.3. The other evaluations that were performed during this initial phase of work provide baseline performance data for comparing VEs and VMs to purely native execution. In Section 4.2 we performed tests using the High-Performance Computing Conjugate Gradient (HPCCG) benchmark to establish baseline performance for a scientific application when run on the Native (host) machine in contrast with execution under Docker and KVM. Our tests verified prior studies showing roughly 2-4% overheads in application execution time & MFlops when running in hypervisor-base environments (VMs) as compared to near native performance with VEs. For more details, see Figures 4.5 (page 28), 4.6 (page 28), and 4.7 (page 29). Additionally, in Section 4.3 we include network measurements for TCP bandwidth performance over the 10GigE interface in our testbed. The Native and Docker based tests achieved >= ~9Gbits/sec, while the KVM configuration only achieved 2.5Gbits/sec (Table 4.6 on page 32). This may be a configuration issue with our KVM installation, and is a point for further testing as we refine the network settings in the testbed. The initial network tests were done using a bridged networking configuration. The report outline is as follows: - Section 1 introduces the report and clarifies the scope of the proj...« less

Adaptive Multilevel Middleware for Object Systems

DTIC Science & Technology

2006-12-01

the system at the system-call level or using the CORBA-standard Extensible Transport Framework ( ETF ). Transparent insertion is highly desirable from an...often as it needs to. This is remedied by using the real-time scheduling class in a stock Linux kernel. We used schedsetscheduler system call (with...real-time scheduling class (SCHEDFIFO) for all the ML-NFD programs, later experiments with CPU load indicate that a stock Linux kernel is not

NAVO MSRC Navigator. Fall 2006

DTIC Science & Technology

2006-01-01

UNIX Manual Pages: xdm (1x). 7. Buddenhagen, Oswald, “The KDM Handbook,” KDE Documentation, http://docs.kde.org/development/ en /kdebase/kdm/. 8... Linux Opteron cluster was recently determined through a series of simulations that employed both fixed and adaptive meshes. The fixed-mesh scalability...approximately eight in the total number of cells in the 3-D simulation. The fixed-mesh and AMR scalability results on the Linux Opteron cluster are

AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs.

PubMed

Gorjanc, Gregor; Hickey, John M

2018-05-02

AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimisation can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimisation objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier. Executable versions of AlphaMate for Windows, Mac, and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate. gregor.gorjanc@roslin.ed.ack.uk.

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the parameter values for each operation. The knowledge of CRS-Stack processing procedure is still preserved in the software, which is easy and efficient to be learned. The software will still be developed in the future. Any new innovative seismic processing workflow will also be added into this GUI software.

Data Collection and Recording on the Wisconsin/GSFC X-ray Quantum Calorimeter

NASA Astrophysics Data System (ADS)

O'Neill, Laura; X-ray Astrophysics Group at the University of Wisconsin-Madison

2016-01-01

The Wisconsin/GSFC X-ray Quantum Calorimeter (XQC) is an astronomical X-ray sounding rocket payload which uses a micro-calorimeter array to detect low (less than1keV) X-rays. Three different devices were evaluated to upgrade XQC's data collection and recording system. The system takes incoming data from XQC's pixel sensors and stores it to a memory card. The upgrade is a much smaller board and much more compact storage device. The Terasic DE0-Nano, Terasic DE0-Nano SoC, and the BeagleBone Black were tested to determine which would suit the needs of XQC best. The device needed to take incoming data, store it to an SD card, and be able to output it through a USB connection. The Terasic DE0-Nano is a simple FPGA, but needed some peripheral additions for an SD card slot and USB readout. The Terasic DE0-Nano SoC was a powerful FPGA and hard processor running Linux combined. It was able to do what was needed, but pulled too much power in the process. The BeagleBone Black had a microcontroller and also ran Linux. This last device ended up being the best choice, as it did not require too much power and had a very easy system already in place for USB readout. The only difficulty to deal with was programming the microcontroller in assembly language. This device is necessary due to the telemetry on XQC not being able to send all of the data down during the flight. It records valuable data about low energy X-rays so that the X-ray Astrophysics Groups at the University of Wisconsin-Madison and Goddard Space Flight Center can analyze and resolve the spectrum of the soft X-ray background.Later, using the digital logic on a Terasic DE0-Nano FPGA, a data simulator for the BeagleBone Black data collection and recording device was created. Programmed with Quartus II, the simulator uses basic digital logic components to fabricate trackable data signals and related timing signals to send to the data management device, as well as other timing signals that are asynchronous to the rest of the circuit, a failsafe enable for outputs, and several user feedback components

PGOPHER in the Classroom and the Laboratory

NASA Astrophysics Data System (ADS)

Western, Colin

2015-06-01

PGOPHER is a general purpose program for simulating and fitting rotational, vibrational and electronic spectra. As it uses a graphical user interface the basic operation is sufficiently straightforward to make it suitable for use in undergraduate practicals and computer based classes. This talk will present two experiments that have been in regular use by Bristol undergraduates for some years based on the analysis of infra-red spectra of cigarette smoke and, for more advanced students, visible and near ultra-violet spectra of a nitrogen discharge and a hydrocarbon flame. For all of these the rotational structure is analysed and used to explore ideas of bonding. The talk will discuss the requirements for the apparatus and the support required. Other ideas for other possible experiments and computer based exercises will also be presented, including a group exercise. The PGOPHER program is open source, and is available for Microsoft Windows, Apple Mac and Linux. It can be freely downloaded from the supporting website http://pgopher.chm.bris.ac.uk. The program does not require any installation process, so can be run on student's own machines or easily setup on classroom or laboratory computers. PGOPHER, a Program for Simulating Rotational, Vibrational and Electronic Structure, C. M. Western, University of Bristol, http://pgopher.chm.bris.ac.uk PGOPHER version 8.0, C M Western, 2014, University of Bristol Research Data Repository, doi:10.5523/bris.huflggvpcuc1zvliqed497r2

Source Code Analysis Laboratory (SCALe) for Energy Delivery Systems

DTIC Science & Technology

2010-12-01

the software for reevaluation. Once the ree- valuation process is completed, CERT provides the client a report detailing the software’s con - formance...Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8% Wine...inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with energy system software will help

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Covert Android Rootkit Detection: Evaluating Linux Kernel Level Rootkits on the Android Operating System

DTIC Science & Technology

2012-06-14

the attacker . Thus, this race condition causes a privilege escalation . 2.2.5 Summary This section reviewed software exploitation of a Linux kernel...has led to increased targeting by malware writers. Android attacks have naturally sparked interest in researching protections for Android . This...release, Android 4.0 Ice Cream Sandwich. These rootkits focused on covert techniques to hide the presence of data used by an attacker to infect a

The Ubuntu Chat Corpus for Multiparticipant Chat Analysis

DTIC Science & Technology

2013-03-01

Intelligence (www.aaai.org). All rights reserved. the # LINUX corpus (Elsner and Charniak 2010), and the #IPHONE/#PHYSICS/#PYTHON corpus (Adams 2008). For many...made publicly available, making it difficult to comparatively evaluate dif- ferent techniques. Corpus Description Ubuntu, a Linux -based operating...Kubuntu (Ubuntu with KDE ) support #ubuntu-devel 2 112 074 12 140 53.7 2004-10-01 Developmental team coordination #ubuntu+1 1 621 680 26 805 52.6 2007-04-04

MVC for Content Management on the Cloud

DTIC Science & Technology

2011-09-01

Windows, Linux , MacOS, PalmOS and other customized ones (Qiu). Figure 20 illustrates implementation of MVC architecture. Qiu examines a “universal...Listing of Unzipped Text Document (From O’Reilly & Associates, Inc, 2005) Figure 37 shows the results of unzipping this file in Linux . The contents of the...ODF Adoption TC, and the ODF Alliance include members from Adobe, BBC, Bristol City Council, Bull, Corel, EDS, EMC, GNOME, IBM, Intel, KDE , MySQL

[Making a low cost IPSec router on Linux and the assessment for practical use].

PubMed

Amiki, M; Horio, M

2001-09-01

We installed Linux and FreeS/WAN on a PC/AT compatible machine to make an IPSec router. We measured the time of ping/ftp, only in the university, between the university and the external network. Between the university and the external network (the Internet), there were no differences. Therefore, we concluded that CPU load was not remarkable at low speed networks, because packets exchanged via the Internet are small, or compressions of VPN are more effective than encoding and decoding. On the other hand, in the university, the IPSec router performed down about 20-30% compared with normal IP communication, but this is not a serious problem for practical use. Recently, VPN machines are becoming cheaper, but they do not function sufficiently to create a fundamental VPN environment. Therefore, if one wants a fundamental VPN environment at a low cost, we believe you should select a VPN router on Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayan Ghosh, Jeff Hammond

OpenSHMEM is a community effort to unifyt and standardize the SHMEM programming model. MPI (Message Passing Interface) is a well-known community standard for parallel programming using distributed memory. The most recen t release of MPI, version 3.0, was designed in part to support programming models like SHMEM.OSHMPI is an implementation of the OpenSHMEM standard using MPI-3 for the Linux operating system. It is the first implementation of SHMEM over MPI one-sided communication and has the potential to be widely adopted due to the portability and widely availability of Linux and MPI-3. OSHMPI has been tested on a variety of systemsmore » and implementations of MPI-3, includingInfiniBand clusters using MVAPICH2 and SGI shared-memory supercomputers using MPICH. Current support is limited to Linux but may be extended to Apple OSX if there is sufficient interest. The code is opensource via https://github.com/jeffhammond/oshmpi« less

Timing characterization and analysis of the Linux-based, closed loop control computer for the Subaru Telescope laser guide star adaptive optics system

NASA Astrophysics Data System (ADS)

Dinkins, Matthew; Colley, Stephen

2008-07-01

Hardware and software specialized for real time control reduce the timing jitter of executables when compared to off-the-shelf hardware and software. However, these specialized environments are costly in both money and development time. While conventional systems have a cost advantage, the jitter in these systems is much larger and potentially problematic. This study analyzes the timing characterstics of a standard Dell server running a fully featured Linux operating system to determine if such a system would be capable of meeting the timing requirements for closed loop operations. Investigations are preformed on the effectiveness of tools designed to make off-the-shelf system performance closer to specialized real time systems. The Gnu Compiler Collection (gcc) is compared to the Intel C Compiler (icc), compiler optimizations are investigated, and real-time extensions to Linux are evaluated.

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.

PubMed

Simillion, Cedric; Janssens, Koen; Sterck, Lieven; Van de Peer, Yves

2008-01-01

i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes. The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/

MaxReport: An Enhanced Proteomic Result Reporting Tool for MaxQuant.

PubMed

Zhou, Tao; Li, Chuyu; Zhao, Wene; Wang, Xinru; Wang, Fuqiang; Sha, Jiahao

2016-01-01

MaxQuant is a proteomic software widely used for large-scale tandem mass spectrometry data. We have designed and developed an enhanced result reporting tool for MaxQuant, named as MaxReport. This tool can optimize the results of MaxQuant and provide additional functions for result interpretation. MaxReport can generate report tables for protein N-terminal modifications. It also supports isobaric labelling based relative quantification at the protein, peptide or site level. To obtain an overview of the results, MaxReport performs general descriptive statistical analyses for both identification and quantification results. The output results of MaxReport are well organized and therefore helpful for proteomic users to better understand and share their data. The script of MaxReport, which is freely available at http://websdoor.net/bioinfo/maxreport/, is developed using Python code and is compatible across multiple systems including Windows and Linux.

Implementation of a Portable Personal EKG Signal Monitoring System

NASA Astrophysics Data System (ADS)

Tan, Tan-Hsu; Chang, Ching-Su; Chen, Yung-Fu; Lee, Cheng

This research develops a portable personal EKG signal monitoring system to help patients monitor their EKG signals instantly to avoid the occurrence of tragedies. This system is built with two main units: signal pro-cessing unit and monitoring and evaluation unit. The first unit consists of EKG signal sensor, signal amplifier, digitalization circuit, and related control circuits. The second unit is a software tool developed on an embedded Linux platform (called CSA). Experimental result indicates that the proposed system has the practical potential for users in health monitoring. It is demonstrated to be more convenient and with greater portability than the conventional PC-based EKG signal monitoring systems. Furthermore, all the application units embedded in the system are built with open source codes, no licensed fee is required for operating systems and authorized applications. Thus, the building cost is much lower than the traditional systems.

Geospatial Authentication

NASA Technical Reports Server (NTRS)

Lyle, Stacey D.

2009-01-01

A software package that has been designed to allow authentication for determining if the rover(s) is/are within a set of boundaries or a specific area to access critical geospatial information by using GPS signal structures as a means to authenticate mobile devices into a network wirelessly and in real-time has been developed. The advantage lies in that the system only allows those with designated geospatial boundaries or areas into the server. The Geospatial Authentication software has two parts Server and Client. The server software is a virtual private network (VPN) developed in Linux operating system using Perl programming language. The server can be a stand-alone VPN server or can be combined with other applications and services. The client software is a GUI Windows CE software, or Mobile Graphical Software, that allows users to authenticate into a network. The purpose of the client software is to pass the needed satellite information to the server for authentication.

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

PubMed Central

Fried, Jake Y.; Luna, Augustin

2013-01-01

Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License. Contact: augustin@mail.nih.gov or jakeyfried@gmail.com PMID:23547033

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.

PubMed

Liu, Bin; Wu, Hao; Zhang, Deyuan; Wang, Xiaolong; Chou, Kuo-Chen

2017-02-21

To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples. All the aforementioned tedious jobs can be automatically done by the computer. Moreover, the multiprocessing technique was adopted to enhance computational speed by about 6 folds. The Pse-Analysis Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/Pse-Analysis/, and can be directly run on Windows, Linux, and Unix.

Perl Extension to the Bproc Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grunau, Daryl W.

2004-06-07

The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less

BOLDMirror: a global mirror system of DNA barcode data.

PubMed

Liu, D; Liu, L; Guo, G; Wang, W; Sun, Q; Parani, M; Ma, J

2013-11-01

DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding. © 2012 John Wiley & Sons Ltd.

Millisecond timing on PCs and Macs.

PubMed

MacInnes, W J; Taylor, T L

2001-05-01

A real-time, object-oriented solution for displaying stimuli on Windows 95/98, MacOS and Linux platforms is presented. The program, written in C++, utilizes a special-purpose window class (GLWindow), OpenGL, and 32-bit graphics acceleration; it avoids display timing uncertainty by substituting the new window class for the default window code for each system. We report the outcome of tests for real-time capability across PC and Mac platforms running a variety of operating systems. The test program, which can be used as a shell for programming real-time experiments and testing specific processors, is available at http://www.cs.dal.ca/~macinnwj. We propose to provide researchers with a sense of the usefulness of our program, highlight the ability of many multitasking environments to achieve real time, as well as caution users about systems that may not achieve real time, even under optimal conditions.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

Snoopy--a unifying Petri net framework to investigate biomolecular networks.

PubMed

Rohr, Christian; Marwan, Wolfgang; Heiner, Monika

2010-04-01

To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design. Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).

The Trick Simulation Toolkit: A NASA/Opensource Framework for Running Time Based Physics Models

NASA Technical Reports Server (NTRS)

Penn, John M.

2016-01-01

The Trick Simulation Toolkit is a simulation development environment used to create high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. Its purpose is to generate a simulation executable from a collection of user-supplied models and a simulation definition file. For each Trick-based simulation, Trick automatically provides job scheduling, numerical integration, the ability to write and restore human readable checkpoints, data recording, interactive variable manipulation, a run-time interpreter, and many other commonly needed capabilities. This allows simulation developers to concentrate on their domain expertise and the algorithms and equations of their models. Also included in Trick are tools for plotting recorded data and various other supporting utilities and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX computer operating systems. This paper describes Trick's design and use at NASA Johnson Space Center.

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.

PubMed

Jossinet, Fabrice; Westhof, Eric

2005-08-01

Efficient RNA sequence manipulations (such as multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures similar to those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information. Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S has been implemented using the Java language and has been developed and tested under UNIX systems, such as Linux and MacOSX. S2S is available at http://bioinformatics.org/S2S/.

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

PubMed

Gaponov, Yurii; Igarashi, Noriyuki; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Suzuki, Mamoru; Kosuge, Takashi; Wakatsuki, Soichi

2004-01-01

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

The Benefits and Complexities of Operating Geographic Information Systems (GIS) in a High Performance Computing (HPC) Environment

NASA Astrophysics Data System (ADS)

Shute, J.; Carriere, L.; Duffy, D.; Hoy, E.; Peters, J.; Shen, Y.; Kirschbaum, D.

2017-12-01

The NASA Center for Climate Simulation (NCCS) at the Goddard Space Flight Center is building and maintaining an Enterprise GIS capability for its stakeholders, to include NASA scientists, industry partners, and the public. This platform is powered by three GIS subsystems operating in a highly-available, virtualized environment: 1) the Spatial Analytics Platform is the primary NCCS GIS and provides users discoverability of the vast DigitalGlobe/NGA raster assets within the NCCS environment; 2) the Disaster Mapping Platform provides mapping and analytics services to NASA's Disaster Response Group; and 3) the internal (Advanced Data Analytics Platform/ADAPT) enterprise GIS provides users with the full suite of Esri and open source GIS software applications and services. All systems benefit from NCCS's cutting edge infrastructure, to include an InfiniBand network for high speed data transfers; a mixed/heterogeneous environment featuring seamless sharing of information between Linux and Windows subsystems; and in-depth system monitoring and warning systems. Due to its co-location with the NCCS Discover High Performance Computing (HPC) environment and the Advanced Data Analytics Platform (ADAPT), the GIS platform has direct access to several large NCCS datasets including DigitalGlobe/NGA, Landsat, MERRA, and MERRA2. Additionally, the NCCS ArcGIS Desktop Windows virtual machines utilize existing NetCDF and OPeNDAP assets for visualization, modelling, and analysis - thus eliminating the need for data duplication. With the advent of this platform, Earth scientists have full access to vast data repositories and the industry-leading tools required for successful management and analysis of these multi-petabyte, global datasets. The full system architecture and integration with scientific datasets will be presented. Additionally, key applications and scientific analyses will be explained, to include the NASA Global Landslide Catalog (GLC) Reporter crowdsourcing application, the NASA GLC Viewer discovery and analysis tool, the DigitalGlobe/NGA Data Discovery Tool, the NASA Disaster Response Group Mapping Platform (https://maps.disasters.nasa.gov), and support for NASA's Arctic - Boreal Vulnerability Experiment (ABoVE).

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

PubMed

Krojer, Tobias; Talon, Romain; Pearce, Nicholas; Collins, Patrick; Douangamath, Alice; Brandao-Neto, Jose; Dias, Alexandre; Marsden, Brian; von Delft, Frank

2017-03-01

XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

GoPhast: a graphical user interface for PHAST

USGS Publications Warehouse

Winston, Richard B.

2006-01-01

GoPhast is a graphical user interface (GUI) for the USGS model PHAST. PHAST simulates multicomponent, reactive solute transport in three-dimensional, saturated, ground-water flow systems. PHAST can model both equilibrium and kinetic geochemical reactions. PHAST is derived from HST3D (flow and transport) and PHREEQC (geochemical calculations). The flow and transport calculations are restricted to constant fluid density and constant temperature. The complexity of the input required by PHAST makes manual construction of its input files tedious and error-prone. GoPhast streamlines the creation of the input file and helps reduce errors. GoPhast allows the user to define the spatial input for the PHAST flow and transport data file by drawing points, lines, or polygons on top, front, and side views of the model domain. These objects can have up to two associated formulas that define their extent perpendicular to the view plane, allowing the objects to be three-dimensional. Formulas are also used to specify the values of spatial data (data sets) both globally and for individual objects. Objects can be used to specify the values of data sets independent of the spatial and temporal discretization of the model. Thus, the grid and simulation periods for the model can be changed without respecifying spatial data pertaining to the hydrogeologic framework and boundary conditions. This report describes the operation of GoPhast and demonstrates its use with examples. GoPhast runs on Windows 2000, Windows XP, and Linux operating systems.

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

Our purpose was to build and test a lightweight solution for generating clinical research information systems (CRIS) that would allow non-IT professionals with basic knowledge of computer usage to quickly define and build a ready-to-use, safe and secure web-based clinical research system for data management. We use the acronym MAGIC (Medical Application Generator InteraCtive) for the system. The generated CRIS should be very easy to build and use, so a common LAMP (Linux Apache MySQL Perl) platform was used, which also enables short development cycles. The application was built and tested using eXtreme Programming (XP) principles by a small development team consisting of one informatics specialist, one physician and one graphical designer/programmer. The parameter and graphical user interface (GUI) definitions for the CRIS can be made by non-IT professionals using an intuitive English-language-like formalism called application definition language (ADL). From these definitions, the MAGIC builds an end-user CRIS that can be used on a wide variety of platforms (from standard workstations to hand-held devices). A working example of a national health-care-quality assessment program is presented to illustrate this process. The lightweight application for generating CRIS (MAGIC) has proven to be useful for both clinical and analytical users in real working environment. To achieve better performance and interoperability, we are planning to recompile the application using XML schemas (XSD) in HL7 CDA or openEHR archetypes formats used for parameters definition and for data interchange between different information systems.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

docBUILDER - Building Your Useful Metadata for Earth Science Data and Services.

NASA Astrophysics Data System (ADS)

Weir, H. M.; Pollack, J.; Olsen, L. M.; Major, G. R.

2005-12-01

The docBUILDER tool, created by NASA's Global Change Master Directory (GCMD), assists the scientific community in efficiently creating quality data and services metadata. Metadata authors are asked to complete five required fields to ensure enough information is provided for users to discover the data and related services they seek. After the metadata record is submitted to the GCMD, it is reviewed for semantic and syntactic consistency. Currently, two versions are available - a Web-based tool accessible with most browsers (docBUILDERweb) and a stand-alone desktop application (docBUILDERsolo). The Web version is available through the GCMD website, at http://gcmd.nasa.gov/User/authoring.html. This version has been updated and now offers: personalized templates to ease entering similar information for multiple data sets/services; automatic population of Data Center/Service Provider URLs based on the selected center/provider; three-color support to indicate required, recommended, and optional fields; an editable text window containing the XML record, to allow for quick editing; and improved overall performance and presentation. The docBUILDERsolo version offers the ability to create metadata records on a computer wherever you are. Except for installation and the occasional update of keywords, data/service providers are not required to have an Internet connection. This freedom will allow users with portable computers (Windows, Mac, and Linux) to create records in field campaigns, whether in Antarctica or the Australian Outback. This version also offers a spell-checker, in addition to all of the features found in the Web version.

The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination

PubMed Central

Krojer, Tobias; Talon, Romain; Pearce, Nicholas; Douangamath, Alice; Brandao-Neto, Jose; Dias, Alexandre; Marsden, Brian

2017-01-01

XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein–ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallo­graphic software packages such as CCP4 [Winn et al. (2011 ▸), Acta Cryst. D67, 235–242] or PHENIX [Adams et al. (2010 ▸), Acta Cryst. D66, 213–221] have entrenched the paradigm that a ‘project’ is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects. PMID:28291762

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

System Data Model (SDM) Source Code

DTIC Science & Technology

2012-08-23

CROSS_COMPILE=/opt/gumstix/build_arm_nofpu/staging_dir/bin/arm-linux-uclibcgnueabi- 8 : CC=$(CROSS_COMPILE)gcc 9: CXX=$(CROSS_COMPILE)g++ 10 : AR...and flags to pass to it 6: LEX=flex 7: LEXFLAGS=-B 8 : 9: ## The parser generator to invoke and flags to pass to it 10 : YACC=bison 11: YACCFLAGS...5: # Point to default PetaLinux root directory 6: ifndef ROOTDIR 7: ROOTDIR=$(PETALINUX)/software/petalinux-dist 8 : endif 9: 10 : PATH:=$(PATH

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

Navigation/Prop Software Suite

NASA Technical Reports Server (NTRS)

Bruchmiller, Tomas; Tran, Sanh; Lee, Mathew; Bucker, Scott; Bupane, Catherine; Bennett, Charles; Cantu, Sergio; Kwong, Ping; Propst, Carolyn

2012-01-01

Navigation (Nav)/Prop software is used to support shuttle mission analysis, production, and some operations tasks. The Nav/Prop suite containing configuration items (CIs) resides on IPS/Linux workstations. It features lifecycle documents, and data files used for shuttle navigation and propellant analysis for all flight segments. This suite also includes trajectory server, archive server, and RAT software residing on MCC/Linux workstations. Navigation/Prop represents tool versions established during or after IPS Equipment Rehost-3 or after the MCC Rehost.

Malware Memory Analysis of the IVYL Linux Rootkit: Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-04-01

report is to examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills ...The skills amassed by incident handlers and investigators alike while using Volatility to examine Windows memory images will be of some help...bin/pulseaudio --start --log-target=syslog 1362 1000 1000 nautilus 1366 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1370 1000 1000 nm-applet

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

Porting and refurbishment of the WSS TNG control software

NASA Astrophysics Data System (ADS)

Caproni, Alessandro; Zacchei, Andrea; Vuerli, Claudio; Pucillo, Mauro

2004-09-01

The Workstation Software Sytem (WSS) is the high level control software of the Italian Galileo Galilei Telescope settled in La Palma Canary Island developed at the beginning of '90 for HP-UX workstations. WSS may be seen as a middle layer software system that manages the communications between the real time systems (VME), different workstations and high level applications providing a uniform distributed environment. The project to port the control software from the HP workstation to Linux environment started at the end of 2001. It is aimed to refurbish the control software introducing some of the new software technologies and languages, available for free in the Linux operating system. The project was realized by gradually substituting each HP workstation with a Linux PC with the goal to avoid main changes in the original software running under HP-UX. Three main phases characterized the project: creation of a simulated control room with several Linux PCs running WSS (to check all the functionality); insertion in the simulated control room of some HPs (to check the mixed environment); substitution of HP workstation in the real control room. From a software point of view, the project introduces some new technologies, like multi-threading, and the possibility to develop high level WSS applications with almost every programming language that implements the Berkley sockets. A library to develop java applications has also been created and tested.

DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

PubMed Central

Gouws, André; Woods, Will; Millman, Rebecca; Morland, Antony; Green, Gary

2008-01-01

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data. PMID:19352444

A Quality-Control-Oriented Database for a Mesoscale Meteorological Observation Network

NASA Astrophysics Data System (ADS)

Lussana, C.; Ranci, M.; Uboldi, F.

2012-04-01

In the operational context of a local weather service, data accessibility and quality related issues must be managed by taking into account a wide set of user needs. This work describes the structure and the operational choices made for the operational implementation of a database system storing data from highly automated observing stations, metadata and information on data quality. Lombardy's environmental protection agency, ARPA Lombardia, manages a highly automated mesoscale meteorological network. A Quality Assurance System (QAS) ensures that reliable observational information is collected and disseminated to the users. The weather unit in ARPA Lombardia, at the same time an important QAS component and an intensive data user, has developed a database specifically aimed to: 1) providing quick access to data for operational activities and 2) ensuring data quality for real-time applications, by means of an Automatic Data Quality Control (ADQC) procedure. Quantities stored in the archive include hourly aggregated observations of: precipitation amount, temperature, wind, relative humidity, pressure, global and net solar radiation. The ADQC performs several independent tests on raw data and compares their results in a decision-making procedure. An important ADQC component is the Spatial Consistency Test based on Optimal Interpolation. Interpolated and Cross-Validation analysis values are also stored in the database, providing further information to human operators and useful estimates in case of missing data. The technical solution adopted is based on a LAMP (Linux, Apache, MySQL and Php) system, constituting an open source environment suitable for both development and operational practice. The ADQC procedure itself is performed by R scripts directly interacting with the MySQL database. Users and network managers can access the database by using a set of web-based Php applications.

A Unified and Comprehensible View of Parametric and Kernel Methods for Genomic Prediction with Application to Rice.

PubMed

Jacquin, Laval; Cao, Tuong-Vi; Ahmadi, Nourollah

2016-01-01

One objective of this study was to provide readers with a clear and unified understanding of parametric statistical and kernel methods, used for genomic prediction, and to compare some of these in the context of rice breeding for quantitative traits. Furthermore, another objective was to provide a simple and user-friendly R package, named KRMM, which allows users to perform RKHS regression with several kernels. After introducing the concept of regularized empirical risk minimization, the connections between well-known parametric and kernel methods such as Ridge regression [i.e., genomic best linear unbiased predictor (GBLUP)] and reproducing kernel Hilbert space (RKHS) regression were reviewed. Ridge regression was then reformulated so as to show and emphasize the advantage of the kernel "trick" concept, exploited by kernel methods in the context of epistatic genetic architectures, over parametric frameworks used by conventional methods. Some parametric and kernel methods; least absolute shrinkage and selection operator (LASSO), GBLUP, support vector machine regression (SVR) and RKHS regression were thereupon compared for their genomic predictive ability in the context of rice breeding using three real data sets. Among the compared methods, RKHS regression and SVR were often the most accurate methods for prediction followed by GBLUP and LASSO. An R function which allows users to perform RR-BLUP of marker effects, GBLUP and RKHS regression, with a Gaussian, Laplacian, polynomial or ANOVA kernel, in a reasonable computation time has been developed. Moreover, a modified version of this function, which allows users to tune kernels for RKHS regression, has also been developed and parallelized for HPC Linux clusters. The corresponding KRMM package and all scripts have been made publicly available.

AESS: Accelerated Exact Stochastic Simulation

NASA Astrophysics Data System (ADS)

Jenkins, David D.; Peterson, Gregory D.

2011-12-01

The Stochastic Simulation Algorithm (SSA) developed by Gillespie provides a powerful mechanism for exploring the behavior of chemical systems with small species populations or with important noise contributions. Gene circuit simulations for systems biology commonly employ the SSA method, as do ecological applications. This algorithm tends to be computationally expensive, so researchers seek an efficient implementation of SSA. In this program package, the Accelerated Exact Stochastic Simulation Algorithm (AESS) contains optimized implementations of Gillespie's SSA that improve the performance of individual simulation runs or ensembles of simulations used for sweeping parameters or to provide statistically significant results. Program summaryProgram title: AESS Catalogue identifier: AEJW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: University of Tennessee copyright agreement No. of lines in distributed program, including test data, etc.: 10 861 No. of bytes in distributed program, including test data, etc.: 394 631 Distribution format: tar.gz Programming language: C for processors, CUDA for NVIDIA GPUs Computer: Developed and tested on various x86 computers and NVIDIA C1060 Tesla and GTX 480 Fermi GPUs. The system targets x86 workstations, optionally with multicore processors or NVIDIA GPUs as accelerators. Operating system: Tested under Ubuntu Linux OS and CentOS 5.5 Linux OS Classification: 3, 16.12 Nature of problem: Simulation of chemical systems, particularly with low species populations, can be accurately performed using Gillespie's method of stochastic simulation. Numerous variations on the original stochastic simulation algorithm have been developed, including approaches that produce results with statistics that exactly match the chemical master equation (CME) as well as other approaches that approximate the CME. Solution method: The Accelerated Exact Stochastic Simulation (AESS) tool provides implementations of a wide variety of popular variations on the Gillespie method. Users can select the specific algorithm considered most appropriate. Comparisons between the methods and with other available implementations indicate that AESS provides the fastest known implementation of Gillespie's method for a variety of test models. Users may wish to execute ensembles of simulations to sweep parameters or to obtain better statistical results, so AESS supports acceleration of ensembles of simulation using parallel processing with MPI, SSE vector units on x86 processors, and/or using NVIDIA GPUs with CUDA.

An upgraded version of the generator BCVEGPY2.0 for hadronic production of B meson and its excited states

NASA Astrophysics Data System (ADS)

Chang, Chao-Hsi; Wang, Jian-Xiong; Wu, Xing-Gang

2006-11-01

An upgraded version of the package BCVEGPY2.0: [C.-H. Chang, J.-X. Wang, X.-G. Wu, Comput. Phys. Commun. 174 (2006) 241] is presented, which works under LINUX system and is named as BCVEGPY2.1. With the version and a GNU C compiler additionally, users may simulate the B-events in various experimental environments very conveniently. It has been manipulated in better modularity and code reusability (less cross communication among various modules) than BCVEGPY2.0 has. Furthermore, in the upgraded version a special execution is arranged as that the GNU command make compiles a requested code with the help of a master makefile in main code directory, and then builds an executable file with the default name run. Finally, this paper may also be considered as an erratum, i.e., typo errors in BCVEGPY2.0 and corrections accordingly have been listed. New version program (BCVEGPY2.1) summaryTitle of program: BCVEGPY2.1 Catalogue identifier: ADTJ_v2_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTJ_v2_1 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Reference to original program: BCVEGPY2.0 Reference in CPC: Comput. Phys. Commun. 174 (2006) 241 Does the new version supersede the old program: No Computer: Any LINUX based on PC with FORTRAN 77 or FORTRAN 90 and GNU C compiler as well Operating systems: LINUX Programming language used: FORTRAN 77/90 Memory required to execute with typical data: About 2.0 MB No. of lines in distributed program, including test data, etc.: 31 521 No. of bytes in distributed program, including test data, etc.: 1 310 179 Distribution format: tar.gz Nature of physical problem: Hadronic production of B meson itself and its excited states Method of solution: The code with option can generate weighted and unweighted events. An interface to PYTHIA is provided to meet the needs of jets hadronization in the production. Restrictions on the complexity of the problem: The hadronic production of (cb¯)-quarkonium in S-wave and P-wave states via the mechanism of gluon-gluon fusion are given by the so-called 'complete calculation' approach. Reasons for new version: Responding to the feedback from users, we rearrange the program in a convenient way and then it can be easily adopted by the users to do the simulations according to their own experimental environment (e.g. detector acceptances and experimental cuts). We have paid many efforts to rearrange the program into several modules with less cross communication among the modules, the main program is slimmed down and all the further actions are decoupled from the main program and can be easily called for various purposes. Typical running time: The typical running time is machine and user-parameters dependent. Typically, for production of the S-wave (cb¯)-quarkonium, when IDWTUP = 1, it takes about 20 hour on a 1.8 GHz Intel P4-processor machine to generate 1000 events; however, when IDWTUP = 3, to generate 10 6 events it takes about 40 minutes only. Of the production, the time for the P-wave (cb¯)-quarkonium will take almost two times longer than that for its S-wave quarkonium. Summary of the changes (improvements): (1) The structure and organization of the program have been changed a lot. The new version package BCVEGPY2.1 has been divided into several modules with less cross communication among the modules (some old version source files are divided into several parts for the purpose). The main program is slimmed down and all the further actions are decoupled from the main program so that they can be easily called for various applications. All of the Fortran codes are organized in the main code directory named as bcvegpy2.1, which contains the main program, all of its prerequisite files and subsidiary 'folders' (subdirectory to the main code directory). The method for setting the parameter is the same as that of the previous versions [C.-H. Chang, C. Driouich, P. Eerola, X.-G. Wu, Comput. Phys. Commun. 159 (2004) 192, hep-ph/0309120. [1

ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

PubMed

Li, Guipeng; Li, Ming; Zhang, Yiwei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q

2014-01-01

Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide" in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request.

minimega v. 3.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crussell, Jonathan; Erickson, Jeremy; Fritz, David

minimega is an emulytics platform for creating testbeds of networked devices. The platoform consists of easily deployable tools to facilitate bringing up large networks of virtual machines including Windows, Linux, and Android. minimega allows experiments to be brought up quickly with almost no configuration. minimega also includes tools for simple cluster, management, as well as tools for creating Linux-based virtual machines. This release of minimega includes new emulated sensors for Android devices to improve the fidelity of testbeds that include mobile devices. Emulated sensors include GPS and

genepop'007: a complete re-implementation of the genepop software for Windows and Linux.

PubMed

Rousset, François

2008-01-01

This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls. © 2007 The Author.

Empirical tests of Zipf's law mechanism in open source Linux distribution.

PubMed

Maillart, T; Sornette, D; Spaeth, S; von Krogh, G

2008-11-21

Zipf's power law is a ubiquitous empirical regularity found in many systems, thought to result from proportional growth. Here, we establish empirically the usually assumed ingredients of stochastic growth models that have been previously conjectured to be at the origin of Zipf's law. We use exceptionally detailed data on the evolution of open source software projects in Linux distributions, which offer a remarkable example of a growing complex self-organizing adaptive system, exhibiting Zipf's law over four full decades.

Development of a Low-Latency, High Data Rate, Differential GPS Relative Positioning System for UAV Formation Flight Control

DTIC Science & Technology

2006-09-01

spiral development cycle involved transporting the software processes from a Windows XP / MATLAB environment to a Linux / C++ environment. This...tested on. Additionally, in the case of the GUMSTIX PC boards, the LINUX operating system is burned into the read-only memory. Lastly, both PC-104 and...both the real-time environment and the post-processed en - vironment. When the system operates in real-time mode, an output file is generated which

MONO FOR CROSS-PLATFORM CONTROL SYSTEM ENVIRONMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Hiroshi; Timossi, Chris

2006-10-19

Mono is an independent implementation of the .NET Frameworkby Novell that runs on multiple operating systems (including Windows,Linux and Macintosh) and allows any .NET compatible application to rununmodified. For instance Mono can run programs with graphical userinterfaces (GUI) developed with the C# language on Windows with VisualStudio (a full port of WinForm for Mono is in progress). We present theresults of tests we performed to evaluate the portability of our controlssystem .NET applications from MS Windows to Linux.

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

PubMed

Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

2010-09-21

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

jSynthesizer: A Java based first-motion synthetic seismogram tool

NASA Astrophysics Data System (ADS)

Sullivan, Mark

2009-10-01

Both researchers and educators need software tools to create synthetic seismograms to model earthquake sources. We have developed a program that generates first-motion synthetic seismograms that is highly interactive and suited to the needs of both research and education audiences. Implemented in the Java programming language, our program is available for use on Windows, Mac OS X and Linux operating systems. Our program allows the user to input the fault parameters strike, dip and slip angle, numerically or graphically using a lower hemisphere equal-area stereographic projection of the focal sphere of the earthquake. This representation is familiar to geologists and seismologists as the standard way of displaying the orientation of a fault in space. The user is also able to enter the relative location of the seismograph and the depth and crustal velocity structure in the vicinity of the earthquake. The direct P wave along with reflections off of layer boundaries near the source are generated using a constant ray-parameter approximation. The instrument response functions used by the Worldwide Standardized Seismogram Network and the attenuation response of the Earth's mantle are generated in the frequency domain and applied to generate the synthetic seismogram. Planned enhancements to this program will allow the simultaneous generation of seismograms at many stations as well as more complicated crustal structures.

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

PubMed Central

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

System level traffic shaping in disk servers with heterogeneous protocols

NASA Astrophysics Data System (ADS)

Cano, Eric; Kruse, Daniele Francesco

2014-06-01

Disk access and tape migrations compete for network bandwidth in CASTORs disk servers, over various protocols: RFIO, Xroot, root and GridFTP. As there are a limited number of tape drives, it is important to keep them busy all the time, at their nominal speed. With potentially 100s of user read streams per server, the bandwidth for the tape migrations has to be guaranteed to a controlled level, and not the fair share the system gives by default. Xroot provides a prioritization mechanism, but using it implies moving exclusively to the Xroot protocol, which is not possible in short to mid-term time frame, as users are equally using all protocols. The greatest commonality of all those protocols is not more than the usage of TCP/IP. We investigated the Linux kernel traffic shaper to control TCP/ IP bandwidth. The performance and limitations of the traffic shaper have been understood in test environment, and satisfactory working point has been found for production. Notably, TCP offload engines' negative impact on traffic shaping, and the limitations of the length of the traffic shaping rules were discovered and measured. A suitable working point has been found and the traffic shaping is now successfully deployed in the CASTOR production systems at CERN. This system level approach could be transposed easily to other environments.

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

PubMed

Garcia-Martin, Juan Antonio; Dotu, Ivan; Clote, Peter

2015-07-01

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

NASA Astrophysics Data System (ADS)

Conrad, O.; Bechtel, B.; Bock, M.; Dietrich, H.; Fischer, E.; Gerlitz, L.; Wehberg, J.; Wichmann, V.; Böhner, J.

2015-07-01

The System for Automated Geoscientific Analyses (SAGA) is an open source geographic information system (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, a user friendly graphical user interface with many visualization options, a command line interpreter, and interfaces to interpreted languages like R and Python. The current version 2.1.4 offers more than 600 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Furthermore, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies, with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

TELICS—A Telescope Instrument Control System for Small/Medium Sized Astronomical Observatories

NASA Astrophysics Data System (ADS)

Srivastava, Mudit K.; Ramaprakash, A. N.; Burse, Mahesh P.; Chordia, Pravin A.; Chillal, Kalpesh S.; Mestry, Vilas B.; Das, Hillol K.; Kohok, Abhay A.

2009-10-01

For any modern astronomical observatory, it is essential to have an efficient interface between the telescope and its back-end instruments. However, for small and medium-sized observatories, this requirement is often limited by tight financial constraints. Therefore a simple yet versatile and low-cost control system is required for such observatories to minimize cost and effort. Here we report the development of a modern, multipurpose instrument control system TELICS (Telescope Instrument Control System) to integrate the controls of various instruments and devices mounted on the telescope. TELICS consists of an embedded hardware unit known as a common control unit (CCU) in combination with Linux-based data acquisition and user interface. The hardware of the CCU is built around the ATmega 128 microcontroller (Atmel Corp.) and is designed with a backplane, master-slave architecture. A Qt-based graphical user interface (GUI) has been developed and the back-end application software is based on C/C++. TELICS provides feedback mechanisms that give the operator good visibility and a quick-look display of the status and modes of instruments as well as data. TELICS has been used for regular science observations since 2008 March on the 2 m, f/10 IUCAA Telescope located at Girawali in Pune, India.

Unsteady, Cooled Turbine Simulation Using a PC-Linux Analysis System

NASA Technical Reports Server (NTRS)

List, Michael G.; Turner, Mark G.; Chen, Jen-Pimg; Remotigue, Michael G.; Veres, Joseph P.

2004-01-01

The fist stage of the high-pressure turbine (HPT) of the GE90 engine was simulated with a three-dimensional unsteady Navier-Sokes solver, MSU Turbo, which uses source terms to simulate the cooling flows. In addition to the solver, its pre-processor, GUMBO, and a post-processing and visualization tool, Turbomachinery Visual3 (TV3) were run in a Linux environment to carry out the simulation and analysis. The solver was run both with and without cooling. The introduction of cooling flow on the blade surfaces, case, and hub and its effects on both rotor-vane interaction as well the effects on the blades themselves were the principle motivations for this study. The studies of the cooling flow show the large amount of unsteadiness in the turbine and the corresponding hot streak migration phenomenon. This research on the GE90 turbomachinery has also led to a procedure for running unsteady, cooled turbine analysis on commodity PC's running the Linux operating system.

BigWig and BigBed: enabling browsing of large distributed datasets.

PubMed

Kent, W J; Zweig, A S; Barber, G; Hinrichs, A S; Karolchik, D

2010-09-01

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

Development of EPA Protocol Information Enquiry Service System Based on Embedded ARM Linux

NASA Astrophysics Data System (ADS)

Peng, Daogang; Zhang, Hao; Weng, Jiannian; Li, Hui; Xia, Fei

Industrial Ethernet is a new technology for industrial network communications developed in recent years. In the field of industrial automation in China, EPA is the first standard accepted and published by ISO, and has been included in the fourth edition IEC61158 Fieldbus of NO.14 type. According to EPA standard, Field devices such as industrial field controller, actuator and other instruments are all able to realize communication based on the Ethernet standard. The Atmel AT91RM9200 embedded development board and open source embedded Linux are used to develop an information inquiry service system of EPA protocol based on embedded ARM Linux in this paper. The system is capable of designing an EPA Server program for EPA data acquisition procedures, the EPA information inquiry service is available for programs in local or remote host through Socket interface. The EPA client can access data and information of other EPA equipments on the EPA network when it establishes connection with the monitoring port of the server.

An Interactive Web-Based Analysis Framework for Remote Sensing Cloud Computing

NASA Astrophysics Data System (ADS)

Wang, X. Z.; Zhang, H. M.; Zhao, J. H.; Lin, Q. H.; Zhou, Y. C.; Li, J. H.

2015-07-01

Spatiotemporal data, especially remote sensing data, are widely used in ecological, geographical, agriculture, and military research and applications. With the development of remote sensing technology, more and more remote sensing data are accumulated and stored in the cloud. An effective way for cloud users to access and analyse these massive spatiotemporal data in the web clients becomes an urgent issue. In this paper, we proposed a new scalable, interactive and web-based cloud computing solution for massive remote sensing data analysis. We build a spatiotemporal analysis platform to provide the end-user with a safe and convenient way to access massive remote sensing data stored in the cloud. The lightweight cloud storage system used to store public data and users' private data is constructed based on open source distributed file system. In it, massive remote sensing data are stored as public data, while the intermediate and input data are stored as private data. The elastic, scalable, and flexible cloud computing environment is built using Docker, which is a technology of open-source lightweight cloud computing container in the Linux operating system. In the Docker container, open-source software such as IPython, NumPy, GDAL, and Grass GIS etc., are deployed. Users can write scripts in the IPython Notebook web page through the web browser to process data, and the scripts will be submitted to IPython kernel to be executed. By comparing the performance of remote sensing data analysis tasks executed in Docker container, KVM virtual machines and physical machines respectively, we can conclude that the cloud computing environment built by Docker makes the greatest use of the host system resources, and can handle more concurrent spatial-temporal computing tasks. Docker technology provides resource isolation mechanism in aspects of IO, CPU, and memory etc., which offers security guarantee when processing remote sensing data in the IPython Notebook. Users can write complex data processing code on the web directly, so they can design their own data processing algorithm.

Web tools for large-scale 3D biological images and atlases

PubMed Central

2012-01-01

Background Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. Results The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Conclusions Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume. PMID:22676296

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.

PubMed

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-05-28

Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4-15.9 times faster, while Unphased jobs performed 1.1-18.6 times faster compared to the accumulated computation duration. Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance.

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

PubMed Central

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-01-01

Background Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Results Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Conclusion Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance. PMID:18541045

The TSO Logic and G2 Software Product

NASA Technical Reports Server (NTRS)

Davis, Derrick D.

2014-01-01

This internship assignment for spring 2014 was at John F. Kennedy Space Center (KSC), in NASAs Engineering and Technology (NE) group in support of the Control and Data Systems Division (NE-C) within the Systems Hardware Engineering Branch. (NEC-4) The primary focus was in system integration and benchmarking utilizing two separate computer software products. The first half of this 2014 internship is spent in assisting NE-C4s Electronics and Embedded Systems Engineer, Kelvin Ruiz and fellow intern Scott Ditto with the evaluation of a newly piece of software, called G2. Its developed by the Gensym Corporation and introduced to the group as a tool used in monitoring launch environments. All fellow interns and employees of the G2 group have been working together in order to better understand the significance of the G2 application and how KSC can benefit from its capabilities. The second stage of this Spring project is to assist with an ongoing integration of a benchmarking tool, developed by a group of engineers from a Canadian based organization known as TSO Logic. Guided by NE-C4s Computer Engineer, Allen Villorin, NASA 2014 interns put forth great effort in helping to integrate TSOs software into the Spaceport Processing Systems Development Laboratory (SPSDL) for further testing and evaluating. The TSO Logic group claims that their software is designed for, monitoring and reducing energy consumption at in-house server farms and large data centers, allows data centers to control the power state of servers, without impacting availability or performance and without changes to infrastructure and the focus of the assignment is to test this theory. TSOs Aaron Rallo Founder and CEO, and Chris Tivel CTO, both came to KSC to assist with the installation of their software in the SPSDL laboratory. TSOs software is installed onto 24 individual workstations running three different operating systems. The workstations were divided into three groups of 8 with each group having its own operating system. The first group is comprised of Ubuntus Debian -based Linux the second group is windows 7 Professional and the third group ran Red Hat Linux. The highlight of this portion of the assignment is to compose documentation expressing the overall impression of the software and its capabilities.

[Design of an embedded stroke rehabilitation apparatus system based on Linux computer engineering].

PubMed

Zhuang, Pengfei; Tian, XueLong; Zhu, Lin

2014-04-01

A realizaton project of electrical stimulator aimed at motor dysfunction of stroke is proposed in this paper. Based on neurophysiological biofeedback, this system, using an ARM9 S3C2440 as the core processor, integrates collection and display of surface electromyography (sEMG) signal, as well as neuromuscular electrical stimulation (NMES) into one system. By embedding Linux system, the project is able to use Qt/Embedded as a graphical interface design tool to accomplish the design of stroke rehabilitation apparatus. Experiments showed that this system worked well.

LCG MCDB—a knowledgebase of Monte-Carlo simulated events

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Galkin, E.; Gusev, A.; Pokorski, W.; Sherstnev, A.

2008-02-01

In this paper we report on LCG Monte-Carlo Data Base (MCDB) and software which has been developed to operate MCDB. The main purpose of the LCG MCDB project is to provide a storage and documentation system for sophisticated event samples simulated for the LHC Collaborations by experts. In many cases, the modern Monte-Carlo simulation of physical processes requires expert knowledge in Monte-Carlo generators or significant amount of CPU time to produce the events. MCDB is a knowledgebase mainly dedicated to accumulate simulated events of this type. The main motivation behind LCG MCDB is to make the sophisticated MC event samples available for various physical groups. All the data from MCDB is accessible in several convenient ways. LCG MCDB is being developed within the CERN LCG Application Area Simulation project. Program summaryProgram title: LCG Monte-Carlo Data Base Catalogue identifier: ADZX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 30 129 No. of bytes in distributed program, including test data, etc.: 216 943 Distribution format: tar.gz Programming language: Perl Computer: CPU: Intel Pentium 4, RAM: 1 Gb, HDD: 100 Gb Operating system: Scientific Linux CERN 3/4 RAM: 1 073 741 824 bytes (1 Gb) Classification: 9 External routines:perl >= 5.8.5; Perl modules DBD-mysql >= 2.9004, File::Basename, GD::SecurityImage, GD::SecurityImage::AC, Linux::Statistics, XML::LibXML > 1.6, XML::SAX, XML::NamespaceSupport; Apache HTTP Server >= 2.0.59; mod auth external >= 2.2.9; edg-utils-system RPM package; gd >= 2.0.28; rpm package CASTOR-client >= 2.1.2-4; arc-server (optional) Nature of problem: Often, different groups of experimentalists prepare similar samples of particle collision events or turn to the same group of authors of Monte-Carlo (MC) generators to prepare the events. For example, the same MC samples of Standard Model (SM) processes can be employed for the investigations either in the SM analyses (as a signal) or in searches for new phenomena in Beyond Standard Model analyses (as a background). If the samples are made available publicly and equipped with corresponding and comprehensive documentation, it can speed up cross checks of the samples themselves and physical models applied. Some event samples require a lot of computing resources for preparation. So, a central storage of the samples prevents possible waste of researcher time and computing resources, which can be used to prepare the same events many times. Solution method: Creation of a special knowledgebase (MCDB) designed to keep event samples for the LHC experimental and phenomenological community. The knowledgebase is realized as a separate web-server ( http://mcdb.cern.ch). All event samples are kept on types at CERN. Documentation describing the events is the main contents of MCDB. Users can browse the knowledgebase, read and comment articles (documentation), and download event samples. Authors can upload new event samples, create new articles, and edit own articles. Restrictions: The software is adopted to solve the problems, described in the article and there are no any additional restrictions. Unusual features: The software provides a framework to store and document large files with flexible authentication and authorization system. Different external storages with large capacity can be used to keep the files. The WEB Content Management System provides all of the necessary interfaces for the authors of the files, end-users and administrators. Running time: Real time operations. References: [1] The main LCG MCDB server, http://mcdb.cern.ch/. [2] P. Bartalini, L. Dudko, A. Kryukov, I.V. Selyuzhenkov, A. Sherstnev, A. Vologdin, LCG Monte-Carlo data base, hep-ph/0404241. [3] J.P. Baud, B. Couturier, C. Curran, J.D. Durand, E. Knezo, S. Occhetti, O. Barring, CASTOR: status and evolution, cs.oh/0305047.

SHIELD-HIT12A - a Monte Carlo particle transport program for ion therapy research

NASA Astrophysics Data System (ADS)

Bassler, N.; Hansen, D. C.; Lühr, A.; Thomsen, B.; Petersen, J. B.; Sobolevsky, N.

2014-03-01

Purpose: The Monte Carlo (MC) code SHIELD-HIT simulates the transport of ions through matter. Since SHIELD-HIT08 we added numerous features that improves speed, usability and underlying physics and thereby the user experience. The "-A" fork of SHIELD-HIT also aims to attach SHIELD-HIT to a heavy ion dose optimization algorithm to provide MC-optimized treatment plans that include radiobiology. Methods: SHIELD-HIT12A is written in FORTRAN and carefully retains platform independence. A powerful scoring engine is implemented scoring relevant quantities such as dose and track-average LET. It supports native formats compatible with the heavy ion treatment planning system TRiP. Stopping power files follow ICRU standard and are generated using the libdEdx library, which allows the user to choose from a multitude of stopping power tables. Results: SHIELD-HIT12A runs on Linux and Windows platforms. We experienced that new users quickly learn to use SHIELD-HIT12A and setup new geometries. Contrary to previous versions of SHIELD-HIT, the 12A distribution comes along with easy-to-use example files and an English manual. A new implementation of Vavilov straggling resulted in a massive reduction of computation time. Scheduled for later release are CT import and photon-electron transport. Conclusions: SHIELD-HIT12A is an interesting alternative ion transport engine. Apart from being a flexible particle therapy research tool, it can also serve as a back end for a MC ion treatment planning system. More information about SHIELD-HIT12A and a demo version can be found on http://www.shieldhit.org.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

PubMed Central

2012-01-01

Background The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context. Results We have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. In particular the ouput of the program entails, depending on user's requirement: 1) the generalized Born radius of each atom; 2) the electrostatic solvation free energy; 3) the electrostatic forces on each atom (currently in a dvelopmental stage); 4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18; 5) the pKa of all ionizable groups; 6) the electrostatic potential at the surface of the molecule; 7) the electrostatic potential in a volume surrounding the molecule; Conclusions Although at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material. PMID:22536964

CERN alerter—RSS based system for information broadcast to all CERN offices

NASA Astrophysics Data System (ADS)

Otto, R.

2008-07-01

Nearly every large organization uses a tool to broadcast messages and information across the internal campus (messages like alerts announcing interruption in services or just information about upcoming events). These tools typically allow administrators (operators) to send 'targeted' messages which are sent only to specific groups of users or computers, e/g only those located in a specified building or connected to a particular computing service. CERN has a long history of such tools: CERNVMS's SPM_quotMESSAGE command, Zephyr [2] and the most recent the NICE Alerter based on the NNTP protocol. The NICE Alerter used on all Windows-based computers had to be phased out as a consequence of phasing out NNTP at CERN. The new solution to broadcast information messages on the CERN campus continues to provide the service based on cross-platform technologies, hence minimizing custom developments and relying on commercial software as much as possible. The new system, called CERN Alerter, is based on RSS (Really Simple Syndication) [9] for the transport protocol and uses Microsoft SharePoint as the backend for database and posting interface. The windows-based client relies on Internet Explorer 7.0 with custom code to trigger the window pop-ups and the notifications for new events. Linux and Mac OS X clients could also rely on any RSS readers to subscribe to targeted notifications. The paper covers the architecture and implementation aspects of the new system.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

NASA Astrophysics Data System (ADS)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

Implementing Journaling in a Linux Shared Disk File System

NASA Technical Reports Server (NTRS)

Preslan, Kenneth W.; Barry, Andrew; Brassow, Jonathan; Cattelan, Russell; Manthei, Adam; Nygaard, Erling; VanOort, Seth; Teigland, David; Tilstra, Mike; O'Keefe, Matthew;

Berkeley lab checkpoint/restart (BLCR) for Linux clusters

DOE PAGES

Hargrove, Paul H.; Duell, Jason C.

2006-09-01

This article describes the motivation, design and implementation of Berkeley Lab Checkpoint/Restart (BLCR), a system-level checkpoint/restart implementation for Linux clusters that targets the space of typical High Performance Computing applications, including MPI. Application-level solutions, including both checkpointing and fault-tolerant algorithms, are recognized as more time and space efficient than system-level checkpoints, which cannot make use of any application-specific knowledge. However, system-level checkpointing allows for preemption, making it suitable for responding to fault precursors (for instance, elevated error rates from ECC memory or network CRCs, or elevated temperature from sensors). Preemption can also increase the efficiency of batch scheduling; for instancemore » reducing idle cycles (by allowing for shutdown without any queue draining period or reallocation of resources to eliminate idle nodes when better fitting jobs are queued), and reducing the average queued time (by limiting large jobs to running during off-peak hours, without the need to limit the length of such jobs). Each of these potential uses makes BLCR a valuable tool for efficient resource management in Linux clusters. © 2006 IOP Publishing Ltd.« less

The LINC-NIRVANA fringe and flexure tracker: Linux real-time solutions

NASA Astrophysics Data System (ADS)

Wang, Yeping; Bertram, Thomas; Straubmeier, Christian; Rost, Steffen; Eckart, Andreas

2006-06-01

The correction of atmospheric differential piston and instrumental flexure effects is mandatory for optimum interferometric performance of the LBT NIR interferometric imaging camera LINC-NIRVANA. The task of the Fringe and Flexure Tracking System (FFTS) is to detect and correct these effects in a real-time closed loop. On a timescale of milliseconds, image data of the order of 4K bytes has to be retrieved from the FFTS detector, analyzed, and the results have to be sent to the control system. The need for a reliable communication between several processes within a confined period of time calls for solutions with good real-time performance. We investigated two soft real-time options for the Linux platform. The design we present takes advantage of several features that follow the POSIX standard with improved real-time performance, which were implemented in the new Linux kernel (2.6.12). Several concepts, such as synchronization, shared memory, and preemptive scheduling are considered and the performance of the most time-critical parts of the FFTS software is tested.

PAPARA(ZZ)I: An open-source software interface for annotating photographs of the deep-sea

NASA Astrophysics Data System (ADS)

Marcon, Yann; Purser, Autun

PAPARA(ZZ)I is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment). If Internet access is available, PAPARA(ZZ)I can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS). Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon). These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZ)I is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

Kubios HRV--heart rate variability analysis software.

PubMed

Tarvainen, Mika P; Niskanen, Juha-Pekka; Lipponen, Jukka A; Ranta-Aho, Perttu O; Karjalainen, Pasi A

2014-01-01

Kubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data. It includes an adaptive QRS detection algorithm and tools for artifact correction, trend removal and analysis sample selection. The software computes all the commonly used time-domain and frequency-domain HRV parameters and several nonlinear parameters. There are several adjustable analysis settings through which the analysis methods can be optimized for different data. The ECG derived respiratory frequency is also computed, which is important for reliable interpretation of the analysis results. The analysis results can be saved as an ASCII text file (easy to import into MS Excel or SPSS), Matlab MAT-file, or as a PDF report. The software is easy to use through its compact graphical user interface. The software is available free of charge for Windows and Linux operating systems at http://kubios.uef.fi. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Fast data transmission in dynamic data acquisition system for plasma diagnostics

NASA Astrophysics Data System (ADS)

Byszuk, Adrian; Poźniak, Krzysztof; Zabołotny, Wojciech M.; Kasprowicz, Grzegorz; Wojeński, Andrzej; Cieszewski, Radosław; Juszczyk, Bartłomiej; Kolasiński, Piotr; Zienkiewicz, Paweł; Chernyshova, Maryna; Czarski, Tomasz

2014-11-01

This paper describes architecture of a new data acquisition system (DAQ) targeted mainly at plasma diagnostic experiments. Modular architecture, in combination with selected hardware components, allows for straightforward reconfiguration of the whole system, both offline and online. Main emphasis will be put into the implementation of data transmission subsystem in said system. One of the biggest advantages of described system is modular architecture with well defined boundaries between main components: analog frontend (AFE), digital backplane and acquisition/control software. Usage of a FPGA chips allows for a high flexibility in design of analog frontends, including ADC <--> FPGA interface. Data transmission between backplane boards and user software was accomplished with the use of industry-standard PCI Express (PCIe) technology. PCIe implementation includes both FPGA firmware and Linux device driver. High flexibility of PCIe connections was accomplished due to use of configurable PCIe switch. Whenever it's possible, described DAQ system tries to make use of standard off-the-shelf (OTF) components, including typical x86 CPU & motherboard (acting as PCIe controller) and cabling.

Community-driven computational biology with Debian Linux.

PubMed

Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

2010-12-21

The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

ChronQC: a quality control monitoring system for clinical next generation sequencing.

PubMed

Tawari, Nilesh R; Seow, Justine Jia Wen; Perumal, Dharuman; Ow, Jack L; Ang, Shimin; Devasia, Arun George; Ng, Pauline C

2018-05-15

ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. ChronQC facilitates regular monitoring of clinical NGS to enable adherence to high quality clinical standards. ChronQC is freely available on GitHub (https://github.com/nilesh-tawari/ChronQC), Docker (https://hub.docker.com/r/nileshtawari/chronqc/) and the Python Package Index. ChronQC is implemented in Python and runs on all common operating systems (Windows, Linux and Mac OS X). tawari.nilesh@gmail.com or pauline.c.ng@gmail.com. Supplementary data are available at Bioinformatics online.

GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.

PubMed

Tahsin, Tasnia; Weissenbacher, Davy; O'Connor, Karen; Magge, Arjun; Scotch, Matthew; Gonzalez-Hernandez, Graciela

2018-05-01

GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH. Binaries and resources required for running GeoBoost are packed into a single zipped file and freely available for download at https://tinyurl.com/geoboost. A video tutorial is included to help users quickly and easily install and run the software. The software is implemented in Java 1.8, and supported on MS Windows and Linux platforms. gragon@upenn.edu. Supplementary data are available at Bioinformatics online.

Software for Analyzing Sequences of Flow-Related Images

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2004-01-01

Spotlight is a computer program for analysis of sequences of images generated in combustion and fluid physics experiments. Spotlight can perform analysis of a single image in an interactive mode or a sequence of images in an automated fashion. The primary type of analysis is tracking of positions of objects over sequences of frames. Features and objects that are typically tracked include flame fronts, particles, droplets, and fluid interfaces. Spotlight automates the analysis of object parameters, such as centroid position, velocity, acceleration, size, shape, intensity, and color. Images can be processed to enhance them before statistical and measurement operations are performed. An unlimited number of objects can be analyzed simultaneously. Spotlight saves results of analyses in a text file that can be exported to other programs for graphing or further analysis. Spotlight is a graphical-user-interface-based program that at present can be executed on Microsoft Windows and Linux operating systems. A version that runs on Macintosh computers is being considered.

S2PLOT: Three-dimensional (3D) Plotting Library

NASA Astrophysics Data System (ADS)

Barnes, D. G.; Fluke, C. J.; Bourke, P. D.; Parry, O. T.

2011-03-01

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.

An Advanced, Three-Dimensional Plotting Library for Astronomy

NASA Astrophysics Data System (ADS)

Barnes, David G.; Fluke, Christopher J.; Bourke, Paul D.; Parry, Owen T.

2006-07-01

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - s2plot - is written in c and can be used by c, c++, and fortran programs on GNU/Linux and Apple/OSX systems. s2plot draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a pgplot-inspired interface, s2plot provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The s2plot architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce s2plot to the astronomical community, describe its potential applications, and present some example uses of the library.

Speckle interferometry. Data acquisition and control for the SPID instrument.

NASA Astrophysics Data System (ADS)

Altarac, S.; Tallon, M.; Thiebaut, E.; Foy, R.

1998-08-01

SPID (SPeckle Imaging by Deconvolution) is a new speckle camera currently under construction at CRAL-Observatoire de Lyon. Its high spectral resolution and high image restoration capabilities open new astrophysical programs. The instrument SPID is composed of four main optical modules which are fully automated and computer controlled by a software written in Tcl/Tk/Tix and C. This software provides an intelligent assistance to the user by choosing observational parameters as a function of atmospheric parameters, computed in real time, and the desired restored image quality. Data acquisition is made by a photon-counting detector (CP40). A VME-based computer under OS9 controls the detector and stocks the data. The intelligent system runs under Linux on a PC. A slave PC under DOS commands the motors. These 3 computers communicate through an Ethernet network. SPID can be considered as a precursor for VLT's (Very Large Telescope, four 8-meter telescopes currently built in Chile by European Southern Observatory) very high spatial resolution camera.

SVGMap: configurable image browser for experimental data.

PubMed

Rafael-Palou, Xavier; Schroeder, Michael P; Lopez-Bigas, Nuria

2012-01-01

Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. nuria.lopez@upf.edu

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment1

PubMed Central

Johnson, Matthew G.; Gardner, Elliot M.; Liu, Yang; Medina, Rafael; Goffinet, Bernard; Shaw, A. Jonathan; Zerega, Nyree J. C.; Wickett, Norman J.

2016-01-01

Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. PMID:27437175

DSISoft—a MATLAB VSP data processing package

NASA Astrophysics Data System (ADS)

Beaty, K. S.; Perron, G.; Kay, I.; Adam, E.

2002-05-01

DSISoft is a public domain vertical seismic profile processing software package developed at the Geological Survey of Canada. DSISoft runs under MATLAB version 5.0 and above and hence is portable between computer operating systems supported by MATLAB (i.e. Unix, Windows, Macintosh, Linux). The package includes processing modules for reading and writing various standard seismic data formats, performing data editing, sorting, filtering, and other basic processing modules. The processing sequence can be scripted allowing batch processing and easy documentation. A structured format has been developed to ensure future additions to the package are compatible with existing modules. Interactive modules have been created using MATLAB's graphical user interface builder for displaying seismic data, picking first break times, examining frequency spectra, doing f- k filtering, and plotting the trace header information. DSISoft modular design facilitates the incorporation of new processing algorithms as they are developed. This paper gives an overview of the scope of the software and serves as a guide for the addition of new modules.

Testing Task Schedulers on Linux System

NASA Astrophysics Data System (ADS)

Jelenković, Leonardo; Groš, Stjepan; Jakobović, Domagoj

Testing task schedulers on Linux operating system proves to be a challenging task. There are two main problems. The first one is to identify which properties of the scheduler to test. The second problem is how to perform it, e.g., which API to use that is sufficiently precise and in the same time supported on most platforms. This paper discusses the problems in realizing test framework for testing task schedulers and presents one potential solution. Observed behavior of the scheduler is the one used for “normal” task scheduling (SCHED_OTHER), unlike one used for real-time tasks (SCHED_FIFO, SCHED_RR).

Comparative Analysis of Active and Passive Mapping Techniques in an Internet-Based Local Area Network

DTIC Science & Technology

2004-03-01

PIII/500 (K) 512 A11 3C905 Honeynet PIII/1000 (C) 512 A11 3C905 Generator PIII/800 (C) 256 A11 3C905 Each system is running Debian GNU / Linux “unstable...Network,” September 2000. http://www.issues.af.mil/notams/notam00-5.html; accessed January 16, 2004. 5. “Debian GNU / Linux 3.0 Released,” Debian News...interact with those servers. 1.5 Summary The remainder of this document is organized into four chapters. Chapter 2 con - tains the literature review where

Dataset for forensic analysis of B-tree file system.

PubMed

Wani, Mohamad Ahtisham; Bhat, Wasim Ahmad

2018-06-01

Since B-tree file system (Btrfs) is set to become de facto standard file system on Linux (and Linux based) operating systems, Btrfs dataset for forensic analysis is of great interest and immense value to forensic community. This article presents a novel dataset for forensic analysis of Btrfs that was collected using a proposed data-recovery procedure. The dataset identifies various generalized and common file system layouts and operations, specific node-balancing mechanisms triggered, logical addresses of various data structures, on-disk records, recovered-data as directory entries and extent data from leaf and internal nodes, and percentage of data recovered.

Assigning unique identification numbers to new user accounts and groups in a computing environment with multiple registries

DOEpatents

DeRobertis, Christopher V.; Lu, Yantian T.

2010-02-23

A method, system, and program storage device for creating a new user account or user group with a unique identification number in a computing environment having multiple user registries is provided. In response to receiving a command to create a new user account or user group, an operating system of a clustered computing environment automatically checks multiple registries configured for the operating system to determine whether a candidate identification number for the new user account or user group has been assigned already to one or more existing user accounts or groups, respectively. The operating system automatically assigns the candidate identification number to the new user account or user group created in a target user registry if the checking indicates that the candidate identification number has not been assigned already to any of the existing user accounts or user groups, respectively.

Using McIDAS-V data analysis and visualization software as an educational tool for understanding the atmosphere

NASA Astrophysics Data System (ADS)

Achtor, T. H.; Rink, T.

2010-12-01

The University of Wisconsin’s Space Science and Engineering Center (SSEC) has been at the forefront in developing data analysis and visualization tools for environmental satellites and other geophysical data. The fifth generation of the Man-computer Interactive Data Access System (McIDAS-V) is Java-based, open-source, freely available software that operates on Linux, Macintosh and Windows systems. The software tools provide powerful new data manipulation and visualization capabilities that work with geophysical data in research, operational and educational environments. McIDAS-V provides unique capabilities to support innovative techniques for evaluating research results, teaching and training. McIDAS-V is based on three powerful software elements. VisAD is a Java library for building interactive, collaborative, 4 dimensional visualization and analysis tools. The Integrated Data Viewer (IDV) is a reference application based on the VisAD system and developed by the Unidata program that demonstrates the flexibility that is needed in this evolving environment, using a modern, object-oriented software design approach. The third tool, HYDRA, allows users to build, display and interrogate multi and hyperspectral environmental satellite data in powerful ways. The McIDAS-V software is being used for training and education in several settings. The McIDAS User Group provides training workshops at its annual meeting. Numerous online tutorials with training data sets have been developed to aid users in learning simple and more complex operations in McIDAS-V, all are available online. In a University of Wisconsin-Madison undergraduate course in Radar and Satellite Meteorology, McIDAS-V is used to create and deliver laboratory exercises using case study and real time data. At the high school level, McIDAS-V is used in several exercises in our annual Summer Workshop in Earth and Atmospheric Sciences to provide young scientists the opportunity to examine data with friendly and powerful tools. This presentation will describe the McIDAS-V software and demonstrate some of the capabilities of McIDAS-V to analyze and display many types of global data. The presentation will also focus on describing how McIDAS-V can be used as an educational window to examine global geophysical data. Consecutive polar orbiting passes of NASA MODIS and CALIPSO observations

Automated Synthesis of Long Communication Delays for Testing

NASA Technical Reports Server (NTRS)

Seibert, Marc; McKim, James

2005-01-01

Planetary-Ohio Network Emulator (p- ONE) is a computer program for local laboratory testing of high bandwidth data-communication systems subject to long delays in propagation over interplanetary distances. p-ONE is installed on a personal computer connected to two bidirectional Ethernet interfaces, denoted A and B, that represent local-area networks at opposite ends of a long propagation path. Traffic that is to be passed between A and B is encapsulated in IP (Internet Protocol) packets (e.g., User Data Protocol, UDP). Intercepting this traffic between A and B in both directions, p-ONE time-tags each packet and stores it in memory or on the hard disk of the computer for a user-specified interval that equals the propagation delay to be synthesized. At the expiration of its storage time, each such packet is sent to its destination (that is, if it was received from A, it is sent to B, or vice versa). The accuracy of the p-ONE software is very high, with zero packet loss through the system and negligible latency. Optionally, p-ONE can be configured to delay all network traffic to and from all network addresses on each Ethernet interface or to selectively delay traffic between specific addresses or traffic of specific types. p-ONE works well with Linux and is also designed to be compatible with other operating systems.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

Dendroscope: An interactive viewer for large phylogenetic trees

PubMed Central

Huson, Daniel H; Richter, Daniel C; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula

2007-01-01

Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. PMID:18034891

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

Scilab software package for the study of dynamical systems

NASA Astrophysics Data System (ADS)

Bordeianu, C. C.; Beşliu, C.; Jipa, Al.; Felea, D.; Grossu, I. V.

2008-05-01

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE. Program summaryProgram title: Chaos Catalogue identifier: AEAP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 885 No. of bytes in distributed program, including test data, etc.: 5925 Distribution format: tar.gz Programming language: Scilab 3.1.1 Computer: PC-compatible running Scilab on MS Windows or Linux Operating system: Windows XP, Linux RAM: below 100 Megabytes Classification: 6.2 Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE). Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies. Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem. Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Additional deployment of ocean bottom gravity meter and ocean bottom electro-magnetic meter for the multidisciplinary cabled observation in Sagami Bay, Japan

NASA Astrophysics Data System (ADS)

Mitsuzawa, K.; Goto, T.; Araki, E.; Watanabe, T.; Sugioka, H.; Kasaya, T.; Sayanagi, K.; Mikada, H.; Fujimoto, H.; Nagao, T.; Koizumi, K.; Asakawa, K.

2005-12-01

Western part of the Sagami Bay central Pacific side of Japan, is known as one of the high active tectonic areas. In this area, Teishi Knoll, volcanic seamount, erupted in 1989 and the earthquake swarms occurs repeatedly every few years in the eastern coast of the Izu Peninsula. The real-time deep sea floor observatory was deployed about 7 km off Hatsushima Island, Sagami Bay, at a depth of 1174 m in 1993 to monitor seismic activities, underwater pressure, water temperature and deep currents. The video camera and lights were also mounted in the observatory to monitor the relations among biological activities associated with the tectonic activities. The observation system including submarine electro-optical cable with a length of 8 km was completely renewed in 2000. The several underwater-mateable connectors are installed in the new observatory for additional observation instruments. A precise pressure sensor, ocean bottom gravity meter and ocean bottom electro-magnetic meter were installed using ROV Hyper-Dolphin in the cruise of R/V Natsushima from January 9 to 14, 2005. We start to operate them at February 10, 2005 after checking those of data qualities. We also installed an underwater internet interface, which is called Linux Box, as a prototype of underwater network system which was operated by Linux operating system. The Linux Box is a key network system for multidisciplinary observation network. It will be able to connect much kind of observation instruments as using internet connection. We put the precise pressure sensor as a sensor of the Linux Box in this experiment.

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

PubMed Central

Varsos, Constantinos; Patkos, Theodore; Pavloudi, Christina; Gougousis, Alexandros; Ijaz, Umer Zeeshan; Filiopoulou, Irene; Pattakos, Nikolaos; Vanden Berghe, Edward; Fernández-Guerra, Antonio; Faulwetter, Sarah; Chatzinikolaou, Eva; Pafilis, Evangelos; Bekiari, Chryssoula; Doerr, Martin; Arvanitidis, Christos

2016-01-01

Abstract Background Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data – Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pc-linux-gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https://portal.lifewatchgreece.eu/ PMID:27932907

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab).

PubMed

Varsos, Constantinos; Patkos, Theodore; Oulas, Anastasis; Pavloudi, Christina; Gougousis, Alexandros; Ijaz, Umer Zeeshan; Filiopoulou, Irene; Pattakos, Nikolaos; Vanden Berghe, Edward; Fernández-Guerra, Antonio; Faulwetter, Sarah; Chatzinikolaou, Eva; Pafilis, Evangelos; Bekiari, Chryssoula; Doerr, Martin; Arvanitidis, Christos

2016-01-01

Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data - Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pc-linux-gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https://portal.lifewatchgreece.eu/.

MARTe: A Multiplatform Real-Time Framework

NASA Astrophysics Data System (ADS)

Neto, André C.; Sartori, Filippo; Piccolo, Fabio; Vitelli, Riccardo; De Tommasi, Gianmaria; Zabeo, Luca; Barbalace, Antonio; Fernandes, Horacio; Valcarcel, Daniel F.; Batista, Antonio J. N.

2010-04-01

Development of real-time applications is usually associated with nonportable code targeted at specific real-time operating systems. The boundary between hardware drivers, system services, and user code is commonly not well defined, making the development in the target host significantly difficult. The Multithreaded Application Real-Time executor (MARTe) is a framework built over a multiplatform library that allows the execution of the same code in different operating systems. The framework provides the high-level interfaces with hardware, external configuration programs, and user interfaces, assuring at the same time hard real-time performances. End-users of the framework are required to define and implement algorithms inside a well-defined block of software, named Generic Application Module (GAM), that is executed by the real-time scheduler. Each GAM is reconfigurable with a set of predefined configuration meta-parameters and interchanges information using a set of data pipes that are provided as inputs and required as output. Using these connections, different GAMs can be chained either in series or parallel. GAMs can be developed and debugged in a non-real-time system and, only once the robustness of the code and correctness of the algorithm are verified, deployed to the real-time system. The software also supplies a large set of utilities that greatly ease the interaction and debugging of a running system. Among the most useful are a highly efficient real-time logger, HTTP introspection of real-time objects, and HTTP remote configuration. MARTe is currently being used to successfully drive the plasma vertical stabilization controller on the largest magnetic confinement fusion device in the world, with a control loop cycle of 50 ?s and a jitter under 1 ?s. In this particular project, MARTe is used with the Real-Time Application Interface (RTAI)/Linux operating system exploiting the new ?86 multicore processors technology.

Quantifying medical student clinical experiences via an ICD Code Logging App.

PubMed

Rawlins, Fred; Sumpter, Cameron; Sutphin, Dean; Garner, Harold R

2018-03-01

The logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students' clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status. We have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers. For each patient interaction, users enter ICD diagnostic, procedure, and drug codes via a hierarchical or search entry interface, as well as patient demographics (age range and gender, but no personal identifiers), and free-text notes. Users and administrators can review and edit input via a series of output interfaces. The user interface and back-end database are provided via dual redundant failover Linux servers. Students master the interface in ten minutes, and thereafter complete entries in less than one minute. Five hundred-forty 3rd year VCOM students each averaged 100 entries in the first four week clinical rotation. Data accumulated in various Appalachian clinics and Central American medical mission trips has demonstrated the public health surveillance utility of the application. PC and mobile apps can be used to collect medical trainee experience in real time or near real-time, quickly, and efficiently. This system has collected 75,596 entries to date, less than 2% of trainees have needed assistance to become proficient, and medical school administrators are using the various summaries to evaluate students and compare different rotation sites. Copyright © 2017. Published by Elsevier B.V.

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Goulet, C.; Silva, F.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2015-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100Hz) ground motions for earthquakes at regional scales. The BBP scientific software modules implement kinematic rupture generation, low and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, seismogram ground motion amplitude calculations, and goodness of fit measurements. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground motion seismograms, using multiple alternative ground motion simulation methods, and software utilities that can generate plots, charts, and maps. The BBP has been developed over the last five years in a collaborative scientific, engineering, and software development project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The SCEC BBP software released in 2015 can be compiled and run on recent Linux systems with GNU compilers. It includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, updated ground motion simulation methods, and a simplified command line user interface.

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Goulet, C. A.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2016-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100 Hz) ground motions for earthquakes at regional scales. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The BBP scientific software modules implement kinematic rupture generation, low- and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, several ground motion intensity measure calculations, and various ground motion goodness-of-fit tools. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground-motion seismograms, using multiple alternative ground motion simulation methods, and software utilities to generate tables, plots, and maps. The BBP has been developed over the last five years in a collaborative project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The SCEC BBP software released in 2016 can be compiled and run on recent Linux and Mac OS X systems with GNU compilers. It includes five simulation methods, seven simulation regions covering California, Japan, and Eastern North America, and the ability to compare simulation results against empirical ground motion models (aka GMPEs). The latest version includes updated ground motion simulation methods, a suite of new validation metrics and a simplified command line user interface.

ZENO: N-body and SPH Simulation Codes

NASA Astrophysics Data System (ADS)

Barnes, Joshua E.

2011-02-01

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere. Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include: Structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems.Snapshot generation routines create particle distributions with various properties. Systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium.Snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.Simulation codes include both pure N-body and combined N-body/SPH programs: Pure N-body codes are available in both uniprocessor and parallel versions.SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions.Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

LHCb Dockerized Build Environment

NASA Astrophysics Data System (ADS)

Clemencic, M.; Belin, M.; Closier, J.; Couturier, B.

2017-10-01

Used as lightweight virtual machines or as enhanced chroot environments, Linux containers, and in particular the Docker abstraction over them, are more and more popular in the virtualization communities. The LHCb Core Software team decided to investigate how to use Docker containers to provide stable and reliable build environments for the different supported platforms, including the obsolete ones which cannot be installed on modern hardware, to be used in integration builds, releases and by any developer. We present here the techniques and procedures set up to define and maintain the Docker images and how these images can be used to develop on modern Linux distributions for platforms otherwise not accessible.

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

Millisecond accuracy video display using OpenGL under Linux.

PubMed

Stewart, Neil

2006-02-01

To measure people's reaction times to the nearest millisecond, it is necessary to know exactly when a stimulus is displayed. This article describes how to display stimuli with millisecond accuracy on a normal CRT monitor, using a PC running Linux. A simple C program is presented to illustrate how this may be done within X Windows using the OpenGL rendering system. A test of this system is reported that demonstrates that stimuli may be consistently displayed with millisecond accuracy. An algorithm is presented that allows the exact time of stimulus presentation to be deduced, even if there are relatively large errors in measuring the display time.

Improving Memory Error Handling Using Linux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlton, Michael Andrew; Blanchard, Sean P.; Debardeleben, Nathan A.

As supercomputers continue to get faster and more powerful in the future, they will also have more nodes. If nothing is done, then the amount of memory in supercomputer clusters will soon grow large enough that memory failures will be unmanageable to deal with by manually replacing memory DIMMs. "Improving Memory Error Handling Using Linux" is a process oriented method to solve this problem by using the Linux kernel to disable (offline) faulty memory pages containing bad addresses, preventing them from being used again by a process. The process of offlining memory pages simplifies error handling and results in reducingmore » both hardware and manpower costs required to run Los Alamos National Laboratory (LANL) clusters. This process will be necessary for the future of supercomputing to allow the development of exascale computers. It will not be feasible without memory error handling to manually replace the number of DIMMs that will fail daily on a machine consisting of 32-128 petabytes of memory. Testing reveals the process of offlining memory pages works and is relatively simple to use. As more and more testing is conducted, the entire process will be automated within the high-performance computing (HPC) monitoring software, Zenoss, at LANL.« less

Cloud flexibility using DIRAC interware

NASA Astrophysics Data System (ADS)

Fernandez Albor, Víctor; Seco Miguelez, Marcos; Fernandez Pena, Tomas; Mendez Muñoz, Victor; Saborido Silva, Juan Jose; Graciani Diaz, Ricardo

2014-06-01

Communities of different locations are running their computing jobs on dedicated infrastructures without the need to worry about software, hardware or even the site where their programs are going to be executed. Nevertheless, this usually implies that they are restricted to use certain types or versions of an Operating System because either their software needs an definite version of a system library or a specific platform is required by the collaboration to which they belong. On this scenario, if a data center wants to service software to incompatible communities, it has to split its physical resources among those communities. This splitting will inevitably lead to an underuse of resources because the data centers are bound to have periods where one or more of its subclusters are idle. It is, in this situation, where Cloud Computing provides the flexibility and reduction in computational cost that data centers are searching for. This paper describes a set of realistic tests that we ran on one of such implementations. The test comprise software from three different HEP communities (Auger, LHCb and QCD phenomelogists) and the Parsec Benchmark Suite running on one or more of three Linux flavors (SL5, Ubuntu 10.04 and Fedora 13). The implemented infrastructure has, at the cloud level, CloudStack that manages the virtual machines (VM) and the hosts on which they run, and, at the user level, the DIRAC framework along with a VM extension that will submit, monitorize and keep track of the user jobs and also requests CloudStack to start or stop the necessary VM's. In this infrastructure, the community software is distributed via the CernVM-FS, which has been proven to be a reliable and scalable software distribution system. With the resulting infrastructure, users are allowed to send their jobs transparently to the Data Center. The main purpose of this system is the creation of flexible cluster, multiplatform with an scalable method for software distribution for several VOs. Users from different communities do not need to care about the installation of the standard software that is available at the nodes, nor the operating system of the host machine, which is transparent to the user.

Individual and Group-Based Engagement in an Online Physical Activity Monitoring Program in Georgia.

PubMed

Smith, Matthew Lee; Durrett, Nicholas K; Bowie, Maria; Berg, Alison; McCullick, Bryan A; LoPilato, Alexander C; Murray, Deborah

2018-06-07

Given the rising prevalence of obesity in the United States, innovative methods are needed to increase physical activity (PA) in community settings. Evidence suggests that individuals are more likely to engage in PA if they are given a choice of activities and have support from others (for encouragement, motivation, and accountability). The objective of this study was to describe the use of the online Walk Georgia PA tracking platform according to whether the user was an individual user or group user. Walk Georgia is a free, interactive online tracking platform that enables users to log PA by duration, activity, and perceived difficulty, and then converts these data into points based on metabolic equivalents. Users join individually or in groups and are encouraged to set weekly PA goals. Data were examined for 6,639 users (65.8% were group users) over 28 months. We used independent sample t tests and Mann-Whitney U tests to compare means between individual and group users. Two linear regression models were fitted to identify factors associated with activity logging. Users logged 218,766 activities (15,119,249 minutes of PA spanning 592,714 miles [41,858,446 points]). On average, group users had created accounts more recently than individual users (P < .001); however, group users logged more activities (P < .001). On average, group users logged more minutes of PA (P < .001) and earned more points (P < .001). Being in a group was associated with a larger proportion of weeks in which 150 minutes or more of weekly PA was logged (B = 20.47, P < .001). Use of Walk Georgia was significantly higher among group users than among individual users. To expand use and dissemination of online tracking of PA, programs should target naturally occurring groups (eg, workplaces, schools, faith-based groups).

How to create successful Open Hardware projects — About White Rabbits and open fields

NASA Astrophysics Data System (ADS)

van der Bij, E.; Arruat, M.; Cattin, M.; Daniluk, G.; Gonzalez Cobas, J. D.; Gousiou, E.; Lewis, J.; Lipinski, M. M.; Serrano, J.; Stana, T.; Voumard, N.; Wlostowski, T.

2013-12-01

CERN's accelerator control group has embraced ''Open Hardware'' (OH) to facilitate peer review, avoid vendor lock-in and make support tasks scalable. A web-based tool for easing collaborative work was set up and the CERN OH Licence was created. New ADC, TDC, fine delay and carrier cards based on VITA and PCI-SIG standards were designed and drivers for Linux were written. Often industry was paid for developments, while quality and documentation was controlled by CERN. An innovative timing network was also developed with the OH paradigm. Industry now sells and supports these designs that find their way into new fields.

Effective user management with high strength crypto -key in dynamic group environment in cloud

NASA Astrophysics Data System (ADS)

Kumar, P. J.; Suganya, P.; Karthik, G.

2017-11-01

Cloud Clusters consists of various collections of files which are being accessed by multiple users of Cloud. The users are managed as a group and the association of the user to a particular group is dynamic in nature. Every group has a manager who handles the membership of a user to a particular group by issuing keys for encryption and decryption. Due to the dynamic nature of a user he/she may leave the group very frequently. But an attempt can be made by the user who has recently left the group to access a file maintained by that group. Key distribution becomes a critical issue while the behavior of the user is dynamic. Existing techniques to manage the users of group in terms of security and key distribution has been investigated so that to arrive at an objective to identify the scopes to increase security and key management scheme in cloud. The usage of various key combinations to measure the strength of security and efficiency of user management in dynamic cloud environment has been investigated.

Evaluating user reputation in online rating systems via an iterative group-based ranking method

NASA Astrophysics Data System (ADS)

Gao, Jian; Zhou, Tao

2017-05-01

Reputation is a valuable asset in online social lives and it has drawn increased attention. Due to the existence of noisy ratings and spamming attacks, how to evaluate user reputation in online rating systems is especially significant. However, most of the previous ranking-based methods either follow a debatable assumption or have unsatisfied robustness. In this paper, we propose an iterative group-based ranking method by introducing an iterative reputation-allocation process into the original group-based ranking method. More specifically, the reputation of users is calculated based on the weighted sizes of the user rating groups after grouping all users by their rating similarities, and the high reputation users' ratings have larger weights in dominating the corresponding user rating groups. The reputation of users and the user rating group sizes are iteratively updated until they become stable. Results on two real data sets with artificial spammers suggest that the proposed method has better performance than the state-of-the-art methods and its robustness is considerably improved comparing with the original group-based ranking method. Our work highlights the positive role of considering users' grouping behaviors towards a better online user reputation evaluation.

Managing Rock and Paleomagnetic Data Flow with the MagIC Database: from Measurement and Analysis to Comprehensive Archive and Visualization

NASA Astrophysics Data System (ADS)

Koppers, A. A.; Minnett, R. C.; Tauxe, L.; Constable, C.; Donadini, F.

2008-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by rock and paleomagnetic data. The goal of MagIC is to archive all measurements and derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Organizing data for presentation in peer-reviewed publications or for ingestion into databases is a time-consuming task, and to facilitate these activities, three tightly integrated tools have been developed: MagIC-PY, the MagIC Console Software, and the MagIC Online Database. A suite of Python scripts is available to help users port their data into the MagIC data format. They allow the user to add important metadata, perform basic interpretations, and average results at the specimen, sample and site levels. These scripts have been validated for use as Open Source software under the UNIX, Linux, PC and Macintosh© operating systems. We have also developed the MagIC Console Software program to assist in collating rock and paleomagnetic data for upload to the MagIC database. The program runs in Microsoft Excel© on both Macintosh© computers and PCs. It performs routine consistency checks on data entries, and assists users in preparing data for uploading into the online MagIC database. The MagIC website is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual FlashMap interface to browse and select locations. Users can also browse the database by data type (inclination, intensity, VGP, hysteresis, susceptibility) or by data compilation to view all contributions associated with previous databases, such as PINT, GMPDB or TAFI or other user-defined compilations. Query results are displayed in a digestible tabular format allowing the user to descend from locations to sites, samples, specimens and measurements. At each stage, the result set can be saved and, when supported by the data, can be visualized by plotting global location maps, equal area, XY, age, and depth plots, or typical Zijderveld, hysteresis, magnetization and remanence diagrams.

Impact on TRMM Products of Conversion to Linux

NASA Technical Reports Server (NTRS)

Stocker, Erich Franz; Kwiatkowski, John

2008-01-01

In June 2008, TRMM data processing will be assumed by the Precipitation Processing System (PPS). This change will also mean a change in the hardware production environment from an SGI 32 bit IRIX processing environment to a Linux (Beowulf) 64 bit processing environment. This change of platform and operating system addressing (32 to 64) has some influence on data values in the TRMM data products. This paper will describe the transition architecture and scheduling. It will also provide an analysis of what the nature of the product differences will be. It will demonstrate that the differences are not scientifically significant and are generally not visible. However, they are not always identical with those which the SGI would produce.

Software for Processing of Digitized Astronegatives from Archives and Databases of Virtual Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu. I.; Andruk, V. N.; Kazantseva, L. V.

The paper discusses and illustrates the steps of basic processing of digitized image of astro negatives. Software for obtaining of a rectangular coordinates and photometric values of objects on photographic plates was created in the environment LINUX / MIDAS / ROMAFOT. The program can automatically process the specified number of files in FITS format with sizes up to 20000 x 20000 pixels. Other programs were made in FORTRAN and PASCAL with the ability to work in an environment of LINUX or WINDOWS. They were used for: identification of stars, separation and exclusion of diffraction satellites and double and triple exposures, elimination of image defects, reduction to the equatorial coordinates and magnitudes of a reference catalogs.

User's Guide for MapIMG 2: Map Image Re-projection Software Package

USGS Publications Warehouse

Finn, Michael P.; Trent, Jason R.; Buehler, Robert A.

2006-01-01

BACKGROUND Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in commercial software packages, but implementation with data other than points requires specific adaptation of the transformation equations or prior preparation of the data to allow the transformation to succeed. It seems that some of these packages use the U.S. Geological Survey's (USGS) General Cartographic Transformation Package (GCTP) or similar point transformations without adaptation to the specific characteristics of raster data (Usery and others, 2003a). Usery and others (2003b) compiled and tabulated the accuracy of categorical areas in projected raster datasets of global extent. Based on the shortcomings identified in these studies, geographers and applications programmers at the USGS expanded and evolved a USGS software package, MapIMG, for raster map projection transformation (Finn and Trent, 2004). Daniel R. Steinwand of Science Applications International Corporation, National Center for Earth Resources Observation and Science, originally developed MapIMG for the USGS, basing it on GCTP. Through previous and continuing efforts at the USGS' National Geospatial Technical Operations Center, this program has been transformed from an application based on command line input into a software package based on a graphical user interface for Windows, Linux, and other UNIX machines.

Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.

2004-05-12

An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view,more » create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.« less

Wolf Testing: Open Source Testing Software

NASA Astrophysics Data System (ADS)

Braasch, P.; Gay, P. L.

2004-12-01

Wolf Testing is software for easily creating and editing exams. Wolf Testing allows the user to create an exam from a database of questions, view it on screen, and easily print it along with the corresponding answer guide. The questions can be multiple choice, short answer, long answer, or true and false varieties. This software can be accessed securely from any location, allowing the user to easily create exams from home. New questions, which can include associated pictures, can be added through a web-interface. After adding in questions, they can be edited, deleted, or duplicated into multiple versions. Long-term test creation is simplified, as you are able to quickly see what questions you have asked in the past and insert them, with or without editing, into future tests. All tests are archived in the database. Written in PHP and MySQL, this software can be installed on any UNIX / Linux platform, including Macintosh OS X. The secure interface keeps students out, and allows you to decide who can create tests and who can edit information already in the database. Tests can be output as either html with pictures or rich text without pictures, and there are plans to add PDF and MS Word formats as well. We would like to thank Dr. Wolfgang Rueckner and the Harvard University Science Center for providing incentive to start this project, computers and resources to complete this project, and inspiration for the project's name. We would also like to thank Dr. Ronald Newburgh for his assistance in beta testing.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

PubMed

Pandey, Manmohan; Kumar, Ravindra; Srivastava, Prachi; Agarwal, Suyash; Srivastava, Shreya; Nagpure, Naresh S; Jena, Joy K; Kushwaha, Basdeo

2018-03-16

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.

SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

USGS Publications Warehouse

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

[Computer simulation of a clinical magnet resonance tomography scanner for training purposes].

PubMed

Hackländer, T; Mertens, H; Cramer, B M

2004-08-01

The idea for this project was born by the necessity to offer medical students an easy approach to the theoretical basics of magnetic resonance imaging. The aim was to simulate the features and functions of such a scanner on a commercially available computer by means of a computer program. The simulation was programmed in pure Java under the GNU General Public License and is freely available for a commercially available computer with Windows, Macintosh or Linux operating system. The graphic user interface is oriented to a real scanner. In an external program parameter, images for the proton density and the relaxation times T1 and T2 are calculated on the basis of clinical examinations. From this, the image calculation is carried out in the simulation program pixel by pixel on the basis of a pulse sequence chosen and modified by the user. The images can be stored and printed. In addition, it is possible to display and modify k-space images. Seven classes of pulse sequences are implemented and up to 14 relevant sequence parameters, such as repetition time and echo time, can be altered. Aliasing and motion artifacts can be simulated. As the image calculation only takes a few seconds, interactive working is possible. The simulation has been used in the university education for more than 1 year, successfully illustrating the dependence of the MR images on the measuring parameters. This should facititate the approach of students to the understanding MR imaging in the future.

MOLAR: Modular Linux and Adaptive Runtime Support for HEC OS/R Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frank Mueller

2009-02-05

MOLAR is a multi-institution research effort that concentrates on adaptive, reliable,and efficient operating and runtime system solutions for ultra-scale high-end scientific computing on the next generation of supercomputers. This research addresses the challenges outlined by the FAST-OS - forum to address scalable technology for runtime and operating systems --- and HECRTF --- high-end computing revitalization task force --- activities by providing a modular Linux and adaptable runtime support for high-end computing operating and runtime systems. The MOLAR research has the following goals to address these issues. (1) Create a modular and configurable Linux system that allows customized changes based onmore » the requirements of the applications, runtime systems, and cluster management software. (2) Build runtime systems that leverage the OS modularity and configurability to improve efficiency, reliability, scalability, ease-of-use, and provide support to legacy and promising programming models. (3) Advance computer reliability, availability and serviceability (RAS) management systems to work cooperatively with the OS/R to identify and preemptively resolve system issues. (4) Explore the use of advanced monitoring and adaptation to improve application performance and predictability of system interruptions. The overall goal of the research conducted at NCSU is to develop scalable algorithms for high-availability without single points of failure and without single points of control.« less

Development and application of remote video monitoring system for combine harvester based on embedded Linux

NASA Astrophysics Data System (ADS)

Chen, Jin; Wang, Yifan; Wang, Xuelei; Wang, Yuehong; Hu, Rui

2017-01-01

Combine harvester usually works in sparsely populated areas with harsh environment. In order to achieve the remote real-time video monitoring of the working state of combine harvester. A remote video monitoring system based on ARM11 and embedded Linux is developed. The system uses USB camera for capturing working state video data of the main parts of combine harvester, including the granary, threshing drum, cab and cut table. Using JPEG image compression standard to compress video data then transferring monitoring screen to remote monitoring center over the network for long-range monitoring and management. At the beginning of this paper it describes the necessity of the design of the system. Then it introduces realization methods of hardware and software briefly. And then it describes detailedly the configuration and compilation of embedded Linux operating system and the compiling and transplanting of video server program are elaborated. At the end of the paper, we carried out equipment installation and commissioning on combine harvester and then tested the system and showed the test results. In the experiment testing, the remote video monitoring system for combine harvester can achieve 30fps with the resolution of 800x600, and the response delay in the public network is about 40ms.

Computing and combustion

NASA Technical Reports Server (NTRS)

Thompson, Daniel

2004-01-01

Coming into the Combustion Branch of the Turbomachinery and Propulsion Systems Division, there was not any set project planned out for me to work on. This was understandable, considering I am only at my sophmore year in college. Also, my mentor was a division chief and it was expected that I would be passed down the line. It took about a week for me to be placed with somebody who could use me. My first project was to write a macro for TecPlot. Commonly, a person would have a 3D contour volume modeling something such as a combustion engine. This 3D volume needed to have slices extracted from it and made into 2D scientific plots with all of the appropriate axis and titles. This was very tedious to do by hand. My macro needed to automate the process. There was some education I needed before I could start, however. First, TecPlot ran on Unix and Linux, like a growing majority of scientific applications. I knew a little about Linux, but I would need to know more to use the software at hand. I took two classes at the Learning Center on Unix and am now comfortable with Linux and Unix. I already had taken Computer Science I and II, and had undergone the transformation from Computer Programmer to Procedural Epistemologist. I knew how to design efficient algorithms, I just needed to learn the macro language. After a little less than a week, I had learned the basics of the language. Like most languages, the best way to learn more of it was by using it. It was decided that it was best that I do the macro in layers, starting simple and adding features as I went. The macro started out slicing with respect to only one axis, and did not make 2D plots out of the slices. Instead, it lined them up inside the solid. Next, I allowed for more than one axis and placed each slice in a separate frame. After this, I added code that transformed each individual slice-frame into a scientific plot. I also made frames for composite volumes, which showed all of the slices in the same XYZ space. I then designed an addition companion macro that exported each frame into its own image file. I then distributed the macros to a test group, and am awaiting feedback. In the meantime, a am researching the possible applications of distributed computing on the National Combustor Code. Many of our Linux boxes were idle for most of the day. The department thinks that it would be wonderful if we could get all of these idle processors to work on a problem under the NCC code. The client software would have to be easily distributed, such as in screensaver format or as a program that only ran when the computer was not in use. This project proves to be an interesting challenge.

Virtualizing access to scientific applications with the Application Hosting Environment

NASA Astrophysics Data System (ADS)

Zasada, S. J.; Coveney, P. V.

2009-12-01

The growing power and number of high performance computing resources made available through computational grids present major opportunities as well as a number of challenges to the user. At issue is how these resources can be accessed and how their power can be effectively exploited. In this paper we first present our views on the usability of contemporary high-performance computational resources. We introduce the concept of grid application virtualization as a solution to some of the problems with grid-based HPC usability. We then describe a middleware tool that we have developed to realize the virtualization of grid applications, the Application Hosting Environment (AHE), and describe the features of the new release, AHE 2.0, which provides access to a common platform of federated computational grid resources in standard and non-standard ways. Finally, we describe a case study showing how AHE supports clinical use of whole brain blood flow modelling in a routine and automated fashion. Program summaryProgram title: Application Hosting Environment 2.0 Catalogue identifier: AEEJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence, Version 2 No. of lines in distributed program, including test data, etc.: not applicable No. of bytes in distributed program, including test data, etc.: 1 685 603 766 Distribution format: tar.gz Programming language: Perl (server), Java (Client) Computer: x86 Operating system: Linux (Server), Linux/Windows/MacOS (Client) RAM: 134 217 728 (server), 67 108 864 (client) bytes Classification: 6.5 External routines: VirtualBox (server), Java (client) Nature of problem: The middleware that makes grid computing possible has been found by many users to be too unwieldy, and presents an obstacle to use rather than providing assistance [1,2]. Such problems are compounded when one attempts to harness the power of a grid, or a federation of different grids, rather than just a single resource on the grid. Solution method: To address the above problem, we have developed AHE, a lightweight interface, designed to simplify the process of running scientific codes on a grid of HPC and local resources. AHE does this by introducing a layer of middleware between the user and the grid, which encapsulates much of the complexity associated with launching grid applications. Unusual features: The server is distributed as a VirtualBox virtual machine. VirtualBox ( http://www.virtualbox.org) must be downloaded and installed in order to run the AHE server virtual machine. Details of how to do this are given in the AHE 2.0 Quick Start Guide. Running time: Not applicable References:J. Chin, P.V. Coveney, Towards tractable toolkits for the grid: A plea for lightweight, useable middleware, NeSC Technical Report, 2004, http://nesc.ac.uk/technical_papers/UKeS-2004-01.pdf. P.V. Coveney, R.S. Saksena, S.J. Zasada, M. McKeown, S. Pickles, The Application Hosting Environment: Lightweight middleware for grid-based computational science, Computer Physics Communications 176 (2007) 406-418.

Tropical Cyclone Information System

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Knosp, Brian W.; Vu, Quoc A.; Yi, Chao; Hristova-Veleva, Svetla M.

2009-01-01

The JPL Tropical Cyclone Infor ma tion System (TCIS) is a Web portal (http://tropicalcyclone.jpl.nasa.gov) that provides researchers with an extensive set of observed hurricane parameters together with large-scale and convection resolving model outputs. It provides a comprehensive set of high-resolution satellite (see figure), airborne, and in-situ observations in both image and data formats. Large-scale datasets depict the surrounding environmental parameters such as SST (Sea Surface Temperature) and aerosol loading. Model outputs and analysis tools are provided to evaluate model performance and compare observations from different platforms. The system pertains to the thermodynamic and microphysical structure of the storm, the air-sea interaction processes, and the larger-scale environment as depicted by ocean heat content and the aerosol loading of the environment. Currently, the TCIS is populated with satellite observations of all tropical cyclones observed globally during 2005. There is a plan to extend the database both forward in time till present as well as backward to 1998. The portal is powered by a MySQL database and an Apache/Tomcat Web server on a Linux system. The interactive graphic user interface is provided by Google Map.

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

PubMed

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Bioinformatics on the cloud computing platform Azure.

PubMed

Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

Ligand.Info small-molecule Meta-Database.

PubMed

von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek

2004-12-01

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

Bioinformatics on the Cloud Computing Platform Azure

PubMed Central

Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

Using Tablet for visual exploration of second-generation sequencing data.

PubMed

Milne, Iain; Stephen, Gordon; Bayer, Micha; Cock, Peter J A; Pritchard, Leighton; Cardle, Linda; Shaw, Paul D; Marshall, David

2013-03-01

The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet-a high-performance graphical viewer for visualization of 2GS assemblies and read mappings-plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded from http://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

PubMed

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. Copyright © 2012 Wiley Periodicals, Inc.

SASfit: a tool for small-angle scattering data analysis using a library of analytical expressions.

PubMed

Breßler, Ingo; Kohlbrecher, Joachim; Thünemann, Andreas F

2015-10-01

SASfit is one of the mature programs for small-angle scattering data analysis and has been available for many years. This article describes the basic data processing and analysis workflow along with recent developments in the SASfit program package (version 0.94.6). They include (i) advanced algorithms for reduction of oversampled data sets, (ii) improved confidence assessment in the optimized model parameters and (iii) a flexible plug-in system for custom user-provided models. A scattering function of a mass fractal model of branched polymers in solution is provided as an example for implementing a plug-in. The new SASfit release is available for major platforms such as Windows, Linux and MacOS. To facilitate usage, it includes comprehensive indexed documentation as well as a web-based wiki for peer collaboration and online videos demonstrating basic usage. The use of SASfit is illustrated by interpretation of the small-angle X-ray scattering curves of monomodal gold nanoparticles (NIST reference material 8011) and bimodal silica nanoparticles (EU reference material ERM-FD-102).

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

PubMed

Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro

2016-07-01

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Digital time stamping system based on open source technologies.

PubMed

Miskinis, Rimantas; Smirnov, Dmitrij; Urba, Emilis; Burokas, Andrius; Malysko, Bogdan; Laud, Peeter; Zuliani, Francesco

2010-03-01

A digital time stamping system based on open source technologies (LINUX-UBUNTU, OpenTSA, OpenSSL, MySQL) is described in detail, including all important testing results. The system, called BALTICTIME, was developed under a project sponsored by the European Commission under the Program FP 6. It was designed to meet the requirements posed to the systems of legal and accountable time stamping and to be applicable to the hardware commonly used by the national time metrology laboratories. The BALTICTIME system is intended for the use of governmental and other institutions as well as personal bodies. Testing results demonstrate that the time stamps issued to the user by BALTICTIME and saved in BALTICTIME's archives (which implies that the time stamps are accountable) meet all the regulatory requirements. Moreover, the BALTICTIME in its present implementation is able to issue more than 10 digital time stamps per second. The system can be enhanced if needed. The test version of the BALTICTIME service is free and available at http://baltictime. pfi.lt:8080/btws/ and http://baltictime.lnmc.lv:8080/btws/.

Orthos, an alarm system for the ALICE DAQ operations

NASA Astrophysics Data System (ADS)

Chapeland, Sylvain; Carena, Franco; Carena, Wisla; Chibante Barroso, Vasco; Costa, Filippo; Denes, Ervin; Divia, Roberto; Fuchs, Ulrich; Grigore, Alexandru; Simonetti, Giuseppe; Soos, Csaba; Telesca, Adriana; Vande Vyvre, Pierre; von Haller, Barthelemy

2012-12-01

ALICE (A Large Ion Collider Experiment) is the heavy-ion detector studying the physics of strongly interacting matter and the quark-gluon plasma at the CERN LHC (Large Hadron Collider). The DAQ (Data Acquisition System) facilities handle the data flow from the detectors electronics up to the mass storage. The DAQ system is based on a large farm of commodity hardware consisting of more than 600 devices (Linux PCs, storage, network switches), and controls hundreds of distributed hardware and software components interacting together. This paper presents Orthos, the alarm system used to detect, log, report, and follow-up abnormal situations on the DAQ machines at the experimental area. The main objective of this package is to integrate alarm detection and notification mechanisms with a full-featured issues tracker, in order to prioritize, assign, and fix system failures optimally. This tool relies on a database repository with a logic engine, SQL interfaces to inject or query metrics, and dynamic web pages for user interaction. We describe the system architecture, the technologies used for the implementation, and the integration with existing monitoring tools.

Internet Distribution of Spacecraft Telemetry Data

NASA Technical Reports Server (NTRS)

Specht, Ted; Noble, David

2006-01-01

Remote Access Multi-mission Processing and Analysis Ground Environment (RAMPAGE) is a Java-language server computer program that enables near-real-time display of spacecraft telemetry data on any authorized client computer that has access to the Internet and is equipped with Web-browser software. In addition to providing a variety of displays of the latest available telemetry data, RAMPAGE can deliver notification of an alarm by electronic mail. Subscribers can then use RAMPAGE displays to determine the state of the spacecraft and formulate a response to the alarm, if necessary. A user can query spacecraft mission data in either binary or comma-separated-value format by use of a Web form or a Practical Extraction and Reporting Language (PERL) script to automate the query process. RAMPAGE runs on Linux and Solaris server computers in the Ground Data System (GDS) of NASA's Jet Propulsion Laboratory and includes components designed specifically to make it compatible with legacy GDS software. The client/server architecture of RAMPAGE and the use of the Java programming language make it possible to utilize a variety of competitive server and client computers, thereby also helping to minimize costs.

Serial Interface through Stream Protocol on EPICS Platform for Distributed Control and Monitoring

NASA Astrophysics Data System (ADS)

Das Gupta, Arnab; Srivastava, Amit K.; Sunil, S.; Khan, Ziauddin

2017-04-01

Remote operation of any equipment or device is implemented in distributed systems in order to control and proper monitoring of process values. For such remote operations, Experimental Physics and Industrial Control System (EPICS) is used as one of the important software tool for control and monitoring of a wide range of scientific parameters. A hardware interface is developed for implementation of EPICS software so that different equipment such as data converters, power supplies, pump controllers etc. could be remotely operated through stream protocol. EPICS base was setup on windows as well as Linux operating system for control and monitoring while EPICS modules such as asyn and stream device were used to interface the equipment with standard RS-232/RS-485 protocol. Stream Device protocol communicates with the serial line with an interface to asyn drivers. Graphical user interface and alarm handling were implemented with Motif Editor and Display Manager (MEDM) and Alarm Handler (ALH) command line channel access utility tools. This paper will describe the developed application which was tested with different equipment and devices serially interfaced to the PCs on a distributed network.

Google Sky: A Digital View of the Night Sky

NASA Astrophysics Data System (ADS)

Connolly, A. Scranton, R.; Ornduff, T.

2008-11-01

From its inception Astronomy has been a visual science, from careful observations of the sky using the naked eye, to the use of telescopes and photographs to map the distribution of stars and galaxies, to the current era of digital cameras that can image the sky over many decades of the electromagnetic spectrum. Sky in Google Earth (http://earth.google.com) and Google Sky (http://www.google.com/sky) continue this tradition, providing an intuitive visual interface to some of the largest astronomical imaging surveys of the sky. Streaming multi-color imagery, catalogs, time domain data, as well as annotating interesting astronomical sources and events with placemarks, podcasts and videos, Sky provides a panchromatic view of the universe accessible to anyone with a computer. Beyond a simple exploration of the sky Google Sky enables users to create and share content with others around the world. With an open interface available on Linux, Mac OS X and Windows, and translations of the content into over 20 different languages we present Sky as the embodiment of a virtual telescope for discovery and sharing the excitement of astronomy and science as a whole.

Grid Visualization Tool

NASA Technical Reports Server (NTRS)

Chouinard, Caroline; Fisher, Forest; Estlin, Tara; Gaines, Daniel; Schaffer, Steven

2005-01-01

The Grid Visualization Tool (GVT) is a computer program for displaying the path of a mobile robotic explorer (rover) on a terrain map. The GVT reads a map-data file in either portable graymap (PGM) or portable pixmap (PPM) format, representing a gray-scale or color map image, respectively. The GVT also accepts input from path-planning and activity-planning software. From these inputs, the GVT generates a map overlaid with one or more rover path(s), waypoints, locations of targets to be explored, and/or target-status information (indicating success or failure in exploring each target). The display can also indicate different types of paths or path segments, such as the path actually traveled versus a planned path or the path traveled to the present position versus planned future movement along a path. The program provides for updating of the display in real time to facilitate visualization of progress. The size of the display and the map scale can be changed as desired by the user. The GVT was written in the C++ language using the Open Graphics Library (OpenGL) software. It has been compiled for both Sun Solaris and Linux operating systems.

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

Irma 5.1 multisensor signature prediction model

NASA Astrophysics Data System (ADS)

Savage, James; Coker, Charles; Thai, Bea; Aboutalib, Omar; Yamaoka, Neil; Kim, Charles

2005-05-01

The Irma synthetic signature prediction code is being developed to facilitate the research and development of multisensor systems. Irma was one of the first high resolution Infrared (IR) target and background signature models to be developed for tactical weapon application. Originally developed in 1980 by the Munitions Directorate of the Air Force Research Laboratory (AFRL/MN), the Irma model was used exclusively to generate IR scenes. In 1988, a number of significant upgrades to Irma were initiated including the addition of a laser (or active) channel. This two-channel version was released to the user community in 1990. In 1992, an improved scene generator was incorporated into the Irma model, which supported correlated frame-to-frame imagery. A passive IR/millimeter wave (MMW) code was completed in 1994. This served as the cornerstone for the development of the co-registered active/passive IR/MMW model, Irma 4.0. In 2000, Irma version 5.0 was released which encompassed several upgrades to both the physical models and software. Circular polarization was added to the passive channel and the doppler capability was added to the active MMW channel. In 2002, the multibounce technique was added to the Irma passive channel. In the ladar channel, a user-friendly Ladar Sensor Assistant (LSA) was incorporated which provides capability and flexibility for sensor modeling. Irma 5.0 runs on several platforms including Windows, Linux, Solaris, and SGI Irix. Since 2000, additional capabilities and enhancements have been added to the ladar channel including polarization and speckle effect. Work is still ongoing to add time-jittering model to the ladar channel. A new user interface has been introduced to aid users in the mechanism of scene generation and running the Irma code. The user interface provides a canvas where a user can add and remove objects using mouse clicks to construct a scene. The scene can then be visualized to find the desired sensor position. The synthetic ladar signatures have been validated twice and underwent a third validation test near the end of 04. These capabilities will be integrated into the next release, Irma 5.1, scheduled for completion in the summer of FY05. Irma is currently being used to support a number of civilian and military applications. The Irma user base includes over 130 agencies within the Air Force, Army, Navy, DARPA, NASA, Department of Transportation, academia, and industry. The purpose of this paper is to report the progress of the Irma 5.1 development effort.

Mobile phones and social structures: an exploration of a closed user group in rural Ghana

PubMed Central

2013-01-01

Background In the Millennium Villages Project site of Bonsaaso, Ghana, the Health Team is using a mobile phone closed user group to place calls amongst one another at no cost. Methods In order to determine the utilization and acceptability of the closed user group amongst users, social network analysis and qualitative methods were used. Key informants were identified and interviewed. The key informants also kept prospective call journals. Billing statements and de-identified call data from the closed user group were used to generate data for analyzing the social structure revealed by the network traffic. Results The majority of communication within the closed user group was personal and not for professional purposes. The members of the CUG felt that the group improved their efficiency at work. Conclusions The methods used present an interesting way to investigate the social structure surrounding communication via mobile phones. In addition, the benefits identified from the exploration of this closed user group make a case for supporting mobile phone closed user groups amongst professional groups. PMID:24007331

Cloud prediction of protein structure and function with PredictProtein for Debian.

PubMed

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

PubMed Central

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032