Sample records for zachary wasserman python

  1. Ball python

    NSDL National Science Digital Library

    Patrick Jean (muséum d'histoire naturelle de Nantes; )

    2004-02-10

    All reptiles are cold-blooded, meaning that they gather their warmth from the environment around them. Reptiles in captivity, like this ball python, need a sun lamp to stay warm. They could die if they get too cold.

  2. Alligator and Python Struggle

    USGS Multimedia Gallery

    An American alligator and a Burmese python locked in a struggle to prevail in Everglades National Park. This python appears to be losing, but snakes in similar situations have apparently escaped unharmed, and in other situations pythons have eaten alligators....

  3. Python Programming Language

    NSDL National Science Digital Library

    Python is often compared to Tcl, Perl, Scheme or Java and runs on many brands of UNIX, on Windows, OS/2, Mac, Amiga, and many other platforms. The most recent version of Python is available for free from this website. Also included are Python 2.3.3 Documentation (released December 19, 2003), the interpreter program that reads Python programs and carries out their instructions, tutorials for non-programmers and programmers, some examples and sample code, information for developers, and links to the programming community user groups. "The Python implementation is copyrighted but freely usable and distributable, even for commercial use."

  4. Python Script Analysis

    NSDL National Science Digital Library

    IMPART RET Program, College of Information Science & Technology,

    Working in small groups, students complete and run functioning Python codes. They begin by determining the missing commands in a sample piece of Python code that doubles all the elements of a given input and sums the resulting values. Then students modify more advanced Python code, which numerically computes the slope of a tangent line by finding the slopes of progressively closer secant lines; to this code they add explanatory comments to describe the function of each line of code. This requires students to understand the logic employed in the Python code. Finally, students make modifications to the code in order to find the slopes of tangents to a variety of functions.

  5. NEURON and Python

    PubMed Central

    Hines, Michael L.; Davison, Andrew P.; Muller, Eilif

    2008-01-01

    The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications. PMID:19198661

  6. Invent with Python

    NSDL National Science Digital Library

    Sweigart, Al

    Have you ever wanted to learn how to make your own computer games? This is now a possibility, and all one needs to do is look over the excellent "Invent Your Own Computer Games with Python" site. The guide has been written to be understood by people as young as 10 and each chapter gives users the complete source guide, then teaches the programming concepts from the example. There are twenty chapters here, including "Using the Debugger," "Hangman," "Tic Tac Toe," and "Installing Python." Each chapter includes graphics and flow-charts designed to help neophytes get acclimated to the entire experience and process. The work is rounded out by the inclusion of four appendices, including "Common Error Messages in Python."

  7. Biologists Remove Python from Everglades

    USGS Multimedia Gallery

    This 16 1/2-foot python, being removed from the wild by USGS and NPS personnel, was captured in a thicket in Everglades National Park in May 2012. The python was equipped with a radio-transmitter and an accelerometer as part of one of the Burmese python projects led by USGS to learn more about the b...

  8. Python microgravity accelerometer system

    NASA Astrophysics Data System (ADS)

    Nijhawan, V.; Arrott, A. P.; Grimes, R. S.

    1989-01-01

    A microgravity accelerometer system developed for use in the Space Shuttle middeck locker is described. The system, known as PYTHON, is a microcomputer-based digital acceleration-measurement system that uses primarily off-the-shelf qualified space hardware and modular software. It can be operated on-board in real time and on the ground either during the flight or post-flight. The sensor head consists of an accelerometer, which measures acceleration in three orthogonal axes, and an internal thermister for temperature compensation; threshold and resolution are better than 0.000001 g. The results of acceleration measurements with PYTHON carried out during parabolic maneuvers aboard the NASA's KC-135 aircraft are presented.

  9. Thermal properties of iron at high pressures and temperatures Evgeny Wasserman and Lars Stixrude

    E-print Network

    Stixrude, Lars

    Thermal properties of iron at high pressures and temperatures Evgeny Wasserman and Lars Stixrude important sources of experimental information on the thermal properties and subsolidus phase diagram of iron by more than a thousand degrees. Theo- retical calculations of thermal properties can help to resolve

  10. A comparison of C++, Java and Python 

    E-print Network

    Chou, Ling

    1997-01-01

    and Embedding the Python Interpreter, http: //www. ida. liu. se/imported/python/python-ext/ext. html [18] Gvmo VAN RossvM, 1997, Python Tutorial, http: //www. wcmh. corn/uworld /archives/95/tutorial/005. html [19] BJARNE STROUSTRUP, 1995, The Design...

  11. NICI Python Data Reduction

    NASA Astrophysics Data System (ADS)

    Zarate, N.; Artigua, E.; Hartung, M.; Labrie, K.

    2010-12-01

    NICI, the new adaptive-optics supported Near Infrared Coronagraphic Imager of the Gemini Observatory (South), has recently been commissioned and offered to the astronomical community. We describe its reduction package and design of the different modules. The software has been written in Python using numerical routines from Numpy, Scipy and Ndimage, as well as the Gemini module Astrodata dealing with Gemini’s fits-file structure. We discuss science data preparation, and basic reduction steps as well as the implementation of the Angular and Spectral Differential Imaging (ADI/SDI) reduction algorithm, and the LOCI method (Locally Optimized Combination of Images) producing the final set of reduced science FITS files for high-contrast imaging.

  12. Python fiber optic seal

    SciTech Connect

    Ystesund, K.; Bartberger, J.; Brusseau, C.; Fleming, P.; Insch, K.; Tolk, K.

    1993-08-01

    Sandia National Laboratories has developed a high security fiber optic seal that incorporates tamper resistance features that are not available in commercial fiber optic seals. The Python Seal is a passive fiber optic loop seal designed to give indication of unauthorized entry. The seal includes a fingerprint feature that provides seal identity information in addition to the unique fiber optic pattern created when the seal is installed. The fiber optic cable used for the seal loop is produced with tamper resistant features that increase the difficulty of attacking that component of a seal. A Seal Reader has been developed that will record the seal signature and the fingerprint feature of the seal. A Correlator software program then compares seal images to establish a match or mismatch. SNL is also developing a Polaroid reader to permit hard copies of the seal patterns to be obtained directly from the seal.

  13. Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

    E-print Network

    Ceder, Gerbrand

    Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis-throughput a b s t r a c t We present the Python Materials Genomics (pymatgen) library, a robust, open

  14. Python programming --Semantic Web Finn Arup Nielsen

    E-print Network

    Python programming -- Semantic Web Finn °Arup Nielsen DTU Compute Technical University of Denmark October 9, 2013 #12;Python programming -- Semantic Web What is Semantic Web? Semantic Web = Triple data 9, 2013 #12;Python programming -- Semantic Web Why the Semantic Web? IBM's Watson supercomputer

  15. Web Interfaces 1 Python Scripts in Browsers

    E-print Network

    Verschelde, Jan

    Web Interfaces 1 Python Scripts in Browsers the web server Apache processing forms with Python scripts Python code to write HTML 2 Web Interfaces for the Determinant dynamic interactive forms passing, 28 October 2013 Scientific Software (MCS 507 L-27) web interfaces 28 October 2013 1 / 42 #12;Web

  16. Building Facebook Application using Python

    E-print Network

    Wu, S. Felix

    Building Facebook Application using Python ECS-15, Fall 2010 Prantik Bhattacharyya #12;· Farmville ­ Game ­ 57.5m users ­ http://www.facebook.com/FarmVille · Causes ­ Issues/Movement ­ 26.4m users ­ http://www.facebook.com/causes Facebook Applications #12;Outline · Facebook Applications · Writing Applications · Development

  17. Statistical Tools in Python A NASA AISR Project

    E-print Network

    Loredo, Thomas J.

    Statistical Tools in Python A NASA AISR Project Tom Loredo, Alanna Connors, Travis Oliphant Cornell: Python Single implementation facilitates depth/breadth Python's VHL features speed development Python's simplicity allows easy access · Outreach #12;A Bit About Python · Very simple syntax--resembles "pseudo code

  18. A Burmese Python and an Alligator Encounter in South Florida

    USGS Multimedia Gallery

    A Burmese python (Python molurus) peeks over the head of an alligator that holds the python's body in its mouth in Everglades National Park. Photo courtesy of Lori Oberhofer, National Park Service....

  19. Biopython: Python tools for computational biology

    Microsoft Academic Search

    Brad Chapman; Jeffrey Chang

    2000-01-01

    The Biopython project was formed in August 1999 as a collaboration to collect and produce open source bioinformatics tools written in Python, an object-oriented scripting language. It is modeled on the highly successful Bioperl project, but has the goal of making libraries available for people doing computations in Python. The philosophy of all the Bio* projects is that part of

  20. A field test of attractant traps for invasive Burmese pythons (Python molurus bivittatus) in southern Florida

    USGS Publications Warehouse

    Reed, R.N.; Hart, K.M.; Rodda, G.H.; Mazzotti, F.J.; Snow, R.W.; Cherkiss, M.; Rozar, R.; Goetz, S.

    2011-01-01

    Context. Invasive Burmese pythons (Python molurus bivittatus) are established over thousands of square kilometres of southern Florida, USA, and consume a wide range of native vertebrates. Few tools are available to control the python population, and none of the available tools have been validated in the field to assess capture success as a proportion of pythons available to be captured. Aims. Our primary aim was to conduct a trap trial for capturing invasive pythons in an area east of Everglades National Park, where many pythons had been captured in previous years, to assess the efficacy of traps for population control.Wealso aimed to compare results of visual surveys with trap capture rates, to determine capture rates of non-target species, and to assess capture rates as a proportion of resident pythons in the study area. Methods.Weconducted a medium-scale (6053 trap nights) experiment using two types of attractant traps baited with live rats in the Frog Pond area east of Everglades National Park.Wealso conducted standardised and opportunistic visual surveys in the trapping area. Following the trap trial, the area was disc harrowed to expose pythons and allow calculation of an index of the number of resident pythons. Key results. We captured three pythons and 69 individuals of various rodent, amphibian, and reptile species in traps. Eleven pythons were discovered during disc harrowing operations, as were large numbers of rodents. Conclusions. The trap trial captured a relatively small proportion of the pythons that appeared to be present in the study area, although previous research suggests that trap capture rates improve with additional testing of alternative trap designs. Potential negative impacts to non-target species were minimal. Low python capture rates may have been associated with extremely high local prey abundances during the trap experiment. Implications. Results of this trial illustrate many of the challenges in implementing and interpreting results from tests of control tools for large cryptic predators such as Burmese pythons. ?? CSIRO 2011.

  1. Effect of nest temperature on egg-brooding dynamics in Children's pythons Zachary R. Stahlschmidt , Dale F. DeNardo

    E-print Network

    Denardo, Dale

    Facultative endothermy Parental care Respiratory gas exchange Snake Thermal relations Trade-off Water balance to other ectothermic boid snakes (1.9­5.7) and Tclutch conformed to Tnest at the constant, cool temperature treatment. Females coiled tightly around eggs more often during cooling than during warming. Further

  2. A comparison of C++, Java and Python

    E-print Network

    Chou, Ling

    1997-01-01

    APPENDIX B. VITA 1V V1 12 12 16 18 19 24 28 31 34 36 38 42 44 vs LIST OF FIGURES FIGURE Page 1. C++ Distribution Model 2. Java Distribution Model . 3. Python Distribution Model 4. An Overview 5. Java's Security Model 10 13 25... of run-time checking. Java eliminates the usage of pointers to avoid memory leaking problems and enforce system security. Starting 1990, Guido Van Rossum began to create a descendant scripting language of ABC which is called Python (after Monty Python...

  3. Wrappy, a Python Wrapper Generator for C++ Classes

    Microsoft Academic Search

    Gregory S. Couch

    1999-01-01

    Wrappy generates a Python extension module from annotated C++ header files. Wrappy's power comes from how it translates C++ features to Python features: standard C++ container classes are mapped to Python lists and dictionaries; C++ classes are con-verted to Python types (or a Python-subclassable extension class [Ful98]); public member data and accessor member functions are mapped to attributes; C++ exceptions

  4. ParselTongue: AIPS Python Interface

    NASA Astrophysics Data System (ADS)

    Kettenis, Mark; Sipior, Mike

    2012-08-01

    ParselTongue is a Python interface to classic AIPS, Obit and possibly other task-based data reduction packages. It serves as the software infrastructure for some of the ALBUS implementation. It allows you to run AIPS tasks, and access AIPS headers and extension tables from Python. There is also support for running Obit tasks and accessing data in FITS files. Full access to the visibilities in AIPS UV data is also available.

  5. The Python Interface to Antelope and Applications

    NASA Astrophysics Data System (ADS)

    Lindquist, K. G.; Clemesha, A.; Newman, R. L.; Vernon, F. L.

    2008-12-01

    The Antelope Environmental Monitoring System from Boulder Real-Time Technologies, Inc. (http://www.brtt.com) is widely used for acquiring, processing, distributing, and archiving near-real-time monitoring data, especially in seismological networks. We have contributed a new Python interface to the Antelope toolkit, paralleling other commercial and open-source language interfaces in Matlab, PHP, TCL/Tk, and C. The Python programming language (http://www.python.org) is well suited both to scientific computing applications and to interactive web-based applications. In the latter, Python serves as the programming interface through which to connect to standardized open-source frameworks. Community development of these frameworks has advanced in parallel with cross-browser standardization and increasing broadband data transfer rates, making web-based applications the defacto standard for platform-agnostic access to large, heterogeneous datasets. These web-based solutions are starting to mirror some of the capabilities of standard desktop-based applications. We describe the functionality of the new Python interface to Antelope, applications of the interface to the interactive exploration of time-series data on the web using the Twisted open-source framework, and web-based prototype tools developed for the Earthscope Array Network Facility to provide community access to network monitoring and seismic event datasets.

  6. Runtime Optimization for a Secure Router Infrastructure Zachary Goodman, Russell Tessier and Tilman Wolf

    E-print Network

    Mountziaris, T. J.

    Runtime Optimization for a Secure Router Infrastructure Zachary Goodman, Russell Tessier and Tilman graph reloads Motivation · Modern network routers use vulnerable network processors and can be protected an algorithm that directs router traffic to processors and connects monitors to them in a way that minimizes

  7. Alien Presence in the Home: The Design of Tableau Mario Romero, Zachary Pousman, Michael Mateas

    E-print Network

    Mateas, Michael

    Alien Presence in the Home: The Design of Tableau Machine Mario Romero, Zachary Pousman, Michael a design strategy, alien presence, which combines work in Human-Computer Interaction, Artificial of daily activities. An alien presence actively interprets and characterizes daily activity and reflects

  8. Reading Period Resolution Sponsors: Zachary Malter `13, Mari Jarris `14, Sam Ebb `13

    E-print Network

    Royer, Dana

    Reading Period Resolution Sponsors: Zachary Malter `13, Mari Jarris `14, Sam Ebb `13 Recognizing continuing the practice of 4 days of finals and 4 days of reading period or expanding reading period, Bearing of reading period, especially for advanced courses that require long final assignments", Aware

  9. Measuring the Length of a Captured Burmese Python

    USGS Multimedia Gallery

    Skip Snow (National Park Service) measures the length of a captured Burmese python (Python molurus) at the South Florida Research Center, Everglades National Park. Photo courtesy of Lori Oberhofer, NPS. ...

  10. A field test of attractant traps for invasive Burmese pythons (Python molurus bivittatus) in southern Florida

    USGS Publications Warehouse

    Reed, Robert N.; Hart, Kristen M.; Rodda, Gordon H.; Mazzotti, Frank J.; Snow, Ray W.; Cherkiss, Michael; Rozar, Rondald; Goetz, Scott

    2011-01-01

    Conclusions: The trap trial captured a relatively small proportion of the pythons that appeared to be present in the study area, although previous research suggests that trap capture rates improve with additional testing of alternative trap designs. Potential negative impacts to non-target species were minimal. Low python capture rates may have been associated with extremely high local prey abundances during the trap experiment. Implications: Results of this trial illustrate many of the challenges in implementing and interpreting results from tests of control tools for large cryptic predators such as Burmese pythons.

  11. Non-Programmers Tutorial For Python Josh Cogliati

    E-print Network

    Kimbrough, Steven Orla

    Non-Programmers Tutorial For Python Josh Cogliati November 20, 2001 #12;Copyright(c) 1999-2001 Josh, provided also that they carry prominent notices stating who last altered them. All example python source it under any license you please. #12;Abstract Non-Programmers Tutorial For Python is a tutorial designed

  12. Implanting a Radio Transmitter in a Burmese Python

    USGS Multimedia Gallery

    Researchers implant a radio transmitter in a 16-foot, 155-pound female Burmese python (Python molurus) at the South Florida Research Center, Everglades National Park. Radio-tracking builds understanding of where pythons spend their time and therefore where they can be controlled in practice. Photo c...

  13. Compiling Little Languages in Python John Aycock

    E-print Network

    Aycock, John

    Compiling Little Languages in Python John Aycock Department of Computer Science University of Victoria Victoria, B.C., Canada aycock@csc.uvic.ca Abstract Little languages" such as con guration les or HTML documents are commonplace in computing. This paper divides the work of implementinga little

  14. A Record-Breaking Invasive Burmese Python

    USGS Multimedia Gallery

    This female Burmese python broke the records for her length -- 17 feet, 7 inches – and the number of eggs she contained: 87. She was first captured in Everglades National Park by USGS researchers in the spring of 2012, when they followed a

  15. Burmese Python Caught in the Everglades

    USGS Multimedia Gallery

    This large Burmese python, weighing 162 pounds and more than 15 feet long at the time of its capture in 2009, was caught alive in the Everglades and was found to have eaten an American alligator that measured about 6 feet in length. University of Florida researchers in the photo: Michael Rochford is...

  16. A Record-Breaking Invasive Burmese Python

    USGS Multimedia Gallery

    This female Burmese python broke the records for her length - 17 feet, 7 inches - and the number of eggs she contained: 87. She was first captured in Everglades National Park by USGS researchers in the spring of 2012, when they followed a

  17. Compiling Python to a hybrid execution environment

    Microsoft Academic Search

    Rahul Garg; José Nelson Amaral

    2010-01-01

    A new compilation framework enables the execution of numerical-intensive applications, written in Python, on a hybrid execution environment formed by a CPU and a GPU. This compiler automatically computes the set of memory locations that need to be transferred to the GPU, and produces the correct mapping between the CPU and the GPU address spaces. Thus, the programming model implements

  18. Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

    USGS Publications Warehouse

    Hart, K.M.; Schofield, P.J.; Gregoire, D.R.

    2012-01-01

    In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios. ?? 2011.

  19. Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

    USGS Publications Warehouse

    Hart, Kristen M.; Schofield, Pamela J.; Gregoire, Denise R.

    2012-01-01

    In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios.

  20. Meteor Shower Identification and Characterization with Python

    NASA Technical Reports Server (NTRS)

    Moorhead, Althea

    2015-01-01

    The short development time associated with Python and the number of astronomical packages available have led to increased usage within NASA. The Meteoroid Environment Office in particular uses the Python language for a number of applications, including daily meteor shower activity reporting, searches for potential parent bodies of meteor showers, and short dynamical simulations. We present our development of a meteor shower identification code that identifies statistically significant groups of meteors on similar orbits. This code overcomes several challenging characteristics of meteor showers such as drastic differences in uncertainties between meteors and between the orbital elements of a single meteor, and the variation of shower characteristics such as duration with age or planetary perturbations. This code has been proven to successfully and quickly identify unusual meteor activity such as the 2014 kappa Cygnid outburst. We present our algorithm along with these successes and discuss our plans for further code development.

  1. Stimfit: quantifying electrophysiological data with Python

    PubMed Central

    Guzman, Segundo J.; Schlögl, Alois; Schmidt-Hieber, Christoph

    2013-01-01

    Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals. PMID:24600389

  2. Stimfit: quantifying electrophysiological data with Python.

    PubMed

    Guzman, Segundo J; Schlögl, Alois; Schmidt-Hieber, Christoph

    2014-01-01

    Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals. PMID:24600389

  3. Simulation of Planetary Formation using Python

    NASA Astrophysics Data System (ADS)

    Bufkin, James; Bixler, David

    2015-03-01

    A program to simulate planetary formation was developed in the Python programming language. The program consists of randomly placed and massed bodies surrounding a central massive object in order to approximate a protoplanetary disk. The orbits of these bodies are time-stepped, with accelerations, velocities and new positions calculated in each step. Bodies are allowed to merge if their disks intersect. Numerous parameters (orbital distance, masses, number of particles, etc.) were varied in order to optimize the program. The program uses an iterative difference equation approach to solve the equations of motion using a kinematic model. Conservation of energy and angular momentum are not specifically forced, but conservation of momentum is forced during the merging of bodies. The initial program was created in Visual Python (VPython) but the current intention is to allow for higher particle count and faster processing by utilizing PyOpenCl and PyOpenGl. Current results and progress will be reported.

  4. Feeding a large-scale physics application to Python

    SciTech Connect

    Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States). Theoretical Div.

    1997-10-01

    The authors describe their experiences using Python with the SPaSM molecular dynamics code at Los Alamos National Laboratory. Originally developed as a large monolithic application for massive parallel processing systems, they have used Python to transform their application into a flexible, highly modular, and extremely powerful system for performing simulation, data analysis, and visualization. In addition, they describe how Python has solved a number of important problems related to the development, debugging, deployment, and maintenance of scientific software.

  5. The Virtual Observatory for the Python Programmer

    NASA Astrophysics Data System (ADS)

    Plante, Raymond L.; Fitzpatrick, M. J.; Graham, M.; Tody, D.; Virtual Astronomical Observatory, US

    2014-01-01

    The web of astronomical data centers that we refer to as the virtual observatory (VO) has led to the development of a variety of web and desktop applications that can discover and download data from most archives around the world. These are made possible by standard interfaces which archives provide and the applications understand that provide a common way to search for information and retrieve discovered datasets. For some applications, retrieving data through the VO is simply an extra feature that enhances the main purpose of the tool. Despite the accessibility to VO data provided by such tools, the VO offers greater flexibility to developers that access the standard services directly within their own software. This applies not only to those who build tools but also to research astronomers that create highly-customized scripts for data analysis. One of the goals of the US Virtual Astronomical Observatory (VAO) project is to make the VO more accessible to both tool developers and astronomer-programmers. To this end, we announce the release of two products with a special focus on supporting access to the VO via Python. PyVO (http://dev.usvao.org/pyvo) is a pure Python library built on Astropy (astropy.org) that can be used to discover data in the VO. In particular, one can search the registry for archives with data, search archives for images and spectra, and query remote catalogs and spectral line databases. While it provides full support for the VO standards, its API is designed to make processing the most common types of queries simple without requiring knowledge about the underlying standards. It also makes available the full power of Astropy for processing tabular information. VOClient (http://dev.usvao.org/voclient), which provides scripting and programming libraries for a variety of languages, also supports Python programming. While the two products share a common API, VOClient provides higher level interfaces that assist with managing data from many archives. It also features support for SAMP, a protocol that can be used to drive other desktop tools such Topcat and Aladin from a Python script. Finally, it provides a framework for making compiled legacy software callable from Python.

  6. Leveraging Python Interoperability Tools to Improve Sapphire's Usability

    SciTech Connect

    Gezahegne, A; Love, N S

    2007-12-10

    The Sapphire project at the Center for Applied Scientific Computing (CASC) develops and applies an extensive set of data mining algorithms for the analysis of large data sets. Sapphire's algorithms are currently available as a set of C++ libraries. However many users prefer higher level scripting languages such as Python for their ease of use and flexibility. In this report, we evaluate four interoperability tools for the purpose of wrapping Sapphire's core functionality with Python. Exposing Sapphire's functionality through a Python interface would increase its usability and connect its algorithms to existing Python tools.

  7. Re-imagining a Stata/Python Combination

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2013-01-01

    At last year's Stata Conference, I presented some ideas for combining Stata and the Python programming language within a single interface. Two methods were presented: in one, Python was used to automate Stata; in the other, Python was used to send simulated keystrokes to the Stata GUI. The first method has the drawback of only working in Windows, and the second can be slow and subject to character input limits. In this presentation, I will demonstrate a method for achieving interaction between Stata and Python that does not suffer these drawbacks, and I will present some examples to show how this interaction can be useful.

  8. Ureka: A Distribution of Python and IRAF Software for Astronomy

    NASA Astrophysics Data System (ADS)

    Hirst, P.; Slocum, C.; Turner, J.; Sienkiewicz, M.; Greenfield, P.; Hogan, E.; Simpson, M.; Labrie, K.

    2014-05-01

    As astronomical data processing expands from our historical platforms into modern Python applications, users are faced with installing and maintaining large numbers of heterogeneous dependencies. A handful of scientific Python distributions make installing key packages easy, but don't cater for specific needs such as integration with IRAF. We have therefore recently released a beta version of a new astronomical software distribution for Linux and OSX, known as Ureka. Ureka is based around STScI Python and dependencies, notably Python, NumPy, IRAF, SciPy, AstroPy, Matplotlib and Tk. It also contains data reduction packages for Gemini, HST, JWST and other observatories, alongside various complementary tools.

  9. 75 FR 11808 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ...environments (Reed and Rodda 2009). Biology The Indian python's life history is...at any time (Reed and Rodda 2009). Biology The reticulated python is most likely...northern localities (Reed and Rodda 2009). Biology Northern African pythons are...

  10. scikit-image: image processing in Python

    PubMed Central

    Schönberger, Johannes L.; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D.; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

    2014-01-01

    scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org. PMID:25024921

  11. Pcigale: Porting Code Investigating Galaxy Emission to Python

    NASA Astrophysics Data System (ADS)

    Roehlly, Y.; Burgarella, D.; Buat, V.; Boquien, M.; Ciesla, L.; Heinis, S.

    2014-05-01

    We present pcigale, the port to Python of CIGALE (Code Investigating Galaxy Emission) a Fortran spectral energy distribution (SED) fitting code developed at the Laboratoire d'Astrophysique de Marseille. After recalling the specifics of the SED fitting method, we show the gains in modularity and versatility offered by Python, as well as the drawbacks compared to the compiled code.

  12. PuLP: A Linear Programming Toolkit for Python

    E-print Network

    2011-09-05

    Sep 5, 2011 ... Python language and allows the user to create programs using expressions that are natural to ... sions into “raw” numbers (i.e. sparse matrix and vector representations of the ... In addition to the Python standard library there are over 10,000 third-party pack- ..... Thus this advantage will typically be wasted in.

  13. Building Scalable Services in Microsoft Azure with Python

    E-print Network

    Narasayya, Vivek

    Building Scalable Services in Microsoft Azure with Python This paper demonstrates how to use Microsoft Azure and the Python programming language to implement the compute nodes of a scalable scientific. It uses a Microsoft Azure Service Bus Queue and Microsoft Azure Table service to communicate with the back

  14. SunPy: Solar Physics in Python

    NASA Astrophysics Data System (ADS)

    Ryan, Daniel; Christe, Steven; Mumford, Stuart; Perez Suarez, David; Ireland, Jack; Shih, Albert Y.; Inglis, Andrew; Liedtke, Simon; Hewett, Russel

    2015-04-01

    SunPy is a community-developed open-source software library for solar physics. It is written in Python, a free, cross-platform, general-purpose, high-level programming language which is being increasingly adopted throughout the scientific community as well as further afield. This has resulted in a wide array of software packages useful for scientific computing, from numerical computation (NumPy, SciPy, etc.), to machine learning (scifitlearn), to visualization and plotting (matplotlib). SunPy aims to provide required specialised software for analysing solar and heliospheric datasets in Python. The current version is 0.5 with 0.6 expected to be released later this year. SunPy provides solar data access through integration with the Virtual Solar Observatory (VSO), the Heliophysics Event Knowledgebase (HEK), and the HELiophysics Integrated Observatory (HELIO) webservices. It supports common data types from major solar missions such as images (SDO/AIA, STEREO, PROBA2/SWAP etc.), time series (GOES/XRS, SDO/EVE, PROBA2/LYRA), and radio spectra (e-Callisto, STEREO/WAVES). SunPy’s code base is publicly available through github.com and can be contributed to by anyone. In this poster we demonstrate SunPy’s functionality and future goals of the project. We also encourage interested users to become involved in further developing SunPy.

  15. Message Passing Interface for Python 1 the Message Passing Interface (MPI)

    E-print Network

    Verschelde, Jan

    Message Passing Interface for Python 1 the Message Passing Interface (MPI) MPI and MPI for Python hello world with mpi4py point-to-point communication 2 Collective Communication broadcast, scatter L-38) MPI for Python 22 November 2013 1 / 37 #12;Message Passing Interface for Python 1 the Message

  16. Multi-Focused Geospatial Analysis Using Probes Thomas Butkiewicz, Wenwen Dou, Zachary Wartell, William Ribarsky, and Remco Chang

    E-print Network

    Wartell, Zachary

    Multi-Focused Geospatial Analysis Using Probes Thomas Butkiewicz, Wenwen Dou, Zachary Wartell, William Ribarsky, and Remco Chang Abstract--Traditional geospatial information visualizations often be incorporated into a variety of geospatial visualizations to empower users with the ability to observe

  17. Visual analysis for live LIDAR battlefield change detection Thomas Butkiewicz, Remco Chang, Zachary Wartell, and William Ribarsky

    E-print Network

    Wartell, Zachary

    to deploy on multiple military unmanned aerial vehicles (UAVs), it is particularly attractive to be ableVisual analysis for live LIDAR battlefield change detection Thomas Butkiewicz, Remco Chang, Zachary of airborne LIDAR range data in a highly interactive visual interface. The system consists of three major

  18. Responses of python gastrointestinal regulatory peptides to feeding

    PubMed Central

    Secor, Stephen M.; Fehsenfeld, Drew; Diamond, Jared; Adrian, Thomas E.

    2001-01-01

    In the Burmese python (Python molurus), the rapid up-regulation of gastrointestinal (GI) function and morphology after feeding, and subsequent down-regulation on completing digestion, are expected to be mediated by GI hormones and neuropeptides. Hence, we examined postfeeding changes in plasma and tissue concentrations of 11 GI hormones and neuropeptides in the python. Circulating levels of cholecystokinin (CCK), glucose-dependent insulinotropic peptide (GIP), glucagon, and neurotensin increase by respective factors of 25-, 6-, 6-, and 3.3-fold within 24 h after feeding. In digesting pythons, the regulatory peptides neurotensin, somatostatin, motilin, and vasoactive intestinal peptide occur largely in the stomach, GIP and glucagon in the pancreas, and CCK and substance P in the small intestine. Tissue concentrations of CCK, GIP, and neurotensin decline with feeding. Tissue distributions and molecular forms (as determined by gel-permeation chromatography) of many python GI peptides are similar or identical to those of their mammalian counterparts. The postfeeding release of GI peptides from tissues, and their concurrent rise in plasma concentrations, suggests that they play a role in regulating python-digestive responses. These large postfeeding responses, and similarities of peptide structure with mammals, make pythons an attractive model for studying GI peptides. PMID:11707600

  19. Responses of python gastrointestinal regulatory peptides to feeding.

    PubMed

    Secor, S M; Fehsenfeld, D; Diamond, J; Adrian, T E

    2001-11-20

    In the Burmese python (Python molurus), the rapid up-regulation of gastrointestinal (GI) function and morphology after feeding, and subsequent down-regulation on completing digestion, are expected to be mediated by GI hormones and neuropeptides. Hence, we examined postfeeding changes in plasma and tissue concentrations of 11 GI hormones and neuropeptides in the python. Circulating levels of cholecystokinin (CCK), glucose-dependent insulinotropic peptide (GIP), glucagon, and neurotensin increase by respective factors of 25-, 6-, 6-, and 3.3-fold within 24 h after feeding. In digesting pythons, the regulatory peptides neurotensin, somatostatin, motilin, and vasoactive intestinal peptide occur largely in the stomach, GIP and glucagon in the pancreas, and CCK and substance P in the small intestine. Tissue concentrations of CCK, GIP, and neurotensin decline with feeding. Tissue distributions and molecular forms (as determined by gel-permeation chromatography) of many python GI peptides are similar or identical to those of their mammalian counterparts. The postfeeding release of GI peptides from tissues, and their concurrent rise in plasma concentrations, suggests that they play a role in regulating python-digestive responses. These large postfeeding responses, and similarities of peptide structure with mammals, make pythons an attractive model for studying GI peptides. PMID:11707600

  20. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)

    PubMed Central

    2011-01-01

    Background Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python is the premier model for studying extremes of metabolic fluctuation and physiological remodelling. In this species, the consumption of large infrequent meals can induce a 40-fold increase in metabolic rate and more than a doubling in size of some organs. To provide a foundation for research utilizing the python, our aim was to assemble and annotate a transcriptome reference from the heart and liver. To accomplish this aim, we used the 454-FLX sequencing platform to collect sequence data from multiple cDNA libraries. Results We collected nearly 1 million 454 sequence reads, and assembled these into 37,245 contigs with a combined length of 13,409,006 bp. To identify known genes, these contigs were compared to chicken and lizard gene sets, and to all Genbank sequences. A total of 13,286 of these contigs were annotated based on similarity to known genes or Genbank sequences. We used gene ontology (GO) assignments to characterize the types of genes in this transcriptome resource. The raw data, transcript contig assembly, and transcript annotations are made available online for use by the broader research community. Conclusion These data should facilitate future studies using pythons and snakes in general, helping to further contribute to the utilization of snakes as a model evolutionary and physiological system. This sequence collection represents a major genomic resource for the Burmese python, and the large number of transcript sequences characterized should contribute to future research in this and other snake species. PMID:21867488

  1. COSMOS: Python library for massively parallel workflows

    PubMed Central

    Gafni, Erik; Luquette, Lovelace J.; Lancaster, Alex K.; Hawkins, Jared B.; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P.; Tonellato, Peter J.

    2014-01-01

    Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24982428

  2. Selection Performance Based on Classes of Bimanual Actions Amy C. Ulinski* Zachary Wartell* Paula Goolkasian* Evan A. Suma* Larry F. Hodges

    E-print Network

    Wartell, Zachary

    Selection Performance Based on Classes of Bimanual Actions Amy C. Ulinski* Zachary Wartell* Paula different classes of bimanual actions [10]. The Bimanual symmetric classification involves each hand. Therefore, four distinct classes of bimanual actions exist: · Symmetric-Synchronous · Symmetric

  3. galpy: A python Library for Galactic Dynamics

    NASA Astrophysics Data System (ADS)

    Bovy, Jo

    2015-02-01

    I describe the design, implementation, and usage of galpy, a python package for galactic-dynamics calculations. At its core, galpy consists of a general framework for representing galactic potentials both in python and in C (for accelerated computations); galpy functions, objects, and methods can generally take arbitrary combinations of these as arguments. Numerical orbit integration is supported with a variety of Runge-Kutta-type and symplectic integrators. For planar orbits, integration of the phase-space volume is also possible. galpy supports the calculation of action-angle coordinates and orbital frequencies for a given phase-space point for general spherical potentials, using state-of-the-art numerical approximations for axisymmetric potentials, and making use of a recent general approximation for any static potential. A number of different distribution functions (DFs) are also included in the current release; currently, these consist of two-dimensional axisymmetric and non-axisymmetric disk DFs, a three-dimensional disk DF, and a DF framework for tidal streams. I provide several examples to illustrate the use of the code. I present a simple model for the Milky Way's gravitational potential consistent with the latest observations. I also numerically calculate the Oort functions for different tracer populations of stars and compare them to a new analytical approximation. Additionally, I characterize the response of a kinematically warm disk to an elliptical m = 2 perturbation in detail. Overall, galpy consists of about 54,000 lines, including 23,000 lines of code in the module, 11,000 lines of test code, and about 20,000 lines of documentation. The test suite covers 99.6% of the code. galpy is available at http://github.com/jobovy/galpy with extensive documentation available at http://galpy.readthedocs.org/en/latest.

  4. Rabacus: A Python Package for Analytic Cosmological Radiative Transfer Calculations

    E-print Network

    Altay, Gabriel

    2015-01-01

    We describe Rabacus, a Python package for calculating the transfer of hydrogen ionizing radiation in simplified geometries relevant to astronomy and cosmology. We present example solutions for three specific cases: 1) a semi-infinite slab gas distribution in a homogeneous isotropic background, 2) a spherically symmetric gas distribution with a point source at the center, and 3) a spherically symmetric gas distribution in a homogeneous isotropic background. All problems can accommodate arbitrary spectra and density profiles as input. The solutions include a treatment of both hydrogen and helium, a self-consistent calculation of equilibrium temperatures, and the transfer of recombination radiation. The core routines are written in Fortran 90 and then wrapped in Python leading to execution speeds thousands of times faster than equivalent routines written in pure Python. In addition, all variables have associated units for ease of analysis. The software is part of the Python Package Index and the source code is a...

  5. Rapid Development of Interferometric Software Using MIRIAD and Python

    NASA Astrophysics Data System (ADS)

    Williams, Peter K. G.; Law, Casey J.; Bower, Geoffrey C.

    2012-06-01

    State-of-the-art radio interferometers are complex systems that unleash torrents of data. If current and planned instruments are to routinely meet their performance goals, standard analysis techniques must be significantly improved, becoming simultaneously more sophisticated, more automatic, and more scalable. While there is no shortage of ideas for next-generation algorithms, there is a shortage of development resources, so it is vital that programming environments for interferometric software allow for rapid, flexible development. We present an open-source software package, miriad-python, that provides access to the MIRIAD interferometric reduction system in the Python programming language. The modular design of MIRIAD and the high productivity and accessibility of Python provide an excellent foundation for rapid development of interferometric software. Several other projects with similar goals exist, and we describe them and compare miriad-python with them in detail. Along with an overview of the package design, we present sample code and applications, including the detection of millisecond astrophysical transients, determination and application of nonstandard calibration parameters, interactive data visualization, and a reduction pipeline using a directed acyclic graph dependency model analogous to that of the traditional UNIX tool make. The key aspects of the miriad-python software project are documented. We find that miriad-python provides an extremely effective environment for prototyping new interferometric software, though certain existing packages provide far more infrastructure for some applications. While equivalent software written in compiled languages can be much faster than Python, there are many situations in which execution time is profitably exchanged for speed of development, code readability, accessibility to nonexpert programmers, quick interlinking with foreign software packages, and other virtues of the Python language.

  6. MEG and EEG data analysis with MNE-Python

    PubMed Central

    Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A.; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

    2013-01-01

    Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne. PMID:24431986

  7. Ecological correlates of invasion impact for Burmese pythons in Florida

    USGS Publications Warehouse

    Reed, R.N.; Willson, J.D.; Rodda, G.H.; Dorcas, M.E.

    2012-01-01

    An invasive population of Burmese pythons (Python molurus bivittatus) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species.

  8. Discrimination of integumentary prey chemicals and strike-induced chemosensory searching in the ball python, Python regius

    Microsoft Academic Search

    1991-01-01

    Experimental tests show that the ball python (Python regius) has the ability to discriminate prey chemicals from control substances by tongue-flicking and exhibits a poststrike elevation\\u000a in tongue-flicking rate (PETF). Prey chemical discrimination was revealed by significantly higher number of tongue-flicks\\u000a and tongue-flick attack score in response to integumental chemicals from mice than to cologne or distilled water and by

  9. Hydropy: Python package for hydrological time series handling based on Python Pandas

    NASA Astrophysics Data System (ADS)

    Van Hoey, Stijn; Balemans, Sophie; Nopens, Ingmar; Seuntjens, Piet

    2015-04-01

    Most hydrologists are dealing with time series frequently. Reading in time series, transforming them and extracting specific periods for visualisation are part of the daily work. Spreadsheet software is used a lot for these operations, but has some major drawbacks. It is mostly not reproducible, it is prone to errors and not easy to automate, which results in repetitive work when dealing with large amounts of data. Scripting languages like R and Python on the other hand, provide flexibility, enable automation and reproducibility and, hence, increase efficiency. Python has gained popularity over the last years and currently, tools for many aspects of scientific computing are readily available in Python. An increased support in controlling and managing the dependencies between packages (e.g. the Anaconda environment) allows for a wide audience to use the huge variety of available packages. Pandas is a powerful Python package for data analysis and has a lot of functionalities related to time series. As such, the package is of special interest to hydrologists. Some other packages, focussing on hydrology (e.g. Hydroclimpy by Pierre Gerard-Marchant and Hydropy by Javier Rovegno Campos), stopped active development, mainly due to the superior implementation of Pandas. We present a (revised) version of the Hydropy package that is inspired by the aforementioned packages and builds on the power of Pandas. The main idea is to add hydrological domain knowledge to the already existing Pandas functionalities. Besides, the package attempts to make the time series handling intuitive and easy to perform, thus with a clear syntax. Some illustrative examples of the current implementation starting from a Pandas DataFrame named flowdata: Creating the object flow to work with: flow = HydroAnalysis(flowdata) Retrieve only the data during winter (across all years): flow.get_season('winter') Retrieve only the data during summer of 2010: flow.get_season('summer').get_year('2010') which is equivalent to flow.get_year('2010').get_season('summer') Retrieve only the data of July and get the peak values above the 95 percentile: flow.get_season('july').get_highpeaks(above_percentile=0.95) Retrieve only the data between two specified days and selecting only the rising limbs flow.get_date_range('01/10/2008', '15/2/2014').get_climbing() Calculate the annual sum and make a plot of it: flow.frequency_resample('A', 'sum').plot()

  10. Python algorithms in particle tracking microrheology

    PubMed Central

    2012-01-01

    Background Particle tracking passive microrheology relates recorded trajectories of microbeads, embedded in soft samples, to the local mechanical properties of the sample. The method requires intensive numerical data processing and tools allowing control of the calculation errors. Results We report the development of a software package collecting functions and scripts written in Python for automated and manual data processing, to extract viscoelastic information about the sample using recorded particle trajectories. The resulting program package analyzes the fundamental diffusion characteristics of particle trajectories and calculates the frequency dependent complex shear modulus using methods published in the literature. In order to increase conversion accuracy, segmentwise, double step, range-adaptive fitting and dynamic sampling algorithms are introduced to interpolate the data in a splinelike manner. Conclusions The presented set of algorithms allows for flexible data processing for particle tracking microrheology. The package presents improved algorithms for mean square displacement estimation, controlling effects of frame loss during recording, and a novel numerical conversion method using segmentwise interpolation, decreasing the conversion error from about 100% to the order of 1%. PMID:23186362

  11. Python-Assisted MODFLOW Application and Code Development

    NASA Astrophysics Data System (ADS)

    Langevin, C.

    2013-12-01

    The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

  12. Stochastic spatio-temporal modelling with PCRaster Python

    NASA Astrophysics Data System (ADS)

    Karssenberg, D.; Schmitz, O.; de Jong, K.

    2012-04-01

    PCRaster Python is a software framework for building spatio-temporal models of land surface processes (Karssenberg, Schmitz, Salamon, De Jong, & Bierkens, 2010; PCRaster, 2012). Building blocks of models are spatial operations on raster maps, including a large suite of operations for water and sediment routing. These operations, developed in C++, are available to model builders as Python functions. Users create models by combining these functions in a Python script. As construction of large iterative models is often difficult and time consuming for non-specialists in programming, the software comes with a set of Python framework classes that provide control flow for static modelling, temporal modelling, stochastic modelling using Monte Carlo simulation, and data assimilation techniques including the Ensemble Kalman filter and the Particle Filter. A framework for integrating model components with different time steps and spatial discretization is currently available as a prototype (Schmitz, de Jong, & Karssenberg, in review). The software includes routines for visualisation of stochastic spatio-temporal data for prompt, interactive, visualisation of model inputs and outputs. Visualisation techniques include animated maps, time series, probability distributions, and animated maps with exceedance probabilities. The PCRaster Python software is used by researchers from a large range of disciplines, including hydrology, ecology, sedimentology, and land use change studies. Applications include global scale hydrological modelling and error propagation in large-scale land use change models. The software runs on MS Windows and Linux operating systems, and OS X (under development).

  13. Python-based Tools and Web Services for Structural

    E-print Network

    Lumsdaine, Andrew

    Tools/Services for Mutation Data wVis tools (UCSF Chimera, PyMOL) wWeb Services (Axis, Pywebsvcs tools u UCSF Chimera (www.cgl.ucsf.edu/chimera) u PyMOL (pymol.sourceforge.net) u Python-based tools to protein structure u Extension in Chimera queries MutDB #12;PyMol Extension Controller window identifies

  14. Paternal alleles enhance female reproductive success in tropical pythons

    Microsoft Academic Search

    THOMAS MADSEN; BEATA UJVARI; MATS OLSSON; RICHARD SHINE

    2005-01-01

    The conventional view that female reproductive success is unlikely to benefit from multiple mating has come under strong challenge in recent years. In the present study, we demon- strate that the time wild-caught reproductive female water pythons ( Liasis fuscus ) spent in the laboratory prior to oviposition affected both hatching success and the number of male microsatellite alleles detected

  15. PyKrige: Development of a Kriging Toolkit for Python

    NASA Astrophysics Data System (ADS)

    Murphy, B. S.

    2014-12-01

    While Python continues to grow in popularity as a convenient and powerful means of data manipulation and analysis, the language still lacks a package that provides easy access to commonly utilized geostatistical routines. PyKrige is a new contribution that attempts to create a Python library that can be used for basic geostatistical tasks, such as creating water level maps using Ordinary and Universal Kriging. While written in pure Python, the code makes extensive use of NumPy in order to enable fast processing. Supported drift terms for Universal Kriging currently include a regional linear drift (such as would be used to simulate an overall groundwater gradient, as discussed in Tonkin and Larson, Groundwater, 2002), a point-logarithmic drift (such as would be used to simulate wells, as discussed in Tonkin and Larson, Groundwater, 2002), and an external digital elevation model drift (such as would be used to simulate a topographically controlled groundwater surface, as discussed in Desbarats et al., Journal of Hydrology, 2002). The package is intended primarily for kriging of two-dimensional data, but limited support for three-dimensional kriging is currently under development. Though similar tools already exist for other commonly utilized scientific languages, such as R and MATLAB, PyKrige is intended to ease data processing by providing further functionality in Python that can be implemented in a single analysis pipeline. The code will be made available on GitHub.

  16. PyMC: Bayesian Stochastic Modelling in Python

    NASA Astrophysics Data System (ADS)

    Fonnesbeck, Chris; Patil, Anand; Huard, David; Salvatier, John

    2015-06-01

    PyMC is a python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo. Its flexibility and extensibility make it applicable to a large suite of problems. Along with core sampling functionality, PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics.

  17. Enjoying python, processing, and Java in CS1

    Microsoft Academic Search

    Olle Bälter; Duane A. Bailey

    2010-01-01

    Here we describe an introductory course in computer science where we combined Python, Processing, and core Java. The main reason for this structure was to make the initial contact with programming as gentle, enjoyable, and understandable as possible, while still having the power of graphics and sufficient Java knowledge for more advanced courses in computer science. This course was designed

  18. Python Robotics: An Environment for Exploring Robotics Beyond LEGOs

    E-print Network

    Blank, Douglas

    Python Robotics: An Environment for Exploring Robotics Beyond LEGOs Douglas Blank Computer Science Mawr, PA 19010 dkumar@cs.brynmawr.edu Abstract This paper describes Pyro, a robotics programming en- vironment designed to allow inexperienced undergradu- ates to explore topics in advanced robotics. Pyro

  19. Python Robotics: An Environment for Exploring Robotics Beyond LEGOs

    E-print Network

    Blank, Douglas

    Python Robotics: An Environment for Exploring Robotics Beyond LEGOs Douglas Blank Computer Science Mawr, PA 19010 dkumar@cs.brynmawr.edu Abstract This paper describes Pyro, a robotics programming en­ vironment designed to allow inexperienced undergradu­ ates to explore topics in advanced robotics. Pyro

  20. OMPC: an Open-Source MATLAB®-to-Python Compiler

    PubMed Central

    Jurica, Peter; van Leeuwen, Cees

    2008-01-01

    Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

  1. Cold-induced mortality of invasive Burmese pythons in south Florida

    USGS Publications Warehouse

    Mazzotti, Frank J.; Cherkiss, Michael S.; Hart, Kristen M.; Snow, Ray W.; Rochford, Michael R.; Dorcas, Michael E.; Reed, Robert N.

    2011-01-01

    A recent record cold spell in southern Florida (2-11 January 2010) provided an opportunity to evaluate responses of an established population of Burmese pythons (Python molurus bivittatus) to a prolonged period of unusually cold weather. We observed behavior, characterized thermal biology, determined fate of radio-telemetered (n = 10) and non-telemetered (n = 104) Burmese pythons, and analyzed habitat and environmental conditions experienced by pythons during and after a historic cold spell. Telemetered pythons had been implanted with radio-transmitters and temperature-recording data loggers prior to the cold snap. Only one of 10 telemetered pythons survived the cold snap, whereas 59 of 99 (60%) non-telemetered pythons for which we determined fate survived. Body temperatures of eight dead telemetered pythons fluctuated regularly prior to 9 January 2010, then declined substantially during the cold period (9-11 January) and exhibited no further evidence of active thermoregulation indicating they were likely dead. Unusually cold temperatures in January 2010 were clearly associated with mortality of Burmese pythons in the Everglades. Some radiotelemetered pythons appeared to exhibit maladaptive behavior during the cold spell, including attempting to bask instead of retreating to sheltered refugia. We discuss implications of our findings for persistence and spread of introduced Burmese pythons in the United States and for maximizing their rate of removal.

  2. Flexible Environmental Modeling with Python and Open - GIS

    NASA Astrophysics Data System (ADS)

    Pryet, Alexandre; Atteia, Olivier; Delottier, Hugo; Cousquer, Yohann

    2015-04-01

    Numerical modeling now represents a prominent task of environmental studies. During the last decades, numerous commercial programs have been made available to environmental modelers. These software applications offer user-friendly graphical user interfaces that allow an efficient management of many case studies. However, they suffer from a lack of flexibility and closed-source policies impede source code reviewing and enhancement for original studies. Advanced modeling studies require flexible tools capable of managing thousands of model runs for parameter optimization, uncertainty and sensitivity analysis. In addition, there is a growing need for the coupling of various numerical models associating, for instance, groundwater flow modeling to multi-species geochemical reactions. Researchers have produced hundreds of open-source powerful command line programs. However, there is a need for a flexible graphical user interface allowing an efficient processing of geospatial data that comes along any environmental study. Here, we present the advantages of using the free and open-source Qgis platform and the Python scripting language for conducting environmental modeling studies. The interactive graphical user interface is first used for the visualization and pre-processing of input geospatial datasets. Python scripting language is then employed for further input data processing, call to one or several models, and post-processing of model outputs. Model results are eventually sent back to the GIS program, processed and visualized. This approach combines the advantages of interactive graphical interfaces and the flexibility of Python scripting language for data processing and model calls. The numerous python modules available facilitate geospatial data processing and numerical analysis of model outputs. Once input data has been prepared with the graphical user interface, models may be run thousands of times from the command line with sequential or parallel calls. We illustrate this approach with several case studies in groundwater hydrology and geochemistry and provide links to several python libraries that facilitate pre- and post-processing operations.

  3. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

    PubMed Central

    2011-01-01

    The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline. PMID:21801464

  4. Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python—Python molurus bivittatus—Management

    PubMed Central

    Hunter, Margaret E.; Hart, Kristen M.

    2013-01-01

    Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae. PMID:23449030

  5. TOPOLOGICAL INFERENCE Larry Wasserman

    E-print Network

    ) (thanks to Yen-Chi Chen) 4 / 76 #12;Part I: Summary: Manifold Estimation q q q q q q q q qq q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q qq q q q q q q qq q q q q q q q qq q q q qq q q qq q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q

  6. UBC Social Ecological Economic Development Studies (SEEDS) Student Report David Chen, Della Anggabrata, Emma Brown, Haney Wang, Rocky Zhang, Zachary Bailey

    E-print Network

    Anggabrata, Emma Brown, Haney Wang, Rocky Zhang, Zachary Bailey UBC BOTANICAL GARDEN RENEWAL CIVL 446 April UBC Botanical Garden (UBCBG) Renewal Project intends to deliver a project that will help UBCBG achieve Botanical Garden. Emma Brown Project Manager April 4, 2014 #12;ii | P a g e CONTENTS 1 Introduction

  7. UBC Social Ecological Economic Development Studies (SEEDS) Student Report Della Anggabrata, Emma Brown, Haney Wang, Mike Harvard, Terrence Gardiner, Zachary Bailey

    E-print Network

    Zachary Bailey GROWING FORWARD AT THE UBC BOTANICAL GARDEN "...and leaf-ing the past behind" #12;ii | P on the Botanical Garden. The solutions that were selected to be most effective are a multi-use building, signage will identify a comprehensive plan to ensure a beneficial redevelopment of the UBC Botanical Garden

  8. Brian: a simulator for spiking neural networks in python.

    PubMed

    Goodman, Dan; Brette, Romain

    2008-01-01

    "Brian" is a new simulator for spiking neural networks, written in Python (http://brian. di.ens.fr). It is an intuitive and highly flexible tool for rapidly developing new models, especially networks of single-compartment neurons. In addition to using standard types of neuron models, users can define models by writing arbitrary differential equations in ordinary mathematical notation. Python scientific libraries can also be used for defining models and analysing data. Vectorisation techniques allow efficient simulations despite the overheads of an interpreted language. Brian will be especially valuable for working on non-standard neuron models not easily covered by existing software, and as an alternative to using Matlab or C for simulations. With its easy and intuitive syntax, Brian is also very well suited for teaching computational neuroscience. PMID:19115011

  9. Expyriment: a Python library for cognitive and neuroscientific experiments.

    PubMed

    Krause, Florian; Lindemann, Oliver

    2014-06-01

    Expyriment is an open-source and platform-independent lightweight Python library for designing and conducting timing-critical behavioral and neuroimaging experiments. The major goal is to provide a well-structured Python library for script-based experiment development, with a high priority being the readability of the resulting program code. Expyriment has been tested extensively under Linux and Windows and is an all-in-one solution, as it handles stimulus presentation, the recording of input/output events, communication with other devices, and the collection and preprocessing of data. Furthermore, it offers a hierarchical design structure, which allows for an intuitive transition from the experimental design to a running program. It is therefore also suited for students, as well as for experimental psychologists and neuroscientists with little programming experience. PMID:24142834

  10. The Crates Library: The Redesigned Python Interface for Scripting Languages

    NASA Astrophysics Data System (ADS)

    Lyn, J.; Burke, D.; Cresitello-Dittmar, M.; Evans, I.; Evans, J. D.

    2011-07-01

    Crates is a Python module produced by the Chandra X-ray Center (CXC) that provides a convenient high-level user interface for accessing and manipulating data stored in a variety of formats. Crates is currently utilized by Chandra's plotting, modeling and fitting tools. This paper will highlight the design changes and improvements made to Crates. This version of Crates has been completely rewritten in Python and has been optimized to conserve time and memory resources through lazy initialization. It provides increased functionality for data and metadata manipulation along with better memory management. In addition, Crates will be able to interface with several different backend modules, allowing the user to effortlessly switch between the CXC Data Model (DM), Virtual Observatory (VO), and pyFITS formats.

  11. PyRAT - python radiography analysis tool (u)

    SciTech Connect

    Temple, Brian A [Los Alamos National Laboratory; Buescher, Kevin L [Los Alamos National Laboratory; Armstrong, Jerawan C [Los Alamos National Laboratory

    2011-01-14

    PyRAT is a radiography analysis tool used to reconstruction images of unknown 1-0 objects. The tool is written in Python and developed for use on LINUX and Windows platforms. The tool is capable of performing nonlinear inversions of the images with minimal manual interaction in the optimization process. The tool utilizes the NOMAD mixed variable optimization tool to perform the optimization.

  12. ObsPy: A Python Toolbox for Seismology

    NASA Astrophysics Data System (ADS)

    Wassermann, J. M.; Krischer, L.; Megies, T.; Barsch, R.; Beyreuther, M.

    2013-12-01

    Python combines the power of a full-blown programming language with the flexibility and accessibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. ObsPy is a community-driven, open-source project extending Python's capabilities to fit the specific needs that arise when working with seismological data. It a) comes with a continuously growing signal processing toolbox that covers most tasks common in seismological analysis, b) provides read and write support for many common waveform, station and event metadata formats and c) enables access to various data centers, webservices and databases to retrieve waveform data and station/event metadata. In combination with mature and free Python packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy makes it possible to develop complete workflows in Python, ranging from reading locally stored data or requesting data from one or more different data centers via signal analysis and data processing to visualization in GUI and web applications, output of modified/derived data and the creation of publication-quality figures. All functionality is extensively documented and the ObsPy Tutorial and Gallery give a good impression of the wide range of possible use cases. ObsPy is tested and running on Linux, OS X and Windows and comes with installation routines for these systems. ObsPy is developed in a test-driven approach and is available under the LGPLv3 open source licence. Users are welcome to request help, report bugs, propose enhancements or contribute code via either the user mailing list or the project page on GitHub.

  13. A Community Python Library for Solar Physics (SunPy)

    NASA Astrophysics Data System (ADS)

    Christe, Steven; Shih, A. Y.; Ireland, J.; Perez-Suarez, D.; Mumford, S.; Hughitt, V. K.; Hewett, R.; Mayer, F.; SunPy Dev Team

    2013-07-01

    Python, a free, cross platform, general purpose, high-level programming language, has seen widespread adoption among the scientific community resulting in the availability of a large range of software, from numerical computation (NumPy, SciPy) and machine learning to spectral analysis and visualization (Matplotlib). SunPy is a data analysis toolkit specializing in providing the software necessary to analyze solar and heliospheric datasets in Python. It aims to provide a free and open-source alternative to the IDL-based SolarSoft (SSW) solar data analysis environment. We present the latest release of SunPy (0.3). This release includes a major refactor of the main SunPy code to improve ease of use for the user as well as a more consistent interface. SunPy provides downloading capability through integration with the Virtual Solar Observatory (VSO) and the the Heliophysics Event Knowledgebase (HEK). It can open image fits files from major solar missions (SDO/AIA, SOHO/EIT, SOHO/LASCO, STEREO) into WCS-aware maps. SunPy provides advanced time-series tools for data from mission such as GOES, SDO/EVE, and Proba2/LYRA as well as support for radio spectra (e.g. e-Callisto). We present examples of solar data analysis in SunPy, and show how Python-based solar data-analysis can leverage the many existing data analysis tools already available in Python. We discuss the future goals of the project and encourage interested users to become involved in the planning and development of SunPy.

  14. Characterization of carbonic anhydrase XIII in the erythrocytes of the Burmese python, Python molurus bivittatus.

    PubMed

    Esbaugh, A J; Secor, S M; Grosell, M

    2015-09-01

    Carbonic anhydrase (CA) is one of the most abundant proteins found in vertebrate erythrocytes with the majority of species expressing a low activity CA I and high activity CA II. However, several phylogenetic gaps remain in our understanding of the expansion of cytoplasmic CA in vertebrate erythrocytes. In particular, very little is known about isoforms from reptiles. The current study sought to characterize the erythrocyte isoforms from two squamate species, Python molurus and Nerodia rhombifer, which was combined with information from recent genome projects to address this important phylogenetic gap. Obtained sequences grouped closely with CA XIII in phylogenetic analyses. CA II mRNA transcripts were also found in erythrocytes, but found at less than half the levels of CA XIII. Structural analysis suggested similar biochemical activity as the respective mammalian isoforms, with CA XIII being a low activity isoform. Biochemical characterization verified that the majority of CA activity in the erythrocytes was due to a high activity CA II-like isoform; however, titration with copper supported the presence of two CA pools. The CA II-like pool accounted for 90 % of the total activity. To assess potential disparate roles of these isoforms a feeding stress was used to up-regulate CO2 excretion pathways. Significant up-regulation of CA II and the anion exchanger was observed; CA XIII was strongly down-regulated. While these results do not provide insight into the role of CA XIII in the erythrocytes, they do suggest that the presence of two isoforms is not simply a case of physiological redundancy. PMID:26005204

  15. BioC implementations in Go, Perl, Python and Ruby

    PubMed Central

    Liu, Wanli; Islamaj Do?an, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

    2014-01-01

    As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

  16. Python for Information Theoretic Analysis of Neural Data

    PubMed Central

    Ince, Robin A. A.; Petersen, Rasmus S.; Swan, Daniel C.; Panzeri, Stefano

    2008-01-01

    Information theory, the mathematical theory of communication in the presence of noise, is playing an increasingly important role in modern quantitative neuroscience. It makes it possible to treat neural systems as stochastic communication channels and gain valuable, quantitative insights into their sensory coding function. These techniques provide results on how neurons encode stimuli in a way which is independent of any specific assumptions on which part of the neuronal response is signal and which is noise, and they can be usefully applied even to highly non-linear systems where traditional techniques fail. In this article, we describe our work and experiences using Python for information theoretic analysis. We outline some of the algorithmic, statistical and numerical challenges in the computation of information theoretic quantities from neural data. In particular, we consider the problems arising from limited sampling bias and from calculation of maximum entropy distributions in the presence of constraints representing the effects of different orders of interaction in the system. We explain how and why using Python has allowed us to significantly improve the speed and domain of applicability of the information theoretic algorithms, allowing analysis of data sets characterized by larger numbers of variables. We also discuss how our use of Python is facilitating integration with collaborative databases and centralised computational resources. PMID:19242557

  17. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

    PubMed Central

    Dale, Ryan K.; Pedersen, Brent S.; Quinlan, Aaron R.

    2011-01-01

    Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses. Availability: pybedtools is maintained under the GPL license. Stable versions of pybedtools as well as documentation are available on the Python Package Index at http://pypi.python.org/pypi/pybedtools. Contact: dalerr@niddk.nih.gov; arq5x@virginia.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21949271

  18. Climate Map for Northern African Python: Areas Potentially Suitable for Invasion

    USGS Multimedia Gallery

    The Northern African Python ( Python sebae ) occurs naturally in a diverse collection of localities in central Africa. The climate-matched portions of the U.S. include peninsular Florida, extreme south Texas, Puerto Rico (right inset), Hawaii (left inset), and the other island territories (not shown...

  19. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

    PubMed Central

    O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

    2008-01-01

    Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

  20. Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

    PubMed

    Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

    2013-02-01

    Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com. PMID:23292976

  1. New Python-based methods for data processing

    PubMed Central

    Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel

    2013-01-01

    Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2?TB?h?1) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femto­second crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units. PMID:23793153

  2. Temporal and spatial complexity of maternal thermoregulation in tropical pythons.

    PubMed

    Stahlschmidt, Zachary Ross; Shine, Richard; Denardo, Dale F

    2012-01-01

    Parental care is a widespread adaptation that evolved independently in a broad range of taxa. Although the dynamics by which two parents meet the developmental needs of offspring are well studied in birds, we lack understanding about the temporal and spatial complexity of parental care in taxa exhibiting female-only care, the predominant mode of parental care. Thus, we examined the behavioral and physiological mechanisms by which female water pythons Liasis fuscus meet a widespread developmental need (thermoregulation) in a natural setting. Although female L. fuscus were not facultatively thermogenic, they did use behaviors on multiple spatial scales (e.g., shifts in egg-brooding postures and surface activity patterns) to balance the thermal needs of their offspring throughout reproduction (gravidity and egg brooding). Maternal behaviors in L. fuscus varied by stage within reproduction and were mediated by interindividual variation in body size and fecundity. Female pythons with relatively larger clutch sizes were cooler during egg brooding, suggesting a trade-off between reproductive quantity (size of clutch) and quality (developmental temperature). In nature, caregiving parents of all taxa must navigate both extrinsic factors (temporal and spatial complexity) and intrinsic factors (body size and fecundity) to meet the needs of their offspring. Our study used a comprehensive approach that can be used as a general template for future research examining the dynamics by which parents meet other developmental needs (e.g., predation risk or energy balance). PMID:22494978

  3. SCoT: a Python toolbox for EEG source connectivity

    PubMed Central

    Billinger, Martin; Brunner, Clemens; Müller-Putz, Gernot R.

    2014-01-01

    Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG). Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs) require single-trial estimation methods. In this paper, we present SCoT—a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with the MVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR) models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting. We demonstrate basic usage of SCoT on motor imagery (MI) data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1) brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2) offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT. PMID:24653694

  4. CMCpy: Genetic Code-Message Coevolution Models in Python

    PubMed Central

    Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

    2013-01-01

    Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

  5. Programming biological models in Python using PySB.

    PubMed

    Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

    2013-01-01

    Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis. PMID:23423320

  6. Programming biological models in Python using PySB

    PubMed Central

    Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

    2013-01-01

    Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis. PMID:23423320

  7. SClib, a hack for straightforward embedded C functions in Python

    E-print Network

    Fuentes, Esteban

    2014-01-01

    We present SClib, a simple hack that allows easy and straightforward evaluation of C functions within Python code, boosting flexibility for better trade-off between computation power and feature availability, such as visualization and existing computation routines in SciPy. We also present two cases were SClib has been used. In the first set of applications we use SClib to write a port to Python of a Schr\\"odinger equation solver that has been extensively used the literature, the resulting script presents a speed-up of about 150x with respect to the original one. A review of the situations where the speeded-up script has been used is presented. We also describe the solution to the related problem of solving a set of coupled Schr\\"odinger-like equations where SClib is used to implement the speed-critical parts of the code. We argue that when using SClib within IPython we can use NumPy and Matplotlib for the manipulation and visualization of the solutions in an interactive environment with no performance compro...

  8. Pythran: enabling static optimization of scientific Python programs

    NASA Astrophysics Data System (ADS)

    Guelton, Serge; Brunet, Pierrick; Amini, Mehdi; Merlini, Adrien; Corbillon, Xavier; Raynaud, Alan

    2015-01-01

    Pythran is an open source static compiler that turns modules written in a subset of Python language into native ones. Assuming that scientific modules do not rely much on the dynamic features of the language, it trades them for powerful, possibly inter-procedural, optimizations. These optimizations include detection of pure functions, temporary allocation removal, constant folding, Numpy ufunc fusion and parallelization, explicit thread-level parallelism through OpenMP annotations, false variable polymorphism pruning, and automatic vector instruction generation such as AVX or SSE. In addition to these compilation steps, Pythran provides a C++ runtime library that leverages the C++ STL to provide generic containers, and the Numeric Template Toolbox for Numpy support. It takes advantage of modern C++11 features such as variadic templates, type inference, move semantics and perfect forwarding, as well as classical idioms such as expression templates. Unlike the Cython approach, Pythran input code remains compatible with the Python interpreter. Output code is generally as efficient as the annotated Cython equivalent, if not more, but without the backward compatibility loss.

  9. PyRAT (python radiography analysis tool): overview

    SciTech Connect

    Armstrong, Jerawan C [Los Alamos National Laboratory; Temple, Brian A [Los Alamos National Laboratory; Buescher, Kevin L [Los Alamos National Laboratory

    2011-01-14

    PyRAT was developed as a quantitative tool for robustly characterizing objects from radiographs to solve problems such as the hybrid nonlinear inverse problem. The optimization software library that was used is the nonsmooth optimization by MADS algorithm (NOMAD). Some of PyRAT's features are: (1) hybrid nonlinear inverse problem with calculated x-ray spectrum and detector response; (2) optimization based inversion approach with goal of identifying unknown object configurations - MVO problem; (3) using functionalities of Python libraries for radiographic image processing and analysis; (4) using the Tikhonov regularization method of linear inverse problem to recover partial information of object configurations; (5) using a priori knowledge of problem solutions to define feasible region and discrete neighbor for the MVO problem - initial data analysis + material library {yields} a priori knowledge; and (6) using the NOMAD (C++ version) software in the object.

  10. Intraspecific scaling of arterial blood pressure in the Burmese python.

    PubMed

    Enok, Sanne; Slay, Christopher; Abe, Augusto S; Hicks, James W; Wang, Tobias

    2014-07-01

    Interspecific allometric analyses indicate that mean arterial blood pressure (MAP) increases with body mass of snakes and mammals. In snakes, MAP increases in proportion to the increased distance between the heart and the head, when the heart-head vertical distance is expressed as ?gh (where ? is the density of blood, G: is acceleration due to gravity and h is the vertical distance above the heart), and the rise in MAP is associated with a larger heart to normalize wall stress in the ventricular wall. Based on measurements of MAP in Burmese pythons ranging from 0.9 to 3.7 m in length (0.20-27 kg), we demonstrate that although MAP increases with body mass, the rise in MAP is merely half of that predicted by heart-head distance. Scaling relationships within individual species, therefore, may not be accurately predicted by existing interspecific analyses. PMID:24737752

  11. One-dimensional statistical parametric mapping in Python.

    PubMed

    Pataky, Todd C

    2012-01-01

    Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/. PMID:21756121

  12. PYTRANSIT: fast and easy exoplanet transit modelling in PYTHON

    NASA Astrophysics Data System (ADS)

    Parviainen, Hannu

    2015-07-01

    We present a fast and user friendly exoplanet transit light-curve modelling package PYTRANSIT, implementing optimized versions of the Giménez and Mandel & Agol transit models. The package offers an object-oriented PYTHON interface to access the two models implemented natively in FORTRAN with OpenMP parallelization. A partial OpenCL version of the quadratic Mandel-Agol model is also included for GPU-accelerated computations. The aim of PYTRANSIT is to facilitate the analysis of photometric time series of exoplanet transits consisting of hundreds of thousands of data points, and of multipassband transit light curves from spectrophotometric observations, as a part of a researcher's programming toolkit for building complex, problem-specific analyses.

  13. Python package for model STructure ANalysis (pySTAN)

    NASA Astrophysics Data System (ADS)

    Van Hoey, Stijn; van der Kwast, Johannes; Nopens, Ingmar; Seuntjens, Piet

    2013-04-01

    The selection and identification of a suitable hydrological model structure is more than fitting parameters of a model structure to reproduce a measured hydrograph. The procedure is highly dependent on various criteria, i.e. the modelling objective, the characteristics and the scale of the system under investigation as well as the available data. Rigorous analysis of the candidate model structures is needed to support and objectify the selection of the most appropriate structure for a specific case (or eventually justify the use of a proposed ensemble of structures). This holds both in the situation of choosing between a limited set of different structures as well as in the framework of flexible model structures with interchangeable components. Many different methods to evaluate and analyse model structures exist. This leads to a sprawl of available methods, all characterized by different assumptions, changing conditions of application and various code implementations. Methods typically focus on optimization, sensitivity analysis or uncertainty analysis, with backgrounds from optimization, machine-learning or statistics amongst others. These methods also need an evaluation metric (objective function) to compare the model outcome with some observed data. However, for current methods described in literature, implementations are not always transparent and reproducible (if available at all). No standard procedures exist to share code and the popularity (and amount of applications) of the methods is sometimes more dependent on the availability than the merits of the method. Moreover, new implementations of existing methods are difficult to verify and the different theoretical backgrounds make it difficult for environmental scientists to decide about the usefulness of a specific method. A common and open framework with a large set of methods can support users in deciding about the most appropriate method. Hence, it enables to simultaneously apply and compare different methods on a fair basis. We developed and present pySTAN (python framework for STructure Analysis), a python package containing a set of functions for model structure evaluation to provide the analysis of (hydrological) model structures. A selected set of algorithms for optimization, uncertainty and sensitivity analysis is currently available, together with a set of evaluation (objective) functions and input distributions to sample from. The methods are implemented model-independent and the python language provides the wrapper functions to apply administer external model codes. Different objective functions can be considered simultaneously with both statistical metrics and more hydrology specific metrics. By using so-called reStructuredText (sphinx documentation generator) and Python documentation strings (docstrings), the generation of manual pages is semi-automated and a specific environment is available to enhance both the readability and transparency of the code. It thereby enables a larger group of users to apply and compare these methods and to extend the functionalities.

  14. PyORBIT: A Python Shell For ORBIT

    SciTech Connect

    Jean-Francois Ostiguy; Jeffrey Holmes

    2003-07-01

    ORBIT is code developed at SNS to simulate beam dynamics in accumulation rings and synchrotrons. The code is structured as a collection of external C++ modules for SuperCode, a high level interpreter shell developed at LLNL in the early 1990s. SuperCode is no longer actively supported and there has for some time been interest in replacing it by a modern scripting language, while preserving the feel of the original ORBIT program. In this paper, we describe a new version of ORBIT where the role of SuperCode is assumed by Python, a free, well-documented and widely supported object-oriented scripting language. We also compare PyORBIT to ORBIT from the standpoint of features, performance and future expandability.

  15. 6.189 A Gentle Introduction to Programming Using Python, January IAP 2010

    E-print Network

    Canelake, Sarina

    2010-01-01

    This 6-unit P/D/F course will provide a gentle introduction to programming using Python for highly motivated students with little or no prior experience in programming computers over the first two weeks of IAP. The course ...

  16. INSTALLING PYTHON THIS appendix explains how to install on your computer the software you

    E-print Network

    Newman, Mark

    on using it. If so, you can do that, but you need to take one extra precaution. There are a few small that can be installed using the standard software installer.) 2. Having installed the Python language you

  17. Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons.

    PubMed

    Hunter, Margaret E; Oyler-McCance, Sara J; Dorazio, Robert M; Fike, Jennifer A; Smith, Brian J; Hunter, Charles T; Reed, Robert N; Hart, Kristen M

    2015-01-01

    Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models. PMID:25874630

  18. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons

    USGS Publications Warehouse

    Hunter, Margaret E.; Oyler-McCance, Sara J.; Dorazio, Robert M.; Fike, Jennifer A.; Smith, Brian J.; Hunter, Charles T.; Reed, Robert N.; Hart, Kristen M.

    2015-01-01

    Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.

  19. Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park

    PubMed Central

    Dorcas, Michael E.; Willson, John D.; Reed, Robert N.; Snow, Ray W.; Rochford, Michael R.; Miller, Melissa A.; Meshaka, Walter E.; Andreadis, Paul T.; Mazzotti, Frank J.; Romagosa, Christina M.; Hart, Kristen M.

    2012-01-01

    Invasive species represent a significant threat to global biodiversity and a substantial economic burden. Burmese pythons, giant constricting snakes native to Asia, now are found throughout much of southern Florida, including all of Everglades National Park (ENP). Pythons have increased dramatically in both abundance and geographic range since 2000 and consume a wide variety of mammals and birds. Here we report severe apparent declines in mammal populations that coincide temporally and spatially with the proliferation of pythons in ENP. Before 2000, mammals were encountered frequently during nocturnal road surveys within ENP. In contrast, road surveys totaling 56,971 km from 2003–2011 documented a 99.3% decrease in the frequency of raccoon observations, decreases of 98.9% and 87.5% for opossum and bobcat observations, respectively, and failed to detect rabbits. Road surveys also revealed that these species are more common in areas where pythons have been discovered only recently and are most abundant outside the python's current introduced range. These findings suggest that predation by pythons has resulted in dramatic declines in mammals within ENP and that introduced apex predators, such as giant constrictors, can exert significant top-down pressure on prey populations. Severe declines in easily observed and/or common mammals, such as raccoons and bobcats, bode poorly for species of conservation concern, which often are more difficult to sample and occur at lower densities. PMID:22308381

  20. Paternal alleles enhance female reproductive success in tropical pythons.

    PubMed

    Madsen, Thomas; Ujvari, Beata; Olsson, Mats; Shine, Richard

    2005-05-01

    The conventional view that female reproductive success is unlikely to benefit from multiple mating has come under strong challenge in recent years. In the present study, we demonstrate that the time wild-caught reproductive female water pythons (Liasis fuscus) spent in the laboratory prior to oviposition affected both hatching success and the number of male microsatellite alleles detected in the broods. A negative correlation between time in captivity and number of male alleles observed in the broods suggests that reduced hatching success was most likely not caused by environmental factors such as non-optimal temperatures, but rather by restricted mating opportunities. Maternal nutritional status and mean hatchling mass did not affect brood viability. However, our results revealed a positive correlation between number of male microsatellite alleles observed in the broods and hatching success, suggesting that increased paternal genetic variability enhanced female reproductive success. As microsatellite loci are unlikely to be direct targets of selection, we suggest that variability at these loci may cosegregate with other polymorphic genes directly linked to fitness. PMID:15836649

  1. SIMA: Python software for analysis of dynamic fluorescence imaging data

    PubMed Central

    Kaifosh, Patrick; Zaremba, Jeffrey D.; Danielson, Nathan B.; Losonczy, Attila

    2014-01-01

    Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/. PMID:25295002

  2. Short Telomeres in Hatchling Snakes: Erythrocyte Telomere Dynamics and Longevity in Tropical Pythons

    PubMed Central

    Ujvari, Beata; Madsen, Thomas

    2009-01-01

    Background Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be induced by changes in the protected status of the telomeres rather than the loss of TL. In the present study we explore whether age- and sex-specific telomere dynamics affect life span in a long-lived snake, the water python (Liasis fuscus). Methodology/Principal Findings Erythrocyte TL was measured using the Telo TAGGG TL Assay Kit (Roche). In contrast to other vertebrates, TL of hatchling pythons was significantly shorter than that of older snakes. However, during their first year of life hatchling TL increased substantially. While TL of older snakes decreased with age, we did not observe any correlation between TL and age in cross-sectional sampling. In older snakes, female TL was longer than that of males. When using recapture as a proxy for survival, our results do not support that longer telomeres resulted in an increased water python survival/longevity. Conclusions/Significance In fish high telomerase activity has been observed in somatic cells exhibiting high proliferation rates. Hatchling pythons show similar high somatic cell proliferation rates. Thus, the increase in TL of this group may have been caused by increased telomerase activity. In older humans female TL is longer than that of males. This has been suggested to be caused by high estrogen levels that stimulate increased telomerase activity. Thus, high estrogen levels may also have caused the longer telomeres in female pythons. The lack of correlation between TL and age among old snakes and the fact that longer telomeres did not appear to affect python survival do not support that erythrocyte telomere dynamics has a major impact on water python longevity. PMID:19834611

  3. Review of the reticulated python (Python reticulatus Schneider, 1801) with the description of new subspecies from Indonesia

    NASA Astrophysics Data System (ADS)

    Auliya, M.; Mausfeld, P.; Schmitz, A.; Böhme, W.

    2002-04-01

    The geographically widespread Python reticulatus, the world's longest snake, has been largely neglected by taxonomists. Dwarfed individuals from Tanahjampea Island, Indonesia, differ strikingly in morphology. Phylogenetic relationships were analyzed using a 345-bp fragment of the cytochrome b gene for 12 specimens from different populations. Both genetic differences and morphological characters distinctly revealed two taxonomic subunits. The island populations of Tanahjampea and Selayar form two monophyletic lineages, supported by high bootstrap values, with distinct differences in color pattern and scalation. We consider these forms to represent two new subspecies. The Tanahjampea form is genetically related to populations of the Sunda Islands and mainland Southeast Asia, whereas the Selayar form is related to populations of Southwest Sulawesi. We conclude that, due to strong directional surface currents in this region, gene flow between Tanahjampea and Selayar is prevented. Sea-level changes during the Pleistocene probably contributed to the isolation of the two taxa described. Aspects of ecology and conservation status are briefly discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0320-4.

  4. High prevalence of Hepatozoon spp. (Apicomplexa, Hepatozoidae) infection in water pythons (Liasis fuscus) from tropical Australia.

    PubMed

    Ujvari, Beata; Madsen, Thomas; Olsson, Mats

    2004-06-01

    Molecular methods were used to identify blood parasites frequently observed in blood smears of water pythons (Liasis fuscus) captured in our study area in the Northern Territory of Australia. A nested polymerase chain reaction (PCR) using primers amplifying the 18s ribosomal RNA (rRNA) nuclear gene resulted in a short PCR product (180 bp) matching this region in the genus Hepatozoon. However, because of the short sequence obtained. 2 new primers were designed based on 18s rRNA sequences of 3 Hepatozoon taxa available in GenBank. Using these primers, approximately 600 bp of the parasite's 18s rRNA gene was amplified successfully and sequenced from 2 water python samples. The new primers were used to investigate the prevalence of blood parasites in 100 pythons. In 25 of these samples we did not observe any blood parasites when examining stained slides. All the samples revealed a 600-bp PCR product, demonstrating that pythons in which we did not visually observe any parasites were infected by Hepatozoon spp. We also analyzed the nucleotide sequences of blood parasites in 4 other reptile taxa commonly encountered in our study area. The sequences obtained from water pythons and from 1 of these taxa were identical, suggesting that the parasite is capable of infecting hosts at different taxonomic levels. PMID:15270125

  5. ObsPy: a bridge for seismology into the scientific Python ecosystem

    NASA Astrophysics Data System (ADS)

    Krischer, Lion; Megies, Tobias; Barsch, Robert; Beyreuther, Moritz; Lecocq, Thomas; Caudron, Corentin; Wassermann, Joachim

    2015-01-01

    The Python libraries NumPy and SciPy are extremely powerful tools for numerical processing and analysis well suited to a large variety of applications. We developed ObsPy (http://obspy.org), a Python library for seismology intended to facilitate the development of seismological software packages and workflows, to utilize these abilities and provide a bridge for seismology into the larger scientific Python ecosystem. Scientists in many domains who wish to convert their existing tools and applications to take advantage of a platform like the one Python provides are confronted with several hurdles such as special file formats, unknown terminology, and no suitable replacement for a non-trivial piece of software. We present an approach to implement a domain-specific time series library on top of the scientific NumPy stack. In so doing, we show a realization of an abstract internal representation of time series data permitting I/O support for a diverse collection of file formats. Then we detail the integration and repurposing of well established legacy codes, enabling them to be used in modern workflows composed in Python. Finally we present a case study on how to integrate research code into ObsPy, opening it to the broader community. While the implementations presented in this work are specific to seismology, many of the described concepts and abstractions are directly applicable to other sciences, especially to those with an emphasis on time series analysis.

  6. SunPy - Python for Solar Physics, Version 0.4

    NASA Astrophysics Data System (ADS)

    Christe, Steven; Mumford, Stuart; Perez-Suarez, David; Ireland, Jack; Shih, Albert Y.; Inglis, Andrew; Liedtke, Simon; Hewett, Russel

    2014-06-01

    We presents version 0.4 of SunPy, a community-developed Python package for solar physics. Python, a free, cross-platform, general-purpose, high-level programming language, has seen widespread adoption among the scientific community, resulting in the availability of a large number of software packages, from numerical computation NumPy, SciPy and machine learning (scikit-learn) to visualisation and plotting (matplotlib).SunPy is a data-analysis environment specialising in providing the software necessary to analyse solar and heliospheric datasets in Python. SunPy is open-source software (BSD licence) and has an open and transparent development workflow that anyone can contribute to. SunPy provides access to solar data through integration with the Virtual Solar Observatory (VSO), the Heliophysics Event Knowledgebase (HEK), and the HELiophysics Integrated Observatory (HELIO) webservices. It currently supports image data from major solar missions (e.g., SDO, SOHO, STEREO, and IRIS), time-series data from missions such as GOES, SDO/EVE, and PROBA2/LYRA, and radio spectra from e-Callisto and STEREO/SWAVES. We describe SunPy's functionality, provide examples of solar data analysis in SunPy, and show how Python-based solar data-analysis can leverage the many existing tools already available in Python. We discuss the future goals of the project and encourage interested users to become involved in the planning and development of SunPy.

  7. Charming the Snake: Student Experiences with Python Programming as a Data Analysis Tool

    NASA Astrophysics Data System (ADS)

    Booker, Melissa; Ivers, C. B.; Piper, M.; Powers, L.; Ali, B.

    2014-01-01

    During the past year, twelve high school students and one undergraduate student participated in the NASA/IPAC Teacher Archive Research Program (NITARP) alongside three high school educators and one informal educator, gaining experience in using Python as a tool for analyzing the vast amount of photometry data available from the Herschel and Spitzer telescopes in the NGC 281 region. Use of Python appeared to produce two main positive gains: (1) a gain in student ability to successfully write and execute Python programs for the bulk analysis of data, and (2) a change in their perceptions of the utility of computer programming and of the students’ abilities to use programming to solve problems. We outline the trials, tribulations, successes, and failures of the teachers and students through this learning exercise and provide some recommendations for incorporating programming in scientific learning.

  8. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

    PubMed

    Yesylevskyy, Semen O

    2015-07-15

    Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc. PMID:25974373

  9. Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

    NASA Astrophysics Data System (ADS)

    Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

    2015-04-01

    GRASS GIS 7 is a free and open source GIS software developed and used by many scientists (Neteler et al., 2012). While some users of GRASS GIS prefer its graphical user interface, significant part of the scientific community takes advantage of various scripting and programing interfaces offered by GRASS GIS to develop new models and algorithms. Here we will present different interfaces added to GRASS GIS 7 and available in Python, a popular programming language and environment in geosciences. These Python interfaces are designed to satisfy the needs of scientists and programmers under various circumstances. PyGRASS (Zambelli et al., 2013) is a new object-oriented interface to GRASS GIS modules and libraries. The GRASS GIS libraries are implemented in C to ensure maximum performance and the PyGRASS interface provides an intuitive, pythonic access to their functionality. GRASS GIS Python scripting library is another way of accessing GRASS GIS modules. It combines the simplicity of Bash and the efficiency of the Python syntax. When full access to all low-level and advanced functions and structures from GRASS GIS library is required, Python programmers can use an interface based on the Python ctypes package. Ctypes interface provides complete, direct access to all functionality as it would be available to C programmers. GRASS GIS provides specialized Python library for managing and analyzing spatio-temporal data (Gebbert and Pebesma, 2014). The temporal library introduces space time datasets representing time series of raster, 3D raster or vector maps and allows users to combine various spatio-temporal operations including queries, aggregation, sampling or the analysis of spatio-temporal topology. We will also discuss the advantages of implementing scientific algorithm as a GRASS GIS module and we will show how to write such module in Python. To facilitate the development of the module, GRASS GIS provides a Python library for testing (Petras and Gebbert, 2014) which helps researchers to ensure the robustness of the algorithm, correctness of the results in edge cases as well as the detection of changes in results due to new development. For all modules GRASS GIS automatically creates standardized command line and graphical user interfaces and documentation. Finally, we will show how GRASS GIS can be used together with powerful Python tools such as the NumPy package and the IPython Notebook. References: Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environmental Modelling & Software 53, 1-12. Neteler, M., Bowman, M.H., Landa, M. and Metz, M., 2012. GRASS GIS: a multi-purpose Open Source GIS. Environmental Modelling & Software 31: 124-130. Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201-219.

  10. Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models

    Microsoft Academic Search

    R. Alexander Pyron; Frank T. Burbrink; Timothy J. Guiher

    2008-01-01

    Background: Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python

  11. Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models

    Microsoft Academic Search

    R. Alexander Pyron; Frank T. Burbrink; Timothy J. Guiher; Andy Hector

    2008-01-01

    BackgroundRecent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are

  12. Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling

    E-print Network

    Revell, Liam

    Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65

  13. HOPE: A Python just-in-time compiler for astrophysical computations

    NASA Astrophysics Data System (ADS)

    Akeret, J.; Gamper, L.; Amara, A.; Refregier, A.

    2015-04-01

    The Python programming language is becoming increasingly popular for scientific applications due to its simplicity, versatility, and the broad range of its libraries. A drawback of this dynamic language, however, is its low runtime performance which limits its applicability for large simulations and for the analysis of large data sets, as is common in astrophysics and cosmology. While various frameworks have been developed to address this limitation, most focus on covering the complete language set, and either force the user to alter the code or are not able to reach the full speed of an optimised native compiled language. In order to combine the ease of Python and the speed of C++, we developed HOPE, a specialised Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimisation on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. We assess the performance of HOPE by performing a series of benchmarks and compare its execution speed with that of plain Python, C++ and the other existing frameworks. We find that HOPE improves the performance compared to plain Python by a factor of 2 to 120, achieves speeds comparable to that of C++, and often exceeds the speed of the existing solutions. We discuss the differences between HOPE and the other frameworks, as well as future extensions of its capabilities. The fully documented HOPE package is available at

  14. SPOTting model parameters using a ready-made Python package

    NASA Astrophysics Data System (ADS)

    Houska, Tobias; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for optimization methods. Here we see simple algorithms like the MCMC struggling to find the global optimum of the function, while algorithms like SCE-UA and DE-MCZ show their strengths. Thirdly, we apply an uncertainty analysis of a one-dimensional physically based hydrological model build with the Catchment Modelling Framework (CMF). The model is driven by meteorological and groundwater data from a Free Air Carbon Enrichment (FACE) experiment in Linden (Hesse, Germany). Simulation results are evaluated with measured soil moisture data. We search for optimal parameter sets of the van Genuchten-Mualem function and find different equally optimal solutions with some of the algorithms. The case studies reveal that the implemented SPOT methods work sufficiently well. They further show the benefit of having one tool at hand that includes a number of parameter search methods, likelihood functions and a priori parameter distributions within one platform independent package.

  15. Light and electron microscopic observations of the life cycle of Sarcocystis orientalis sp. n. in the rat ( Rattus norvegicus ) and the Malaysian reticulated python ( Python reticulatus )

    Microsoft Academic Search

    V. Zaman; Frederick C. Colley

    1975-01-01

    A light and electron microscopic study of Sarcocystis orientalis sp. n. was made. The life cycle of this parasite is in two hosts. Gametogony is in the intestinal epithelial cells of a predator, Python reticulatus. Isospora-like oocysts developed. Sporocysts average 9.1 by 7.7 µm. Rats (Rattus norvegicus) were infected with sporocysts and asexual stages developed. Ten days after infection large

  16. COSMIC MICROWAVE BACKGROUND ANISOTROPY MEASUREMENT FROM PYTHON V K. Coble, 1,2 S. Dodelson, 1,3 M. Dragovan, 4 K. Ganga, 5 L. Knox, 6 J. Kovac, 1 B. Ratra, 7 and T. Souradeep 7,8

    E-print Network

    Souradeep, Tarun

    COSMIC MICROWAVE BACKGROUND ANISOTROPY MEASUREMENT FROM PYTHON V K. Coble, 1,2 S. Dodelson, 1,3 M; accepted 2002 October 22 ABSTRACT We analyze observations of the microwave sky made with the Python in the early universe. We compare this Python V map to a map made from data taken in the third year of Python

  17. A Comparison of C, MATLAB, and Python as Teaching Languages in Engineering

    Microsoft Academic Search

    Hans Fangohr

    2004-01-01

    We describe and compare the programming languages C, MATLAB and Python as teaching languages for engineering students. We distinguish between two distinct phases in the process of converting a given problem into a computer program that can provide a solution: (i) finding an algorithmic solution and (ii) implementing this in a partic- ular programming language. It is argued that it

  18. Biopython: freely available Python tools for computational molecular biology and bioinformatics

    Microsoft Academic Search

    Peter J. A. Cock; Tiago Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. De Hoon

    2009-01-01

    Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW, and EMBOSS, accessing key online databases, as well

  19. 77 FR 3329 - Injurious Wildlife Species; Listing Three Python Species and One Anaconda Species as Injurious...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-23

    ...will compete for food with native species; in other words, baby pythons will eat small prey, and the size of their...investment-grade'' ones, because the average person is hesitant to buy a new pet.'' We also note that part of the snake...

  20. Close-Up of a Radio Transmitter on an Invasive Burmese Python

    USGS Multimedia Gallery

    This close-up is of the radio-transmitter on a 16 1/2-foot python. The snake, being removed from the wild by USGS and NPS personnel, was re-captured in a thicket in Everglades National Park in April 2012. After its first capture, the snake was equipped with a radio-transmitter and an accelerometer a...

  1. Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data

    PubMed Central

    Shah, Abhik; Woolf, Peter

    2009-01-01

    Summary In this paper, we introduce pebl, a Python library and application for learning Bayesian network structure from data and prior knowledge that provides features unmatched by alternative software packages: the ability to use interventional data, flexible specification of structural priors, modeling with hidden variables and exploitation of parallel processing. PMID:20161541

  2. Automating Disk Forensic Processing with SleuthKit, XML and Python

    Microsoft Academic Search

    Simson L. Garfinkel

    2009-01-01

    We have developed a program called fiwalk which produces detailed XML describing all of the partitions and files on a hard drive or disk image, as well as any extractable metadata from the document files themselves. We show how it is relatively simple to create automated disk forensic applications using a Python module we have written that reads fiwalk's XML

  3. PyCOOL — A Cosmological Object-Oriented Lattice code written in Python

    Microsoft Academic Search

    J. Sainio

    2012-01-01

    There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet

  4. A Python-Based Analog Layout Generation Tool For Nanometer CMOS Technologies

    E-print Network

    Boyer, Edmond

    A Python-Based Analog Layout Generation Tool For Nanometer CMOS Technologies Stephanie YOUSSEF based analog layout generation tool for nanometer CMOS technologies. To demon- strate the ease of use for two layout techniques of a differential pair device (interdigited and symmetric). I. INTRODUCTION

  5. Python and Roles of Variables in Introductory Programming: Experiences from Three Educational Institutions

    ERIC Educational Resources Information Center

    Nikula, Uolevi; Sajaniemi, Jorma; Tedre, Matti; Wray, Stuart

    2007-01-01

    Students often find that learning to program is hard. Introductory programming courses have high drop-out rates and students do not learn to program well. This paper presents experiences from three educational institutions where introductory programming courses were improved by adopting Python as the first programming language and roles of…

  6. Old pythons stay fit; effects of haematozoan infections on life history traits of a large tropical predator.

    PubMed

    Madsen, Thomas; Ujvari, Beata; Olsson, Mats

    2005-01-01

    We document the impact of blood parasite infections caused by Hepatozoon sp. on water python (Liasis fuscus) life history traits such as growth rates, condition, reproductive output and survival. Individual snakes maintained similar among-year parasite loads. Hepatozoon infections affected python growth rate, i.e. snakes suffering from high infection levels exhibited significantly slower growth compared to individuals with low parasite loads. Our results suggest that the parasites also affected the pythons' nutritional status (condition), as snakes with low condition scores suffered from higher parasite infection levels than snakes with high scores. Furthermore, our data suggest that parasitaemia may affect female reproductive output, as reproductive female pythons harboured lower parasite loads compared to non-reproductive adult females. High levels of parasite infections also affected juvenile python survival, as recaptured snakes harboured significantly lower parasite loads compared to non-recaptured yearling pythons. In our study area, water python have very few natural predators and, hence, experience low mortality rates and commonly reach an age of >15 years. In contrast to results obtained in other studies, parasite loads in larger/older pythons were lower compared to younger snakes, suggesting that only snakes harbouring lower levels of parasitaemia were able to survive to old age. We suggest that a possible cause for the opposing results regarding parasite prevalence and host age may be due to different levels of extrinsic mortality rates and longevity. Long-lived organisms, such as water pythons, may invest relatively more into crucial self-maintenance functions such as parasite defence, compared to short-lived organisms. PMID:15517406

  7. GMES: A Python package for solving Maxwell’s equations using the FDTD method

    NASA Astrophysics Data System (ADS)

    Chun, Kyungwon; Kim, Huioon; Kim, Hyounggyu; Jung, Kil Su; Chung, Youngjoo

    2013-04-01

    This paper describes GMES, a free Python package for solving Maxwell’s equations using the finite-difference time-domain (FDTD) method. The design of GMES follows the object-oriented programming (OOP) approach and adopts a unique design strategy where the voxels in the computational domain are grouped and then updated according to its material type. This piecewise updating scheme ensures that GMES can adopt OOP without losing its simple structure and time-stepping speed. The users can easily add various material types, sources, and boundary conditions into their code using the Python programming language. The key design features, along with the supported material types, excitation sources, boundary conditions and parallel calculations employed in GMES are also described in detail. Catalog identifier: AEOK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOK_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 17700 No. of bytes in distributed program, including test data, etc.: 89878 Distribution format: tar.gz Programming language: C++, Python. Computer: Any computer with a Unix-like system with a C++ compiler, and a Python interpreter; developed on 2.53 GHz Intel CoreTM i3. Operating system: Any Unix-like system; developed under Ubuntu 12.04 LTS 64 bit. Has the code been vectorized or parallelized?: Yes. Parallelized with MPI directives (optional). RAM: Problem dependent (a simulation with real valued electromagnetic field uses roughly 0.18 KB per Yee cell.) Classification: 10. External routines: SWIG [1], Cython [2], NumPy [3], SciPy [4], matplotlib [5], MPI for Python [6] Nature of problem: Classical electrodynamics Solution method: Finite-difference time-domain (FDTD) method Additional comments: This article describes version 0.9.5. The most recent version can be downloaded at the GMES project homepage [7]. Running time: Problem dependent (a simulation with real valued electromagnetic field takes typically about 0.16 ?s per Yee cell per time-step.) SWIG, http://www.swig.org. Cython, http://www.cython.org. NumPy, http://numpy.scipy.org. SciPy, http://www.scipy.org. matplotlib, http://matplotlib.sourceforge.net. MPI for Python, http://mpi4py.scipy.org. GMES, http://sourceforge.net/projects/gmes.

  8. Python-Based Scientific Analysis and Visualization of Precipitation Systems at NASA Marshall Space Flight Center

    NASA Technical Reports Server (NTRS)

    Lang, Timothy J.

    2015-01-01

    At NASA Marshall Space Flight Center (MSFC), Python is used several different ways to analyze and visualize precipitating weather systems. A number of different Python-based software packages have been developed, which are available to the larger scientific community. The approach in all these packages is to utilize pre-existing Python modules as well as to be object-oriented and scalable. The first package that will be described and demonstrated is the Python Advanced Microwave Precipitation Radiometer (AMPR) Data Toolkit, or PyAMPR for short. PyAMPR reads geolocated brightness temperature data from any flight of the AMPR airborne instrument over its 25-year history into a common data structure suitable for user-defined analyses. It features rapid, simplified (i.e., one line of code) production of quick-look imagery, including Google Earth overlays, swath plots of individual channels, and strip charts showing multiple channels at once. These plotting routines are also capable of significant customization for detailed, publication-ready figures. Deconvolution of the polarization-varying channels to static horizontally and vertically polarized scenes is also available. Examples will be given of PyAMPR's contribution toward real-time AMPR data display during the Integrated Precipitation and Hydrology Experiment (IPHEx), which took place in the Carolinas during May-June 2014. The second software package is the Marshall Multi-Radar/Multi-Sensor (MRMS) Mosaic Python Toolkit, or MMM-Py for short. MMM-Py was designed to read, analyze, and display three-dimensional national mosaicked reflectivity data produced by the NOAA National Severe Storms Laboratory (NSSL). MMM-Py can read MRMS mosaics from either their unique binary format or their converted NetCDF format. It can also read and properly interpret the current mosaic design (4 regional tiles) as well as mosaics produced prior to late July 2013 (8 tiles). MMM-Py can easily stitch multiple tiles together to provide a larger regional or national picture of precipitating weather systems. Composites, horizontal and vertical crosssections, and combinations thereof are easily displayed using as little as one line of code. MMM-Py can also write to the native MRMS binary format, and sub-sectioning of tiles (or multiple stitched tiles) is anticipated to be in place by the time of this meeting. Thus, MMM-Py also can be used to power the creation of custom mosaics for targeted regional studies. Overlays of other data (e.g., lightning observations) are easily accomplished. Demonstrations of MMM-Py, including the creation of animations, will be shown. Finally, Marshall has done significant work to interface Python-based analysis routines with the U.S. Department of Energy's Py-ART software package for radar data ingest, processing, and analysis. One example of this is the Python Turbulence Detection Algorithm (PyTDA), an MSFC-based implementation of the National Center for Atmospheric Research (NCAR) Turbulence Detection Algorithm (NTDA) for the purposes of convective-scale analysis, situational awareness, and forensic meteorology. PyTDA exploits Py-ART's radar data ingest routines and data model to rapidly produce aviation-relevant turbulence estimates from Doppler radar data. Work toward processing speed optimization and better integration within the Py-ART framework will be highlighted. Python-based analysis within the Py-ART framework is also being done for new research related to intercomparison of ground-based radar data with satellite estimates of ocean winds, as well as research on the electrification of pyrocumulus clouds.

  9. Galactic Foreground Constraints from the Python V Cosmic Microwave Background Anisotropy Data

    E-print Network

    Pia Mukherjee; Kim Coble; Mark Dragovan; Ken Ganga; John Kovac; Bharat Ratra; Tarun Souradeep

    2003-04-24

    We constrain Galactic foreground contamination of the Python V cosmic microwave background anisotropy data by cross correlating it with foreground contaminant emission templates. To model foreground emission we use 100 and 12 $\\mu$m dust emission templates and two point source templates based on the PMN survey. The analysis takes account of inter-modulation correlations in 8 modulations of the data that are sensitive to a large range of angular scales and also densely sample a large area of sky. As a consequence the analysis here is highly constraining. We find little evidence for foreground contamination in an analysis of the whole data set. However, there is indication that foregrounds are present in the data from the larger-angular-scale modulations of those Python V fields that overlap the region scanned earlier by the UCSB South Pole 1994 experiment. This is an independent consistency cross-check of findings from the South Pole 1994 data.

  10. And now for something completely different: Inattentional blindness during a Monty Python's Flying Circus sketch

    PubMed Central

    Wiseman, Richard; Watt, Caroline

    2015-01-01

    Perceptual science has frequently benefited from studying illusions created outside of academia. Here, we describe a striking, but little-known, example of inattentional blindness from the British comedy series “Monty Python's Flying Circus.” Viewers fail to attend to several highly incongruous characters in the sketch, despite these characters being clearly visible onscreen. The sketch has the potential to be a valuable research and teaching resource, as well as providing a vivid illustration of how people often fail to see something completely different.

  11. Calculations of lattice vibrational mode lifetimes using Jazz: a Python wrapper for LAMMPS

    NASA Astrophysics Data System (ADS)

    Gao, Y.; Wang, H.; Daw, M. S.

    2015-06-01

    Jazz is a new python wrapper for LAMMPS [1], implemented to calculate the lifetimes of vibrational normal modes based on forces as calculated for any interatomic potential available in that package. The anharmonic character of the normal modes is analyzed via the Monte Carlo-based moments approximation as is described in Gao and Daw [2]. It is distributed as open-source software and can be downloaded from the website http://jazz.sourceforge.net/.

  12. A new open-source Python-based Space Weather data access, visualization, and analysis toolkit

    NASA Astrophysics Data System (ADS)

    de Larquier, S.; Ribeiro, A.; Frissell, N. A.; Spaleta, J.; Kunduri, B.; Thomas, E. G.; Ruohoniemi, J.; Baker, J. B.

    2013-12-01

    Space weather research relies heavily on combining and comparing data from multiple observational platforms. Current frameworks exist to aggregate some of the data sources, most based on file downloads via web or ftp interfaces. Empirical models are mostly fortran based and lack interfaces with more useful scripting languages. In an effort to improve data and model access, the SuperDARN community has been developing a Python-based Space Science Data Visualization Toolkit (DaViTpy). At the center of this development was a redesign of how our data (from 30 years of SuperDARN radars) was made available. Several access solutions are now wrapped into one convenient Python interface which probes local directories, a new remote NoSQL database, and an FTP server to retrieve the requested data based on availability. Motivated by the efficiency of this interface and the inherent need for data from multiple instruments, we implemented similar modules for other space science datasets (POES, OMNI, Kp, AE...), and also included fundamental empirical models with Python interfaces to enhance data analysis (IRI, HWM, MSIS...). All these modules and more are gathered in a single convenient toolkit, which is collaboratively developed and distributed using Github and continues to grow. While still in its early stages, we expect this toolkit will facilitate multi-instrument space weather research and improve scientific productivity.

  13. NEVESIM: event-driven neural simulation framework with a Python interface

    PubMed Central

    Pecevski, Dejan; Kappel, David; Jonke, Zeno

    2014-01-01

    NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies. PMID:25177291

  14. NEVESIM: event-driven neural simulation framework with a Python interface.

    PubMed

    Pecevski, Dejan; Kappel, David; Jonke, Zeno

    2014-01-01

    NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies. PMID:25177291

  15. Food composition influences metabolism, heart rate and organ growth during digestion in Python regius.

    PubMed

    Henriksen, Poul Secher; Enok, Sanne; Overgaard, Johannes; Wang, Tobias

    2015-05-01

    Digestion in pythons is associated with a large increase in oxygen consumption (SDA), increased cardiac output and growth in visceral organs assisting in digestion. The processes leading to the large postprandial rise in metabolism in snakes is subject to opposing views. Gastric work, protein synthesis and organ growth have each been speculated to be major contributors to the SDA. To investigate the role of food composition on SDA, heart rate (HR) and organ growth, 48 ball pythons (Python regius) were fed meals of either fat, glucose, protein or protein combined with carbonate. Our study shows that protein, in the absence or presence of carbonate causes a large SDA response, while glucose caused a significantly smaller SDA response and digestion of fat failed to affect metabolism. Addition of carbonate to the diet to stimulate gastric acid secretion did not increase the SDA response. These results support protein synthesis as a major contributor to the SDA response and show that increased gastric acid secretion occurs at a low metabolic cost. The increase in metabolism was supported by tachycardia caused by altered autonomic regulation as well as an increased non-adrenergic, non-cholinergic (NANC) tone in response to all diets, except for the lipid meal. Organ growth only occurred in the small intestine and liver in snakes fed on a high protein diet. PMID:25553896

  16. Python scripting libraries for subsurface fluid and heat flow simulations with TOUGH2 and SHEMAT

    NASA Astrophysics Data System (ADS)

    Florian Wellmann, J.; Croucher, Adrian; Regenauer-Lieb, Klaus

    2012-06-01

    Numerical simulations of subsurface fluid and heat flow are commonly controlled manually via input files or from graphical user interfaces (GUIs). Manual editing of input files is often tedious and error-prone, while GUIs typically limit the full capability of the simulator. Neither approach lends itself to automation, which is desirable for more complex simulations. We propose an alternative approach based on the use of scripting. To this end we have developed Python libraries for scripting subsurface simulations using the SHEMAT and TOUGH2 simulators. For many problems the entire modeling process including grid generation, model setup, execution, post-processing and analysis of results can be carried out from a single Python script. Through example problems we demonstrate some of the potential power of the scripting approach, which does not only make model setup simpler and less error-prone, but also facilitates more complex simulations involving, for example, multiple model runs with varying parameters (e.g. permeabilities, heat inputs, and the level of grid refinement). It is also possible to apply the developed methods for extending the functionality of graphical user interfaces. Basing our approach on the Python language makes it simple to take advantage of other libraries available for scientific computation, with sophisticated analysis of results often a matter of a single function call. We envisage many other possible applications of the approach, including linking with geological modeling software, running stochastic ensembles of models and hybrid modeling using multiple interacting simulators.

  17. PyCOOL - a Cosmological Object-Oriented Lattice code written in Python

    E-print Network

    Sainio, Jani

    2012-01-01

    There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet spot of speed, accuracy and user friendliness. This has been achieved by using the Python language with the PyCUDA interface to make a program that is easy to adapt to different scalar field models. In this paper we derive the symplectic dynamics that govern the evolution of the system and then present the implementation of the program in Python and PyCUDA. The functionality of the program is tested in a chaotic inflation preheating model, a single field oscillon case and in a supersymmetric curvaton model which leads to Q-ball production. We have also compared the performance of a consumer graphics card to a professional Tesla compute...

  18. A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

    PubMed Central

    Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

    2015-01-01

    Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

  19. ObsPy: A Python Toolbox for Seismology - Recent Developments and Applications

    NASA Astrophysics Data System (ADS)

    Megies, T.; Krischer, L.; Barsch, R.; Sales de Andrade, E.; Beyreuther, M.

    2014-12-01

    ObsPy (http://www.obspy.org) is a community-driven, open-source project dedicated to building a bridge for seismology into the scientific Python ecosystem. It offersa) read and write support for essentially all commonly used waveform, station, and event metadata file formats with a unified interface,b) a comprehensive signal processing toolbox tuned to the needs of seismologists,c) integrated access to all large data centers, web services and databases, andd) convenient wrappers to legacy codes like libtau and evalresp.Python, currently the most popular language for teaching introductory computer science courses at top-ranked U.S. departments, is a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. Together with packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy enables the construction of complete workflows in Python. These vary from reading locally stored data or requesting data from one or more different data centers through to signal analysis and data processing and on to visualizations in GUI and web applications, output of modified/derived data and the creation of publication-quality figures.ObsPy enjoys a large world-wide rate of adoption in the community. Applications successfully using it include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. All functionality is extensively documented and the ObsPy tutorial and gallery give a good impression of the wide range of possible use cases.We will present the basic features of ObsPy, new developments and applications, and a roadmap for the near future and discuss the sustainability of our open-source development model.

  20. PyCOOL — A Cosmological Object-Oriented Lattice code written in Python

    SciTech Connect

    Sainio, J., E-mail: jani.sainio@utu.fi [Turku School of Economics, University of Turku, Rehtorinpellonkatu 3, FI-20500 Turku (Finland); Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland)

    2012-04-01

    There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet spot of speed, accuracy and user friendliness. This has been achieved by using the Python language with the PyCUDA interface to make a program that is easy to adapt to different scalar field models. In this paper we derive the symplectic dynamics that govern the evolution of the system and then present the implementation of the program in Python and PyCUDA. The functionality of the program is tested in a chaotic inflation preheating model, a single field oscillon case and in a supersymmetric curvaton model which leads to Q-ball production. We have also compared the performance of a consumer graphics card to a professional Tesla compute card in these simulations. We find that the program is not only accurate but also very fast. To further increase the usefulness of the program we have equipped it with numerous post-processing functions that provide useful information about the cosmological model. These include various spectra and statistics of the fields. The program can be additionally used to calculate the generated curvature perturbation. The program is publicly available under GNU General Public License at https://github.com/jtksai/PyCOOL. Some additional information can be found from http://www.physics.utu.fi/tiedostot/theory/particlecosmology/pycool/.

  1. AIMBAT: A Python/Matplotlib Tool for Measuring Teleseismic Arrival Times

    NASA Astrophysics Data System (ADS)

    Lou, X.; van der Lee, S.; Lloyd, S.

    2013-12-01

    Python is an open-source, platform-independent, and object-oriented scripting language. It became more popular in the seismologist community since the appearance of ObsPy (Beyreuther et al. 2010, Megies et al. 2011), which provides a powerful framework for seismic data access and processing. This study introduces a new Python-based tool named AIMBAT (Automated and Interactive Measurement of Body-wave Arrival Times) for measuring teleseismic body-wave arrival times on large-scale seismic event data (Lou et al. 2013). Compared to ObsPy, AIMBAT is a lighter tool that is more focused on a particular aspect of seismic data processing. It originates from the widely used MCCC (Multi-Channel Cross-Correlation) method developed by VanDecar and Crosson (1990). On top of the original MCCC procedure, AIMBAT is automated in initial phase picking and is interactive in quality control. The core cross-correlation function is implemented in Fortran to boost up performance in addition to Python. The GUI (graphical user interface) of AIMBAT depends on Matplotlib's GUI-neutral widgets and event-handling API. A number of sorting and (de)selecting options are designed to facilitate the quality control of seismograms. By using AIMBAT, both relative and absolute teleseismic body-wave arrival times are measured. AIMBAT significantly improves efficiency and quality of the measurements. User interaction is needed only to pick the target phase arrival and to set a time window on the array stack. The package is easy to install and use, open-source, and is publicly available. Graphical user interface of AIMBAT.

  2. Development of Conceptual Benchmark Models to Evaluate Complex Hydrologic Model Calibration in Managed Basins Using Python

    NASA Astrophysics Data System (ADS)

    Hughes, J. D.; White, J.

    2013-12-01

    For many numerical hydrologic models it is a challenge to quantitatively demonstrate that complex models are preferable to simpler models. Typically, a decision is made to develop and calibrate a complex model at the beginning of a study. The value of selecting a complex model over simpler models is commonly inferred from use of a model with fewer simplifications of the governing equations because it can be time consuming to develop another numerical code with data processing and parameter estimation functionality. High-level programming languages like Python can greatly reduce the effort required to develop and calibrate simple models that can be used to quantitatively demonstrate the increased value of a complex model. We have developed and calibrated a spatially-distributed surface-water/groundwater flow model for managed basins in southeast Florida, USA, to (1) evaluate the effect of municipal groundwater pumpage on surface-water/groundwater exchange, (2) investigate how the study area will respond to sea-level rise, and (3) explore combinations of these forcing functions. To demonstrate the increased value of this complex model, we developed a two-parameter conceptual-benchmark-discharge model for each basin in the study area. The conceptual-benchmark-discharge model includes seasonal scaling and lag parameters and is driven by basin rainfall. The conceptual-benchmark-discharge models were developed in the Python programming language and used weekly rainfall data. Calibration was implemented with the Broyden-Fletcher-Goldfarb-Shanno method available in the Scientific Python (SciPy) library. Normalized benchmark efficiencies calculated using output from the complex model and the corresponding conceptual-benchmark-discharge model indicate that the complex model has more explanatory power than the simple model driven only by rainfall.

  3. GPUs and Python: A Recipe for Lightning-Fast Data Pipelines

    NASA Astrophysics Data System (ADS)

    Warner, C.; Packham, C.; Eikenberry, S. S.; Gonzalez, A.

    2012-09-01

    As arrays increase their pixel numbers and mosaics of arrays become more prevalent, the volume of data being produced per night is increasing rapidly. As we look forward to the LSST era, where 30TB of data per night will be produced, streamlined and rapid data reduction processes are becoming critical. Recent developments in the computer industry have led to the production of Graphics Processing Units (GPUs) which can contain hundreds of processing cores, each of which can process hundreds of threads concurrently. Nvidia's Compute Unified Device Architecture (CUDA) platform has allowed developers to take advantage of these modern GPUs and design massively parallel algorithms which can provide huge speed-ups of up to around a factor of 100 over CPU implementations. Data pipelines are perfectly suited to reap the benefits of massive parallelization because many of the algorithms in data processing are performed on a per-pixel basis on ever larger sets of images. In addition, the PyCUDA (http://mathema.tician.de/software/pycuda) module and python native C-API allow for CUDA code to be easily integrated into python code. Python has continued to gain momentum in the astronomical community, particularly as an attractive alternative to IDL or C code for data pipelines. Thus, the ability to link GPU-optimized CUDA code directly into python allows for existing data pipeline frameworks to be reused with new parallel algorithms. We present the initial results of parallelizing many of the more CPU-intensive algorithms in the Florida Analysis Tool Born Of Yearning for high quality scientific data (FATBOY) and discuss the implications for the future of data pipelines. We use an Nvidia 580 GTX GPU for our tests and find that the 580 GTX produces a speed-up of anywhere from a factor of around 10 up to a factor of 300 over CPU implementations for individual routines. We believe that it is possible to obtain an overall pipeline speed gain of a factor of 10-25 over traditionally built data pipelines. A speed gain of this magnitude would for the first time allow for near real-time data processing - data sets that previously required hours to process could be reduced in minutes concurrent with continuing observations, considerably optimizing the observational process.

  4. Digesting pythons quickly oxidize the proteins in their meals and save the lipids for later.

    PubMed

    McCue, Marshall D; Guzman, R Marena; Passement, Celeste A

    2015-07-01

    Pythons digesting rodent meals exhibit up to 10-fold increases in their resting metabolic rate (RMR); this increase in RMR is termed specific dynamic action (SDA). Studies have shown that SDA is partially fueled by oxidizing dietary nutrients, yet it remains unclear whether the proteins and the lipids in their meals contribute equally to this energy demand. We raised two populations of mice on diets labeled with either [(13)C]leucine or [(13)C]palmitic acid to intrinsically enrich the proteins and lipids in their bodies, respectively. Ball pythons (Python regius) were fed whole mice (and pureed mice 3 weeks later), after which we measured their metabolic rates and the ?(13)C in the breath. The ?(13)C values in the whole bodies of the protein- and lipid-labeled mice were generally similar (i.e. 5.7±4.7‰ and 2.8±5.4‰, respectively) but the oxidative kinetics of these two macronutrient pools were quite different. We found that the snakes oxidized 5% of the protein and only 0.24% of the lipids in their meals within 14?days. Oxidation of the dietary proteins peaked 24?h after ingestion, at which point these proteins provided ?90% of the metabolic requirement of the snakes, and by 14?days the oxidation of these proteins decreased to nearly zero. The oxidation of the dietary lipids peaked 1 day later, at which point these lipids supplied ?25% of the energy demand. Fourteen days after ingestion, these lipids were still being oxidized and continued to account for ?25% of the metabolic rate. Pureeing the mice reduced the cost of gastric digestion and decreased SDA by 24%. Pureeing also reduced the oxidation of dietary proteins by 43%, but it had no effect on the rates of dietary lipid oxidation. Collectively, these results demonstrate that pythons are able to effectively partition the two primary metabolic fuels in their meals. This approach of uniquely labeling the different components of the diet will allow researchers to examine new questions about how and when animals use the nutrients in their meals. PMID:25987734

  5. ObsPy: A Python toolbox for Seismology, a Data Center Perspective

    NASA Astrophysics Data System (ADS)

    Beyreuther, Moritz; Barsch, Robert; Krischer, Lion; Megies, Tobias; Behr, Yannik; Wassermann, Joachim

    2010-05-01

    ObsPy: A Python toolbox for seismology (http://www.obspy.org) aims at filling the gap between interactive analysis and automatic data acquistion systems. Automatic batch analysis of continuous data streams or feeding a so far unknown formatted data stream into an acquistion system are two possible applications. Python provides a platform independent, free and open source interpreter language including a large collection of scientific open-source modules thus allowing rapid development of prototype code. ObsPy extends Python by providing the seismologist with basic seismological routines, e.g. MiniSEED, SAC, GSE2 read and write support, various pickers, filters, instrument correction... The data itself is stored in numpy.ndarrays allowing powerful numerical array-programming modules like NumPy (http://numpy.scipy.org) or SciPy (http://scipy.org) to be used. Also SeisComP3 has a Python API which makes use of the previous mentioned modules, thus making it easy to extend SeisComP3 with the help of the ObsPy library. Especially for data centers the ObsPy ArcLink and XSEED modules are of special interest. The ArcLink module makes it possible to easily automatically access the data via ArcLink or for testing the servers functionality. The XSEED module allows to convert data from dataless SEED to XML-SEED and back. The XML-SEED format is very verbose and easy extensible for internal purposes. For "public" distribution the resulting extended XML-SEED can always be converted back to the standard exchange format dataless SEED (loosing the additionally fields). An application of ObsPy is running on the Azores. Here, seismic data are continuous recorded with National Instruments digitizers which are writing data in an binary format every 10s. ObsPy is used to feed the data in EarthWorm and SeisComP3 by decoding the binary format every 30s and appending the new data to a MiniSEED file. The MiniSEED file is continuously scanned by the mseed_scan module of the seedlink server and allows EarthWorm as well as SeisComP3 to access the data.

  6. cloudPEST - A python module for cloud-computing deployment of PEST, a program for parameter estimation

    USGS Publications Warehouse

    Fienen, Michael N.; Kunicki, Thomas C.; Kester, Daniel E.

    2011-01-01

    This report documents cloudPEST-a Python module with functions to facilitate deployment of the model-independent parameter estimation code PEST on a cloud-computing environment. cloudPEST makes use of low-level, freely available command-line tools that interface with the Amazon Elastic Compute Cloud (EC2(TradeMark)) that are unlikely to change dramatically. This report describes the preliminary setup for both Python and EC2 tools and subsequently describes the functions themselves. The code and guidelines have been tested primarily on the Windows(Registered) operating system but are extensible to Linux(Registered).

  7. PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data

    PubMed Central

    Hanke, Michael; Halchenko, Yaroslav O.; Sederberg, Per B.; Hanson, Stephen José; Haxby, James V.; Pollmann, Stefan

    2009-01-01

    Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine-learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability. PMID:19184561

  8. A multi-model Python wrapper for operational oil spill transport forecasts

    NASA Astrophysics Data System (ADS)

    Hou, X.; Hodges, B. R.; Negusse, S.; Barker, C.

    2015-01-01

    The Hydrodynamic and oil spill modeling system for Python (HyosPy) is presented as an example of a multi-model wrapper that ties together existing models, web access to forecast data and visualization techniques as part of an adaptable operational forecast system. The system is designed to automatically run a continual sequence of hindcast/forecast hydrodynamic models so that multiple predictions of the time-and-space-varying velocity fields are already available when a spill is reported. Once the user provides the estimated spill parameters, the system runs multiple oil spill prediction models using the output from the hydrodynamic models. As new wind and tide data become available, they are downloaded from the web, used as forcing conditions for a new instance of the hydrodynamic model and then applied to a new instance of the oil spill model. The predicted spill trajectories from multiple oil spill models are visualized through Python methods invoking Google MapTM and Google EarthTM functions. HyosPy is designed in modules that allow easy future adaptation to new models, new data sources or new visualization tools.

  9. Using Python to generate AHPS-based precipitation simulations over CONUS using Amazon distributed computing

    NASA Astrophysics Data System (ADS)

    Machalek, P.; Kim, S. M.; Berry, R. D.; Liang, A.; Small, T.; Brevdo, E.; Kuznetsova, A.

    2012-12-01

    We describe how the Climate Corporation uses Python and Clojure, a language impleneted on top of Java, to generate climatological forecasts for precipitation based on the Advanced Hydrologic Prediction Service (AHPS) radar based daily precipitation measurements. A 2-year-long forecasts is generated on each of the ~650,000 CONUS land based 4-km AHPS grids by constructing 10,000 ensembles sampled from a 30-year reconstructed AHPS history for each grid. The spatial and temporal correlations between neighboring AHPS grids and the sampling of the analogues are handled by Python. The parallelization for all the 650,000 CONUS stations is further achieved by utilizing the MAP-REDUCE framework (http://code.google.com/edu/parallel/mapreduce-tutorial.html). Each full scale computational run requires hundreds of nodes with up to 8 processors each on the Amazon Elastic MapReduce (http://aws.amazon.com/elasticmapreduce/) distributed computing service resulting in 3 terabyte datasets. We further describe how we have productionalized a monthly run of the simulations process at full scale of the 4km AHPS grids and how the resultant terabyte sized datasets are handled.

  10. Species identification of protected carpet pythons suitable for degraded forensic samples.

    PubMed

    Ciavaglia, Sherryn; Donnellan, Stephen; Henry, Julianne; Linacre, Adrian

    2014-09-01

    In this paper we report on the identification of a section of mitochondrial DNA that can be used to identify the species of protected and illegally traded pythons of the genus Morelia. Successful enforcement of wildlife laws requires forensic tests that can identify the species nominated in the relevant legislation. The potentially degraded state of evidentiary samples requires that forensic investigation using molecular genetic species identification is optimized to interrogate small fragments of DNA. DNA was isolated from 35 samples of Morelia spilota from which the complete cytochrome b was sequenced. The ND6 gene was also sequenced in 32 of these samples. Additional DNA sequences were generated from 9 additional species of Morelia. The sequences were aligned by Geneious and imported into MEGA to create phylogenetic trees based on the entire complex of approximately 1,706 base pairs (bp). To mimic degraded DNA, which is usually found in forensic cases, short sub-sections of the full alignment were used to generate phylogenetic trees. The sub-sections that had the greatest DNA sequence information were in parts of the cytochrome b gene. Our results highlight that legislation is presently informed by inadequate taxonomy. We demonstrated that a 278 bp region of the cytochrome b gene recovered the topology of the phylogenetic tree found with the entire gene sequence and correctly identified species of Morelia with a high degree of confidence. The locus described in this report will assist in the successful prosecution of alleged illegal trade in python species. PMID:24915762

  11. Multi-resolution Image Registration Algorithm (MIRA): Robust Automated Image Registration Using Python

    NASA Astrophysics Data System (ADS)

    Hack, W. J.; Dencheva, N.

    2007-10-01

    A primary problem with combining images taken at different epochs is the difficulty in determining the offset between the images in an automated manner. Automated multi-scale techniques have been adopted for use in aligning images taken with ground-based telescopes with great success. However, several characteristics of Hubble Space Telescope (HST) images made direct application of the ground-based multi-scale techniques problematic. This paper describes how an algorithm developed for automated image alignment of Earth observing satellite imagery was merged with a multi-scale analysis of the images to produce a new image registration task. This task was developed using Python, with C extensions for efficiency, and has undergone initial testing to successfully align HST images of the core of 47Tuc and, separately, mosaics of HST images of the Orion Nebula without any differences in the parameter settings. More work needs to be done to improve the run time and to generalize it to work on non-HST images before making it publicly available on all platforms which run Python.

  12. Optimization of Industrial Code with Python: Development of a Graphical User Interface A SURE project by Nicholas Speal

    E-print Network

    Barthelat, Francois

    Optimization of Industrial Code with Python: Development of a Graphical User Interface A SURE phenomenon under a variety of conditions Objective ·To design a graphical user interface (GUI) to facilitate that allows a user to specify simulation parameters, launch routines, and then interpret the feedback provided

  13. An ecological risk assessment of nonnative boas and pythons as potentially invasive species in the United States.

    PubMed

    Reed, Robert N

    2005-06-01

    The growing international trade in live wildlife has the potential to result in continuing establishment of nonnative animal populations in the United States. Snakes may pose particularly high risks as potentially invasive species, as exemplified by the decimation of Guam's vertebrate fauna by the accidentally introduced brown tree snake. Herein, ecological and commercial predictors of the likelihood of establishment of invasive populations were used to model risk associated with legal commercial imports of 23 species of boas, pythons, and relatives into the United States during the period 1989-2000. Data on ecological variables were collected from multiple sources, while data on commercial variables were collated from import records maintained by the U.S. Fish and Wildlife Service. Results of the risk-assessment models indicate that species including boa constrictors (Boa constrictor), ball pythons (Python regius), and reticulated pythons (P. reticulatus) may pose particularly high risks as potentially invasive species. Recommendations for reducing risk of establishment of invasive populations of snakes and/or pathogens include temporary quarantine of imports to increase detection rates of nonnative pathogens, increasing research attention to reptile pathogens, reducing the risk that nonnative snakes will reach certain areas with high numbers of federally listed species (such as the Florida Keys), and attempting to better educate individuals purchasing reptiles. PMID:16022706

  14. Escript: Open Source Environment For Solving Large-Scale Geophysical Joint Inversion Problems in Python

    NASA Astrophysics Data System (ADS)

    Gross, Lutz; Altinay, Cihan; Fenwick, Joel; Smith, Troy

    2014-05-01

    The program package escript has been designed for solving mathematical modeling problems using python, see Gross et al. (2013). Its development and maintenance has been funded by the Australian Commonwealth to provide open source software infrastructure for the Australian Earth Science community (recent funding by the Australian Geophysical Observing System EIF (AGOS) and the AuScope Collaborative Research Infrastructure Scheme (CRIS)). The key concepts of escript are based on the terminology of spatial functions and partial differential equations (PDEs) - an approach providing abstraction from the underlying spatial discretization method (i.e. the finite element method (FEM)). This feature presents a programming environment to the user which is easy to use even for complex models. Due to the fact that implementations are independent from data structures simulations are easily portable across desktop computers and scalable compute clusters without modifications to the program code. escript has been successfully applied in a variety of applications including modeling mantel convection, melting processes, volcanic flow, earthquakes, faulting, multi-phase flow, block caving and mineralization (see Poulet et al. 2013). The recent escript release (see Gross et al. (2013)) provides an open framework for solving joint inversion problems for geophysical data sets (potential field, seismic and electro-magnetic). The strategy bases on the idea to formulate the inversion problem as an optimization problem with PDE constraints where the cost function is defined by the data defect and the regularization term for the rock properties, see Gross & Kemp (2013). This approach of first-optimize-then-discretize avoids the assemblage of the - in general- dense sensitivity matrix as used in conventional approaches where discrete programming techniques are applied to the discretized problem (first-discretize-then-optimize). In this paper we will discuss the mathematical framework for inversion and appropriate solution schemes in escript. We will also give a brief introduction into escript's open framework for defining and solving geophysical inversion problems. Finally we will show some benchmark results to demonstrate the computational scalability of the inversion method across a large number of cores and compute nodes in a parallel computing environment. References: - L. Gross et al. (2013): Escript Solving Partial Differential Equations in Python Version 3.4, The University of Queensland, https://launchpad.net/escript-finley - L. Gross and C. Kemp (2013) Large Scale Joint Inversion of Geophysical Data using the Finite Element Method in escript. ASEG Extended Abstracts 2013, http://dx.doi.org/10.1071/ASEG2013ab306 - T. Poulet, L. Gross, D. Georgiev, J. Cleverley (2012): escript-RT: Reactive transport simulation in Python using escript, Computers & Geosciences, Volume 45, 168-176. http://dx.doi.org/10.1016/j.cageo.2011.11.005.

  15. SpacePy - a Python-based library of tools for the space sciences

    SciTech Connect

    Morley, Steven K [Los Alamos National Laboratory; Welling, Daniel T [Los Alamos National Laboratory; Koller, Josef [Los Alamos National Laboratory; Larsen, Brian A [Los Alamos National Laboratory; Henderson, Michael G [Los Alamos National Laboratory

    2010-01-01

    Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above - at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation. SpacePy is a package for Python, targeted at the space sciences, that aims to make basic data analysis, modeling and visualization easier. It builds on the capabilities of the well-known NumPy and MatPlotLib packages. Publication quality output direct from analyses is emphasized. The SpacePy project seeks to promote accurate and open research standards by providing an open environment for code development. In the space physics community there has long been a significant reliance on proprietary languages that restrict free transfer of data and reproducibility of results. By providing a comprehensive, open-source library of widely used analysis and visualization tools in a free, modern and intuitive language, we hope that this reliance will be diminished. SpacePy includes implementations of widely used empirical models, statistical techniques used frequently in space science (e.g. superposed epoch analysis), and interfaces to advanced tools such as electron drift shell calculations for radiation belt studies. SpacePy also provides analysis and visualization tools for components of the Space Weather Modeling Framework - currently this only includes the BATS-R-US 3-D magnetohydrodynamic model and the RAM ring current model - including streamline tracing in vector fields. Further development is currently underway. External libraries, which include well-known magnetic field models, high-precision time conversions and coordinate transformations are wrapped for access from Python using SWIG and f2py. The rest of the tools have been implemented directly in Python. The provision of open-source tools to perform common tasks will provide openness in the analysis methods employed in scientific studies and will give access to advanced tools to all space scientists regardless of affiliation or circumstance.

  16. ABC-SysBio—approximate Bayesian computation in Python with GPU support

    PubMed Central

    Liepe, Juliane; Barnes, Chris; Cule, Erika; Erguler, Kamil; Kirk, Paul; Toni, Tina; Stumpf, Michael P.H.

    2010-01-01

    Motivation: The growing field of systems biology has driven demand for flexible tools to model and simulate biological systems. Two established problems in the modeling of biological processes are model selection and the estimation of associated parameters. A number of statistical approaches, both frequentist and Bayesian, have been proposed to answer these questions. Results: Here we present a Python package, ABC-SysBio, that implements parameter inference and model selection for dynamical systems in an approximate Bayesian computation (ABC) framework. ABC-SysBio combines three algorithms: ABC rejection sampler, ABC SMC for parameter inference and ABC SMC for model selection. It is designed to work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic models can be analyzed in ABC-SysBio. Availability: http://abc-sysbio.sourceforge.net Contact: christopher.barnes@imperial.ac.uk; ttoni@imperial.ac.uk PMID:20591907

  17. Dracunculus mulbus n. sp. (Nematoda: Spirurida) from the water python Liasis fuscus (Serpentes: Boidae) in northern Australia.

    PubMed

    Jones, Hugh I; Mulder, Eridani

    2007-03-01

    A new species of Dracunculus Reichard, 1759 (Nematoda: Spirurida) is described from the tissues surrounding organs in the body-cavity of the water python Liasis fuscus Peters in northern Australia. One to 14 worms were recovered from 22% (27/120) of pythons examined. Males were located principally around the lungs, liver and heart of the hosts, and females were recovered from peritoneal tissue surrounding the intestines and lining the body-cavity. This species differs from previously described species of Dracunculus in the position of the papillae at the posterior end in males, and in the possession of thick, narrow caudal alae. Submedian cephalic papillae are single in both sexes. Dorsal and ventral anterior cephalic papillae are absent in males. This is the first report of a species of Dracunculus from the Australian region. PMID:16972152

  18. Python Processing and Version Control using VisTrails for the Netherlands Hydrological Instrument (Invited)

    NASA Astrophysics Data System (ADS)

    Verkaik, J.

    2013-12-01

    The Netherlands Hydrological Instrument (NHI) model predicts water demands in periods of drought, supporting the Dutch decision makers in taking operational as well as long-term decisions with respect to the water supply. Other applications of NHI are predicting fresh-salt interaction, nutrient loadings, and agriculture change. The NHI model consists of several coupled models: a saturated groundwater model (MODFLOW), an unsaturated groundwater model (MetaSWAP), a sub-catchment surface water model (MOZART), and a distribution network of surface waters model (DM/SOBEK). Each of these models requires specific, usually large, input data that may be the result of sophisticated schematization workflows. Input data can also be dependent on each other, for example, the precipitation data is input for the unsaturated zone model (cells) as well as for the surface water models (polygons). For efficient data management, we developed several Python tools such that the modeler or stakeholder can use the model in a user-friendly manner, and data is managed in a consistent, transparent and reproducible way. Two open source Python tools are presented here: the data version control module for the workflow manager VisTrails called FileSync, and the NHI model control script that uses FileSync. VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. Since VisTrails does not directly support version control we developed a version control module called FileSync. With this generic module, the user can synchronize data from and to his workflow through a dialog window. The FileSync dialog calls the FileSync script that is command-line based and performs the actual data synchronization. This script allows the user to easily create a model repository, upload and download data, create releases and define scenarios. The data synchronization approach applied here differs from systems as Subversion or Git, since these systems do not perform well for large (binary) model data files. For this reason, a new concept of parameterization and data splitting has been implemented. Each file, or set of files, is uniquely labeled as a parameter, and for this parameter metadata is maintained by Subversion. The metadata data contains file hashes to identify data content and the location where the actual bulk data are stored that can be reached by FTP. The NHI model control script is a command-line driven Python script for pre-processing, running, and post-processing the NHI model and uses one single configuration file for all computational kernels. This configuration file is an easy-to-use, keyword-driven, Windows INI-file, having separate sections for all the kernels. It also includes a FileSync data section where the user can specify version controlled model data to be used as input. The NHI control script keeps all the data consistent during the pre-processing. Furthermore, this script is able to do model state handling when the NHI model is used for ensemble forecasting.

  19. Using the Python language and the CMOR2 library to create PMIPn-CMIPn compliant model output

    NASA Astrophysics Data System (ADS)

    Peterschmitt, Jean-Yves; Doutriaux, Charles

    2015-04-01

    The Paleoclimate Modelling Intercomparison Project (PMIP) is a long standing initiative that has provided an efficient mechanism for coordinating paleoclimate modelling activities that provide valuable information on the mechanisms of climate change, the identification of key feedbacks operating in the climate system and, through model evaluation, the capability of climate models to reproduce climates different from today. The third phase of PMIP (aka PMIP 3) started in 2009 (the fourth phase is about to start) and followed the requirements specified by CMIP5 (Coupled Model Intercomparison Project). Generating data files following strict Model Intercomparison Projects (MIPs) standards (NetCDF format, file and variable names, file structure, metadata information, directory hierarchy, etc…) has been a key to the success of many recent Model Intercomparison Projects. It is unfortunately not always easy to convert proprietary model output format to the required standards, and this has prevented some smaller modelling groups from sharing their data. We will present how the Python version of the CMOR2 (Climate Model Output Rewriter) library bundled with the UV-CDAT Python distribution (Ultrascale Visualization Climate Data Analysis Tools) can be used to easily convert raw model output to the appropriate MIP shareable format. References: http://pmip3.lsce.ipsl.fr/ http://cmip-pcmdi.llnl.gov/cmip5/output_req.html http://www2-pcmdi.llnl.gov/cmor http://uvcdat.llnl.gov/ https://www.python.org/

  20. FMC: a one-liner Python program to manage, classify and plot focal mechanisms

    NASA Astrophysics Data System (ADS)

    Álvarez-Gómez, José A.

    2014-05-01

    The analysis of earthquake focal mechanisms (or Seismic Moment Tensor, SMT) is a key tool on seismotectonics research. Each focal mechanism is characterized by several location parameters of the earthquake hypocenter, the earthquake size (magnitude and scalar moment tensor) and some geometrical characteristics of the rupture (nodal planes orientations, SMT components and/or SMT main axes orientations). The aim of FMC is to provide a simple but powerful tool to manage focal mechanism data. The data should be input to the program formatted as one of two of the focal mechanisms formatting options of the GMT (Generic Mapping Tools) package (Wessel and Smith, 1998): the Harvard CMT convention and the single nodal plane Aki and Richards (1980) convention. The former is a SMT format that can be downloaded directly from the Global CMT site (http://www.globalcmt.org/), while the later is the simplest way to describe earthquake rupture data. FMC is programmed in Python language, which is distributed as Open Source GPL-compatible, and therefore can be used to develop Free Software. Python runs on almost any machine, and has a wide support and presence in any operative system. The program has been conceived with the modularity and versatility of the classical UNIX-like tools. Is called from the command line and can be easily integrated into shell scripts (*NIX systems) or batch files (DOS/Windows systems). The program input and outputs can be done by means of ASCII files or using standard input (or redirection "<"), standard output (screen or redirection ">") and pipes ("|"). By default FMC will read the input and write the output as a Harvard CMT (psmeca formatted) ASCII file, although other formats can be used. Optionally FMC will produce a classification diagram representing the rupture type of the focal mechanisms processed. In order to count with a detailed classification of the focal mechanisms I decided to classify the focal mechanism in a series of fields that include the oblique slip regimes. This approximation is similar to the Johnston et al. (1994) classification; with 7 classes of earthquakes: 1) Normal; 2) Normal - Strike-slip; 3) Strike-slip - Normal; 4) Strike-slip; 5) Strike-slip - Reverse; 6) Reverse - strike-slip and 7) Reverse. FMC uses by default this classification in the resulting diagram, based on the Kaverina et al. (1996) projection, which improves the Frohlich and Apperson (1992) ternary diagram.

  1. A World Without Referees Larry Wasserman1

    E-print Network

    that the stamp of approval by having a paper accepted by the refereeing process is crucial for maintaining having papers rejected because of unfair referee reports. Some of this can be written off as sour grapes seen many cases where one referee rejected a paper and another equally qualified referee accepted it. I

  2. Living History of Physiology: Karlman Wasserman

    NSDL National Science Digital Library

    2009-10-01

    In 2005, the American Physiological Society (APS) initiated the Living History Project to recognize senior members who have made extraordinary contributions during their career to the advancement of the discipline and profession of physiology. The videos provided to date focus on the physiologist's training, careers and their professional interactions.

  3. Quantity or quality? Determinants of maternal reproductive success in tropical pythons (Liasis fuscus)

    PubMed Central

    Madsen, T.; Shine, R.

    1998-01-01

    A female's reproductive output (size and number of offspring) may say little about her reproductive success; the 'quality' of her progeny and the time that they are produced may be more important in this respect. We marked and released 1224 hatchling water pythons (Liasis fuscus) from 116 clutches of laboratory-incubated eggs, in a study site in tropical Australia. Clutches varied widely in the number of eggs, mean offspring sizes, the proportion of eggs that hatched, and recapture rates of offspring. Clutch size was not significantly correlated with the number of recaptured hatchlings in either year, nor was mean offspring size related to recapture probability. Instead, offspring recapture rates varied as a function of the time of hatching. Recapture rates were higher for hatchlings released in a year with high prey availability than in a year with few prey. In addition, recapture rates were higher for earlier-hatching clutches in the year with few prey. The other significant effect on recapture rates involved offspring viability: some clutches had a much higher proportion of surviving offspring than did others, and recapture rates were higher from clutches with higher hatching success (i.e. proportion of eggs hatching). Hence, the usual measures of reproductive output (clutch size and offspring size) offer only a poor index of a female's reproductive success in this system.

  4. The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation

    SciTech Connect

    Foley, Samantha S [ORNL; Elwasif, Wael R [ORNL; Bernholdt, David E [ORNL

    2011-11-01

    High-fidelity coupled multiphysics simulations are an increasingly important aspect of computational science. In many domains, however, there has been very limited experience with simulations of this sort, therefore research in coupled multiphysics often requires computational frameworks with significant flexibility to respond to the changing directions of the physics and mathematics. This paper presents the Integrated Plasma Simulator (IPS), a framework designed for loosely coupled simulations of fusion plasmas. The IPS provides users with a simple component architecture into which a wide range of existing plasma physics codes can be inserted as components. Simulations can take advantage of multiple levels of parallelism supported in the IPS, and can be controlled by a high-level ``driver'' component, or by other coordination mechanisms, such as an asynchronous event service. We describe the requirements and design of the framework, and how they were implemented in the Python language. We also illustrate the flexibility of the framework by providing examples of different types of simulations that utilize various features of the IPS.

  5. ScalPy: A Python Package For Late Time Scalar Field Cosmology

    E-print Network

    Kumar, Sumit; Sen, Anjan A

    2015-01-01

    We present a python package "ScalPy" for studying the late time scalar field cosmology for a wide variety of scalar field models, namely the quintessence, tachyon and Galileon model. The package solves the autonomous system of equations for power law and exponential potential. But it can be easily generalized to add more complicated potential. For completeness, we also include the standard parameterization for dark energy models, e.g. the $\\Lambda$CDM, $w$CDM, $w_{0}w_{a}$CDM as well as the GCG parameterization. The package also solves the linear growth equation for matter perturbations on sub-horizon scales. All the important observables related to background universe as well as to the perturbed universe, e.g. luminosity distance ($D_{L}(z)$), angular diameter distance ($D_{A}(z)$), normalized Hubble parameter ($h(z)$), lookback time ($t_{L}$), equation of state for the dark energy ($w(z)$), growth rate ($f=\\frac{d \\ln\\delta}{d \\ln a}$), linear matter power spectra ($P(k)$), and its normalization $\\sigma_{8}...

  6. Analysis and Visualization of Multi-Scale Astrophysical Simulations using Python and NumPy

    SciTech Connect

    Turk, M.; /KIPAC, Menlo Park

    2008-09-30

    The study the origins of cosmic structure requires large-scale computer simulations beginning with well-constrained, observationally-determined, initial conditions. We use Adaptive Mesh Refinement to conduct multi-resolution simulations spanning twelve orders of magnitude in spatial dimensions and over twenty orders of magnitude in density. These simulations must be analyzed and visualized in a manner that is fast, accurate, and reproducible. I present 'yt,' a cross-platform analysis toolkit written in Python. 'yt' consists of a data-management layer for transporting and tracking simulation outputs, a plotting layer, a parallel analysis layer for handling mesh-based and particle-based data, as well as several interfaces. I demonstrate how the origins of cosmic structure--from the scale of clusters of galaxies down to the formation of individual stars--can be analyzed and visualized using a NumPy-based toolkit. Additionally, I discuss efforts to port this analysis code to other adaptive mesh refinement data formats, enabling direct comparison of data between research groups using different methods to simulate the same objects.

  7. Dispel4py: An Open-Source Python library for Data-Intensive Seismology

    NASA Astrophysics Data System (ADS)

    Filgueira, Rosa; Krause, Amrey; Spinuso, Alessandro; Klampanos, Iraklis; Danecek, Peter; Atkinson, Malcolm

    2015-04-01

    Scientific workflows are a necessary tool for many scientific communities as they enable easy composition and execution of applications on computing resources while scientists can focus on their research without being distracted by the computation management. Nowadays, scientific communities (e.g. Seismology) have access to a large variety of computing resources and their computational problems are best addressed using parallel computing technology. However, successful use of these technologies requires a lot of additional machinery whose use is not straightforward for non-experts: different parallel frameworks (MPI, Storm, multiprocessing, etc.) must be used depending on the computing resources (local machines, grids, clouds, clusters) where applications are run. This implies that for achieving the best applications' performance, users usually have to change their codes depending on the features of the platform selected for running them. This work presents dispel4py, a new open-source Python library for describing abstract stream-based workflows for distributed data-intensive applications. Special care has been taken to provide dispel4py with the ability to map abstract workflows to different platforms dynamically at run-time. Currently dispel4py has four mappings: Apache Storm, MPI, multi-threading and sequential. The main goal of dispel4py is to provide an easy-to-use tool to develop and test workflows in local resources by using the sequential mode with a small dataset. Later, once a workflow is ready for long runs, it can be automatically executed on different parallel resources. dispel4py takes care of the underlying mappings by performing an efficient parallelisation. Processing Elements (PE) represent the basic computational activities of any dispel4Py workflow, which can be a seismologic algorithm, or a data transformation process. For creating a dispel4py workflow, users only have to write very few lines of code to describe their PEs and how they are connected by using Python, which is widely supported on many platforms and is popular in many scientific domains, such as in geosciences. Once, a dispel4py workflow is written, a user only has to select which mapping they would like to use, and everything else (parallelisation, distribution of data) is carried on by dispel4py without any cost to the user. Among all dispel4py features we would like to highlight the following: * The PEs are connected by streams and not by writing to and reading from intermediate files, avoiding many IO operations. * The PEs can be stored into a registry. Therefore, different users can recombine PEs in many different workflows. * dispel4py has been enriched with a provenance mechanism to support runtime provenance analysis. We have adopted the W3C-PROV data model, which is accessible via a prototypal browser-based user interface and a web API. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data, which may be selectively stored at runtime, into dedicated data archives. dispel4py has been already used by seismologists in the VERCE project to develop different seismic workflows. One of them is the Seismic Ambient Noise Cross-Correlation workflow, which preprocesses and cross-correlates traces from several stations. First, this workflow was tested on a local machine by using a small number of stations as input data. Later, it was executed on different parallel platforms (SuperMUC cluster, and Terracorrelator machine), automatically scaling up by using MPI and multiprocessing mappings and up to 1000 stations as input data. The results show that the dispel4py achieves scalable performance in both mappings tested on different parallel platforms.

  8. A novel protein from the serum of Python sebae, structurally homologous with type-? phospholipase A(2) inhibitor, displays antitumour activity.

    PubMed

    Donnini, Sandra; Finetti, Federica; Francese, Simona; Boscaro, Francesca; Dani, Francesca R; Maset, Fabio; Frasson, Roberta; Palmieri, Michele; Pazzagli, Mario; De Filippis, Vincenzo; Garaci, Enrico; Ziche, Marina

    2011-12-01

    Cytotoxic and antitumour factors have been documented in the venom of snakes, although little information is available on the identification of cytotoxic products in snake serum. In the present study, we purified and characterized a new cytotoxic factor from serum of the non-venomous African rock python (Python sebae), endowed with antitumour activity. PSS (P. sebae serum) exerted a cytotoxic activity and reduced dose-dependently the viability of several different tumour cell lines. In a model of human squamous cell carcinoma xenograft (A431), subcutaneous injection of PSS in proximity of the tumour mass reduced the tumour volume by 20%. Fractionation of PSS by ion-exchange chromatography yielded an active protein fraction, F5, which significantly reduced tumour cell viability in vitro and, strikingly, tumour growth in vivo. F5 is composed of P1 (peak 1) and P2 subunits interacting in a 1:1 stoichiometric ratio to form a heterotetramer in equilibrium with a hexameric form, which retained biological activity only when assembled. The two peptides share sequence similarity with PIP {PLI-? [type-? PLA(2) (phospholipase A(2)) inhibitor] from Python reticulatus}, existing as a homohexamer. More importantly, although PIP inhibits the hydrolytic activity of PLA(2), the anti-PLA(2) function of F5 is negligible. Using high-resolution MS, we covered 87 and 97% of the sequences of P1 and P2 respectively. In conclusion, in the present study we have identified and thoroughly characterized a novel protein displaying high sequence similarity to PLI-? and possessing remarkable cytotoxic and antitumour effects that can be exploited for potential pharmacological applications. PMID:21834793

  9. Distribution of lipids from the yolk to the tissues during development of the water python (Liasis fuscus).

    PubMed

    Speake, B K; Thompson, M B; Thacker, F E; Bedford, G S

    2003-09-01

    Energy metabolism during embryonic development of snakes differs in several respects from the patterns displayed by other reptiles. There are, however, no previous reports describing the main energy source for development, the yolk lipids, in snake eggs. There is also no information on the distribution of yolk fatty acids to the tissues during snake development. In eggs of the water python ( Liasis fuscus), we report that triacylglycerol, phospholipid, cholesteryl ester and free cholesterol, respectively, form 70.3%, 14.1%, 5.7% and 2.1% of the total lipid. The main polyunsaturate of the yolk lipid classes is 18:2n-6. The yolk phospholipid contains 20:4n-6 and 22:6n-3 at 13.0% and 3.6% (w/w), respectively. Approximately 10% and 30% of the initial egg lipids are respectively recovered in the residual yolk and the fat body of the hatchling. A major function of yolk lipid is, therefore, to provision the neonate with large energy reserves. The proportion of 22:6n-3 in brain phospholipid of the hatchling is 11.1% (w/w): this represents only 0.24% of the amount of 22:6n-3 originally present in the egg. This also contrasts with values for free-living avian species where the proportion of DHA in neonatal brain phospholipid is 16-19%. In the liver of the newly hatched python, triacylglycerol, phospholipid and cholesteryl ester, respectively, form 68.2%, 7.7% and 14.3% of total lipid. This contrasts with embryos of birds where cholesteryl ester forms up to 80% of total liver lipid and suggests that the mechanism of lipid transfer in the water python embryo differs in some respects from the avian situation. PMID:12827419

  10. Annotated checklist of the recent and extinct pythons (Serpentes, Pythonidae), with notes on nomenclature, taxonomy, and distribution

    PubMed Central

    Schleip, Wulf D.; O’Shea, Mark

    2010-01-01

    Abstract McDiarmid et al. (1999) published the first part of their planned taxonomic catalog of the snakes of the world. Since then, several new python taxa have been described in both the scientific literature and non-peer-reviewed publications. This checklist evaluates the nomenclatural status of the names and discusses the taxonomic status of the new taxa, and aims to continue the work of McDiarmid et al. (1999) for the family Pythonidae, covering the period 1999 to 2010. Numerous new taxa are listed, and where appropriate recent synonymies are included and annotations are made. A checklist and a taxonomic identification key of valid taxa are provided. PMID:21594030

  11. Team: Katherine Ahern Zachary Gillen

    E-print Network

    Militzer, Burkhard

    Billing OTHER MEDICAL CENTER Alternate Internet Based View Emergency Department (Manual Input) Clinician STAND-ALONE SYSTEMS HL7 Based Messaging System Other Lab System Inpatient Pharmacy RADIOLOGY Medical Records Coding LABORATORY (GEN/BB/MICRO) Electronic Medical Record System CLINICALS Operating Room GI Lab

  12. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.

    PubMed

    Andrew, Audra L; Card, Daren C; Ruggiero, Robert P; Schield, Drew R; Adams, Richard H; Pollock, David D; Secor, Stephen M; Castoe, Todd A

    2015-05-01

    Snakes provide a unique and valuable model system for studying the extremes of physiological remodeling because of the ability of some species to rapidly upregulate organ form and function upon feeding. The predominant model species used to study such extreme responses has been the Burmese python because of the extreme nature of postfeeding response in this species. We analyzed the Burmese python intestine across a time series, before, during, and after feeding to understand the patterns and timing of changes in gene expression and their relationship to changes in intestinal form and function upon feeding. Our results indicate that >2,000 genes show significant changes in expression in the small intestine following feeding, including genes involved in intestinal morphology and function (e.g., hydrolases, microvillus proteins, trafficking and transport proteins), as well as genes involved in cell division and apoptosis. Extensive changes in gene expression occur surprisingly rapidly, within the first 6 h of feeding, coincide with changes in intestinal morphology, and effectively return to prefeeding levels within 10 days. Collectively, our results provide an unprecedented portrait of parallel changes in gene expression and intestinal morphology and physiology on a scale that is extreme both in the magnitude of changes, as well as in the incredibly short time frame of these changes, with up- and downregulation of expression and function occurring in the span of 10 days. Our results also identify conserved vertebrate signaling pathways that modulate these responses, which may suggest pathways for therapeutic modulation of intestinal function in humans. PMID:25670730

  13. Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages

    PubMed Central

    Nunez-Iglesias, Juan; Kennedy, Ryan; Plaza, Stephen M.; Chakraborty, Anirban; Katz, William T.

    2014-01-01

    The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. PMID:24772079

  14. Review: Giant Constrictors: Biological and Management Profiles and an Establishment Risk Assessment for Nine Large Species of Pythons, Anacondas, and the Boa Constrictor

    Microsoft Academic Search

    Robert N. Reed; Gordon H. Rodda; David G. Barker; Tracy M. Barker

    2010-01-01

    Summary Burmese Pythons may eat Ivory-billed W oodpeckers. As surprising as that statement may seem, it's listed as a genuine possibility in Table 4.2 on page 69 of this report. There is no better illustration of the extraordinary degree of bias and unfounded speculation that comprises the bulk of this report. W e make the following observations to summarize this

  15. SimorLP.,R.Whittaker, andR.Shine. 7999. Morelb spilota(AustraliancarPet python) Caudalluring. HerpetologicalReview 30:102-103.

    E-print Network

    Shine, Rick

    . HerpetologicalReview 30:102-103. MORELIA SPILOTA (Aus.ralian Carpet Pvthon) CAUDAL LURJNG. Snakesof sevnl abovetheheadandcompleted six morevibrations. Weusdframcby-ftame analysisof lhe film to quantifyseveral attsiburesof thetail latrseizedandconsumedby thesnake.Panof thisfilm sequence wasincludedin thecompletedfilm ('Python, TheSly Strangler." RogerWhittakerFilms

  16. Using Python for scientific computing: Efficient and flexible evaluation of the statistical characteristics of functions with multivariate random inputs

    NASA Astrophysics Data System (ADS)

    Chudoba, R.; Sadílek, V.; Rypl, R.; Vo?echovský, M.

    2013-02-01

    This paper examines the feasibility of high-level Python based utilities for numerically intensive applications via an example of a multidimensional integration for the evaluation of the statistical characteristics of a random variable. We discuss the approaches to the implementation of mathematically formulated incremental expressions using high-level scripting code and low-level compiled code. Due to the dynamic typing of the Python language, components of the algorithm can be easily coded in a generic way as algorithmic templates. Using the Enthought Development Suite they can be effectively assembled into a flexible computational framework that can be configured to execute the code for arbitrary combinations of integration schemes and versions of instantiated code. The paper describes the development cycle using a simple running example involving averaging of a random two-parametric function that includes discontinuity. This example is also used to compare the performance of the available algorithmic and executional features. The implemented package including further examples and the results of performance studies have been made available via the free repository [1] and CPCP library. Program summaryProgram title: spirrid Catalogue identifier: AENL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special licence provided by the author No. of lines in distributed program, including test data, etc.: 10722 No. of bytes in distributed program, including test data, etc.: 157099 Distribution format: tar.gz Programming language: Python and C. Computer: PC. Operating system: LINUX, UNIX, Windows. Classification: 4.13, 6.2. External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.com) Nature of problem: Evaluation of the statistical moments of a function of random variables. Solution method: Direct multidimensional integration. Running time: Depending on the number of random variables the time needed for the numerical estimation of the mean value of a function with a sufficiently low level of numerical error varies. For orientation, the time needed for two included examples: examples/fiber_tt_2p/fiber_tt_2p.py with 2 random variables: few milliseconds examples/fiber_po_8p/fiber_po_8p.py with 8 random variables: few seconds

  17. Processing of terabytes of data for seismic noise analysis with the Python codes of the Whisper Suite. (Invited)

    NASA Astrophysics Data System (ADS)

    Briand, X.; Campillo, M.; Brenguier, F.; Boue, P.; Poli, P.; Roux, P.; Takeda, T.

    2013-12-01

    The Whisper Suite, as part of the ERC project Whisper (whisper.obs.ujf-grenoble.fr), is developed with the high-level programming language Python and uses intensively the scientific libraries Scipy and Obspy, which is dedicated to the seismological community (www.obspy.org). The Whisper Suite consists of several tools. It provides a flexible way to specify a pipeline of seismogram processing. The user can define his own sequence of treatments, can use the Python libraries he needs and eventually, can add his processing procedure to the Whisper Suite. Another package is dedicated to the computation of correlations. When dealing with large data set, computational time becomes a major difficulty and we devoted a lot of efforts to make possible the fast processing of the large data sets produced by the present day dense seismic networks. With the Whisper Suite, we manage currently more than 150TB of data for ambient noise analysis. For the computations of 68 millions correlations (daily, 5Hz, correlation window 3600s) on a 50 core cluster, with a dedicated disk array, the required time is 4 days. With a distributed storage (Irods) and a grid of clusters (mode best effort), both provided by the University of Grenoble, we compute currently one year of 4-hours correlations for 550 3C stations of the Hi-Net Japanese Network in one day (about 350 millions individual correlations) . Note that the quadratic space complexity can be critical. We developed also codes for the analysis of the correlations. The Whisper Suite is used to make challenging observations using cross-correlation techniques at various scales in the Earth. We present some examples of applications. Using a global data set of available broadband stations, we discuss the emergence of the complete teleseismic body wave wave field, including the deep phases used for imaging of the mantle and the core. The giant 2011 Tohoku-oki earthquake and the records of the dense Hi-Net array offer an opportunity to analyze what are the changes in the elastic properties of the crust at large scale, including the co-seismic non linear response of the shallow layers and the signatures of the different processes affecting the crust at depth, such as postseismic slip and viscoelastic relaxation.

  18. C++QEDv2 Milestone 10: A C++/Python application-programming framework for simulating open quantum dynamics

    NASA Astrophysics Data System (ADS)

    Sandner, Raimar; Vukics, András

    2014-09-01

    The v2 Milestone 10 release of C++QED is primarily a feature release, which also corrects some problems of the previous release, especially as regards the build system. The adoption of C++11 features has led to many simplifications in the codebase. A full doxygen-based API manual [1] is now provided together with updated user guides. A largely automated, versatile new testsuite directed both towards computational and physics features allows for quickly spotting arising errors. The states of trajectories are now savable and recoverable with full binary precision, allowing for trajectory continuation regardless of evolution method (single/ensemble Monte Carlo wave-function or Master equation trajectory). As the main new feature, the framework now presents Python bindings to the highest-level programming interface, so that actual simulations for given composite quantum systems can now be performed from Python. Catalogue identifier: AELU_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELU_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 492422 No. of bytes in distributed program, including test data, etc.: 8070987 Distribution format: tar.gz Programming language: C++/Python. Computer: i386-i686, x86 64. Operating system: In principle cross-platform, as yet tested only on UNIX-like systems (including Mac OS X). RAM: The framework itself takes about 60MB, which is fully shared. The additional memory taken by the program which defines the actual physical system (script) is typically less than 1MB. The memory storing the actual data scales with the system dimension for state-vector manipulations, and the square of the dimension for density-operator manipulations. This might easily be GBs, and often the memory of the machine limits the size of the simulated system. Classification: 4.3, 4.13, 6.2. External routines: Boost C++ libraries, GNU Scientific Library, Blitz++, FLENS, NumPy, SciPy Catalogue identifier of previous version: AELU_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1381 Does the new version supersede the previous version?: Yes Nature of problem: Definition of (open) composite quantum systems out of elementary building blocks [2,3]. Manipulation of such systems, with emphasis on dynamical simulations such as Master-equation evolution [4] and Monte Carlo wave-function simulation [5]. Solution method: Master equation, Monte Carlo wave-function method Reasons for new version: The new version is mainly a feature release, but it does correct some problems of the previous version, especially as regards the build system. Summary of revisions: We give an example for a typical Python script implementing the ring-cavity system presented in Sec. 3.3 of Ref. [2]: Restrictions: Total dimensionality of the system. Master equation-few thousands. Monte Carlo wave-function trajectory-several millions. Unusual features: Because of the heavy use of compile-time algorithms, compilation of programs written in the framework may take a long time and much memory (up to several GBs). Additional comments: The framework is not a program, but provides and implements an application-programming interface for developing simulations in the indicated problem domain. We use several C++11 features which limits the range of supported compilers (g++ 4.7, clang++ 3.1) Documentation, http://cppqed.sourceforge.net/ Running time: Depending on the magnitude of the problem, can vary from a few seconds to weeks. References: [1] Entry point: http://cppqed.sf.net [2] A. Vukics, C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems, Comp. Phys. Comm. 183(2012)1381. [3] A. Vukics, H. Ritsch, C++QED: an object-oriented framework for wave-function simulations of cavity QED systems, Eur. Phys. J. D 44 (2007) 585. [4] H. J. Carmichael, An Open Systems Approach to Quantum Optics, Springer, 1993. [5] J. Dalibard, Y. Castin, K. Molmer, Wave-f

  19. NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.

    PubMed

    Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

    2013-06-01

    To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings. PMID:23678341

  20. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.

    PubMed

    Cooper, Christopher D; Bardhan, Jaydeep P; Barba, L A

    2014-03-01

    The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license. PMID:25284826

  1. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

    PubMed Central

    Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L. A.

    2014-01-01

    The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1–2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license. PMID:25284826

  2. Forecast of spatially distributed runoff dynamics in the Finger Lakes region using an interactive web tool and Python

    NASA Astrophysics Data System (ADS)

    Dahlke, H. E.; Easton, Z. M.; Fuka, D. R.; Rao, N. S.; Steenhuis, T. S.

    2008-12-01

    To optimize NPS pollution reduction efficiency of Best Management Practices (BMPs) in NY State, various models have been developed that can effectively delineate runoff and contaminant source areas in the landscape. In the Finger Lakes region with shallow, permeable soils, underlain by a restricting layer, saturation excess runoff is the dominant mechanism of nutrient transport. In watersheds characterized by these conditions, runoff originates from areas in the landscape that expand and contract seasonally and are therefore often termed as variable source areas (VSAs). Hence, consideration should be given to the spatial distribution of VSA in the watershed during the planning process of BMPs. However, in practice the applied hydrological models often require extensive expertise and effort to be used on a routine basis for BMP planning. In order to simplify the BMP planning process, we developed an interactive web-based tool for Salmon Creek watershed, NY that locates VSA and calculates their probability of saturation. The interactive web tool incorporates hydrologic, geographic and land management information in an ESRI ArcIMS framework and presents the resulting VSA maps online. For the web tool we developed a Python-based application that calculates the surface runoff potential of the 230 km2 Salmon Creek watershed on the basis of a water balance model and free precipitation and temperature data from the National Climatic Data Center. Areas of high surface runoff potential are distributed via a soil topographic index to capture VSA dynamics. Further, the application is used to calculate a one to two day prediction of the spatial extent of VSA using free web- provided weather forecasts. The web tool is designed to interactively assist planners and especially farmers in the BMP planning process on a simplified expertise level. It can be used on a daily basis to locate fields with low runoff risk that could, potentially receive more liberal nutrient applications without increasing the risk of NPS pollution.

  3. On the tradeoffs of programming language choice for numerical modelling in geoscience. A case study comparing modern Fortran, C++/Blitz++ and Python/NumPy.

    NASA Astrophysics Data System (ADS)

    Jarecka, D.; Arabas, S.; Fijalkowski, M.; Gaynor, A.

    2012-04-01

    The language of choice for numerical modelling in geoscience has long been Fortran. A choice of a particular language and coding paradigm comes with different set of tradeoffs such as that between performance, ease of use (and ease of abuse), code clarity, maintainability and reusability, availability of open source compilers, debugging tools, adequate external libraries and parallelisation mechanisms. The availability of trained personnel and the scale and activeness of the developer community is of importance as well. We present a short comparison study aimed at identification and quantification of these tradeoffs for a particular example of an object oriented implementation of a parallel 2D-advection-equation solver in Python/NumPy, C++/Blitz++ and modern Fortran. The main angles of comparison will be complexity of implementation, performance of various compilers or interpreters and characterisation of the "added value" gained by a particular choice of the language. The choice of the numerical problem is dictated by the aim to make the comparison useful and meaningful to geoscientists. Python is chosen as a language that traditionally is associated with ease of use, elegant syntax but limited performance. C++ is chosen for its traditional association with high performance but even higher complexity and syntax obscurity. Fortran is included in the comparison for its widespread use in geoscience often attributed to its performance. We confront the validity of these traditional views. We point out how the usability of a particular language in geoscience depends on the characteristics of the language itself and the availability of pre-existing software libraries (e.g. NumPy, SciPy, PyNGL, PyNIO, MPI4Py for Python and Blitz++, Boost.Units, Boost.MPI for C++). Having in mind the limited complexity of the considered numerical problem, we present a tentative comparison of performance of the three implementations with different open source compilers including CPython and PyPy, Clang++ and GNU g++, and GNU gfortran.

  4. The contribution of gastric digestion and ingestion of amino acids on the postprandial rise in oxygen consumption, heart rate and growth of visceral organs in pythons.

    PubMed

    Enok, Sanne; Simonsen, Lasse Stærdal; Wang, Tobias

    2013-05-01

    To investigate the contribution of gastric and intestinal processes to the postprandial rise in metabolism in pythons (Python regius), we measured oxygen consumption after ligation of the pyloric sphincter to prevent the chyme from entering the intestine. Pyloric blockade reduced the postprandial rise in metabolism during the first 18h after ingestion of mice amounting to 18% of the snake's body mass by 60%. In another series of the experiments, we showed that infusion of amino acids directly into the stomach or the intestine elicited similar metabolic responses. This indicates a lower gastric contribution to the SDA response than previously reported. To include an assessment of the gastric contribution to the postprandial cardiovascular response, we also measured blood and heart rate. While heart rate increased during digestion in snakes with pyloric blockade, there was no rise in the double-blocked heart rates compared to fasting controls. Thus, the non-adrenergic-non-cholinergic factor that stimulates heart rate during digestion does not stem from the stomach. Finally, there was no growth of the visceral organs in response to digestion when chyme was prevented from reaching the intestine. PMID:23384684

  5. metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA

    PubMed Central

    Dale, Ryan K.; Matzat, Leah H.; Lei, Elissa P.

    2014-01-01

    Here we introduce metaseq, a software library written in Python, which enables loading multiple genomic data formats into standard Python data structures and allows flexible, customized manipulation and visualization of data from high-throughput sequencing studies. We demonstrate its practical use by analyzing multiple datasets related to chromatin insulators, which are DNA–protein complexes proposed to organize the genome into distinct transcriptional domains. Recent studies in Drosophila and mammals have implicated RNA in the regulation of chromatin insulator activities. Moreover, the Drosophila RNA-binding protein Shep has been shown to antagonize gypsy insulator activity in a tissue-specific manner, but the precise role of RNA in this process remains unclear. Better understanding of chromatin insulator regulation requires integration of multiple datasets, including those from chromatin-binding, RNA-binding, and gene expression experiments. We use metaseq to integrate RIP- and ChIP-seq data for Shep and the core gypsy insulator protein Su(Hw) in two different cell types, along with publicly available ChIP-chip and RNA-seq data. Based on the metaseq-enabled analysis presented here, we propose a model where Shep associates with chromatin cotranscriptionally, then is recruited to insulator complexes in trans where it plays a negative role in insulator activity. PMID:25063299

  6. Journal of Machine Learning Research 12 (2011) 2825-2830 Submitted 3/11; Revised 8/11; Published 10/11 Scikit-learn: Machine Learning in Python

    E-print Network

    Paris-Sud XI, Université de

    2011-01-01

    Journal of Machine Learning Research 12 (2011) 2825-2830 Submitted 3/11; Revised 8/11; Published 10/11 Scikit-learn: Machine Learning in Python Fabian Pedregosa fabian.pedregosa@inria.fr Ga¨el Varoquaux gael integrating a wide range of state-of-the-art machine learn- ing algorithms for medium-scale supervised

  7. Journal of Machine Learning Research 12 (2011) 2825-2830 Submitted 3/11; Revised 8/11; Published 10/11 Scikit-learn: Machine Learning in Python

    E-print Network

    Paris-Sud XI, Université de

    2011-01-01

    Journal of Machine Learning Research 12 (2011) 2825-2830 Submitted 3/11; Revised 8/11; Published 10/11 Scikit-learn: Machine Learning in Python Fabian Pedregosa fabian.pedregosa@inria.fr Ga¨el Varoquaux gael manuscript, published in "Journal of Machine Learning Research (2011)" #12;Pedregosa, Varoquaux, Gramfort et

  8. Data and Schema Matching Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    of Disparate Data Sources: A Machine Learning Approach," by Doan et al, SIGMOD 01 Some slides on LSD courtesy of the things they want to do: Y E-commerce exchanges Y Data integration/warehousing Y Semantic web § Goal: make are implications for instance-level vs. schema- level? #12;12 What Makes Matching Complicated 1/2 How do we deal

  9. Data Integration Systems Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    Integration Design Points (from Monday) Garlic [Haas+97] ­ IBM Almaden (now in DB2) Focus: intranet, SQL, few of mediated schema #12;4 Garlic: small-scale, controlled integration of heterogeneous data DB2 data Limited query engine for combining data afterwards What's interesting about Garlic: Commercially

  10. Pipe dream? Envisioning a grassroots Python ecosystem of open, common software tools and data access in support of river and coastal biogeochemical research (Invited)

    NASA Astrophysics Data System (ADS)

    Mayorga, E.

    2013-12-01

    Practical, problem oriented software developed by scientists and graduate students in domains lacking a strong software development tradition is often balkanized into the scripting environments provided by dominant, typically proprietary tools. In environmental fields, these tools include ArcGIS, Matlab, SAS, Excel and others, and are often constrained to specific operating systems. While this situation is the outcome of rational choices, it limits the dissemination of useful tools and their integration into loosely coupled frameworks that can meet wider needs and be developed organically by groups addressing their own needs. Open-source dynamic languages offer the advantages of an accessible programming syntax, a wealth of pre-existing libraries, multi-platform access, linkage to community libraries developed in lower level languages such as C or FORTRAN, and access to web service infrastructure. Python in particular has seen a large and increasing uptake in scientific communities, as evidenced by the continued growth of the annual SciPy conference. Ecosystems with distinctive physical structures and organization, and mechanistic processes that are well characterized, are both factors that have often led to the grass-roots development of useful code meeting the needs of a range of communities. In aquatic applications, examples include river and watershed analysis tools (River Tools, Taudem, etc), and geochemical modules such as CO2SYS, PHREEQ and LOADEST. I will review the state of affairs and explore the potential offered by a Python tool ecosystem in supporting aquatic biogeochemistry and water quality research. This potential is multi-faceted and broadly involves accessibility to lone grad students, access to a wide community of programmers and problem solvers via online resources such as StackExchange, and opportunities to leverage broader cyberinfrastructure efforts and tools, including those from widely different domains. Collaborative development of such tools can provide the additional advantage of enhancing cohesion and communication across specific research areas, and reducing research obstacles in a range of disciplines.

  11. Honorable Zachary J. Lemnios The Honorable Zachary J. Lemnios was sworn in as Director, Defense Research

    E-print Network

    Research Projects Agency (DARPA) Microsystems Technology Office (MTO) as well as the Deputy Director organizations and represented DARPA on various national committees. Mr. Lemnios' also served as a Senior Staff Manager at DARPA. Additionally, he held various positions within industry at Hughes Aircraft Company

  12. Data for giant constrictors - Biological management profiles and an establishment risk assessment for nine large species of pythons, anacondas, and the boa constrictor

    USGS Publications Warehouse

    Jarnevich, C.S.; Rodda, G.H.; Reed, R.N.

    2011-01-01

    Giant Constrictors' Climate Space The giant constrictors' climate space data set represents the information needed to recreate the climate space and climate matching analyses in Reed and Rodda (2009). A detailed methodology and results are included in that report. The data include locations for nine species of large constrictors including Python molurus, Broghammerus reticulatus, P. sebae, P. natalensis, Boa constrictor, Eunectes notaeus, E. deschauenseei, E. beniensis, and E. murinus. The locations are from published sources. Climate data are included for monthly precipitation and average monthly temperature along with the species locations. The individual spreadsheets of location data match the figures in the Reed and Rodda (2009) report, illustrating areas of the mainland United States that match the climate envelope of the native range. The precipitation and temperature data at each location were used to determine the climate space for each species. Graphs of climate space formed the basis for the algorithms in the data set, and more details can be found in Reed and Rodda (2009). These algorithms were used in ArcGIS to generate maps of areas in the United States that matched the climate space of locations of the snakes in their native range. We discovered a rounding error in ArcGIS in the implementation of the algorithms, which has been corrected here. Therefore the shapefiles are slightly different than those appearing in the risk assessment figures illustrating areas of the United States that match the climate envelope of the species in their native ranges. However, the suitable localities are not different at the scale of intended use for these maps, although there are more noticeable differences between areas classified as 'too cold' and 'too hot'.

  13. PyBetVH: A Python tool for probabilistic volcanic hazard assessment and for generation of Bayesian hazard curves and maps

    NASA Astrophysics Data System (ADS)

    Tonini, Roberto; Sandri, Laura; Anne Thompson, Mary

    2015-06-01

    PyBetVH is a completely new, free, open-source and cross-platform software implementation of the Bayesian Event Tree for Volcanic Hazard (BET_VH), a tool for estimating the probability of any magmatic hazardous phenomenon occurring in a selected time frame, accounting for all the uncertainties. New capabilities of this implementation include the ability to calculate hazard curves which describe the distribution of the exceedance probability as a function of intensity (e.g., tephra load) on a grid of points covering the target area. The computed hazard curves are (i) absolute (accounting for the probability of eruption in a given time frame, and for all the possible vent locations and eruptive sizes) and (ii) Bayesian (computed at different percentiles, in order to quantify the epistemic uncertainty). Such curves allow representation of the full information contained in the probabilistic volcanic hazard assessment (PVHA) and are well suited to become a main input to quantitative risk analyses. PyBetVH allows for interactive visualization of both the computed hazard curves, and the corresponding Bayesian hazard/probability maps. PyBetVH is designed to minimize the efforts of end users, making PVHA results accessible to people who may be less experienced in probabilistic methodologies, e.g. decision makers. The broad compatibility of Python language has also allowed PyBetVH to be installed on the VHub cyber-infrastructure, where it can be run online or downloaded at no cost. PyBetVH can be used to assess any type of magmatic hazard from any volcano. Here we illustrate how to perform a PVHA through PyBetVH using the example of analyzing tephra fallout from the Okataina Volcanic Centre (OVC), New Zealand, and highlight the range of outputs that the tool can generate.

  14. Python Optimization Modeling Objects (Pyomo)

    E-print Network

    2009-12-29

    Dec 29, 2009 ... Pyomo leverages the capabilities of the Coopr software library, which .... ing high reliability of the software still requires careful software management and a ... external optimization executables (e.g., through the use of system.

  15. ArcNEMO, a spatially distributed nutrient emission model developed in Python to quantify losses of nitrogen and phosphorous from agriculture to surface waters

    NASA Astrophysics Data System (ADS)

    Van Opstal, Mattias; Tits, Mia; Beckers, Veronique; Batelaan, Okke; Van Orshoven, Jos; Elsen, Annemie; Diels, Jan; D'heygere, Tom; Van Hoof, Kor

    2014-05-01

    Pollution of surface water bodies with nitrogen (N) and phosphorous (P) from agricultural sources is a major problem in areas with intensive agriculture in Europe. The Flemish Environment Agency requires information on how spatially explicit policy measures on manure and fertilizer use, and changes in land use and soil management affect the N and P concentration in the surface waters in the region of Flanders, Belgium. To assist in this, a new spatially distributed, mechanistic nutrient emission model was developed in the open-source language Python. The model is called ArcNEMO (Nutrient Emission MOdel). The model is fully integrated in ArcGIS, but could be easily adapted to work with open-source GIS software. In Flanders, detailed information is available each year on the delineation of each agricultural parcel and the crops grown on them. Parcels are linked to farms, and for each farm yearly manure and fertilizer use is available. To take full advantage of this information and to be able to simulate nutrient losses to the high-density surface water network, the model makes use of grid cells of 50 by 50m. A fertilizer allocation model was developed to calculate from the yearly parcel and farm data the fertilizer and manure input per grid cell for further use in the ArcNEMO-model. The model architecture was chosen such that the model can be used to simulate spatially explicit monthly discharge and losses of N and P to the surface water for the whole of Flanders (13,500 km²) over periods of 10-20 years. The extended time period is necessary because residence times in groundwater and the rates of organic matter turnover imply that water quality reacts slowly to changes of land use and fertilization practices. Vertical water flow and nutrient transport in the unsaturated zone are described per grid cell using a cascading bucket-type model with daily time steps. Groundwater flow is described by solving the 2D-groundwater flow equation using an explicit numerical solution with daily time steps. Solute transport is described using a mixing cell concept in the unsaturated zone, and by numerically solving the 2D solute transport equation in the groundwater. Denitrification in soil and groundwater is described as a first order process. Mineralisation of organic N and P in the top soil of every grid cell is modelled according to the principles of the RothC model and by assigning C:N and C:P ratios to organic matter pools. As mineralization is a slow process, it is modelled with monthly rather than daily time steps. Soil erosion and N and P transport with sediment flow is modelled in line with the WaTEM/SEDEM spatially distributed soil erosion and sediment delivery model, also with monthly time steps. The performance of the model was evaluated with discharge and water quality time series from small catchments in Flanders.

  16. FEBRUARY 2013 BRADLEY C. PARKS AND ZACHARY J. RICE

    E-print Network

    Fashing, Norman

    Verde; Luis Cosenza, the former Minister of the Presidency of Honduras; John Evans, the former U in the Technical Secretariat of the Presidency of El Salvador, and Said Abdou Salime, the former Secretary General

  17. Diseases and pests of honey bees Zachary Huang

    E-print Network

    Huang, Zachary

    Acid gloves Finley photo 7. Using screen bottom board Effect of traps on mite infestation June June Aug;5 Healthy brood frame Unhealthy brood pattern Punctured Cappings, Cheesy Smell False tongue #12;6 1.Sunken

  18. FIXED POINT METHODS IN NONLINEAR ANALYSIS ZACHARY SMITH

    E-print Network

    May, J. Peter

    . Contents 1. Introduction 1 2. Differential Calculus on Banach Spaces 2 2.1. Banach Fixed Point Theory 2 2 Point Theory 7 3.1. Brouwer Fixed Point Theory 7 3.2. Ascoli-Arzel`a Theory 8 3.3. Schauder Fixed Point Spaces 2.1. Banach Fixed Point Theory. Definition 2.1. Let (X, d) be a metric space and T : M X X

  19. Darwin and evolutionary tales in leukemia. The Ham-Wasserman Lecture.

    PubMed

    Greaves, Mel

    2009-01-01

    All cancers evolve by a process of genetic diversification and "natural selection" akin to the process first described by Charles Darwin for species evolution. The evolutionary, natural history of childhood acute lymphoblastic leukemia (ALL) is almost entirely covert, clinically silent and well advanced by the point of diagnosis. It has, however, been possible to backtrack this process by molecular scrutiny of appropriate clinical samples: (i) leukemic clones in monozygotic twins that are either concordant or discordant for ALL; (ii) archived neonatal blood spots or Guthrie cards from individuals who later developed leukemia; and (iii) stored, viable cord blood cells. These studies indicate prenatal initiation of leukemia by chromosome translocation and gene fusion (or hyperdiploidy) and the post-natal acquisition of multiple, gene copy number alterations (CNAs), mostly deletions. The prenatal or first "hit" occurs very commonly, exceeding the clinical rate of ALL by some 100x and indicating a low rate of penetrance or evolutionary progression. The acquisition of the critical, secondary CNAs requires some Darwinian selective advantage to expand numbers of cells at risk, and the cytokine TGF beta is able to exercise this function. The clonal architecture of ALL has been investigated by single cell analysis with multicolor probes to mutant genes. The data reveal not a linear sequence of mutation acquisition with clonal succession but rather considerable complexity with a tree-like or branching structure of genetically distinct subclones very reminiscent of Darwin's original 1837 evolutionary divergence diagram. This evolutionary pattern has important implications for stem cells in ALL, for the origins of relapse and for therapeutic targeting. PMID:20008176

  20. Conventional and non-conventional Drosophila Toll signaling Scott A. Lindsay, Steven A. Wasserman

    E-print Network

    , the organization of signaling events at and beneath membranes, the sorting of information flow, and the existence, and parasites, multicellular organisms defend themselves. Receptors that re- spond to conserved microbial molecules trigger signaling cascades that direct expression of a battery of antimicrobial peptides, cyto

  1. Arsenic and manganese exposure and children's intellectual function Gail A. Wasserman a,b,

    E-print Network

    van Geen, Alexander

    toxins (Bellinger, 2009). As an example, among Korean school children, while current levels of both blood lead (BPb) and blood Mn (BMn) were independently associated with lower intelligence scores, evidence of household wells. When adjusted only for each other, both As and Mn in whole blood (BAs; BMn) were

  2. Python Programming: Lecture 2 Lili Dworkin

    E-print Network

    Plotkin, Joshua B.

    in b True >>> 6 not in b True #12;Lists: Iteration >>> a = ["apple", "orange", "banana"] >>> range(len(a)) [0, 1, 2] >>> for i in range(len(a)): # Bad! ... print a[i] ... apple orange banana >>> for i in a: # Good! ... print i ... apple orange banana #12;Lists: Insertion >>> a = ["apple", "orange", "banana

  3. Py4Science 3 Python "names"

    E-print Network

    Delene, David J.

    ]: f1header[0].split()[0] Out[3]: '83' #12;Loading the ASCII files - week 2 # Open file f1 = open) f1header = [f1.readline() for lines in range(skiprows)] # Close the file f1.close() # Read whole section of the file 3-) # Extract the header 4-) # How many variables in the file and what they are 5

  4. PyDrizzle: Python version of Drizzle

    NASA Astrophysics Data System (ADS)

    Hack, Warren; Blakeslee, John; Meurer, Gerhardt; Hook, Richard

    2014-01-01

    PyDrizzle provides a semi-automated interface for computing the parameters necessary for running Drizzle. PyDrizzle performs the task of determining the parameters necessary for aligning images based on the WCS information in the input image headers, as well as any supplemental alignment information provided in shift files, and combines the images onto the same WCS. Though it does not identify cosmic rays, it has the ability to ignore pixels flagged as bad, such as pixels identified by other programs as affected by cosmic rays.

  5. Why Python? 1) readable, compact, simple syntax

    E-print Network

    Spang, Rainer

    **alf Parameters def alfify(x = 1,y = 2,alf = 1): return x**-alf + y**alf alfify() alfify(y=3) Litt managed 4) types inferred at run-time 5) dynamic: classes are objects 6) batteries included: extensive

  6. Python programming --Pandas Finn Arup Nielsen

    E-print Network

    Get some data from R Get a standard dataset, Pima, from R: $ R > library(MASS) > write.csv(Pima.te, "pima.csv") pima.csv now contains comma-separated values: "","npreg pandas as pd >>> pima = pd.read_csv("pima.csv") "pima" is now what Pandas call a DataFrame object

  7. Projet gratuit et open source Ecrit en python (compatible python 2.3 et +)

    E-print Network

    Tichit, Laurent

    biologiques ExPASy -- http://www.expasy.org/ Entrez (NCBI) -- http://www.ncbi.nlm.nih.gov/Entrez/ PubMed (NCBI) -- http://www.ncbi.nlm.nih.gov/PubMed/ SCOP -- http://scop.mrc-lmb.cam.ac.uk/scop/ #12;Requête

  8. Wasserman et al. BMC Public Health 2010, 10:192 http://www.biomedcentral.com/1471-2458/10/192

    E-print Network

    Paris-Sud XI, Université de

    Balazs3, Julia Bobes4, Renata Bracale13, Romuald Brunner5, Cendrine Bursztein-Lipsicas2, Paul Corcoran6-Pierre Kahn9, Michael Kaess5, Helen Keeley6, Dragan Marusic11, Bogdan Nemes7, Vita Postuvan11, Stella Reiter

  9. Zachary O. Dugas Toups Curriculum Vitae ztoups@nmsu.edu http://cs.nmsu.edu/~ztoups

    E-print Network

    Toups, Zach

    2014­Aug 2014 TEES Asst. Research Engineer, Texas Center for Applied Technology College Station, Texas, USA Apr 2012­Jul 2013 TEES Asst. Research Professor of Computer Science and Engineering, Texas A Asst. Research Engineer, TCAT / TEEX Disaster Preparedness & Response, Crisis Response Innovative

  10. Relationship Between Data Smoothing and the Regularization of Inverse Problems William Menke and Zachary Eilon

    E-print Network

    Menke, William

    tomographic images). We consider the general inverse problem, in its continuum limit. By deconstruction and few, if any, drawbacks. Keywords: Inverse Theory; Tomography; Spatial Analysis; Damping; Smoothing the inversion process, are damped through the addition of prior information, which quantifies expectations about

  11. Electrothermal ac electro-osmosis Zachary R. Gagnon and Hsueh-Chia Changa

    E-print Network

    Chang, Hsueh-Chia

    - ing down peristaltic, diaphragm, or other popular macroscale mechanical pumps to microscale dimensions Debye layer on the channel wall, and through viscous dissipation drives a characteristic Smolu- chowski

  12. An Autonomous Robot Photographer Zachary Byers Michael Dixon Kevin Goodier Cindy M. Grimm William D. Smart

    E-print Network

    Dixon, Michael

    for investigating algorithms for standard robot tasks, such as navigation and localization, as well as novel human-robot interaction methodologies. The system we describe below is a baseline from which we can explore more advanced of how changing a component affects the entire system. The current system is entirely event

  13. Visual Analysis of Urban Terrain Dynamics Thomas Butkiewicz, Remco Chang, William Ribarsky, and Zachary Wartell

    E-print Network

    Wartell, Zachary

    with multivalent heights and non-genus-0 topologies. Overhangs, subways, subterranean rooms and passages, bridges that a comprehensive modeling approach must deal with overlapping patches or volumes from #12;3 different sensors

  14. Designing a Statically-Typed Scripting Language Pottayil Harisanker Menon Zachary Palmer Alexander Rozenshteyn Scott Smith

    E-print Network

    Smith, Scott F.

    that we call the onion. Onions aim to unify imperative, object-oriented, and functional pro- gramming of this paper describes the onion data com- binator, the process of typechecking Big Bang, and some prac- tical considerations involved in its implementation. Onion-Oriented Programming At the core of Big Bang

  15. Compressive Coded Aperture Imaging Roummel F. Marcia, Zachary T. Harmany, and Rebecca M. Willett

    E-print Network

    of constraints on the focal plane array size. In particular, we describe a novel yet practical approach a single focal plane array to increase field of view. Specifically, the proposed method superimposes coded In a wide variety of video applications, keeping the focal plan array (FPA) small is useful or even critical

  16. Startle Reduces Recall of a Recently Learned Internal Model Zachary Wright, James L. Patton

    E-print Network

    Patton, James

    early from subcortical areas by the using a startling acoustic stimulus (SAS). Our question is whether to as the feedforward mode of motor control, whereby an internal model is constantly modified and acquired through motor as they would if undisturbed [2]. When unexpectedly turned off and people return to the "normal" world

  17. Gully measurement strategies in a pixel using python

    NASA Astrophysics Data System (ADS)

    Wells, Robert; Momm, Henrique; Bennett, Sean; Dabney, Seth

    2015-04-01

    Gullies are often the single largest sediment sources within the landscape; however, measurement and process description of these channels presents challenges that have limited complete understanding. A strategy currently being employed in the field and laboratory to measure topography of gullies utilizes inexpensive, off-the-shelf cameras and software. Photogrammetry may be entering an enlightened period, as users have numerous choices (cameras, lenses, and software) and many are utilizing the technology to define their surroundings; however, the key for those seeking answers will be what happens once topography is represented as a three-dimensional digital surface model. Perhaps the model can be compared with another model to visualize change, either in topography or in vegetation cover, or both. With these models of our landscape, prediction technology should be rejuvenated and/or reinvented. Over the past several decades, researchers have endeavored to capture the erosion process and transfer these observations through oral and written word. Several have hypothesized a fundamental system for gully expression in the landscape; however, this understanding has not transferred well into our prediction technology. Unlike many materials, soils often times do not behave in a predictable fashion. Which soil physical properties lend themselves to erosion process description? In most cases, several disciplines are required to visualize the erosion process and its impact on our landscape. With a small camera, the landscape becomes more accessible and this accessibility will lead to a deeper understanding and development of uncompromised erosion theory. Why? Conservation of our soil resources is inherently linked to a complete understanding of soil wasting.

  18. Supplement: Regular Expressions For Introduction to Programming Using Python

    E-print Network

    Liang, Y. Daniel

    expression (abbreviated regex) is a string that describes a pattern for matching a set of strings. Regular, replacing, and splitting strings. 1 Getting Started To use regex, import the re module. You can use the split function in the module to split a string. For example, re.split(" ", "ab bc cd") splits "ab bc cd

  19. Spatial ecology and habitat use of carpet pythons (Morelia spilota)

    E-print Network

    Canberra, University of

    Certificate of authorship of thesis Except as specifically indicated in footnotes, quotations of Requirements for a Thesis issued by the University Higher Degrees Committee. Signature of Author............................................................ Copyright This thesis may be freely copied and distributed for private use and study. However, no part

  20. PySP: Modeling and Solving Stochastic Programs in Python

    E-print Network

    2010-09-07

    Sep 6, 2010 ... Abstract Although stochastic programming is a powerful tool for ...... partment of Energy's National Nuclear Security Administration under contract DE- .... Sustainable Infrastructure System Modeling under Uncertainties and Dy-.

  1. Client HTTP en Python HyperText Transfer Protocol

    E-print Network

    Tichit, Laurent

    2014 : url = http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi et pour les données : 'db obtenez le bon résultat, ouvrez votre navigateur sur : http://eutils.ncbi.nlm.nih.gov articles au format texte : url = http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi et pour les

  2. Peristaltic pumping in an elastic tube: feeding the hungry python

    NASA Astrophysics Data System (ADS)

    Takagi, Daisuke; Balmforth, Neil

    2010-11-01

    Biological ducts convey contents like food in the digestive system by peristaltic action, propagating waves of muscular contraction and relaxation. The motion is investigated theoretically by considering a radial force of sinusoidal or Gaussian form moving steadily down a fluid-filled axisymmetric tube. Effects of the prescribed force on the resultant fluid flow and elastic deformation of the tube wall are presented. The flow can induce a rigid object suspended in the fluid to propel in different ways, as demonstrated in numerous examples.

  3. Initiation l'algorithmique et la programmation en langage Python

    E-print Network

    Tichit, Laurent

    'Informatique Bât TPR1, entrée G, 6ème étage - sujets des TP - supports cours et documentations - annonces diverses des opérations précédentes soit acquises depuis l'extérieur (clavier, appareil de mesure, etc

  4. Crates and Transform: Python Interfaces for Data Analysis

    NASA Astrophysics Data System (ADS)

    Lyn, J.; Cresitello-Dittmar, M.; Evans, I.; Evans, J. D.

    2014-05-01

    With its flexible design and ease-of-use, Crates and Transform have been incorporated into the Chandra X-Ray Center's (CXC) data visualization and fitting tools and data processing scripts to facilitate a wide variety of tasks. Chandra's fitting and modeling application, called Sherpa, uses Crates as an underlying data access module, taking advantage of its ability to interpret standard Flexible Image Transport System (FITS) files, such as Redistribution Matrix Files (RMF), Auxiliary Response Files(ARF), and both types of Pulse Height Analysis (PHA) files. The Chandra Imaging and Plotting System (ChIPS) tool utilizes the associated Transform module for visualizing data in different World Coordinate Systems (WCS). By using the CXC DataModel (DM) as a backend, Crates can perform advanced filtering and binning techniques on data. This capability, combined with its simple Application Programming Interface, make it ideal for incorporation into our data analysis scripts, aiding with operations from simple keyword manipulation to creating and writing multiple Header Definition Unit (HDU) files. Crates and Transform are available respectively as the pycrates and pytransform modules within the Chandra Interactive Analysis of Observations (CIAO) environment to assist users with their own analysis threads. In this paper, we will illustrate the capabilities of the Crates and Transform modules and how they are being used within the CXC for analysis.

  5. Amikacin pharmacokinetics and the effects of ambient temperature on the dosage regimen in ball pythons (Python reguis) 

    E-print Network

    Johnson, James Harvey

    1995-01-01

    ,880, 4,320, 5,760, and 8,640 minutes after administration of amikacin. A 28-day washout period occurred between each study. Drug concentration versus time curves following IC administration at both temperatures best fit a two-compartment open model...

  6. Agarwal, Margene Kennedy, David A Bluemke and Joo A.C. Lima Milind Y. Desai, Annabelle Rodriguez, Bruce A. Wasserman, Gary Gerstenblith, Sachin

    E-print Network

    Terasaki, Mark

    -sectional study of consecutively enrolled initial 28 patients who were part of an ongoing randomized trial testing the effects of extended release Niacin versus placebo station top of baseline therapy on carotid plaque

  7. STATE OF UTAH CONTRACT NUMBER: MA543 March 12, 2014 Page 1 of 16 Amendment number: Purchasing Agent: Zachary Derr

    E-print Network

    Capecchi, Mario R.

    STATE OF UTAH CONTRACT NUMBER: MA543 March 12, 2014 Page 1 of 16 Amendment number: Purchasing Agent Systems, Wireless Interactive Pads, Interactive Panels, and Software. This contract is one of five available contracts for same/like items. Examine all contracts when making a selection. The other available

  8. Design, Analysis, and Learning Control of a Robotic Wind Turbine J. Zico Kolter, Zachary Jackowski, Russ Tedrake*

    E-print Network

    Jackson, Daniel

    , Russ Tedrake* Abstract-- Wind power represents one of the most promising sources of renewable energy continues to grow rapidly [1]. Wind power represents one of the most promising sources of renewable energy predicted by turbine simulation software developed at the National Renewable Energy Laboratory; the results

  9. Vocal resonance as a passive biometric Cory Cornelius, Zachary Marois, Jacob Sorber, Ron Peterson, Shrirang Mare, David Kotz

    E-print Network

    with other devices nearby (e.g., entertainment systems, climate-control systems, or medical devices). Sensor of pervasive wearable devices, whether for health monitoring, personal assistance, entertainment, or home automation. In our vision, the user can simply wear the desired set of devices, and they "just work

  10. Equilibria and Efficiency Loss in Games on Joshua R. Davis, Zachary Goldman, Jacob Hilty, Elizabeth N. Koch,

    E-print Network

    Sharp, Alexa

    , Elizabeth N. Koch, David Liben-Nowell, Alexa Sharp, Tom Wexler, and Emma Zhou Carleton College; Northfield grant CCF-0728779. This work was also supported by grants from Carleton College, Oberlin College, MN Denison University; Granville, OH Oberlin College; Oberlin, OH joshuardavis@q.com, goldma z

  11. Compressive Coded Apertures for High-Resolution Imaging Roummel F. Marciaa, Zachary T. Harmanyb, and Rebecca M. Willettb

    E-print Network

    such measurements. Specifically, we describe how given a fixed size focal plane array, compressive measurements allow relatively small focal plane arrays (FPAs) to be used to generate high-resolution im- agery

  12. STATE OF UTAH CONTRACT NUMBER: MA513 March 12, 2014 Page 1 of 17 Revision number: Purchasing Agent: Zachary Derr

    E-print Network

    Capecchi, Mario R.

    , Lightspeed, Crestron, Extron, Sanyo, Chief, Interwrite Price: See Attached Pricing Terms: Net 30 Effective: Other conditions: New Contract awarded to same vendor. RT14036-1 This contract covers only those items

  13. Organic light-emitting devices with laminated top contacts Daniel A. Bernards, Tomasz Biegala, Zachary A. Samuels, Jason D. Slinker,

    E-print Network

    Rogers, John A.

    Organic light-emitting devices with laminated top contacts Daniel A. Bernards, Tomasz Biegala; accepted 22 March 2004; published online 20 April 2004 We demonstrate the fabrication of organic light into the organic layer s and recombine, giving rise to light emission. The fabrication of OLEDs re- quires

  14. A Trade Space Model for Robotic Lunar Exploration

    E-print Network

    A Trade Space Model for Robotic Lunar Exploration Zachary James Bailey, David W. Miller June 2010 SSL # 11-10 #12;#12;A Trade Space Model for Robotic Lunar Exploration Zachary James Bailey, David W of Technology. #12;2 #12;A Trade Space Model for Robotic Lunar Exploration by Zachary James Bailey Submitted

  15. A standard python environment for software applications at the Robert C. Byrd Green Bank Telescope (GBT)

    NASA Astrophysics Data System (ADS)

    Radziwill, Nicole M.; Shelton, Amy L.

    2006-06-01

    Since 2003, the monitor and control software systems for the Robert C. Byrd Green Bank Telescope (GBT) have been substantially redesigned to make the telescope easier to use. The result is the release of the Astronomer's Integrated Desktop (Astrid), an observation management platform used to create and submit scheduling blocks, monitor their progress on the telescope, and provide a real time, quick look data display. Using Astrid, the astronomer launches one application and has access to all of the software, documentation, and feedback facilities that are required to conduct an interactive observing session. These systems together provide a common look and feel for GBT software applications, enable offline observation preparation, and facilitate dynamic scheduling and remote observing.

  16. Copyright Y. Daniel Liang, 2012 For Introduction to Programming Using Python

    E-print Network

    Liang, Y. Daniel

    . A megabyte is roughly a million bytes. cable modem Uses the TV cable line maintained by the cable company. A cable modem is as fast as a DSL. calling a function In programming terminology, when you use a function subscriber line) Uses a phone line and can transfer data in a speed 20 times faster than a regular modem

  17. Combs: open source python library for RVE generation. Application to microscale diffusion simulations in cementitious materials

    NASA Astrophysics Data System (ADS)

    Bourcier, C.; Dridi, W.; Chomat, L.; Laucoin, E.; Bary, B.; Adam, E.

    2014-06-01

    The developed tools are used to create a representative volume element (RVE) of cementitious materials and then assess the diffusive properties. The algorithms developed in Combs target a fast placement of the inclusions and a fast generation of the RVE shape and its mesh. Two application cases are considered: the unaltered material diffusivity and the degraded material diffusivity. The first case of application focuses on the description of the capillary porosity. The second application case focuses on the description of the degradation of cementitious material (mineral and porosity) and the diffusive properties associated. The reliability of the analytical effective medium approximations (MT and SC) is confirmed from 3D finite elements (FE) calculations performed on a matrix-inclusions microstructure obtained by RVE generation with Combs. The results also show the need to take into account the percolation behavior.

  18. 75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

    ...and Four Anaconda Species as Injurious Reptiles AGENCY: Fish and Wildlife Service...beniensis) to the list of injurious reptiles under the Lacey Act. If you have previously...anaconda (Eunectes beniensis) as injurious reptiles under the Lacey Act (18...

  19. CS Circles: An In-Browser Python Course for Beginners David Pritchard

    E-print Network

    Vasiga, Troy

    of exercises. Our position is that such a framework puts students at risk of losing interest mid. To compensate for these issues we have added a human touch by letting students eas- ily send a"Help"message when

  20. The Python Project: A Unique Model for Extending Research Opportunities to Undergraduate Students

    PubMed Central

    Harvey, Pamela A.; Wall, Christopher; Luckey, Stephen W.; Langer, Stephen

    2014-01-01

    Undergraduate science education curricula are traditionally composed of didactic instruction with a small number of laboratory courses that provide introductory training in research techniques. Research on learning methodologies suggests this model is relatively ineffective, whereas participation in independent research projects promotes enhanced knowledge acquisition and improves retention of students in science. However, availability of faculty mentors and limited departmental budgets prevent the majority of students from participating in research. A need therefore exists for this important component in undergraduate education in both small and large university settings. A course was designed to provide students with the opportunity to engage in a research project in a classroom setting. Importantly, the course collaborates with a sponsor's laboratory, producing a symbiotic relationship between the classroom and the laboratory and an evolving course curriculum. Students conduct a novel gene expression study, with their collective data being relevant to the ongoing research project in the sponsor's lab. The success of this course was assessed based on the quality of the data produced by the students, student perception data, student learning gains, and on whether the course promoted interest in and preparation for careers in science. In this paper, we describe the strategies and outcomes of this course, which represents a model for efficiently providing research opportunities to undergraduates. PMID:25452492

  1. Physics 212E Classical and Modern Physics Spring 2012 Python Class 10: Quantum Dynamics

    E-print Network

    Vollmayr-Lee, Ben

    t # then some new stuff will go here draw() t = t + dt ioff() show() 4 Stuff to Initialize · Constants We For animations, we need to create first a plot object and then in the while loop we can change the ydata below should all come before the draw() command. · Calculate (x, t) For our initial case of just being

  2. High-Performance Parallel Computations Using Python as High-Level Language

    Microsoft Academic Search

    Stefano Masini; Paolo Bientinesi

    \\u000a High-performance and parallel computations have always represented a challenge in terms of code optimization and memory usage,\\u000a and have typically been tackled with languages that allow a low-level management of resources, like Fortran, C and C++. Nowadays,\\u000a most of the implementation effort goes into constructing the bookkeeping logic that binds together functionalities taken from\\u000a standard libraries. Because of the increasing

  3. A Comparison of C, MATLAB and Python as Teaching Languages in Engineering

    E-print Network

    of computer programming and the efforts to implement the algorithm using a particular programming language distinct phases in the process of converting a given problem into a computer program that can provide step whereas the actual implementation in a programming language is of secondary importance

  4. Sir Bedevere's Revelation (from Witch Scene in Monty Python's Holy Grail)

    E-print Network

    Bringsjord, Selmer

    's permission to burn her. King Arthur has just rode into the village and is watching the scene from a distance o Not happy - Made of wood o Likes - Burning not permitted/not desired o Dislikes - Burning not to wish to burn a daft object AND you do not wish to burn an intellegent object. 4 Goals o

  5. Sir Bedevere's Revelation (from Witch Scene in Monty Python's Holy Grail)

    E-print Network

    Bringsjord, Selmer

    is a witch. They would like Sir Bedevere's permission to burn her. King Arthur has just rode into the village ­ Burning not permitted/not desired ffl Dislikes ­ Burning permitted/desired 3 Given Information ffl F're a judge only if you do not to wish to burn a daft object AND you do not wish to burn an intellegent object

  6. OOF ?: A Python engine for automating regional and coastal ocean forecasts

    Microsoft Academic Search

    Martinho Marta-Almeida; Manuel Ruiz-Villarreal; Pablo Otero; Marcos Cobas; Alvaro Peliz; Rita Nolasco; Mauro Cirano; Janini Pereira

    2011-01-01

    Coastal and regional ocean forecasts can be currently performed on a daily basis due to the advances in numerical techniques and in computational resources. Maintenance of routine forecasts is a demanding task from the point of view of software engineering since it involves a number of new additional tasks difficult to code efficiently in the compiled languages in which ocean

  7. DEVSimPy:A Collaborative Python Software for Modeling and Simulation of DEVS Systems

    E-print Network

    Paris-Sud XI, Université de

    multidisciplinary approach. In the same time, computer simulations have been becoming increasingly complex of the models and also their validation much easier [4,5,6]. Storing models in a common generic library has several benefits. First, the genericity of this storage service can be offered to various modeling

  8. PyMVPA: a Python Toolbox for Multivariate Pattern Analysis of fMRI Data

    Microsoft Academic Search

    Michael Hanke; Yaroslav O. Halchenko; Per B. Sederberg; Stephen José Hanson; James V. Haxby; Stefan Pollmann

    2009-01-01

    Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard\\u000a univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent\\u000a (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual\\u000a tasks. Recently, researchers have begun to explore new multivariate

  9. STATE OF THE ART OF SOAP LIBRARIES IN PYTHON AND RUBY

    E-print Network

    Myllymäki, Petri

    libraries for prototyping. A simple REST interface is created for a commercial Web service called SyncShield. #12;Chapter 1 Introduction The ITEA Services for all (S4All) research project aimed to create a world a visionary software component called a Service Composer which is used to combine public small-scale web-services

  10. Blank, Kumar, Meeden, and Yanco. JERIC 2005. Pyro: A Python-based Versatile Programming

    E-print Network

    Blank, Douglas

    ]: Robotics ­ Autonomous vehicles; K.3 [Computers and Education]: Computer and Information Science Environments General Terms: Mobile robotics, education, robot abstractions, autonomous control, programming for Teaching Robotics DOUGLAS BLANK Bryn Mawr College DEEPAK KUMAR Bryn Mawr College LISA MEEDEN Swarthmore

  11. Tabizi Pythons and Clendro Hawks: Using Imaginary Animals to Achieve Real Knowledge about Ecosystems

    NSDL National Science Digital Library

    Michael Rockow

    2007-01-01

    In the engaging unit described here, imaginary organisms are used to teach a variety of topics related to ecosystems--food chains and energy flow, food webs, limiting factors, carrying capacity, and the effects of natural and human-made events on ecosystems. By inventing organisms, the teacher is able to control the level of complexity, and the number of organisms can be modified to meet each student's level. Because the organisms are figments of the imagination, the assignment is not complicated by students' prior knowledge. Once the unit is finished, the class can discuss the ecosystem and how it is similar to and different from real ecosystems.

  12. IE 172 Laboratory 1: Algorithm Analysis and Python Tools Dr. T.K. Ralphs

    E-print Network

    Ralphs, Ted

    . Conway's game of life is a simulation of the growth of a population that follows several very simple game board. We can store the current state of the population in a two-dimensional matrix. The challenge rules. The population is represented by cells represented by locations in a two-dimensional grid

  13. Recent advances in the source inversion of W-Phase Zacharie Duputel1, Luis A. Rivera1 and Hiroo Kanamori2

    E-print Network

    Duputel, Zacharie

    , we now incorporate horizontal ones. We also develop a real-time im- plementation of the inversion response and the bandpass filtering is performed in real-time using time domain recursive filters. Several, and non-linear inversions based on a centroid time delay grid search and a centroid location grid search

  14. Protein degradation in a TX-TL cell-free expression system using ClpXP protease Zachary Z. Sun1

    E-print Network

    Murray, Richard M.

    -based Escherichia coli expression system ("Transcription-Translation", or "TX-TL") has been developed! 1! Protein degradation in a TX-TL cell-free expression system using ClpXP protease AUTHORS that play an important role for in vivo circuit dynamics ­ namely protein degradation and protein dilution

  15. Darkroom: Compiling High-Level Image Processing Code into Hardware Pipelines James Hegarty John Brunhaver Zachary DeVito Jonathan Ragan-Kelley

    E-print Network

    Stanford University

    requires painstaking manual design in hardware. Based on this pattern, we present Darkroom, a language Hanrahan Stanford University MIT CSAIL Line-buffered pipeline ISP Corner Detection Edge Detection bx-level language for image processing into a line-buffered pipeline, modeled after optimized image signal processor

  16. 77 FR 7967 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-13

    ...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera Legal Authority...African python, Southern African python, boa constrictor, yellow anaconda,...

  17. 76 FR 40082 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-07

    ...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species from Python, Boa, and Eunectes Genera Legal Authority...African python, Southern African python, boa constrictor, yellow anaconda,...

  18. Initial Ph.D. Job Placement University of Tennessee Department of Economics

    E-print Network

    Tennessee, University of

    University, Moon Township, Pennsylvania 2010 Omer Bayar University of Evansville, Evansville, Indiana & Comptroller School, Ira C. Eaker Center for Professional Development, Maxwell Air Force Base, Alabama Zachary

  19. Python review sheet: Exam 3 A collection of items of any type: [10, 3, 22], ["sh", "ch"

    E-print Network

    Rusu, Adrian

    be used as an alternative to extend. L = ["apple", "banana"] print L Prints ["apple", "banana"] L.append("peach") Adds "raisin" to the end of L print L Prints ["apple", "banana", "raisin"] L.extend(["plum", "peach"] Adds "plum" and "peach" to the end of L print L Prints ["apple", "banana", "raisin", "plum", "peach

  20. Expression of Venom Gene Homologs in Diverse Python Tissues Suggests a New Model for the Evolution of Snake Venom

    E-print Network

    Castoe, Todd A.

    for the Evolution of Snake Venom Jacobo Reyes-Velasco,1 Daren C. Card,1 Audra L. Andrew,1 Kyle J. Shaney,1 Richard H Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across

  1. SAE2.py : a python script to automate parameter studies using SCREAMER with application to magnetic switching on Z.

    SciTech Connect

    Orndorff-Plunkett, Franklin

    2011-05-01

    The SCREAMER simulation code is widely used at Sandia National Laboratories for designing and simulating pulsed power accelerator experiments on super power accelerators. A preliminary parameter study of Z with a magnetic switching retrofit illustrates the utility of the automating script for optimizing pulsed power designs. SCREAMER is a circuit based code commonly used in pulsed-power design and requires numerous iterations to find optimal configurations. System optimization using simulations like SCREAMER is by nature inefficient and incomplete when done manually. This is especially the case when the system has many interactive elements whose emergent effects may be unforeseeable and complicated. For increased completeness, efficiency and robustness, investigators should probe a suitably confined parameter space using deterministic, genetic, cultural, ant-colony algorithms or other computational intelligence methods. I have developed SAE2 - a user-friendly, deterministic script that automates the search for optima of pulsed-power designs with SCREAMER. This manual demonstrates how to make input decks for SAE2 and optimize any pulsed-power design that can be modeled using SCREAMER. Application of SAE2 to magnetic switching on model of a potential Z refurbishment illustrates the power of SAE2. With respect to the manual optimization, the automated optimization resulted in 5% greater peak current (10% greater energy) and a 25% increase in safety factor for the most highly stressed element.

  2. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

    E-print Network

    Cooper, Christopher D; Barba, L A

    2013-01-01

    The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2%, then the simpler, single-surface model can be used. When calculating b...

  3. An Ecological Risk Assessment of Nonnative Boas and Pythons as Potentially Invasive Species in the United States

    Microsoft Academic Search

    Robert N. Reed

    2005-01-01

    The growing international trade in live wildlife has the potential to result in continuing establishment of nonnative animal populations in the United States. Snakes may pose particularly high risks as potentially invasive species, as exemplified by the decimation of Guam's vertebrate fauna by the accidentally introduced brown tree snake. Herein, ecological and commercial predictors of the likelihood of establishment of

  4. SADAATL 2014 COLING Workshop on Synchronic and Diachronic

    E-print Network

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Jargon-Term Extraction by Chunking Adam Meyers, Zachary Glass, Angus Grieve-Smith, Yifan He:30 Jargon-Term Extraction by Chunking Adam Meyers, Zachary Glass, Angus Grieve-Smith, Yifan He, Shasha Liao to Analyzing Technical Language (SADAATL 2014) Adam Meyers, Yifan He and Ralph Grishman (eds.) ii #12

  5. Journal of Comparative Physiology A Neuroethology, Sensory, Neural, and

    E-print Network

    Stockin, Karen

    avian lineages: paleognaths, parrots, and passerines Zachary Aidala, Leon Huynen, Patricia L. R. Brennan: paleognaths, parrots, and passerines Zachary Aidala · Leon Huynen · Patricia L. R. Brennan · Jacob Musser, including extinct moa (Emeidae), and parrots, including the nocturnal and flightless kakapo (Strigops

  6. 76 FR 6351 - Great Lakes Pilotage: 2011 Annual Review and Adjustment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-04

    ...USCG-2010-0517] RIN 1625-AB48 Great Lakes Pilotage: 2011 Annual Review and...rates for pilotage service on the Great Lakes to generate sufficient revenue...e-mail Mr. Paul Wasserman, Chief, Great Lakes Pilotage Division,...

  7. 75 FR 51191 - Great Lakes Pilotage Rates-2011 Annual Review and Adjustment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-19

    ...USCG-2010-0517] RIN 1625-AB48 Great Lakes Pilotage Rates--2011 Annual...increase the rates for pilotage on the Great Lakes to generate sufficient revenue...Paul M. Wasserman, Chief, Great Lakes Pilotage Division,...

  8. This summer, Zachary O'Hagan '11 will be studying a highly endangered Peruvian language--not in the classroom, but in a remote village in northeastern Peru, where

    E-print Network

    California at Berkeley, University of

    --not in the classroom, but in a remote village in northeastern Peru, where the last two native speakers live. Omagua in the Amazon Basin. Led by linguistics professor Lev Michael, Zach and three other students will travel to Peru contributing to our understanding of indigenous populations before the advent of Europeans. His work in Peru

  9. Provided by the College of Charleston Office of New Student Programs ~ parents@cofc.edu Resources for Parents

    E-print Network

    Kasman, Alex

    Rising by Neil Howe Rising Millennials Face Worldview Conflict by Shirley A. Carson The Naked Roommate: Lauren Schaffer and Sandy Fleischl Wasserman Almost Grown: Launching Your Child from High School

  10. 78 FR 54255 - HRSA's Bureau of Health Professions Advanced Education Nursing Traineeship Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-03

    ...Health Professions Advanced Education Nursing Traineeship Program AGENCY: Health Resources...announcing a change to its Advanced Education Nursing Traineeship (AENT) program. Effective...Joan Wasserman, DrPH, RN, Advanced Nursing Education Branch Chief, Division of...

  11. 1.1:1111 , , , 573.) (

    E-print Network

    Segall, Adrian

    ) ­. , , python( . www.python.org .)-interactive shell .-shell ( print "Hello world") ( Hello", "copyright", "credits" or "license" for more information. >>> print "Hello world" Hello world >>> ,Ctrl+D. , , hello.py: Print "Hello world from a file." , ,-python: ~$ python hello.py Hello world from a file

  12. Wildlife laundering through breeding farms: Illegal harvest, population declines and a means of regulating the trade of green pythons ( Morelia viridis) from Indonesia

    Microsoft Academic Search

    Jessica A. Lyons; Daniel J. D. Natusch

    Wildlife breeding farms have been promoted to aid biodiversity conservation by alleviating the pressure of harvest on wild populations. There is, however, growing concern that many breeding farms are being used to launder illegally caught wildlife. Surveys of wildlife traders in the Indonesian provinces of Maluku, West Papua and Papua were conducted between August 2009 and April 2011 to assess

  13. Investigation of sea-ice\\/Climate Interaction Models That Feature Abrupt, Switch-Like Behavior Using Python, a Low-Level Programming Language Useful for Climate Research

    Microsoft Academic Search

    I. D. Turnbull; G. Eshel; R. T. Pierrehumbert

    2005-01-01

    Recent study of interactions between sea ice, ocean circulation, and continental ice sheet advance and retreat have suggested that rapid, switch-like behavior may explain abrupt climate change evident in paleoclimatic records [Sayag et al., 2004]. The authors of this study theorized that the last glacial period was marked by periods of rapidly advancing sea ice cover in the northern hemisphere

  14. Python Challenge 2013 If you are interested in visiting the Center for Wildlife Education, please call at (912) 478-0831 or

    E-print Network

    Hutcheon, James M.

    ) A pinky tip dipped in black paint (or a dot from a marker once painting is dry) is the eye and the final touch for your eagle! 7) Set aside to dry. Additional crafting: Once your eagle painting is dry, you can

  15. Correction for "The Burmese python genome reveals the molec-ular basis for extreme adaptation in snakes," by Todd A. Castoe,

    E-print Network

    Chang, Belinda

    , David A. Ray, Federico G. Hoffmann, Robert Bogden, Eric N. Smith, Belinda S. W. Chang, Freek J. Vonk, Federico G. Hoffmann, Robert Bogden, Eric N. Smith, Belinda S. W. Chang, Freek J. Vonk, Nicholas R G. Hoffmanni,n , Robert Bogdenh , Eric N. Smithb , Belinda S. W. Changk , Freek J. Vonko

  16. Architecture and the Arts May 11, 2013 Class of 2013

    E-print Network

    Illinois at Chicago, University of

    in architecture, art and design, art history, and theatre and music. The curricula in each of the units also give and Music Sharon Haar Associate Dean, College of Architecture and the Arts Zachary Sherwood Candidate Architecture

  17. The relationship between depressive symptoms and error monitoring during response switching

    E-print Network

    Liu, Taosheng

    . Schroder & Tim P. Moran & Zachary P. Infantolino & Jason S. Moser Published online: 25 June 2013 material, which is available to authorized users. H. S. Schroder :T. P. Moran :J. S. Moser (*) Department of

  18. Fax +41 61 306 12 34 E-Mail karger@karger.ch

    E-print Network

    Murphy, Troy G.

    -Backed Orioles (Icterus pustulatus) Zachary J. Hall a Scott A. MacDougall-Shackleton a, b Marcela Osorio of the streak-backed oriole (Icterus pustulatus), a New World blackbird with a female bias in song rate

  19. Towards a Prototyping Tool for Behavior Oriented Authoring of Conversational Agents for Educational Applications

    E-print Network

    Rose, Carolyn Penstein

    Applications Gahgene Gweon, Jaime Arguello, Carol Pai, Regan Carey, Zachary Zaiss, Carolyn Rosé Human is reported in (Jordan, Ro- sé, & VanLehn, 2001; Aleven & Rosé, 2004; Rosé & Torrey, 2004). In this paper we

  20. presented by Thursday, March 14, 2013, 10am-1pm

    E-print Network

    Engel, Robert

    and Robert Engel Department of Chemistry and Biochemistry, Queens College-CUNY, Flushing, NY 11367 We Ligand Zachary M Adler, Thomas C. Strekas and Robert Engel Department of Chemistry & Biochemistry, Queens

  1. BAYESIAN SEGMENTATION OF CHEST TUMORS IN PET SCANS USING A POISSON-GAMMA MIXTURE MODEL

    E-print Network

    Dobigeon, Nicolas

    BAYESIAN SEGMENTATION OF CHEST TUMORS IN PET SCANS USING A POISSON-GAMMA MIXTURE MODEL Zacharie and real data. Experimental results on real chest PET images suggest that the proposed method can correctly

  2. HonorsConvocation TexasTechUniversity

    E-print Network

    Gelfond, Michael

    Engineering Nicholas Lehman Mechanical Engineering Elise Welsh Chemical Engineering Jenn Welsh Chemical Smith Justin Lee Talavera Kevin R Thomas Evan Wang Isaac Zachary Whitley Nolan Ryan Williams SUMMA CUM

  3. Ohio Valley Entomological Association 2009 Annual Business Meeting Minutes

    E-print Network

    Pittendrigh, Barry

    DerLaan, Purdue University ii. Second Place: Zachary Phillips, Ohio State University iii. Third Place: Jeffrey ii. Second Place: Kapil Raje, Purdue University iii. Third Place: Marissa McDonough, Purdue

  4. DigiSwitch: A device to allow older adults to monitor and direct the collection and transmission of health information collected at home

    E-print Network

    Camp, L. Jean

    of health information collected at home Kelly E. Caine, Celine Y. Zimmerman, Zachary Schall-Zimmerman adult, Privacy. Reference: Caine, K. E., Zimmerman, C. Y., Schall-Zimmerman, Z., Hazlewood, W. R., Camp

  5. 5320 J. Am. Chem. SOC.1993,115. 5320-5321 An Iodide Ion Complex of a Hydrophobic Tetraphenyl

    E-print Network

    Zheng, Zhiping

    5320 J. Am. Chem. SOC.1993,115. 5320-5321 An Iodide Ion Complex of a Hydrophobic Tetraphenyl [12.; Zacharie, B. J.Am. Chem.Soc. 1986,108, 73. (c) Wuest, J. D.; Zacharie, B. J. Am. Chem.Soc. 1987, 109. H.; Blanda, M.T.; Squattrito, P. J. J.Am. Chem. Soc. 1989,111,6294. (f) Newcomb, M.;Blanda, M. T

  6. Sage for Power Users William Stein

    E-print Network

    Stein, William

    Sage for Power Users William Stein February 13, 2012 #12;Contents 1 Introduction to Sage 5 1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2 What is Sage Programming Sage 11 2 Python 12 2.1 What is Python

  7. 50 CFR 16.15 - Importation of live reptiles or their eggs.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...prohibited except as provided under the terms and conditions set forth in § 16.22: (1) Boiga irregulari s (brown tree snake). (2) Python molurus (including P. molurus molurus (Indian python) and P. molurus bivittatus (Burmese...

  8. 50 CFR 16.15 - Importation of live reptiles or their eggs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...prohibited except as provided under the terms and conditions set forth in § 16.22: (1) Boiga irregulari s (brown tree snake). (2) Python molurus (including P. molurus molurus (Indian python) and P. molurus bivittatus (Burmese...

  9. 50 CFR 16.15 - Importation of live reptiles or their eggs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...prohibited except as provided under the terms and conditions set forth in § 16.22: (1) Boiga irregulari s (brown tree snake). (2) Python molurus (including P. molurus molurus (Indian python) and P. molurus bivittatus (Burmese...

  10. Prof. Amenta TA Jesse Smith

    E-print Network

    California at Davis, University of

    , you need lots of languages... Web pages ­ HTML5 and CSS Browser programs ­ Javascript and JQuery-oriented Python HTML5 and CSS Javascript Django-Python server framework This will be enough to make some

  11. 78 FR 44275 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-23

    ...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera Legal Authority...green anaconda, and Beni anaconda. The boa constrictor is still under...

  12. Why, When, and What: Analyzing Stack Overflow Questions by Topic, Type, and Code

    E-print Network

    Edinburgh, University of

    210799 android CSS 86961 css, css3 SQL 218326 sql, mysql, sql-server, postgresql, databases Version Used Category Count Related Stack Overflow Tags Java 281508 java, java-ee Python 122708 python Android is to find differences among c

  13. "Face new challenges, seize new opportunities, test your resources

    E-print Network

    Ginzel, Matthew

    . Raymond Daniel P. Aldrich Betty Bugusu Thomas W. Hertel Klein Ileleji Matthew Huber Sophie A. Lelièvre in statistical analysis and connecting them to para- metric estimation and change-point detection for Levy models computations in order to turn complex raw data into meaningful information. Adam Wasserman (chemistry

  14. Design and Spectroscopic Characterization of Peptide Models for the Plastocyanin Copper-Binding Loop

    E-print Network

    Gibney, Brian R.

    .; Wasserman, Z. R.; Lear, J. D. Science 1989, 243, 622-628. (4) Gibney, B. R.; Mulholland, S. E.; Rabanal, F.; Doughty, M. B. J. Am. Chem. Soc. 1995, 117, 8502-8510. (6) Mulholland, S. E.; Gibney, B. R.; Rabanal, F

  15. Bayesian Model Selection: Analysis of a Survival Model with a Surviving Fraction

    E-print Network

    , Joel Greenhouse, and Larry Wasserman Department of Statistics Carnegie Mellon University 232 Baker Hall, with low values reflecting more severe depression (Endicott, et al. 1976). For our data the GAS scores of recurrence, has been seen in studies of toxicants (Farewell 1982) and of treatment of pediatric malignancy

  16. Political Cartooning in the Age of Reagan

    Microsoft Academic Search

    Dan Wasserman

    1990-01-01

    Dan Wasserman, syndicated political cartoonist for the Boston Globe, speaks about his political caricatures of Reagan, Bush, Dukakis, and others, much of it during the 1988 election campaign.\\u000aThis talk was delivered at Sacred Heart University on November 15, 1988 as part of a lecture series dedicated to the memory of Daniel Friedman Gottlieb and Max Dickstein.

  17. Regression Analysis Department of Statistics 36-707 Fall 2010

    E-print Network

    Roeder, Kathryn

    : A Concise Course in Statistical Inference, by Larry Wasserman. 6. All of Nonparametric Statistics, by Larry, by Sanford Weisberg OTHER REFERENCES: 1. The Elements of Statistical Learning: Data Mining, Inference, and Prediction, by Trevor Hastie, Robert Tibshirani and Jerome Friedman. 2. Modern Applied Statistics With S

  18. 75 FR 7958 - 2010 Rates for Pilotage on the Great Lakes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ...2010 Rates for Pilotage on the Great Lakes AGENCY: Coast Guard, DHS. ACTION...rates for pilotage service on the Great Lakes by an average of 5.07% to generate...call Mr. Paul Wasserman, Chief, Great Lakes Pilotage Branch,...

  19. Our Growing Planet

    NSDL National Science Digital Library

    Elizabeth Lener

    2001-05-01

    Children are naturally curious and passionate about taking care of the world around them. To capitalize on these interests, the unit described in this article was the result of a schoolwide theme entitled People and the Planet (Wasserman 1996). The unit h

  20. A program to calculate bootstrap confidence intervals for the process capability index Cpk

    Microsoft Academic Search

    Gary S. Wasserman; Hassan A. Mohsen; LeRoy A. Franklin

    1991-01-01

    Franklin and Wasserman (1991) introduced the use of Bootstrap sampling procedures for deriving nonparametric confidence intervals for the process capability index, Cpk, which are applicable for instances when at least twenty data points are available. This represents a significant reduction in the usually recommended sample requirement of 100 observations (see Gunther 1989). To facilitate and encourage the use of these

  1. Fabrication of 5 nm linewidth and 14 nm pitch features by nanoimprint lithography

    E-print Network

    ) Haixiong Ge,b) Wei Wu,b) Mingtao Li,b) Zhaoning Yu,b) D. Wasserman, S. A. Lyon, and Stephen Y. ChoubFabrication of 5 nm linewidth and 14 nm pitch features by nanoimprint lithography Michael D. Austin,a),b. In photocurable nanoimprint lithography (P-NIL) (shown in Fig. 1), a mold is pressed into a low viscosity

  2. Papers and Proceedings of the Combined Annual Meetings of the Midwest History of Education Society and the History of Education Society (Chicago, Illinois, October 27-29, 1978).

    ERIC Educational Resources Information Center

    Rutkowski, Edward, Ed.

    1979-01-01

    The selected papers presented in this document include topics on normal schools in Wisconsin and Minnesota, George S. Counts, and segregated schooling in Kansas. "Wisconsin Normal Schools and the Educational Hierarchy, 1860-1890" (J. Wasserman) describes the struggle of normal schools to be perceived as teacher training institutions rather than…

  3. Attempted transfer of a learned geotropic response via injections of whole brain homogenate 

    E-print Network

    Smith, Douglas Calvin

    1973-01-01

    nomyci n-0 ~ h ' ~ RNA sy the 1 6 o emoty. Jou 1 of ~Neurochemist 1964, 11, 187-195. eyrne, W. L. (Ed. ) Mole ul r A h to ~tea i d M~emo Ne Yo h, Ne Yo ~a eml Pr , NTO. Byrne, W. L. , Samuel, D. , Bennett, E. I. , Rosensweig, M. R. , Wasserman, E...

  4. Pupil Dilation and Object Permanence in Infants

    ERIC Educational Resources Information Center

    Sirois, Sylvain; Jackson, Iain R.

    2012-01-01

    This paper examines the relative merits of looking time and pupil diameter measures in the study of early cognitive abilities of infants. Ten-month-old infants took part in a modified version of the classic drawbridge experiment used to study object permanence (Baillargeon, Spelke, & Wasserman, 1985). The study involved a factorial design where…

  5. Structural Balance and Transitivity

    E-print Network

    Liu, Huan

    Structural Balance and Transitivity Social Network Analysis, Chapter 6 Wasserman and Faust #12;Balance Theory Concerned with how an individual's attitudes or opinions coincide with those of others in a network balance vs dissonance if two actors that are "friends" have the same "attitude" toward a third

  6. Dryden: A Collection of Critical Essays. Twentieth Century Views Series.

    ERIC Educational Resources Information Center

    Schilling, Bernard N., Ed.

    One of a series of works aimed at presenting contemporary critical opinion on major authors, this collection includes essays by Bernard Schilling, T. S. Eliot, Louis I. Bredvold, James M. Osborn, Reuben A. Brower, Edwin Morgan, Earl Wasserman, R. J. Kaufmann, Moody E. Prior, Earl W. Miner, Edward N. Hooker, E. M. W. Tillyard, John Hollander,…

  7. 76 FR 8990 - Hours of Service of Drivers; Availability of Supplemental Documents and Corrections to Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-16

    ...Calcagno, J.A., Davis, W.T., Boulet, J.A.M. & Wasserman, J.F., ``Improving Heavy-Duty Diesel Truck Ergonomics to Reduce Fatigue and Improve Driver Health and Performance,'' FMCSA, December 2010. 3. Page 82179. Correct the...

  8. Belloni, A. and Chernozhukov, V. (2011). High Dimensional Sparse Econometric Models: An Introduction. arXiv:1106.5242

    E-print Network

    2011-01-01

    Belloni, A. and Chernozhukov, V. (2011). High Dimensional Sparse Econometric Models economet- ric models. arXiv:1201.0220. Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert. (2008 graphical models. Statistical Science, 27, 519-537. Wasserman, Larry and Kolar, Mladen and Rinaldo

  9. Keats: A Collection of Critical Essays. Twentieth Century Views Series.

    ERIC Educational Resources Information Center

    Bate, Walter Jackson, Ed.

    One of a series of works aimed at presenting contemporary critical opinion on major authors, this collection includes essays by Walter Jackson Bate, T. S. Eliot, Douglas Bush, Richard H. Fogle, Jack Stillinger, Harold Bloom, David Perkins, Earl Wasserman, and D. G. James--all dealing with the biography and literary work of John Keats. Designed for…

  10. Research: Deborah Smithen, Imam Uddin, Estelle Marchal, November 2010 Cassandra Hawco and Alison Thompson

    E-print Network

    Dellaire, Graham

    Communications 2007, 2701-2703. (6) Regourd, J.; Ali, A. A.-S.; Thompson, A. Journal of Medicinal Chemistry 2007.-C.; Yohannes, D.; Wasserman, H. H. Bioorganic and Medicinal Chemistry Letters 2006, 16, 701-704. (2) Dairi, K of Medicinal Chemistry 2000, 43, 2557-2565. (8) D'Alessio, R.; Rossi, A. Synlett 1996, 513-514. #12;

  11. Effects of Stimulus Duration and Choice Delay on Visual Categorization in Pigeons

    ERIC Educational Resources Information Center

    Lazareva, Olga F.; Wasserman, Edward A.

    2009-01-01

    We [Lazareva, O. F., Freiburger, K. L., & Wasserman, E. A. (2004). "Pigeons concurrently categorize photographs at both basic and superordinate levels." "Psychonomic Bulletin and Review," 11, 1111-1117] previously trained four pigeons to classify color photographs into their basic-level categories (cars, chairs, flowers, or people) or into their…

  12. IACMM Israel Association for Computational Methods in Mechanics Israel Symposium on Computational Mechanics (ISCM-29)

    E-print Network

    Adler, Joan

    in Mechanics with Neural Network Predictions 10:30 Coffee break 10:50 Lecture session A (10:50) Mark Wasserman Berrie Nanotechnology Institute, Technion Simulation of vibrational frequencies of carbon nanotubes (11 with Large Strains 15:25 Coffee break (15:40) Ofir Shor, Rafael Advanced Defence Systems Probabilistic

  13. Membrane Vesicles as a Vaccine Platform For Salmonella

    E-print Network

    Hinkley, Megan L

    2012-07-11

    Natl Acad Sci USA 80: 1159-1163 13. Murphy, J. R, L. Grez, L. Schlesinger, C. Ferreccio, S. Baqar, C. Mu?oz, S.S. Wasserman, G. Losonsky, J.G. Olson, and M.M. Levine. 1991. Immunogenicity of Salmonella typhi Ty21a vaccine for young children...

  14. Analysis of microarray data for treated fat cells Nicoleta Serban

    E-print Network

    Spirtes, Peter

    treatment. The analysis of the response to the drug treatment is based on two approaches: multiple hypothesis testing with rejection decision according to False Discovery Rate and cluster analysisAnalysis of microarray data for treated fat cells Nicoleta Serban Larry Wasserman , David Peters

  15. STAT 5103: Introduction to Probability Theory "Our world, our life, our destiny, are dom-

    E-print Network

    Petris, Giovanni

    ), Probability and Statistics (3rd ed.); Evans & Rosenthal (2004), Probability and Statistics; Wasserman (2004 mean) and their large-sample behavior. Assessment: Your final grade will be based on three in and not copied from someone else. Course grade: The course grade is equally divided between homework, midterms

  16. STAT 5103: Introduction to Probability Theory "Our world, our life, our destiny, are dominated by

    E-print Network

    Petris, Giovanni

    ), Probability and Statistics (3rd ed.); Evans & Rosenthal (2004), Probability and Statistics; Wasserman (2004) and their large-sample behavior. Assessment: Your final grade will be based on three in-class midterm examinations from someone else. Course grade: The course grade is equally divided between homework, midterms

  17. Stata Hybrids: Updates and Ideas

    NASA Technical Reports Server (NTRS)

    Fieldler, James

    2014-01-01

    At last year's Stata conference I presented two projects for using Python with Stata: a plugin that embeds the Python programming language within Stata and code for using Stata data sets in Python. In this talk I will describe some small improvements being made to these projects, and I will present other ideas for combining tools with Stata. Some of these ideas use Python, some use JavaScript and a web browser.

  18. Prof. Dr. Rdiger Brause Markus Hildebrand Robert-Mayer-Str. 11-15 markhild@stud.uni-frankfurt.de

    E-print Network

    Brause, R.

    ) Programmieren Sie ein neuronales Netz mit der Perzeptron-Lernregel in Python. Verwenden Sie dafür die Lernre neuronales Netz mit der Perzeptron-Lernregel in Python. Verwenden Sie dafür die Lernre- gel ,,Perzeptron1) Programmieren Sie nun ein weiteres Neuronales Netz in Python, diesmal ein AdaLinE. Verwenden sie die folgen- de

  19. Principles of Modern Molecular Simulation Methods

    E-print Network

    Shell, M. Scott

    · minimization (structures) · molecular dynamics (thermo & kinetics) · Monte Carlo (thermo) Free energy & phase will use Python programming language NumPy and SciPy Fortran (basics, for numerically intense routines only (exceeds?) commercial packages like Matlab, but is open source #12;Why Python + Fortran? Python alone

  20. A scripting interface for doubly linked face list based polygonal meshes 

    E-print Network

    Tett, Stuart Tosten

    2009-05-15

    rinding (Left: before peeling; Right: after peeling) . . . . . . . . . . . . . . 12 9 A simple handle creation (Left: before handle; Right: after handle) . . . . . . . . . . 13 10 Python ?Hello, world!? code... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 11 C++ ?Hello, world!? code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 12 Example Python code with results . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 13 An example of a dictionary in Python...

  1. A scripting interface for doubly linked face list based polygonal meshes 

    E-print Network

    Tett, Stuart Tosten

    2008-10-10

    rinding (Left: before peeling; Right: after peeling) . . . . . . . . . . . . . . 12 9 A simple handle creation (Left: before handle; Right: after handle) . . . . . . . . . . 13 10 Python “Hello, world!” code... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 11 C++ “Hello, world!” code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 12 Example Python code with results . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 13 An example of a dictionary in Python...

  2. Interactive Computing 1 Input/Output and Complex Arithmetic

    E-print Network

    Verschelde, Jan

    Interactive Computing 1 Input/Output and Complex Arithmetic interactive Python scripts complex Software (MCS 507 L-3) Interactive Computing 30 August 2013 1 / 33 #12;Interactive Computing 1 Input/Output and Complex Arithmetic interactive Python scripts complex arithmetic 2 Python Coding Style and pylint coding

  3. Dim light at night disrupts the short-day response in Siberian hamsters Tomoko Ikeno

    E-print Network

    Nelson, Randy J.

    Light pollution Pelage Immune function a b s t r a c t Photoperiodic regulation of physiologyDim light at night disrupts the short-day response in Siberian hamsters Tomoko Ikeno , Zachary M of melatonin under the control of a circadian clock. How- ever, artificial light at night caused by recent

  4. Subscriber access provided by Indiana University Analytical Chemistry is published by the American Chemical Society. 1155

    E-print Network

    Clemmer, David E.

    of Chemistry, Indiana University, Bloomington, Indiana 47405 A novel ion mobility spectrometry instrument in developing new ion mobility spectrometry (IMS) technologies that couple with mass spectrometry (MS) analyses Mobility Spectrometry Samuel I. Merenbloom, Rebecca S. Glaskin, Zachary B. Henson, and David E. Clemmer

  5. Bilingual Education in Texas: Exploring Best Practices

    E-print Network

    Ghosh, Banashwar; Hokom, Meghan; Hunt, Zachary; Magdaleno, Miriam; Su, Baoqiang

    2008-01-01

    ? ? ? ? ? Bilingual?Education?in?Texas:?Exploring?Best?Practices?? Final?Report? ? ? ? ? ? ? ? ? Project?Conducted?by:? Banashwar?Ghosh? Meghan?Hokom? Zachary?Hunt? Miriam?Magdaleno? Baoqiang?Su? ? Supervised?by?Lori?L.?Taylor,?PhD? Bush............................................................................................................................... 1 Bilingual?Education?through?a?Texas?Perspective..................................................................... 2 Limited?Education?Proficiency?Student?Demographics............................................................... 2 The...

  6. Water usage dropping on campus, but UT hopes to lower it more

    E-print Network

    Johnston, Daniel

    Water usage dropping on campus, but UT hopes to lower it more Photo Credit: Zachary Strain | Daily six years, UT has worked to decrease its water usage, but the University still has a ways to go if it the University was using one billion gallons of water per year. Across buildings, irrigation, chilling stations

  7. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (85th, Miami, Florida, August 5-8, 2002). Commission on the Status of Women Division.

    ERIC Educational Resources Information Center

    2002

    The Commission on the Status of Women Division of the proceedings contains the following 6 papers: "Relationship Content in Four Men's and Women's Magazines" (Alexis Zachary and Bryan Denham); "Mind the Gender Gap: Gender Differences in Motivation to Contribute Online Content" (Cindy Royal); "Peering through the Glass Ceiling of the Boys' Club:…

  8. Oracle-Based Optimization Applied to Climate Model Calibration

    E-print Network

    Beltran-Royo, Cesar

    Oracle-Based Optimization Applied to Climate Model Calibration C. Beltran N.R. Edwards A. B. Haurie J.-P. Vial§ D. S. Zachary¶ September 14, 2005 Abstract In this paper, we show how oracle by using an oracle-based optimization tool, Proximal-ACCPM. The oracle is a procedure which finds, for each

  9. Ambient Information Systems: Evaluation in Two Paradigms

    E-print Network

    Stasko, John T.

    Ambient Information Systems: Evaluation in Two Paradigms Zachary Pousman, John Stasko School, and apply their as- sumptions to the evaluation of ambient information systems. Ambient information Systems. Evaluating Ambient Information Systems (AISs) is a process of explaining how often an AIS is used, how much

  10. Previous Fires Moderate Burn Severity of Subsequent Wildland

    E-print Network

    Previous Fires Moderate Burn Severity of Subsequent Wildland Fires in Two Large Western US Wilderness Areas Sean A. Parks,1,2 * Carol Miller,1 Cara R. Nelson,2 and Zachary A. Holden3 1 U.S.D.A. Forest, Mis- soula, Montana 59801, USA; 2 Department of Ecosystem and Conservation Sciences, College

  11. STAT-MD Training Workshop Early identification of ASD for pediatric health care providers

    E-print Network

    Cui, Yan

    STAT-MD Training Workshop Early identification of ASD for pediatric health care providers Tues consultation and screening procedures to pediatric medical providers serving young children. This 1-day · Zachary Warren, Ph.D. Clinical Psychologist, Associate Professor of Pediatrics, Psychiatry and Special

  12. Opening the Black Box of Social Cognitive Mapping

    ERIC Educational Resources Information Center

    Neal, Zachary P.; Neal, Jennifer Watling

    2013-01-01

    This article provides Zachary P. Neal and Jennifer Watling Neal's response to Thomas W. Farmer and Hongling Xie's commentary on Neal and Neal's "Multiple Meanings of Peer Groups in Social Cognitive Mapping." Neal and Neal assert that many of Farmer and Xie's comments highlight the motivation behind their original…

  13. GameMath! Embedding Secondary Mathematics into a Game Making Curriculum

    E-print Network

    Kim, Jihie

    GameMath! Embedding Secondary Mathematics into a Game Making Curriculum Erin Shaw, Zachary Boehm experiences designing GameMath!, a mathematics learning track for a new game making curriculum called strategies to embed mathematics in authentic contexts. The curriculum is being developed and implemented

  14. Harmonic Syntax in the "Serial" Works of Dmitri Shostakovich

    E-print Network

    Webber, Miriam Brack

    2013-05-31

    ....................................................18 Andrey Volkonsky .............................................................................................................19 Musica Stricta: Analysis... with Shostakovich: both composers utilize multiple twelve-tone rows. Zachary Cairns’ discussion of multiple rows in the Russian serial music of Andrey Denisov may shed some further light on this phenomenon. Cairns defines the use of multiple rows as more than one...

  15. DEAN'S LIST Spring Semester 2013

    E-print Network

    Wong, Pak Kin

    , Linda C. Alyousef, Hassan Ammann, Kaitlyn R. Anderson, Zachary C. Andrews, William Michael Armstrong Michael Blum, Aidan Io Boles, Hanah Veronica Bollig, Michael Jean-Luc Boone, Cory Stefan Bradbury, Alison, Daniel Andrew Grady, Ryan P. Graves, Logan Rodriguez Greivenkamp, Jake E. Groff, Dustin M. Gudvangen

  16. DEAN'S LIST Spring Semester 2013

    E-print Network

    Wong, Pak Kin

    , Abdullah Allee, Linda C. Alyousef, Hassan Ammann, Kaitlyn R. Anderson, Zachary C. Andrews, William Michael Beyak, Ethan Samuel Blum, Aidan Io Boles, Hanah Veronica Bollig, Michael Jean-Luc Boone, Cory Stefan Gorin, Daniel Andrew Grady, Ryan P. Graves, Logan Rodriguez Gudvangen, Kjel Thomas Hart, Matthew R. Heet

  17. BIOINFORMATICS ORIGINAL PAPER Vol. 24 no. 21 2008, pages 24982504

    E-print Network

    Jakobsson, Mattias

    informative when populations are studied for highly variable multiallelic markers, such as microsatellites/btn478 Genetics and population analysis ADZE: a rarefaction approach for counting alleles private to combinations of populations Zachary A. Szpiech1,, Mattias Jakobsson1,2,3 and Noah A. Rosenberg1,2,4 1Center

  18. Effects of Experience on Short-and Long-term Foraging Performance in Bumblebees

    E-print Network

    Dukas, Reuven

    Effects of Experience on Short- and Long-term Foraging Performance in Bumblebees Zachary Durisko*, Les Shipp & Reuven Dukas* * Animal Behaviour Group, Department of Psychology, Neuroscience on performance are widely appreciated in humans (Ericsson et al. 2006), but have rarely been closely examined

  19. Leveraging Light-Weight Analyses to Aid Software Maintenance Ph.D. Dissertation Proposal

    E-print Network

    Weimer, Westley

    Leveraging Light-Weight Analyses to Aid Software Maintenance Ph.D. Dissertation Proposal Zachary P of finding and fixing bugs (e.g. [4, 15, 20, 23, 30, 31, 45, 47, 53, 71]) and to ensure long-term system-of-the-art work in many of these areas and full practical adoption. We aim to close that gap by using light

  20. The University of New Hampshire Department of Music

    E-print Network

    Pohl, Karsten

    Program 4:00 Jazz Band To be selected from the following: Four, Five, Six Frank Foster Bitter Jug Paul McKee/W. King/arr. Paul McKee El Gatote Matt Harris Nathan Jorgensen, director INTERMISSION Smoking, food, drink Andrew LeFoley Guitar Richie Smith Bass Gardner Rulon-Miller Jason Emmond Drums Zachary King Dominic

  1. Minutes taken by Secretary Christopher Kulesza Page 1 of 8 >Dr. James Westman, Director, Purdue University Student Health Center

    E-print Network

    Ginzel, Matthew

    . > Emergency room copay has been decreased. >No concern for visits outside of network. Will be paid regardless decreased. >Copayments have been decreased for prescriptions. >Contraceptives are now payable. >Preventative Absences (Proxies Sent and Other Emergencies) Steve Kimble (Christine Keller) Zachary Davis (Joel Davis

  2. Significance of the concentration gradients associated with dunite bodies in the Josephine and Trinity ophiolites

    E-print Network

    and Trinity ophiolites Zachary Morgan and Yan Liang Department of Geological Sciences, Brown University bodies in the Josephine and Trinity ophiolites. The major peridotite lithologies sampled in the Josephine this study and those from other ophiolite studies also demonstrate that concentration profiles in dunite

  3. VISUAL QUERY OF TIME-DEPENDENT 3D WEATHER IN A GLOBAL GEOSPATIAL

    E-print Network

    Shaw, Chris

    1 VISUAL QUERY OF TIME-DEPENDENT 3D WEATHER IN A GLOBAL GEOSPATIAL ENVIRONMENT William Ribarsky WEATHER IN A GLOBAL GEOSPATIAL ENVIRONMENT William Ribarsky, Nickolas Faust, Zachary Wartell, Christopher stream of large scale, time-dependent, 3D weather data in a global environment. The structure supports

  4. nATuRE CommunICATIons | 2:510 | DoI: 10.1038/ncomms1518 | www.nature.com/naturecommunications 2011 Macmillan Publishers Limited. All rights reserved.

    E-print Network

    Yanik, Mehmet Fatih

    screening of synaptogenesis. our platform enables the induction of synaptic structures in regular arrays that improve neuroligin-1-induced synaptogenesis by modulating class-I HDACs. We also found a structure molecules that enhance synaptogenesis Peng shi1, , mark A. scott1 , Balaram Ghosh2 , Dongpeng Wan2 , Zachary

  5. Photoperiod Mediated Changes in Olfactory Bulb Neurogenesis and Olfactory Behavior in Male White-

    E-print Network

    Nelson, Randy J.

    - Footed Mice (Peromyscus leucopus) James C. Walton*. , Leah M. Pyter.¤ , Zachary M. Weil, Randy J. Nelson. Several small rodent species, including Peromyscus leucopus, display seasonal (photoperiodic) brain olfactory bulb neurogenesis and olfactory behavior in Peromyscus leucopus. Citation: Walton JC, Pyter LM

  6. Chronobiology International, 2013; 30(9): 10891100 ! Informa Healthcare USA, Inc.

    E-print Network

    Nelson, Randy J.

    of hippocampal neuronal morphology of siberian hamsters Tomoko Ikeno, Zachary M. Weil, and Randy J. Nelson clock gene, Bmal1, in the hippocampus of Siberian hamsters. Diurnal rhythms in total length of dendrites, seasonality, Siberian hamsters, trkb, VEGF INTRODUCTION Many organisms are able to respond to annual cycles

  7. Tutors Spring 2014 Name Email Address

    E-print Network

    Indiana University

    Tutors Spring 2014 INFO-I 101 Name Email Address Hammel, Ashley hammela@indiana.edu Melendy, Jacob@indiana.edu Santiago, Gabriel gabsanti@indiana.edu INFO-I 201 Name Email Address Vaughan, Zachary zvaughan@indiana.edu Mannfeld, Jordan jmannfel@indiana.edu Nguyen, Tiffany tpnguyen@indiana.edu INFO-I 202 Name Email Address

  8. Analysis of Over 10,000 Cases Finds No Association between Previously-Reported Candidate Polymorphisms and Ovarian

    E-print Network

    Salzman, Daniel

    Polymorphisms and Ovarian Cancer Outcome Kristin L. White1, Robert A. Vierkant2, Zachary C. Fogarty2, Bridget Lester22, Weiva Sieh21, Valerie McGuire21, Joseph H. Rothstein21, Argyrios Ziogas20, Jan Lubiski19 of Public Health and Primary Care, University of Cambridge, Cambridge, UK. 7Cancer Division, Queensland

  9. 44 Scientific American, January 2013 Photograph by Tktk Tktk quantum physics

    E-print Network

    44 Scientific American, January 2013 Photograph by Tktk Tktk quantum physics Strange and StringyIllustration by Artist Name Photograph by Zachary Zavislak MAGNET is being levitated by an unseen superconductor in which countless trillions of electrons form a vast interconnected quan- tum state. Astoundingly, the quantum state

  10. Moniliformis moniliformis Infection Has No Effect on Some Behaviors of the Cockroach Diploptera punctata

    E-print Network

    Gotelli, Nicholas J.

    Moniliformis moniliformis Infection Has No Effect on Some Behaviors of the Cockroach Diploptera MoniliformismoniliformisInfectionHasNo Effecton Some Behaviorsof the CockroachDiplopterapunctata ZacharyAllely,Janice Moore, 1991; Gotelli and Moore, 1992), the behavioral responses of sev- eral cockroach host species

  11. "Creating Unity from Diversity: Finding Our Commonalities, Respecting Our Differences." Presenter Abstracts of the Annual National Conference of the National Multicultural Institute (9th, Washington, D.C., May 19-22, 1994).

    ERIC Educational Resources Information Center

    National Multicultural Inst., Washington, DC.

    This is primarily a collection of abstracts for training workshops for professionals in the field of multicultural education. The abstracts are: (1) "An Exploration of the Unspoken: A Group Relations Approach to Multicultural Dialogue" (Zachary G. Green); (2) "Exploring Our Cultural Assumptions" (Daniel Rivera); (3) "Challenging Homophobia:…

  12. I N T H E N E W S Founder's Column 2

    E-print Network

    Detwiler, Russell

    generation (SHG). The microscope used in this study is a novel clinical instrument, the "MPT-flex," developed- photon microscopy," by M. Balu, K. M. Kelly, C. B. Zachary, R. M. Harris, T. B. Krasieva, K. König, A. J on laser- scanning multiphoton microscopy (MPM). MPM "sees" through the skin surface by generating 3D imag

  13. Combining Self-Assembled Monolayers and Mass

    E-print Network

    Mrksich, Milan

    Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips Zachary A. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well current work with self-assembled monolayers (SAMs) to tailor the interfacial layer, and emphasize current

  14. THE JOURNAL OF CHEMICAL PHYSICS 136, 174101 (2012) Optimizing transition states via kernel-based machine learning

    E-print Network

    Henkelman, Graeme

    2012-01-01

    -based machine learning Zachary D. Pozun,1,2 Katja Hansen,1,3,a) Daniel Sheppard,1,2,b) Matthias Rupp,1,3,c, Austin, Texas 78712-0165, USA 3 Machine Learning Group, Computer Science Department, Technische mechanisms. To generate optimal dividing surfaces, we apply a cycle of machine-learning and refinement

  15. The Need for Predictable Garbage Collection Alastair Reid, John McCorquodale, Jason Baker,

    E-print Network

    Utah, University of

    in part by the Defense Advanced Re­ search Projects Agency, monitored by the Department of the Army under­ resenting official views or policies, either expressed or implied, of the Defense Advanced Research Projects Hsieh, Joseph Zachary Department of Computer Science University of Utah Abstract Modern programming

  16. March 26, 2013 Strozier Library

    E-print Network

    Sura, Philip

    . Eric Wiebelhaus-Brahm, Political Science An ERP Investigation of the Automatic Evaluation Effect Cody Therapy Roxy Marrese Faculty Mentor: Dr. Thomas Smith, Social Work If You've Got It, Flaunt It: Why Men and Women Flaunt Attractive Partners Zachary Kustin Research Mentor: Bo Winegard, Psychology Image Analyses

  17. Psychology of Success 1 The Science of Success

    E-print Network

    Liu, Taosheng

    from a hat.) This person can be an athlete, politician, artist, musician, scientist, entrepreneurPsychology of Success 1 PSY493 The Science of Success TU/TH: 3:004:20 PM 314 Berkey Hall D. Zachary Hambrick, Ph.D. Office Hours: TU/TH, 1:302:30, Room 298B, Psychology Overview

  18. A general protocol for the crystallization of membrane proteins for X-ray structural investigation

    E-print Network

    Zachary E R Newby1, Joseph D O'Connell III1, Franz Gruswitz1, Franklin A Hays1, William E C Harries1, Ian in the membranes of cells. To accomplish this, membrane proteins first need to be either heterologously expressed and then proceeds through cell membrane isolation, solubilization, purification, identification of conditions

  19. Vol. IV No. 1 Spring 2010

    E-print Network

    Finzi, Adrien

    Ruxandra Iordache Jenna Kreyche Nicholas Kyriacou Andrew J. Pellitieri William Seltzer AaronTsang ARCHÉ ADVISING EDITOR Zachary Bos ART DIRECTOR Elenor F.Amari FACULTYADVISOR Walter Hopp, Ph.D. EXTERNAL REVIEWERS Jarrod L. Schaeffer Stacey Goguen John Grey Josh McDonald Peter Moore Richard Cipolla ASSISTANT

  20. Updated On: 11/16/2012 15:38 Teams: Reptar on Ice points The Dangle Berries points

    E-print Network

    Sridhar, Srinivas

    Joe Ryder 1 Susanne Hudis 0 Ryan Beauchesne 0 Connor Nolan 2 Matt Lagarto 0 Daniel Monohan 1 0 Barakat 0 Hannah Berry #12;Bruno Ravioli points Dont Toews Me Bro points Nicholas Berns points Zachary Rassam - C 1 Thomas Lewis - C 3 Nicholas Berns - C 2 Dave Margolius 0 Matthew Cassista 4 Nicholas Lau 1

  1. An Integrated Science Plan for the Lake Tahoe Basin: Conceptual Framework and Research Strategies Patricia N. Manley,

    E-print Network

    Standiford, Richard B.

    Strategies Patricia N. Manley, 2 Dennis D. Murphy, 3 and Zachary P. Hymanson 4 Introduction Uncertainties. Conceptual framework for an integrated science program. In: Hymanson, Z.P.; Collopy, M.W., eds. An integrated: 19­35. Chapter 2. 2 Pacific Southwest Research Station, USDA Forest Service, Davis, CA 95618. 3

  2. Reliable Storage and Querying for Collaborative Data Sharing Systems

    E-print Network

    Pennsylvania, University of

    Reliable Storage and Querying for Collaborative Data Sharing Systems Nicholas E. Taylor and Zachary G. Ives Computer and Information Science Department, University of Pennsylvania Philadelphia, PA, U DBMSs, com- bined with archived storage of all database versions. ORCHESTRA adopts a peer

  3. Tableau Machine: A Creative Alien Presence , Mario Romero

    E-print Network

    California at Santa Cruz, University of

    Tableau Machine: A Creative Alien Presence Adam Smith , Mario Romero , Zachary Pousman of what we call "alien presence": an ambient, non-human, embodied, intelligent agent. From overhead video as emergent visual properties detected by a pixel-level image analysis. TM was designed as an alien presence

  4. Numerical Simulations of Interactions between Gravity Waves and Deep Moist Convection

    E-print Network

    Randall, David A.

    Numerical Simulations of Interactions between Gravity Waves and Deep Moist Convection ZACHARY A gravity waves that it generates. A large number of trajectories are used to evaluate the behavior; Pandya and Alexander 1999; Lane et al. 2001) studies, gravity waves have been shown to propagate

  5. Mode and Carrier Choice in the Quebec City -Windsor Corridor: A Random Parameters

    E-print Network

    Bierlaire, Michel

    Mode and Carrier Choice in the Quebec City - Windsor Corridor: A Random Parameters Approach Zachary Ontario M5B 2K3, Canada. Email: murtaza.haider@ryerson.ca 1 #12;Abstract The Quebec City-Windsor corridor presents the findings of a random parameters mixed-logit model of shipper carrier choice in the Quebec City

  6. ORIGINAL PAPER DigiSwitch: A Device to Allow Older Adults to Monitor

    E-print Network

    Connelly, Kay

    and Transmission of Health Information Collected at Home Kelly E. Caine & Celine Y. Zimmerman & Zachary Schall-Zimmerman K. E. Caine (*) :C. Y. Zimmerman :Z. Schall-Zimmerman : W. R. Hazlewood :L. Jean Camp :K. H, IN 47408, USA e-mail: caine@indiana.edu C. Y. Zimmerman e-mail: celzimme@indiana.edu Z. Schall-Zimmerman e

  7. Analysis of Preoperative Factors for Time-Independent and Time-Dependent Outcomes

    E-print Network

    DeUgarte, Daniel A.

    2013-01-01

    Author Contributions Literature search, study design, dataDaniel DeUgarte, MD * Literature search, study design, dataZachary Burke * Literature search, study design, data

  8. The Price of Civil Society Russell Buehler1

    E-print Network

    Liben-Nowell, David

    . The new social game has its own equilibria, and the price of civil society denotes the ratio of the social. We initiate the study of the price of civil society in the context of a simple class of gamesThe Price of Civil Society Russell Buehler1 , Zachary Goldman2 , David Liben-Nowell1 , Yuechao Pei2

  9. The Price of Civil Society Russell Buehler1

    E-print Network

    Sharp, Alexa

    . We initiate the study of the price of civil society in the context of a simple class of gamesThe Price of Civil Society Russell Buehler1 , Zachary Goldman2 , David Liben-Nowell1 , Yuechao Pei2 work in algorithmic game theory assumes that players ignore costs incurred by their fellow players

  10. Referral Web: combining social networks and collaborative filtering

    Microsoft Academic Search

    Henry A. Kautz; Bart Selman; Mehul A. Shah

    1997-01-01

    This paper appears in the Communications of the ACM,vol. 40 no. 3, March, 1997.Numerous studies have shown that one of the most the most effective channelsfor dissemination of information and expertise within an organization is itsinformal network of collaborators, colleagues, and friends (Granovetter 1973;Kraut 1990; Wasserman and Galaskiewicz 1994). Indeed, the social network1is as least as important as the official

  11. O N L I N E P R E S E N TAT I O N WELCOME & INTRODUCTIONS

    E-print Network

    Williams, Gary A.

    -Based Scholarships ­ 1st year Need-Based Grants, Lew & Edie Wasserman Grants. #12;HISTORY OF ALUMNI SCHOLARSHIPS D I R E C T O R , A L U M N I S C H O L A R S H I P S P R O G R A M #12;THE UCLA ALUMNI SCHOLARSHIPS PROGRAM #12;WHAT IS AN ALUMNI SCHOLARSHIP Since 1936, thousands of UCLA students, loyal alumni, dedicated

  12. Molecular Binding Energies from Partition Density Functional Theory

    SciTech Connect

    Nafziger, J.; Wu, Q.; Wasserman, A.

    2011-12-21

    Approximate molecular calculations via standard Kohn-Sham density functional theory are exactly reproduced by performing self-consistent calculations on isolated fragments via partition density functional theory [P. Elliott, K. Burke, M. H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.

  13. Quiz Section 1 Tanya Grancharova

    E-print Network

    Borenstein, Elhanan

    file containing one line print "Hello, world!" · Be sure to end line with enter · Save file as hello.py in present working directory · In terminal type "python hello.py" > python hello.py Hello, world! #12;Objects, and then prints them on the same line with a colon in between > python print-two-args.py hello world hello : world

  14. Jonathan Faubert: jonfaub@gmail.com : (352) 514 -6145 Jonathan Faubert

    E-print Network

    Verbrugge, Clark

    ADDITIONAL SKILLS AND COMPETENCIES Languages Spoken and Written: French, English Personal Traits Excellent SKILLS Languages Proficient in: Java, C, TCL, Oracle sqlplus, ENOVIA MQL. Familiar with: C++, Python

  15. Southwest Research Institute ) is working to enhance

    E-print Network

    Chapman, Clark R.

    a unique combination of advanced capabilities in computer engineering coupled with extensive expertise including: · Fortran · C/C++ · Python Advanced Application Programming Interfaces and Compiler Tools

  16. Infrastructure Hans de Vries

    E-print Network

    Vries, Hans de

    Other questions Software Easier installation (congure) Python interfaces EMS Choose usercode menu performance External services Web servers Offices KNMI-WAN Data communication Firewall Storage SANTape

  17. "A Carpenter Is Only as Good as His or Her Tools": Doing Good Science

    E-print Network

    Lin, Johnny

    tools: Rawinsondes, radar, satellites, etc. Experimental tools: Wind tunnels, rotating tables, chemical (AOS) users interested in learning Python. Experienced AOS users to learn of recent advances, support

  18. Protecting Cattle from Horn Flies 

    E-print Network

    Tomberlin, Jeffery K.

    2004-05-24

    Force GardStar Plus Atroban, Deckem, Expar, GardStar, Z-Permethrin Fenvalerate 8.6% Ectrin Cyfluthrin 10% Cutter Gold Lambda-cyhalothrin 10% + PBO 13% Saber Extra Zetacypermethrin 10% + PBO 20% Python Magnum Zeta Gard Python Combination ear tags...

  19. Genome 373 Spring 2012 -Problemset 3 -Due Thu April 19, by 8am (12 pts) 1. You're studying a particular gene and have used PCR to amplify a fragment of

    E-print Network

    Borenstein, Elhanan

    exactly two. >python choose2.py apple orange banana pear apple orange apple banana apple pear orange banana orange pear banana pear total: 6 (8 pts) 2. Write a program, items.txt: Apple Orange Banana >python choose2fromfile.py items.txt apple orange apple banana

  20. Projektbericht Marina Shvalova und Oliver Bestmann

    E-print Network

    Parallelrechnerevaluation PySpank: Python Interface zu SPANK Betreuer: Julian Kunkel Wissenschaftliches Rechnen Department-ins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3 SPANK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3 PySPANK 10.1 Motivation und Zielsetzung Im Rahmen dieser Arbeit wird ein Python Interface PySPANK zu einer Plug-in Schnitt

  1. doi:10.1152/ajpregu.00664.2005 290:1407-1412, 2006. First published Dec 22, 2005;Am J Physiol Regul Integr Comp Physiol

    E-print Network

    Bennett, Albert F.

    of the Burmese python ( Postprandial increase of oleoylethanolamide You might find this additional information.physiology.orgDownloadedfrom #12;Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python, Albert F. Bennett, James W. Hicks, and Daniele Piomelli. Postprandial increase of oleoylethanolamide

  2. Lizards & Snakes: Alive! Coloring Book

    NSDL National Science Digital Library

    This seven-page printable handout includes pictures of the following squamates for kids to color: Rhinoceros Iguana (Cyclura cornuta), Veiled Chameleon (Chamaeleo calyptratus,) Madagascan Giant Day Gecko (Phelsuma madagascariensis), Water Monitor (Varanus salvator), Gabon Viper (Bitis gabonica)and Burmese Python (Python molurus).

  3. Physics 440/740 -1-Fall 2012 SFSU Physics 440/740: Computational Phyics

    E-print Network

    Barranco, Joseph

    data; coupled ordinary differential equations for initial value problems; Fast Fourier Transforms (FFTs; compilers for FORTRAN90, C, C++, or Python (4) LaTex document preparation software package Important or Engineering 213 or an equivalent class in basic programming in FORTRAN, C, C++, Python, etc. Please see me

  4. Basics of MPI 1 Message Passing Interface

    E-print Network

    Verschelde, Jan

    Basics of MPI 1 Message Passing Interface one program to code manager/worker model hello world to broadcast an array of doubles 3 MPI for Python bindings of MPI for Python hello world with mpi4py to Supercomputing (MCS 572) Basics of MPI L-4 22 January 2014 1 / 37 #12;Basics of MPI 1 Message Passing Interface

  5. Annotation Tools for Large-Scale Corpus Development: Using AGTK at the Linguistic Data Consortium

    E-print Network

    Pennsylvania, University of

    . Producing large volumes of richly annotated data under strict deadlines demands sub- stantial infrastructureEndOffset, SetFeature, GetFeature ¯ GetAnnotationSet, Load, Store The core AG library is implemented in C Python, Tcl, Perl and Java. All annotation tools described in this paper are written in Python. Another

  6. CPSC 235 Fall 2013 Assignment 3: Drawing A Recursive Curve

    E-print Network

    Li, Zongpeng

    CPSC 235 ­ Fall 2013 Assignment 3: Drawing A Recursive Curve Due: October 23 2010, before mid above. In this assignment, your task is to write a Python program that prints QuickDraw commands to draw. For example, $ python3 a3.py 3 should draw the curve at level 3. Recall that by including from sys import argv

  7. Frontiers in Neuroinformatics www.frontiersin.org February 2009 | Volume 3 | Article 3 | 1 NEUROINFORMATICS

    E-print Network

    Sederberg, Per B.

    for Behavioral Brain Sciences, Magdeburg, Germany 14 Center for Cognitive Neuroscience, Dartmouth College. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can recordings, machine learning, Python applicability to humans, and the corresponding neural correlates

  8. Jednooci jednookym 2011 FEniCS -very short introduction

    E-print Network

    Cerveny, Vlastislav

    element Automatic Tabulator (curently Lagrange, mixed FE) Instant Python module that allows for instant inlining of C and C++ code in Python UFC Uni ed Form-assembly Code is a uni ed framework for nite element assembly UFL Uni ed Form Language is speci c language for declaration of nite element discretizations

  9. Wild populations of Argen-tine tegu lizards, also known

    E-print Network

    Jawitz, James W.

    outcompete natives in Hawaii Egg-eating Pythons Invasive species news for busy Extension professionals T h e : Focal Species: Argentine Tegu 1 Science: Egg- eating Pythons 2 Science: Florida Herp Invasions 2 Science and their invasion pathway and determined their current invasion status. Of these 137 species, they found that 56

  10. Orbital stability in combined uniform axial and three-dimensional wiggler magnetic fields for free-electron lasers

    NASA Technical Reports Server (NTRS)

    Johnston, S.

    1984-01-01

    Zachary Phys. Rev. A 29 (6), 3224 (1984) recently analyzed the instability of relativistic-electron helical trajectories in combined uniform axial and helical wiggler magnetic fields when the radial variation of the wiggler field is taken into account. It is shown here that the type 2 instability comprised of secular terms growing linearly in time, identified by Zachary and earlier by Diament Phys. Rev. A 23 (5), 2537 (1981), is an artifact of simple perturbation theory. A multiple-time-scale perturbation analysis reveals a nonsecular evolution on a slower time scale which accommodates an arbitrary initial perturbation. It is shown that, in the absence of exponential instability, the electron seeks a modified helical orbit more appropriate to its perturbed state and oscillates stably about it. Thus, the perturbed motion is oscillatory but nonsecular, and hence the helical orbits are stable.

  11. Factors Mediating Alcohol Craving and Relapse: Stress, Compulsivity, and Genetics

    PubMed Central

    Rodd, Zachary A.; Anstrom, Kristin K; Knapp, Darin J.; Racz, Ildiko; Zimmer, Andreas; Serra, Salvatore; Bell, Richard L.; Woodward, Donald J.; Breese, George R.; Colombo, Giancarlo

    2010-01-01

    This article represents the proceedings of a symposium at the 2004 annual meeting of the International Society for Biomedical Research on Alcoholism in Heidelberg, Germany. The symposium was organized by Zachary A. Rodd and Giancarlo Colombo. The presentations were (1) Pharmacological reversal of cycled withdrawal-sensitized or stress-sensitized withdrawal anxiety and enhanced ethanol drinking, by Darin J. Knapp and George R. Breese, (2) Alcohol craving and relapse in rats genetically selected for high alcohol preference, by Zachary A. Rodd and Richard L. Bell, (3) Exposure to stress increases dopaminergic burst firing in awake rats, by Kristin Anstrom and Donald J. Woodward, (4) Involvement of cannabinoid CB1 and GABAB receptors in the control of relapse-like drinking in alcohol-preferring Sardinian alcohol-preferring rats by Giancarlo Colombo and Salvatore Serra, and (5) Stress-induced ethanol drinking in CB1?/?, POMC, and PENK knockout mice, by Idiko Racz and Andreas Zimmer. PMID:16088996

  12. JPython 1.0

    NSDL National Science Digital Library

    The JPython 1.0 programming environment, created under the aegis of the Corporation for National Research Initiatives, implements the popular Python programming language in the Java environment. JPython leverages the power and portability of Java by compiling Python directly to portable Java bytecodes which can be run on any Java Virtual Machine (VM). Beyond allowing standard Python to run on a Java VM, the system also seamlessly integrates Java classes into Python, allowing the programmer to use libraries such as the Abstract Window Toolkit (AWT) within a Python script. While this version has some bugs and incompatibilities, it is still an interesting and useful tool for experimentation and development. JPython 1.0 is certified as 100% Pure Java and is freely available for both commercial and non-commercial use.

  13. The morphology of polymer modified asphalt and its relationship to rheology and durability

    E-print Network

    Kraus, Zachary Rothman

    2008-10-10

    binders in Figures 2-4 and 2-5 perhaps due to polymer-asphalt interactions. These interactions may serve to disperse asphaltene associations thereby decreasing the asphaltene content from the base binder. The decrease in asphaltene content showed... THE MORPHOLOGY OF POLYMER MODIFIED ASPHALT AND ITS RELATIONSHIP TO RHEOLOGY AND DURABILITY A Thesis by ZACHARY ROTHMAN KRAUS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment...

  14. Non-Mimetic Simulation Games: Teaching Team Coordination from a Grounding in Practice 

    E-print Network

    Dugas Toups, Zachary Oliver

    2011-10-21

    for the degree of DOCTOR OF PHILOSOPHY August 2010 Major Subject: Computer Science Non-mimetic Simulation Games: Teaching Team Coordination from a Grounding in Practice Copyright 2010 Zachary Oliver Dugas Toups NON-MIMETIC SIMULATION GAMES: TEACHING TEAM... of Committee, Andruid Kerne Committee Members, Richard Furuta Charles D. Samuelson Scott Schaefer Head of Department, Valerie E. Taylor August 2010 Major Subject: Computer Science iii ABSTRACT Non-mimetic Simulation Games: Teaching Team Coordination...

  15. An operational analysis of protected-permitted lead-lag left-turn phasing 

    E-print Network

    Gaston, Gilmer D

    1991-01-01

    number of sneakers are presented. This research also illustrates the importance of considering the impacts of progression quality in delay estimation. DEDICATION This thesis is dedicated to my wife, Connie, and son Zachary. I have sacrificed many... Observations 71 Accepted and Rejected Headway Analysis . . . . . . . . , . 74 Critical Gap Analysis 77 Left-Turn Headway Data 78 Average Number of Left-Turn Sneakers. . . . . . . . . . . . . 79 Observed Leading and Lagging Delay Measurements . . . 82...

  16. VPython

    NSDL National Science Digital Library

    Python (from www.vpython.org) Python is a powerful object-oriented programming language initiated by Guido van Rossum in 1990. See the essay by van Rossum on "Programming for Everybody," www.python.org/cp4e. It is easy to start writing simple programs in Python, and even using classes and objects involves a relatively gentle learning curve. Python is cross-platform (Windows, Mac, Linux). It is open source (and therefore free) and supported by a sizable developer community. Python is a general-purpose programming language with significant numerical capabilities, though a common use of Python is managing servers, administering systems, etc. See the extensive web site, www.python.org. A good textbook is Learning Python by Mark Lutz and David Ascher, O'Reilly 1999. Realtime 3D Graphics: Visual Python itself does not provide graphics output. The Tk graphics library can be used to create 2D graphics, but it is difficult to use. In the spring of 2000, while a sophomore in computer science at Carnegie Mellon University, David Scherer created a 3D graphics module for Python, called "Visual," that is exceptionally easy to use. A program can create 3D objects (such as spheres, curves, etc.) and position them in 3D space. Visual, running in a separate thread, automatically updates a 3D scene many times per second, to reflect the current positions of the objects. The programmer does not need to deal with display management, but can focus on the computational aspects of the program. The user can navigate in the 3D scene by using the mouse to zoom and rotate while the program is running. Visual supports full vector algebra. Use in Classrooms Students in introductory physics courses have been using VPython to do computer modeling. VPython lets students focus on the physics computations without having to write explicit graphics statements yet obtain 3D visualization. Students can do true vector computations, which improves their understanding of the utility of vectors and vector notation. Platforms Supported The Python language itself is cross-platform. The Visual module, and the Idle integrated development environment, work with Python on Windows and Unix/Linux/MacOSX. Published Articles A journal article about VPython has been published: Scherer, D., Dubois, P., & Sherwood, B. (2000). VPython: 3D Interactive Scientific Graphics for Students, Computing in Science and Engineering, Sept./Oct. 2000, 82-88.

  17. Epitaxial film growth study of single crystal V/Ce prepared by molecular-beam epitaxy on sapphire

    SciTech Connect

    Homma, H.; Yang, K.Y.; Schuller, I.K.

    1986-11-01

    The growth of epitaxial films of cerium (Ce)/vanadium (V)/on single crystal sapphires (..cap alpha..-Al/sub 2/O/sub 3/) was studied by in-situ reflection high energy electron diffraction and x-ray scattering. For the first time Ce(111) single crystal films was grown on V(110)/Al/sub 2/O/sub 3/(1120) in the Frank-van der Merwe mode. A new epitaxial orientation, different from the well known Nishiyama-Wasserman or Kurdjumov-Sachs orientations is found in the present study. Subsequent V(110) layers grow epitaxially with three equivalent domains.

  18. Variable structure motifs for transcription factor binding sites

    E-print Network

    Reid, John E; Evans, Kenneth J; Dyer, Nigel; Wernisch, Lorenz; Ott, Sascha

    2010-01-14

    . The improvement in the definition of the binding motif is also visible in the logos for the two transcription factors. These are in addition to the 10 PWMs where gaps had already been introduced in the sequences to define the PWMs published in TRANSFAC... , Lewicki-Potapov B, Saxel H, Kel AE, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34(Database issue):D108–D110. [7] Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR...

  19. The occultation of Epsilon Geminorum by Mars as observed at Princeton

    NASA Technical Reports Server (NTRS)

    Groth, E. J.; Klopfenstein, J. B.; Wickes, W. C.; Caldwell, J.

    1978-01-01

    Results are reported for two-color (red and blue) high-speed photometric observations of the April 8, 1976, occultation of Epsilon Gem by Mars. The observing system is briefly described, fits to an isothermal atmospheric model of the event are presented, and the blue data are used to derive temperature profiles of the Martian atmosphere in the manner of Wasserman and Veverka (1973). The results are compared with those of Elliot et al. (1977), which were obtained from the NASA Kuiper Airborne Observatory.

  20. CyNEST: a maintainable Cython-based interface for the NEST simulator

    PubMed Central

    Zaytsev, Yury V.; Morrison, Abigail

    2014-01-01

    NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, 2007). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., 1999). The introduction of PyNEST (Eppler et al., 2008), the Python interface for NEST, enabled users to control simulations using Python. As the majority of NEST users found PyNEST easier to use and to combine with other applications, it immediately displaced SLI as the default NEST interface. However, developing and maintaining PyNEST has become increasingly difficult over time. This is partly because adding new features requires writing low-level C++ code intermixed with calls to the Python/C API, which is unrewarding. Moreover, the Python/C API evolves with each new version of Python, which results in a proliferation of version-dependent code branches. In this contribution we present the re-implementation of PyNEST in the Cython language, a superset of Python that additionally supports the declaration of C/C++ types for variables and class attributes, and provides a convenient foreign function interface (FFI) for invoking C/C++ routines (Behnel et al., 2011). Code generation via Cython allows the production of smaller and more maintainable bindings, including increased compatibility with all supported Python releases without additional burden for NEST developers. Furthermore, this novel approach opens up the possibility to support alternative implementations of the Python language at no cost given a functional Cython back-end for the corresponding implementation, and also enables cross-compilation of Python bindings for embedded systems and supercomputers alike. PMID:24672470

  1. isochrones: Stellar model grid package

    NASA Astrophysics Data System (ADS)

    Morton, Timothy D.

    2015-03-01

    Isochrones, written in Python, simplifies common tasks often done with stellar model grids, such as simulating synthetic stellar populations, plotting evolution tracks or isochrones, or estimating the physical properties of a star given photometric and/or spectroscopic observations.

  2. VESPA: False positive probabilities calculator

    NASA Astrophysics Data System (ADS)

    Morton, Timothy D.

    2015-03-01

    Validation of Exoplanet Signals using a Probabilistic Algorithm (VESPA) calculates false positive probabilities and statistically validates transiting exoplanets. Written in Python, it uses isochrones [ascl:1503.010] and the package simpledist.

  3. AUVNetSim: a Simulator for Underwater Acoustics Networks

    E-print Network

    Montana, Josep Miquel Jornet

    AUVNetSim is a simulation library for testing acoustic networking algorithms. It is written in Python and makes extensive use of the SimPy discrete event simulation package. AUVNetSim is interesting for both end users and ...

  4. STEM Incubator in Cyber Security (Haxor) Wednesdays 4:00 -5:00pm, Manchester 244 Spring 2014

    E-print Network

    Fulp, Errin W.

    , hacking tools, Backtrack Networks and sniffing Sniffing, wireshark Unix Aufkl and Python tools Network and web exploits System evaluation and defense Hack this = all STEM sections meet curity. Students will experiment with ethical hacking, cyber defense, and reverse engineering techniques

  5. UNIVERSITY OF CALGARY DEPARTMENT OF COMPUTER SCIENCE

    E-print Network

    Stephenson, Ben

    follows a zero tolerance policy regarding dishonesty. Please read the sections of the University Calendar/herself with these regulations. 5. Text: Starting Out with Python Tony Gaddis, Pearson Education ISBN-13: 978

  6. Fabio Soldo Interests and Specialties

    E-print Network

    Markopoulou, Athina

    . 2010 Supervisor: Ahmed Metwally - Click Fraud o Implementation of a Sawzall/Python pipeline to estimate% the prediction accuracy of state-of-the-art mechanisms. - Characterization of Malicious IP Traffic o Data

  7. Ecology, 92(9), 2011, pp. 18581864 2011 by the Ecological Society of America

    E-print Network

    Shine, Rick

    , such as are predicted under models of anthropogenically caused global warming (Easterling et al. 2000). Although; Rattus colletti; reaction norms; snake; tropical Australia; water python. INTRODUCTION In their natural

  8. Is a Puffersphere an effective medium for visualising real-time global earthquake events? 

    E-print Network

    Scougal, Callum

    2014-11-27

    information by mapping live earthquakes across the globe for a weekly period. In order to conduct this research, a Python script was developed to automatically retrieve and plot United States Geological Survey data against a satellite base map...

  9. Prototyping Symbolic Execution Engines for Interpreted Languages

    E-print Network

    Candea, George

    Prototyping Symbolic Execution Engines for Interpreted Languages Stefan Bucur Ã?cole Polytechnique are written in dynamic interpreted languages like Python. Building a new symbolic execution engine language specifications lead to their implementation in a symbolic execution engine potentially differing

  10. Comparison of MDO Architectures within a Universal Framework

    Microsoft Academic Search

    Nathan Tedford

    2006-01-01

    Abstract Comparison of MDO Architectures within a Universal Framework Nathan Tedford Masters of Applied Science Graduate Department of Aerospace Engineering University of Toronto 2006 A new MDO framework has been developed in Python to provide an ideal platform

  11. Senior Example Recruiting/Engineering angieneer@fas.harvard.edu

    E-print Network

    a productivity add-on for Office using C# and VSTO in .NET framework to automate and synchronize activity Programming: .NET, C, C++, C#, PHP/MySQL, Scheme, Perl, Python, MATLAB, JavaScript, OCaml. Operating Systems

  12. Introductions Espces cls, espces envahissantes, communauts

    E-print Network

    Blouin-Demers, Gabriel

    of evidence implicate the introduced brown tree snake (Boiga irregularis) as the cause of the range reductions) 342: 1166-1167 #12;PNAS (2012) 109: 2418-2422 « Burmese pythons, giant constricting snakes native

  13. Jonas Michel http://www.jonasmichel.com/ CONTACT 201 E. 24th

    E-print Network

    Julien, Christine

    trajectory data model for pervasive computing applications (Java, Python, C/C++, Android, iOS, Arduino, OMNe for unmanned aerial system missions (PHP, Javascript). The project was awarded a Small Business Innovation

  14. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

    Microsoft Academic Search

    Sidhartha Chaudhury; Sergey Lyskov; Jeffrey J. Gray

    2010-01-01

    Summary: PyRosetta is a stand-alone Python-based implementa- tion of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies, and running Monte Carlo-based simulations. PyRosetta can

  15. Synergies in scientific computing by combining multi-paradigmatic languages for high-performance applications

    Microsoft Academic Search

    Philipp Schwaha; René Heinzl; Franz Stimpfl; Siegfried Selberherr

    2009-01-01

    The challenging art of multi-paradigmatic application development, which only few languages currently support, greatly aids the development of highly efficient and reusable software components. A link of two such languages, namely Python and C++, is presented. Thereby data structures and algorithms realised in C++ using features such as compile-time meta-programming are made available to the run-time environment of Python. Several

  16. Problem Solving - Programming

    NSDL National Science Digital Library

    kajigga

    2009-09-23

    Learn some basic math skills while at the same time learning some programming skills This short lesson focuses on solving simple math problem using computer programming. In this case, the examples given will be in Python (click on this link for more information: Official Tutorial for the Python programming language.). Computer programming can and has often been used to solve very complex mathematical problems along the lines of calculating ? ...

  17. Book Review:

    NASA Astrophysics Data System (ADS)

    Dray, T.

    2005-10-01

    I have had a love/hate relationship with this book ever since it first came out. On the one hand, this is an excellent introduction for mathematicians to the differential geometry underlying general relativity. On the other hand, this is definitely a book for mathematicians. The book's greatest strength is its clear, precise presentation of the basic ideas in differential geometry, combined with equally clear and precise applications to theoretical physics, notably general relativity. But the book's precision is also its greatest weakness; this is not an easy book to read for non-mathematicians, who may not appreciate the notational complexity, some of which is nonstandard. The present edition is very similar to the original, published in 1992. In addition to minor revisions and clarifications of the material, there is now a brief introduction to fibre bundles, and a (very) brief discussion of the gauge theory description of fundamental particles. The index to the symbols used is also a more complete than in the past, but without the descriptive material present in the previous edition. The bulk of the book consists of a careful introduction to tensors and their properties. Tensors are introduced first as linear maps on vector spaces, and only later generalized to tensor fields on manifolds. The differentiation and integration of differential forms is discussed in detail, including Stokes' theorem, Lie differentiation and Hodge duality, and connections, curvature and torsion. To this point, Wasserman's text can be viewed as an expanded version of Bishop and Goldberg's classic text [1], one major difference being Wasserman's inclusion of the pseudo-Riemannian case from the beginning (in particular, when discussing Hodge duality). Whether one prefers Wasserman's approach to Bishop and Goldberg's is largely a matter of taste: Wasserman's treatment is both more complete and more precise, making it easier to check calculations in detail, but occasionally more difficult to remember what one is calculating. An instructor using this text would be well advised to think carefully about which topics to cover, rather than trying to do everything. The remainder of the book contains applications to mechanics, relativity and gauge theory. In each case, better treatments exist elsewhere. However, each such treatment typically introduces its own notation; it is not without some truth that differential geometry is often described as the study of objects under changes of notation. Having several short treatments of these different topics in one place makes it easy for the instructor to choose those he or she wishes to emphasize, while providing a clear transition to more advanced treatments. The presentation does have some idiosyncrasies. The key concept of a derivation is not clearly defined. Some subtleties are referred to in cryptic comments ('This space is too large') which are never explained. The occasionally nonstandard notation is not always easy to follow, although this is a common criticism of introductory texts in differential geometry, which must balance precision with understanding. And appropriate cross references are not always given in sentences of the form 'Recall that ...', which on occasion contained (correct) results which I did not find obvious, and which I could not quickly find explicitly stated in earlier sections. I also have one minor gripe about the publishing format, namely that the outside margins are too small, at only 1 cm; I found this extremely distracting. But all of these criticisms are minor. Wasserman's book would unquestionably be an excellent introduction to tensor analysis for mathematicians, especially those who are interested in the physics applications. The readers of Classical and Quantum Gravity will want to know whether the book is equally suitable as a text for an introductory course in general relativity. At first glance, this text appears to fill a niche in mathematical sophistication between, say, the undergraduate texts by Schutz [2] or d'Inverno [3], which do not require prior background

  18. Evolution of the complementary sex-determination gene of honey bees: Balancing selection and trans-species polymorphisms

    E-print Network

    Cho, Soochin; Huang, Zachary Y.; Green, Daniel R.; Smith, Deborah R.; Zhang, Jianzhi

    2006-10-25

    Evolution of the complementary sex-determination gene of honey bees: Balancing selection and trans-species polymorphisms Soochin Cho,1 Zachary Y. Huang,2 Daniel R. Green,1 Deborah R. Smith,3 and Jianzhi Zhang1,4 1Department of Ecology... sequences. DnaSP (Rozas et al. 2003) was used for all population genetic analyses. Acknowledgments We thank Xiaoxia Wang for technical assistance and Wendy Grus and Peng Shi for valuable comments. We also thank the Honey Bee Genome Project at the Baylor...

  19. Textual Liberation - Slides and Paper 

    E-print Network

    Coker, Catherine

    2010-08-11

    are the aca-fan?s own words, purposefully stated as a critique of popular media and as a liberation?or even transformation?of ?sexy? hero to stalker. Though it is perhaps better articulated than other such works, it is by no means an isolated piece... Zachary Quinto. Her behavior is described variously as ?attacking? or ?raping? him in the turbolift scene. An illustrative example reads: I will admit, it was a sexy scene. But imagine we switched the genders. A young woman...

  20. HISTORICAL GEOGRAPHY OF THE CATHOLIC CHURCH IN KANSAS CITY, MISSOURI: 1822-1930

    E-print Network

    Hornbeck, Thomas

    2008-01-01

    questions. I thank my spiritual directors, Father Zachary of the Mother of God and Troy Henkel, in particular for instructing me to finish my thesis before pursing other goals. The community of St. Lawrence was my base for the last two years. I know..., Matt Nagle, Jasmine Pasimio and Anna Warfield. A final thanks to my spiritual friends in heaven who have been with me on this journey: Nancy Elliott, Margaret Hornbeck, Greg Nichols, Pope John Paul the Great, Blessed Charles of Jesus (a geographer...

  1. 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.

  2. The Clawpack Community of Codes

    NASA Astrophysics Data System (ADS)

    Mandli, K. T.; LeVeque, R. J.; Ketcheson, D.; Ahmadia, A. J.

    2014-12-01

    Clawpack, the Conservation Laws Package, has long been one of the standards for solving hyperbolic conservation laws but over the years has extended well beyond this role. Today a community of open-source codes have been developed that address a multitude of different needs including non-conservative balance laws, high-order accurate methods, and parallelism while remaining extensible and easy to use, largely by the judicious use of Python and the original Fortran codes that it wraps. This talk will present some of the recent developments in projects under the Clawpack umbrella, notably the GeoClaw and PyClaw projects. GeoClaw was originally developed as a tool for simulating tsunamis using adaptive mesh refinement but has since encompassed a large number of other geophysically relevant flows including storm surge and debris-flows. PyClaw originated as a Python version of the original Clawpack algorithms but has since been both a testing ground for new algorithmic advances in the Clawpack framework but also an easily extensible framework for solving hyperbolic balance laws. Some of these extensions include the addition of WENO high-order methods, massively parallel capabilities, and adaptive mesh refinement technologies, made possible largely by the flexibility of the Python language and community libraries such as NumPy and PETSc. Because of the tight integration with Python tecnologies, both packages have benefited also from the focus on reproducibility in the Python community, notably IPython notebooks.

  3. Nonparametric Bayes Factors Based On Empirical Likelihood Ratios

    PubMed Central

    Vexler, Albert; Deng, Wei; Wilding, Gregory E.

    2012-01-01

    Bayes methodology provides posterior distribution functions based on parametric likelihoods adjusted for prior distributions. A distribution-free alternative to the parametric likelihood is use of empirical likelihood (EL) techniques, well known in the context of nonparametric testing of statistical hypotheses. Empirical likelihoods have been shown to exhibit many of the properties of conventional parametric likelihoods. In this article, we propose and examine Bayes factors (BF) methods that are derived via the EL ratio approach. Following Kass & Wasserman [10], we consider Bayes factors type decision rules in the context of standard statistical testing techniques. We show that the asymptotic properties of the proposed procedure are similar to the classical BF’s asymptotic operating characteristics. Although we focus on hypothesis testing, the proposed approach also yields confidence interval estimators of unknown parameters. Monte Carlo simulations were conducted to evaluate the theoretical results as well as to demonstrate the power of the proposed test. PMID:23180904

  4. Reasoning Backwards by Design: Commentary on "Moral Reasoning among HEC Members".

    PubMed

    Stephens, Ashley L; Heitman, Elizabeth

    2015-01-01

    Empirical assessment of the practice of clinical ethics is made difficult by the limited standardization of settings, structures, processes, roles, and training for ethics consultation, as well as by whether individual ethics consultants or hospital ethics committees (HECs) provide consultation. Efforts to study the relationship between theory and practice in the work of HECs likewise require the spelling out of assumptions and definition of key variables, based in knowledge of the core concepts of clinical ethics and logistics of clinical consultation. The survey of HEC members reported by Wasserman and colleagues illustrates the difficulty of such research and calls attention to need for studies of real-time, complex decision making to inform conclusions about how theory affects practice. PMID:26132058

  5. Simple Illustration of Partition Theory

    NASA Astrophysics Data System (ADS)

    Wasserman, Adam; Cohen, Morrel; Burke, Kieron; Car, Roberto

    2009-03-01

    In Partition Theory (PT) [M.H. Cohen and A. Wasserman, J.Phys. Chem. A 2007, 111, 2229], the density of a system is decomposed exactly into a superposition of the densities of its parts through the introduction of a common partition potential acting on each of the parts as if they were isolated. In this talk we illustrate PT on a simple one-dimensional model of a heteronuclear diatomic molecule. We show that a sharp definition for the charge of the fragments emerges from PT, and that the ensuing population analysis can be used to study how charge redistributes during dissociation. By studying the preservation of the shapes of the parts as different parameters of the model are varied, we address the issue of transferability of the parts. We find good transferability within the chemically meaningful parameter regime, raising hopes that PT will prove useful in chemical applications.

  6. An Equation for the Prediction of Oxygen Consumption in a Brazilian Population

    PubMed Central

    de Almeida, Antonio Eduardo Monteiro; Stefani, Charles de Moraes; do Nascimento, João Agnaldo; de Almeida, Narla Miranda; Santos, Amilton da Cruz; Stein, Ricardo

    2014-01-01

    Background The equations predicting maximal oxygen uptake (VO2max or peak) presently in use in cardiopulmonary exercise testing (CPET) softwares in Brazil have not been adequately validated. These equations are very important for the diagnostic capacity of this method. Objective Build and validate a Brazilian Equation (BE) for prediction of VO2peak in comparison to the equation cited by Jones (JE) and the Wasserman algorithm (WA). Methods Treadmill evaluation was performed on 3119 individuals with CPET (breath by breath). The construction group (CG) of the equation consisted of 2495 healthy participants. The other 624 individuals were allocated to the external validation group (EVG). At the BE (derived from a multivariate regression model), age, gender, body mass index (BMI) and physical activity level were considered. The same equation was also tested in the EVG. Dispersion graphs and Bland-Altman analyses were built. Results In the CG, the mean age was 42.6 years, 51.5% were male, the average BMI was 27.2, and the physical activity distribution level was: 51.3% sedentary, 44.4% active and 4.3% athletes. An optimal correlation between the BE and the CPET measured VO2peak was observed (0.807). On the other hand, difference came up between the average VO2peak expected by the JE and WA and the CPET measured VO2peak, as well as the one gotten from the BE (p = 0.001). Conclusion BE presents VO2peak values close to those directly measured by CPET, while Jones and Wasserman differ significantly from the real VO2peak. PMID:25352504

  7. Results from the 2010 Feb 14 and July 4 Pluto Occultations

    NASA Astrophysics Data System (ADS)

    Young, Leslie; Sicardy, B.; Widemann, T.; Brucker, M. J.; Buie, M. W.; Fraser, B.; Van Heerden, H.; Howell, R. R.; Lonergan, K.; Olkin, C. B.; Reitsema, H. J.; Richter, A.; Sepersky, T.; Wasserman, L. H.; Young, E. F.

    2010-10-01

    The Portable High-speed Occultation Telescope (PHOT) group observed two occultations by Pluto in 2010. The first, of a I=9.3 magnitudue star on 2010 Feb 14, was organized by the Meudon occultation group, with the PHOT group as collaborators. For this bright but low-elevation event, we deployed to three sites in Europe: Obs. Haute Provence, France (0.8-m; L. Young, H. Reitsema), Leopold Figl, Austria (1.5-m; E. Young), and Apline Astrovillage, Lu, Switzerland (0.36-m; C. Olkin, L. Wasserman). We obtained a lightcurve at Lu under clear conditions, which will be combined with two other lightcurves from the Meudon group, from Sisteron and Pic du Midi, France. We observed the second Pluto occultation, of a I=13.2 star on 2010 July 4 UT, from four sites in South Africa: with our portable telescope near Upington (0.36-m; M. Buie, L. Wasserman), the Boyden telescope in Bloemfontein (1.5-m; L. Young, M. Brucker), the Innes telescope in Johannesburg (0.67-m; T. Sepersky, B. Fraser), and the telescope at Aloe Ridge north of Johannesburg (0.62-m; R. Howell, K. Lonergan, A. Richter). Upington was cloudy, Boyden had heavy scattered clouds, and Innes suffered from haze and telescope mechanical problems. A lightcurve was obtained from Aloe Ridge under clear conditions. Data was also obtained by Karl-Ludwig Bath & Thomas Sauer at Hakos, Namibia and by Berto Monard of ASSA near Pretoria, South Africa. The length of the Aloe Ridge chord suggests it is nearly central. These observations give us four contiguous years in which we observed one or more Pluto occultations, providing constraints on the seasonal evolution of Pluto's atmosphere. Thanks are due to Marcelo Assafin and Jim Elliot for sharing predictions prior to the July event. This work was supported, in part, by NASA PAST NNX08A062G.

  8. VOLTTRON: An Agent Execution Platform for the Electric Power System

    SciTech Connect

    Akyol, Bora A.; Haack, Jereme N.; Ciraci, Selim; Carpenter, Brandon J.; Vlachopoulou, Maria; Tews, Cody W.

    2012-06-05

    Volttron is an agent execution platform that is engineered for use in the electric power system. Volttron provides resource guarantees for agents and the platform including memory and processor utilization; authentication and authorization services; directory services for agent and resource location; and agent mobility. Unlike most other agent platforms, Volttron does not depend on a single agent authoring language. Instead, we chose to design and implement Volttron as a platform service and framework that is decoupled from the agent execution environment. A prototype implementation of Volttron has been written in Python (using Python v2.7.2) and we have executed agents written in Python and Java and as shell scripts. The intended use of Volttron is in the power distribution system for managing distributed generation, demand-response, and plug-in electric vehicles.

  9. AstroML: "better, faster, cheaper" towards state-of-the-art data mining and machine learning

    NASA Astrophysics Data System (ADS)

    Ivezic, Zeljko; Connolly, Andrew J.; Vanderplas, Jacob

    2015-01-01

    We present AstroML, a Python module for machine learning and data mining built on numpy, scipy, scikit-learn, matplotlib, and astropy, and distributed under an open license. AstroML contains a growing library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical datasets (such as SDSS and other recent major surveys), and a large suite of examples of analyzing and visualizing astronomical datasets. AstroML is especially suitable for introducing undergraduate students to numerical research projects and for graduate students to rapidly undertake cutting-edge research. The long-term goal of astroML is to provide a community repository for fast Python implementations of common tools and routines used for statistical data analysis in astronomy and astrophysics (see http://www.astroml.org).

  10. Hunter-gatherers and other primates as prey, predators, and competitors of snakes.

    PubMed

    Headland, Thomas N; Greene, Harry W

    2011-12-27

    Relationships between primates and snakes are of widespread interest from anthropological, psychological, and evolutionary perspectives, but surprisingly, little is known about the dangers that serpents have posed to people with prehistoric lifestyles and nonhuman primates. Here, we report ethnographic observations of 120 Philippine Agta Negritos when they were still preliterate hunter-gatherers, among whom 26% of adult males had survived predation attempts by reticulated pythons. Six fatal attacks occurred between 1934 and 1973. Agta ate pythons as well as deer, wild pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocally prey, predators, and potential competitors. Natural history data document snake predation on tree shrews and 26 species of nonhuman primates as well as many species of primates approaching, mobbing, killing, and sometimes eating snakes. These findings, interpreted within the context of snake and primate phylogenies, corroborate the hypothesis that complex ecological interactions have long characterized our shared evolutionary history. PMID:22160702

  11. 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.

  12. CADRE: The CArma Data REduction pipeline

    E-print Network

    Friedel, D N

    2013-01-01

    The Combined Array for Millimeter-wave Astronomy (CARMA) data reduction pipeline (CADRE) has been developed to give investigators a first look at a fully reduced set of their data. It runs automatically on all data produced by the telescope as they arrive in the CARMA data archive. CADRE is written in Python and uses Python wrappers for MIRIAD subroutines for direct access to the data. It goes through the typical reduction procedures for radio telescope array data and produces a set of continuum and spectral line maps in both MIRIAD and FITS format. CADRE has been in production for nearly two years and this paper presents the current capabilities and planned development.

  13. ALOHA: Automatic Libraries Of Helicity Amplitudes for Feynman diagram computations

    E-print Network

    de Aquino, Priscila; Maltoni, Fabio; Mattelaer, Olivier; Stelzer, Tim

    2011-01-01

    We present an application that automatically writes the Helas library corresponding to the Feynman rules of any Lagrangian, renormalizable or not, in quantum field theory. The code, written in Python, takes the Universal FeynRules Output as an input and produces the complete set of routines (wave-functions and amplitudes) that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent and outputs in Fortran, C++, Python are currently available. A few key sample applications implemented in the MadGraph5 framework are presented.

  14. Pentastomes (Pentastomida, Armillifer armillatus Wyman, 1848) in snakes from Zambia.

    PubMed

    De Meneghi, D

    1999-12-01

    Twenty-three snakes, belonging to eight different species, were collected from rural areas of Zambia and inspected for the presence of pentastomes. Pentastomid parasites were found in four snakes: one African rock python (Python sebae), one puff adder (Bitis arietans) and two Mozambique spitting cobras (Naja mossambica) were infested with a small number of Armillifer armillatus, respectively five, two and one adult parasites. As humans can be incidental/intermediate hosts for reptilian pentastomes, the zoonotic potential of these parasites, especially in tropical countries, is discussed. PMID:10870563

  15. Système de Construction Automatisé d'Archives d'Installation

    E-print Network

    Vessière, Damien

    In order to optimize people's time in charge of asset computer management, I created Python software able to automate the creation of install archives on various LHCb’s computer in use. To conduct this realization, I had access to different servers and virtual machines at CERN and on my own workstation. The handling of these machines was performed by the "libvirt" library in python and has many modules like "pyGTK" for the graphical user interface. With my software it is now possible to run commands on remote systems to create installer and finally bring them back on the workstation.

  16. ALOHA: Automatic Libraries Of Helicity Amplitudes for Feynman diagram computations

    E-print Network

    Priscila de Aquino; William Link; Fabio Maltoni; Olivier Mattelaer; Tim Stelzer

    2012-07-31

    We present an application that automatically writes the Helas library corresponding to the Feynman rules of any Lagrangian, renormalizable or not, in quantum field theory. The code, written in Python, takes the Universal FeynRules Output as an input and produces the complete set of routines (wave-functions and amplitudes) that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent and outputs in Fortran, C++, Python are currently available. A few key sample applications implemented in the MadGraph5 framework are presented.

  17. The CARMA Data Reduction Pipeline

    NASA Astrophysics Data System (ADS)

    Friedel, D. N.

    2013-10-01

    The Combined Array for Millimeter-wave Astronomy (CARMA) data reduction pipeline (CADRE) has been developed to give investigators a first look at a fully reduced set of their data. It runs automatically on all data produced by the telescope as they arrive in the data archive. CADRE is written in Python and uses Python wrappers for MIRIAD subroutines for direct access to the data. It applies passband, gain and flux calibration to the data sets and produces a set of continuum and spectral line maps in both MIRIAD and FITS format. CADRE has been in production for a year and this poster will discuss the current capabilities and planned improvements.

  18. CADRE: The CArma Data REduction pipeline

    NASA Astrophysics Data System (ADS)

    Friedel, D. N.

    2013-08-01

    The Combined Array for Millimeter-wave Astronomy (CARMA) data reduction pipeline (CADRE) has been developed to give investigators a first look at a fully reduced set of their data. It runs automatically on all data produced by the telescope as they arrive in the CARMA data archive. CADRE is written in Python and uses Python wrappers for MIRIAD subroutines for direct access to the data. It goes through the typical reduction procedures for radio telescope array data and produces a set of continuum and spectral line maps in both MIRIAD and FITS format. CADRE has been in production for nearly two years and this paper presents the current capabilities and planned development.

  19. Vectorized algorithms for spiking neural network simulation.

    PubMed

    Brette, Romain; Goodman, Dan F M

    2011-06-01

    High-level languages (Matlab, Python) are popular in neuroscience because they are flexible and accelerate development. However, for simulating spiking neural networks, the cost of interpretation is a bottleneck. We describe a set of algorithms to simulate large spiking neural networks efficiently with high-level languages using vector-based operations. These algorithms constitute the core of Brian, a spiking neural network simulator written in the Python language. Vectorized simulation makes it possible to combine the flexibility of high-level languages with the computational efficiency usually associated with compiled languages. PMID:21395437

  20. On the nature of the omega tri-layer periodicity in rapidly cooled Ti-15Mo

    E-print Network

    Bennett, J.M.; Barnard, J.S.; Stone, H.J.; Midgley, P.A.; Rugg, D.; Jones, N.G.

    2015-06-04

    Figure 2 The simultaneously acquired raw ADF and EELS data are contained within FIG2-A and FIG2-B dm3 files. The Ti edge was extracted from the FIG2-B datacube using JMBFIG2.txt (which needs to be renamed as *.py and run using python). The bulk Ti... #Script written by JMB in 2014 #This script extracts the independent components from an EELS data cube to isolate the bulk Ti edge. #This script calls the program HYPERSPY #The script needs to be renamed as *.py before running using Python from...

  1. PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes

    Microsoft Academic Search

    Swanand P. Gore; David F. Burke; Tom L. Blundell

    2005-01-01

    Summary: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized soft- ware (Qhull, Pymol etc.) into a pipeline. The calculation component of

  2. Molecular and morphological description of a Hepatozoon species in reptiles and their ticks in the Northern Territory, Australia.

    PubMed

    Vilcins, Inger-Marie E; Ujvari, Beata; Old, Julie M; Deane, Elizabeth

    2009-04-01

    Ticks, representing 3 species of Amblyomma, were collected from the water python (Liasis fuscus) and 3 additional reptile species in the Northern Territory, Australia, and tested for the presence of Hepatozoon sp., the most common blood parasites of snakes. In addition, blood smears were collected from 5 reptiles, including the water python, and examined for the presence of the parasite. Hepatozoon sp. DNA was detected in all tick and reptile species, with 57.7% of tick samples (n = 187) and 35.6% of blood smears (n=35) showing evidence of infection. Phylogenetic analysis of the 18S rRNA gene demonstrated that half of the sequences obtained from positive tick samples matched closest with a Hepatozoon species previously identified in the water python population. The remaining sequences were found to be more closely related to mammalian and amphibian Hepatozoon species. This study confirms that species of Amblyomma harbor DNA of the same Hepatozoon species detected in the water pythons. The detection of an additional genotype suggests the ticks may be exposed to 2 Hepatozoon species, providing further opportunity to study multiple host-vector-parasite relationships. PMID:18710299

  3. Introduction to Programming with JES Titus Winters & Josef Spjut

    E-print Network

    Zordan, Victor

    ). If you are just trying stuff out, trying to see what things do, you can use the interactive window introductory programming, and we are going to use it to do some fun stuff with graphics. JES1 is a free the message in quotes. In Python, a bit of text in quotes is called a "string". You can do things with strings

  4. Frank Nielsen 2011 Fundamentals of 3D

    E-print Network

    Nielsen, Frank

    -Maximization + Overview of computational photography Frank Nielsen nielsen@lix.polytechnique.fr 30 Novembre 2011 #12 2011 En Java, http://www.lix.polytechnique.fr/~nielsen/MEF/ Modeling images with Gaussian mixture models RGB+XY= Point in 5D En Python, http://www.lix.polytechnique.fr/~schwander/pyMEF/ #12;© Frank

  5. Astronomical Data Analysis Software and Systems XV P.4 ASP Conference Series, Vol. XXX, 2005

    E-print Network

    van Langevelde, Huib Jan

    as a scripting inter- face for doing complicated data reduction on large data sets. It is also used as a coding to automate things like collecting calibration data. 1. ParselTongue ParselTongue1 provides a Python interfaceNet's Advance Long Baseline User Software (ALBUS)4 project, but is useful in its own right for things like

  6. CPSC 231 Assignment 5 Due: Friday April 17, 2009 at 1:00pm

    E-print Network

    Stephenson, Ben

    (nicely formatted, but without any comments): · Loading the Maze: Less than 25 lines · Displaying the Maze: Less than 30 lines · Solving the Maze: Less than 25 lines · Everything Else: Less than 50 lines In this assignment, you will create a Python program which reads a maze from a file and finds a solution to that maze

  7. WALi User Manual Nicholas Kidd

    E-print Network

    Liblit, Ben

    papers see http://www.cs.wisc.edu/wpis/wpds.) 2 Installation WALi has been compiled on Linux, Cygwin file of the WALi source tree. 2.1 Linux and Cygwin WALi requires a working Python installation2;This will compile and link the WALi library in the directory WALi-1.2/lib. (For cygwin, a static

  8. The findings and conclusions in this presentation have not been formally disseminated by the Centers for Disease Control and Prevention and should not be construed to represent any agency determination or policy. The Office of Management and Budget (OMB)

    E-print Network

    Wright, Dawn Jeannine

    in the Geospatial Line of Business. The framework is mostly open-source (Apache, JBOSS, Python, etc) and works frameworks including a framework called the Public Health Distributed Geospatial Intelligence Network (PH and Prevention (CDC) DGInet History: The Distributed Geospatial Intelligence Network (DGInet) was built by ESRI

  9. abcpmc: Approximate Bayesian Computation for Population Monte-Carlo code

    NASA Astrophysics Data System (ADS)

    Akeret, Joel

    2015-04-01

    abcpmc is a Python Approximate Bayesian Computing (ABC) Population Monte Carlo (PMC) implementation based on Sequential Monte Carlo (SMC) with Particle Filtering techniques. It is extendable with k-nearest neighbour (KNN) or optimal local covariance matrix (OLCM) pertubation kernels and has built-in support for massively parallelized sampling on a cluster using MPI.

  10. Demo Abstract: Cascades: An Extensible Heterogeneous Sensor Networking Framework

    Microsoft Academic Search

    Phillip Sitbon; Nirupama Bulusu; Wu-Chi Feng

    This demonstration shows a powerful high-level, heterogeneous sensor networking framework, Cascades. We intend to demonstrate how, with this framework, application designers have great control over implementation designs without the requirement of in- depth development. Several key components and example applications will be demonstrated, along with some important concepts used in this Python-based framework. The emphasis will be on video sensing

  11. A Mutation in the Mitochondrial Fission Gene Dnm1l Leads to Cardiomyopathy

    PubMed Central

    Ashrafian, Houman; Docherty, Louise; Leo, Vincenzo; Towlson, Christopher; Neilan, Monica; Steeples, Violetta; Lygate, Craig A.; Hough, Tertius; Townsend, Stuart; Williams, Debbie; Wells, Sara; Norris, Dominic; Glyn-Jones, Sarah; Land, John; Barbaric, Ivana; Lalanne, Zuzanne; Denny, Paul; Szumska, Dorota; Bhattacharya, Shoumo; Griffin, Julian L.; Hargreaves, Iain; Fernandez-Fuentes, Narcis; Cheeseman, Michael; Watkins, Hugh; Dear, T. Neil

    2010-01-01

    Mutations in a number of genes have been linked to inherited dilated cardiomyopathy (DCM). However, such mutations account for only a small proportion of the clinical cases emphasising the need for alternative discovery approaches to uncovering novel pathogenic mutations in hitherto unidentified pathways. Accordingly, as part of a large-scale N-ethyl-N-nitrosourea mutagenesis screen, we identified a mouse mutant, Python, which develops DCM. We demonstrate that the Python phenotype is attributable to a dominant fully penetrant mutation in the dynamin-1-like (Dnm1l) gene, which has been shown to be critical for mitochondrial fission. The C452F mutation is in a highly conserved region of the M domain of Dnm1l that alters protein interactions in a yeast two-hybrid system, suggesting that the mutation might alter intramolecular interactions within the Dnm1l monomer. Heterozygous Python fibroblasts exhibit abnormal mitochondria and peroxisomes. Homozygosity for the mutation results in the death of embryos midway though gestation. Heterozygous Python hearts show reduced levels of mitochondria enzyme complexes and suffer from cardiac ATP depletion. The resulting energy deficiency may contribute to cardiomyopathy. This is the first demonstration that a defect in a gene involved in mitochondrial remodelling can result in cardiomyopathy, showing that the function of this gene is needed for the maintenance of normal cellular function in a relatively tissue-specific manner. This disease model attests to the importance of mitochondrial remodelling in the heart; similar defects might underlie human heart muscle disease. PMID:20585624

  12. Midterm Test --Solutions Fall 20l2 Question 1. [4 marks

    E-print Network

    Toronto, University of

    height > 0.92 or with_adult Part (d) [1 mark] Fill in the box with Python code that will make the program;Midterm Test -- Solutions Fall 20l2 Part (b) [5 marks] The estimated cooking time for potatoes is usually 5 minutes per potato, but if the potatoes are extra large, it is 7 minutes per potato. When cooking

  13. CSC 108H1 F 2012 Midterm Test Duration --50 minutes

    E-print Network

    Toronto, University of

    is with an adult as indicated by with_adult.''' return Part (d) [1 mark] Fill in the box with Python code^^le' >>> merge_views('^ppl^', '^pp^e') '^pple' ''' Page 4 of 6 #12;Part (b) [5 marks] The estimated cooking time. When cooking more than 2 potatoes of any size, the cooking time calculated is too long, so 3 minutes

  14. Language-side Foreign Function Interfaces with NativeBoost

    E-print Network

    Paris-Sud XI, Université de

    on the top of a virtual ma- chine (VM) such as Pharo3 , Lua4 or Python5 . Figure 1 depicts four possibilities of view, only the generic FFI VM- plugin has to be implemented on all platforms. 3 http://pharo.org/ 4

  15. MDLab: A Molecular Dynamics Simulation Prototyping Environment

    E-print Network

    Izaguirre, Jesús A.

    MDLab: A Molecular Dynamics Simulation Prototyping Environment Trevor Cickovski1 ,Santanu level sampling protocols that run several instances of molecular dynamics. For computationally demanding-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Key words: molecular dynamics, sampling, Python

  16. Sage: Open Source Mathematical Software: Symbolic Computation, Combinatorial Species,

    E-print Network

    Stein, William

    Sage: Open Source Mathematical Software: Symbolic Computation, Combinatorial Species, Backtracking March 21, 2008 1 Introduction Sage brings together Python and the best existing open source mathemat to fund work by four students on Sage. Each of the four students (two graduate and two undergraduate) have

  17. William A. Stein Project Description (858) 220-6876 wstein@math.washington.edu http://sage.math.washington.edu

    E-print Network

    Stein, William

    William A. Stein Project Description (858) 220-6876 wstein@math.washington.edu http://sage.math.washington.edu SAGE: Software for Algebra and Geometry Experimentation Major Points · SAGE is free open source. · SAGE is an environment for rigorous mathematical computation built using Python, GAP, Maxima, Singular

  18. 6/8/13 ADAM 2013 --Sage localhost:8080/home/admin/7/ 1/18

    E-print Network

    Veroff, Robert

    6/8/13 ADAM 2013 -- Sage localhost:8080/home/admin/7/ 1/18 ADAM 2013 last edited Jun 6, 2013 10:16:48 PM by admin Save Save & quit Discard & quit File... Action... Data... sage Typeset Print Worksheet Edit Text Revisions Share Publish Prover9 and other provers with Sage/Python/LaTeX input

  19. Sage: Unifying Mathematical Software for Scientists, Engineers, and Mathematicians

    E-print Network

    Stein, William

    Sage: Unifying Mathematical Software for Scientists, Engineers, and Mathematicians 1 Introduction The goal of this proposal is to further the development of Sage, which is comprehensive unified open source and tools. Sage [12] uses Python, one of the world's most popular general-purpose interpreted programming

  20. PHENIX: Developing new software for automated crystallographic structure determination

    Microsoft Academic Search

    Paul D. Adams; Ralf W. Grosse-Kunstleve; Li-Wei Hung; Thomas R. Ioerger; Airlie J. McCoy; Nigel W. Moriarty; Randy J. Read; James C. Sacchettini; Nicholas K. Sautera; Thomas C. Terwilligerf

    2002-01-01

    Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed.

  1. Augmented Tangible Molecular Models Suzanne Weghorst

    E-print Network

    Washington at Seattle, University of

    , and augmenting them with a variety of interface modalities, including augmented visual overlays, haptic reality approach is integrated around PMV, TSRI's Python-based molecular visualization software. Results haptic feedback. Using multi-modal interaction, computational models can be queried and studied

  2. State of the Toolbox: an overview of the Computational Crystallography Toolbox (CCTBX)

    E-print Network

    Grosse-Kunstleve, Ralf

    - mats. At the moment the iotbx contains C++ and Python interfaces for reading CCP4 MTZ files and ADSC X-ray detector images. 3. The beach in the box If you go to the beach you will find massive amounts of a material here is the cctbx way of playing in the sandbox: from cctbx import xray from cctbx import crystal from

  3. STEM Incubator in Cyber Security (Haxor) Wednesdays 4:00 5:00pm, Manchester 244 Spring 2014

    E-print Network

    Fulp, Errin W.

    , and the Garmon law Attacks, hacking tools, Backtrack # Networks and sni#ng Sni#ng, wireshark # Unix Aufkl and Python tools Network and web exploits # System evaluation and defense Hack this # # = all STEM sections curity. Students will experiment with ethical hacking, cyber defense, and reverse engineering techniques

  4. Embarrassingly parallel mesh refinement by edge subdivision

    Microsoft Academic Search

    David C. Thompson; Philippe P. Pébay

    2006-01-01

    We have previously proposed a new technique for the communication-free adaptive refinement of tet- rahedral meshes that works for all configurations. Implementations of the scheme must deal with all pos- sible geometric configurations, which results in a large number of cases that in turn result in practical pro- gramming issues. In this article, we address this issue with a Python

  5. Christopher R. Gagne Gagnecr@gmail.com

    E-print Network

    Badre, David

    manipulation and image scrambling routines in Matlab and Python. Compiled a database of stimuli for the lab types of consumer loyalty cards. Advs. Caron Merrill CVS Pharmacy Pharmacy Technician Summer 09 ­ Fall 2010 Worked in the retail pharmacy, completing all the necessary steps from prescription drop

  6. Sage 2008: Sage on Microsoft Windows William Stein

    E-print Network

    Stein, William

    Sage 2008: Sage on Microsoft Windows William Stein January 2008 1 Introduction Stein started by Sage, and improve support for using Sage on Solaris and Microsoft Windows. Sage is the only serious supported by Microsoft via the IronPython project: http://www

  7. AN EFFICIENT WAY TO PERFORM THE ASSEMBLY OF FINITE ELEMENT MATRICES IN VECTOR LANGUAGES

    E-print Network

    Paris-Sud XI, Université de

    to perform the assembly of finite element matrices in vector languages (e.g. Matlab, Octave, Python), fromAN EFFICIENT WAY TO PERFORM THE ASSEMBLY OF FINITE ELEMENT MATRICES IN VECTOR LANGUAGES FRANC¸ OIS finite elements case, with an application to linear elasticity. We present numerical results which

  8. New Features in AST - a WCS Management and Manipulation Library

    E-print Network

    Berry, David

    2012-01-01

    Recent developments in the AST library are described, including a Python interface, support for the FITS-WCS "-TAB" system for storing tabular co-ordinate information, and extended support for representing distortions in spatial projections, using several schemes in common use (IRAF TNX/ZPX, Spitzer SIP, NOAO TPV and SCAMP).

  9. BIOINFORMATICS ORIGINAL PAPER Vol. 26 no. 12 2010, pages 15061512

    E-print Network

    Lee, Doheon

    in accordance with the rules. By applying the present approach to publicly available prostate cancer datasets are consistent with known prostate cancer biology. Availability: Scripts written in Python and R are available); to develop gene expression signatures for cancer diagnosis, prognosis or prediction of drug responsiveness

  10. Welcome to MCS 507 1 About the Course

    E-print Network

    Verschelde, Jan

    Welcome to MCS 507 1 About the Course content and organization expectations of the course 2 Python for MCS 507 Lecture 1 Mathematical, Statistical and Scientific Software Jan Verschelde, 25 August 2014 Scientific Software (MCS 507 L-1) Welcome to MCS 507 25 Aug 2014 1 / 28 #12;Welcome to MCS 507 1 About

  11. Welcome to MCS 507 1 About the Course

    E-print Network

    Verschelde, Jan

    Welcome to MCS 507 1 About the Course content and organization expectations of the course 2 Python for MCS 507 Lecture 1 Mathematical, Statistical and Scientific Software Jan Verschelde, 26 August 2013 Scientific Software (MCS 507 L-1) Welcome to MCS 507 26 Aug 2013 1 / 28 #12;Welcome to MCS 507 1 About

  12. Demystifying software What is software?

    E-print Network

    Prodiæ, Aleksandar

    as you think } ECE 468: Computer Security } Hackers? Hackers! } ECE 444/450: Software Engineering } HowDing Yuan Demystifying software #12;What is software? 2 } Anyone? } Computer programs, or the non-tangible parts of computer #12;Myth #1: programming is too hard 3 Too many languages: C, Java, Python

  13. Comprehensive data reduction package for the Immersion GRating INfrared Spectrograph: IGRINS

    E-print Network

    Pak, Soojong

    2014 Available online 10 March 2014 Abstract We present a Python-based data reduction pipeline package correction of the target spectra, the intrinsic hydrogen absorption features of the standard A star pipeline is to provide stable quality of data reduction process with minimal human intervention. The full

  14. Proceedings of the ASME 2012 Summer Heat Transfer Conference July 8-12, 2012, Rio Grande, Puerto Rico

    E-print Network

    Kostic, Milivoje M.

    Proceedings of the ASME 2012 Summer Heat Transfer Conference HT2012 July 8-12, 2012, Rio Grande CODE FOR FLOW SCOURING AROUND BRIDGE PIERS Phani Ganesh Elapolu Department of Mechanical Engineering+ commercial CFD code. A computational methodology has been developed using Python and Java Macros

  15. Basic Lisp Techniques David J. Cooper, Jr.

    E-print Network

    Reed, Nancy E.

    Basic Lisp Techniques David J. Cooper, Jr. January 28, 2002 #12;ii 0 Copyright c 2002, Franz Inc needed to support future technological expectations. Common Lisp (CL) is one of the few languages. Perl, Python, Java, C++, C# -- they all incorporate some of the features that give Lisp its power

  16. Optimization of Computations Used in Information Theory Applied to Base Pair Analysis

    E-print Network

    Gobbert, Matthias K.

    Concurrent Collec- tions (CnC) programming paradigm moreover show that tools from parallel computing can times using the exhaustive Python program, more efficient MATLAB program, and translated serial C program. Times are given in seconds. O.M represents Out of Memory. The number of unique DNA sequences

  17. ORIGINAL PAPER Sexual variation in assimilation efficiency: its link to phenotype

    E-print Network

    Denardo, Dale

    phenomenon among animals, and both dietary intake and resource allocation strategies influence sexually efficiency (AE), an intermediate step between die- tary intake and allocation, can also vary between) and AE of total energy, crude protein, and crude fat in post-reproductive adult Children's pythons (which

  18. The Portable Extensible Toolkit for Scientific computing Day 1: Usage and Algorithms

    E-print Network

    ;Introduction Portable Extensible Toolkit for Scientific computing · Architecture · tightly coupled (XT5, BG/P, Earth Simulator, Sun Blade, SGI Altix) · loosely coupled such as network of workstations · Operating/double precision, 32/64-bit int · Usable from C, C++, Fortran 77/90, and Python · Free to everyone (BSD

  19. Coupling ReaxFF with Temperature Accelerated

    E-print Network

    Goddard III, William A.

    Coupling ReaxFF with Temperature Accelerated Dynamics CMDF: Summer 2005 Daniel Yi, Caltech `07 #12: TAD standalone code - FORTRAN 77 CMDF - Python based #12;CMDF Module: TADTOOLS #12;Seamless;TAD ReaxFF Coupled Example: Hydrogen adatom on Platinum min = 5 x 1011 sec-1 , = .01 [100] Platinum

  20. THE COMPUTATION OF PERIODIC SOLUTIONS OF THE 3-BODY PROBLEM USING THE NUMERICAL

    E-print Network

    Doedel, Eusebius

    model for space mission design because it has many of the essential features of a more complex high-#12 of conservative systems. This software package has a number of features that make it useful as a space mission analysis and design tool. Using scripts written in the object-oriented scripting language Python to drive