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1

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

E-print Network

captive Children's pythons (Antaresia childreni) to assess their facultative endothermic capability are not facultatively endothermic because brooding unit temperature coefficient (Q10) for VO2 and VCO2 was similar endothermic, they are capable of assessing the Tnest­Tclutch gradient and making behavioral adjustments

Denardo, Dale

2

FEBRUARY 2013 BRADLEY C. PARKS AND ZACHARY J. RICE  

E-print Network

FEBRUARY 2013 BRADLEY C. PARKS AND ZACHARY J. RICE Millennium Challenge Corporation: A Survey of the Millennium Challenge Corporation: A Survey-Based Approach Bradley C. Parks and Zachary J. Rice Making Reform

Fashing, Norman

3

Ball python  

NSDL National Science Digital Library

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.

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

2004-02-10

4

Python Calculus  

NSDL National Science Digital Library

Students analyze a cartoon of a Rube Goldberg machine and a Python programming language script to practice engineering analysis. In both cases, they study the examples to determine how the different systems operate and the function of each component. This exercise in juxtaposition enables students to see the parallels between a more traditional mechanical engineering design and computer programming. Students also gain practice in analyzing two very different systems to fully understand how they work, similar to how engineers analyze systems and determine how they function and how changes to the system might affect the system.

IMPART RET Program, College of Information Science & Technology,

5

Python and Turtle  

NSDL National Science Digital Library

Learn a little bit of Python as well as how it can be used to graph simple shapes and pictures. This lesson can be used to learn the basic concepts of programming and logical processes. $.beautyOfCode.init({ brushes: ['Xml', 'JScript', 'CSharp', 'Plain', 'Php','Python'] }); Python - Turtle This lesson will focus around simple python programming concepts. ...

Kajigga

2009-09-21

6

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."

7

A Human Study of Fault Localization Accuracy Zachary P. Fry  

E-print Network

A Human Study of Fault Localization Accuracy Zachary P. Fry University of Virginia Email: zpf5a to debug, however. We present formal models, backed by a human study involving 65 participants (from both to human accuracy at locating errors. Our study involves example code from Java textbooks, helping us

Weimer, Westley

8

Algorithms for Designing Pop-Up Cards Zachary Abel1  

E-print Network

Algorithms for Designing Pop-Up Cards Zachary Abel1 , Erik D. Demaine2 , Martin L. Demaine2 , Sarah for delivering babies. Dean & Sons' Little Red Riding Hood (1850) is the first known movable book where a flat ­ Leibniz-Zentrum für Informatik, Dagstuhl Publishing, Germany #12;2 Algorithms for Designing Pop-Up Cards

Demaine, Erik

9

Minimizing Movement in Mobile Facility Location Problems Zachary Friggstad  

E-print Network

Minimizing Movement in Mobile Facility Location Problems Zachary Friggstad Mohammad R. Salavatipour,mreza@cs.ualberta.ca Abstract In the mobile facility location problem, which is a variant of the classical facility location facility location problem while an approximation for the minimum total movement variant and hardness

Salavatipour, Mohammad R.

10

Linkage Analysis With Sequential Imputation Zachary Skrivanek, Shili Linn  

E-print Network

Linkage Analysis With Sequential Imputation Zachary Skrivanek, Shili Linn , and Mark Irwin information on all pedigree members, are important for linkage analysis. Exact calculation methods in linkage. In this article, we propose a Monte Carlo method for linkage analysis based on sequential imputation. Unlike exact

Irwin, Mark E.

11

Teaching and Learning Python  

NSDL National Science Digital Library

Python is an introductory programming language considered ideal for learning the basic concepts of programming. This website offers examples of educational uses and lesson plans for Python. "LiveWires" is used to teach Python to children ages 12-15 at a summer camp in Britain. The lesson materials are free online and include a series of worksheets, reference sheets and game sheets for use with the LiveWires package (Python modules). Also on this website are a list of possible activities that will be offered in the 2004 summer session, interviews with current and former LiveWires people, and a typical timetable.

2007-07-24

12

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

E-print Network

Arsenic and manganese exposure and children's intellectual function Gail A. Wasserman a neurobehavioral function and exposure to arsenic (As) via drinking water or industrial sources (Calderon et al Accepted 21 March 2011 Available online 29 March 2011 Keywords: Arsenic Manganese Children Water Bangladesh

van Geen, Alexander

13

Molecular Recognition and Self-Organization in Fluorinated Hydrocarbons Frank H. Stlllinger" and Zelda Wasserman  

E-print Network

" and Zelda Wasserman Bell Laboratories, Murray Hill, New Jersey 07974 (Received November 16, 1977 in section 11, can achieve this objective with carefully selected partial fluorination. The patterns of hydrogen and fluorineatoms borne by those molecules provide information storage, in binary form

Stillinger, Frank

14

Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1  

E-print Network

is a genetic microar- ray experiment but the method is very general. The method includes: transformationCATS: Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1 Department of Statistics Carnegie Mellon University August 11, 2004 CATS ­ Clustering After Transformation and Smoothing

Serban, Nicoleta

15

Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1  

E-print Network

CATS: Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1 Department of Statistics Carnegie Mellon University CATS ­ Clustering After Transformation and Smoothing ­ is a technique for nonparametrically estimating and clustering a large number of curves. Our motivating example is a genetic microar

16

Python to learn programming  

NASA Astrophysics Data System (ADS)

Today we have a lot of programming languages that can realize our needs, but the most important question is how to teach programming to beginner students. In this paper we suggest using Python for this purpose, because it is a programming language that has neatly organized syntax and powerful tools to solve any task. Moreover it is very close to simple math thinking. Python is chosen as a primary programming language for freshmen in most of leading universities. Writing code in python is easy. In this paper we give some examples of program codes written in Java, C++ and Python language, and we make a comparison between them. Firstly, this paper proposes advantages of Python language in relation to C++ and JAVA. Then it shows the results of a comparison of short program codes written in three different languages, followed by a discussion on how students understand programming. Finally experimental results of students' success in programming courses are shown.

Bogdanchikov, A.; Zhaparov, M.; Suliyev, R.

2013-04-01

17

Monte Python: Monte Carlo code for CLASS in Python  

NASA Astrophysics Data System (ADS)

Monte Python is a parameter inference code which combines the flexibility of the python language and the robustness of the cosmological code CLASS into a simple and easy to manipulate Monte Carlo Markov Chain code.

Audren, Benjamin; Lesgourgues, Julien; Benabed, Karim; Prunet, Simon

2013-07-01

18

Web Interfaces 1 Python Scripts in Browsers  

E-print Network

Web Interfaces 1 Python Scripts in Browsers the web server Apache processing forms with Python Interfaces 1 Python Scripts in Browsers the web server Apache processing forms with Python scripts Python web forms we can call Python scripts from a browser give our programs a web interface make software

Verschelde, Jan

19

Programmation en Python -Cours 2 : Premiers programmes  

E-print Network

Programmation en Python - Cours 2 : Premiers programmes MPSI1 - Lyc´ee Thiers 2013/2014 #12;Diverses utilisations de python Programmation en python Exercices Diverses utilisations de python Utilisation en mode interactif Ecriture d'un programme python Programmation en python Saisie de donn´ees par l

Préaux, Jean-Philippe

20

Invent with Python  

NSDL National Science Digital Library

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."

Sweigart, Al

21

Python and computer vision  

SciTech Connect

This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, and (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.

Doak, J. E. (Justin E.); Prasad, Lakshman

2002-01-01

22

Programmation python Utilisation des listes  

E-print Network

TD 3 - Programmation python Utilisation des listes Informatique MPSI1 - Lyc´ee Thiers 2013/2014 #12 : Chiffrement de C´esar Enonc´e Solution Informatique MPSI1 - Lyc´ee Thiers TD 3 - Programmation python'ex´ecution est du m^eme ordre de grandeur. Informatique MPSI1 - Lyc´ee Thiers TD 3 - Programmation python

Préaux, Jean-Philippe

23

Pythons in Burma: Short-tailed python (Reptilia: Squamata)  

USGS Publications Warehouse

Short-tailed pythons, Python curtus species group, occur predominantly in the Malayan Peninsula, Sumatra, and Borneo. The discovery of an adult female in Mon State, Myanmar, led to a review of the distribution of all group members (spot-mapping of all localities of confirmed occurrence) and an examination of morphological variation in P. brongersmai. The resulting maps demonstrate a limited occurrence of these pythons within peninsular Malaya, Sumatra, and Borneo with broad absences in these regions. Our small samples limit the recognition of regional differentiation in the morphology of P. brongersmai populations; however, the presence of unique traits in the Myanmar python and its strong allopatry indicate that it is a unique genetic lineage, and it is described as Python kyaiktiyo new species.

Zug, George R.; Gotte, Steve W.; Jacobs, Jeremy F.

2011-01-01

24

Porting Perl To Python Techniques for migrating legacy, untested Perl to Python  

E-print Network

Porting Perl To Python Techniques for migrating legacy, untested Perl to Python Skill Level-automatically, generate unit tests for legacy systems written in Python." Additionally, you can define entry points

25

Computational Physics Education with Python  

NSDL National Science Digital Library

Educators at an institution in Germany have started using Python to teach computational physics. The author describes how graphical visualizations also play an important role, which he illustrates here with a few simple examples.

Bcker, Arnd

2008-06-07

26

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

E-print Network

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

Royer, Dana

27

Characterizing Image Fusion Techniques in Stereoscopic HTDs Zachary Wartell, Larry F. Hodges, William Ribarsky  

E-print Network

Characterizing Image Fusion Techniques in Stereoscopic HTDs Zachary Wartell, Larry F. Hodges image. Researchers have used a number of software methods to reduce fusion problems. We are particularly of the user. Ideally the user's visual system combines the stereo image pairs into a single, 3D perceived

Wartell, Zachary

28

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

E-print Network

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

Mountziaris, T. J.

29

Sensitivity of soil respiration and microbial communities to altered snowfall Zachary T. Aanderud a,1  

E-print Network

Sensitivity of soil respiration and microbial communities to altered snowfall Zachary T. Aanderud a in winter soil respiration may be in uenced by the effects of snowfall on microbial communities effects on other features of the soil microbial community at spring thaw. Our results suggest

Fierer, Noah

30

Tracking Provenance in ORNL's Flexible Research Platforms Zachary Hensley (zphensley42@students.tntech.edu),1  

E-print Network

Tracking Provenance in ORNL's Flexible Research Platforms Zachary Hensley (zphensley42@students information about the use of sensor data in their experiments on ORNL's Flexible Research Platforms (FRPs of the information as part of the information's workflow. The concept of provenance and its usage in science

Wang, Xiaorui "Ray"

31

Effects of Early-Life Experience on Learning Ability in Fruit Flies Zachary Durisko & Reuven Dukas  

E-print Network

associated with learning and memory. Learning and memory require brain tissue, which is metabolically). Specifically, learning requires both the initial constitutive, or global, investment to develop the brainEffects of Early-Life Experience on Learning Ability in Fruit Flies Zachary Durisko & Reuven Dukas

Dukas, Reuven

32

Pynamic: the Python Dynamic Benchmark  

SciTech Connect

Python is widely used in scientific computing to facilitate application development and to support features such as computational steering. Making full use of some of Python's popular features, which improve programmer productivity, leads to applications that access extremely high numbers of dynamically linked libraries (DLLs). As a result, some important Python-based applications severely stress a system's dynamic linking and loading capabilities and also cause significant difficulties for most development environment tools, such as debuggers. Furthermore, using the Python paradigm for large scale MPI-based applications can create significant file IO and further stress tools and operating systems. In this paper, we present Pynamic, the first benchmark program to support configurable emulation of a wide-range of the DLL usage of Python-based applications for large scale systems. Pynamic has already accurately reproduced system software and tool issues encountered by important large Python-based scientific applications on our supercomputers. Pynamic provided insight for our system software and tool vendors, and our application developers, into the impact of several design decisions. As we describe the Pynamic benchmark, we will highlight some of the issues discovered in our large scale system software and tools using Pynamic.

Lee, G L; Ahn, D H; de Supinksi, B R; Gyllenhaal, J C; Miller, P J

2007-07-10

33

Breadth-First CS 1 for Scientists Zachary Dodds, Christine Alvarado, Geoff Kuenning, Ran Libeskind-Hadas  

E-print Network

Breadth-First CS 1 for Scientists Zachary Dodds, Christine Alvarado, Geoff Kuenning, Ran Libeskind-607-1813 {dodds, alvarado, geoff, hadas}@cs.hmc.edu ABSTRACT This paper describes an introductory CS course

Alvarado, Christine

34

Introduction into Python Python 3: Further Lists and Other Data Structures  

E-print Network

: Introduction into Python ­ p.7/?? Filtering Tools Code def even(x): return x % 2 == 0 Input >>> filterIntroduction into Python Python 3: Further Lists and Other Data Structures Daniel Polani Daniel Polani: Introduction into Python ­ p.1/?? More List Operations (Methods) Note: help(list) will give you

Polani, Daniel

35

Accessing the VO with Python  

NASA Astrophysics Data System (ADS)

We introduce two products for accessing the VO from Python: PyVO and VOClient. PyVO is built on the widely-used Astropy package and is well suited for integrating automated access to astronomical data into highly customizable scripts and applications for data analysis in Python. VOClient is built on a collection of C-libraries and is well suited for integrating with multi-language analysis packages. It also provides a framework for integrating legacy software into the Python environment. In this demo, we will run through several examples demonstrate basic data discovery and retrieval of data. This includes finding archives containing data of interest (VO registry), retrieving datasets (SIA, SSA), and exploring (Cone Search, SLAP). VOClient features some extended capabilities including the ability to communicate to other desktop applications from a script using the SAMP protocol.

Plante, R.; Fitzpatrick, M.; Graham, M.; Tody, D.; Young, W.

2014-05-01

36

Programmation python Recherche d'elements  

E-print Network

TD 4 - Programmation python Recherche d'´el´ements : Dichotomie, M´ethode de Newton Informatique´ement return True return False # Cas d'´echec Informatique MPSI1 - Lyc´ee Thiers TD 4 - Programmation python'intervalle [a, b]. Informatique MPSI1 - Lyc´ee Thiers TD 4 - Programmation python Recherche d

Préaux, Jean-Philippe

37

Introduction into Python Python 5: Classes, Exceptions, Generators and more  

E-print Network

Thought: "An example class" answer = 42 # class global variable def respond(self): # always use 'self' as first method argument return self.answer # DeepThought.answer would also have worked # as a class++, this is done with a concept called constructors, but in Python, the mechanism is different. Use __init(self

Polani, Daniel

38

Python programming --introduction to Python Finn Arup Nielsen  

E-print Network

August 28, 2009 #12;Python programming -- introduction Output from the print function "Autoblog Green",http://www.opensecrets.org/news/atom.xml Causecast,http://feeds.feedburner.com/causecast/latest_news.rss "Clean Fuels Blog Outout from the print function ['Autoblog Green', 'http

39

MontePython: Implementing Quantum Monte Carlo using Python  

NASA Astrophysics Data System (ADS)

We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and diffusion Monte Carlo and we describe how to implement theses methods in pure C++ and C++/Python. Furthermore we check the efficiency of the implementations in serial and parallel cases to show that the overhead using Python can be negligible. Program summaryProgram title: MontePython Catalogue identifier: ADZP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 49 519 No. of bytes in distributed program, including test data, etc.: 114 484 Distribution format: tar.gz Programming language: C++, Python Computer: PC, IBM RS6000/320, HP, ALPHA Operating system: LINUX Has the code been vectorised or parallelized?: Yes, parallelized with MPI Number of processors used: 1-96 RAM: Depends on physical system to be simulated Classification: 7.6; 16.1 Nature of problem: Investigating ab initio quantum mechanical systems, specifically Bose-Einstein condensation in dilute gases of 87Rb Solution method: Quantum Monte Carlo Running time: 225 min with 20 particles (with 4800 walkers moved in 1750 time steps) on 1 AMD Opteron TM Processor 2218 processor; Production run for, e.g., 200 particles takes around 24 hours on 32 such processors.

Nilsen, Jon Kristian

2007-11-01

40

Imagining a Stata / Python Combination  

NASA Technical Reports Server (NTRS)

There are occasions when a task is difficult in Stata, but fairly easy in a more general programming language. Python is a popular language for a range of uses. It is easy to use, has many high ]quality packages, and programs can be written relatively quickly. Is there any advantage in combining Stata and Python within a single interface? Stata already offers support for user-written programs, which allow extensive control over calculations, but somewhat less control over graphics. Also, except for specifying output, the user has minimal programmatic control over the user interface. Python can be used in a way that allows more control over the interface and graphics, and in so doing provide a roundabout method for satisfying some user requests (e.g., transparency levels in graphics and the ability to clear the results window). My talk will explore these ideas, present a possible method for combining Stata and Python, and give examples to demonstrate how this combination might be useful.

Fiedler, James

2012-01-01

41

Geophysical data analysis using Python  

Microsoft Academic Search

A set of routines designed for geophysical data analysis that make extensive use of the numerical extensions to the computer language Python are presented. The routines perform some typical tasks during multivariate analysis of geophysical fields, such as principal component analysis and related tasks (truncation rules by means of analytical and Monte Carlo techniques). Other functions perform singular value decomposition

Jon Senz; Juan Zubillaga; Jess Fernndez

2002-01-01

42

Building Facebook Application using Python  

E-print Network

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

Wu, S. Felix

43

Python on Ranger and Lonestar  

NSDL National Science Digital Library

While Python is a scripting language, it has plenty of facilities for high performance computing. This article covers some of its features and libraries that are particularly helpful when moving scientific code to a large cluster resource. It also includes specific recipes for compilation and execution on the TACC clusters.

44

Geophysical data analysis using Python  

NASA Astrophysics Data System (ADS)

A set of routines designed for geophysical data analysis that make extensive use of the numerical extensions to the computer language Python are presented. The routines perform some typical tasks during multivariate analysis of geophysical fields, such as principal component analysis and related tasks (truncation rules by means of analytical and Monte Carlo techniques). Other functions perform singular value decomposition of covariance matrices and canonical correlation analysis for coupled variability of geophysical fields. Other parts of the package allow access to a library of statistical distribution functions, multivariate digital filters, time-handling routines, kernel-based probability density function estimation and differential operators over the sphere for gridded data sets. As they rely on the numerical extensions to the Python language, they are fast for numerical analysis. The programs make the analysis of geophysical data sets both easier and faster.

Senz, Jon; Zubillaga, Juan; Fernndez, Jess

2002-05-01

45

Steering object-oriented computations with Python  

SciTech Connect

We have described current approaches and future plans for steering C++ application, running Python on parallel platforms, and combination of Tk interface and Python interpreter in steering computations. In addition, there has been significant enhancement in the Gist module. Tk mega widgets has been implemented for a few physics applications. We have also written Python interface to SIJLO, a data storage package used as an interface to a visualization system named MeshTv. Python is being used to control large-scale simulations (molecular dynamics in particular) running on the CM-5 and T3D at LANL as well. A few other code development projects at LLNL are either using or considering Python as their steering shells. In summary, the merits of Python have been appreciated by more and more people in the scientific computation community.

Yang, T.-Y.B.; Dubois, P.F.; Furnish, G. [Lawrence Livermore National Lab., CA (United States); Beazley, D.M. [Utah Univ., Salt Lake City, UT (United States). Dept. of Computer Science

1996-10-01

46

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....

2009-10-12

47

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

Federal Register 2010, 2011, 2012, 2013

...Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda Species as Injurious Reptiles...proposed rule to amend our regulations to add Indian python (Python molurus, including Burmese python Python molurus...

2010-07-01

48

Computed tomography of ball pythons (Python regius) in curled recumbency.  

PubMed

Anesthesia and tube restraint methods are often required for computed tomography (CT) of snakes due to their natural tendency to curl up. However, these restraint methods may cause animal stress. The aim of this study was to determine whether the CT appearance of the lungs differs for ball pythons in a curled position vs. tube restraint. Whole body CT was performed on ten clinically healthy ball pythons, first in curled and then in straight positions restrained in a tube. Curved multiplanar reformatted (MPR) lung images from curled position scans were compared with standard MPR lung images from straight position scans. Lung attenuation and thickness were measured at three locations for each scan. Time for positioning and scanning was 12 5 min shorter for curled snakes compared to tube restraint. Lung parenchyma thickness and attenuation declined from cranial to caudal on both straight and curled position images. Mean lung parenchyma thickness was greater in curled images at locations 1 (P = 0.048) and 3 (P = 0.044). Mean lung parenchyma thickness decreased between location 1 and 2 by 86-87% (straight: curled) and between location 1 and 3 by 51-50% (straight: curled). Mean lung attenuation at location 1 was significantly greater on curled position images than tube restraint images (P = 0.043). Findings indicated that CT evaluation of the lungs is feasible for ball pythons positioned in curled recumbency if curved MPR is available. However, lung parenchyma thickness and attenuation in some locations may vary from those acquired using tube restraint. PMID:24438485

Hedley, Joanna; Eatwell, Kevin; Schwarz, Tobias

2014-01-01

49

PYCHEM: a multivariate analysis package for python  

Microsoft Academic Search

Summary: We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a

Roger M. Jarvis; David Broadhurst; Helen E. Johnson; Noel M. O'boyle; Royston Goodacre

2006-01-01

50

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

USGS Publications Warehouse

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.

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

2011-01-01

51

Punishing the Lies on the Rio Grande: Catholic and Immigrant Volunteers in Zachary Taylor's Army and the Fight against Nativism  

Microsoft Academic Search

:In May 1846, in the midst of the largest wave of immigration up to that point in its history, the United States went to war with Mexico. The nation's attention became focused on northern Mexico as General Zachary Taylor's army marched up the Rio Grande and fought Mexican forces in the major battles of Monterrey and Buena Vista. Hundreds of

Tyler V. Johnson

2010-01-01

52

Punishing the Lies on the Rio Grande: Catholic and Immigrant Volunteers in Zachary Taylor's Army and the Fight against Nativism  

Microsoft Academic Search

In May 1846, in the midst of the largest wave of immigration up to that point in its history, the United States went to war with Mexico. The nation's attention became focused on northern Mexico as General Zachary Taylor's army marched up the Rio Grande and fought Mexican forces in the major battles of Monterrey and Buena Vista. Hundreds of

Tyler V. Johnson

2010-01-01

53

Say Cheese!: Experiences with a Robot Photographer Zachary Byers and Michael Dixon and William D. Smart and Cindy M. Grimm  

E-print Network

Say Cheese!: Experiences with a Robot Photographer Zachary Byers and Michael Dixon and William D an autonomous robot system that takes well-composed photographs of people at social events, such as weddings and conference receptions. The robot, Lewis, navigates through the environment, opportunistically taking

Dixon, Michael

54

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

E-print Network

Visual 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, the cycle is completed by the generation of a goal map for the LIDAR collection hardware that instructs

Wartell, Zachary

55

Transport and Dynamics of the Panay Sill Overflow in the Philippine Seas* ZACHARY D. TESSLER AND ARNOLD L. GORDON  

E-print Network

Transport and Dynamics of the Panay Sill Overflow in the Philippine Seas* ZACHARY D. TESSLER via Luzon Strait, investigated by Chao et al. (1996) and Qu et al. (2006b). Similarly, the seas of the Philippines region are com- posed of numerous isolated deep basins, though the circulation patterns

Gordon, Arnold L.

56

Reflection-Based Python-C++ Bindings  

SciTech Connect

Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access C++ libraries with essentially no preparation on the users' behalf. In addition, and in a similar way, PyROOT gives ROOT users access to Python libraries.

Generowicz, Jacek; Lavrijsen, Wim T.L.P.; Marino, Massimo; Mato, Pere

2004-10-14

57

Grid Programming in Java and Python  

NSDL National Science Digital Library

Introduction to Grids, the Globus Toolkit, and the Commodity Grid (CoG) Kit. Using and programming grids with the Java and Python CoG Kits, including secure access to remote resources, remote job submission and data access.

Von Laszewski, Gregor; Jackson, Keith

58

Python Optimization Modeling Objects (Pyomo) - Optimization Online  

E-print Network

Dec 29, 2009 ... ages define Python objects that can be used to express models, but they can be dis- tinguished according ...... instance is legal given the dynamic update of the CUTS set. Additionally, we .... risks in drinking water. INFORMS...

2009-12-29

59

A comparison of C++, Java and Python  

E-print Network

of new OOP languages have emerged. These languages provide powerful application tools on some specific areas. Java and Python are two excellent next-generation languages. They inherit most praising features from C++, provide simpler user interfaces...

Chou, Ling

2012-06-07

60

Astropy: Community Python Software for Astronomy  

NASA Astrophysics Data System (ADS)

The Astropy Project is a community effort to develop an open source Python package of common data structures and routines for use by other, more specialized astronomy software in Python in order to foster software interoperability in the astronomical community. The project encompasses Astropy's core and affiliated" packages that adopt Astropys coding, testing and documentation standards. By doing so we aim to improve interoperability with other Python packages in astronomy, and help a broader community implement more Pythonic solutions to astronomy computing problems while minimizing duplication of effort. The project provides a template for other projects that use Astropy to reuse much of Astropys development framework without reinventing the wheel. Here we present an overview of the key features of the core package (existing and upcoming), current and planned affiliated packages, and how we manage a large open source project with a diverse community of contributors.

Greenfield, Perry; Tollerud, E. J.; Robitaille, T.; Developers, Astropy

2014-01-01

61

Python-Based Applications for Hydrogeological Modeling  

NASA Astrophysics Data System (ADS)

Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Add-on packages supporting fast array computation (numpy), plotting (matplotlib), scientific /mathematical Functions (scipy), have resulted in a powerful ecosystem for scientists interested in exploratory data analysis, high-performance computing and data visualization. Three examples are provided to demonstrate the applicability of the Python environment in hydrogeological applications. Python programs were used to model an aquifer test and estimate aquifer parameters at a Superfund site. The aquifer test conducted at a Groundwater Circulation Well was modeled with the Python/FORTRAN-based TTIM Analytic Element Code. The aquifer parameters were estimated with PEST such that a good match was produced between the simulated and observed drawdowns. Python scripts were written to interface with PEST and visualize the results. A convolution-based approach was used to estimate source concentration histories based on observed concentrations at receptor locations. Unit Response Functions (URFs) that relate the receptor concentrations to a unit release at the source were derived with the ATRANS code. The impact of any releases at the source could then be estimated by convolving the source release history with the URFs. Python scripts were written to compute and visualize receptor concentrations for user-specified source histories. The framework provided a simple and elegant way to test various hypotheses about the site. A Python/FORTRAN-based program TYPECURVEGRID-Py was developed to compute and visualize groundwater elevations and drawdown through time in response to a regional uniform hydraulic gradient and the influence of pumping wells using either the Theis solution for a fully-confined aquifer or the Hantush-Jacob solution for a leaky confined aquifer. The program supports an arbitrary number of wells that can operate according to arbitrary schedules. The python wrapper invokes the underlying FORTRAN layer to compute transient groundwater elevations and processes this information to create time-series and 2D plots.

Khambhammettu, P.

2013-12-01

62

Identification and Characterization of Two Closely Related Unclassifiable Endogenous Retroviruses in Pythons (Python molurus and Python curtus)  

PubMed Central

Boid inclusion body disease (BIBD) is a fatal disorder of boid snakes that is suspected to be caused by a retrovirus. In order to identify this agent, leukocyte cultures (established from Python molurus specimens with symptoms of BIBD or kept together with such diseased animals) were assessed for reverse transcriptase (RT) activity. Virus from cultures exhibiting high RT activity was banded on sucrose density gradients, and the RT peak fraction was subjected to highly efficient procedures for the identification of unknown particle-associated retroviral RNA. A 7-kb full retroviral sequence was identified, cloned, and sequenced. This virus contained intact open reading frames (ORFs) for gag, pro, pol, and env, as well as another ORF of unknown function within pol. Phylogenetic analysis showed that the virus is distantly related to viruses from both the B and D types and the mammalian C type but cannot be classified. It is present as a highly expressed endogenous retrovirus in all P. molurus individuals; a closely related, but much less expressed virus was found in all tested Python curtus individuals. All other boid snakes tested, including Python regius, Python reticulatus, Boa constrictor, Eunectes notaeus, and Morelia spilota, were virus negative, independent of whether they had BIBD or not. Virus isolated from P. molurus could not be transmitted to the peripheral blood mononuclear cells of B. constrictor or P. regius. Thus, there is no indication that this novel virus, which we propose to name python endogenous retrovirus (PyERV), is causally linked with BIBD. PMID:12097574

Huder, Jon B.; Boni, Jurg; Hatt, Jean-Michel; Soldati, Guido; Lutz, Hans; Schupbach, Jorg

2002-01-01

63

The Python Interface to Antelope and Applications  

NASA Astrophysics Data System (ADS)

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.

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

2008-12-01

64

Python for Education: Computational Methods for Nonlinear Systems  

NSDL National Science Digital Library

The authors' interdisciplinary computational methods course uses Python and associated numerical and visualization libraries to enable students to implement simulations for several different course modules, which highlight the breadth and flexibility of Python-powered computational environments.

Myers, Christopher; Sethna, James

2008-07-23

65

Starkiller : a static type inferencer and compiler for Python  

E-print Network

Starkiller is a type inferencer and compiler for the dynamic language Python designed to generate fast native code. It analyzes Python source programs and converts them into equivalent C++ programs. Starkiller's type ...

Salib, Michael, 1978-

2004-01-01

66

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

USGS Publications Warehouse

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.

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

2011-01-01

67

Consumption of bird eggs by invasive Burmese Pythons in Florida  

USGS Publications Warehouse

Burmese Pythons (Python molurus bivittatus or P. bivittatus) have been reported to consume 25 species of adult birds in Everglades National Park, Florida (Dove et al. 2011), but until now no records documented this species eating bird eggs. Here we report three recent cases of bird-egg consumption by Burmese Pythons and discuss egg-eating in basal snakes.

Dove, Carla J.; Reed, Robert N.; Snow, Ray W.

2012-01-01

68

Programming in Java, Pizza and Python Extra Credit (not required)  

E-print Network

CS 538 Project #4 Programming in Java, Pizza and Python Extra Credit (not required) Not accepted an infinite LazyList containing val in // every position } static LazyList filter(LazyList control, Lazy (lazy lists and the ``Sieve of Erastosthenes'') in Python. Since Python is dynamically typed, you may

Fischer, Charles N.

69

A New Python Library for Spectroscopic Analysis with MIDAS Style  

NASA Astrophysics Data System (ADS)

The ESO MIDAS is a system for astronomers to analyze data which many astronomers are using. Python is a high level script language and there are many applications for astronomical data process. We are releasing a new Python library which realizes some MIDAS commands in Python. People can use it to write a MIDAS style Python code. We call it PydasLib. It is a Python library based on ESO MIDAS functions, which is easily used by astronomers who are familiar with the usage of MIDAS.

Song, Y.; Luo, A.; Zhao, Y.

2013-10-01

70

Identifying plausible scenarios for the establishment of invasive Burmese pythons ( Python molurus ) in Southern Florida  

Microsoft Academic Search

Successful invasions of secretive alien species often go unrecognized until spread has exceeded the point where control or\\u000a eradication is feasible. In such situations, understanding factors that contributed to establishment can be critical to preventing\\u000a subsequent introductions of previously-successful invaders or ecologically similar species. The Burmese python (Python molurus bivittatus), a native to Southeast Asia, is abundant in the pet

John D. WillsonMichael; Michael E. Dorcas; Raymond W. Snow

2011-01-01

71

Compiling Little Languages in Python John Aycock  

E-print Network

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

Aycock, John

72

A Python Library for Historical Comparative Linguistics  

E-print Network

;Language History pater father 1 padre Vater 1 Historical Linguistics 3 / 33 hprints-00758536,version1-28Nov. . . .. . . A Python Library for Historical Comparative Linguistics Steven Moran1 & Johann 2012, Brussels : Belgium (2012)" #12;Talk Map . . .1 Language History . . .2 Traditional Language

Paris-Sud XI, Université de

73

Implementation of Kalman Filter with Python Language  

Microsoft Academic Search

In this paper, we investigate the implementation of a Python code for a Kalman Filter using the Numpy package. A Kalman Filtering is carried out in two steps: Prediction and Update. Each step is investigated an d coded as a function with matrix input and output. These different functions are exp lained and an example of a Kalman Filter application

Mohamed LAARAIEDH

74

Python Scripting in the Nengo Simulator  

PubMed Central

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models. PMID:19352442

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

75

PyXNAT: XNAT in Python.  

PubMed

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line. PMID:22654752

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gal; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

2012-01-01

76

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

USGS Publications Warehouse

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.

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

2012-01-01

77

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

USGS Publications Warehouse

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.

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

2012-01-01

78

Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius  

PubMed Central

ABSTRACT A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (Python regius) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order Nidovirales. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (n = 8) but was not detected in healthy pythons or other snakes (n = 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in Torovirinae subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease. PMID:25205093

Stenglein, Mark D.; Jacobson, Elliott R.; Wozniak, Edward J.; Wellehan, James F. X.; Kincaid, Anne; Gordon, Marcus; Porter, Brian F.; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S.

2014-01-01

79

Implementation of Kalman Filter with Python Language  

E-print Network

In this paper, we investigate the implementation of a Python code for a Kalman Filter using the Numpy package. A Kalman Filtering is carried out in two steps: Prediction and Update. Each step is investigated and coded as a function with matrix input and output. These different functions are explained and an example of a Kalman Filter application for the localization of mobile in wireless networks is given.

Laaraiedh, Mohamed

2012-01-01

80

Cosmic Microwave Background Anisotropy: Python V Results  

Microsoft Academic Search

Observations of the microwave sky using the Python telescope in its fifth season of operation at the Amundsen-Scott South Pole Station in Antarctica are presented. The system consists of a 0.75 m off-axis telescope instrumented with a HEMT amplifier-based radiometer having continuum sensitivity from 37-45 GHz in two frequency bands. With a 0.91 x 1.02 deg beam the instrument fully

K. Coble; M. Dragovan; J. Kovac; N. W. Halverson; W. L. Holzapfel; L. Knox; S. Dodelson; K. Ganga; J. B. Peterson; D. Alvarez; G. Griffin; M. Newcomb; K. Miller; S. R. Platt; G. Novak

1999-01-01

81

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

82

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

83

HOPE: Just-in-time Python compiler for astrophysical computations  

NASA Astrophysics Data System (ADS)

HOPE is a specialized 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 optimization on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. By using HOPE, the user benefits from being able to write common numerical code in Python while getting the performance of compiled implementation.

Akeret, Joel; Gamper, Lukas; Amara, Adam; Refregier, Alexandre

2014-11-01

84

Feeding a large-scale physics application to Python  

SciTech Connect

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.

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

85

Re-imagining a Stata/Python Combination  

NASA Technical Reports Server (NTRS)

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.

Fiedler, James

2013-01-01

86

The Virtual Observatory for the Python Programmer  

NASA Astrophysics Data System (ADS)

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.

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

2014-01-01

87

Stably extracting text contents from email messages with Python  

Microsoft Academic Search

Extracting text contents from email messages is a fundamental task in email processing, such as spam mail identifying and email filtering. Although Python is a rapid application development language, there is not a library in Python which can efficiently and stably accomplish this task when facing versatile email formats in a real application. This paper proposes an approach to fulfill

S. Sun

2009-01-01

88

Implementation of Kalman Filter with Python Language Mohamed LAARAIEDH  

E-print Network

- 1 - Implementation of Kalman Filter with Python Language Mohamed LAARAIEDH IETR Labs, University of a Python code for a Kalman Filter using the Numpy package. A Kalman Filtering is carried out in two steps. These different functions are explained and an example of a Kalman Filter application for the localization

Paris-Sud XI, Université de

89

PuLP: A Linear Programming Toolkit for Python  

E-print Network

Sep 5, 2011 ... guage. PuLP is a high-level modelling library that leverages the power of the ... any system that has a Python interpreter, as it has no dependencies on any other software ... uses Python's control structures and arithmetic operators (see section 3). In con- ..... and any separation between them is arbitrary.

2011-09-05

90

How to Think Like a Computer Scientist Learning with Python  

E-print Network

How to Think Like a Computer Scientist Learning with Python #12;#12;How to Think Like a Computer://www.thinkpython.com Publisher's Cataloging-in-Publication (provided by Quality Books, Inc.) Downey, Allen How to think like Scientist Learning with Python Allen Downey Jeffrey Elkner Chris Meyers Green Tea Press Wellesley

Reluga, Tim

91

Python for Education: Computational Methods for Nonlinear Systems  

E-print Network

We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in complex networks, biomechanics, pattern formation, and gene regulation are highlighted to illustrate the breadth and flexibility of Python-powered computational environments.

Christopher R. Myers; James. P. Sethna

2007-04-24

92

scikit-image: image processing in Python  

PubMed Central

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

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

2014-01-01

93

scikit-image: image processing in Python.  

PubMed

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

van der Walt, Stfan; Schnberger, Johannes L; Nunez-Iglesias, Juan; Boulogne, Franois; Warner, Joshua D; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

94

Python erythrocytes are resistant to ?-hemolysin from Escherichia coli.  

PubMed

?-Hemolysin (HlyA) from Escherichia coli lyses mammalian erythrocytes by creating nonselective cation pores in the membrane. Pore insertion triggers ATP release and subsequent P2X receptor and pannexin channel activation. Blockage of either P2X receptors or pannexin channels reduces HlyA-induced hemolysis. We found that erythrocytes from Python regius and Python molurus are remarkably resistant to HlyA-induced hemolysis compared to human and Trachemys scripta erythrocytes. HlyA concentrations that induced maximal hemolysis of human erythrocytes did not affect python erythrocytes, but increasing the HlyA concentration 40-fold did induce hemolysis. Python erythrocytes were more resistant to osmotic stress than human erythrocytes, but osmotic stress tolerance per se did not confer HlyA resistance. Erythrocytes from T. scripta, which showed higher osmotic resistance than python erythrocytes, were as susceptible to HlyA as human erythrocytes. Therefore, we tested whether python erythrocytes lack the purinergic signalling known to amplify HlyA-induced hemolysis in human erythrocytes. P. regius erythrocytes increased intracellular Ca? concentration and reduced cell volume when exposed to 3 mM ATP, indicating the presence of a P2X?-like receptor. In addition, scavenging extracellular ATP or blocking P2 receptors or pannexin channels reduced the HlyA-induced hemolysis. We tested whether the low HlyA sensitivity resulted from low affinity of HlyA to the python erythrocyte membrane. We found comparable incorporation of HlyA into human and python erythrocyte membranes. Taken together, the remarkable HlyA resistance of python erythrocytes was not explained by increased osmotic resistance, lack of purinergic hemolysis amplification, or differences in HlyA affinity. PMID:22064954

Larsen, Casper K; Skals, Marianne; Wang, Tobias; Cheema, Muhammad U; Leipziger, Jens; Praetorius, Helle A

2011-12-01

95

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

PubMed Central

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

2011-01-01

96

Implementation of quantum game theory simulations using Python  

NASA Astrophysics Data System (ADS)

This paper provides some examples about quantum games simulated in Python's programming language. The quantum games have been developed with the Sympy Python library, which permits solving quantum problems in a symbolic form. The application of these methods of quantum mechanics to game theory gives us more possibility to achieve results not possible before. To illustrate the results of these methods, in particular, there have been simulated the quantum battle of the sexes, the prisoner's dilemma and card games. These solutions are able to exceed the classic bottle neck and obtain optimal quantum strategies. In this form, python demonstrated that is possible to do more advanced and complicated quantum games algorithms.

Madrid S., A.

2013-05-01

97

Multi-scale Analysis with Python  

NASA Astrophysics Data System (ADS)

This talk will discuss the SphereBlur package, written in Python and available in the Ultra-scale Visualization Climate Data AnalysisTools (UV-CDAT) environment. SphereBlur provides a flexible multi-scale analysis toolkit for climate data based on linear scale space. Scale space methods, common in image processing, draw upon the well-studied physics of diffusion to obtain a multi-scale representation of data. A simple extension of these methods to the sphere provides flexible analysis tools for climate data. We use this framework to evaluate model performance at multiple spatial scales and to design filters to isolate scales of interest. We show how these methods can be used to simultaneously detect points and scales of interest in data, and to track the appearance and evolution of features such as corners, edges, and "blobs" in observational and model data. Prepared by LLNL under Contract DE-AC52-07NA27344.

Marvel, K. D.

2012-12-01

98

COSMOS: Python library for massively parallel workflows  

PubMed Central

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

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

99

Using Python to teach mathematics, physics, and acoustics.  

PubMed

Advanced technical courses often suffer from a lack of interactive materials. Common tools to remedy this deficiency include MATLAB and Mathematica, both of which can be prohibitively expensive to obtain outside of the university environment. Python is a scripted language that is easy to read and use and is rapidly emerging as a lingua franca for scientific computing due to the flexibility and facility of the language, the large and active community, and the large number of high quality scientific libraries that are available in Python. Python provides a free and open source tool to develop classroom materials that students can modify and extend. We discuss the use of Python in teaching advanced topics in mathematics, physics, and acoustics. Examples are drawn from courses in acoustics, mechanics, and mathematical and computational physics. PMID:25235062

Thomas, Derek C; Christensen, Benjamin Y

2014-04-01

100

MEG and EEG data analysis with MNE-Python  

PubMed Central

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

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

2013-01-01

101

MEG and EEG data analysis with MNE-Python.  

PubMed

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

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

2013-12-26

102

Rapid Development of Interferometric Software Using MIRIAD and Python  

NASA Astrophysics Data System (ADS)

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.

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

2012-06-01

103

Anisotropy in the Cosmic Microwave Background: Results from Python V  

Microsoft Academic Search

We present observations of the microwave sky made with the Python experiment in its fifth year of operation at the Amundsen-Scott South Pole Station in Antarctica. The Python telescope was fitted with a HEMT amplifier-based radiometer, yielding sensitivity to the microwave sky from 37-45 GHz in two frequency bands for each pixel in a 1 x 2 array, each pixel

K. Coble; J. Kovac; M. Dragovan; N. Halverson; W. Holzapfel; D. Alvarez; J. B. Peterson; G. Griffin; M. Newcomb; K. Miller; S. R. Platt; G. Novak; S. Dodelson; K. Ganga; L. Knox

1998-01-01

104

Sexual size dimorphism and natural history traits are correlated with intersexual dietary divergence in royal pythons (python regius) from the rainforests of southeastern Nigeria  

Microsoft Academic Search

Food habits of the royal python (Python regius) were studied in some localities of southeastern Nigeria by means both of faeces analysis and forced regurgitation of living individuals. Female pythons were significantly longer than the males. Both sexes preyed exclusively upon birds and mammals, but there were significant intersexual differences in terms of dietary, composition. Males preyed more frequently upon

Luca Luiselli; Francesco Maria Angelici

1998-01-01

105

Ecological correlates of invasion impact for Burmese pythons in Florida  

USGS Publications Warehouse

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.

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

2012-01-01

106

Ecological correlates of invasion impact for Burmese pythons in Florida.  

PubMed

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. PMID:22938523

Reed, Robert N; Willson, John D; Rodda, Gordon H; Dorcas, Michael E

2012-09-01

107

Pythons metabolize prey to fuel the response to feeding.  

PubMed Central

We investigated the energy source fuelling the post-feeding metabolic upregulation (specific dynamic action, SDA) in pythons (Python regius). Our goal was to distinguish between two alternatives: (i) snakes fuel SDA by metabolizing energy depots from their tissues; or (ii) snakes fuel SDA by metabolizing their prey. To characterize the postprandial response of pythons we used transcutaneous ultrasonography to measure organ-size changes and respirometry to record oxygen consumption. To discriminate unequivocally between the two hypotheses, we enriched mice (= prey) with the stable isotope of carbon (13C). For two weeks after feeding we quantified the CO2 exhaled by pythons and determined its isotopic 13C/12C signature. Ultrasonography and respirometry showed typical postprandial responses in pythons. After feeding, the isotope ratio of the exhaled breath changed rapidly to values that characterized enriched mouse tissue, followed by a very slow change towards less enriched values over a period of two weeks after feeding. We conclude that pythons metabolize their prey to fuel SDA. The slowly declining delta13C values indicate that less enriched tissues (bone, cartilage and collagen) from the mouse become available after several days of digestion. PMID:15255044

Starck, J. Matthias; Moser, Patrick; Werner, Roland A.; Linke, Petra

2004-01-01

108

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

Microsoft Academic Search

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

1991-01-01

109

MTpy: A Python toolbox for magnetotellurics  

NASA Astrophysics Data System (ADS)

We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

Krieger, Lars; Peacock, Jared R.

2014-11-01

110

Technical instructions for submitting the Python program Go to http://www.python.org/download/, download the Python 3.3.2 installer  

E-print Network

are satisfied that your agent runs properly, change the name of the file StudentName.py to your own (true) name, change the name of the class, replacing StudentName by the name of the file (e.g., to Agent of an implementation of an agent, the class AgentStudentName (class is a technical term in Python). This serves

111

Cosmic Microwave Background Anisotropy Measurement from Python V  

NASA Astrophysics Data System (ADS)

We analyze observations of the microwave sky made with the Python experiment in its fifth year of operation at the Amundsen-Scott South Pole Station in Antarctica. After modeling the noise and constructing a map, we extract the cosmic signal from the data. We simultaneously estimate the angular power spectrum in eight bands ranging from large (l~40) to small (l~260) angular scales, with power detected in the first six bands. There is a significant rise in the power spectrum from large to smaller (l~200) scales, consistent with that expected from acoustic oscillations in the early universe. We compare this Python V map to a map made from data taken in the third year of Python. Python III observations were made at a frequency of 90 GHz and covered a subset of the region of the sky covered by Python V observations, which were made at 40 GHz. Good agreement is obtained both visually (with a filtered version of the map) and via a likelihood ratio test.

Coble, K.; Dodelson, S.; Dragovan, M.; Ganga, K.; Knox, L.; Kovac, J.; Ratra, B.; Souradeep, T.

2003-02-01

112

Stochastic spatio-temporal modelling with PCRaster Python  

NASA Astrophysics Data System (ADS)

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).

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

2012-04-01

113

pyam: Python Implementation of YaM  

NASA Technical Reports Server (NTRS)

pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

Myint, Steven; Jain, Abhinandan

2012-01-01

114

Synthetic seismogram web service and Python tools  

NASA Astrophysics Data System (ADS)

Many geophysical methods require knowledge of Green's functions (GF) or synthetic seismograms in dependence of ranges of source and receiver coordinates. Examples include synthetic seismogram generation, moment tensor inversion, the modeling of depth phases for regional and teleseismic earthquakes, or the modeling of pressure diffusion induced static displacement and strain. Calculation of Green's functions is a computationally expensive operation and it can be of advantage to calculate them in advance: the same Green's function traces can then be reused several or many times as required in a typical application. Regarding Green's function computation as an independent step in a use-case's processing chain encourages to store these in an application independent form. They can then be shared between different applications and they can also be passed to other researchers, e.g. via a web service. Starting now, we provide such a web service to the seismological community (http://kinherd.org/), where a researcher can share Green's function stores and retrieve synthetic seismograms for various point and extended earthquake source models for many different earth models at local, regional and global scale. This web service is part of a rich new toolset for the creation and handling of Green's functions and synthetic seismograms (http://emolch.github.com/pyrocko/gf). It can be used off-line or in client mode. Its core features are: greatly simplified generation of Green's function stores supports various codes for Green's function computation extensible Green's function storage format flexible spacial indexing of Green's functions integrated travel time computation support for other types of Green's functions; e.g. poro-elastic GFs written in Python

Heimann, Sebastian; Cesca, Simone; Kriegerowski, Marius; Dahm, Torsten

2014-05-01

115

Record length, mass, and clutch size in the nonindigenous Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), in Florida  

USGS Publications Warehouse

The Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), is indigenous to northern India,east to southern China, and south to Vietnam and a few islands in Indonesia (Barker and Barker 2008, Reed and Rodda 2009). This species has been introduced since at least 1979 in southern Florida, USA, where it likely began reproducing and became established during the 1980s (Meshaka et al. 2000, Snowet al. 2007b,Kraus 2009, Krysko et al. 2011, Willson et al. 2011). Python bivittatus has been documented in Florida consuming a variety of mammals and birds, and the American Alligator(Alligator mississippiensis) (Snowet al. 2007a, 2007b; Harvey et al. 2008; Rochford et al. 2010b; Holbrook and Chesnes 2011), many of which are protected species. Herein, we provide details on two of the largest known wild P. bivittatus in Florida to date, including current records on length,mass,clutch size, and diet.

Krysko, Kenneth L.; Hart, Kristen M.; Smith, Brian J.; Selby, Thomas H.; Cherkiss, Michael S.; Coutu, Nicholas T.; Reichart, Rebecca M.; Nuez, Leroy P.; Mazzotti, Frank J.; Snow, Ray W.

2012-01-01

116

pyGadgetReader: GADGET snapshot reader for python  

NASA Astrophysics Data System (ADS)

pyGadgetReader is a universal GADGET snapshot reader for python that supports type-1, type-2, HDF5, and TIPSY (ascl:1111.015) binary formats. It additionally supports reading binary outputs from FoF_Special, P-StarGroupFinder, Rockstar (ascl:1210.008), and Rockstar-Galaxies.

Thompson, Robert

2014-11-01

117

PyTrilinos : a parallel python interface to Trilinos.  

SciTech Connect

PyTrilinos provides python access to selected Trilinos packages: emerging from early stages, portability, completeness; parallelism; rapid prototyping; application development; unit testing; and numeric compatibility (migrating to NumPy). PyTrilinos complements and supplements the SciPy package.

Spotz, William F.

2006-02-01

118

Finite Element Modeling of Contact and Impact Problems Using Python  

Microsoft Academic Search

This paper discusses an on going project to improve the accuracy of automotive crash simulations. Two likely causes for discrepancy between simulations and the results of real, physical tests are discussed. An existing Python package for finite element anal- ysis, SfePy, is presented along with plans to con- tribute additional features in support of this work, including nonlinear material modeling

Ryan Krauss

119

Cosmic Microwave Background Anisotropy Measurement from Python V  

Microsoft Academic Search

We analyze observations of the microwave sky made with the Python experiment in its fifth year of operation at the Amundsen-Scott South Pole Station in Antarctica. After modeling the noise and constructing a map, we extract the cosmic signal from the data. We simultaneously estimate the angular power spectrum in eight bands ranging from large (l~40) to small (l~260) angular

K. Coble; S. Dodelson; M. Dragovan; K. Ganga; L. Knox; J. Kovac; B. Ratra; T. Souradeep

2003-01-01

120

Python for Unified Research in Econometrics and Statistics Roseline Bilina  

E-print Network

Python for Unified Research in Econometrics and Statistics Roseline Bilina Steve Lawford Cornell-alone applications in econometrics and statistics, and as a tool for gluing different applications together. (It methods and programming), C87 (Econometric software), C88 (Other computer software). Keywords: Object

Boyer, Edmond

121

Python Robotics: An Environment for Exploring Robotics Beyond LEGOs  

E-print Network

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

Blank, Douglas

122

Python Robotics: An Environment for Exploring Robotics Beyond LEGOs  

E-print Network

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

Blank, Douglas

123

Cold-induced mortality of invasive Burmese pythons in south Florida  

USGS Publications Warehouse

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.

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

2011-01-01

124

Rapid microsatellite marker development using next generation pyrosequencing to inform invasive Burmese python -- Python molurus bivittatus -- management  

USGS Publications Warehouse

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 (26) 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.

Hunter, Margaret E.; Hart, Kristen M.

2013-01-01

125

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

PubMed Central

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

2011-01-01

126

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

PubMed Central

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 (26) 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

Hunter, Margaret E.; Hart, Kristen M.

2013-01-01

127

Using Virtual Observatory with Python: querying remote astronomical databases  

E-print Network

This tutorial is devoted to extending an existing catalogue with data taken elsewhere, either from CDS Vizier or Simbad database. As an example, we used the so-called 'Spectroscopic Survey of Stars in the Solar Neighborhood' (aka. S4N, Allende Prieto et al. 2004) in order to retrieve all objects with available data for the set of fundamental stellar parameters effective temperature, surface gravity and metallicity. Then for each object in this dataset we query Simbad database to retrieve the projected rotational velocity. This combines Vizier and Simbad queries made using Python astroquery module. The tutorial covers remote database access, filtering tables with arbitrary criteria, creating and writing your own tables, and basics of plotting in Python.

Paletou, F

2014-01-01

128

Expyriment: a Python library for cognitive and neuroscientific experiments.  

PubMed

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

Krause, Florian; Lindemann, Oliver

2014-06-01

129

Brian: a simulator for spiking neural networks in python.  

PubMed

"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

Goodman, Dan; Brette, Romain

2008-01-01

130

The Crates Library: The Redesigned Python Interface for Scripting Languages  

NASA Astrophysics Data System (ADS)

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.

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

2011-07-01

131

PyRAT - python radiography analysis tool (u)  

SciTech Connect

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.

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

2011-01-14

132

Python as a Federation Tool for GENESIS 3.0  

PubMed Central

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be glued together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience. PMID:22276101

Cornelis, Hugo; Rodriguez, Armando L.; Coop, Allan D.; Bower, James M.

2012-01-01

133

A Community Python Library for Solar Physics (SunPy)  

NASA Astrophysics Data System (ADS)

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.

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

134

Python as a federation tool for GENESIS 3.0.  

PubMed

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be 'glued' together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience. PMID:22276101

Cornelis, Hugo; Rodriguez, Armando L; Coop, Allan D; Bower, James M

2012-01-01

135

ObsPy: A Python Toolbox for Seismology  

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

136

Python for Information Theoretic Analysis of Neural Data  

PubMed Central

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

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

2008-01-01

137

Parallel astronomical data processing with Python: Recipes for multicore machines  

NASA Astrophysics Data System (ADS)

High performance computing has been used in various fields of astrophysical research. But most of it is implemented on massively parallel systems (supercomputers) or graphical processing unit clusters. With the advent of multicore processors in the last decade, many serial software codes have been re-implemented in parallel mode to utilize the full potential of these processors. In this paper, we propose parallel processing recipes for multicore machines for astronomical data processing. The target audience is astronomers who use Python as their preferred scripting language and who may be using PyRAF/IRAF for data processing. Three problems of varied complexity were benchmarked on three different types of multicore processors to demonstrate the benefits, in terms of execution time, of parallelizing data processing tasks. The native multiprocessing module available in Python makes it a relatively trivial task to implement the parallel code. We have also compared the three multiprocessing approaches-Pool/Map, Process/Queue and Parallel Python. Our test codes are freely available and can be downloaded from our website.

Singh, Navtej; Browne, Lisa-Marie; Butler, Ray

2013-08-01

138

BioC implementations in Go, Perl, Python and Ruby  

PubMed Central

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

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

2014-01-01

139

Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius.  

PubMed

Snakes lack both an outer ear and a tympanic middle ear, which in most tetrapods provide impedance matching between the air and inner ear fluids and hence improve pressure hearing in air. Snakes would therefore be expected to have very poor pressure hearing and generally be insensitive to airborne sound, whereas the connection of the middle ear bone to the jaw bones in snakes should confer acute sensitivity to substrate vibrations. Some studies have nevertheless claimed that snakes are quite sensitive to both vibration and sound pressure. Here we test the two hypotheses that: (1) snakes are sensitive to sound pressure and (2) snakes are sensitive to vibrations, but cannot hear the sound pressure per se. Vibration and sound-pressure sensitivities were quantified by measuring brainstem evoked potentials in 11 royal pythons, Python regius. Vibrograms and audiograms showed greatest sensitivity at low frequencies of 80-160 Hz, with sensitivities of -54 dB re. 1 m s(-2) and 78 dB re. 20 ?Pa, respectively. To investigate whether pythons detect sound pressure or sound-induced head vibrations, we measured the sound-induced head vibrations in three dimensions when snakes were exposed to sound pressure at threshold levels. In general, head vibrations induced by threshold-level sound pressure were equal to or greater than those induced by threshold-level vibrations, and therefore sound-pressure sensitivity can be explained by sound-induced head vibration. From this we conclude that pythons, and possibly all snakes, lost effective pressure hearing with the complete reduction of a functional outer and middle ear, but have an acute vibration sensitivity that may be used for communication and detection of predators and prey. PMID:22189777

Christensen, Christian Bech; Christensen-Dalsgaard, Jakob; Brandt, Christian; Madsen, Peter Teglberg

2012-01-15

140

ObsPy - A Bridge to Utilize Python's Big Data Capabilities for Seismology  

NASA Astrophysics Data System (ADS)

Numerous packages for handling and analysing big data sets with Python surfaced in the last couple of years. Seismology has similarly seen a rapid increase in the amount of available data to the point where the tools commonly employed can no longer deal with them in a reasonable fashion. ObsPy is a community-driven, open-source project dedicated to provide a Python framework for seismological data enabling users to easily utilize Python 's aforementioned big data modules for their research. This contribution presents a short overview of the current landscape of Python's big data ecosystem along with selected applications in seismology.

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

2013-12-01

141

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

PubMed Central

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

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

2011-01-01

142

Zachary Kaplan Math 547  

E-print Network

is affected. If this factor is greater than one then the image is lightened, while or darkened with relative ease. This text is in color. (R=12,B=80,G=69) This text in the field. In general this is normalized to a value between negative one and one

Marzuola, Jeremy

143

Zachary Gagnon Jason Gordon  

E-print Network

Article Bovine red blood cell starvation age discrimination through a glutaraldehyde- amplified the concept of membrane cross-linking- induced dielectrophoretic discrimination of bovine red blood cells (b reaction that allows for sensitive di- electrophoretic analysis and discrimination of bovine red blood

Chang, Hsueh-Chia

144

MTpy - Python Tools for Magnetotelluric Data Processing and Analysis  

NASA Astrophysics Data System (ADS)

We present the Python package MTpy, which provides functions for the processing, analysis, and handling of magnetotelluric (MT) data sets. MT is a relatively immature and not widely applied geophysical method in comparison to other geophysical techniques such as seismology. As a result, the data processing within the academic MT community is not thoroughly standardised and is often based on a loose collection of software, adapted to the respective local specifications. We have developed MTpy to overcome problems that arise from missing standards, and to provide a simplification of the general handling of MT data. MTpy is written in Python, and the open-source code is freely available from a GitHub repository. The setup follows the modular approach of successful geoscience software packages such as GMT or Obspy. It contains sub-packages and modules for the various tasks within the standard work-flow of MT data processing and interpretation. In order to allow the inclusion of already existing and well established software, MTpy does not only provide pure Python classes and functions, but also wrapping command-line scripts to run standalone tools, e.g. modelling and inversion codes. Our aim is to provide a flexible framework, which is open for future dynamic extensions. MTpy has the potential to promote the standardisation of processing procedures and at same time be a versatile supplement for existing algorithms. Here, we introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing, interpretation, and visualisation utilising MTpy on example data sets collected over different regions of Australia and the USA.

Krieger, Lars; Peacock, Jared; Thiel, Stephan; Inverarity, Kent; Kirkby, Alison; Robertson, Kate; Soeffky, Paul; Didana, Yohannes

2014-05-01

145

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit  

Microsoft Academic Search

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

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

2008-01-01

146

Programming in Java, C#, Pizza and Python Extra Credit (not required)  

E-print Network

CS 538 Project #4 Programming in Java, C#, Pizza and Python Extra Credit (not required an infinite LazyList containing val in // every position } static LazyList filter(LazyList control, Lazy. You are to redo Question 4 of Project #2 (lazy lists and the "Sieve of Erastosthenes") in Python

Fischer, Charles N.

147

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

Federal Register 2010, 2011, 2012, 2013

...requirements? (13) Why we should or should...silent hunters that lie in wait along pathways...numerous sources of people being bitten...if harassed by people. Although African...python for reasons why the Southern African...such will often lie in wait to attack...python for reasons why the boa...

2010-03-12

148

PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI  

E-print Network

PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data Michael Hanke1,2 , Yaroslav-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written theory in their analysis of fMRI data1. For example, two such classifier-based studies by Haynes and Rees

Sederberg, Per B.

149

Python for Software Design: How to Think Like a Computer Scientist  

Microsoft Academic Search

Python for Software Design is a concise introduction to software design using the Python programming language. Intended for people with no programming experience, this book starts with the most basic concepts and gradually adds new material. Some of the ideas students find most challenging, like recursion and object-oriented programming, are divided into a sequence of smaller steps and introduced over

Allen B. Downey

2009-01-01

150

Amateur Image Pipeline Processing using Python plus PyRAF  

NASA Astrophysics Data System (ADS)

A template pipeline spanning observing planning to publishing is offered as a basis for establishing a long term observing program. The data reduction pipeline encapsulates all policy and procedures, providing an accountable framework for data analysis and a teaching framework for IRAF. This paper introduces the technical details of a complete pipeline processing environment using Python, PyRAF and a few other languages. The pipeline encapsulates all processing decisions within an auditable framework. The framework quickly handles the heavy lifting of image processing. It also serves as an excellent teaching environment for astronomical data management and IRAF reduction decisions.

Green, Wayne

2012-05-01

151

Pyteomicsa Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics  

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

152

Novel divergent nidovirus in a python with pneumonia.  

PubMed

The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33?000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales. PMID:25063552

Bodewes, Rogier; Lempp, Charlotte; Schrch, Anita C; Habierski, Andre; Hahn, Kerstin; Lamers, Mart; von Drnberg, Katja; Wohlsein, Peter; Drexler, Jan Felix; Haagmans, Bart L; Smits, Saskia L; Baumgrtner, Wolfgang; Osterhaus, Albert D M E

2014-11-01

153

New Python-based methods for data processing  

PubMed Central

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

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

2013-01-01

154

Programming biological models in Python using PySB  

PubMed Central

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

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

2013-01-01

155

Programming biological models in Python using PySB.  

PubMed

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

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

2013-01-01

156

A cross-validation package driving Netica with python  

USGS Publications Warehouse

Bayesian networks (BNs) are powerful tools for probabilistically simulating natural systems and emulating process models. Cross validation is a technique to avoid overfitting resulting from overly complex BNs. Overfitting reduces predictive skill. Cross-validation for BNs is known but rarely implemented due partly to a lack of software tools designed to work with available BN packages. CVNetica is open-source, written in Python, and extends the Netica software package to perform cross-validation and read, rebuild, and learn BNs from data. Insights gained from cross-validation and implications on prediction versus description are illustrated with: a data-driven oceanographic application; and a model-emulation application. These examples show that overfitting occurs when BNs become more complex than allowed by supporting data and overfitting incurs computational costs as well as causing a reduction in prediction skill. CVNetica evaluates overfitting using several complexity metrics (we used level of discretization) and its impact on performance metrics (we used skill).

Fienen, Michael N.; Plant, Nathaniel G.

2014-01-01

157

Intraspecific scaling of arterial blood pressure in the Burmese python.  

PubMed

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

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

2014-07-01

158

Oxygen transport is not compromised at high temperature in pythons.  

PubMed

To evaluate whether the 'oxygen and capacity limited thermal tolerance' model (OCLTT) applies to an air-breathing ectothermic vertebrate, we measured oxygen uptake (), cardiac performance and arterial blood gases during a progressive rise of temperature from 30 to 40C in the snake Python regius. of fasting snakes increased exponentially with temperature whereas of digesting snakes at high temperatures plateaued at a level 3- to 4-fold above fasting. The high and sustained aerobic metabolism over the entire temperature range was supported by pronounced tachycardia at all temperatures, and both fasting and digesting snakes maintained a normal acid-base balance without any indication of anaerobic metabolism. All snakes also maintained high arterial PO2 , even at temperatures close to the upper lethal temperature. Thus, there is no evidence of a reduced capacity for oxygen transport at high temperatures in either fasting or digesting snakes, suggesting that the upper thermal tolerance of this species is limited by other factors. PMID:25267848

Fobian, Dannie; Overgaard, Johannes; Wang, Tobias

2014-11-15

159

PyRAT (python radiography analysis tool): overview  

SciTech Connect

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.

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

2011-01-14

160

A Pseudo-Parallel Python Environment for Database Curation  

NASA Astrophysics Data System (ADS)

One of the major challenges providing large databases like the WFCAM Science Archive (WSA) is to minimize ingest times for pixel/image metadata and catalogue data. In this article we describe how the pipeline processed data are ingested into the database as the first stage in building a release database which will be succeeded by advanced processing (source merging, seaming, detection quality flagging etc.). To accomplish the ingestion procedure as fast as possible we use a mixed Python/C++ environment and run the required tasks in a simple parallel modus operandi where the data are split into daily chunks and then processed on different computers. The created data files can be ingested into the database immediately as they are available. This flexible way of handling the data allows the most usage of the available CPUs as the comparison with sequential processing shows.

Sutorius, E.; Bryant, J.; Collins, R.; Cross, N.; Hambly, N.; Read, M.

2008-08-01

161

PyMidas--A Python Interface to ESO-MIDAS  

NASA Astrophysics Data System (ADS)

Finland joined the European Southern Observatory in 2004, providing a contribution in kind of software expertise as part of its joining fee. This significant resource, called the Sampo project, will be devoted to exploring the options for the future of data reduction and analysis in an ESO context, to understanding user requirements and to performing a series of major pilot projects to investigate different technologies, approaches and architectures. The Sampo project {http://www.eso.org/sampo} will run for three years and aims to prepare the ESO community for the data analysis and reduction challenges of the next decades. The first major Sampo project is PyMidas, an interface from Python to the ESO-MIDAS data analysis and reduction system. This paper describes the motivation for this project, how it has been implemented and gives some examples of PyMidas in action.

Hook, R. N.; Maisala, S.; Oittinen, T.; Ullgren, M.; Vasko, K.; Savolainen, V.; Lindroos, J.; Anttila, M.; Solin, O.; Mller, P. M.; Banse, K.; Peron, M.

2006-07-01

162

One-dimensional statistical parametric mapping in Python.  

PubMed

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

Pataky, Todd C

2012-01-01

163

Python package for model STructure ANalysis (pySTAN)  

NASA Astrophysics Data System (ADS)

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.

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

2013-04-01

164

Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes.  

PubMed

Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21-36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km of the original capture location. Translocated snakes moved straighter and faster than control snakes and displayed movement path structure indicative of oriented movement. This study provides evidence that Burmese pythons have navigational map and compass senses and has implications for predictions of spatial spread and impacts as well as our understanding of reptile cognitive abilities. PMID:24647727

Pittman, Shannon E; Hart, Kristen M; Cherkiss, Michael S; Snow, Ray W; Fujisaki, Ikuko; Smith, Brian J; Mazzotti, Frank J; Dorcas, Michael E

2014-03-01

165

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes  

E-print Network

, Stephen P. Mackessyt , Anne M. Bronikowskiu , Mark Yandellj , Wesley C. Warrenl , Stephen M. Secorv compare the python and king cobra genomes along with genomic samples from other snakes and perform

Feschotte, Cedric

166

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

E-print Network

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 ...

Canelake, Sarina

2010-01-01

167

Synthesized N-Point Chopping Pattern Analysis of the Python Data  

Microsoft Academic Search

We report initial results from a new analysis method for data taken with the Python microwave background anisotropy experiment. The Python telescope performs a three-beam chop on the sky at multiple azimuth positions. The original analysis involved subtracting neighboring pairs of three-beam observations to produce a four-beam pattern on the sky. This talk generalizes the original analysis in three ways

D. L. Alvarez; M. Dragovan; J. E. Ruhl; J. Kovac; S. R. Platt; J. Peterson

1995-01-01

168

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

Microsoft Academic Search

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

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

2010-01-01

169

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

USGS Publications Warehouse

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 20032011 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.

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

2012-01-01

170

Environmental temperatures, physiology and behavior limit the range expansion of invasive Burmese pythons in southeastern USA.  

PubMed

A well-established population of Burmese pythons resides in the Everglades of southern Florida. Prompted in part by a report that identified much of southern USA as suitable habitat for expansion or establishment of the Burmese python, we examined the plausibility of this snake to survive winters at sites north of the Everglades. We integrated daily low and high temperatures recorded from October to February from 2005-2011 at Homestead, Orlando and Gainesville, Florida; and Aiken, South Carolina, with minimum temperatures projected for python digestion (16 C), activity (5 C) and survival (0 C). Mean low and high temperatures decreased northward from Homestead to Aiken and the number of days of freezing temperatures increased northward. Digestion was impaired or inhibited for 2 months in the Everglades and up to at least 5 months in Aiken, and activity was increasingly limited northward during these months. Reports of overwinter survivorship document that a single bout of low and freezing temperatures results in python death. The capacity for Burmese pythons to successfully overwinter in more temperate regions of the USA is seemingly prohibited because they lack the behaviors to seek refuge from, and the physiology to tolerate, cold temperatures. As tropical Southeast Asia is the source of the Everglades Burmese pythons, we predict it is unlikely that they will be able to successfully expand to or colonize more temperate areas of Florida and adjoining states due to their lack of behavioral and physiological traits to seek refuge from cold temperatures. PMID:22938524

Jacobson, Elliott R; Barker, David G; Barker, Tracy M; Mauldin, Richard; Avery, Michael L; Engeman, Richard; Secor, Stephen

2012-09-01

171

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

PubMed

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

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

2012-02-14

172

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

PubMed Central

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 20032011 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

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

173

Using Python as a first programming environment for computational physics in developing countries  

NASA Astrophysics Data System (ADS)

Python unique features such its interpretative, multiplatform and object oriented nature as well as being a free and open source software creates the possibility that any user connected to the internet can download the entire package into any platform, install it and immediately begin to use it. Thus Python is gaining reputation as a preferred environment for introducing students and new beginners to programming. Therefore in Africa, the Python African Tour project has been launched and we are coordinating its use in computational science. We examine here the challenges and prospects of using Python for computational physics (CP) education in developing countries (DC). Then we present our project on using Python to simulate and aid the learning of laboratory experiments illustrated here by modeling of the simple pendulum and also to visualize phenomena in physics illustrated here by demonstrating the wave motion of a particle in a varying potential. This project which is to train both the teachers and our students on CP using Python can easily be adopted in other DC.

Akpojotor, Godfrey; Ehwerhemuepha, Louis; Echenim, Myron; Akpojotor, Famous

2011-03-01

174

A Survey of Computational Physics: Python Multimodal eBook  

NSDL National Science Digital Library

This upper-division text surveys many of the topics of modern computational physics from a computational science point of view. Its emphasis on learning by doing is assisted by many available model programs, using Python. The text is designed for a one- or two-semester undergraduate or beginning graduate course. The text overlaps the lower-division "A First Course in Scientific Computing" by Landau, to provide computational science/physics materials at all levels of undergraduate curriculum. Of particular note is the eTextBook's links to video-based lecture modules specifically created for most every topic in the text. Individual lectures can be streamed for viewing on the web. The video modules contain a video picture-in-picture of a lecture or demonstration, along with active slides coordinated with the lecture, a dynamic table of contents, and links to codes, applets, and slides. The set of lectures makes the text particularly useful for a blended or online course where an instructor can use some or all of the text's lectures or slides, or even insert his or her own materials within the text and lectures. The Table of Contents (440 KB) and the full textbook (22 MB) are available for download.

Landau, Rubin; Paez, Manuel J.; Bordeianu, Cristian

2011-12-03

175

SIMA: Python software for analysis of dynamic fluorescence imaging data  

PubMed Central

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

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

2014-01-01

176

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

PubMed

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

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

2014-01-01

177

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

PubMed Central

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

Ujvari, Beata; Madsen, Thomas

2009-01-01

178

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

NASA Astrophysics Data System (ADS)

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.

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

2002-04-01

179

PESO - The Python Based Control System of the Ondrejov 2m Telescope  

NASA Astrophysics Data System (ADS)

Python has been gaining a good reputation and respectability in many areas of software development. We have chosen Python after getting the new CCD detector for the coud spectrograph of Ond?ejov observatory 2m telescope. The VersArray detector from Roper Scientific came only with the closed source library PVCAM of low-level camera control functions for Linux, so we had to write the whole astronomical data acquisition system from scratch and integrate it with the current spectrograph and telescope control systems. The final result of our effort, PESO (Python Exposure System for Ond?ejov) is a highly comfortable GUI-based environment allowing the observer to change the spectrograph configuration, choose the detector acquisition mode, select the exposure parameters, and monitor the exposure progress. All of the relevant information from the control computers is written into the FITS headers by the PyFITS module, and the acquired CCD frame is immediately displayed in an SAO DS9 window using XPA calls. The GTK-based front end design was drawn in the Glade visual development tool, giving the shape and position of all widgets in single XML file, which is used in Python by a simple call of the PyGlade module. We describe our experience with the design and implementation of PESO, stressing the easiness of quick changes of the GUI, together with the capability of separate testing of every module using the Python debugger, IPython.

Skoda, P.; Fuchs, J.; Honsa, J.

2005-12-01

180

SunPy - Python for Solar Physics, Version 0.4  

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

181

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

E-print Network

Optimization of Industrial Code with Python: Development of a Graphical User Interface A SURE and Vibrations laboratory ·Goal is to achieve a better understanding of nonlinear phenomena arising within modern by the computer ·Toimporovefunctionalityandwork-flowofaGUIoriginallyde- signedinMATLABusingtheopen-sourcelanguage,Python

Barthelat, Francois

182

Object-oriented implementations of the MPDATA advection equation solver in C++, Python and Fortran  

E-print Network

Three object-oriented implementations of a prototype solver of the advection equation are introduced. Presented programs are based on Blitz++ (C++), NumPy (Python), and Fortran's built-in array containers. The solvers include an implementation of the Multidimensional Positive-Definite Advective Transport Algorithm (MPDATA). The introduced codes exemplify how the application of object-oriented programming (OOP) techniques allows to reproduce the mathematical notation used in the literature within the program code. The introduced codes serve as a basis for discussion on the tradeoffs of the programming language choice. The main angles of comparison are code brevity and syntax clarity (and hence maintainability and auditability) as well as performance. In case of Python, a significant performance gain is observed when switching from the standard interpreter (CPython) to the PyPy implementation of Python. Entire source code of all three implementations is embedded in the text and is licensed under the terms of th...

Arabas, Sylwester; Jaruga, Anna; Fija?kowski, Maciej

2013-01-01

183

Python-based geometry preparation and simulation visualization toolkits for STEPS  

PubMed Central

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. PMID:24782754

Chen, Weiliang; De Schutter, Erik

2014-01-01

184

A World Without Referees Larry Wasserman1  

E-print Network

and democratize our approach to scientific publishing. 1 Introduction The peer review system that we use on arxiv. If the paper is good, people will read it. If they find mistakes, you can thank them a post

185

History Revenged: Monty Python Translates Chretien de Troyes's "Perceval, or the Story of the Grail" (Again).  

ERIC Educational Resources Information Center

Finds "Monty Python and the Holy Grail" functions as a "surprisingly accurate cultural translation" of de Troyes's "Perceval" text. Suggests that using such films helps students open a door upon film studies and discursive studies that will serve them well as they adapt to their own historical moment. (PA)

Murrell, Elizabeth

1998-01-01

186

Using Python Packages in 6D (Py)Ferret: EOF Analysis, OPeNDAP Sequence Data  

NASA Astrophysics Data System (ADS)

PyFerret was designed to provide the easy methods of access, analysis, and display of data found in the Ferret under the simple yet powerful Python scripting/programming language. This has enabled PyFerret to take advantage of a large and expanding collection of third-party scientific Python modules. Furthermore, ensemble and forecast axes have been added to Ferret and PyFerret for creating and working with collections of related data in Ferret's delayed-evaluation and minimal-data-access mode of operation. These axes simplify processing and visualization of these collections of related data. As one example, an empirical orthogonal function (EOF) analysis Python module was developed, taking advantage of the linear algebra module and other standard functionality in NumPy for efficient numerical array processing. This EOF analysis module is used in a Ferret function to provide an ensemble of levels of data explained by each EOF and Time Amplitude Function (TAF) product. Another example makes use of the PyDAP Python module to provide OPeNDAP sequence data for use in Ferret with minimal data access characteristic of Ferret.

Smith, K. M.; Manke, A.; Hankin, S. C.

2012-12-01

187

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

E-print Network

economic burden. Burmese pythons, giant constricting snakes native to Asia, now are found throughout much and ecosystem function (1). In the United States the cost of invasive species management exceeds $120 billion annually (2). Invasive species affect native ecosystems via alteration of habitat structure (3

Dorcas, Michael E.

188

Safe Asynchronous Exceptions For Python Williams College Technical Note 02-2002, Dec. 2002  

E-print Network

of asynchrony and exception handling, and propose a modification of the Python lan- guage that restores signal language. When the operating system raises a signal, control is transferred to a signal handler, i that they treat error conditions. For example, a program may recover from an error writing to an open file

Freund, Stephen N.

189

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

E-print Network

. Daniel Liang Chapter 1 .py Python script file extension name. assembler A software used to translate The components are connected through a subsystem called a bus that transfers data or power between them. byte subscriber line) Uses a phone line and can transfer data in a speed 20 times faster than a regular modem

Liang, Y. Daniel

190

Automating Disk Forensic Processing with SleuthKit, XML and Python  

Microsoft Academic Search

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

Simson L. Garfinkel

2009-01-01

191

A MythTV Python API to complement the JustPlay Network  

E-print Network

In this thesis, I developed an API to control a MythTV backend. This API is called PyMythTV. It allows one to develop software that can take advantage of a PVR device, MythTV. The API was written in Python, which allows ...

Deonier, Christian

2008-01-01

192

The importance of snakes, and the Burmese python, as model organisms  

E-print Network

to the python (which is non-venomous), venomous snake species are also important for bio- medical research of organ performance and regeneration. These animals are also readily obtained from commercial breeders, non-aggressive, and easier and cheaper to care for than laboratory rats. The scientific potential

Ray, David

193

Using Python and QuickDraw to Foster Student Engagement in CS1  

E-print Network

Using Python and QuickDraw to Foster Student Engagement in CS1 Ben Stephenson Department Projects, Student Engagement Permission to make digital or hard copies of all or part of this work students enrolling in introductory computer science courses today have grown up working exclusively

Stephenson, Ben

194

Assessing risks to humans from invasive Burmese pythons in Everglades National Park, Florida, USA  

USGS Publications Warehouse

Invasive Burmese pythons (Python molurus bivittatus) are now established across a large area of southern Florida, USA, including all of Everglades National Park (NP). The presence of these large-bodied snakes in the continental United States has attracted intense media attention, including regular reference to the possibility of these snakes preying on humans. Over the course of a decade (20032012), we solicited reports of apparently unprovoked strikes directed at humans in Everglades NP. We summarize the circumstances surrounding each of the 5 reported incidents, which occurred between 2006 and 2012. All strikes were directed toward biologists moving through flooded wetlands; 2 strikes resulted in minor injury and none resulted in constriction. We consider most of these strikes to be cases of mistaken identity, in which the python initiated a strike at a potential prey item but aborted its predatory behavior prior to constriction and ingestion. No strikes are known to have been directed at park visitors despite visitation rates averaging over one million per year during this period. We conclude that while risks to humans should not be completely discounted, the relative risk of a human being killed by a python in Everglades NP appears to be extremely low.

Reed, Robert N.; Snow, Ray W.

2014-01-01

195

ScattPy: A new Python package for light scattering computations  

Microsoft Academic Search

We present a Python package developed for computing optical properties of non-spherical particles. It gives a user friendly flexible framework that takes advantage of programming with the modern language supported by the abundant library of scientific packages. The framework is designed to include the methods and interfaces to third-party codes required to treat scatterers of different shape and structure. We

A. A. Vinokurov; V. B. Ilin; V. G. Farafonov

2011-01-01

196

Automating Geographic Information Systems (GIS) through Python for the Hydrological Sciences  

NASA Astrophysics Data System (ADS)

Geographic Information Systems (GIS) have many applications in the hydrological sciences. However, GIS software is often expensive and difficult to automate. This paper will demonstrate how to automate GRASS GIS software using the Python programming language. Both GRASS GIS and Python are open source projects that are free for anyone to use. Automation of GIS processes is important when dealing with large-scale geographic studies, as large GIS maps are usually divided into discrete tiles. When conducting GIS transformations on such maps, the user must repeat the action for each tile, a process that is greatly expedited through automation. The paper will work through several examples of automated GIS processes and provide complete Python codes that demonstrate correct syntax for working with GRASS GIS applications. The provided examples will demonstrate automation of the following processes 1.) using raster math to calculate foliage thickness from LIDAR and DEM data; 2.) conducting raster interpolation from a set of vector points to develop a continuous hydraulic conductivity coverage; 3.) automating raster coloration to sync the coloration of a large number of raster tiles for website display, and 4.) constructing contoured vector lines from topography rasters. These examples programs will serve as the building blocks for readers, giving them the tools to automate any GIS process using Python and GRASS GIS.

Madsen, K.

2013-12-01

197

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

ERIC Educational Resources Information Center

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

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

2007-01-01

198

Math 311w-01 Laboratory 2: Introduction to Linux and Python  

E-print Network

to Linux and Python Date: 2011-09-09 =================================================== Goals for today. If it is not on, please turn it on. Push the Linux button in the front of the Belkin box, if it isn't pressed. Wait for Redhat Linux to give you a login box. Find the menu at the bottom of the screen labeled

Reluga, Tim

199

PyMercury: Interactive Python for the Mercury Monte Carlo Particle Transport Code  

SciTech Connect

Monte Carlo particle transport applications are often written in low-level languages (C/C++) for optimal performance on clusters and supercomputers. However, this development approach often sacrifices straightforward usability and testing in the interest of fast application performance. To improve usability, some high-performance computing applications employ mixed-language programming with high-level and low-level languages. In this study, we consider the benefits of incorporating an interactive Python interface into a Monte Carlo application. With PyMercury, a new Python extension to the Mercury general-purpose Monte Carlo particle transport code, we improve application usability without diminishing performance. In two case studies, we illustrate how PyMercury improves usability and simplifies testing and validation in a Monte Carlo application. In short, PyMercury demonstrates the value of interactive Python for Monte Carlo particle transport applications. In the future, we expect interactive Python to play an increasingly significant role in Monte Carlo usage and testing.

Iandola, F N; O'Brien, M J; Procassini, R J

2010-11-29

200

Team: Katherine Ahern Zachary Gillen  

E-print Network

Server Ancillary Ancillary Ancillary Radiology Imaging Critical Care Alternate Financial System Inventory STAND-ALONE SYSTEMS HL7 Based Messaging System Other Lab System Inpatient Pharmacy RADIOLOGY Medical Ancillary Radiology Results ANATOMIC PATHOLOGY TB CLINIC CLINICAL VIROLOGY PROGRESS NOTES FINANCIALS Medical

Militzer, Burkhard

201

GMES: A Python package for solving Maxwells equations using the FDTD method  

NASA Astrophysics Data System (ADS)

This paper describes GMES, a free Python package for solving Maxwells 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, Queens 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.

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

2013-04-01

202

Identification and comparison of marbofloxacin metabolites from the plasma of ball pythons (Python regius) and blue and gold macaws (Ara ararauna).  

PubMed

Marbofloxacin is a veterinary only, synthetic, broad spectrum fluoroquinolone antimicrobial agent. In mammals, approximately 40% of the oral dose of marbofloxacin is excreted unchanged in the urine; the remaining is excreted via the bile as unchanged drug in the feces. The Vd ranges from 1.1 (cattle) to 1.3 (dog, goat, swine) L/kg. Because of extra-label use of marbofloxacin in birds and reptiles, this study was designed to determine the profile of metabolites in plasma and compare the circulating metabolite profile between a reptile and an avian species. Six adult ball pythons (Python regius) and 10 blue and gold macaws (Ara ararauna) were used in this study. The macaws were dosed both i.v. and p.o. with a single 2.5 mg/kg administration where as the pythons received a single 10 mg/kg dose both i.v. and p.o. The metabolite profiles of marbofloxacin in the plasma of these species were determined using a high performance liquid chromatography system with a mass spectrometer for detection (LC/MS/MS). Mass spectra data generated from the snake and bird plasma samples were compared with previously reported LC/MS/MS mass spectral data. Evidence does not suggest differences due to route of administration (i.v. vs. p.o.) in either species. Four chromatographic peaks with resulting daughter spectrum were identified and represent 12 possible metabolite structures. All of the proposed metabolites, except for the N-oxide, appear to be unique to macaws. The potential metabolites identified in macaws appear to be very different than those reported for chickens. PMID:17472658

Hunter, R P; Koch, D E; Coke, R L; Carpenter, J W; Isaza, R

2007-06-01

203

Climate-induced reaction norms for life-history traits in pythons.  

PubMed

Climate change modelers predict increasingly frequent "extreme events," so it is critical to quantify whether organismal responses (such as reproductive output) measured over the range of usual climatic conditions can predict responses under more extreme conditions. In a 20-year field study on water pythons (Liasis fuscus), we quantified the effects of climatically driven annual variation in food supply on demographic traits of female pythons (feeding rate, body size, body mass, and reproductive output). Reaction norms linking food supply to feeding rates and residual body mass were broadly linear, whereas norms linking food supply to female body size became curvilinear when a dramatic (flooding-induced) famine reduced the mean body size at sexual maturity. Thus, the reaction norms recorded over 16 years of mal" (albeit highly variable) climatic conditions gave little insight into the population's response to a more extreme nutritional crisis. PMID:21939082

Ujvari, Beata; Shine, Richard; Luiselli, Luca; Madsen, Thomas

2011-09-01

204

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.  

PubMed

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome. PMID:24297902

Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurlie; Minx, Patrick; Feschotte, Cdric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

2013-12-17

205

Data reduction and analysis of the Python V cosmic microwave background anisotropy experiment  

Microsoft Academic Search

Observations of the microwave sky using the Python telescope in its fifth season of operation at the Amundsen-Scott South Pole Station in Antarctica are presented. The system consists of a 0.75 m off-axis telescope instrumented with a HEMT amplifier-based radiometer having continuum sensitivity from 37-5 GHz in two frequency bands. With a 0.91 1.02 beam the instrument fully sampled

Kimberly Ann Coble

1999-01-01

206

Anisotropy in the Cosmic Microwave Background at Degree Angular Scales: Python V Results  

Microsoft Academic Search

Observations of the microwave sky using the Python telescope in its fifth season of operation at the Amundsen-Scott South Pole Station in Antarctica are presented. The system consists of a 0.75 m off-axis telescope instrumented with a HEMT amplifier-based radiometer having continuum sensitivity from 37 to 45 GHz in two frequency bands. With a 0.91dx1.02d beam, the instrument fully sampled

K. Coble; M. Dragovan; J. Kovac; N. W. Halverson; W. L. Holzapfel; L. Knox; S. Dodelson; K. Ganga; D. Alvarez; J. B. Peterson; G. Griffin; M. Newcomb; K. Miller; S. R. Platt; G. Novak

1999-01-01

207

Anisotropy in the Microwave Sky at 90 GHz: Results from Python II  

Microsoft Academic Search

We report on additional observations of degree-scale anisotropy at 90 GHz from the Amundsen-Scott South Pole Station in Antarctica. Observations during the first season with the Python instrument yielded a statistically significant sky signal with an amplitude of Delta T\\/T ~ 3.5 x 10-5 for a Gaussian autocorrelation function model with a coherence angle theta c = 1 deg. In

J. E. Ruhl; M. Dragovan; S. R. Platt; J. Kovac; G. Novak

1995-01-01

208

A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites.  

PubMed

Neuropeptides and hormones are signaling molecules that support cell-cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html), a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides. PMID:19169350

Southey, Bruce R; Sweedler, Jonathan V; Rodriguez-Zas, Sandra L

2008-01-01

209

Synthesized N-Point Chopping Pattern Analysis of the Python Data  

NASA Astrophysics Data System (ADS)

We report initial results from a new analysis method for data taken with the Python microwave background anisotropy experiment. The Python telescope performs a three-beam chop on the sky at multiple azimuth positions. The original analysis involved subtracting neighboring pairs of three-beam observations to produce a four-beam pattern on the sky. This talk generalizes the original analysis in three ways and presents preliminary results of a reanalysis of the previous Python data. First, we decompose the three-beam chop data into four independent modes. Two of these are signal modes which contain information from the sky. The other two are dark modes which have zero response to signals on the sky but non-zero response to instrumental effects. Second, we allow more general methods of combining three-point observations (at neighboring azimuth positions and/or from independent detectors) to produce synthesized n-point chopping patterns. Third, we synthesize n-beam chopping patterns which constitute optimal filters for estimating cosmological parameters. This work was supported by the National Science Foundation under a cooperative agreement with the Center for Astrophysical Research in Antarctica (CARA), grant number NSF OPP 89-20223, M.D.'s PYI grant NSF AST 90-57089, and the James S. McDonnell Foundation. CARA is a National Science Foundation Science and Technology Center.

Alvarez, D. L.; Dragovan, M.; Ruhl, J. E.; Kovac, J.; Platt, S. R.; Peterson, J.

1995-05-01

210

Data Reduction and Analysis of the Python V Cosmic Microwave Background Anisotropy Experiment  

NASA Astrophysics Data System (ADS)

Observations of the microwave sky using the Python telescope in its fifth season of operation at the Amundsen-Scott South Pole Station in Antarctica are presented. The system consists of a 0.75 m off-axis telescope instrumented with a HEMT amplifier-based radiometer having continuum sensitivity from 37-45 GHz in two frequency bands. With a 0.91() 1.02() beam the instrument fully sampled 598 deg(2) of sky, including fields measured during the previous four seasons of Python observations. Interpreting the observed fluctuations as anisotropy in the cosmic microwave background, we place constraints on the angular power spectrum of fluctuations in eight multipole bands up to l 260. The observed spectrum is consistent with both the COBE experiment and previous Python results. Total-power Wiener-filtered maps of the CMB are also presented. There is no significant contamination from known foregrounds. The results show a discernible rise in the angular power spectrum from large (l 40) to small (l 200) angular scales.

Coble, Kimberly Ann

1999-11-01

211

Anisotropy in the Cosmic Microwave Background at Degree Angular Scales: Python V Results  

E-print Network

Observations of the microwave sky using the Python telescope in its fifth season of operation at the Amundsen-Scott South Pole Station in Antarctica are presented. The system consists of a 0.75 m off-axis telescope instrumented with a HEMT amplifier-based radiometer having continuum sensitivity from 37-45 GHz in two frequency bands. With a 0.91 deg x 1.02 deg beam the instrument fully sampled 598 deg^2 of sky, including fields measured during the previous four seasons of Python observations. Interpreting the observed fluctuations as anisotropy in the cosmic microwave background, we place constraints on the angular power spectrum of fluctuations in eight multipole bands up to l ~ 260. The observed spectrum is consistent with both the COBE experiment and previous Python results. There is no significant contamination from known foregrounds. The results show a discernible rise in the angular power spectrum from large (l ~ 40) to small (l ~ 200) angular scales. The shape of the observed power spectrum is not a simple linear rise but has a sharply increasing slope starting at l ~ 150.

K. Coble; M. Dragovan; J. Kovac; N. W. Halverson; W. L. Holzapfel; L. Knox; S. Dodelson; K. Ganga; D. Alvarez; J. B. Peterson; G. Griffin; M. Newcomb; K. Miller; S. R. Platt; G. Novak

1999-02-15

212

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

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

213

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

PubMed

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

Pecevski, Dejan; Kappel, David; Jonke, Zeno

2014-01-01

214

SMMP v. 3.0Simulating proteins and protein interactions in Python and Fortran  

NASA Astrophysics Data System (ADS)

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more. Program summaryTitle of program:SMMP Catalogue identifier:ADOJ_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.html Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language used:FORTRAN, Python No. of lines in distributed program, including test data, etc.:52 105 No. of bytes in distributed program, including test data, etc.:599 150 Distribution format:tar.gz Computer:Platform independent Operating system:OS independent RAM:2 Mbytes Classification:3 Does the new version supersede the previous version?:Yes Nature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins. Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles. Reasons for new version:API changes and increased functionality. Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings. Restrictions:The consumed CPU time increases with the size of protein molecule. Running time:Depends on the size of the simulated molecule.

Meinke, Jan H.; Mohanty, Sandipan; Eisenmenger, Frank; Hansmann, Ulrich H. E.

2008-03-01

215

Interfacing MATLAB and Python Optimizers to Black-Box Environmental Simulation Models  

NASA Astrophysics Data System (ADS)

A common approach for utilizing environmental models in a management or policy-analysis context is to incorporate them into a simulation-optimization framework - where an underlying process-based environmental model is linked with an optimization search algorithm. The optimization search algorithm iteratively adjusts various model inputs (i.e. parameters or design variables) in order to minimize an application-specific objective function computed on the basis of model outputs (i.e. response variables). Numerous optimization algorithms have been applied to the simulation-optimization of environmental systems and this research investigated the use of optimization libraries and toolboxes that are readily available in MATLAB and Python - two popular high-level programming languages. Inspired by model-independent calibration codes (e.g. PEST and UCODE), a small piece of interface software (known as PIGEON) was developed. PIGEON allows users to interface Python and MATLAB optimizers with arbitrary black-box environmental models without writing any additional interface code. An initial set of benchmark tests (involving more than 20 MATLAB and Python optimization algorithms) were performed to validate the interface software - results highlight the need to carefully consider such issues as numerical precision in output files and enforcement (or not) of parameter limits. Additional benchmark testing considered the problem of fitting isotherm expressions to laboratory data - with an emphasis on dual-mode expressions combining non-linear isotherms with a linear partitioning component. With respect to the selected isotherm fitting problems, derivative-free search algorithms significantly outperformed gradient-based algorithms. Attempts to improve gradient-based performance, via parameter tuning and also via several alternative multi-start approaches, were largely unsuccessful.

Matott, L. S.; Leung, K.; Tolson, B.

2009-12-01

216

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

NASA Astrophysics Data System (ADS)

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.

Hughes, J. D.; White, J.

2013-12-01

217

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

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

218

Py4CAtS - Python tools for line-by-line modelling of infrared atmospheric radiative transfer  

NASA Astrophysics Data System (ADS)

Py4CAtS Python scripts for Computational ATmospheric Spectroscopy is a Python re-implementation of the Fortran infrared radiative transfer code GARLIC, where compute-intensive code sections utilize the Numeric/Scientific Python modules for highly optimized array-processing. The individual steps of an infrared or microwave radiative transfer computation are implemented in separate scripts to extract lines of relevant molecules in the spectral range of interest, to compute line-by-line cross sections for given pressure(s) and temperature(s), to combine cross sections to absorption coefficients and optical depths, and to integrate along the line-of-sight to transmission and radiance/intensity. The basic design of the package, numerical and computational aspects relevant for optimization, and a sketch of the typical workflow are presented.

Schreier, Franz; Garca, Sebastin Gimeno

2013-05-01

219

PREdator: a python based GUI for data analysis, evaluation and fitting  

PubMed Central

The analysis of a series of experimental data is an essential procedure in virtually every field of research. The information contained in the data is extracted by fitting the experimental data to a mathematical model. The type of the mathematical model (linear, exponential, logarithmic, etc.) reflects the physical laws that underlie the experimental data. Here, we aim to provide a readily accessible, user-friendly python script for data analysis, evaluation and fitting. PREdator is presented at the example of NMR paramagnetic relaxation enhancement analysis.

2014-01-01

220

ObsPy: A Python Toolbox for Seismology/Seismological Observatories  

NASA Astrophysics Data System (ADS)

Python enables the user to combine the possibilities of a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and many freely available high quality scientific modules cover most needs in developing scientific processing workflows. The goal of the ObsPy project (http://www.obspy.org) is to facilitate rapid application development for seismology by extending Python's capabilities to fit the specific needs that arise when working with seismological data. It provides read and write support for many common waveform file formats (e.g. MiniSEED, SAC, GSE2, SEISAN, ...) and metadata formats (e.g. SEED, Dataless SEED, XML-SEED, RESP, ...). Several available client modules make it possible to directly acquire waveform data and metadata as well as earthquake event data from data centers communicating with ArcLink (http://www.webdc.eu), Fissures (http://www.iris.edu/dhi) and SeisHub servers (http://www.seishub.org) and by connecting to webservices provided by IRIS (http://www.iris.edu/ws/) and NERIES (http://www.seismicportal.eu/). Finally there is a growing signal processing toolbox that covers many often needed routines for filtering, triggering, instrument correction/simulation, complex trace analysis, array analysis and many more. Recent additions to ObsPy include calculation of probabilistic power spectral densities, relative instrument calibration and wrappers for the IASPEI-tau traveltime package and IRIS's evalresp. In combination with well developed, free Python packages like NumPy (http://numpy.scipy.org), SciPy (http://scipy.org), IPython (http://ipython.scipy.org), Matplotlib (http://matplotlib.sourceforge.net) and PyQt (http://www.riverbankcomputing.co.uk/software/pyqt), ObsPy makes it possible to develop complete workflows in Python, ranging from reading/requesting data via signal analysis and data processing to visualization in GUI applications and output of modified or derived data. ObsPy is developed in a test-driven approach, it has a modular architecture which aims at minimizing the dependencies and is available under the GPL/LGPLv3 licences. ObsPy is tested and running on Linux, MacOSX and Windows XP/Vista/7.

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

2011-12-01

221

Data Reduction and Analysis of the Python V Cosmic Microwave Background Anisotropy Experiment  

Microsoft Academic Search

Observations of the microwave sky using the Python telescope in its fifth\\u000aseason of operation at the Amundsen-Scott South Pole Station in Antarctica are\\u000apresented. The system consists of a 0.75 m off-axis telescope instrumented with\\u000aa HEMT amplifier-based radiometer having continuum sensitivity from 37-45 GHz\\u000ain two frequency bands. With a $0.91^{\\\\circ} \\\\times 1.02^{\\\\circ} $ beam the\\u000ainstrument fully

Kimberly Ann Coble

1999-01-01

222

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

NASA Astrophysics Data System (ADS)

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.

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

2010-05-01

223

Mushu, a free- and open source BCI signal acquisition, written in Python.  

PubMed

The following paper describes Mushu, a signal acquisition software for retrieval and online streaming of Electroencephalography (EEG) data. It is written, but not limited, to the needs of Brain Computer Interfacing (BCI). It's main goal is to provide a unified interface to EEG data regardless of the amplifiers used. It runs under all major operating systems, like Windows, Mac OS and Linux, is written in Python and is free- and open source software licensed under the terms of the GNU General Public License. PMID:23366257

Venthur, Bastian; Blankertz, Benjamin

2012-01-01

224

i-PI: A Python interface for ab initio path integral molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

225

TelluSim: A Python Plug-in Based Computational Framework for Spatially Distributed Environmental and Earth Sciences Modelling  

NASA Astrophysics Data System (ADS)

TelluSim is a python-based computational framework for integrating and manipulating modules written in a variety of computer languages. TelluSim consists of a main program that dynamically, at run time, assembles a series of modules. These modules can be written in any language that can be accessed by Python. Currently we have modules in Fortran and Python, with C to be supported soon. New modules are incorporated as plug-ins like done for a browser or Photoshop, simply by copying the module binary into a plug-in directory. TelluSim automatically generates a GUI for parameter and state I/O, and automatically creates the intermodule communication mechanisms needed for the computations. A decision to use Python was arrived at after detailed trials using other languages including C, Tcl/Tk and Fortran. An important aspect of the design of TelluSim was to minimise the overhead in interfacing the modules with TelluSim, and minimise any requirement for recoding of existing software, so eliminating a major disadvantage of more complex frameworks (e.g. JAMS, openMI). Several significant Fortran codes developed by the author have been incorporated as part of the design process and as proof of concept. In particular the SIBERIA landform evolution code (a high performance F90 code, including parallel capability) has been broken up into a series of TelluSim modules, so that the SIBERIA now consists of a Python script of 20 lines. These 20 lines assemble and run the underlying modules (about 50,000 lines of Fortran code). The presentation will discuss in more detail the design of TelluSim, and our experiences of the advantages and disadvantages of using Python relative to other approaches.

Willgoose, G. R.

2008-12-01

226

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

PubMed

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

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

2014-09-01

227

Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).  

PubMed

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny. PMID:22331485

Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

2012-07-01

228

Python for Development of OpenMP and CUDA Kernels for Multidimensional Data  

SciTech Connect

Design of data structures for high performance computing (HPC) is one of the principal challenges facing researchers looking to utilize heterogeneous computing machinery. Heterogeneous systems derive cost, power, and speed efficiency by being composed of the appropriate hardware for the task. Yet, each type of processor requires a specific organization of the application state in order to achieve peak performance. Discovering this and refactoring the code can be a challenging and time-consuming task for the researcher, as the data structures and the computational model must be co-designed. We present a methodology that uses Python as the environment for which to explore tradeoffs in both the data structure design as well as the code executing on the computation accelerator. Our method enables multi-dimensional arrays to be used effectively in any target environment. We have chosen to focus on OpenMP and CUDA environments, thus exploring the development of optimized kernels for the two most common classes of computing hardware available today: multi-core CPU and GPU. Python s large palette of file and network access routines, its associative indexing syntax and support for common HPC environments makes it relevant for diverse hardware ranging from laptops through computing clusters to the highest performance supercomputers. Our work enables researchers to accelerate the development of their codes on the computing hardware of their choice.

Bell, Zane W [ORNL; Davidson, Gregory G [ORNL; D'Azevedo, Ed F [ORNL; Evans, Thomas M [ORNL; Joubert, Wayne [ORNL; Munro Jr, John K [ORNL; Patlolla, Dilip Reddy [ORNL; Vacaliuc, Bogdan [ORNL

2011-01-01

229

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

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

230

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data  

PubMed Central

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

231

Pyff - a pythonic framework for feedback applications and stimulus presentation in neuroscience.  

PubMed

This paper introduces Pyff, the Pythonic feedback framework for feedback applications and stimulus presentation. Pyff provides a platform-independent framework that allows users to develop and run neuroscientific experiments in the programming language Python. Existing solutions have mostly been implemented in C++, which makes for a rather tedious programming task for non-computer-scientists, or in Matlab, which is not well suited for more advanced visual or auditory applications. Pyff was designed to make experimental paradigms (i.e., feedback and stimulus applications) easily programmable. It includes base classes for various types of common feedbacks and stimuli as well as useful libraries for external hardware such as eyetrackers. Pyff is also equipped with a steadily growing set of ready-to-use feedbacks and stimuli. It can be used as a standalone application, for instance providing stimulus presentation in psychophysics experiments, or within a closed loop such as in biofeedback or brain-computer interfacing experiments. Pyff communicates with other systems via a standardized communication protocol and is therefore suitable to be used with any system that may be adapted to send its data in the specified format. Having such a general, open-source framework will help foster a fruitful exchange of experimental paradigms between research groups. In particular, it will decrease the need of reprogramming standard paradigms, ease the reproducibility of published results, and naturally entail some standardization of stimulus presentation. PMID:21160550

Venthur, Bastian; Scholler, Simon; Williamson, John; Dhne, Sven; Treder, Matthias S; Kramarek, Maria T; Mller, Klaus-Robert; Blankertz, Benjamin

2010-01-01

232

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.  

PubMed

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

233

Installation Instructions The first thing to ensure is you have python, most linux distributions will have it. Galaxy requires  

E-print Network

--------------------------------------------------------------------------------------------------------------------------- Installing ZSI To install ZSI 2.1 go to http://sourceforge.net/projects/pywebsvcs/files/ and download- %sudo python setup.py install If you want ZSI 2.0 You will need to make modifications to wsdl2path

Kissinger, Jessica

234

A NEW SPECIES OF HEPATOZOON (APICOMPLEXA: ADELEORINA) FROM PYTHON REGIUS (SERPENTES: PYTHONIDAE) AND ITS EXPERIMENTAL TRANSMISSION BY A MOSQUITO VECTOR  

Microsoft Academic Search

Hepatozoon ayorgbor n. sp. is described from specimens of Python regius imported from Ghana. Gametocytes were found in the peripheral blood of 43 of 55 snakes examined. Localization of gametocytes was mainly inside the erythrocytes; free gametocytes were found in 15 (34.9%) positive specimens. Infections of laboratory-reared Culex quinquefasciatus feeding on infected snakes, as well as experimental infection of juvenile

Michal Sloboda; Martin Kamler; Jana Bulantov; Jan Votpka; David Modr

2007-01-01

235

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

SciTech Connect

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.

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

236

A Pure-Python Robust Frequency Band Automatic Phase Picker for Seismic Monitoring  

NASA Astrophysics Data System (ADS)

We modify the FPPICK algorithm of Lomax et al. (2012) and implement an automatic phase picking algorithm implemented in Python. The algorithm takes advantage of existing seismological Python libraries, Obspy. The algorithm is designed to work on a variety of instrumentation and automatically adapts to different sampling rates. The time series signals are band-pass filtered for each band, octave, considered within the picker algorithm. The energy of the signal is calculated over an averaging window and multiplied by the instantaneous energy of the signal. This energy time-series is the statistic we can then examine for each frequency band considered. The summary statistic, which allows the identification of a trigger, is simply the maximum value of any frequency bands energy statistic at each sample time. A trigger is identified by using a control chart type statistic to identify when our statistics summary is changing rapidly and exceeds a specified number of standard deviations from the mean of the summary energy statistic. This has the advantage that the picker parameters don't necessarily need to be modified when processing data from a wide variety of instrumentation with different response characteristics. The algorithm also contains a method to determine the first motion direction associated with a pick as well as an uncertainty for the pick. As with any automatic phase identification system false picks can and do occur. A few simple algorithms are implemented to avoid false-picks, the picker can be configured not to include these checks. These algorithms remove picks that occur very close in time, and picks for which a phase has a smaller RMS than the previous time interval. The algorithm uses many techniques within Numpy to improve computation times. The algorithm effectively picks both P- and S-phase from local and regional earthquakes with only small amounts of picker parameter modifications. The picker can pick both P and S phases on local and regional earthquakes from a wide variety of instrumentation with no modifications by instrument type or sample rate. We demonstrate the robustness and effectiveness of this picker by comparing manual picked earthquake phase arrivals with those obtained from this picker. In addition, because the picker picks both P- and S-phase arrivals, pick association algorithms can be enhanced by the additional phase arrival picks. We demonstrate the effectiveness of a local earthquake phase associator algorithm written in Python.

Chen, C.; Holland, A. A.

2013-12-01

237

Data Provenance as a Tool for Debugging Hydrological Models based on Python  

NASA Astrophysics Data System (ADS)

There is an increase in data volume used in hydrological modeling. The increasing data volume requires additional efforts in debugging models since a single output value is influenced by a multitude of input values. Thus, it is difficult to keep an overview among the data dependencies. Further, knowing these dependencies, it is a tedious job to infer all the relevant data values. The aforementioned data dependencies are also known as data provenance, i.e. the determination of how a particular value has been created and processed. The proposed tool infers the data provenance automatically from a python script and visualizes the dependencies as a graph without executing the script. To debug the model the user specifies the value of interest in space and time. The tool infers all related data values and displays them in the graph. The tool has been evaluated by hydrologists developing a model for estimating the global water demand [1]. The model uses multiple different data sources. The script we analysed has 120 lines of codes and used more than 3000 individual files, each of them representing a raster map of 360*720 cells. After importing the data of the files into a SQLite database, the data consumes around 40 GB of memory. Using the proposed tool a modeler is able to select individual values and infer which values have been used to calculate the value. Especially in cases of outliers or missing values it is a beneficial tool to provide the modeler with efficient information to investigate the unexpected behavior of the model. The proposed tool can be applied to many python scripts and has been tested with other scripts in different contexts. In case a python code contains an unknown function or class the tool requests additional information about the used function or class to enable the inference. This information has to be entered only once and can be shared with colleagues or in the community. Reference [1] Y. Wada, L. P. H. van Beek, D. Viviroli, H. H. Drr, R. Weingartner, and M. F. P. Bierkens, "Global monthly water stress: II. water demand and severity of water," Water Resources Research, vol. 47, 2011.

Wombacher, A.; Huq, M.; Wada, Y.; Van Beek, R.

2012-12-01

238

Effect of water deprivation on baseline and stress-induced corticosterone levels in the Children's python (Antaresia childreni).  

PubMed

Corticosterone (CORT) secretion is influenced by endogenous factors (e.g., physiological status) and environmental stressors (e.g., ambient temperature). Heretofore, the impact of water deprivation on CORT plasma levels has not been thoroughly investigated. However, both baseline CORT and stress-induced CORT are expected to respond to water deprivation not only because of hydric stress per se, but also because CORT is an important mineralocorticoid in vertebrates. We assessed the effects of water deprivation on baseline CORT and stress-induced CORT, in Children's pythons (Antaresia childreni), a species that experiences seasonal droughts in natural conditions. We imposed a 52-day water deprivation on a group of unfed Children's pythons (i.e., water-deprived treatment) and provided water ad libitum to another group (i.e., control treatment). We examined body mass variations throughout the experiment, and baseline CORT and stress-induced CORT at the end of the treatments. Relative body mass loss averaged ~10% in pythons without water, a value 2 to 4 times higher compared to control snakes. Following re-exposition to water, pythons from the water-deprived treatment drank readily and abundantly and attained a body mass similar to pythons from the control treatment. Together, these results suggest a substantial dehydration as a consequence of water deprivation. Interestingly, stress-induced but not baseline CORT level was significantly higher in water-deprived snakes, suggesting that baseline CORT might not respond to this degree of dehydration. Therefore, possible mineralocorticoid role of CORT needs to be clarified in snakes. Because dehydration usually induces adjustments (reduced movements, lowered body temperature) to limit water loss, and decreases locomotor performances, elevated stress-induced CORT in water-deprived snakes might therefore compensate for altered locomotor performances. Future studies should test this hypothesis. PMID:24231466

Dupou, Andraz; Angelier, Frdric; Lourdais, Olivier; Bonnet, Xavier; Brischoux, Franois

2014-02-01

239

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.  

PubMed

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. PMID:24795618

Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

2014-01-01

240

MSNoise: a Python Package for Monitoring Seismic Velocity Changes using Ambient Seismic Noise  

NASA Astrophysics Data System (ADS)

We present MSNoise, a complete software suite to compute relative seismic velocity changes under a seismic network, using ambient seismic noise. The whole is written in Python, from the monitoring of data archives, to the production of high quality figures. All steps have been optimized to only compute the necessary steps and to use 'job'-based processing. All steps can be changed by matching the in/outs. MSNoise exposes an API for communication with the data archive and the database. We present a validation of the software on a dataset acquired during the UnderVolc project on the Piton de la Fournaise Volcano, La Runion Island, France, for which precursory relative changes of seismic velocity are visible for three eruptions betwee 2009 and 2011. MSNoise is available on http://www.msnoise.org

Lecocq, Thomas; Caudron, Corentin; Brenguier, Florent

2014-05-01

241

i-PI: A Python interface for ab initio path integral molecular dynamics simulations  

E-print Network

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.

Ceriotti, Michele; Manolopoulos, David E

2014-01-01

242

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.  

PubMed

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license. PMID:24688855

Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

2014-01-01

243

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models  

PubMed Central

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license. PMID:24688855

Hamelryck, Thomas; Jensen, Jan H.

2014-01-01

244

morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python.  

PubMed

The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

Hull, Michael J; Willshaw, David J

2013-01-01

245

morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python  

PubMed Central

The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

Hull, Michael J.; Willshaw, David J.

2014-01-01

246

Application of MATLAB and Python optimizers to two case studies involving groundwater flow and contaminant transport modeling  

Microsoft Academic Search

One approach for utilizing geoscience models for management or policy analysis is via a simulation-based optimization frameworkwhere an underlying model is linked with an optimization search algorithm. In this regard, MATLAB and Python are high-level programming languages that implement numerous optimization routines, including gradient-based, heuristic, and direct-search optimizers. The ever-expanding number of available algorithms makes it challenging for practitioners to

L. Shawn Matott; Kenny Leung; Junyoung Sim

2011-01-01

247

Raman spectroscopic studies of the skins of the Sahara sand viper, the carpet python and the American black rat snake  

NASA Astrophysics Data System (ADS)

Vibrational Raman spectra of the skins of the snakes Cerastes vipera (Sahara sand viper) and Morelia argus (carpet python) have been recorded for the first time using visible and IR laser excitation. Full vibrational assignments are proposed and comparisons made with vibrational Raman spectra of the snake Elaphe obsoleta (American black rat snake); such studies may be important in correlating the permeabilities of human and snake skins to drugs and contaminants.

Edwards, H. G. M.; Farwell, D. W.; Williams, A. C.; Barry, B. W.

1993-07-01

248

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

NASA Astrophysics Data System (ADS)

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.

Verkaik, J.

2013-12-01

249

Using Python Scripting and Web Frameworks to Access Spatial and Temporal Data via KML  

NASA Astrophysics Data System (ADS)

Ever increasing volumes of spatial and temporal data about our world are being made available for download by various organizations. However, the data formats used are generally well-suited for storing large volumes of data but are not directly usable without specialized software. Also in recent years, there has been a wide adoption of easy-to-use virtual globe browsers (such as Google Earth) for viewing spatial and temporal datasets, but these applications cannot directly work with many large datasets due to the formats and/or the size of the datasets. This work presents several examples of Python-based data systems for accessing, filtering, and transforming large and complex spatial and temporal datasets into KML, an Open Geospatial Consortium (OGC) standard used for visualization and annotation of two-dimensional and three-dimensional data. Precipitable water forecasted by the NCEP Global Forecast System (GFS) model. Soil moisture content for December 2024 predicted by an IPCC model (GFDL R30).

Erickson, T. A.; Koziol, B. W.

2010-12-01

250

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

SciTech Connect

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.

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

2011-11-01

251

Nengo: a Python tool for building large-scale functional brain models  

PubMed Central

Neuroscience currently lacks a comprehensive theory of how cognitive processes can be implemented in a biological substrate. The Neural Engineering Framework (NEF) proposes one such theory, but has not yet gathered significant empirical support, partly due to the technical challenge of building and simulating large-scale models with the NEF. Nengo is a software tool that can be used to build and simulate large-scale models based on the NEF; currently, it is the primary resource for both teaching how the NEF is used, and for doing research that generates specific NEF models to explain experimental data. Nengo 1.4, which was implemented in Java, was used to create Spaun, the world's largest functional brain model (Eliasmith et al., 2012). Simulating Spaun highlighted limitations in Nengo 1.4's ability to support model construction with simple syntax, to simulate large models quickly, and to collect large amounts of data for subsequent analysis. This paper describes Nengo 2.0, which is implemented in Python and overcomes these limitations. It uses simple and extendable syntax, simulates a benchmark model on the scale of Spaun 50 times faster than Nengo 1.4, and has a flexible mechanism for collecting simulation results. PMID:24431999

Bekolay, Trevor; Bergstra, James; Hunsberger, Eric; DeWolf, Travis; Stewart, Terrence C.; Rasmussen, Daniel; Choo, Xuan; Voelker, Aaron Russell; Eliasmith, Chris

2014-01-01

252

Open-Source Python Modules to Estimate Level Ice Thickness from Ice Charts  

NASA Astrophysics Data System (ADS)

A collaborative research effort between the University of Delaware (UD) and National Ice Center (NIC) addresses the task of providing open-source translations of sea ice stage-of-development into level ice thickness estimates on a 4km grid for the Interactive Multisensor Snow and Ice Mapping System (IMS). The characteristics for stage-of-development are quantified from remote sensing imagery with estimates of level ice thickness categories originating from World Meteorological Organization (WMO) egg coded ice charts codified since the 1970s. Conversions utilize Python scripting modules which transform electronic ice charts with WMO egg code characteristics into five level ice thickness categories, in centimeters, (0-10, 10-30, 30-70, 70-120, >120cm) and five ice types (open water, first year pack ice, fast ice, multiyear ice, and glacial ice with a reserve slot for deformed ice fractions). Both level ice thickness categories and ice concentration fractions are reported with uncertainties propagated based on WMO ice stage ranges which serve as proxy estimates for standard deviation. These products are in preparation for use by NCEP, CMC, and NAVO by 2014 based on their modeling requirements for daily products in near-real time. In addition to development, continuing research tests the value of these estimated products against in situ observations to improve both value and uncertainty estimates.

Geiger, C. A.; Deliberty, T. L.; Bernstein, E. R.; Helfrich, S.

2012-12-01

253

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

SciTech Connect

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.

Turk, M.; /KIPAC, Menlo Park

2008-09-30

254

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

PubMed Central

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.

Madsen, T.; Shine, R.

1998-01-01

255

Data and Schema Matching Zachary G. Ives  

E-print Network

of Disparate Data Sources: A Machine Learning Approach," by Doan et al, SIGMOD 01 Some slides on LSD courtesy projects you've been working on! § Slides are allowed (but not required) Y What did you do? Y What were § What are some key attributes of this approach? Can also use data mining and probabilistic machine

Ives, Zachary G.

256

Wilson-Cowan Model Zachary P. Kilpatrick*  

E-print Network

.1007/978-1-4614-7320-6_80-1 # Springer Science+Business Media New York 2013 Page 1 of 5 #12;Thus, the activity variables ae,i(t) obey. The nonlinearities are typically chosen to be sigmoidal Fj�x� � 1 1 � e�gj x�yj� � ; j � e; i; (2) where the gain gj and threshold yj can depend on the population type j � e,i. The argument x is a weighted sum of the proportion

Kilpatrick, Zachary P.

257

2010. 3. 28 324 . 1 Zachary  

E-print Network

)[11] (in- novators), (early adopters), (early majority), (late majority), (laggards) 5 . . . Twitter . Twitter 140 . Twitter follow follow . follow ( tweet , tweet retweet , mention [1]. follower retweet . follower degree tweet

Moon, Sue B.

258

Data Integration Systems Zachary G. Ives  

E-print Network

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

Ives, Zachary G.

259

Zachary Horowitz David Evans and Associates  

E-print Network

· Transcontinental railroad · US line mileage peaked ­ 1916 · 142,000 miles of track today · UP's Bailey Yard #12;CTS Analysis of Class I Railroad Cooperation in the Columbia Gorge #12;Outline · Intro · Background · Geography ­ October 12, 2007 Did You Know? · Track gauge, flanged wheel · B&O Railroad ­ 1827 · Signaling

Bertini, Robert L.

260

Sun-Sentinel Red hot email heats up Wasserman Schultz,  

E-print Network

, degrading attitudes toward women because he contributed a column to a biker magazine that contained words and images about women that some found misogynistic and offensive. That really bothered West. He brought Schultz was motivated by gender. "Congressman West does not hate women. He has been married to a PHD

Belogay, Eugene A.

261

pyLIDEM: A Python-Based Tool to Delineate Coastal Watersheds Using LIDAR Data  

NASA Astrophysics Data System (ADS)

Accurately identifying the boundary of a watershed is one of the most fundamental and important steps in any hydrological assessment. Representative applications include defining a study area, predicting overland flow, estimating groundwater infiltration, modeling pollutant accumulation and wash-off rates, and evaluating effectiveness of pollutant mitigation measures. The United States Environmental Protection Agency (USEPA) Total Maximum Daily Load (TMDL) program, the most comprehensive water quality management program in the United States (US), is just one example of an application in which accurate and efficient watershed delineation tools play a critical role. For example, many impaired water bodies currently being addressed through the TMDL program drain small coastal watersheds with relatively flat terrain, making watershed delineation particularly challenging. Most of these TMDL studies use 30-meter digital elevation models (DEMs) that rarely capture all of the small elevation changes in coastal watersheds, leading to errors not only in watershed boundary delineation, but in subsequent model predictions (such as watershed runoff flow and pollutant deposition rate predictions) for which watershed attributes are key inputs. Manually delineating these low-relief coastal watersheds through the use of expert knowledge of local water flow patterns, often produces relatively accurate (and often more accurate) watershed boundaries as compared to the boundaries generated by the 30-meter DEMs. Yet, manual delineation is a costly and time consuming procedure that is often not opted for. There is a growing need, therefore, particularly to address the ongoing needs of the TMDL program (and similar environmental management programs), for software tools which can utilize high resolution topography data to more accurately delineate coastal watersheds. Here, we address this need by developing pyLIDEM (python LIdar DEM), a python-based tool which processes bare earth high-resolution Light Detection and Ranging (LIDAR) data, generates fine scale DEMs, and delineates watershed boundaries for a given pour point. Because LIDAR data are typically distributed in large sets of predefined tiles, our tool is capable of combining only the minimum number of bare earth LIDAR tiles required to delineate a watershed of interest. Our tool then processes the LIDAR data into Triangulated Irregular Networks, generates DEMs at user- specified cell sizes, and creates the required files needed to delineate watersheds within ArcGIS. To make pyLIDEM more accessible to the modeling community, we have bundled it within an ArcGIS toolbox, which also allows users to run it directly from an ArcGIS platform. We assess pyLIDEM functionality and accuracy by delineating several impaired small coastal watersheds in the Newport River Estuary in Eastern North Carolina using LIDAR data collected for the North Carolina Flood Mapping Program. We then compare the pyLIDAR-based watershed boundaries with those generated manually and with those generated using the 30-meter DEMs, and find that the pyLIDAR-based boundaries are more accurate than the 30-meter DEMs, and provide a significant time savings compared to manual delineation, particularly in cases where multiple watersheds need to be delineated for a single project.

O'Banion, R.; Alameddine, I.; Gronewold, A.; Reckhow, K.

2008-12-01

262

HDDM: Hierarchical Bayesian estimation of the Drift-Diffusion Model in Python  

PubMed Central

The diffusion model is a commonly used tool to infer latent psychological processes underlying decision-making, and to link them to neural mechanisms based on response times. Although efficient open source software has been made available to quantitatively fit the model to data, current estimation methods require an abundance of response time measurements to recover meaningful parameters, and only provide point estimates of each parameter. In contrast, hierarchical Bayesian parameter estimation methods are useful for enhancing statistical power, allowing for simultaneous estimation of individual subject parameters and the group distribution that they are drawn from, while also providing measures of uncertainty in these parameters in the posterior distribution. Here, we present a novel Python-based toolbox called HDDM (hierarchical drift diffusion model), which allows fast and flexible estimation of the the drift-diffusion model and the related linear ballistic accumulator model. HDDM requires fewer data per subject/condition than non-hierarchical methods, allows for full Bayesian data analysis, and can handle outliers in the data. Finally, HDDM supports the estimation of how trial-by-trial measurements (e.g., fMRI) influence decision-making parameters. This paper will first describe the theoretical background of the drift diffusion model and Bayesian inference. We then illustrate usage of the toolbox on a real-world data set from our lab. Finally, parameter recovery studies show that HDDM beats alternative fitting methods like the ?2-quantile method as well as maximum likelihood estimation. The software and documentation can be downloaded at: http://ski.clps.brown.edu/hddm_docs/ PMID:23935581

Wiecki, Thomas V.; Sofer, Imri; Frank, Michael J.

2013-01-01

263

Structural and performance costs of reproduction in a pure capital breeder, the Children's python Antaresia childreni.  

PubMed

Females often manage the high energy demands associated with reproduction by accumulating and storing energy in the form of fat before initiating their reproductive effort. However, fat stores cannot satisfy all reproductive resource demands, which include considerable investment of amino acids (e.g., for the production of yolk proteins or gluconeogenesis). Because capital breeders generally do not eat during reproduction, these amino acids must come from internal resources, typically muscle proteins. Although the energetic costs of reproduction have been fairly well studied, there are limited data on structural and performance costs associated with the muscle degradation required to meet amino acid demands. Thus, we examined structural changes (epaxial muscle width) and performance costs (constriction and strength) over the course of reproduction in a pure capital breeder, the children's python (Antaresia childreni). We found that both egg production (i.e., direct resource allocation) and maternal care (egg brooding) induce muscle catabolism and affect performance of the female. Although epaxial muscle loss was minimal in nonreproductive females, it reached up to 22% (in females after oviposition) and 34% (in females after brooding) of initial muscle width. Interestingly, we found that individuals with higher initial muscular condition allocated more of their muscle into reproduction. The amount of muscle loss was significantly linked to clutch mass, underscoring the role of structural protein in egg production. Egg brooding significantly increased proteolysis and epaxial loss despite no direct allocation to the offspring. Muscle loss was linked to a significant reduction in performance in postreproductive females. Overall, these results demonstrate that capital-breeding females experience dramatic costs that consume structural resources and jeopardize performance. PMID:23434777

Lourdais, Olivier; Lorioux, Sophie; DeNardo, Dale F

2013-01-01

264

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python  

PubMed Central

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research. PMID:21897815

Gorgolewski, Krzysztof; Burns, Christopher D.; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O.; Waskom, Michael L.; Ghosh, Satrajit S.

2011-01-01

265

Application of MATLAB and Python optimizers to two case studies involving groundwater flow and contaminant transport modeling  

NASA Astrophysics Data System (ADS)

One approach for utilizing geoscience models for management or policy analysis is via a simulation-based optimization frameworkwhere an underlying model is linked with an optimization search algorithm. In this regard, MATLAB and Python are high-level programming languages that implement numerous optimization routines, including gradient-based, heuristic, and direct-search optimizers. The ever-expanding number of available algorithms makes it challenging for practitioners to identify optimizers that deliver good performance when applied to problems of interest. Thus, the primary contribution of this paper is to present a series of numerical experiments that investigated the performance of various MATLAB and Python optimizers. The experiments considered two simulation-based optimization case studies involving groundwater flow and contaminant transport. One case study examined the design of a pump-and-treat system for groundwater remediation, while the other considered least-squares calibration of a model of strontium (Sr) transport. Using these case studies, the performance of 12 different MATLAB and Python optimizers was compared. Overall, the Hooke-Jeeves direct search algorithm yielded the best performance in terms of identifying least-cost and best-fit solutions to the design and calibration problems, respectively. The IFFCO (implicit filtering for constrained optimization) direct search algorithm and the dynamically dimensioned search (DDS) heuristic algorithm also consistently yielded good performance and were up to 80% more efficient than Hooke-Jeeves when applied to the pump-and-treat problem. These results provide empirical evidence that, relative to gradient- and population-based alternatives, direct search algorithms and heuristic variants, such as DDS, are good choices for application to simulation-based optimization problems involving groundwater management.

Matott, L. Shawn; Leung, Kenny; Sim, Junyoung

2011-11-01

266

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

PubMed

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers. PMID:24315866

Graham Reynolds, R; Niemiller, Matthew L; Revell, Liam J

2014-02-01

267

Weighing empirical and hypothetical evidence for assessing potential invasive species range limits: a review of the case of Burmese pythons in the USA.  

PubMed

Range expansion potential is an important consideration for prioritizing management actions against an invasive species. Understanding the potential for range expansion by invasive reptiles such as the Burmese python can be challenging, because the lack of knowledge on fundamental physiological and behavioral constraints initially forces reliance on modeling to predict hypothetical invasive range potential. Hypothetical predictions for Burmese python range limits in the USA have been highly divergent, from only extreme South Florida and the extreme southern Gulf edge of Texas to a broad swath over the southern third of the continental USA. Empirical observations on python thermal tolerances and behavioral abilities to cope with more temperate temperatures became evident during a cold spell in December 2009-January 2010. We review and highlight important considerations for improving invasive range estimation methodology, deciding between competing range predictions, and the importance of having, and applying, empirical data to aid in decision making. PMID:24943887

Engeman, Richard; Avery, Michael L; Jacobson, Elliott

2014-10-01

268

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator  

PubMed Central

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading glue tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS. PMID:19506707

Drewes, Rich; Zou, Quan; Goodman, Philip H.

2008-01-01

269

CCMR: Creating Elemental Arrays in the Python Numeric Module and Band Gaps of High Temperature Superconductor Crystals  

NSDL National Science Digital Library

Numeric allows one to enter many different types of data in an array, ranging from integers and floating points to Python objects. Unfortunately, other arrays could not be assigned as data elements of an array. This project was to modify the C code for Numeric so that it would gain this functionality. The problem with the original code was that if one was given an array a of dimension 2x3, and a new array b was created: b = array([[a,a],[a,a

Friesen, Michael

2005-08-17

270

Combustion-chamber Performance Characteristics of a Python Turbine-propeller Engine Investigated in Altitude Wind Tunnel  

NASA Technical Reports Server (NTRS)

Combustion-chamber performance characteristics of a Python turbine-propeller engine were determined from investigation of a complete engine over a range of engine speeds and shaft horsepowers at simulated altitudes. Results indicated the effect of engine operating conditions and altitude on combustion efficiency and combustion-chamber total pressure losses. Performance of this vaporizing type combustion chamber was also compared with several atomizing type combustion chambers. Over the range of test conditions investigated, combustion efficiency varied from approximately 0.95 to 0.99.

Campbell, Carl E

1951-01-01

271

The Social Tunnel Versus the Python: A New Way to Understand the Impact of Baby Booms and Baby Busts on a Society.  

ERIC Educational Resources Information Center

Maintains that the "python analogy," often used to help students understand the negative societal impact of unusually small or large age cohorts, is better replaced by the social tunnel analogy, which is diagramed and illustrated with reference to the educational problems experienced in the United States as a result of the World War II baby boom.

McFalls, Joseph A.; And Others

1986-01-01

272

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

NASA Astrophysics Data System (ADS)

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

Chudoba, R.; Sadlek, V.; Rypl, R.; Vo?echovsk, M.

2013-02-01

273

QuTiP: An open-source Python framework for the dynamics of open quantum systems  

NASA Astrophysics Data System (ADS)

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

274

Wilber 3: A Python-Django Web Application For Acquiring Large-scale Event-oriented Seismic Data  

NASA Astrophysics Data System (ADS)

Since 2001, the IRIS Data Management Center (DMC) WILBER II system has provided a convenient web-based interface for locating seismic data related to a particular event, and requesting a subset of that data for download. Since its launch, both the scale of available data and the technology of web-based applications have developed significantly. Wilber 3 is a ground-up redesign that leverages a number of public and open-source projects to provide an event-oriented data request interface with a high level of interactivity and scalability for multiple data types. Wilber 3 uses the IRIS/Federation of Digital Seismic Networks (FDSN) web services for event data, metadata, and time-series data. Combining a carefully optimized Google Map with the highly scalable SlickGrid data API, the Wilber 3 client-side interface can load tens of thousands of events or networks/stations in a single request, and provide instantly responsive browsing, sorting, and filtering of event and meta data in the web browser, without further reliance on the data service. The server-side of Wilber 3 is a Python-Django application, one of over a dozen developed in the last year at IRIS, whose common framework, components, and administrative overhead represent a massive savings in developer resources. Requests for assembled datasets, which may include thousands of data channels and gigabytes of data, are queued and executed using the Celery distributed Python task scheduler, giving Wilber 3 the ability to operate in parallel across a large number of nodes.

Newman, R. L.; Clark, A.; Trabant, C. M.; Karstens, R.; Hutko, A. R.; Casey, R. E.; Ahern, T. K.

2013-12-01

275

The Zachary Cruz Memorial Scholarship Established by the Zachary Michael Cruz Foundation  

E-print Network

to everyone he met. An avid fan of all things "Cal," Zach loved Golden Bear Football, Big Game Week, Oski and insights that continually surprised us - questions about science, politics, sports, history, and technology. His favorite band was The Beatles. He was a t-ball player, a Dodgers fan, and he loved Legos, Star

Doudna, Jennifer A.

276

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

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

277

Autonomic control of heart rate during orthostasis and the importance of orthostatic-tachycardia in the snake Python molurus.  

PubMed

Orthostasis dramatically influences the hemodynamics of terrestrial vertebrates, especially large and elongated animals such as snakes. When these animals assume a vertical orientation, gravity tends to reduce venous return, cardiac filling, cardiac output and blood pressure to the anterior regions of the body. The hypotension triggers physiological responses, which generally include vasomotor adjustments and tachycardia to normalize blood pressure. While some studies have focused on understanding the regulation of these vasomotor adjustments in ectothermic vertebrates, little is known about regulation and the importance of heart rate in these animals during orthostasis. We acquired heart rate and carotid pulse pressure (P PC) in pythons in their horizontal position, and during 30 and 60 inclinations while the animals were either untreated (control) or upon muscarinic cholinoceptor blockade and a double autonomic blockade. Double autonomic blockade completely eradicated the orthostatic-tachycardia, and without this adjustment, the P PC reduction caused by the tilts became higher than that which was observed in untreated animals. On the other hand, post-inclinatory vasomotor adjustments appeared to be of negligible importance in counterbalancing the hemodynamic effects of gravity. Finally, calculations of cardiac autonomic tones at each position revealed that the orthostatic-tachycardia is almost completely elicited by a withdrawal of vagal drive. PMID:25017862

Armelin, Vinicius Arajo; da Silva Braga, Victor Hugo; Abe, Augusto Shinya; Rantin, Francisco Tadeu; Florindo, Luiz Henrique

2014-10-01

278

Application of python-based Abaqus preprocess and postprocess technique in analysis of gearbox vibration and noise reduction  

NASA Astrophysics Data System (ADS)

To reduce vibration and noise, a damping layer and constraint layer are usually pasted on the inner surface of a gearbox thin shell, and their thicknesses are the main parameters in the vibration and noise reduction design. The normal acceleration of the point on the gearbox surface is the main index that can reflect the vibration and noise of that point, and the normal accelerations of different points can reflect the degree of the vibration and noise of the whole structure. The K-S function is adopted to process many points' normal accelerations as the comprehensive index of the vibration characteristics of the whole structure, and the vibration acceleration level is adopted to measure the degree of the vibration and noise. Secondary development of the Abaqus preprocess and postprocess on the basis of the Python scripting programming automatically modifies the model parameters, submits the job, and restarts the analysis totally, which avoids the tedious work of returning to the Abaqus/CAE for modifying and resubmitting and improves the speed of the preprocess and postprocess and the computational efficiency.

Yi, Guilian; Sui, Yunkang; Du, Jiazheng

2011-06-01

279

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

NASA Astrophysics Data System (ADS)

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

Sandner, Raimar; Vukics, Andrs

2014-09-01

280

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

PubMed

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

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

2013-06-01

281

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

NASA Astrophysics Data System (ADS)

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 on 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.

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

2014-03-01

282

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

PubMed Central

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 DNAprotein 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

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

2014-01-01

283

CS 140 Rock -Paper -Scissors Email copy due Friday, May 4 at 5pm For the in-class project, you must write a Python program to play Rock-Paper-Scissors versus the  

E-print Network

and write small batches of code to create these (preferably as functions that can easily be called inside must write a Python program to play Rock-Paper-Scissors versus the computer in Pygame. At a minimum your main program) Start with the text based version of the game and then work on "converting it

Ramler, Ivan

284

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

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

Paris-Sud XI, Université de

285

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

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

Paris-Sud XI, Université de

286

Performance and Operational Characteristics of a Python Turbine-propeller Engine at Simulated Altitude Conditions / Carl L. Meyer and Lavern A. Johnson  

NASA Technical Reports Server (NTRS)

The performance and operational characteristics of a Python turbine-propeller engine were investigated at simulated altitude conditions in the NACA Lewis altitude wind tunnel. In the performance phase, data were obtained over a range of engine speeds and exhaust nozzle areas at altitudes from 10,000 to 40,000 feet at a single cowl-inlet ram pressure ratio; independent control of engine speed and fuel flow was used to obtain a range of powers at each engine speed. Engine performance data obtained at a given altitude could not be used to predict performance accurately at other altitudes by use of the standard air pressure and temperature generalizing factors. At a given engine speed and turbine-inlet total temperature, a greater portion of the total available energy was converted to propulsive power as the altitude increased.

Meyer, Carl L; Johnson, Lavern A

1952-01-01

287

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)

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.

Mayorga, E.

2013-12-01

288

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA.  

PubMed

Recent studies have demonstrated that detection of environmental DNA (eDNA) from aquatic vertebrates in water bodies is possible. The Burmese python, Python bivittatus, is a semi-aquatic, invasive species in Florida where its elusive nature and cryptic coloration make its detection difficult. Our goal was to develop a diagnostic PCR to detect P.bivittatus from water-borne eDNA, which could assist managers in monitoring this invasive species. First, we used captive P.bivittatus to determine whether reptilian DNA could be isolated and amplified from water samples. We also evaluated the efficacy of two DNA isolation methods and two DNA extraction kits commonly used in eDNA preparation. A fragment of the mitochondrial cytochrome b gene from P.bivittatus was detected in all water samples isolated with the sodium acetate precipitate and the QIAamp DNA Micro Kit. Next, we designed P.bivittatus-specific primers and assessed the degradation rate of eDNA in water. Our primers did not amplify DNA from closely related species, and we found that P.bivittatus DNA was consistently detectable up to 96h. Finally, we sampled water from six field sites in south Florida. Samples from five sites, where P.bivittatus has been observed, tested positive for eDNA. The final site was negative and had no prior documented evidence of P.bivittatus. This study shows P.bivittatus eDNA can be isolated from water samples; thus, this method is a new and promising technique for the management of invasive reptiles. PMID:24119154

Piaggio, Antoinette J; Engeman, Richard M; Hopken, Matthew W; Humphrey, John S; Keacher, Kandy L; Bruce, William E; Avery, Michael L

2014-03-01

289

Diseases and pests of honey bees Zachary Huang  

E-print Network

2001 2002 0 20 40 60 80 100 120 140 Natural mitefall No traps Traps Data from T. Webster 8. Using Drone-Trapping to reduce mites 1. Drone trapping method (works, labor-intensive, ~60%)\\ 2. Mitezapper 9. Stock 1. Use.Hygienic assay 3.Drone stock 4.Control of mating #12;4 Life cycle of Nosema apis · Transmitted by spores

Huang, Zachary

290

Hinged Dissections Exist Timothy G. Abbott #+ Zachary Abel # David Charlton  

E-print Network

#¶ Martin L. Demaine # Scott Duke Kominers # Abstract We prove that any finite collection of polygons, programmable matter, and nanomanufacturing. 1 Introduction Around 1808, Wallace asked whether every two] published the first solution to Wallace's problem in 1814, although Wallace may have also had a solution

Demaine, Erik

291

Zachary Zwerko Senior Analyst, Financial Evaluation and Analysis  

E-print Network

as an International Tax consultant, supporting International Tax services for clients such as Johnson & Johnson Marketing, Manufacturing and Research to evaluate potential business development deals for Merck ,and how actuals to senior managment. Zack was later promoted to Manager of Sales and Marketing Finance. During

Lin, Xiaodong

292

THE LOUISIANA OYSTER INDUSTRY. By F. C. ZACHARIE.  

E-print Network

and Pontchartrain, and following the shore line southward and westward around the mouths of the Mississippi River flavor, can not be excelled the world over. East of the Mississippi River these natural beds are still

293

1. Write a Python program that takes 5 integers from command line (in the argv list) and separates them into two groups, such that the difference between the sum of the first  

E-print Network

Point: def __init__(self, x, y): self.x, self.y = x, y class Triangle: def __init__(self, A=Point(100,100), B=Point(200,100), C=Point(200,200)): self.A, self.B, self.C = A, B, C def get_perimeter(self): pass to the following Python class: class Node: def __init__(self, data=0, left=None, right=None): self.data = data self

Li, Zongpeng

294

Statistical Analysis of Multiple Sociometric Relations Stephen E. Fienberg; Michael M. Meyer; Stanley S. Wasserman  

E-print Network

, cities, or even nation states; relations have ranged from kinship or friendship to transfers of scarce's ideas, focusing on matrix representations of sociometric data, the popularity of actors, mutuality

Fienberg, Stephen E.

295

oFwrsc,o{srN ly2ltt -SHELDoN A. WASSERMAN, MD, FACOG  

E-print Network

¡sin Medical Examining Board "The Medical Exarnining Board and How It Affects Your Life" tt/09il1 - PAULA M. TERMUHLEN, MD Moderator: Panel Discussion - "Hospital Readtnission Rate - Why Should We Care and What Can

296

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

E-print Network

the thermal excitation of electrons. Significant decrease of the elastic constants of hcp iron: the product of thermal expansivity and bulk modulus is found to be nearly independent of compression at high pressure and the logarithmic volume derivative of is found to decrease with compression. In contrast

Stixrude, Lars

297

Creative Computing with Landlab: Open-Source Python Software for Building and Exploring 2D Models of Earth-Surface Dynamics  

NASA Astrophysics Data System (ADS)

Computer models help us explore the consequences of scientific hypotheses at a level of precision and quantification that is impossible for our unaided minds. The process of writing and debugging the necessary code is often time-consuming, however, and this cost can inhibit progress. The code-development barrier can be especially problematic when a field is rapidly unearthing new data and new ideas, as is presently the case in surface dynamics. To help meet the need for rapid, flexible model development, we have written a prototype software framework for two-dimensional numerical modeling of planetary surface processes. The Landlab software can be used to develop new models from scratch, to create models from existing components, or a combination of the two. Landlab provides a gridding module that allows you to create and configure a model grid in just a few lines of code. Grids can be regular or unstructured, and can readily be used to implement staggered-grid numerical solutions to equations for various types of geophysical flow. The gridding module provides built-in functions for common numerical operations, such as calculating gradients and integrating fluxes around the perimeter of cells. Landlab is written in Python, a high-level language that enables rapid code development and takes advantage of a wealth of libraries for scientific computing and graphical output. Landlab also provides a framework for assembling new models from combinations of pre-built components. This capability is illustrated with several examples, including flood inundation, long-term landscape evolution, impact cratering, post-wildfire erosion, and ecohydrology. Interoperability with the Community Surface Dynamics Modeling System (CSDMS) Model-Coupling Framework allows models created in Landlab to be combined with other CSDMS models, which helps to bring frontier problems in landscape and seascape dynamics within closer theoretical reach.

Tucker, G. E.; Hobley, D. E.; Gasparini, N. M.; Hutton, E.; Istanbulluoglu, E.; Nudurupati, S.; Adams, J. M.

2013-12-01

298

Python Optimization Modeling Objects (Pyomo)  

E-print Network

Algebraic Modeling Languages (AMLs) are alternative approach that allows applications to ... guage for formulating optimization problems and the efficiency of the low-level lan- guage for ..... self . obj . min(?4? self .x[1] ? 5? self .x[2]) self . c1...

2008-09-08

299

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

E-print Network

, in addition to preventing suicide, reduce risk behaviors and promote healthier ones as well as improve young. The effects of such interventions in terms of combating unhealthy lifestyles in young people, which often

Paris-Sud XI, Université de

300

Rev. of LIST (Library and Informations Services Today): An International Registry of Research and Innovation, ed. by Paul Wasserman  

E-print Network

. University of Nebraska John Braeman "REMEMBER T H E LADIES;" New Perspectives on Women in American History. Ed. by Carol V. R. George. Syracuse. Syracuse University Press. 1975. $10.00. A useful collection of ten essays on women's history which spans two... works Frank Freidel, editor, assisted by Richard K. Showman. HARVARD GUIDE TO AMERICAN HISTORY. Rev. ed. 2 volumes. Harvard. 1974. $45.00. History. Rev. ed. 2 volumes. Harvard. 1974. $45.00. In every case in which I checked the listings in fields I...

Levine, Stuart

1976-01-01

301

Battlefield Casualty Extraction Device for Unmanned Ground Vehicles Zachary Sabato Jonathan Sente Sajeel Shiromani David Williams  

E-print Network

· Sajeel Shiromani · David Williams 95th Percentile: 350 lbs Motivation: Robotically extract casualties thus keeping medics out of harm's way Lift Gate Articulated Arm Litter Tray 8 DOF End Physics Based Simulation · Stress Testing (Strain Gage) · ANYSYS and ProMECHANICA · Physics

Oh, Paul

302

Validating a New Algorithm for Wind Vector Retrieval in Tropical Zachary Hargrove, UNC Asheville  

E-print Network

-Winds, and (d) the raw wind vector estimates directly from QuickSCAT. (Jones et al. 2011) (C4) (C5) (C2-C3n) (C3 are well out to sea. Estimates in wind strength are extremely important. · Scatterometers are valuable

Hennon, Christopher C.

303

Early Stage Soliton Observations in the Sulu Sea* ZACHARY D. TESSLER AND ARNOLD L. GORDON  

E-print Network

of the soliton generation site near Pearl Bank in the Sulu Archipelago. From here, waves propagate toward been coupled to harbor seiche activity (Giese et al. 1998). To our knowledge, these are the first

Gordon, Arnold L.

304

Women's estradiol predicts preference for facial cues of men's testosterone James R. Roney , Zachary L. Simmons  

E-print Network

Women's estradiol predicts preference for facial cues of men's testosterone James R. Roney testosterone during times in the cycle when conception is most likely, no previous studies have directly demonstrated that women express stronger attraction to higher testosterone men at different times in the cycle

Cosmides, Leda

305

3D Tracking via Body Radio Reflections Fadel Adib Zachary Kabelac Dina Katabi Robert C. Miller  

E-print Network

and occlusions, and human-computer interaction systems like Kinect, which can track a user without instrumenting device in order to be localized. In contrast, systems like Kinect and depth imaging have revolutionized of the user. However, Kinect and imaging systems require a user to stay within the device's line

Polz, Martin

306

Hormonal predictors of sexual motivation in natural menstrual cycles James R. Roney , Zachary L. Simmons  

E-print Network

Menstrual cycle Estradiol Testosterone Progesterone Little is known regarding which hormonal signals may. To address this, we collected daily saliva samples across 1­2 menstrual cycles from a sample of young women; assayed samples for estradiol, progesterone, and testosterone; and also collected daily diary reports

Dever, Jennifer A.

307

Medieval Romances: "Perceval" to "Monty Python."  

ERIC Educational Resources Information Center

A selection of romances from medieval literature can be used successfully in undergraduate literature classes to trace the appearance and relevance of medieval themes, motifs, and characters in works of modern poetry, fiction, and film. New scholarly editions, historiographies, translations, and modernizations give both teachers and students more

Jehle, Dorothy M.

308

Python Engine Installed in Altitude Wind Tunnel  

NASA Technical Reports Server (NTRS)

An engine mechanic checks instrumentation prior to an investigation of engine operating characteristics and thrust control of a large turboprop engine with counter-rotating propellers under high-altitude flight conditions in the 20-foot-dianieter test section of the Altitude Wind Tunnel at the Lewis Flight Propulsion Laboratory of the National Advisory Committee for Aeronautics, Cleveland, Ohio, now known as the John H. Glenn Research Center at Lewis Field.

1949-01-01

309

Why Python? 1) readable, compact, simple syntax  

E-print Network

-based syntax, less brackets · Control flow via indentation if danger : if smaller_than_you(): fight() else: run' for letter in ABC: print(ord(letter)) # hunts for every animal in list zoo zoo = [ 'egg', 'dog', 'duck

Spang, Rainer

310

PyGFit: Python Galaxy Fitter  

NASA Astrophysics Data System (ADS)

PyGFit measures PSF-matched photometry from images with disparate pixel scales and PSF sizes; its primary purpose is to extract robust spectral energy distributions (SEDs) from crowded images. It fits blended sources in crowded, low resolution images with models generated from a higher resolution image, thus minimizing the impact of crowding and also yielding consistently measured fluxes in different filters which minimizes systematic uncertainty in the final SEDs.

Mancone, Conor L.; Gonzalez, Anthony H.; Moustakas, Leonidas A.; Price, Andrew

2014-02-01

311

Neurologic dysfunction in a ball python (python regius) color morph, and Implications for welfare  

E-print Network

for welfare problems in inbred reptiles, and to stimulate further research in this field. A survey of expert opinion was used to establish a description of a heritable disorder, the wobble syndrome, associated with a widely propagated phenotype, the spider...

Rose, Mark P.; Williams, David L.

2014-06-09

312

78 FR 39307 - National Environmental Policy Act: Implementing Procedures; Addition to Categorical Exclusions...  

Federal Register 2010, 2011, 2012, 2013

...carp (Mylopharyngodon piceus, 2007), and four species of large constrictor snakes (Burmese python (Python molurus), Northern African python (Python sebae), Southern African python (Python natalensis), and yellow anaconda...

2013-07-01

313

Vortex Visualization in Ultra Low Reynolds Number Insect Flight Christopher Koehler, Thomas Wischgoll, Haibo Dong, and Zachary Gaston  

E-print Network

forewing and hindwing of a dragonfly during takeoff. Abstract--We present the visual analysis of a biologically inspired CFD simulation of the deformable flapping wings of a dragonfly as it takes off and begins the dragonfly takeoff, parametric surfaces used for wing reconstruction, CFD solver and underlying flapping

314

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

E-print Network

of pervasive wearable devices, whether for health monitoring, personal assistance, entertainment, or home with the correct identity so that it can be stored in the correct health record. (A mixup of sensor data could lead to be properly labeled or personalized behavior to be properly achieved. We use vocal resonance, that is

315

(Not) Interacting with a Robot Photographer William D. Smart and Cindy M. Grimm and Michael Dixon and Zachary Byers  

E-print Network

observation, and possibly used to enhance the quality of the human- robot interaction. The Robot The robot(Not) Interacting with a Robot Photographer William D. Smart and Cindy M. Grimm and Michael Dixon, MO 63130 United States {wds,cmg,msd2,zcb1}@cse.wustl.edu Abstract We have deployed a robot

Dixon, Michael

316

Leveraging Change Blindness for Walking in Virtual Environments Evan A. Suma* Seth Clark Samantha L. Finkelstein Zachary Wartell  

E-print Network

to activate a computer monitor. (c) State 3: The corridor and the door to exit the room are instantly rotated: The user enters the second room and walks to the desk to activate a computer monitor. (f) State 6

Wartell, Zachary

317

ORIGINAL PAPER Can invasive Burmese pythons inhabit temperate regions  

E-print Network

threat to native ecosystems. Recent studies indicate that climate suitable for the species P. molurus-freezing weather. The remaining snakes used refugia but died during an unusually cold period in January 2010. Although all snakes died during the study, most survived extended periods at tempera- tures below those

Dorcas, Michael E.

318

ORIGINAL PAPER Can invasive Burmese pythons inhabit temperate regions  

E-print Network

bivittatus) are established in southern Florida and pose a significant threat to native ecosystems. Recent, but most died after failing to seek appropriate refugia during sub-freezing weather. The remaining snakes used refugia but died during an unusually cold period in January 2010. Although all snakes died during

Willson. J.D.

319

RESEARCH ARTICLE Conservation genetics of Boelen's python (Morelia boeleni)  

E-print Network

and European zoos have active captive breeding programs that have been largely unsuccessful. To understand as one of the world's five High Biodiversity Wilderness Areas (Mittermeier et al. 2003). New Guinea occupies less than 0.6% of global land area yet harbors 5­7% of the world's biodiversity (Beehler 1993

Austin, Christopher C.

320

Non-Programmers Tutorial For Python Josh Cogliati  

E-print Network

to Elizabeth Cogliati for complaining enough :) about the original tutorial,(that is almost unusable for a non welcome questions and comments about this tutorial. I will try to answer any questions you have as best as I can. Thanks go to James A. Brown for writing most of the Windows install info. Thanks also

Kimbrough, Steven Orla

321

Forces driving thermogenesis and parental care in pythons.  

E-print Network

??Parental care provides many benefits to offspring. One widely realized benefit is enhanced regulation of offspring's thermal environment. The developmental thermal environment during development can (more)

Brashears, Jake Alexander

2012-01-01

322

Preliminary Results from the PYTHON Microwave Background Anisotropy Experiment  

Microsoft Academic Search

We will present preliminary results of our experiment to measure the anisotropy of the microwave background on medium (2.75 degree) angular scales. Observations of 14 separate regions (two rows of seven regions) on the sky were made during the 15 day period of 1 Jan to 15 Jan 1993. The observing site, the geographic South Pole, is an ideal location

M. Dragovan; J. Ruhl; G. Novak; S. R. Platt; B. Crone; R. Pernic

1993-01-01

323

Crates and Transform: Python Interfaces for Data Analysis  

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

324

Preliminary Results from the PYTHON Microwave Background Anisotropy Experiment  

NASA Astrophysics Data System (ADS)

We will present preliminary results of our experiment to measure the anisotropy of the microwave background on medium (2.75 degree) angular scales. Observations of 14 separate regions (two rows of seven regions) on the sky were made during the 15 day period of 1 Jan to 15 Jan 1993. The observing site, the geographic South Pole, is an ideal location for microwave background anisotropy studies where long integration times, low sky background (10K at 90GHz), and stable atmospheric conditions are required. The geometric advantage of the Pole is that a patch of sky never rises or sets, allowing 24 hour observations of the patch with no corrections required for changes in elevation. Approximately 100 hours of usable data were obtained during this time. The instrument is a five channel bolometer array, with the detectors operating at 50 mK, cooled by a hybrid (3) He-Adiabatic demagnetization refrigerator. There are four pixels in the focal plane arranged in a square grid so that the angular separation between pixels on the sky is 2.75 degrees. The fifth channel is a dark channel acting as a monitor for extraneous noise or pickup. Individual pixels consist of corrugated feedhorns coupled to waveguide waffle filters combined with glass and plastics to define the high frequency cutoff (110 GHz); the low frequency cutoff is determined by the cutoff of the waveguide (75 GHz). The band was selected for minimal expected contributions from foreground sources such as free-free, synchrotron and cool dust. This detector system is coupled to the sky via a 0.75m off axis parabolic primary. A gradient free 3-beam switching pattern on the sky is obtained by moving a low moment of inertia flat plate quickly (15 msec transition time, with 85 msec spent integrating on the point) between 3 points on the sky. The plate is oriented vertically so the switching is at constant elevation. This work was supported by The Center for Astrophysics in Antarctica, PYI grant NSF AST-9057089 and the James S. McDonnell Foundation.

Dragovan, M.; Ruhl, J.; Novak, G.; Platt, S. R.; Crone, B.; Pernic, R.

1993-05-01

325

Pablo Python Looks at Animals. [Multimedia Educational Kit].  

ERIC Educational Resources Information Center

Teachers and students can view the world of animals together through an exploration of how-and-why questions about animals in this curriculum unit. The problem-solving and critical thinking skills of students are improved through interactive activities involving oral and written communication, mathematics, creative arts, music, dance, and creative

Sullivan, Rick; Green, David

326

PySP: Modeling and Solving Stochastic Programs in Python  

E-print Network

Sep 6, 2010 ... Discrete Math and Complex Systems Department. PO Box 5800, MS ..... programmatic navigation, query, manipulation, and reporting of the scenario tree struc- ture. While hidden ..... chain, e.g., for maintaining an aircraft fleet.

2010-09-07

327

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

E-print Network

ribbon snake (Thamnophis proximus) and the diamond-backed water snake (Natrix rhombifera) were acclimated to the temperatures of 15' and 30'C. The ambient temperature also plays a role in maintaining a functional immune system. In a study using... ribbon snake (Thamnophis proximus) and the diamond-backed water snake (Natrix rhombifera) were acclimated to the temperatures of 15' and 30'C. The ambient temperature also plays a role in maintaining a functional immune system. In a study using...

Johnson, James Harvey

2012-06-07

328

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

E-print Network

! 1! Protein degradation in a TX-TL cell-free expression system using ClpXP protease AUTHORS as an alternative prototyping environment to the cell for synthetic circuits [1-5]. Basic circuit elements-TL � by expressing the proteins off of plasmid DNA or by adding purified protein. We first attempted to express both

Murray, Richard M.

329

Facile Synthesis of a Tungsten Alkylidyne Catalyst for Alkyne Zachary J. Tonzetich, Yan Choi Lam, Peter Muller, and Richard R. Schrock*  

E-print Network

ligands reside above the CalkylOO face, while the tert-butyl group of the neopentyl ligand resides below-Bu)(OAr)2 in 40-50% isolated yield. W(C-t-Bu)(CH2-t-Bu)(OAr)2 is a Versatile entry for preparing W), followed by displacement of the chlorides with alkoxides.8 The key synthesis of volatile, yellow

Müller, Peter

330

One-way entangled-photon autocompensating quantum cryptography Zachary D. Walton,* Ayman F. Abouraddy, Alexander V. Sergienko, Bahaa E. A. Saleh, and Malvin C. Teich  

E-print Network

- cently emerged cf. Ref. 3 , and references therein , the ``no-cloning theorem'' 4 published in 1982 . This method, pioneered by Klyshko, establishes a formal equivalence between the following two optical con

Sergienko, Alexander

331

Zachary-Fort Lauderdale pipeline construction and conversion project: final supplement to final environmental impact statement. Docket No. CP74-192  

SciTech Connect

This Final Supplement to the Final Environmental Impact Statement (Final Supplement) evaluates the economic, engineering, and environmental aspects of newly developed alternatives to an abandonment/conversion project proposed by Florida Gas Transmission Company (Florida Gas). It also updates the staff's previous FEIS and studies revisions to the original proposal. Wherever possible, the staff has adopted portions of its previous FEIS in lieu of reprinting portions of that analysis which require no change. 60 references, 8 figures, 35 tables.

None

1980-05-01

332

1. Thoughts on Space Travel for Spring 2010 Orion: I. Wasserman, 3/31/2010 To derive the relativistic rocket equation, consider what happens when a mass m is  

E-print Network

the relativistic rocket equation, consider what happens when a mass m is ejected in the spaceship's rest frame. If the rocket moves at speed v relative to Earth, then in the Earth frame E = (E0 + vP0) = E0(1 + vv0) P = (P0 + vE0) = E0(v + v0) . (1) Since P = Ev is the rocket momentum relative to Earth, and E = m in the same

Richardson Jr., James E.

333

The Funeral of Froggy the Frog: The Child as Dramatist, Designer, and Realist  

ERIC Educational Resources Information Center

One sunny afternoon, six-year-old Zachary and his friend John Michael, four and a half, discovered a dead frog in a bag of clay in the garage. Zachary proposed, "Let's have a funeral for the frog." This is how the funeral drama of Froggy the Frog began. This article describes the play experiences of Zachary and John Michael as designers,

Cummins, Lauren

2004-01-01

334

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

335

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1, Introducing a Python Edition  

Microsoft Academic Search

The Naval Observatory Vector Astrometry Software (NOVAS) is a source-code library that provides common astrometric quantities and transformations. NOVAS calculations are accurate at the sub-milliarcsecond level. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of

Eric G. Barron; G. H. Kaplan; J. Bangert; J. L. Bartlett; W. Puatua; W. Harris; P. Barrett

2011-01-01

336

Pyro: A Python-Based Versatile Programming Environment for Teaching Robotics  

ERIC Educational Resources Information Center

In this article we describe a programming framework called Pyro, which provides a set of abstractions that allows students to write platform-independent robot programs. This project is unique because of its focus on the pedagogical implications of teaching mobile robotics via a top-down approach. We describe the background of the project, its

Blank, Douglas; Kumar, Deepak; Meeden, Lisa; Yanco, Holly

2004-01-01

337

From Monty Python to Total Recall: A Feature Film Activity for the Cognitive Psychology Course.  

ERIC Educational Resources Information Center

Describes a college psychology course activity designed to help students define the parameters of cognitive psychology. Students selected a feature film and a journal article that represented some aspect of cognitive psychology. They then wrote a paper discussing the theoretical and empirical connections between the sources and the topic. (MJP)

Conner, David B.

1996-01-01

338

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

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

339

Automating Disk Forensic Processing with SleuthKit, XML and Python.  

National Technical Information Service (NTIS)

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 ...

S. L. Garfinkel

2009-01-01

340

Implementing Customized Pivot Rules in COIN-OR's CLP with Python  

E-print Network

works would therefore be more efficient if linear and mixed-integer pro- gramming .... is possible, it has to involve increasing a non-basic variable. The last ...... filter line-search algorithm for large-scale nonlinear programming. Mathemat-.

Mehdi Towhidi, Dominique Orban

2012-05-04

341

Establishing a Novel Modeling Tool: A Python-Based Interface for a Neuromorphic Hardware System  

PubMed Central

Neuromorphic hardware systems provide new possibilities for the neuroscience modeling community. Due to the intrinsic parallelism of the micro-electronic emulation of neural computation, such models are highly scalable without a loss of speed. However, the communities of software simulator users and neuromorphic engineering in neuroscience are rather disjoint. We present a software concept that provides the possibility to establish such hardware devices as valuable modeling tools. It is based on the integration of the hardware interface into a simulator-independent language which allows for unified experiment descriptions that can be run on various simulation platforms without modification, implying experiment portability and a huge simplification of the quantitative comparison of hardware and simulator results. We introduce an accelerated neuromorphic hardware device and describe the implementation of the proposed concept for this system. An example setup and results acquired by utilizing both the hardware system and a software simulator are demonstrated. PMID:19562085

Bruderle, Daniel; Muller, Eric; Davison, Andrew; Muller, Eilif; Schemmel, Johannes; Meier, Karlheinz

2008-01-01

342

A Problem Course in Compilation: From Python to x86 Assembly  

Microsoft Academic Search

ABSTRACT. The primary,goal of this course is to help students acquire an understanding,of what,happens,behind the scenes when,programs,written in high-level languages,are executed,on modern,hardware.,This understanding,is useful for estimating performance,tradeoffs and,debugging,programs.,A secondary goal of the course is to teach students the principles, techniques, and tools that are used in compiler,construction. While an engi- neer seldom,needs to implement,a compiler,for a general purpose language, it

Jeremy G. Siek

343

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

E-print Network

neighbors dies from overcrowding. · Any dead cell with exactly three live neighbors becomes a live cell step in the game, the cell at each grid location is either alive or dead. When transitioning from one.org/wiki/Conway's_Game_of_Life): · Any live cell with fewer than two live neighbors dies due to under-population. · Any live cell

Ralphs, Ted

344

pySPACE-a signal processing and classification environment in Python.  

PubMed

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries. PMID:24399965

Krell, Mario M; Straube, Sirko; Seeland, Anett; Whrle, Hendrik; Teiwes, Johannes; Metzen, Jan H; Kirchner, Elsa A; Kirchner, Frank

2013-01-01

345

Building Components for a Distributed Sentient Framework with Python and CORBA  

Microsoft Academic Search

TRIP (Target Recognition using Image Processing) is a novel vision-based sensor system that uses a combination of visual markers (2-D circular barcode tags, or ringcodes) and conventional video cameras to identify tagged objects in the field of view. A CORBA- based distributed component architecture called Sentient Information Framework has been devised to efficiently manage and distribute to applications the sensor

Diego Lpez de Ipia

2000-01-01

346

ProDaMa: an open source Python library to generate protein structure datasets  

Microsoft Academic Search

BACKGROUND: The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective,

Giuliano Armano; Andrea Manconi

2009-01-01

347

Using Python Scripting and Web Frameworks to Access Spatial and Temporal Data via KML  

Microsoft Academic Search

Ever increasing volumes of spatial and temporal data about our world are being made available for download by various organizations. However, the data formats used are generally well-suited for storing large volumes of data but are not directly usable without specialized software. Also in recent years, there has been a wide adoption of easy-to-use virtual globe browsers (such as Google

T. A. Erickson; B. W. Koziol

2010-01-01

348

gluepy: A Simple Distributed Python Programming Framework for Complex Grid Environments  

Microsoft Academic Search

Problem-solving frameworks in large-scale and wide-area en- vironments must handle connectivity issues (NATs and firewalls), main- tain scalability with respect to connection management, accommodate dynamic processes joining\\/leaving at runtime, and provide simple means to tolerate communication\\/node failures. All of the above must be pre- sented in a simple and flexible programming model. This paper designs and implements such a framework

Ken Hironaka; Hideo Saito; Kei Takahashi; Kenjiro Taura

2008-01-01

349

Phenix - a comprehensive python-based system for macromolecular structure solution  

SciTech Connect

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

2009-01-01

350

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

Microsoft Academic Search

BackgroundTelomere 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

Beata Ujvari; Thomas Madsen; Robert C. Fleischer

2009-01-01

351

DARE: Going Medieval on the Universe Monte Python and the Holy Grail  

E-print Network

--when was our cosmic dawn? Observations and calculations suggest that this phenomenon occurred when the universe, Moon. #12;High-gain Antenna Spacecraft Bus Payload Antenna Support Structure Payload Dipole Antennas (4) Payload Antennas Radials (12) 1.8 m2 Solar Array Instrument Response Function #12;AFT location Forward

Shumway, John

352

Using python and QuickDraw to foster student engagement in CS1  

Microsoft Academic Search

Most students enrolling in introductory computer science courses today have grown up working exclusively with graphical user interfaces. Through this experience, they have come to expect computers to be reasonably intuitive and easy to use. Yet, when students enter an introductory course in computer science, it is commonplace for them to work on exclusively text based assignments using complex programming

Ben Stephenson

2009-01-01

353

Design and Implementation of a Python-Based Active Network Platform for Network Management and  

E-print Network

the creation of Virtual Active Networks. Similar to virtual private networks (VPNs), a customer can "rent" such a virtual active network. Within its active network, the customer (e.g. a company) can exploit AN technology but has no access to the other virtual networks. The goal of the app

Braun, Torsten

354

PyTensor: A Python based Tensor Library Ji Oh Yoo Arvind Ramanathan  

E-print Network

on the MATLAB tensor-toolkit library, available from Sandia National Labs (http://csmr.ca.sandia.gov/ tgkolda@cs.cmu.edu This research was supported by NIH RC2 GM093307-0110, Oak Ridge National Lab's LDRD program, the Na- tional

Langmead, Christopher James

355

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes  

E-print Network

for Child and Maternal Health, Calgary, AB, Canada T2N 4N1; d Department of Human Genetics, University of Education, Nanjing 210096, China; g Department of Biology, Linfield College, McMinnville, OR 97128; h

Castoe, Todd A.

356

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

Microsoft Academic Search

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

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

2009-01-01

357

Implementation of a python version of a scaled boundary finite element method for plate bending analysis  

E-print Network

Common finite element programs for plate bending analysis are complicated and limited by the common plate theories. Such programs are usually not user-friendly for designers to implement. Lately, Hou Man et al. from the ...

Chen, Lingfeng, M. Eng. Massachusetts Institute of Technology

2014-01-01

358

PLANETENSTELSELS -WERKCOLLEGE 1A EN 1B Opdracht 1: Introductie Python  

E-print Network

astronomy # druk de constante G af print astronomy .G # zet snelheid op 0.2 maal de l i c h t s n e l h e i), gebruik dan het reload commando: § ¤ import astronomy as p # druk de constante G af print p .G #herladen (a) de aarde, (b) de maan en (c) de zon. Je mag ervan uitgaan dat het ISS zich op een cirkelbaan op

Hogerheijde, Michiel

359

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

ERIC Educational Resources Information Center

The author describes how he used to teach a unit on food webs and ecosystems using actual food webs as models. However, the models used by the author tend to be either too simplistic or too complicated for his students. A few years ago, he solved these problems by making up his own food web, complete with invented plants and animals. The model has

Rockow, Michael

2007-01-01

360

PHENIX: a comprehensive Python-based system for macromolecular structure solution  

PubMed Central

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. PMID:20124702

Adams, Paul D.; Afonine, Pavel V.; Bunkoczi, Gabor; Chen, Vincent B.; Davis, Ian W.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Kapral, Gary J.; Grosse-Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

2010-01-01

361

A Software Framework in Python for Generating Optimal Isogeometric Kernels on the PowerPC 450  

E-print Network

a pattern #12;Code generation Mako templates writing inline assembly Easy to control unrolling and jamming to standard FEM Can exactly conform to some engineering geometries. Better impedence match with solid modeling (CAD). Fewer degrees of freedom for 4th order problems, e.g. no rotation dofs for shells. More nonzeros

Brown, Jed

362

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

Federal Register 2010, 2011, 2012, 2013

...removal; public education and awareness; spatial ecology and movement studies using radio telemetry, satellite and GPS technology; diet (stomach content analysis); thermal biology (implanted data loggers); trap development and trials;...

2012-01-23

363

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

the highest standards of noir suspense, TheGirlwiththeDragonTattoo.While readers are hooked by cunningGirlwith theDragonTattoo. Is that really a lot? Raymond Chandler'sTheBigSleep and FarewellMy Lovely (roughly they cluster around swamps? Do spells reach farther when they are cast by men or by women? Did spells work

California at Berkeley, University of

364

Friday, September 16, 2011 10am Opening remarks  

E-print Network

: Place, Space and Everyday Infrastructure Japonica Brown-Saracino Krista Paulsen Richard Lloyd Zachary Department of Sociology UIC Department of Political Science Symposium in celebration of Anthony Orum

Illinois at Chicago, University of

365

76 FR 40082 - Semiannual Regulatory Agenda  

Federal Register 2010, 2011, 2012, 2013

...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species from Python, Boa, and Eunectes Genera Legal Authority...the Lacey Act. The species are: Indian python (including Burmese python),...

2011-07-07

366

77 FR 7967 - Semiannual Regulatory Agenda  

Federal Register 2010, 2011, 2012, 2013

...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera Legal Authority...wildlife under the Lacey Act: Indian python (including Burmese python),...

2012-02-13

367

Aeronautics and Astronautics Helen Josephine,helenj@stanford.edu  

E-print Network

Aeronautics and Astronautics Helen Josephine,helenj@stanford.edu African Collection Karen Fung Engineering Helen Josephine,helenj@stanford.edu Engineering Helen Josephine,helenj@stanford.edu Feminist Documents: State and Local Kris Kasianovitz,krisk11@stanford.edu Hebraica and Jewish Studies Zachary Baker,zachary.baker

Wandless, Tom

368

Aligning social welfare and agent preferences to alleviate traffic congestion  

E-print Network

Aligning social welfare and agent preferences to alleviate traffic congestion Kagan Tumer Oregon State University 204 Rogers Hall Corvallis, OR 97331 kagan.tumer@oregonstate.edu Zachary T Welch Oregon traffic congestion, Kagan Tumer, Zachary T Welch and Adrian Agogino, Proc. of 7th Int. Conf. on Autonomous

Tumer, Kagan

369

Application of python-based Abaqus preprocess and postprocess technique in analysis of gearbox vibration and noise reduction  

Microsoft Academic Search

To reduce vibration and noise, a damping layer and constraint layer are usually pasted on the inner surface of a gearbox thin\\u000a shell, and their thicknesses are the main parameters in the vibration and noise reduction design. The normal acceleration\\u000a of the point on the gearbox surface is the main index that can reflect the vibration and noise of that

Guilian Yi; Yunkang Sui; Jiazheng Du

2011-01-01

370

Physics 212E Classical and Modern Physics Spring 2012 VPython Class 1: Introduction to Python/VPython  

E-print Network

= vector(0,1,0) · d = vector(1,0,0) · print(c + d) · print(dot(c,d)) · print(cross(c,d)) · print(mag with a print in it, execute the program you have written. You can do this from the pull-down Run menu, or you the shell window for outputs. · print(6+5) · print(2**3) · print(a-b) (Erase this command when you are done

Vollmayr-Lee, Ben

371

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

SciTech Connect

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.

Orndorff-Plunkett, Franklin

2011-05-01

372

The Unlock Project: a Python-based framework for practical brain-computer interface communication "app" development.  

PubMed

In this paper we present a framework for reducing the development time needed for creating applications for use in non-invasive brain-computer interfaces (BCI). Our framework is primarily focused on facilitating rapid software "app" development akin to current efforts in consumer portable computing (e.g. smart phones and tablets). This is accomplished by handling intermodule communication without direct user or developer implementation, instead relying on a core subsystem for communication of standard, internal data formats. We also provide a library of hardware interfaces for common mobile EEG platforms for immediate use in BCI applications. A use-case example is described in which a user with amyotrophic lateral sclerosis participated in an electroencephalography-based BCI protocol developed using the proposed framework. We show that our software environment is capable of running in real-time with updates occurring 50-60 times per second with limited computational overhead (5 ms system lag) while providing accurate data acquisition and signal analysis. PMID:23366434

Brumberg, Jonathan S; Lorenz, Sean D; Galbraith, Byron V; Guenther, Frank H

2012-01-01

373

Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations  

E-print Network

into close contact (see, for example, Rippe et al., 1995; Wasserman and Cozzarelli, 1986). This site juxtapo, no fruitful analytical approach has been found yet. Several simple theoretical models were proposed to account

Langowski, Jörg

374

EE 527 1: Introduction to Detection and Estimation Theory  

E-print Network

of handwritten digits. RELEVANT REFERENCES: [Kay, 1993, 1998, Hero, 2008, Bickel and Doksum, 2001, Poor, 1994, Gelman et al., 2004, Wasserman, 2003, Johnson, 2013]. Basic Concepts Figure 1: Statistical signal

Dogandzic, Aleksandar

375

Chapter 7 Social network analysis 7.1 Introduction  

E-print Network

and contacts on the Island described the community as "tight-knit", and spoke about extensive and active social social entities, and on the patterns and implications of these relationships" (Wasserman and Faust 1994 p

376

78 FR 44275 - Semiannual Regulatory Agenda  

Federal Register 2010, 2011, 2012, 2013

...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera...Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera Legal Authority...wildlife under the Lacey Act: Reticulated python, DeSchauensee's anaconda, green...

2013-07-23

377

ELLIS, JOSEPH. The RNA World: A Look at Ribonuclease P RNA, Small Nucleolar RNA, 6S RNA, and the Small Ribosomal Subunit. (Under the Direction of James W.  

E-print Network

, and Annabelle. Thank you for always listening, for always caring, and for all the smiles we shared along ACKNOWLEDGEMENTS I would like to thank my family Heather, Lauren, Zachary, and Annabelle for their love

Brown, James W.

378

Concatenations24 delegate feel welcome, but also  

E-print Network

Wells Editor, Designer: Zachary Adams Departnent of French and Italian University of Pittsburgh 1328 as babies and toddlers, but into old age when, as a neuroscientist found, "individuals with a higher degree

Jiang, Huiqiang

379

ALTERNATIVE RESOURCES FOR FUNDING AND SUPPORTING UNDERGRADUATE RESEARCH  

E-print Network

ALTERNATIVE RESOURCES FOR FUNDING AND SUPPORTING UNDERGRADUATE RESEARCH ZACHARY KUDLAK, ZEYNEP TEYMUROGLU, AND CARL YERGER Abstract. In a time where funding for programs on academic campuses around to find. We discuss some suggestions for funding and supporting undergraduate research programs

Yerger, Carl

380

77 FR 22786 - Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company  

Federal Register 2010, 2011, 2012, 2013

...Pinon Tree Holding Company, LLC, SKL Investment Group, LLC; Benjamin I. Lumpkin GRIT, with trustees Steven L. Grissom, all of...Sparks, and Zachary Whitten, all of Albuquerque, New Mexico; Benjamin I. Lumpkin, Chicago, Illinois; Elizabeth L. Celio,...

2012-04-17

381

Errata to the Seventh Printing (February 2005) "Acknowledgements," p. xl  

E-print Network

, David Bover, Logan Browne, Terry Brugger, Gordon Burns, Serdar Cabuk, Raymond Centeno, Yang Chen, Hak, Xiaohui Ye, Lara Whelan, John Zachary, Linfeng Zhang, Aleksandr Zingorenko, and to everyone in my computer

California at Davis, University of

382

Errata to the the Second Printing (March 25, 2003) "Graduate Level," p. xxxix [Steven Alexander  

E-print Network

Bizri, Logan Browne, Terry Brugger, Raymond Centeno, Michael Clifford, Christopher Clifton, Dan Coming Wal- cott, Dan Watson, Chris Wee, Paul Williams, Bonnie Xu, Xiaoduan Ye, Lara Whelan, John Zachary

California at Davis, University of

383

Errata to the Second Printing (December 2004) "Acknowledgements," p. xxxi  

E-print Network

Berman, Rafae Bhatti, Ziad El Bizri, David Bover, Logan Browne, Terry Brugger, Ralph Bunker, Serdar Cabuk Yang, Xiaoduan Ye, Lara Whelan, John Zachary, Linfeng Zhang, Aleksandr Zingorenko, and to everyone

California at Davis, University of

384

DEAN'S LIST HONORABLE MENTION Spring Semester 2013  

E-print Network

. Dischinger, Sarah Marie Dixit, Vineet A. Dogbevi, Kokou Serge Dow, Jessica Louise Doyle, Dakota Shea Drozd. Hays, Sean M. Heiland, Zachary Taylor Hellman, Brandon M. Hernandez, Steven A. Herrera, Brian Edward

Wong, Pak Kin

385

Weatherizing America  

ScienceCinema

As Recovery Act money arrives to expand home weatherization programs across the country, Zachary Stewart of Phoenix, Ariz., and others have found an exciting opportunity not only to start working again, but also to find a calling.

Stewart, Zachary; Bergeron, T.J.; Barth, Dale; Qualis, Xavier; Sewall, Travis; Fransen, Richard; Gill, Tony;

2013-05-29

386

2013/14 Membership MEMBER EMAIL PHONE FUNCTIONAL AREA DIVISION TERM ENDS  

E-print Network

of the President 2014 Mary Beth Zachary mzachar@bgsu.edu 3722054 Athletics Provost Joseph jjoseph@bgsu.edu 3729129 Student Support Provost 2016 Mary Ellen Kellow 2014 Tim Parish tparish@bgsu.edu 3728473 Technology Finance & Administration 2014 Adam

Moore, Paul A.

387

76 FR 72705 - Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company  

Federal Register 2010, 2011, 2012, 2013

...Minnesota, and Jenny Lynn Verner, Victoria, Minnesota, Zachary Miller Zacek...Minnwest Bank, M.V., Redwood Falls, Minnesota; Minnwest Bank South...Minnesota, and Minnwest Bank Sioux Falls, Sioux Falls, South Dakota. Board of...

2011-11-25

388

2012 Spring : Distinguished Honors Distinguished  

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Bailey Margaret Mackinnon Distinguished Baker Katherine Brennan Distinguished Baker Sarah Adrian Distinguished Baker-Whitcomb Annalise Frances Distinguished Bannister Shayna Rachel Distinguished Barber Zachary Distinguished Carrig Emily Anne Distinguished Carroll Kathryn Josephine Distinguished Carron Stephen Christopher

Kasman, Alex

389

Aeronautics and Astronautics Helen Josephine,helenj@stanford.edu  

E-print Network

Aeronautics and Astronautics Helen Josephine,helenj@stanford.edu African Collection Karen Fung Engineering Helen Josephine (Interim),helenj@stanford.edu Engineering Helen Josephine Baker,zachary.baker@stanford.edu History: American and British Benjamin Stone

Wandless, Tom

390

DEAN'S LIST HONORABLE MENTION Fall Semester 2013  

E-print Network

, Johnny Y. Befus, Phillip Michael Benjamin, Alyssa Jeane Bergsma, Ryan Kenneth Blacutt, Owen Humberto Nguyen, Lynn Q. Ning, Huirong Odle, Jesse Q. Oja, Zachary John Ollanik, Jordan Davis Ortiz, Ashton

Wong, Pak Kin

391

The School of Music of the College of Arts and Sciences  

E-print Network

Smerdon, Graduate Assistant and quartet coach Nathan Arnwine, Landon Brady, Tylar Bullion, Thomas, Daniel Styles, Tyler Wadsworth, bass UT Trombone Quartet: Nathan Arnwine, Tylar Bullion, Sean Copeland Robbins DFC's Original Four: Landon Brady, Zachary Cypcar, Kevin Ridder, Daniel Styles Tennessee

Tennessee, University of

392

Proclamation 3 College of Education 4  

E-print Network

.) Ronald V. Hite '64, President Mr. Jeffrey C. Taylor '85, President-Elect Ms. Renee Bays Lockhart '87, '89 of Education Ross Rowland, voting ex-officio, University of Tennessee, Knoxville Zachary Ross Walden, non

Karsai, Istvan

393

Traffic Congestion Management as a Learning Agent Coordination Problem  

E-print Network

Traffic Congestion Management as a Learning Agent Coordination Problem Kagan Tumer Oregon State University kagan.tumer@oregonstate.edu Zachary T. Welch Oregon State University welch@engr.orst.edu Adrian

Tumer, Kagan

394

Non-Mimetic Simulation Games: Teaching Team Coordination from a Grounding in Practice  

E-print Network

NON-MIMETIC SIMULATION GAMES: TEACHING TEAM COORDINATION FROM A GROUNDING IN PRACTICE A Dissertation by ZACHARY OLIVER DUGAS TOUPS Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements... 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...

Dugas Toups, Zachary Oliver

2011-10-21

395

Sculpture, Geometry and Computer Science  

E-print Network

;Python (programming) and VTK (graphics) } Install Python and IPython } Install Notepad++ editor (students used Windows) } Install binary VTK (for Python) [and matplotlib] } Python programming 101: (mention polygonal model) Sources e.g. points Filters e.g. glyphs Mappers Actors Renderer/ Window VTKpipeline from

Lumsdaine, Andrew

396

Labelling Operators (Programming tricks with MAMBA)  

E-print Network

, as erosions and dilations or filters with large structuring elements, can efficiently be designed in Python). However, many of them are implemented in Python. Compared to C, Python brings more flexibility even. In some cases, however, specific operators are needed. Implementing them in Python requires then some

Beucher, Serge

397

Bachelor Thesis June 11, 2012  

E-print Network

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 A.2 How is filtering performed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2 Software Evolution Storylines: The evolution of Python

Lanza, Michele

398

STILTS -Starlink Tables Infrastructure Library Tool Set Version 2.5-2  

E-print Network

.................................................................................................................. 16 4 JyStilts - STILTS from Python............................................................................................................................. 21 4.4 Table filter commands (cmd

Best, Philip

399

ACM Journal of Educational Resources in Computing, Vol. 3. No. 4, December 2003. Article 1. Pyro: A Python-based Versatile Programming  

E-print Network

­ Computer science education; I.6.7 [Simulation and Modeling]: Simulation Support Systems - Environments, advanced sensors, and motors (such as Sony's robot dog, Aibo, and ActivMedia's Pioneer) are becoming is granted without fee provided that the copies are not made or distributed for profit or commercial

Yanco, Holly A.

400

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

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

Jessica A. Lyons; Daniel J. D. Natusch

401

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

E-print Network

, University of Calgary and Alberta Children's Hospital Research Institute for Child and Maternal Health Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China; g

Chang, Belinda

402

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

E-print Network

phylogeneticlineagesutilize caudal luringto attractprey.Caudalluring involvesasnakewavingits tail ripsuchthatit resmblesalive.alcmabovethegroundimmediatelyorientedtowardsthefrog andbegantwitching its tail-tip rapidly.Thetail-tip wasvibrateda totalof 23timesoverthecowseof theoexlseveralhours.Thefirsa 17of thesevibrationsoccurredwith thetail held>2 cm abovethe head.Themale thenraisedits tail

Shine, Rick

403

JOURNAL OF THE EXPERIMENTAL ANALYSIS OF BEHAVIOR EFFECTS OF SPATIAL REARRANGEMENT OF OBJECT COMPONENTS ON  

E-print Network

perception by pigeons (for a review of re- search on pigeons' picture perception, see Wasserman, 1993 visual stimuli. Essential to Bieder- man's formulation is that the visual system parses complex visual in the pigeons' recognition accuracy from a mean of 80.5% correct to the original draw- ings to a mean of 52

Biederman, Irving

404

University Graduate School Academic Bulletin  

E-print Network

Heather Bradshaw*, Joshua Brown*, Brian D'Onofrio*, Karin Harman James*, Thomas W. James*, Michael Jones*, James T. Townsend*, Stanley Wasserman* Chancellors' Professors James C. Craig*, Robert L. Goldstone Jeffrey R. Alberts*, John E. Bates*, Geoffrey Bingham*, Sha- ron Brehm*, Jerome R. Busemeyer*, Thomas A

Indiana University

405

Robust Bayesian Methods for Monitoring Clinical Trials  

E-print Network

Robust Bayesian Methods for Monitoring Clinical Trials Joel B. Greenhouse and Larry Wasserman Revised: July 1994 ­1 #12; Robust Bayesian Methods for Monitoring Clinical Trials Summary Bayesian methods for the analysis of clinical trials data have received increasing attention recently as they offer an approach

406

ON THE IMPOSSIBILITY OF INFERRING CAUSATION FROM ASSOCIATION WITHOUT BACKGROUND KNOWLEDGE  

E-print Network

. Robins Departments of Epidemiology and Biostatistics, Harvard School of Public Health and Larry Wasserman, there exist methods for identifying causal relationships which are asymptotically (in sample size) correct are faithful to the causal graph. We argue that, in observational epidemiologic, econometric, and social

407

Designing and Prototyping Multimodal Commands Marie-Luce Bourguet  

E-print Network

between different interaction techniques. The CARE properties for example (Coutaz, 1995) are a framework in graphical user interfaces (Wasserman, 1985). A FSM typically consists of states, events, transitions and actions (see Figure 1). A transition has a source and a target state and is executed when the FSM

Bourguet, Marie-Luce

408

Experimental constraints on the thermodynamics and sound velocities of hcp-Fe to core pressures  

E-print Network

percent light elements [e.g., McDonough, 2003]. Iron is considered to be the most abundant element explored e-Fe's equation of state in general [e.g., Brown and McQueen, 1986; Mao et al., 1990; Wasserman et] and, in particular, its sound veloc- ities [e.g., Brown and McQueen, 1986; Mao et al., 2001; Nguyen

Jackson, Jennifer M.

409

Forest Density Estimation Anupam Gupta  

E-print Network

Forest Density Estimation Anupam Gupta , John Lafferty , Han Liu , Larry Wasserman , Min Xu School and density estimation in high dimensions, using a family of density estimators based on forest structured undirected graphical models. For density estimation, we do not assume the true distribution corresponds

Guestrin, Carlos

410

Search UNS... go University of Iowa News Release  

E-print Network

because it could be used in developing intelligent robots and visual prosthetics. The journal Current and Sciences Department of Psychology -- Ed Wasserman, Stuit Professor of Experimental Psychology. The fact that people and pigeons are so different gave researchers a better opportunity to see how general

Gosselin, Frédéric

411

Nature Macmillan Publishers Ltd 1998 1. Katz, A. M. Heart Disease and Stroke 1, 151154 (1992).  

E-print Network

Nature © Macmillan Publishers Ltd 1998 8 1. Katz, A. M. Heart Disease and Stroke 1, 151­154 (1992­771 (1996). 6. Komi, P. V. in Biochemistry of Exercise VI (ed. Saltin, B.) 529­575 (Human Kinetics. 3, 117­120 (1988). 12. Wasserman, D. H. & Vranic, M. in Biochemistry of Exercise VI (ed. Saltin, B

Nittler, Larry R.

412

BUSINESS SUBJECT GUIDE -I/S Business communication : building critical skills / Kitty O. Locker, Stephen Kyo  

E-print Network

of Marketing: A Canadian Perspective / David Notman, Jack Wilson HF5415.12.C2 N68 2003 (teacher's resource also and leadership / Edgar H. Schein HD58.7 .S33 2004 Textbooks: (textbooks on the Ontario Trillium List) Grade 9.N. Magnan, Alan Wasserman HF5351 .L54 2001 (teacher's resource also available) The World of Business 5th

Abolmaesumi, Purang

413

ANNUAL RESEARCH REPORT September 2006  

E-print Network

Elizabeth Fox Quality Control Catherine Bourgeois Mara Karapetian Elizabeth Kubicki Rhonda Maynard Anne Wasserman Publication Consultant Cheryl Slowik Proofreading Samuel C. Crooks Mara Karapetian Rhonda Maynard. Printer Next Generation Printing Special thanks to Sam Crooks, Rhonda Maynard, Cheryl Slowik and Anne

Reif, Rafael

414

Learning an object from multiple views enhances its recognition in an orthogonal rotational axis in pigeons  

E-print Network

in pigeons Jessie J. Peissig a,*, Edward A. Wasserman a , Michael E. Young b , Irving Biederman c training with only one view. Pigeons were taught with either five views or one view of each of four single-geon objects. Pigeons trained with five views responded more accurately to novel views of an object than did

Peissig, Jessie J.

415

Stein's Method and The Bootstrap in Low and High Dimensions  

E-print Network

D R A FT Stein's Method and The Bootstrap in Low and High Dimensions: A Tutorial Larry Wasserman February 8 2014 These notes give a brief tutorial on Stein's method and the bootstrap. The notes are divided into two parts. Part I is a review of Stein's method in the low dimensional case. Part II

Singh, Aarti

416

Protein Science (1994), 3:2419-2427. CambridgeUniversity Press. Printed in the USA Copyright 0 1994 The Protein Society  

E-print Network

Protein Science (1994), 3:2419-2427. CambridgeUniversity Press. Printed in the USA Copyright 0 1994 The Protein Society Disulfide crosslinks to probe the structure and flexibility of a designed four-helix bundle protein LYNNE REGAN, ARLENE ROCKWELL,'ZELDA WASSERMAN,' AND WILLIAM DEGRADO' The Experimental

Mochrie, Simon

417

Tuesday, April 23rd, 2013 | Spring 2013: Issue 12 Looking to get involved? Want to make a difference?  

E-print Network

's Hope in North Korea "A Look into North Korea's Unknown: Escape from Camp 14" NonProfit Opportunities for America, Hillel at Binghamton, and the Jewish Graduate Student Network will be presenting the movie "Won Wasserman. Tomorrow's Hope in North Korea "A Look into North Korea's Unknown: Escape from Camp 14" April 26

Suzuki, Masatsugu

418

Our Growing Planet  

NSDL National Science Digital Library

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

Lener, Elizabeth

2001-05-01

419

Exploratory Network Visualization: Simultaneous Display of  

E-print Network

drawing. We outline a customized approach. The advantages of our method are illustrated in a study of pol for substantive research questions. For a comprehensive overview of such methods see Wasserman and Faust (1994@uni-konstanz.de. Part of this research was done while with the Department of Computer Science at Brown University. I

Brandes, Ulrik

420

Stochastic Plans for Robotic Manipulation Kenneth Yigael Goldberg  

E-print Network

fostered a strong sense of solidarity in our lab that made this work a pleasure. I also thank the other discussions with the following colleagues: Srinivas Akella, Peter Allen, Dina Berkowitz, David Bourne, Johann, Dan Sleator, Rick Szeliski, Roy Taylor, Jeff Trinkle, Richard Wallace, Yu Wang, Larry Wasserman, Jon

Goldberg, Ken

421

A large percentage of the population in Bangladesh is highly exposed to arsenic and  

E-print Network

A large percentage of the population in Bangladesh is highly exposed to arsenic and manganese are even higher in portions of Araihazar, Bangladesh (the location of the current study), where 80 population in Araihazar, Bangladesh (Wasserman et al. 2006). Although the impact of manganese expo- sures

van Geen, Alexander

422

Detecting the community structure in complex networks based on quantum mechanics  

NASA Astrophysics Data System (ADS)

In this paper, we develop a novel method to detect the community structure in complex networks. This approach is based on the combination of kernel-based clustering using quantum mechanics, the spectral clustering technique and the concept of the Bayesian information criterion. We test the proposed algorithm on Zacharys karate club network and the world of American college football. Experimental results indicate that our algorithm is efficient and effective at finding both the optimal number of clusters, and the best clustering of community structures.

Niu, Yan Qing; Hu, Bao Qing; Zhang, Wen; Wang, Min

2008-10-01

423

77 FR 40865 - Privacy Act of 1974; System of Records  

Federal Register 2010, 2011, 2012, 2013

...Name: Naval Postgraduate School Education Management System (PYTHON) System Location: U.S. Naval Postgraduate School (NPS...Social Security Number (SSN). Safeguards: Access to the Python web interface occurs over encrypted channels. Periodic...

2012-07-11

424

ISSN0249-6399 de recherche  

E-print Network

of existing software for simulation applications, e.g. Matlab, Scilab, Python, OpenFOAM, Paraview, Python, OpenFoam, ParaView et des codes d'applications. La contribu- tion de ce rapport est une nouvelle

Paris-Sud XI, Université de

425

A toolkit for a Generative Lexicon Patrick HENRY  

E-print Network

it filters the adequate form of anaphoric reference to the modifier in endocentric compounds. 1 Introduction to use and free · Its use is cross-platform PYTHON [http://www.python.org/]: The choice of the language

Paris-Sud XI, Université de

426

30/06/2008 Wei Wang @ SEBD 2008 130/06/2008 1 Similarity Join Algorithms  

E-print Network

;30/06/2008 Wei Wang @ SEBD 2008 430/06/2008 4 Computers are dumb Numerical errors C:\\Users\\weiw>python ActivePython Applications Collaborative filtering Bioinformatics File/Document management systems Match-making services

Wang, Wei

427

A UNIFIED METHODOLOGY FOR SEISMIC WAVEFORM ANALYSIS AND INVERSION  

E-print Network

(sebastien.chevrot@cnes.fr). Other data analysis and inversion tools were developed using Python (http://www.python....................................................36 2.4.1 Effects of Windowing and Narrow-band Filtering on Target Waveform

Chen, Po

428

Prof. Amenta TA Jesse Smith  

E-print Network

, 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

California at Davis, University of

429

Stata Hybrids: Updates and Ideas  

NASA Technical Reports Server (NTRS)

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.

Fieldler, James

2014-01-01

430

Preprint version 3rd Int. Conf. on Simulation, Modeling, and Programming for Autonomous Robots, Tsukuba, Japan (2012) SwarmSimX: Real-time Simulation Environment  

E-print Network

strict constraints on the 1 #12;inner simulation timing (e.g., whenever requiring online processing/filtering be implemented in Python.Python is a highly portable, open source programming language and usually all code an extensive Python API enabling the user to easily add functionality to the simulation or any parts of it

431

Computing for Everyone: Introduction to Computing  

E-print Network

programming image filters, splicing and reversing sounds, im- plementing digital video special effects with a textbook (available now through Prentice-Hall), a programming environment (for Python), and a collaborative a communications skill. 2 Course Curriculum 2.1 Example Programs We teach Python (http://www.python

Guzdial, Mark

432

CSC326 Functional Programming CSC326 Functional Programming  

E-print Network

Programming in Python · Basic elements ­ map( func, list ) ­ reduce( func, list ) ­ filter( func, list Python code for "print big products" ----# bigmuls = lambda xs,ys: filter(lambda (x,y):x*y > 25, combine ) ­ lambda x : expr(x) 2 Eliminating if #------ "Short-circuit" conditional calls in Python -----# # Normal

Zhu, Jianwen

433

Constructing Media as a Context for Teaching Computing and  

E-print Network

programming image filters, splicing and reversing sounds, im- plementing digital video special effects with a textbook (available now through Pearson), a programming environment (for Python), and a collaborative.1 Example Programs We teach Python (http://www.python.org, specifically the Java-based variant Jython http

Guzdial, Mark

434

MobileComputing(EEC687) ProjectReport1  

E-print Network

communication system where components implemented in hardware are implemented in software (ex. Mixer, filters different signal processing functions 2. Python implement main application programming 3. SWIG works as glue between C++ classes and Python language. It is a Linux package that converts the C++ classes into Python

Yu, Chansu

435

Domain-Specific Languages in Few Steps The Neverlang Approach  

E-print Network

or redundant (e.g., Python's map/filter/reduce and list comprehensions) and contribute to make the language the Neverlang framework and try out its benefits in a case study that merges functional programming à la Python programming languages support different program- ming paradigms, such as Erlang [25], Python [19] and Scala

Cazzola, Walter

436

University of Hertfordshire Dept. of Computer Science  

E-print Network

to guess the result first without actually running the Python code. Assignment 4.7 Challenge: Using filter, write a Python function by_3(n) that prints out all numbers up to (but not including) n a particular use). Assignment 4.14 Challenge: Consider the string sequence Data AGAATAGAGAATCGAT Write a Python

Polani, Daniel

437

Adapted from Richard P. Muller 1 OutlineOutline  

E-print Network

.caltech.edu/home/rpm/python_course/python_quick.html Python Quick Reference ­ http://www.ibiblio.org/obp/thinkCSpy How to think like a computer scientist scripts ­ Make file executable: % chmod +x myprogram.py ­ The first line of the program tells the OS how

Reluga, Tim

438

Observation of Quantum Shock Waves Created with Ultra-  

E-print Network

-Einstein Condensate Zachary Dutton,1,2 Michael Budde,1,3 Christopher Slowe,1,2 Lene Vestergaard Hau1,2,3 We have used over which the density of a condensate can adjust. Bose-Einstein condensates (BECs) of al- kali atoms

Hau, Lene Vestergaard

439

Ecology, 93(8), 2012, pp. 18671879 2012 by the Ecological Society of America  

E-print Network

Ecology, 93(8), 2012, pp. 1867­1879 ? 2012 by the Ecological Society of America Mapping the niche space of soil microorganisms using taxonomy and traits JAY T. LENNON,1,2,3 ZACHARY T. AANDERUD,1,4 B. K dry optima (0.3 MPa) and were capable of respiring under low water potentials (?2.0 MPa). Within

Bruns, Tom

440

TheDean'sHonorList 2007-2008 The Faculty of Science congratulates the following students who have earned a place on the Dean's List. To be  

E-print Network

Andrighetti Daniyal Ansari Stefi Anthonipillai Zachary Armstrong Thomas Vining Armstrong Nathan Armstrong Ryan Christine Berger Lesley Bergman Tanya Elizabeth Berkers Kathryn Bezzina Anaita Bharucha Amanpreet Bhathal Justin Thomas E Bondy Hyeeun Boo Hilary Booth Erica Borchiver Jordana Boro Rachael Bosma Cameron Wayne

Sinnamon, Gordon J.

441

Donors to the 2012 Hunter College Mother's Day Scholarship Fund Women who went to Hunter College taught their children a love of learning and the desire to excel.  

E-print Network

. Neil E. and Lesley Green, Dr. Alan I. and Frances Green, Dr. Mark R. and Judith Green of their grandmother Lenora Marcus Gottfried '35 Thomas and Stephen Orphanos in honor of their mother Nunzia D, Thomas Brown and Chagit Steiner; Dr. Caroline and Mark Teichman, Jessica, David, Jared, Zachary

Qiu, Weigang

442

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

E-print Network

BAYESIAN SEGMENTATION OF CHEST TUMORS IN PET SCANS USING A POISSON-GAMMA MIXTURE MODEL Zacharie is derived from PET physics, models tissue activity using a mixture of Poisson- Gamma distributions. Moreover, a Markov field is proposed to model the spatial correlation between mixture compo- nents. Then

Dobigeon, Nicolas

443

Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic  

E-print Network

strategy for glioblastoma Paul H. Huang*, Akitake Mukasa , Rudy Bonavia , Ryan A. Flynn*, Zachary E. Brewer for review May 14, 2007) Glioblastoma multiforme (GBM) is the most aggressive brain tumor in adults transduction tyrosine phosphorylation Glioblastoma multiforme (GBM) is the most aggressive form of adult human

444

The nucleotide receptor P2X7 mediates actin reorganization and membrane blebbing in RAW 264.7 macrophages via  

E-print Network

.7 macrophages via p38 MAP kinase and Rho Zachary A. Pfeiffer, Mini Aga, Usha Prabhu, Jyoti J. Watters,1 David JATP), resulting in Ca2 and Na influx and K efflux [3]. P2X7 also forms a nonselective pore that is permeable

Bertics, Paul J.

445

Dhanya Mary Abraham Reece Larson Adamson  

E-print Network

Curran Tapan Paresh Dalal Tara Lin D'Ambruoso Zachary James D'Amico David Clark Daniels Corey Danko Ian Wilhelm Bentley Janyu Jaimini Bhatt Siena Arcuri Biales Daniel John Bibisi James Alexander Bickerstaff James R Boivie John William Bojorquez Lindsey Elizabeth Bonitz Olivia Ann Bonner Dean's List Spring 2014

Lozano-Robledo, Alvaro

446

Particle Size Classification of Glass Particles Using Aerodynamic Jet Vectoring  

E-print Network

that an air sample con- taining water-like particles can be concentrated by a fac- tor of 10 using AVPSParticle Size Classification of Glass Particles Using Aerodynamic Jet Vectoring Zachary E. Humes processes, it is desir- able that the powder be comprised of particles of a rela- tively uniform size

Smith, Barton L.

447

ORIGINAL RESEARCH ARTICLE published: 01 July 2013  

E-print Network

ORIGINAL RESEARCH ARTICLE published: 01 July 2013 doi: 10.3389/fncom.2013.00085 Short term synaptic depression improves information transfer in perceptual multistability Zachary P. Kilpatrick* Department, Israel Reviewed by: Andre Longtin, University of Ottawa, Canada Paolo Del Giudice, Italian National

Kilpatrick, Zachary P.

448

Attempts at a Feminist and Interdisciplinary Conversation About Strip Clubs  

Microsoft Academic Search

In this essay, we analyze two recent publications in Deviant Behavior on the consumption of exotic dance: Behavioral and Interactional Patterns of Strip Club Patrons: Tipping Techniques and Club Attendance by Zachary Brewster and The Gentlemen in the Club: A Typology of Strip Club Patrons by Erickson and Tewksbury. In so doing, we map their lack of engagement with feminist

R. Danielle Egan; Katherine Frank

2005-01-01

449

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

E-print Network

- 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

Nelson, Randy J.

450

J Neuroimmune Pharmacol DOI 10.1007/s11481-012-9346-3  

E-print Network

of Complement Receptor 1 (CR1/CD35) Protein Clustering in Human Erythrocytes Zachary J. Lapin · Christiane-field optical microscopy. Recent studies have demonstrated that levels of A peptide, associated with Alzheimers-dependent adherence to CR1. It is unknown why patients with AD have a markedly impaired ability to bind A to CR1 via

Novotny, Lukas

451

Smathers Ocean Circulation and its Effect on Climate Change  

E-print Network

1 Ocean Circulation and its Effect on Climate Change Zachary Smathers At the turn of the 20th of warfare. Scientists began asking questions about the climate and how determining the World's oceans were when it came to climate change. Did the chemical makeup of the oceans matter? Why were there trends

Marzuola, Jeremy

452

Book Editors IOS Press, 2003  

E-print Network

for Computer Science Education David E. Price, Ellen Riloff, Joseph L. Zachary School of Computing, University of Utah, Salt Lake City, UT 84112 Abstract. Programming language syntax is a barrier to learning in a lecture (Figure 1). Our goal is to enable students to work at a higher level of abstraction by allowing

Riloff, Ellen

453

Team Project: Team Design Specification CSCE 121 Spring 2011 (507, 508) this work is licensed under a Creative Commons Attribution-ShareAlike 3.0  

E-print Network

. Think about the game you have selected, and consider how the game rules map to code. Take into account game), what options are available to the player? How are those options created in code? (For example under a Creative Commons Attribution-ShareAlike 3.0 Unported License by Zachary O. Toups 1 Team Game

Toups, Zach

454

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

E-print Network

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

Bierlaire, Michel

455

1/28/2014 CFCAM Workshop 2014 1 How to generate ^ PAW Atomic Datasets*  

E-print Network

), Nicholas Lepley , Qi Li (WFU graduate students), James Drewery Cameron Kates, Zachary Pipkorn (WFU undergraduate students), Alan Wright (Sandia National Laboratory), Alan Tackett, Greg Walker, Rachael Hansel code version 4.x series, based on machine optimization approach. (Original idea from Alan Wright

Holzwarth, Natalie

456

A SHAPE ANALYSIS FRAMEWORK FOR SMALL ANIMAL PHENOTYPING WITH APPLICATION TO MICE WITH A TARGETED DISRUPTION OF HOXD11  

E-print Network

A SHAPE ANALYSIS FRAMEWORK FOR SMALL ANIMAL PHENOTYPING WITH APPLICATION TO MICE WITH A TARGETED DISRUPTION OF HOXD11 Joshua Cates , P Thomas Fletcher , Zachary Warnock and Ross Whitaker Scientific Computing and Imaging Institute Howard Hughes Medical Institute University of Utah, Salt Lake City, UT, USA

Utah, University of

457

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

E-print Network

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

Johnston, Daniel

458

Dean's List College of Physical and Mathematical Sciences  

E-print Network

/term. Name Major Jeffrey Thomas Andersen Computer Science Jordan Anderson Mathematics Zachary Scott Anderson Brogan Mathematics Sarah Kaiulani Kimiko Brown Geology Trent Matthew Burke Computer Science Jacob Paul Science Joseph Lawrence Physics Jessica Charlene Leete Mathematics Ty G Lewis Computer Science Jennifer

Hart, Gus

459

VOLUME 76, NUMBER 8 P H Y S I C A L R E V I E W L E T T E R S 19 FEBRUARY 1996 Large Local-Field Corrections in Optical Rotatory Power of Quartz and Selenium  

E-print Network

-Field Corrections in Optical Rotatory Power of Quartz and Selenium Lars Jönsson,1 Zachary H. Levine,1,2 and John W al. [3] calculated the optical rota- tory power for a-quartz and selenium. Their results are too

Wilkins, John

460

FREIGHT RAILROAD CAPACITY ALTERNATIVES IN THE PACIFIC NORTHWEST: AN ANALYSIS OF CLASS I COOPERATION IN THE COLUMBIA RIVER GORGE  

E-print Network

IN THE COLUMBIA RIVER GORGE by ZACHARY HOROWITZ A research project report submitted in partial fulfillment River Gorge Freight railroad traffic volumes are now at or approaching capacity in the Pacific Northwest, especially in the Columbia River corridor. Two Class I carriers operate alongside the river: BNSF Railway

Bertini, Robert L.

461

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

E-print Network

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

Cui, Yan

462

General Assembly Meeting: September 23, 2012 Opening of the Meeting: Meeting called to order at 7:04pm  

E-print Network

for universities and colleges (smaller line graph) 2. Student Charges (72% of the operating Budget) 3. Tuition has gone up significantly (much higher than inflation) a. Roth: The reason why the middle class has been squeezed out b. Zachary Malter: Still the question of whether or not people will apply depending

Royer, Dana

463

Conklin, Lindsey Leigh Cota Carrasco, Daigaro Juan P.  

E-print Network

, Sean M. Hegedus, Kevin R. Henry, Chase Howard Henry, Samantha C. Hernandez, Kari Hernandez, Kenji, Cassie Marie Parades, Carlos A. Petrie, Cody Walker Playford, Alyssa Nicole Prince, Zachary Pyne, Jeffrey Rogan, Sarah C. Rojas, Nicole Marie Ross, Maxwell E. Ruanto, Russell Reyes Rundel, Kira Salsbury, Chase

Wong, Pak Kin

464

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

E-print Network

Effects of Experience on Short- and Long-term Foraging Performance in Bumblebees Zachary Durisko for short-term improvements owing to the factors just mentioned exists for both honeybees and bumblebees (e studied bumblebees foraging on pepper plants inside a greenhouse. This allowed us to combine the global

Dukas, Reuven

465

Local-Search based Approximation Algorithms for Mobile Facility Location Problems  

E-print Network

Local-Search based Approximation Algorithms for Mobile Facility Location Problems Sara Ahmadian Zachary Friggstad Chaitanya Swamy Abstract We consider the mobile facility location (MFL) problem. We is wi times the distance traveled by i. 1 Introduction Facility location problems have been widely

Swamy, Chaitanya

466

LocalSearch based Approximation Algorithms for Mobile Facility Location Problems  

E-print Network

Local­Search based Approximation Algorithms for Mobile Facility Location Problems Sara Ahmadian # Zachary Friggstad # Chaitanya Swamy # Abstract We consider the mobile facility location (MFL) problem. We is w i times the distance traveled by i. 1 Introduction Facility location problems have been widely

Swamy, Chaitanya

467

NODE CONNECTIVITY AND CONDITIONAL DENSITY D. White and F. Harary Definitions of Cohesive Sets in Social Networks  

E-print Network

, are exemplified in the following analysis of conflict and solidarity in a karate club, an excerpt of part IV's Karate Club Zachary's (1975, 1977) two-year ethnographic network study of 34 members of a karate club were the karate teacher (T, #1, Mr. Hi) and the club administrator (A, #34, John) and the dispute

White, Douglas R.

468

DEAN'S LIST Spring Semester 2013  

E-print Network

DeForest, Armand Walter Dennis, Steven T. Dow, Luz M. Duffy, Breanna Durbin, John R. Dwyer, Jonathan.engineering.arizona.edu Abdul-Wahid, Maryam Alia Adkins-Rieck, Ruben C. Akins, David John Alanis, Tyler Aldaghi, Maya M. Aleem Henry Elwood, Teri Alida Espiritu, Daniella M. Ezeugwu, Rita Ferell, Benjamin W. Fier, Zachary Joseph

Wong, Pak Kin

469

Peer Mentoring and Action Learning  

ERIC Educational Resources Information Center

Mentoring has been defined in many different ways. Traditionally, mentoring is seen as a relationship between an older, more experienced mentor and a younger, less experienced protege for the purpose of helping and developing the protege's career. Zachary's (2005) description best fits the process discussed in this article: "Mentoring is best

O'Neil, Judy; Marsick, Victoria J.

2009-01-01

470

"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

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:

National Multicultural Inst., Washington, DC.

471

TO: MEMBERS OF THE UC DAVIS DIVISION OF THE ACADEMIC SENATE SUBJECT: INTEGRATION OF STUDY ABROAD INTO UC DAVIS CURRICULA  

E-print Network

-297-4637) and Zachary Frieders (zjfrieders@ucdavis.edu or 530-297-4638), and Peter Schiffman, Faculty Director--Office of University Outreach and International Programs Peter Schiffman Director, Education Abroad Center #12;FAQs of the Education Abroad Center, Peter Schiffman, and the Academic Integration Coordinators, Joel Shriver

Islam, M. Saif

472

Probing and Controlling Photothermal Heat Generation in Plasmonic Nanostructures  

E-print Network

Probing and Controlling Photothermal Heat Generation in Plasmonic Nanostructures Zachary J. Coppens, Joule heating associated with optically resonant plasmonic structures is exploited to generate nanoscale by incorporating the diabolo antenna into a plasmonic lens. Using a newly developed thermal microscopy method based

Simaan, Nabil

473

Student Name Faculty Advisor Student Name Faculty Advisor Student Name Faculty Advisor Abbadini, Jarred R. H. Elsayed-Ali Batchelder, Kelly M. L. Belfore Carden, Ryan P. R. Joshi  

E-print Network

, Jarred R. H. Elsayed-Ali Batchelder, Kelly M. L. Belfore Carden, Ryan P. R. Joshi Adams, Zachary J. V. Li Dowd, Brian A. R. Joshi Hammock, Thomas V. J. Li Khan, Jafar H. L. Belfore Downs, Amanda J. O. Lakdawala Begay, Seth J. J. Li Carr, Joshua D. L. Belfore Afandi, Esam N. H. Elsayed-Ali Belfore, Harry A. L

474

International Development Interdisciplinary Studies Program Graduate Program Checksheet  

E-print Network

-Socially Responsible Apparel 1 Development in Indian Country Women, Health and Culture Globalization and Cultural Engineering Carol Hammerdofer Global, Social and Sustainable Enterprise Brian Jones Physics Zachary Johnson Children and Youth in Global Context IE/PSY 517 3 Perspectives in Global Health IE/PHIL 550 P 3 Ethics

475

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

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:

2002

476

Paul E. Stanton, Jr. University President  

E-print Network

-008-10 75M Lieutenant General (ret.) Ronald V. Hite '64, President Mr. Jeffrey C. Taylor '85, President-voting ex­officio, Executive Director, State Board of Education Ross Rowland, voting ex­officio, University of Tennessee, Knoxville Zachary Ross Walden, non­voting ex-officio, East Tennessee State University tennessee

Karsai, Istvan

477

Paul E. Stanton, Jr. University P resident  

E-print Network

-008-10 75M Lieutenant General (ret.) Ronald V. Hite '64, President Mr. Jeffrey C. Taylor '85, President-voting ex­officio, Executive Director, State Board of Education Ross Rowland, voting ex­officio, University of Tennessee, Knoxville Zachary Ross Walden, non­voting ex-officio, East Tennessee State University tennessee

Karsai, Istvan

478

University of Southern California Mork Family  

E-print Network

of chemical warfare agents (with Nitin Nair, Fokion Egolfopoulos, and Theodore T. Tsotsis) Zachary LingleyUniversity of Southern California Mork Family Department of Chemical Engineering and Materials embryonic stem cells via an engineered baculoviral vector carrying zinc finger nucleases (with Pin Wang) 12

Southern California, University of

479

Richard M. Lehtinen The College of Wooster  

E-print Network

-Instructor: "Introduction to the Biology of Populations" (BIOL 230), 2003- 2004, 2006. Co-Instructor: "Gateway to Ecology-zygotic isolation mechanism in two species of hybridizing salamanders: Is it effective? Levi Fawcett ('15): Field traits in a captive population of red ruffed lemurs. Zachary Bradley ('14): Surveys of freshwater fish

Wilson, Mark A.

480

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

E-print Network

and Robert Engel Department of Chemistry and Biochemistry, Queens College-CUNY, Flushing, NY 11367 We Geneva S. Meredith, Ya-Ching Hung and Simone V. Gill Department of Family Nutrition and Exercise Sciences Ligand Zachary M Adler, Thomas C. Strekas and Robert Engel Department of Chemistry & Biochemistry, Queens

Engel, Robert

481

Making Colonial Subjects: Education in the Age of Empire  

ERIC Educational Resources Information Center

This article explores two attempts to envisage a new global world, one created by the West, and to create new colonial subjects. One of these attempts was in Sierra Leone in the 1790s, the other in India in the 1830s. The two case studies are seen through the lens of a father and son, Zachary and Thomas Babington Macaulay, each a representative

Hall, Catherine

2008-01-01

482

&U N I V E R S I T Y O F S A S K ATC H E WA N S P R I N G 2014 ALUMNI OF INFLUENCE EDITION  

E-print Network

in a competitive world 14 Arctic Intelligence | Trevor Pritchard (BA'01) Michael Byers, one of Canada's foremost Taggart Tasha Hubbard explores the history of the buffalo through film 22 Portfolio: Zachari Logan | Betsy to Mars & Associate Professor of Chemistry Lee Wilson and students gather in a lab in the Thorvaldson

Saskatchewan, University of

483

Developing operational algorithms using linear and non-linear squares estimation in Python for the identification of Culex pipiens and Culex restuans in a mosquito abatement district (Cook County, Illinois, USA).  

PubMed

In this research, community level spatial models were developed for determining mosquito abundance and environmental factors that could aid in the risk prediction of West Nile virus (WNv) outbreaks. Adult Culex pipiens and Culex restuan mosquitoes and multiple habitat covariates were collected from nine sites within Cook County, Illinois, USA, to provide spatio-temporal information on the abundance of WNv vectors from 2002 to 2005. Regression analyses of the sampled covariates revealed that the adult Culex population was positively associated with temperature throughout the sampling frame. The model output also indicated that precipitation was negatively associated to mosquito abundance in 2002, 2003 and 2005 (P <0.05), but positively associated in 2004 (P <0.05). A land use land cover classification, based on QuickBird visible and near infra-red data, acquired at 0.61 m resolution, was used to investigate possible associations between geographical features and the abundance of sampled Culex oviposition surveillance sites. A maximum likelihood unsupervised classification in ArcInfo 9.2(R) revealed that the highest overall mosquito abundance was found in sites having a low-to-moderate range of built environment (40%) and high forest composition. A set of propagation equations were then designed to model the calibration uncertainties, which revealed that normalized difference vegetation index (NDVI), and two NDVI variants, were informative markers for the sampled mosquito data. Spatial dependence of the covariates of Cx. restuans and Cx. pipiens oviposition sites were indexed using semivariograms, which suggested that all main effects of the explanatory variables were statistically significant in the model. Additionally, a multispectral classification and digital elevation model-based geographical information system method were able to evaluate stream flow direction and accumulation for identification of terrain covariates associated with the sampled habitat data. These results demonstrate that remotely sensed operational indices can be used to identify parameters associated with field-sampled Cx. pipiens and Cx. restuans aquatic habitats. PMID:19440960

Jacob, Benjamin J; Gu, Weidong; Caamano, Erik X; Novak, Robert J

2009-05-01

484

The Hidden Web  

Microsoft Academic Search

d phenomenon;namely, the social network that links all people.In the 1960s, Stanley Milgram's (1967)pioneering work on the small-world problemshowed that any two randomly chosen individualsin the United States are linked by achain of six or fewer first-name acquaintances.Researchers have replicated this phenomenonin many contexts, ranging fromgroups of workers within a corporation(Wasserman and Galaskiewicz 1994; Krackhardtand Hanson 1993) to patterns of

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

1997-01-01

485

Summary of Toward a Global Media Ethics: Theoretical Perspectives  

Microsoft Academic Search

This is a summary of Toward a Global Media Ethics: Theoretical Perspectives, which appeared in Ecquid Novi: African Journalism Studies, 29(2), 2008, 135172. The article was written by Clifford G. Christians, University of Illinois at Urbana-Champaign; Shakuntala Rao, State University of New York-Plattsburgh; Stephen J. A. Ward, University of Wisconsin-Madison; and Herman Wasserman, University of Sheffield. It was the result

Stephen J. A. Ward

2010-01-01

486

The Impact of Electronic Trading Technology  

Microsoft Academic Search

\\u000a ROBERT SCHWARTZ: Rich Holowczak is head of the Wasserman Trading Floor Subotnick Center here at Baruch College. Rich is\\u000a my colleague, a friend and also a co-author. Please welcome him.\\u000a \\u000a \\u000a RICHARD HOLOWCZAK: Thanks Bob. The professor in me wants to get some definitions out of the way. So, my first question for\\u000a the panel is, what do you consider

Richard Holowczak; Leslie Boni; Kevin Callahan; Alfred Eskandar; James Leman; Robert McCooey; Joseph Wald

487

Product Individuality of Commercially Available Low-Molecular-Weight Heparins and Their Generic Versions: Therapeutic Implications  

Microsoft Academic Search

The currently available brand-name low-molecular-weight heparins (LMWHs) in the United States include dalteparin (Pfizer), enoxaparin (Aventis), and tinzaparin (Pharmion). Other products available, in Europe, include certoparin (Novartis), reviparin (Abbott), nadroparin (GlaxoSmithkline), and parnaparin (Alpha-Wasserman). Each of these LMWHs has a characteristic molecular weight profile and biological activity in terms of an anti-FXa and anti-FIIa potency. The mean molecular weight of

Jyothi Maddineni; Jeanine M. Walenga; Walter P. Jeske; Debra A. Hoppensteadt; Jawed Fareed; Rakesh Wahi; Rodger L. Bick

2006-01-01

488

Characterization of the Breakdown of Magnetospheric Polarization Models  

NASA Astrophysics Data System (ADS)

Radio emission from pulsars contain valuable information about geometry of the pulsar. In particular, polarization angle curves can be related to geometry via the popular rotating vector model. A modification to the rotating vector model proposed by Blaskiewicz, Cordes, and Wasserman (1991) allows for the additional measure of the emission height. At large heights, these analytic formulas break down. By comparing the analytic formulas to numerical simulations of emission we have performed probabilistic analysis to more precisely define this breakdown.

Craig, Helen A.; Romani, R. W.

2012-01-01

489

Orbital stability in combined uniform axial and three-dimensional wiggler magnetic fields for free-electron lasers  

NASA Technical Reports Server (NTRS)

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.

Johnston, S.

1984-01-01

490

EcoCast: Interactive, object-oriented macroprogramming for networks of ultra-compact wireless sensor nodes  

Microsoft Academic Search

EcoCast is an execution framework for macroprogramming of wireless sensor networks. Users access sensor nodes as dynamic objects in Python by invoking methods on them without being concerned with network protocols, and type marshalling and demarshalling ensure proper data access. EcoCast extends Pythons functional programming primitives map(), reduce(), and filter() to macroprogramming with several synchrony semantics and job-control options. EcoCast

Yi-Hsuan Tu; Yen-Chiu Li; Ting-Chou Chien; Pai H. Chou

2011-01-01

491

THEJOURNALOF BIOLOGICALCHEMISTRY ( 0 1992 by The American Society for Biochemistryand Molecular Biology, Inc.  

E-print Network

, February20, 1992) Daniel W. Carr, Zachary E. Hausken, lain D. C. Fraser$, RenataE. Stofko-Hahn, and John.E., Fraser, I. D.C., Bishop, S. M., Acott, T. E., Brennan, R. G.,and ScottJ. D. (1991)J. Biol. Chem. 266 sequenceswhich exhibit a high prob- ability of amphipathic helix formation (Carr, D. W., Stofko-Hahn, R

Scott, John D.

492

Combinatorial Laplacian and entropy of simplicial complexes associated with complex networks  

NASA Astrophysics Data System (ADS)

Simplicial complexes represent useful and accurate models of complex networks and complex systems in general. We explore the properties of spectra of combinatorial Laplacian operator of simplicial complexes and show its relationship with connectivity properties of the Q-vector and with connectivities of cliques in the simplicial clique complex. We demonstrate the need for higher order analysis in complex networks and compare the results with ordinary graph spectra. Methods and results are obtained using social network of the Zachary karate club.

Maleti?, S.; Rajkovi?, M.

2012-09-01

493

Local method for detecting communities  

NASA Astrophysics Data System (ADS)

We propose a method of community detection that is computationally inexpensive and possesses physical significance to a member of a social network. This method is unlike many divisive and agglomerative techniques and is local in the sense that a community can be detected within a network without requiring knowledge of the entire network. A global application of this method is also introduced. Several artificial and real-world networks, including the famous Zachary karate club, are analyzed.

Bagrow, James P.; Bollt, Erik M.

2005-10-01

494

Patterns of Cognitive Decline in Alzheimer's Dementia: An Application of Hierarchical Bayesian Multiphase Models  

E-print Network

on at least 9 occasions from archival data in a study of healthy aging and dementia. Positive neuropathol- ogy at autopsy or sustained occupancy in non-zero Clinical Dementia Ratings (CDR) were used to determine disease presence (Section 2.2). A summary...Patterns of Cognitive Decline in Alzheimers Dementia: An Application of Hierarchical Bayesian Multiphase Models By Zachary Denver Langford Submitted to the Department of Psychology and the Faculty of the Graduate School of the University of Kansas...

Langford, Zachary Denver

2012-12-31

495

Are you good at math and science? Spend 4 weeks at MIT this summer  

E-print Network

introduces students to thinking computationally to solve problems and programming in Python, and is designed and sequential logic, transistors, counters, resistor networks, RC filters, operational amplifiers, rectification

Williams, Brian C.

496

McGill University School of Computer Science  

E-print Network

operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3.6 Error.4 VRRuntime performance optimizations . . . . . . . . . . . . . . . . . . . . . . . . . 13 6 Design Speedup of Velociraptor generated code over Python interpreter on machine with Nvidia GPU

Verbrugge, Clark

497

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).

498

ISSN0249-6399 de recherche  

E-print Network

the smooth integration of existing software, e.g. Matlab, Scilab, Python, OpenFOAM, Paraview and user'intégration de logiciels existants comme MatLab, Scilab, Python, OpenFOAM et ParaView et de programmes utilisa

Boyer, Edmond

499

VPython  

NSDL National Science Digital Library

VPython is a 3D programming language developed at Carnegie Mellon University that is useful for presenting visualizations of physical phenomena. VPython is free and open-source. It includes: the