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1

Python programming --Pythonish python Finn Arup Nielsen  

E-print Network

Python programming -- Pythonish python Finn °Arup Nielsen DTU Compute Technical University of Denmark November 4, 2013 #12;Pythonish python Overview "Pythonic": Writing Python the Python way. Langtangen's list of Pythonic programming Special Python constructs: class variables, generators

2

Python programming --numeric Python Finn Arup Nielsen  

E-print Network

Python programming -- numeric Python Finn °Arup Nielsen DTU Compute Technical University of Denmark September 10, 2013 #12;Python programming -- numeric Python Python numerics The problem with Python: >>> [1, 2, 3] * 3 Finn °Arup Nielsen 1 September 10, 2013 #12;Python programming -- numeric Python Python

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

Introduction into Python Python 4: Advanced Features  

E-print Network

Introduction into Python Python 4: Advanced Features Daniel Polani Daniel Polani: Introduction into Python ­ p.1/?? Looping in Dicts Input >>> knights = {'gallahad': 'the pure', 'robin': 'the brave: Introduction into Python ­ p.2/?? Enumerating Iteration Input >>> for i, v in enumerate(['tic', 'tac', 'toe

Polani, Daniel

5

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

E-print Network

-Chair of the Laboratory's New Technology Initiative (NTI) Board. Mr. Lemnios was the Director of the Defense Advanced Research Projects Agency (DARPA) Microsystems Technology Office (MTO) as well as the Deputy DirectorHonorable Zachary J. Lemnios The Honorable Zachary J. Lemnios was sworn in as Director, Defense

6

Sun-Sentinel Red hot email heats up Wasserman Schultz,  

E-print Network

to the kerfuffle. Former U.S. Rep. Mark Foley, R-Palm Beach Gardens, said it was "almost made for the Jerry West's Deerfield Beach campaign headquarters. She charged that West was associated with viciousSun-Sentinel Red hot email heats up Wasserman Schultz, West rift South Florida members of Congress

Belogay, Eugene A.

7

Alligator and Python Struggle  

USGS Multimedia Gallery

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

8

Packaging Python code and Sphinx 1 Python packages  

E-print Network

Packaging Python code and Sphinx 1 Python packages extending Python with your own package making the Python interface phcpy 3 Documenting Software with Sphinx Sphinx generates documentation generating) Packaging Python code and Sphinx 7 October 2013 1 / 41 #12;Packaging Python code and Sphinx 1 Python

Verschelde, Jan

9

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,

10

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

11

Python and Web Development  

E-print Network

Python and Web Development An overview James Crasta Monday, November 23, 2009 #12;Why Python? (in packages · Interactive Console, no recompile cycle Monday, November 23, 2009 #12;Why Python? (on the web, November 23, 2009 #12;Who uses Python? · Google (App Engine) · Amazon.com · NewYork Times (Represent

Ge, Qiaode Jeff

12

Python praktikum Alessandro Mammana  

E-print Network

Python praktikum Alessandro Mammana 10.10.2014 Max Plank Institute for Molecular Genetics #12 (1-2 hours) free time (until 18:00) #12;Python: pros and cons Pros: ­ easy to write and to read(less)+equal+sort(greater) #12;Python is interactive ~> python3 Python 3.3.0 (default, Dec 5 2012, 11:05:54) [GCC 4.7.1] on linux

Spang, Rainer

13

Introduction into Python Python 1: Examples, Variables, Scalars and Lists  

E-print Network

Introduction into Python Python 1: Examples, Variables, Scalars and Lists Daniel Polani Daniel Polani: Introduction into Python ­ p.1/?? Why Python? Properties: minimalistic syntax powerful high procedurality Daniel Polani: Introduction into Python ­ p.2/?? Where to get Python and Learn More? Web Site

Polani, Daniel

14

Data Mining using Python --exercises for numeric Python  

E-print Network

Data Mining using Python -- exercises for numeric Python Finn °Arup Nielsen DTU Compute Technical University of Denmark September 15, 2014 #12;Python programming -- exercises for numeric Python File reading with NumPy! Finn °Arup Nielsen 1 September 15, 2014 #12;Python programming -- exercises for numeric Python

15

Python programming --introduction to Python Finn Arup Nielsen  

E-print Network

Python programming -- introduction to Python Finn °Arup Nielsen DTU Compute Technical University of Denmark September 9, 2013 #12;Python programming -- introduction Content Invoking Python A basic program 9, 2013 #12;Python programming -- introduction Invoking python . . . From the command line

16

Python Java Mathematical Operators  

E-print Network

2/25/2014 1 Python Java 2 Mathematical Operators Python Java + + - - * * / / ** Math.pow(x, y with -- Division · The same in Python and Java 10 / 4 returns 2 10.0 / 4.0 returns 2.5 10.0 / 4 returns 2.5 ints are automatically converted to floats Casting x = 3.3 Python int(x) returns 3 Java (int) x returns 3 Strings · Both

Parker, Gary B.

17

Python Reference Introduction  

E-print Network

Python Reference Introduction These notes contain commands useful for analysing and plotting data using the Python programming language, together with the Numpy and Matplotlib libraries. Installation predecessor, the enthought python distribution (free version). Running If you have Canopy, run it. Start up

Francis, Paul

18

Simulation Programming with Python  

E-print Network

Chapter 4 Simulation Programming with Python This chapter shows how simulations of some of the examples in Chap. 3 can be programmed using Python and the SimPy simulation library[1]. The goals-based discrete-event simulation library for Python. It is open source and released under the M license. Sim

Nelson, Barry L.

19

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."

20

CSC326 Python Sequences CSC326 Python Sequences  

E-print Network

CSC326 Python Sequences i CSC326 Python Sequences #12;CSC326 Python Sequences ii REVISION HISTORY NUMBER DATE DESCRIPTION NAME 1.0 2011-09 JZ #12;CSC326 Python Sequences iii Contents 1 Agenda 1 2 while Matrics 12 13 Prime Number with List Comprehension 12 14 Quick Sort 12 15 Recap 12 #12;CSC326 Python

Zhu, Jianwen

21

Python programming --introduction to Python Finn Arup Nielsen  

E-print Network

Python programming -- introduction to Python Finn °Arup Nielsen Department of Informatics #12;Python programming -- introduction First a case Finn °Arup Nielsen 1 August 28, 2009 #12;Python August 28, 2009 #12;Python programming -- introduction Output from the print function "Autoblog Green

22

Installation of Python and VPython Install Python 2.x  

E-print Network

Installation of Python and VPython OBJECTIVES · Install Python 2.x · Install the VPython 3D graphics module TIME You should finish this installation in about 10 minutes I. Install Python 2.x 1. What is Python? Before writing any code, you will need to install the programming language called Python. What

Texas at Austin. University of

23

Introduction into Python Daniel Polani  

E-print Network

Introduction into Python Daniel Polani Daniel Polani: Introduction into Python ­ p.1/67 Why Python structures functionality procedurality Daniel Polani: Introduction into Pyt Where to get Python and Learn More? Web Site: http://www.python.org/ (also main source for this introduction) UH Availability: in PC

Polani, Daniel

24

Python Programming: Lecture 1 Introduction  

E-print Network

Python Programming: Lecture 1 Introduction Lili Dworkin University of Pennsylvania #12;Welcome;Introduction What is Python? Compromise between shell script and C++/Java program Intuitive syntax Interpreted() { std::cout Python print "hello world" #12

Plotkin, Joshua B.

25

Python genome Supplementary Information 1 SUPPLEMENTARY INFORMATION  

E-print Network

Python genome Supplementary Information 1 SUPPLEMENTARY INFORMATION 1. SUPPLEMENTARY METHODS 1.1 Python Genome Sequencing A single Python molurus bivittatus female was obtained through. #12;Python genome Supplementary Information 2 The SOAPdenovo and Newbler python assemblies

Castoe, Todd A.

26

Python Script Analysis  

NSDL National Science Digital Library

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

IMPART RET Program, College of Information Science & Technology,

27

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

28

Python for Ecology  

EPA Science Inventory

Python is a high-level scripting language that is becoming increasingly popular for scientific computing. This all-day workshop is designed to introduce the basics of Python programming to ecologists. Some scripting/programming experience is recommended (e.g. familiarity with R)....

29

Extending Python with Fortran  

Microsoft Academic Search

Python is a great scripting language. It is portable, free, and has a powerful numerical facility, object oriented features, and a library of modules that enable a huge variety of applications: cryptography, image processing, special effects for movies, Web programming, Web site search engines, and so on. The authors have created a tool, Pyfort, for connecting Fortran routines to Python.

Paul F. Dubois; T.-Y. Yang

1999-01-01

30

Extending Python: speed it upExtending Python: speed it up Python is great for rapid application development  

E-print Network

1 Extending Python: speed it upExtending Python: speed it up · Python is great for rapid, it can be slow at times · Python is fairly easy to profile ­ time.clock() module ­ Python Profiler the program in Python ­ Profile ­ Rewrite slow features in C, Fortran #12;2 Extending Python: reuse code

Reluga, Tim

31

Introduction into Python Python 2: Programming, Control Structures,  

E-print Network

Introduction into Python Python 2: Programming, Control Structures, Functions Daniel Polani Daniel Polani: Introduction into Python ­ p.1/?? Programming Code a = 3 b = 4 print a + b 7 Code a, b = 3, 4 if a > b: print a + b else: print a - b -1 Daniel Polani: Introduction into Python ­ p.2/?? Programming II

Polani, Daniel

32

Python Database Programming For Introduction to Programming Using Python  

E-print Network

Python Database Programming For Introduction to Programming Using Python By Y. Daniel Liang To write database programs using SQL in Python, you need to know RDBM and SQL. An introduction to RDBMS and SQL can be found in http://www.cs.armstrong.edu/liang/intro9e/databasesupplement .html. Python

Liang, Y. Daniel

33

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

E-print Network

Introduction into Python Python 5: Classes, Exceptions, Generators and more Daniel Polani Daniel Polani: Introduction into Python ­ p.1/?? Name Spaces Concept: There are three different types of name Polani: Introduction into Python ­ p.2/?? Classes: Briefest Introduction Idea: the concept of a class

Polani, Daniel

34

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

35

Using Python in Climate and Meteorology  

E-print Network

Using Python in Climate and Meteorology Johnny Wei-Bing Lin Physics Department, North Park;Outline Why Python? Python tools for data analysis: CDAT. Using Python to make models more modular: The qtcm example. #12;Why Python?: Topics What is Python? Advantages and disadvantages. Why Python

Lin, Johnny

36

Amebiasis in four ball pythons, Python reginus.  

PubMed

Between September 13th and November 18th in 1999, four ball pythons, Python reginus kept in the same display, showed anorexia and died one after another. At necropsy, all four snakes had severe hemorrhagic colitis. Microscopically, all snakes had severe necrotizing hemorrhagic colitis, in association with ameba-like protozoa. Some of the protozoa had macrophage-like morphology and others formed protozoal cysts with thickened walls. These protozoa were distributed throughout the wall in the large intestine. Based on the pathological findings, these snakes were infested with a member of Entamoeba sp., presumably with infection by Entamoeba invadens, the most prevalent type of reptilian amoebae. PMID:11789622

Kojimoto, A; Uchida, K; Horii, Y; Okumura, S; Yamaguch, R; Tateyama, S

2001-12-01

37

From Scratch to Python Michael Krisper  

E-print Network

;Ball (Scratch & Python) (live demo) #12;Python ist cool... IEEE Spectrum Programmiersprachen RankingFrom Scratch to Python Michael Krisper Programmieren 0, WS 2014 #12;Inhalt Motivation Installation Python Entwicklungsumgebung Hello World! Scratch --> Python #12;Super Mario Python Beta (live demo) #12

38

Python programming --installation Finn Arup Nielsen  

E-print Network

Python programming -- installation Finn °Arup Nielsen DTU Compute Technical University of Denmark September 3, 2013 #12;Python programming -- installation Overview of Python parts Apart from Python "itself when you start python The Python Standard Library: bundled modules, such as "copy", "string", "re

39

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

40

Python Tutorial Release 2.6.2  

E-print Network

Python Tutorial Release 2.6.2 Guido van Rossum Fred L. Drake, Jr., editor August 04, 2009 Python Software Foundation Email: docs@python.org #12;#12;CONTENTS 1 Whetting Your Appetite 3 2 Using the Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 3 An Informal Introduction to Python 9 3.1 Using Python as a Calculator

Laidlaw, David

41

Python Reference Manual Release 2.0  

E-print Network

Python Reference Manual Release 2.0 Guido van Rossum Fred L. Drake, Jr., editor October 16, 2000 BeOpen PythonLabs E­mail: python­docs@python.org #12; BEOPEN.COM TERMS AND CONDITIONS FOR PYTHON 2.0 BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1 1. This LICENSE AGREEMENT is between BeOpen.com (``Be

Fischer, Charles N.

42

Python Reference Manual Release 2.0  

E-print Network

Python Reference Manual Release 2.0 Guido van Rossum Fred L. Drake, Jr., editor October 16, 2000 BeOpen PythonLabs E-mail: python-docs@python.org #12;BEOPEN.COM TERMS AND CONDITIONS FOR PYTHON 2.0 BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1 1. This LICENSE AGREEMENT is between BeOpen.com ("Be

Fischer, Charles N.

43

Python Tutorial Release 2.0  

E-print Network

Python Tutorial Release 2.0 Guido van Rossum Fred L. Drake, Jr., editor October 16, 2000 BeOpen PythonLabs E­mail: python­docs@python.org #12; BEOPEN.COM TERMS AND CONDITIONS FOR PYTHON 2.0 BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1 1. This LICENSE AGREEMENT is between BeOpen.com (``Be

Fischer, Charles N.

44

Python 2 vs. Python 3 for Carleton CS 111 students Following are the differences between Python 2 and Python 3 that are likely to come  

E-print Network

Python 2 vs. Python 3 for Carleton CS 111 students Following are the differences between Python 2 and Python 3 that are likely to come up for students learning Python 2 in CS 111 but reading the Zelle textbook which uses code examples in Python 3. For a more complete explanation of all

Musicant, Dave

45

Python Tutorial Release 2.0  

E-print Network

Python Tutorial Release 2.0 Guido van Rossum Fred L. Drake, Jr., editor October 16, 2000 BeOpen PythonLabs E-mail: python-docs@python.org #12;BEOPEN.COM TERMS AND CONDITIONS FOR PYTHON 2.0 BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1 1. This LICENSE AGREEMENT is between BeOpen.com ("Be

Fischer, Charles N.

46

Biologists Remove Python from Everglades  

USGS Multimedia Gallery

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

47

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

48

Repast for Python Scripting.  

SciTech Connect

Repast for Python Scripting (RepastPy) is a rapid application development (RAD) tool for producing simulations from the Repast agent simulation framework. Using a point-and-click component based interface, users can easily construct a simulation and then use a special subset of the Python programming language to define agent behaviors. RepastPy is the next generation of Repast visual development tools superceding the older SimBuilder tool and incorporating a streamlined user interface, improved Python language support, and the latest improvements to Repast. RepastPy now provides the ability to export RepastPy models to Java, allowing users to then work in the traditional Repast for Java environment.

Collier, N.; North, M. J.; Decision and Information Sciences

2005-01-01

49

Hemodynamic effects of python neuropeptide ? in the anesthetized python, Python regius  

Microsoft Academic Search

The effects of python neuropeptide gamma (NP?) on hemodynamic parameters have been investigated in the anesthetized ball python (Python regius). Bolus intra-arterial injections of synthetic python NP? (1300 pmol kg?1) produced a dose-dependent decrease in systemic arterial blood pressure (Psys) concomitant with increases in systemic vascular conductance (Gsys), total cardiac output and stroke volume, but only minor effects on heart

Nini Skovgaard; Gina Galli; Edwin W. Taylor; J. Michael Conlon; Tobias Wang

2005-01-01

50

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

51

Zachary O. Dugas Toups Curriculum Vitae ztoups@nmsu.edu  

E-print Network

,000) studied Japanese language and culture in the Asian Studies Program at Kansai University of Foreign Language Studies #12;Zachary O. Dugas Toups ­ ztoups@nmsu.edu CV 2 / 10 RESEARCH EXPERIENCE Texas A systems supporting shopping and wayfinding based on fieldwork with shoppers and concierges JOURNAL ARTICLE

Toups, Zach

52

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

53

Python programming --course introduction Finn Arup Nielsen  

E-print Network

Python programming -- course introduction Finn °Arup Nielsen DTU Compute Technical University of Denmark January 8, 2014 #12;Python programming -- course introduction Python programming DTU course 02819 Data mining using Python. Previously called DTU course 02820 Python programming (study admin- istration

54

All-in-One Python for Scientists  

E-print Network

Py4Science @ UND #12;#12;All-in-One Python for Scientists Enthought Python Distribution Open, NASA, NCAR, NOAA uses "Every pixel counts " #12;Resources 1 What is Python? by Wesley Chun Python 101 and 102 @ PyCon 2009 An Introduction to OO Programming - PyCon 2009 Python 401: Some Advanced Topics @ Py

Delene, David J.

55

Data Mining using Python --exercises for installation  

E-print Network

Data Mining using Python -- exercises for installation Finn °Arup Nielsen DTU Compute Technical University of Denmark September 1, 2014 #12;Python programming -- exercises for installation Install Python Install python and some libraries and check that you can write: $ python >>> import numpy >>> import scipy

56

Python programming --exercises Finn Arup Nielsen  

E-print Network

Python programming -- exercises Finn °Arup Nielsen DTU Compute Technical University of Denmark October 10, 2013 #12;Python programming -- exercises Installation Finn °Arup Nielsen 1 October 10, 2013 #12;Python programming -- exercises Install Python Install python and some libraries Check that you

57

Python programming --course introduction Finn Arup Nielsen  

E-print Network

Python programming -- course introduction Finn °Arup Nielsen Department of Informatics #12;Python programming -- course introduction Python programming DTU course 02820 Python programming and an oral presentation at the poster about a Python program you write in a group. Autumn 2009 first run

58

Parallel distributed computing using Python  

NASA Astrophysics Data System (ADS)

This work presents two software components aimed to relieve the costs of accessing high-performance parallel computing resources within a Python programming environment: MPI for Python and PETSc for Python. MPI for Python is a general-purpose Python package that provides bindings for the Message Passing Interface (MPI) standard using any back-end MPI implementation. Its facilities allow parallel Python programs to easily exploit multiple processors using the message passing paradigm. PETSc for Python provides access to the Portable, Extensible Toolkit for Scientific Computation (PETSc) libraries. Its facilities allow sequential and parallel Python applications to exploit state of the art algorithms and data structures readily available in PETSc for the solution of large-scale problems in science and engineering. MPI for Python and PETSc for Python are fully integrated to PETSc-FEM, an MPI and PETSc based parallel, multiphysics, finite elements code developed at CIMEC laboratory. This software infrastructure supports research activities related to simulation of fluid flows with applications ranging from the design of microfluidic devices for biochemical analysis to modeling of large-scale stream/aquifer interactions.

Dalcin, Lisandro D.; Paz, Rodrigo R.; Kler, Pablo A.; Cosimo, Alejandro

2011-09-01

59

Python programming --machine learning Finn Arup Nielsen  

E-print Network

Python programming -- machine learning Finn °Arup Nielsen DTU Compute Technical University of Denmark October 28, 2013 #12;Python programming -- machine learning Overview Machine learning: Unsupervized and supervized The concept of generalization Overview of Python machine learning packages

60

Python programming --databasing Finn Arup Nielsen  

E-print Network

Python programming -- databasing Finn °Arup Nielsen DTU Compute Technical University of Denmark September 23, 2013 #12;Python programming -- databasing Overview Pickle -- simple format for persistence Key September 23, 2013 #12;Python programming -- databasing Persistence via pickle String representation

61

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

62

Pyro Python Robotics  

NSDL National Science Digital Library

Pyro stands for Python Robotics. The goal of the project is to provide a programming environment for easily exploring advanced topics in artificial intelligence and robotics without having to worry about the low-level details of the underlying hardware. That is not to say that Pyro is just a toy. In fact, Pyro is used for real robotics research as well as courseware.This website is the 2005 recipient of Premier Award for Excellence in Engineering Education Courseware. It includes curriculum, tutorials, modules and documentations.

63

The Effect of Meal Composition on Specific Dynamic Action in Burmese Pythons (Python molurus)  

E-print Network

182 The Effect of Meal Composition on Specific Dynamic Action in Burmese Pythons (Python molurus) M pythons (Python molurus) at 30 C. Each snake was fed a series of experimental meals consisting of amino expenditure of a viperid snake (McCue and Lil- lywhite 2002). Snakes of the genus Python have been proposed

Bennett, Albert F.

64

CSC326 Python Imperative Core (Lec CSC326 Python Imperative Core (Lec 2)  

E-print Network

CSC326 Python Imperative Core (Lec 2) i CSC326 Python Imperative Core (Lec 2) #12;CSC326 Python Imperative Core (Lec 2) ii REVISION HISTORY NUMBER DATE DESCRIPTION NAME 1.0 2011-09 JZ #12;CSC326 Python Imperative Core (Lec 2) iii Contents 1 Agenda 1 2 Invoking Python 1 3 Value, Type, Variable 1 4 Keywords 2 5

Zhu, Jianwen

65

Invasive Species Distribution Notes Reproduction of the Burmese python (Python molurus  

E-print Network

Invasive Species Distribution Notes Reproduction of the Burmese python (Python molurus bivittatus@flmnh.ufl.edu Key data: Python molurus bivittatus; Pythonidae; Burmese python; population; Everglades National Park; 147144-46; 147150; 151398. Python molurus bivittatus is the largest exotic herpetofaunal species

Mazzotti, Frank

66

Use ORNL DAAC TDS Data Resources in Python 1. Python Modules used in this Tutorial  

E-print Network

Use ORNL DAAC TDS Data Resources in Python 1. Python Modules used for interactive computing with Python. Pydap [http://www.pydap.org] Pydap is a pure Python://matplotlib.org] matplotlib is a python 2D plotting library which produces publication quality figures

67

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 legacy Perl to Python can be a daunting task. In this article, learn some of the theory behind dealing vendor APIs are available only in Python. At this point, the monumental feat of porting Perl to Python

68

What advantages has it? The Reasons for Choosing Python  

E-print Network

by #12;What advantages has it? #12;The Reasons for Choosing Python Python is free It is object modules for interfacing with Solids Works #12;Getting Started with Python Python(x,y) package from http://code.google.com/p/pythonxy The Python(x,y) package comes with all numerical and scientific Python modules. Python(x,y) is a free

Stavroulakis, Georgios E.

69

Cardiovascular actions of python bradykinin and substance P in the anesthetized python, Python regius.  

PubMed

The cardiovascular actions of python bradykinin (BK) and substance P (SP) have been investigated in the anesthetized ball python, Python regius. Bolus intra-arterial injections of python BK (0.03-3 nmol/kg) produced concentration-dependent increases in arterial blood pressure, heart rate (HR), and cardiac output concomitant with small decreases in systemic resistance and stroke volume. Intra-arterial injection of 3 nmol/kg python BK produced a tenfold increase in circulating concentration of norepinephrine, but epinephrine levels did not change. BK-induced tachycardia was attenuated (>90%) by the beta-adrenergic receptor antagonist sotalol, and the hypertensive response was attenuated (>70%) by the alpha-adrenergic receptor antagonist prazosin, indicating that effects of python BK are mediated at least in part by activation of the extensive network of adrenergic neurons present in vascular tissues. Bolus intra-arterial injections of python SP in the range 0. 01-30 pmol/kg produced concentration-dependent decreases in arterial blood pressure and systemic peripheral resistance concomitant with increases in cardiac output and stroke volume but with only minor effects on HR. The data suggest that kinins play a physiologically important role in cardiovascular regulation in the python. PMID:10938242

Wang, T; Axelsson, M; Jensen, J; Conlon, J M

2000-08-01

70

Scientific Programming with Python: part II  

E-print Network

Scientific Programming with Python: part II Advanced Research Computing #12;Advanced Research Computing Outline · MPI programming in Python · NumPy (SciPy) arrays · Plotting in Python: ­ bar-charts, pie-charts, mesh-grids · Plotting and image processing in Python ­ image representation, conversion to array

Crawford, T. Daniel

71

Python programming --Testing Finn Arup Nielsen  

E-print Network

Python programming -- Testing Finn °Arup Nielsen DTU Compute Technical University of Denmark January 3, 2014 #12;Python testing Overview Testing frameworks: unittest, nose, py.test, doctest Coverage January 3, 2014 #12;Python testing Testing frameworks unittest: In the Python Standard Library, x

72

Programmation en langage Python Master BBSG 1  

E-print Network

Programmation en langage Python Master BBSG 1 Henri Garreta, Laurent Tichit D´epartement d'Informatique, Facult´e des Sciences de Luminy 6. Python orient´e objets c H. Garreta et L. Tichit, 2014 () Le langage Python 1 / 30 Python orient´e objets Objets et messages L'esprit de la chose Un programme est fait d

Tichit, Laurent

73

Why Python? 1) readable, compact, simple syntax  

E-print Network

Starting with Python #12;Why Python? 1) readable, compact, simple syntax 2) documented 3) memory of programming effective scripting language 10/19/2010 2 #12;Running simple Scripts >python your_file.py >ls() Python course #12;Basic Datatypes 510/19/2010 Type Example Convert boolean True integer 100000000000019

Spang, Rainer

74

Programmation en Python -Cours 3 : les listes  

E-print Network

Programmation en Python - Cours 3 : les listes MPSI1 - Lyc´ee Thiers 2013/2014 #12;Les listes en python la boucle for Les listes en python Les listes Cr´eation de liste avec range() la boucle for Boucle for Exemples MPSI1 - Lyc´ee Thiers Programmation en Python - Cours 3 : les listes #12;Les listes en python la

Préaux, Jean-Philippe

75

Python fiber optic seal  

SciTech Connect

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

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

1993-08-01

76

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

77

DRAFT Python for Science DRAFT David J. Raymond  

E-print Network

DRAFT Python for Science DRAFT David J. Raymond Physics Department and Geophysical Research Center Introduction 1 2 Standard Python 3 2.1 Using Python as a Desk Calculator . . . . . . . . . . . . . . . . . . . . . . . 9 2.3 Python Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2

Raymond, David J.

78

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

79

Python programming --Interfacing with other Finn Arup Nielsen  

E-print Network

Python programming -- Interfacing with other languages Finn °Arup Nielsen DTU Compute Technical approaches. Calling C(++): Boost.Python, ctypes Cython Other ways to make Python faster Embedding Python++ and Fortran functions from Python: Either with "manual" wrapping Or by using a automated wrapper: SWIG, Boost.Python

80

DIFFERENCES BETWEEN PYTHON VERSIONS THE Python programming language is continually being updated and im-  

E-print Network

APPENDIX B DIFFERENCES BETWEEN PYTHON VERSIONS THE Python programming language is continually being rarely.) The programs that appear in this book are written using Python version 3, although, as noted side of the word "future".) This statement tells version 2 of Python to behave in the way version 3

Newman, Mark

81

DIFFERENCES BETWEEN PYTHON VERSIONS THE Python programming language is continually being updated and im-  

E-print Network

APPENDIX B DIFFERENCES BETWEEN PYTHON VERSIONS THE Python programming language is continually being rarely.) The programs that appear in this book are written using Python version 3, although, as noted underscore characters "__" on either side of the word "future".) This statement tells version 2 of Python

Newman, Mark

82

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

E-print Network

Introduction 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 into Python ­ p.2/?? Notes on Using Methods Note: Methods for any structures are invoked by a dot . between

Polani, Daniel

83

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

E-print Network

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

Ceder, Gerbrand

84

6.S897 Algebra and Computation May 9, 2012 Lecturer: Madhu Sudan Scribe: Zachary Abel  

E-print Network

6.S897 Algebra and Computation May 9, 2012 Lecture 24 Lecturer: Madhu Sudan Scribe: Zachary Abel 1 coefficients. We may assume p(0) = 0 by replacing the constant term c0 with c0xm . Let u1, . . . , un

Goldwasser, Shafi

85

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

Verschelde, Jan

86

Python programming --Scripting Finn Arup Nielsen  

E-print Network

Python programming -- Scripting Finn °Arup Nielsen DTU Compute Technical University of Denmark October 2, 2013 #12;Python scripting Overview How to make a command-line script (as oppose to a module October 2, 2013 #12;Python scripting Naming It is not necessary to call a script run from the command

87

Python programming --Profiling Finn Arup Nielsen  

E-print Network

Python programming -- Profiling Finn °Arup Nielsen DTU Compute Technical University of Denmark January 3, 2014 #12;Python profiling Overview time and timeit profiling Finn °Arup Nielsen 1 January 3, 2014 #12;Python profiling Simpel profiling with time time and timeit modules and times() function

88

Programmation en Python -Cours 1 : Premier contact  

E-print Network

Programmation en Python - Cours 1 : Premier contact MPSI1 - Lyc´ee Thiers 2013/2014 #12;Introduction Utilisation en mode console Annexes Introduction Le langage python Utilisation en mode console´ee Thiers Programmation en Python - Cours 1 : Premier contact #12;Introduction Utilisation en mode console

Préaux, Jean-Philippe

89

Python programming --Web serving Finn Arup Nielsen  

E-print Network

Python programming -- Web serving Finn °Arup Nielsen Department of Informatics and Mathematical Modelling Technical University of Denmark September 30, 2013 #12;Python programming -- Web serving Overview Google App Engine Finn °Arup Nielsen 1 September 30, 2013 #12;Python programming -- Web serving Methods

90

Information Processing in Python School COMSC  

E-print Network

Information Processing in Python School COMSC The aim of this module is to introduce techniques to extract, store and process information using the Python programming language. To achieve this, students Language of module delivery English On completion of the module a student will be able to: · Use Python

Martin, Ralph R.

91

Python for Scientific Gateways Development Randy Heiland  

E-print Network

Python for Scientific Gateways Development Randy Heiland Research Technologies Indiana University and technologies that are based on the Python programming language and can be quite useful for scientific gateway, Standardization, Languages. Keywords Python, Web services, Gateways, Web development frameworks. 1. INTRODUCTION

Lumsdaine, Andrew

92

Getting started with Python Dr. Mark Lee  

E-print Network

Getting started with Python Dr. Mark Lee School of Computer Science University of Birmingham B15 2TT m.g.lee@cs.bham.ac.uk Introduction Python a very clear syntax and is an ideal first programming language. It's also very powerful ­ Python

Lee, Mark

93

UCRL-TR-237219 Leveraging Python  

E-print Network

UCRL-TR-237219 Leveraging Python Interoperability Tools to Improve Sapphire's Usability Abel by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. #12;Leveraging Python prefer higher level scripting languages such as Python for their ease of use and flexibility

Kamath, Chandrika

94

Python programming --code comments Finn Arup Nielsen  

E-print Network

Python programming -- code comments Finn °Arup Nielsen DTU Compute Technical University of Denmark November 5, 2013 #12;Python programming -- code comments Code comments Random comments on code provided by students. Finn °Arup Nielsen 1 November 5, 2013 #12;Python programming -- code comments argparse? import

95

Python -die Alternative zu Matlab? Jochen Schulz  

E-print Network

. ...... Python - die Alternative zu Matlab? Jochen Schulz Georg-August Universität Göttingen 1/36 #12;Aufbau ...1 Einleitung ...2 Grundlegende Bedienung Python (Spyder) ...3 3D - Grafik ...4 umständlich sein. Spezialisierter Funktionsumfang macht manche Programmierung schwer. 3/36 #12;Python: Num

Wardetzky, Max

96

COMPARISON OF MATLAB, OCTAVE, AND PYTHON  

E-print Network

COMPARISON OF MATLAB, OCTAVE, AND PYTHON ON EXAMPLES FOR MATH 665 NUMERICAL LINEAR ALGEBRA ED. To download Octave, go to http://www.gnu.org/software/octave/. The general purpose language Python has at the computer language differences, and also the different modes of thought, between Matlab/Octave and Python

Bueler, Ed

97

Python programming --encoding Finn Arup Nielsen  

E-print Network

Python programming -- encoding Finn °Arup Nielsen Department of Informatics and Mathematical September 7, 2012 #12;Python programming -- encoding https://gist.github.com/3667575 Finn °Arup Nielsen 1 September 7, 2012 #12;Python programming -- encoding Character encoding Handling of characters encoding

98

Python programming --a case Finn Arup Nielsen  

E-print Network

Python programming -- a case Finn °Arup Nielsen Department of Informatics and Mathematical Modelling Technical University of Denmark September 2, 2012 #12;Python programming -- a case A case Download) Extract features Topic mining of texts Graph mining of coauthors See Python code at https

99

A PDESolve Interpreter in Python Chris Myers  

E-print Network

A PDESolve Interpreter in Python Chris Myers Beam Technologies, Inc., 110 N. Cayuga St., Ithaca, NY environment that Beam is developing. Recently, we have begun building an interpreted Python interface to PDESolve by wrapping pieces of the library using Beazley's SWIG package 2] to build a Python extension

Myers, Chris

100

A Python Experiment Suite THOMAS RUCKSTIE  

E-print Network

A Python Experiment Suite THOMAS R¨UCKSTIE? Technische Universit¨at M¨unchen, Germany J¨URGEN SCHMIDHUBER Dalle Molle Institute for Artificial Intelligence, Lugano, Switzerland We introduce the Python Experiment Suite, an open source software tool written in Python, that supports scientists, engineers

Schmidhuber, Juergen

101

Scientific Programming with Python: part I  

E-print Network

Scientific Programming with Python: part I Advanced Research Computing #12;Advanced Research Computing Outline · A tour of Python ­ Date types, exceptions ­ Functions, modules, generators ­ Functional programming ­ The Map-reduce data-parallel pattern · Linear algebra in Python ­ Saxpy as a map operation

Crawford, T. Daniel

102

Python programming --Semantic Web Finn Arup Nielsen  

E-print Network

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

103

Data Mining using Python --exercises for introduction  

E-print Network

Data Mining using Python -- exercises for introduction Finn °Arup Nielsen DTU Compute Technical University of Denmark September 8, 2014 #12;Data Mining using Python -- exercises for introduction For loops. Finn °Arup Nielsen 1 September 8, 2014 #12;Data Mining using Python -- exercises for introduction

104

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

105

Anatomy of the python heart.  

PubMed

The hearts of all snakes and lizards consist of two atria and a single incompletely divided ventricle. In general, the squamate ventricle is subdivided into three chambers: cavum arteriosum (left), cavum venosum (medial) and cavum pulmonale (right). Although a similar division also applies to the heart of pythons, this family of snakes is unique amongst snakes in having intracardiac pressure separation. Here we provide a detailed anatomical description of the cardiac structures that confer this functional division. We measured the masses and volumes of the ventricular chambers, and we describe the gross morphology based on dissections of the heart from 13 ball pythons (Python regius) and one Burmese python (P. molurus). The cavum venosum is much reduced in pythons and constitutes approximately 10% of the cavum arteriosum. We suggest that shunts will always be less than 20%, while other studies conclude up to 50%. The high-pressure cavum arteriosum accounted for approximately 75% of the total ventricular mass, and was twice as dense as the low-pressure cavum pulmonale. The reptile ventricle has a core of spongious myocardium, but the three ventricular septa that separate the pulmonary and systemic chambers--the muscular ridge, the bulbuslamelle and the vertical septum--all had layers of compact myocardium. Pythons, however, have unique pads of connective tissue on the site of pressure separation. Because the hearts of varanid lizards, which also are endowed with pressure separation, share many of these morphological specializations, we propose that intraventricular compact myocardium is an indicator of high-pressure systems and possibly pressure separation. PMID:20376590

Jensen, Bjarke; Nyengaard, Jens R; Pedersen, Michael; Wang, Tobias

2010-12-01

106

Hemodynamic effects of python neuropeptide gamma in the anesthetized python, Python regius.  

PubMed

The effects of python neuropeptide gamma (NPgamma) on hemodynamic parameters have been investigated in the anesthetized ball python (Python regius). Bolus intra-arterial injections of synthetic python NPgamma (1-300 pmol kg-1) produced a dose-dependent decrease in systemic arterial blood pressure (Psys) concomitant with increases in systemic vascular conductance (Gsys), total cardiac output and stroke volume, but only minor effects on heart rate. The peptide had no significant effect on pulmonary arterial blood pressure (Ppul) and caused only a small increase in pulmonary conductance (Gpul) at the highest dose. In the systemic circulation, the potency of the NK1 receptor-selective agonist [Sar9,Met(0(2))11] substance P was >100-fold greater than the NK2 receptor-selective agonist [betaAla8] neurokinin A-(4-10)-peptide suggesting that the python cardiovascular system is associated with a receptor that resembles the mammalian NK1 receptor more closely than the NK2 receptor. Administration of the inhibitor of nitric oxide synthesis, L-nitro-arginine-methylester (L-NAME; 150 mg kg-1), resulted in a significant (P<0.05) increase in Psys as well as a decrease in Gsys, but no effect on Ppul and Gpul. Conversely, the nitric oxide donor, sodium nitroprusside (SNP; 60 microg kg-1) produced a significant (P<0.05) decrease in Psys along with an increase in Gsys and pulmonary blood flow. However, neither L-NAME nor indomethacin (10 mg kg-1) reduced the cardiovascular responses to NPgamma. Thus, nitric oxide is involved in regulation of basal vascular tone in the python, but neither nitric oxide nor prostaglandins mediate the vasodilatory action of NPgamma. PMID:15721483

Skovgaard, Nini; Galli, Gina; Taylor, Edwin W; Conlon, J Michael; Wang, Tobias

2005-05-15

107

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.

108

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

109

Pybus -- A Python Software Bus  

SciTech Connect

A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the concept of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.

Lavrijsen, Wim T.L.P.

2004-10-14

110

Python: The Full Monty A Tested Semantics for the  

E-print Network

Python: The Full Monty A Tested Semantics for the Python semantics for the Python programming language. We present both a core language for Python, suitable for tools and proofs, and a translation process for converting Python source to this core. We have tested

Krishnamurthi, Shriram

111

Statistical Tools in Python A NASA AISR Project  

E-print Network

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

Loredo, Thomas J.

112

Master BBSG 1 anne TP Programmation & langage Python TP 1. Premires manipulations -python3 en mode interactif  

E-print Network

Master BBSG 1° année TP Programmation & langage Python TP 1. Premières manipulations - python3 en mode interactif Une fois activé, l'interpréteur Python répète inlassablement le cycle suivant : - Python affiche une invite (le signe >>>), - l'utilisateur compose au clavier une expression Python

Tichit, Laurent

113

Adapted from Richard P. Muller 1 Python GUIs (Graphical User Interfaces)Python GUIs (Graphical User Interfaces)  

E-print Network

Adapted from Richard P. Muller 1 Python GUIs (Graphical User Interfaces)Python GUIs (Graphical User Interfaces) · Tkinter ­ Python's de-facto standard GUI ­ this is the only GUI we will cover · Wx) ­ Many people find Tcl limited ­ Can also drive Tk with Perl, Python · Tkinter is the Python Tk Interface

Reluga, Tim

114

Infectious dermatitis in a ball python (Python regius) colony.  

PubMed

Seven wild-caught ball pythons (Python regius), including six gravid females and one male, were obtained from Africa and were housed in a government animal facility in Research Triangle Park, North Carolina. Upon arrival, the snakes were found to be infested with ticks (Aponomma latus), which were manually removed. Four weeks following arrival, vesicular skin lesions began to appear on the snakes. Despite treatment of all affected female snakes with amikacin (5 mg/kg i.m., every 3 days) and cefotaxime (25 mg/kg i.m., every 3 days), the condition progressed and five of the female snakes died 7 wk after arrival. The remaining male and one female improved after an increase in environmental temperature, with ecdysis followed by healing. Physiologic stress, ectoparasites, and shipping may have predisposed the snakes to sepsis. PMID:10065857

Branch, S; Hall, L; Blackshear, P; Chernoff, N

1998-12-01

115

Assessment of multiple cardiocentesis in ball pythons (Python regius).  

PubMed

This study evaluated the gross and microscopic effects of serial blood collection from six ball pythons (Python regius) by using cardiocentesis. We collected 39 blood samples from each snake over a 120-day period. Cardiocentesis was performed on manually restrained snakes, with each sample requiring approximately 15 sec to collect. No clinically apparent complications were noted in any of the snakes after the cardiocentesis procedures, and all snakes survived until they were euthanized 73 days after the last blood sample. Minimal gross lesions were noted at necropsy; faint brown pigmentation of the pericardium was present in five of six snakes, and three snakes had approximately 0.5 ml dark pigmented fluid in the pericardial space. One snake had a small, organized hematoma in the pericardial space. Microscopic findings were limited to moderate and regularly arranged collagen fibrosis and focal thickening of the epicardium. The pericardial sac in all snakes had a mild infiltrate of hemosiderin-laden macrophages and small numbers of heterophils. The results suggest that serial cardiocentesis is well tolerated in ball pythons. PMID:15636554

Isaza, Ramiro; Andrews, Gordon; Coke, Rob; Hunter, Robert

2004-11-01

116

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

117

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

118

Metabolism, temperature relations, maternal behavior, and reproductive energetics in the ball python ( Python regius )  

Microsoft Academic Search

Thermogenic incubation has been documented in two large species of pythons, but the phenomenon has not been studied in small species with concomitantly large heat transfer coefficients. We describe behavior, metabolic rates, mass changes, and temperature relations for adult ball pythons (Python regius), the smallest member of the genus, during the reproductive cycle. Egg and hatchling metabolism and hatchling growth

Tamir M. Ellis; Mark A. Chappell

1987-01-01

119

Anatomy of the python heart  

Microsoft Academic Search

The hearts of all snakes and lizards consist of two atria and a single incompletely divided ventricle. In general, the squamate\\u000a ventricle is subdivided into three chambers: cavum arteriosum (left), cavum venosum (medial) and cavum pulmonale (right).\\u000a Although a similar division also applies to the heart of pythons, this family of snakes is unique amongst snakes in having\\u000a intracardiac pressure

Bjarke JensenJens; Jens R. Nyengaard; Michael Pedersen; Tobias Wang

2010-01-01

120

Pyomo : Python Optimization Modeling Objects.  

SciTech Connect

The Python Optimization Modeling Objects (Pyomo) package [1] is an open source tool for modeling optimization applications within Python. Pyomo provides an objected-oriented approach to optimization modeling, and it can be used to define symbolic problems, create concrete problem instances, and solve these instances with standard solvers. While Pyomo provides a capability that is commonly associated with algebraic modeling languages such as AMPL, AIMMS, and GAMS, Pyomo's modeling objects are embedded within a full-featured high-level programming language with a rich set of supporting libraries. Pyomo leverages the capabilities of the Coopr software library [2], which integrates Python packages (including Pyomo) for defining optimizers, modeling optimization applications, and managing computational experiments. A central design principle within Pyomo is extensibility. Pyomo is built upon a flexible component architecture [3] that allows users and developers to readily extend the core Pyomo functionality. Through these interface points, extensions and applications can have direct access to an optimization model's expression objects. This facilitates the rapid development and implementation of new modeling constructs and as well as high-level solution strategies (e.g. using decomposition- and reformulation-based techniques). In this presentation, we will give an overview of the Pyomo modeling environment and model syntax, and present several extensions to the core Pyomo environment, including support for Generalized Disjunctive Programming (Coopr GDP), Stochastic Programming (PySP), a generic Progressive Hedging solver [4], and a tailored implementation of Bender's Decomposition.

Siirola, John; Laird, Carl Damon (Texas A& M University, College Station, TX); Hart, William Eugene; Watson, Jean-Paul

2010-11-01

121

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

E-print Network

Technical instructions for submitting the Python program Go to http://www.python.org/download/, download the Python 3.3.2 installer and excute. (This website also contains useful documentation of the Python programming language.) In the course webpage http://www.wisdom.weizmann.ac.il/feige/agt2013.html

122

A Python Software Platform for Cooperatively Tracking Multiple GPS  

E-print Network

A Python Software Platform for Cooperatively Tracking Multiple GPS Receivers Eliot Wycoff and Grace of using the Python Software Receiver over traditional software receivers. Introduction With billions

Gao, Grace Xingxin

123

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

124

Biopython: Python tools for computational biology  

Microsoft Academic Search

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

Brad Chapman; Jeffrey Chang

2000-01-01

125

From Python to PLT Scheme Philippe Meunier Daniel Silva  

E-print Network

From Python to PLT Scheme Philippe Meunier Daniel Silva College of Computer and Information Science an experimental embedding of Python into DrScheme. The core of the system is a compiler, which translates Python programs into equivalent MzScheme pro- grams, and a runtime system to model the Python environ- ment

126

Hands-On Python A Tutorial Introduction for Beginners  

E-print Network

Hands-On Python A Tutorial Introduction for Beginners Dr. Andrew N. Harrington Computer Science Chapter 1. Beginning With Python 4 1.1. Context 4 1.2. The Python Interpreter and Idle, Part I 6 1 Basics 125 4.2. Composing Web Pages in Python 127 4.3. CGI - Dynamic Web Pages 131 4.4. Summary 137 3 #12

Reluga, Tim

127

PyXNAT: XNAT in Python Yannick Schwartz1  

E-print Network

PyXNAT: XNAT in Python Yannick Schwartz1 , Alexis Barbot1 , Benjamin Thyreau1 , Vincent Frouin1 to databases. We introduce here PyXNAT, a Python module that in- teracts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python

Paris-Sud XI, Université de

128

Python for Scientific Computing Bill McLean, UNSW  

E-print Network

Python for Scientific Computing Bill McLean, UNSW Last updated on March 21, 2007 1 #12;Outline: 1. The python language 2. Array processing with numpy 3. Graphics with matplotlib 4. Running compiled code from python 2 #12;The Python Language Originally a teaching language written by Guido van Rossum in the early

Scheichl, Robert

129

Copyright Y. Daniel Liang, 2010 Eclipse Python Tutorial  

E-print Network

© Copyright Y. Daniel Liang, 2010 1 Eclipse Python Tutorial For Introduction to Programming Using Python By Y. Daniel Liang This supplement covers the following topics: Download and install Java if necessary Download and install Eclipse Launch Eclipse Install Python plug-in for Eclipse Add a Python

Liang, Y. Daniel

130

The Python Development Project 5.1 Introduction  

E-print Network

Chapter 5 The Python Development Project 5.1 Introduction This chapter describes the calibration management policy. The project will be referred to as the Python development project and International Chip Inc. (ICI) will refer to the organization responsible for the Python development project. The Python

Ford, David N.

131

Classical Topological Order in Abelian and Non-Abelian Generalized Height Models R. Zachary Lamberty,1  

E-print Network

particular models in which fully local non-Abelian constraints lead to global topological liquid propertiesClassical Topological Order in Abelian and Non-Abelian Generalized Height Models R. Zachary. These models have topological sectors labeled by group products along topologically nontrivial loops

Henley, Christopher L.

132

OPTIMAL INVESTMENT POLICIES FOR THE HORSE RACE MODEL Thomas S. Ferguson and C. Zachary Gilstein  

E-print Network

OPTIMAL INVESTMENT POLICIES FOR THE HORSE RACE MODEL Thomas S. Ferguson and C. Zachary Gilstein strategies for the log, power and exponential utility functions are derived. 1. Introduction. In Ferguson. Models with this utility function were considered in Ferguson [5] for investors whose main concern

Ferguson, Thomas S.

133

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

E-print Network

Early Stage Soliton Observations in the Sulu Sea* ZACHARY D. TESSLER AND ARNOLD L. GORDON Lamont internal waves, identified as solitons, at three locations. Solitary internal waves have since been of the soliton generation site near Pearl Bank in the Sulu Archipelago. From here, waves propagate toward

Gordon, Arnold L.

134

LN FN MN CLS ADVISOR NAME Abbott Zachary Dalton SO Boucheron, Laura E.  

E-print Network

LN FN MN CLS ADVISOR NAME Abbott Zachary Dalton SO Boucheron, Laura E. Abotalebi Shayan JR Dawood Abdulrahman Ali H JR Borah, Deva K. Alyami Mohammed Hussain JR Prasad, Nadipuram Apodaca Michael John SR. Carroll Timothy John FR Rodriguez, Edward A. Carter Samuel P SO Voelz, David G. Castillo Andres Ezequiel

Johnson, Eric E.

135

Dynamics of Social Behavior in Fruit Fly Larvae Zachary Durisko1,2  

E-print Network

Dynamics of Social Behavior in Fruit Fly Larvae Zachary Durisko1,2 *, Rebecca Kemp1 , Rameeshay and dynamics of social interactions among fruit fly larvae over time. Both a wild-type laboratory population and a recently-caught strain of larvae spontaneously formed social foraging groups. Levels of aggregation

Dukas, Reuven

136

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 snow-covered ecosystems Seed banks Sub-zero conditions Winter CO2 ux a b s t r a c t Winter respiration in winter soil respiration may be in uenced by the effects of snowfall on microbial communities

Fierer, Noah

137

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

E-print Network

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

Mateas, Michael

138

Behavioral biology of marine mammal deterrents: A review and Zachary A. Schakner  

E-print Network

Review Behavioral biology of marine mammal deterrents: A review and prospectus Zachary A. Schakner Non-lethal deterrents Marine mammals Depredation Conservation behavior Fear conditioning a b s t r a c t Marine mammal depredation of fisheries is a concern from a scientific, management, and conservation

Blumstein, Daniel T.

139

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

E-print Network

. The results support a functional role for estradiol in calibrating women's mating psychology to indicesWomen's estradiol predicts preference for facial cues of men's testosterone James R. Roney , Zachary L. Simmons Department of Psychology, University of California, Santa Barbara, CA 93106-9660, USA

Cosmides, Leda

140

Parallel, Distributed Scripting with Python  

SciTech Connect

Parallel computers used to be, for the most part, one-of-a-kind systems which were extremely difficult to program portably. With SMP architectures, the advent of the POSIX thread API and OpenMP gave developers ways to portably exploit on-the-box shared memory parallelism. Since these architectures didn't scale cost-effectively, distributed memory clusters were developed. The associated MPI message passing libraries gave these systems a portable paradigm too. Having programmers effectively use this paradigm is a somewhat different question. Distributed data has to be explicitly transported via the messaging system in order for it to be useful. In high level languages, the MPI library gives access to data distribution routines in C, C++, and FORTRAN. But we need more than that. Many reasonable and common tasks are best done in (or as extensions to) scripting languages. Consider sysadm tools such as password crackers, file purgers, etc ... These are simple to write in a scripting language such as Python (an open source, portable, and freely available interpreter). But these tasks beg to be done in parallel. Consider the a password checker that checks an encrypted password against a 25,000 word dictionary. This can take around 10 seconds in Python (6 seconds in C). It is trivial to parallelize if you can distribute the information and co-ordinate the work.

Miller, P J

2002-05-24

141

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

142

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

143

Development of Hemipenes in the Ball Python Snake Python regius.  

PubMed

Within amniotes, external copulatory organs have undergone extensive morphological diversification. One of the most extreme examples is squamate (lizards and snakes) hemipenes, which are paired copulatory organs that extend from the lateral margins of the cloaca. Here, we describe the development of hemipenes in a basal snake, the ball python (Python regius). Snake hemipenes arise as a pair of lateral swellings on either side of the caudal part of the cloaca, and these paired outgrowths persist to form the left and right hemipenes. In non-squamate amniotes, external genitalia form from paired swellings that arise on the anterior side of the cloaca, which then fuse medially to form a single genital tubercle, the anlagen of the penis or clitoris. Whereas in non-squamate amniotes, Sonic hedgehog (Shh)-expressing cells of the cloacal endoderm form the urethral or sulcus epithelium and are required for phallus outgrowth, the hemipenes of squamates lack an endodermal contribution, and the sulcus does not express Shh. Thus, snake hemipenes differ from the genital tubercles of non-squamate amniotes both in their embryonic origins and in at least part of patterning mechanisms, which raises the possibility that hemipenes may not be direct homologs of the unpaired amniote penis. Nonetheless, we find that some developmental genes show similar expression patterns in snake hemipenes buds and non-squamate genital tubercles, suggesting that homologous developmental mechanisms are involved in aspects of external genital development across amniotes, even when these structures may have different developmental origins and may have arisen independently during evolution. 2014 S. Karger AG, Basel. PMID:24970309

Leal, Francisca; Cohn, Martin J

2014-06-20

144

Solve the Master Equation by Python-An Introduction to the Python Computing Environment  

E-print Network

A brief introduction to the Python computing environment is given. By solving the master equation encountered in quantum transport, we give an example of how to solve the ODE problems in Python. The ODE solvers used are the ZVODE routine in Scipy and the bsimp solver in GSL. For the former, the equation can be in its complex-valued form, while for the latter, it has to be rewritten to a real-valued form. The focus is on the detailed workflow of the implementation process, rather than on the syntax of the python language, with the hope to help readers simulate their own models in Python.

Wei Fan; Yan Xu; Bing Chen; Qianqian Ye

2011-05-10

145

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

146

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.

Gregor von Laszewski

147

Why do female ball pythons (Python regius) coil so tightly around their eggs?  

Microsoft Academic Search

Question: What benefits does brooding confer to offspring viability that outweigh its costs to the nest-attending female? Organisms: Thirty captive Python regius females and their clutches. Site: Vicinity of Lom, Togo. Background: It has previously been shown that brooding enhances ball python hatching success by reducing desiccation of eggs. Methods: We captured wild, gravid females just before the time of

Fabien Aubret; Xavier Bonnet; Richard Shine; Stphanie Maumelat

2005-01-01

148

A Python Geospatial Language Toolkit  

NASA Astrophysics Data System (ADS)

The volume and scope of geospatial data archives, such as collections of satellite remote sensing or climate model products, has been rapidly increasing and will continue to do so in the near future. The recently launched (October 2011) Suomi National Polar-orbiting Partnership satellite (NPP) for instance, is the first of a new generation of Earth observation platforms that will monitor the atmosphere, oceans, and ecosystems, and its suite of instruments will generate several terabytes each day in the form of multi-spectral images and derived datasets. Full exploitation of such data for scientific analysis and decision support applications has become a major computational challenge. Geophysical data exploration and knowledge discovery could benefit, in particular, from intelligent mechanisms for extracting and manipulating subsets of data relevant to the problem of interest. Potential developments include enhanced support for natural language queries and directives to geospatial datasets. The translation of natural language (that is, human spoken or written phrases) into complex but unambiguous objects and actions can be based on a context, or knowledge domain, that represents the underlying geospatial concepts. This poster describes a prototype Python module that maps English phrases onto basic geospatial objects and operations. This module, along with the associated computational geometry methods, enables the resolution of natural language directives that include geographic regions of arbitrary shape and complexity.

Fillmore, D.; Pletzer, A.; Galloy, M.

2012-12-01

149

Measuring the Length of a Captured Burmese Python  

USGS Multimedia Gallery

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

2009-10-12

150

Gist: A scientific graphics package for Python  

SciTech Connect

{open_quotes}Gist{close_quotes} is a scientific graphics library written by David H. Munro of Lawrence Livermore National Laboratory (LLNL). It features support for three common graphics output devices: X Windows, (Color) PostScript, and ANSI/ISO Standard Computer Graphics Metafiles (CGM). The library is small (written directly to Xlib), portable, efficient, and full-featured. It produces X versus Y plots with {open_quotes}good{close_quotes} tick marks and tick labels, 2-dimensional quadrilateral mesh plots with contours, vector fields, or pseudo color maps on such meshes, with 3-dimensional plots on the way. The Python Gist module utilizes the new {open_quotes}Numeric{close_quotes} module due to J. Hugunin and others. It is therefore fast and able to handle large datasets. The Gist module includes an X Windows event dispatcher which can be dynamically added (e.g., via importing a dynamically loaded module) to the Python interpreter after a simple two-line modification to the Python core. This makes fast mouse-controlled zoom, pan, and other graphic operations available to the researcher while maintaining the usual Python command-line interface. Munro`s Gist library is already freely available. The Python Gist module is currently under review and is also expected to qualify for unlimited release.

Busby, L.E.

1996-05-08

151

Building a programmable interface for physics codes using numeric python  

SciTech Connect

With its portability, ease to add built-in functions and objects in C, and fast array facility among many other features, Python proved to be an excellent language for creating programmable scientific applications. In addition to the two modules presented, there are also other progresses at LLNL in using Python. For example, Python interfaces are being developed for at least three graphics packages, and Python interpreter and applications have been built on distributed platforms such as meiko and Cray T3D.

Yang, T.-Y.B.; Dubois, P.F.; Motteler, Z.C.

1996-04-16

152

Python and Java: The Best of Both Worlds  

Microsoft Academic Search

This paper describes a new working implementation ofthe Python language; built on top of the Java languageand run-time environment. This is in contrast to theexisting implementation of Python, which has been builton top of the C language and run-time environment.Implementing Python in Java has a number of limitationswhen compared to the current implementation ofPython in C. These include about 1.7X

Jim Hugunin

1997-01-01

153

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

154

Calcolo Numerico in Python Fabio Marcuzzi, Maria Rosaria Russo  

E-print Network

Calcolo Numerico in Python Fabio Marcuzzi, Maria Rosaria Russo Dipartimento di Matematica Pura ed Giugno 2005 #12;F.Marcuzzi - M.R.Russo Contents 1 Introduzione 4 1.1 Sviluppo di programmi in Python . . . . . . . . . . . . . . . . . . . . . . . 4 1.2 Documentazione su Python . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.3 Moduli

155

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

E-print Network

RESEARCH ARTICLE Conservation genetics of Boelen's python (Morelia boeleni) from New Guinea / Published online: 26 May 2009 ? Springer Science+Business Media B.V. 2009 Abstract Boelen's python (Morelia to science, Boelen's Python (Morelia boeleni), is an uncommon snake found only in the New Guinea highlands

Austin, Christopher C.

156

Non-Programmers Tutorial For Python Josh Cogliati  

E-print Network

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

Kimbrough, Steven Orla

157

Feeding a large-scale physics application to Python  

Microsoft Academic Search

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

David M. Beazley; Peter S. Lomdahl

1997-01-01

158

Data Mining with Python (Working draft) Finn Arup Nielsen  

E-print Network

Data Mining with Python (Working draft) Finn °Arup Nielsen September 10, 2014 #12;Contents Contents i List of Figures v List of Tables vii 1 Introduction 1 1.1 Other introductions to Python? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Why Python for data mining

159

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 University ENAC July 27, 2010 Abstract Python is a powerful high-level open source programming language purposes. We motivate the use of Python and its free extension modules for high performance stand

Boyer, Edmond

160

Python and PyDSTool for Scientific Computation  

E-print Network

Python and PyDSTool for Scientific Computation Robert Clewley Neuroscience Institute Georgia State University #12;Python is ideal for scientific computing · High level language, easy to learn · Interpreted computation #12;Python widely adopted · Already used by many government labs and industries ­ NASA, NIST, NCAR

Clewley, Robert

161

Software Engineer-Contract Position Emphasis in Python!  

E-print Network

Software Engineer-Contract Position Emphasis in Python! Perfect career opportunity for your summer experience with Python · Linux experience Additional preferred skills include: · C development · Java and rock-solid experience with Python is necessary for this exciting project. A foundation in software

Ravikumar, B.

162

Proceedings of the 7th Python in Science  

E-print Network

Proceedings of the 7th Python in Science Conference SciPy Conference ­ Pasadena, CA, August 19-24, 2008. Editors: Gaël Varoquaux, Travis Vaught, Jarrod Millman #12;#12;Proceedings of the 7th Python. Hagberg, D. Schult, P. Swart Interval Arithmetic: Python Implementation and Applications 16 S. Taschini

Paris-Sud XI, Université de

163

Computing critical points of polynomial systems using PHCpack and Python  

E-print Network

Computing critical points of polynomial systems using PHCpack and Python BY KATHERINE PIRET B with the development of the Python interface to PHCpack. I would also like to thank the NSF for supporting me . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.4 Building an interface to PHCpack in Python . . . . . . . . . . 12 1.5 Applications: random

Verschelde, Jan

164

Proceedings of the 8th Python in Science  

E-print Network

Proceedings of the 8th Python in Science Conference SciPy Conference ­ Pasadena, CA, August 18. Mueller, A. Lumsdaine Convert-XY: type-safe interchange of C++ and Python containers for NumPy extensions. Kienzle, N. Patel, M. McKerns PaPy: Parallel and distributed data-processing pipelines in Python 41 M

Paris-Sud XI, Université de

165

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 Scientist Learning with Python Allen Downey Jeffrey Elkner Chris Meyers Green Tea Press Wellesley a computer scientist : learning with Python / Allen Downey, Jeffrey Elkner, Chris Meyers. ­ 1st ed. p. cm

Reluga, Tim

166

Python phylogenetics: inference from morphology and mitochondrial DNA  

E-print Network

Python phylogenetics: inference from morphology and mitochondrial DNA LESLEY H. RAWLINGS,1,2 DANIEL among the pythons. We aimed to determine which of two competing hypotheses of relationships of the genera Aspidites and Python best explains the evolutionary and bioegeographical history of the family

Rabosky, Daniel L.

167

2. Programming Fundamentals and Python 2.1 Introduction  

E-print Network

2. Programming Fundamentals and Python 2.1 Introduction This chapter provides a non-technical overview of Python and will give you the know-how to survive the next few chapters. It contains many section below. More advanced programming material is contained in a later tutorial. 2.2 Python

Hearst, Marti

168

Python programming --exercises for text and web mining  

E-print Network

Python programming -- exercises for text and web mining Finn °Arup Nielsen DTU Compute Technical University of Denmark September 22, 2014 #12;Python programming -- exercises for text and web mining Word in Polyteknisk Boghandle. Is 'Text Processing in Python' appropriate for the course? Perhaps! The constructor

169

Implanting a Radio Transmitter in a Burmese Python  

USGS Multimedia Gallery

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

2009-10-12

170

Hemodynamic consequences of cardiac malformations in two juvenile ball pythons (Python regius).  

PubMed

Two cases of bifid ventricles and cardiac malformations in juvenile ball python (Python regius) were investigated by blood pressure measurements and macro- and microscopic sectioning. A study of a normal ball python was included for reference. In both cases, all cardiac chambers were enlarged and abnormally shaped. Internal assessment of the ventricles revealed a pronounced defect of the muscular ridge, which normally is responsible for separating the systemic and pulmonary circuits. Consistent with the small muscular ridge, systolic pressures were identical in the pulmonary and systemic arteries, but, the snakes, nevertheless, lived to reach body weights severalfold of their hatchling weight. PMID:20063822

Jensen, Bjarke; Wang, Tobias

2009-12-01

171

APLpy: Astronomical Plotting Library in Python  

NASA Astrophysics Data System (ADS)

APLpy (the Astronomical Plotting Library in Python) is a Python module for producing publication-quality plots of astronomical imaging data in FITS format. The module uses Matplotlib, a powerful and interactive plotting package. It is capable of creating output files in several graphical formats, including EPS, PDF, PS, PNG, and SVG. Plots can be made interactively or by using scripts, and can generate co-aligned FITS cubes to make three-color RGB images. It also offers different overlay capabilities, including contour sets, markers with customizable symbols, and coordinate grids, and a range of other useful features.

Robitaille, Thomas; Bressert, Eli

2012-08-01

172

Python Ephemeris Module for Radio Astronomy  

NASA Astrophysics Data System (ADS)

An extension of the Python pyephem module was developed for Deep Space Network (DSN) radio astronomy. The class DSS( ) provides the geodetic coordinates of the DSN stations as well as other properties such as antenna diameter. The class Quasar( ) provides positional data for the sources in the National Radio Astronomy Observatory Very Large Array (NRAO VLA) Calibrator Handbook and flux estimates based the University of Michigan Radio Astronomy Observatory (UMRAO) Database or the VLA Calibrator Handbook. Flux calibration data are also available for the bright planets. Class Pulsar( ) provides the data from the Australia Telescope National Facility (ATNF) Pulsar Catalogue in Python format.

Kuiper, T. B.

2013-05-01

173

THE PYTHON SHELL FOR THE ORBIT CODE  

SciTech Connect

A development of a Python driver shell for the ORBIT simulation code is presented. The original ORBIT code uses the SuperCode shell to organize accelerator-related simulations. It is outdated, unsupported, and it is an obstacle to future code development. The necessity and consequences of replacing the old shell language are discussed. A set of core modules and extensions that are currently in PyORBIT are presented. They include particle containers, parsers for MAD and SAD lattice files, a Python wrapper for MPI libraries, space charge calculators, TEAPOT trackers, and a laser stripping extension module.

Shishlo, Andrei P [ORNL] [ORNL; Gorlov, Timofey V [ORNL] [ORNL; Holmes, Jeffrey A [ORNL] [ORNL

2009-01-01

174

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

Microsoft Academic Search

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

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

2002-01-01

175

Ecological divergence among sympatric colour morphs in blood pythons, Python brongersmai  

Microsoft Academic Search

Blood pythons in northeastern Sumatra display a series of discrete colour morphs, even among hatchlings within a single clutch.\\u000a The first step towards understanding the maintenance of this polymorphism is to test the null hypothesis that colour variation\\u000a in this species has no major biological correlates. Data on >2,000 blood pythons killed for the commercial leather industry\\u000a enabled us to

R. Shine; Ambariyanto; Peter S. Harlow; Mumpuni

1998-01-01

176

Python scripting in the nengo simulator.  

PubMed

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

2009-01-01

177

A Record-Breaking Invasive Burmese Python  

USGS Multimedia Gallery

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

178

A Record-Breaking Invasive Burmese Python  

USGS Multimedia Gallery

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

179

A Record-Breaking Invasive Burmese Python  

USGS Multimedia Gallery

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

180

Burmese Python Caught in the Everglades  

USGS Multimedia Gallery

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

181

Laboratory Project Norms for NLP courses (PLN, INLP, 1. Implementation should be done in Python  

E-print Network

in Python Python can be obtained from http://www.python.org/ where relevant documentation and material can tutorial can be found in http://docs.python.org/tutorial/ Whenever pieces of software in other languages (external or built by the student) are used, the corresponding interfaces from Python should be included

Ageno, Alicia

182

Evidence that neurotensin mediates postprandial intestinal hyperemia in the python, Python regius.  

PubMed

Digestion of large meals in pythons produces substantial increases in heart rate and cardiac output, as well as a dilation of the mesenteric vascular bed leading to intestinal hyperemia, but the mediators of these effects are unknown. Bolus intra-arterial injections of python neurotensin ([His(3), Val(4), Ala(7)]NT) (1 - 1,000 pmol/kg) into the anesthetized ball python Python regius (n = 7) produced a dose-dependent vasodilation that was associated with a decrease in systemic pressure (P(sys)) and increase in systemic blood flow (Q(sys)). There was no effect on pulmonary pressure and conductance. A significant (P < 0.05) increase in heart rate (f(H)) and total cardiac output (Q(tot)) was seen only at high doses (>30 pmol/kg). The systemic vasodilation and increase in Q(tot) persisted after beta-adrenergic blockade with propranolol, but the rise in f(H) was abolished. Also, the systemic vasodilation persisted after histamine H(2)-receptor blockade. In unanesthetized pythons (n = 4), bolus injection of python NT in a dose as low as 1 pmol/kg produced a significant increase in blood flow to the mesenteric artery (177% +/- 54%; mean +/- SE) and mesenteric conductance (219% +/- 74%) without any increase in Q(sys), systemic conductance, P(sys), and f(H). The data provide evidence that NT is an important hormonal mediator of postprandial intestinal hyperemia in the python, but its involvement in mediating the cardiac responses to digestion may be relatively minor. PMID:17567714

Skovgaard, Nini; Conlon, J Michael; Wang, Tobias

2007-09-01

183

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

184

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

185

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

E-print Network

: Zachary Derr Phone #: 801-538-3307 Email: zderr@utah.gov Item: Integrated Classroom which includes some or all of the following items: Sound System, Projectors, Document Cameras, White Boards, Student Response: N/A Price guarantee period: One Year Freight: Minimum order: $100 Min shipment without charges

Capecchi, Mario R.

186

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

E-print Network

: Zachary Derr Phone #: (801) 538-3307 Email: zderr@utah.gov Item: Integrated Classroom which includes some or all of the following items: Sound System, Projectors, Document Cameras, White Boards, Student Response: 21 Days Price guarantee period: Freight: Minimum order: $1 Min shipment without charges: New Contract

Capecchi, Mario R.

187

Design of a Modular Snake Robot Cornell Wright, Aaron Johnson, Aaron Peck, Zachary McCord, Allison Naaktgeboren,  

E-print Network

Design of a Modular Snake Robot Cornell Wright, Aaron Johnson, Aaron Peck, Zachary McCord, Allison such as size, power, and weight constrain the design of modular snake robots. Meeting these constraints of the mechanical and electrical architectures results in a robust and versatile robot. I. INTRODUCTION Snake robots

Choset, Howie

188

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

189

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

Federal Register 2010, 2011, 2012, 2013

...1018-AV68 Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...sebae), Southern African python (Python natalensis), boa constrictor (Boa constrictor), yellow anaconda (Eunectes...

2010-07-01

190

Stimfit: quantifying electrophysiological data with Python  

PubMed Central

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

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

2013-01-01

191

matplotlib -- A Portable Python Plotting Package  

NASA Astrophysics Data System (ADS)

matplotlib is a portable 2D plotting and imaging package aimed primarily at visualization of scientific, engineering, and financial data. matplotlib can be used interactively from the Python shell, called from python scripts, or embedded in a GUI application (GTK, Wx, Tk, Windows). Many popular hardcopy outputs are supported including JPEG, PNG, PostScript and SVG. Features include the creation of multiple axes and figures per page, interactive navigation, many predefined line styles and symbols, images, antialiasing, alpha blending, date and financial plots, W3C compliant font management and FreeType2 support, legends and tables, pseudocolor plots, mathematical text and more. It works with both numarray and Numeric. The goals of the package, basic architecture, current features (illustrated with examples), and planned enhancements will be described.

Barrett, P.; Hunter, J.; Miller, J. T.; Hsu, J.-C.; Greenfield, P.

2005-12-01

192

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

193

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

194

Copper Mountain 2011 Algebraic Multigrid Solvers in Python  

E-print Network

Copper Mountain 2011 Algebraic Multigrid Solvers in Python PyAMG Nathan Bell, Nvidia Luke Olson-->Accessories-->Terminal) #12;Task 0.1: Installing PyAMG $ tar -xvf pyamg2.0.tar.gz $ cd pyamg/ $ sudo python setup.py install interactive iPython session, enter: import pyamg pyamg.test() #12;What is PyAMG Algebraic multigrid (AMG

Olson, Luke

195

str's format Method For Introduction to Programming Using Python  

E-print Network

str's format Method For Introduction to Programming Using Python By Y. Daniel Liang The text integer and s for a string. For example, the following code print("{0:8s}{1:8d}{2:8.1f}".format("Python", 1234, 5.68)) displays Python12345.7 8 8 8 where the square box (·) denotes a blank space. Note

Liang, Y. Daniel

196

Saccular lung cannulation in a ball python (Python regius) to treat a tracheal obstruction.  

PubMed

An adult male ball python (Python regius) presented in a state of severe dyspnea characterized by open-mouth breathing and vertical positioning of the head and neck. The animal had copious discharge in the tracheal lumen acting as an obstruction. A tube was placed through the body wall into the caudal saccular aspect of the lung to allow the animal to breathe while treatment was initiated. The ball python's dyspnea immediately improved. Diagnostics confirmed a bacterial respiratory infection with predominantly Providencia rettgeri. The saccular lung (air sac) tube was removed after 13 days. Pulmonary endoscopy before closure showed minimal damage with a small amount of hemorrhage in the surrounding muscle tissue. Respiratory disease is a common occurrence in captive snakes and can be associated with significant morbidity and mortality. Saccular lung cannulation is a relatively simple procedure that can alleviate tracheal narrowing or obstruction, similar to air sac cannulation in birds. PMID:19368267

Myers, Debbie A; Wellehan, James F X; Isaza, Ramiro

2009-03-01

197

Predators in training: operant conditioning of novel behavior in wild Burmese pythons (Python molurus bivitattus).  

PubMed

Large pythons and boas comprise a group of animals whose anatomy and physiology are very different from traditional mammalian, avian and other reptilian models typically used in operant conditioning. In the current study, investigators used a modified shaping procedure involving successive approximations to train wild Burmese pythons (Python molurus bivitattus) to approach and depress an illuminated push button in order to gain access to a food reward. Results show that these large, wild snakes can be trained to accept extremely small food items, associate a stimulus with such rewards via operant conditioning and perform a contingent operant response to gain access to a food reward. The shaping procedure produced robust responses and provides a mechanism for investigating complex behavioral phenomena in massive snakes that are rarely studied in learning research. PMID:25139000

Emer, Sherri A; Mora, Cordula V; Harvey, Mark T; Grace, Michael S

2015-01-01

198

Ureka: A Distribution of Python and IRAF Software for Astronomy  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

199

Extensible message passing application development and debugging with Python  

SciTech Connect

The authors describe how they have parallelized Python, an interpreted object oriented scripting language, and used it to build an extensible message-passing C/C++ applications for the CM-5, Cray T3D, and Sun multiprocessor servers running MPI. Using a parallelized Python interpreter, it is possible to interact with large-scale parallel applications, rapidly prototype new features, and perform application specific debugging. It is even possible to write message passing programs in Python itself. The authors describe some of the tools they have developed to extend Python and applications of this approach.

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.

1996-09-19

200

Leveraging Python Interoperability Tools to Improve Sapphire's Usability  

SciTech Connect

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

Gezahegne, A; Love, N S

2007-12-10

201

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

202

Partial tracheal obstruction due to chondromas in ball pythons (Python regius).  

PubMed

Over a 9-mo period, three adult ball pythons (Python regius) (one male, two females) were evaluated for severe dyspnea. Partial obstructions of the tracheal lumen were identified radiographically and/or visualized with a 3.0-mm rigid laparoscope inserted into the tracheal lumen in all three snakes. Administration of systemic antibiotics and nebulization resulted in partial improvement of the dyspnea. In two snakes, the tracheal lesions were removed with a rigid laparoscope and a flexible biopsy instrument inserted into the tracheal lumen. The other snake died and was necropsied. Histologically, the lesions from two snakes were determined to be benign chondromas. The chondromas were composed of a variably disorganized chondroid matrix populated by quiescent, normal-appearing chondrocytes within lacunae, although the chondrocytes were increased in density compared with normal hyaline cartilage and contained rare mitotic figures. The tracheal masses in one snake grew by expansion, not invasion, and were focally continuous with a mineralized cartilage tracheal ring, suggesting a benign nature. This is the second report of tracheal chondroma in ball pythons. Tracheal chondromas are exceedingly rare in humans and domesticated animals, suggesting a possible predisposition of ball pythons for this neoplasm. PMID:10367658

Drew, M L; Phalen, D N; Berridge, B R; Johnson, T L; Bouley, D; Weeks, B R; Miller, H A; Walker, M A

1999-03-01

203

Trypanosoma cf. varani in an imported ball python (Python reginus) from Ghana.  

PubMed

Peripheral blood from a ball python (Python reginus) imported from Ghana was cultured in Barbour-Stoenner-Kelly (BSK) medium for Borrelia spp. isolation, resulting in the prominent appearance of free, and clusters of, trypanosomes in a variety of morphological forms. The molecular phylogenetic characterization of these cultured trypanosomes, using the small subunit rDNA, indicated that this python was infected with a species closely related to Trypanosoma varani Wenyon, 1908, originally described in the Nile monitor lizard (Varanus niloticus) from Sudan. Furthermore, nucleotide sequences of glycosomal glyceraldehyde-3-phosphate dehydrogenase gene of both isolates showed few differences. Giemsa-stained blood smears, prepared from the infected python 8 mo after the initial observation of trypanosomes in hemoculture, contained trypomastigotes with a broad body and a short, free flagellum; these most closely resembled the original description of T. varani, or T. voltariae Macfie, 1919 recorded in a black-necked spitting cobra (Naja nigricollis) from Ghana. It is highly possible that lizards and snakes could naturally share an identical trypanosome species. Alternatively, lizards and snakes in the same region might have closely related, but distinct, Trypanosoma species as a result of sympatric speciation. From multiple viewpoints, including molecular phylogenetic analyses, reappraisal of trypanosome species from a wide range of reptiles in Africa is needed to clarify the relationship of recorded species, or to unmask unrecorded species. PMID:20050011

Sato, Hiroshi; Takano, Ai; Kawabata, Hiroki; Une, Yumi; Watanabe, Haruo; Mukhtar, Maowia M

2009-08-01

204

Patterns of blood flow during the postprandial response in ball pythons, Python regius  

Microsoft Academic Search

We present evidence supporting the hypothesis that postprandial upregulation of the size of the small intestine and the liver is caused by an increased blood flow volume to the organs. The postprandial response of ball pythons was characterized by measurements of oxygen consumption, organ size changes and histological evaluation of the mucosal epithelium and liver parenchyme. Synchronized with these changes

J. Matthias Starck; Christian Wimmer

2005-01-01

205

Molecular genetic evidence for parthenogenesis in the Burmese python, Python molurus bivittatus  

Microsoft Academic Search

Parthenogenesis among reptiles is rare. Only a few species have the ability to reproduce asexually. Most of these are obligate parthenogenetic species that consist (almost) entirely of females, which can reproduce solely through parthenogenesis. Rarer are sexual species that only sporadically reproduce through parthenogenesis. A female Python molurus bivittatus (Reptilia, Boidae) from the Artis Zoo, Amsterdam, produced eggs in five

T. V. M. Groot; E Bruins; J A J Breeuwer; TVM Groot

2003-01-01

206

Python bite: an unusual cause of hand injury.  

PubMed

We report a patient that sustained a severe hand injury following a python bite. Python bite injuries are rare and we were unable to find guidelines in literature regarding the management of this injury. This report details our experience in managing this case and summarizes the available literature. PMID:24876681

Yak, Ryan Siqi; Lundin, Anna Carin; Peng, Yeong Pin; Sebastin, Sandeep Jacob

2014-06-01

207

Pcigale: Porting Code Investigating Galaxy Emission to Python  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

208

Building Scalable Services in Microsoft Azure with Python  

E-print Network

by the BLAST example. A Service #12;Building Scalable Services in Microsoft Azure with Python 2 Bus QueueBuilding Scalable Services in Microsoft Azure with Python This paper demonstrates how to use computing service. It uses Basic Local Alignment Search Tool (BLAST) queries as an example. BLAST

Narasayya, Vivek

209

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

210

A facility for creating Python extensions in C++  

SciTech Connect

Python extensions are usually created by writing the glue that connects Python to the desired new functionality in the C language. While simple extensions do not require much effort, to do the job correctly with full error checking is tedious and prone to errors in reference counting and to memory leaks, especially when errors occur. The resulting program is difficult to read and maintain. By designing suitable C++ classes to wrap the Python C API, we are able to produce extensions that are correct and which clean up after themselves correctly when errors occur. This facility also integrates the C++ and Python exception facilities. This paper briefly describes our package for this purpose, named CXX. The emphasis is on our design choices and the way these contribute to the construction of accurate Python extensions. We also briefly relate the way CXX's facilities for sequence classes allow use of C++'s Standard Template Library (STL) algorithms on C++ sequences.

Dubois, P F

1998-07-14

211

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

212

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

213

Rodents as intermediate hosts of Hepatozoon ayorgbor (Apicomplexa: Adeleina: Hepatozoidae) from the African ball python, Python regius?  

Microsoft Academic Search

Two experimental trials were performed to elucidate the role of rodents in the life cycle of Hepatozoon species using snakes as intermediate hosts. In one trial, two ball pythons, Python regius Shaw, 1802 were force fed livers of laboratory mice previously inoculated with sporocysts of Hepatozoon ayorgbor Sloboda, Kamler, Bulantov, Votpka et Modr, 2007. Transmis- sion was successful in these

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

214

Somatosensory and visual correlation in the optic tectum of a python, Python regius: a horseradish peroxidase and Golgi study  

Microsoft Academic Search

In snakes with infrared receptors the optic tectum receives infrared input in addition to visual and general somatosensory inputs. In order to observe their rectal termination patterns in ball pythons, Python regius, we injected horseradish peroxidase (HRP) into the nucleus of the lateral descending trigeminal tract (LTTD) which mediates infrared information, the optic nerve, and the nucleus of the trigeminal

Sonou Kobayashi; Fumiaki Amemiya; Reiji Kishida; Richard C. Goris; Toyokazu Kusunoki; Hironobu Ito

1995-01-01

215

Copyright Y. Daniel Liang, 2011 For Introduction to Programming Using Python  

E-print Network

© Copyright Y. Daniel Liang, 2011 1 Using IDLE For Introduction to Programming Using Python By Y environment (IDE) for Python. It is 100% pure Python and developed using Tkinter. It has a text editor with color syntax highlighting and automatic code indent. When you install Python, IDLE is automatically

Liang, Y. Daniel

216

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

E-print Network

PyTensor: A Python based Tensor Library Ji Oh Yoo Arvind Ramanathan Christopher J. Langmead and implementation of a python based library to perform multi-way analysis. Our results show that the python im described in [3]. However, with increasing support from the Python commu- nity for numerical and scientific

Langmead, Christopher James

217

COSMIC MICROWAVE BACKGROUND ANISOTROPY MEASUREMENT FROM PYTHON V K. Coble,1,2  

E-print Network

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

Souradeep, Tarun

218

A Semantics of Python in Isabelle/HOL James F. Ranson,  

E-print Network

A Semantics of Python in Isabelle/HOL James F. Ranson, Howard J. Hamilton and Philip W. L. Fong a formal definition for a programming language called IntegerPython, which is a subset of the Python with strategies for the efficient, executable implementation of the IntegerPython semantics and its extension

Hamilton, Howard J.

219

UCPy: Reverse-Engineering Python John Aycock David Pereira Georges Jodoin  

E-print Network

UCPy: Reverse-Engineering Python John Aycock David Pereira Georges Jodoin Department of Computer Introduction One of the recurring topics in the Python community is how to make Python pro- grams run faster programs into native code; translat- ing Python programs into Parrot/Lisp/.net code; applying research

Aycock, John

220

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

E-print Network

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes Todd A python (Python molurus bivittatus), a model of ex- treme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform

Castoe, Todd A.

221

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

E-print Network

to Linux and Python Date: 2011-09-09 =================================================== Goals for today ---------------------------- - To show you a command-line interpreter for Python - To show you how to use a command-line interpreter interactively - To show you some basics of the python language - To show you how to write python script

Reluga, Tim

222

1 Python Programming The previous Chapter provided an overview of modeling in optimization. The  

E-print Network

1 Python Programming The previous Chapter provided an overview of modeling in optimization. In this Chapter, we discuss a particular software language, namely Python, for developing various optimization algorithms. The reasons for choosing Python, over, say, Matlab or C++, are: (1) Python is free (2

Suresh, Krishnan

223

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

224

Morphological respiratory diffusion capacity of the lungs of ball pythons (Python regius).  

PubMed

This study aims at a functional and morphological characterization of the lung of a boid snake. In particular, we were interested to see if the python's lungs are designed with excess capacity as compared to resting and working oxygen demands. Therefore, the morphological respiratory diffusion capacity of ball pythons (Python regius) was examined following a stereological, hierarchically nested approach. The volume of the respiratory exchange tissue was determined using computed tomography. Tissue compartments were quantified using stereological methods on light microscopic images. The tissue diffusion barrier for oxygen transport was characterized and measured using transmission electron micrographs. We found a significant negative correlation between body mass and the volume of respiratory tissue; the lungs of larger snakes had relatively less respiratory tissue. Therefore, mass-specific respiratory tissue was calculated to exclude effects of body mass. The volume of the lung that contains parenchyma was 11.95.0mm(3)g(-1). The volume fraction, i.e., the actual pulmonary exchange tissue per lung parenchyma, was 63.227.3%; the total respiratory surface was, on average, 0.2140.129m(2); it was significantly negatively correlated to body mass, with larger snakes having proportionally smaller respiratory surfaces. For the air-blood barrier, a harmonic mean of 0.780.05?m was found, with the epithelial layer representing the thickest part of the barrier. Based on these findings, a median diffusion capacity of the tissue barrier ( [Formula: see text] ) of 0.690.38ml O(2)min(-1)mmHg(-1) was calculated. Based on published values for blood oxygen concentration, a total oxygen uptake capacity of 61.16mlO(2)min(-1)kg(-1) can be assumed. This value exceeds the maximum demand for oxygen in ball pythons by a factor of 12. We conclude that healthy individuals of P. regius possess a considerable spare capacity for tissue oxygen exchange. PMID:22770588

Starck, J Matthias; Aupperle, Heike; Kiefer, Ingmar; Weimer, Isabel; Krautwald-Junghanns, Maria-Elisabeth; Pees, Michael

2012-08-01

225

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

226

Preliminary single-dose pharmacokinetics of marbofloxacin in ball pythons (Python regius).  

PubMed

Pharmacokinetics of marbofloxacin in two male and four female adult ball pythons (Python regius) was determined after i.v. and p.o. administration of a single dose. Using a crossover design, each snake was given a single 10 mg/kg dose of marbofloxacin i.v. and p.o. Blood samples were collected prior to and 0.5, 1, 1.5, 3, 6, 12, and 24 hr after marbofloxacin administration. Marbofloxacin was quantitated by use of liquid chromatography-mass spectrometry. Following p.o. administration, marbofloxacin had a peak plasma concentration (Cmax) of 9.40 microg/ml and a time to Cmax (Tmax) of 9.0 hr. Based on the plasma pharmacokinetics generated in this study and pending any further studies to evaluate potential toxicity and multi-dose pharmacokinetics, we suggest a dosage for marbofloxacin in ball pythons of 10 mg/kg p.o. at least every 48 hr, depending on the sensitivity of the pathogen and as a basis for further research. PMID:17312805

Coke, Rob L; Isaza, Ramiro; Koch, David E; Pellerin, Marie A; Hunter, Robert P

2006-03-01

227

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

228

Scripting the Virtual Observatory in Python  

NASA Astrophysics Data System (ADS)

The VOClient package from the US Virtual Astronomical Observatory (VAO) provides a desktop or client-side interface to the Virtual Observatory (VO). The VO integrates data and services from many archives into a single unified system, allowing development of research tools which combine data from multiple sources. VOClient provides both ready to use tools for finding and retrieving data from remote archives, as well as support for user scripting to build custom applications. In this paper we focus on the capabilities provided by VOClient for developing user scripts or other applications which access remote data and services via the VO framework. A companion paper (Fitzpatrick et. al.) describes the user tools provided by VOClient. Initial support for application development using VOClient emphasizes Python scripting. Integration with high level environments such as IRAF and CASA is also provided.

Tody, Douglas; Fitzpatrick, M. J.; Graham, M.; Young, W.

2013-01-01

229

galpy: A python Library for Galactic Dynamics  

NASA Astrophysics Data System (ADS)

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

Bovy, Jo

2015-02-01

230

Neutron Scattering Experiment Automation with Python  

SciTech Connect

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory currently holds the Guinness World Record as the world most powerful pulsed spallation neutron source. Neutrons scattered off atomic nuclei in a sample yield important information about the position, motions, and magnetic properties of atoms in materials. A neutron scattering experiment usually involves sample environment control (temperature, pressure, etc.), mechanical alignment (slits, sample and detector position), magnetic field controllers, neutron velocity selection (choppers) and neutron detectors. The SNS Data Acquisition System (DAS) consists of real-time sub-system (detector read-out with custom electronics, chopper interface), data preprocessing (soft real-time) and a cluster of control and ancillary PCs. The real-time system runs FPGA firmware and programs running on PCs (C++, LabView) typically perform one task such as motor control and communicate via TCP/IP networks. PyDas is a set of Python modules that are used to integrate various components of the SNS DAS system. It enables customized automation of neutron scattering experiments in a rapid and flexible manner. It provides wxPython GUIs for routine experiments as well as IPython command line scripting. Matplotlib and numpy are used for data presentation and simple analysis. We will present an overview of SNS Data Acquisition System and PyDas architectures and implementation along with the examples of use. We will also discuss plans for future development as well as the challenges that have to be met while maintaining PyDas for 20+ different scientific instruments.

Zolnierczuk, Piotr A [ORNL] [ORNL; Riedel, Richard A [ORNL] [ORNL

2010-01-01

231

PyMC: Bayesian Stochastic Modelling in Python  

PubMed Central

This user guide describes a Python package, PyMC, that allows users to efficiently code a probabilistic model and draw samples from its posterior distribution using Markov chain Monte Carlo techniques. PMID:21603108

Patil, Anand; Huard, David; Fonnesbeck, Christopher J.

2010-01-01

232

Rabacus: A Python Package for Analytic Cosmological Radiative Transfer Calculations  

E-print Network

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

Altay, Gabriel

2015-01-01

233

ACPYPE - AnteChamber PYthon Parser interfacE  

E-print Network

AbstractBackgroundACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like...

Sousa da Silva, Alan W; Vranken, Wim F

2012-07-23

234

An Introduction to Python for UNIX\\/C Programmers  

Microsoft Academic Search

Python is an interpreted, object-oriented language suitable for many purposes. It has a clear, intuitive syntax, powerful high-level data structures, and a flexible dynamic type system. Python can be used interactively, in stand-alone scripts, for large programs, or as an extension language for existing applications. The language runs on UNIX, Macintosh, and DOS machines. Source and documentation are available by

Guido van Rossum

1993-01-01

235

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

236

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

237

Using Python to Develop Graphical Interfaces to Scientific Data  

SciTech Connect

At Lawrence Livermore National Laboratory (LLNL), Python has proven to be a convenient language for the development of graphical user interfaces (GUIs) which allow scientists to view, plot, and analyze scientific data. Two such applications are described in this paper. The first, EOSView, is a browser application for an equation of state data library at LLNL. EOSView is used by scientists throughout the laboratory who use simulation codes that access the data library, or who need equation of state data for other purposes. EOSView provides graphical visualization capabilities, as well as the capability to analyze the data in many different ways. The second application, Zimp, is a GUI that allows interactive use of the Stark Line Shape Database. It is used to access and plot data. The quick construction of Zimp from elements of the EOSView code provides a useful lesson in code reuse, and illustrates how the object-oriented nature of Python facilitates this goal. In general, Python has proven to be an appropriate choice of language for applications of this type for several reasons, including the easy access to GUI functionality provided by Tkinter, the ease with which C functions can be called from Python, and the convenient handling of strings in Python. Moreover, the features of the Python language, combined with the fact that it is interpreted rather than compiled, have allowed for extremely quick prototyping.

MacFarland, L; Streletz, G J

1999-09-24

238

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

239

The effects of UV light on calcium metabolism in ball pythons (Python regius).  

PubMed

Despite the popularity of keeping snakes in captivity, there has been limited investigation into the effects of UV radiation on vitamin D levels in snakes. The aim of this study was to investigate the effects of UV-b radiation on plasma 25-hydroxyvitamin D3 levels and ionised calcium concentrations in ball pythons (Python regius). Blood samples were taken from 14 ball pythons, which had never been exposed to UV-b light, to obtain baseline 25-hydroxyvitamin D3 levels and ionised calcium concentrations. Blood samples were then taken again from the same snakes 70 days later after one group (Group 1, n=6 females) were exposed to UV-b radiation daily, and the other group (Group 2, n=5 males and 3 females) were exposed to no UV-b radiation. Meansd 25-hydroxyvitamin D3 levels on day 0 in Group 1 were 19735 nmol/l, and on day 70 were 203.513.8 nmol/l. Meansd 25-hydroxyvitamin D3 levels in Group 2 on day 0 were 77.741.5 nmol/l, and on day 70 were 83.041.9 nmol/l. Meansd ionised calcium levels at day 0 were 1.840.05 mmol/l for Group 1, and on day 70 were 1.780.07 mmol/l. Meansd ionised calcium levels at day 0 were 1.790.07 mmol/l for Group 2, and on day 70 were 1.810.05 mmol/l. No association was demonstrated between exposure to UV-b radiation and plasma 25-hydroxyvitamin D3 and ionised calcium concentrations. These results may provide baseline parameters for future studies in this and other snake species to determine ability to utilise UV-b light for vitamin D production. PMID:24068697

Hedley, J; Eatwell, K

2013-10-12

240

Azithromycin metabolite identification in plasma, bile, and tissues of the ball python (Python regius).  

PubMed

Azithromycin is the first of a class of antibiotics classified as azalides. Six ball pythons (Python regius) were given a single dose of azithromycin at 10 mg/kg p.o. and i.v. in a crossover design. Serial blood samples were collected for unchanged azithromycin and to determine, if possible, the structure and number of circulating azithromycin metabolites. After a 4-month wash-out period, the snakes were given azithromycin p.o. as a single dose of 10 mg/kg for the study of azithromycin metabolism and metabolite tissue distribution. Bile, liver, lung, kidney, and skin samples were analyzed for the metabolites identified from the first experiment. Unchanged azithromycin accounted for 80, 68, and 60% of the total material at 12, 24, and 48 h postadministration in plasma, independent of route of administration. At both 24 and 72 h postadministration, azithromycin accounted for 70% of total azithromycin- associated material in bile. In liver and kidney, unchanged azithromycin accounted for 40% of the total azithromycin-associated material; this doubled in lung and skin. Fifteen metabolites were positively or tentatively identified in plasma, bile, or tissues of all snakes. Four of these possible metabolites: 3'-desamine-3-ene-azithromycin, descladinose dehydroxy-2-ene-azithromycin, 3'-desamine-3-ene descladinose-azithromycin, and 3'-N-nitroso,9a-N-desmethyl-azithromycin are unique to this species. Descladinose-azithromycin, 3'-N-desmethyl,9a-N-desmethyl-azithromycin, and 3'-N-desmethyl, 3'-O-desmethyl-azithromycin were the only metabolites identified in skin. Kidney tissue contained a greater number of metabolites than liver tissue, with 3'-N-didesmethyl-azithromycin being identified only in the kidney. Compared with the dog and cat, a greater number of metabolites were identified in ball python plasma. The percentage of unchanged azithromycin in bile is not different between the three species. PMID:12667181

Hunter, R P; Koch, D E; Coke, R L; Goatley, M A; Isaza, R

2003-04-01

241

PsychoPyPsychophysics software in Python  

PubMed Central

The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits. PMID:17254636

Peirce, Jonathan W.

2007-01-01

242

Python algorithms in particle tracking microrheology  

PubMed Central

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

2012-01-01

243

AJAC: Atomic data calculation tool in Python  

NASA Astrophysics Data System (ADS)

In this work, new features and extensions of a currently used online atomic database management system are reported. A multiplatform flexible computation package is added to the present system, to allow the calculation of various atomic radiative and collisional processes, based on simplifying the use of some existing atomic codes adopted from the literature. The interaction between users and data is facilitated by a rather extensive Python graphical user interface working online and could be installed in personal computers of different classes. In particular, this study gives an overview of the use of one model of the package models (i.e., electron impact collisional excitation model). The accuracy of computing capability of the electron impact collisional excitation in the adopted model, which follows the distorted wave approximation approach, is enhanced by implementing the Dirac R-matrix approximation approach. The validity and utility of this approach are presented through a comparison of the current computed results with earlier available theoretical and experimental results. Finally, the source code is made available under the general public license and being distributed freely in the hope that it will be useful to a wide community of laboratory and astrophysical plasma diagnostics.

Amani, Tahat; Jordi, Marti; Kaher, Tahat; Ali, Khwaldeh

2013-04-01

244

Patterns of blood flow during the postprandial response in ball pythons, Python regius.  

PubMed

We present evidence supporting the hypothesis that postprandial upregulation of the size of the small intestine and the liver is caused by an increased blood flow volume to the organs. The postprandial response of ball pythons was characterized by measurements of oxygen consumption, organ size changes and histological evaluation of the mucosal epithelium and liver parenchyme. Synchronized with these changes in measurements were changes in the patterns of blood flow volume to small intestine and liver. A correlation analysis of organ size change and blood flow volume showed a significant nonlinear relationship, which explained about 50% of the overall variances in organ size (small intestine, liver). Histological analysis indicated that incorporation of lipid droplets in enterocytes and in hepatocytes contributes to an increase of absorptive surface magnification (in small intestine) and hepatocyte size (in liver). Collectively, these data support the concept that in the ball python, postprandial upregulation of organ size does not reflect new mitotic activity, but rather results from increased blood volume in the intestinal villi and incorporation of lipid droplets into enterocytes and hepatocytes, respectively. PMID:15755886

Starck, J Matthias; Wimmer, Christian

2005-03-01

245

The spectacle of the ball python (Python regius): a morphological description.  

PubMed

A detailed morphological description of the spectacle of the ball python (Python regius) is provided. The eyes of 21 snakes were examined by light microscopy and/or transmission electron microscopy. Additionally, eyes of nine live snakes were examined using optical coherence tomography (OCT) and Scheimpflug scanning (Pentacam). The spectacle consists of three layers: outer epithelium, stroma and inner epithelium. The outer epithelium is made up of flat basal cells overlaid by keratin, the stroma consists of organized layers of collagen fibrils with interweaving nerve fibers and blood vessels, and the inner epithelium holds squamous cells containing vesicles and microvilli. At the rim of the spectacle, there is a transition zone, where the spectacle merges with the epidermis and dermis of the periocular scales. This zone is characterized by a greater height of the basal cells of the outer epithelium and a less orderly organization of the stroma compared with the spectacle proper. The thickness of the spectacle was uniform throughout. It averaged 96 10 m in histological specimens and 108 13 m using OCT. The subspectacular space was extremely narrow in the live snakes; however, the space was visible at the periphery of the spectacle with OCT. PMID:24375578

Da Silva, Mari-Ann O; Heegaard, Steffen; Wang, Tobias; Nyengaard, Jens R; Bertelsen, Mads F

2014-05-01

246

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

247

Cold-induced mortality of invasive Burmese pythons in south Florida  

Microsoft Academic Search

A recent record cold spell in southern Florida (211 January 2010) provided an opportunity to evaluate responses of an established\\u000a population of Burmese pythons (Python molurus bivittatus) to a prolonged period of unusually cold weather. We observed behavior, characterized thermal biology, determined fate of\\u000a radio-telemetered (n=10) and non-telemetered (n=104) Burmese pythons, and analyzed habitat and environmental conditions experienced by pythons

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

2011-01-01

248

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

E-print Network

Facile Synthesis of a Tungsten Alkylidyne Catalyst for Alkyne Metathesis Zachary J. Tonzetich, Yan cis double bonds. Tungsten alkylidyne trialkoxide alkyne metathesis catalysts were discovered in 1981 of cleavage of a tungsten-tungsten triple bond upon reaction with an alkyne or nitrile.9 Recent advances

Müller, Peter

249

A Tungsten(VI) Nitride Having a W2(-N)2 Core Zachary J. Tonzetich, Richard R. Schrock,* Keith M. Wampler, Brad C. Bailey,  

E-print Network

A Tungsten(VI) Nitride Having a W2(µ-N)2 Core Zachary J. Tonzetich, Richard R. Schrock,* Keith M-331, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 Received September 27, 2007 The tungsten that the tungsten alkylidyne species W(C-t-Bu)(CH2-t-Bu)(OAr)2 (Ar ) 2,6-diisopropylphenyl) can be prepared readily

Müller, Peter

250

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

251

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

252

Benign chondromy pr?dunice u krajty krlovsk (Python regius)  

Microsoft Academic Search

SUMMARY Hnzdo J., Hes O., Honsa V., Grgrov L. Benign tracheal chondromas in the ball python (Python regius). Veterinrn klinika 2007;4:123-127. The paper describes two cases of ball pythons presented due to acute respiratory distress. In the first case, with clinical examination, radiology and endoscopy the diagnosis of partial obstruction of multiple intratracheal masses was confirmed. Here it was possible

J. HNZDO; V. HONSA

253

L-Py, an open L-systems framework in Python Frdric Boudon1  

E-print Network

L-Py, an open L-systems framework in Python Frédéric Boudon1 , Thomas Cokelaer2 , Christophe Pradal Montpellier Cedex 5, France, frederic.boudon@cirad.fr Keywords: L-systems, Python, Plant Simulation Software with the Python high-level modeling language. In addition to this software module, an integrated visual

Paris-Sud XI, Université de

254

Exomerge user's manual : a lightweight Python interface for manipulating Exodus files.  

SciTech Connect

Exomerge is a lightweight Python module for reading, manipulating and writing data within ExodusII files. It is built upon a Python wrapper around the ExodusII API functions. This module, the Python wrapper, and the ExodusII libraries are available as part of the standard SIERRA installation.

Kostka, Timothy D.

2013-01-01

255

A quick review of basic Python commands and data structures for INFO-I485  

E-print Network

A quick review of basic Python commands and data structures for INFO-I485 Compiled by Santosh Manicka This is a quick review of some basic python should be able to run any piece on its own in python version 2.x

Rocha, Luis

256

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

E-print Network

APPENDIX A INSTALLING PYTHON THIS appendix explains how to install on your computer the software you will need for programming in the Python programming language. All of the software is distributed there are four software pack- ages you should install: the Python language itself, and the packages "numpy

Newman, Mark

257

A Python-based Framework for Distributed Programming and Rapid Prototyping of Distributed Programming Models  

E-print Network

A Python-based Framework for Distributed Programming and Rapid Prototyping of Distributed Python-based Framework for Distributed Programming and Rapid Prototyping of Distributed Programming Models Copyright 2009 by Alexey S. Fedosov ii #12;Abstract River is a Python-based framework for rapid

Fedosov, Alexey

258

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

E-print Network

PLANETENSTELSELS - WERKCOLLEGE 1A EN 1B Opdracht 1: Introductie Python Tijdens dit werkcollege en voorkomende natuurkundige formules. In deze eerste opdracht gaan we een python module maken die de waardes van deze functies en constanten terugkomen. (1) Maak een python module met de naam `astronomy' die

Hogerheijde, Michiel

259

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 that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python- based-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written

Sederberg, Per B.

260

The allometry of life-history traits: insights from a study of giant snakes (Python reticulatus)  

E-print Network

The allometry of life-history traits: insights from a study of giant snakes (Python reticulatus) R pythons from southern Sumatra to ask two questions: (i) do life-history traits show intraspeci at hatching and maximum adult size), these giant pythons were near or beyond the extremes reported for smaller

Keogh, Scott

261

Proceedings of the 7th Python in Science Conference (SciPy 2008)  

E-print Network

Proceedings of the 7th Python in Science Conference (SciPy 2008) Exploring Network Structure NetworkX is a Python language package for explo- ration and analysis of networks and network algo- rithmsX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibil- ity makes

Hagberg, Aric

262

Python-Ubung zur Vorlesung Algorithmische Bioinformatik Freie Universitat Berlin, WS 2012/13  

E-print Network

Python-¨Ubung zur Vorlesung Algorithmische Bioinformatik Freie Universit¨at Berlin, WS 2012¨asens¨ubung (16.10.2012) und dar¨uber hinaus. Freiwillige Abgabe am 22.10.2012 vor Beginn der Vorlesung 1 Python im interaktiven Interpreter Die interaktive Shell von Python bietet sich an, um schnell kleinere

Spang, Rainer

263

Proceedings of the 7th Python in Science Conference (SciPy 2008)  

E-print Network

Proceedings of the 7th Python in Science Conference (SciPy 2008) Mayavi: Making 3D Data to use, both by relying on standard numerical objects (numpy arrays) and by using the features of Python the com- mand line, · An embedded Python shell that can be used to script the application, · The ability

Paris-Sud XI, Université de

264

Technical report: CSVM dictionaries. Extension of CSVM-1 specification: definition, usages, Python toolkit.  

E-print Network

, Python toolkit. Frédéric Rodriguez a,b,* a CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d of concept, Perl and Python toolkits were designed in order to handle CSVM data and objects in workflows supported by the Python toolkit. This report presents a proposal for CSVM dictionaries, a working example

Paris-Sud XI, Université de

265

CptS 111 --Lab #2 Jan. 14, 2014 Exploring Python Basics  

E-print Network

CptS 111 -- Lab #2 Jan. 14, 2014 Exploring Python Basics Goal: There are two goals for this lab: (1) and interactively (using IDLE, an interactive development environment (IDE)) to run a Python program and (2) to use the Python language you've learned so far to implement two different programs. Task #1: Using IDLE and Saving

Broschat, Shira Lynn

266

Instruction Set Architecture of Mamba, a New Virtual Machine for Python  

E-print Network

Instruction Set Architecture of Mamba, a New Virtual Machine for Python David Pereira and John, Canada T2N 1N4 {pereira,aycock}@cpsc.ucalgary.ca TR 2002-706-09 Abstract: Python programs are implemented by compiling them into code for a virtual machine. Mamba is a new virtual machine for Python whose design

Aycock, John

267

A Python-Based Layout-Aware Analog Design Methodology For Nanometric Technologies.  

E-print Network

A Python-Based Layout-Aware Analog Design Methodology For Nanometric Technologies. St. A Python-based layout generation tool generates different layout styles for the same basic analog building and compared for different layout styles. The procedural layout description is written using a Python API

Paris-Sud XI, Université de

268

ACCURACY AND SPEED WE HAVE now seen the basic elements of programming in Python: input  

E-print Network

CHAPTER 4 ACCURACY AND SPEED WE HAVE now seen the basic elements of programming in Python: input. There are many additional features of the Python language that we haven't covered. In later chapters of the book, as well as lists and arrays. Python variables can hold numbers that span a wide range of values, including

Newman, Mark

269

IE 172 Laboratory 0: Setting Up Python and Eclipse Dr. T.K. Ralphs  

E-print Network

IE 172 Laboratory 0: Setting Up Python and Eclipse Dr. T.K. Ralphs Due January 23, 2014 1 of an integrated development environment (IDE). 2. Understand how to install and use the Eclipse IDE with Python and the PyDev. 3. Understand how to develop a simple Python application using Eclipse from scratch. 4

Ralphs, Ted

270

A Python interface with Narcisse graphics  

SciTech Connect

Narcisse is a graphics package developed by our French colleagues at Centre d`Etudes de Limeil Valenton of the Commissariat d`Energie Atomique. Narcisse is quite comprehensive; it can do two-, three-, and four-dimensional plots (the latter meaning that the surface is colored according to the values of an arbitrary function). One can open and send plots to a Narcisse window on a distant machine. Narcisse has a user-friendly graphical user interface (GUI) which, once a graph has appeared, allows the user to change its characteristics interactively. This enables one to find the best appearance for a particular plot without having to graph it repeatedly from the user program. Previously created files in various formats can also be imported directly into the Narcisse GUI and manipulated from there. Narcisse runs independently, as a graphics server. The user program communicates with Narcisse via Unix sockets. This communication is quite low level and very complex. The appearance of a plot is controlled by nearly 150 parameters for determining such things as the color palette, type of shading, axis scales, curve and surface labels, titles, angle and distance of view (for three- and four-dimensional graphs), hidden line removal, etc. Most end users do not wish to spend time learning the tedious details of such interfaces; they would just like to specify data and ask to have it plotted. This paper describes a high level, easy to use graphics interface which hides (as much as possible) the low level details of whatever graphics system is actually being used, so that the low level can be essentially ``plug-and-play.`` Then, whenever a better system becomes available, it should only be necessary to change low level interface routines not normally accessed by ordinary users. Python, with its easy extendability, was ideally suited for this job.

Motteler, Z.C.

1996-04-15

271

Advanced PANIC quick-look tool using Python  

NASA Astrophysics Data System (ADS)

PANIC, the Panoramic Near Infrared Camera, is an instrument for the Calar Alto Observatory currently being integrated in laboratory and whose first light is foreseen for end 2012 or early 2013. We present here how the PANIC Quick-Look tool (PQL) and pipeline (PAPI) are being implemented, using existing rapid programming Python technologies and packages, together with well-known astronomical software suites (Astromatic, IRAF) and parallel processing techniques. We will briefly describe the structure of the PQL tool, whose main characteristics are the use of the SQLite database and PyQt, a Python binding of the GUI toolkit Qt.

Ibez, Jos-Miguel; Garca Segura, Antonio J.; Storz, Clemens; Fried, Josef W.; Fernndez, Matilde; Rodrguez Gmez, Julio F.; Terrn, V.; Crdenas, M. C.

2012-09-01

272

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

273

Rainfall-Discharge Relationships for a Monsoonal Climate in the Ethiopian Highlands1 Ben M. Liu, Amy S. Collick, Gete Zeleke, Enyew Adgo, Zachary M. Easton, and Tammo S. Steenhuis*3  

E-print Network

, Amy S. Collick, Gete Zeleke, Enyew Adgo, Zachary M. Easton, and Tammo S. Steenhuis*3 Department such as TOPMODEL (Beven et al. 1984) and13 SMDR (Easton et al. 2007) have not yet been applied in the Ethiopian

Walter, M.Todd

274

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

E-print Network

Physics 212E Classical and Modern Physics Spring 2012 VPython Class 1: Introduction to Python/VPython 1 Getting Started We will edit and run Python programs (called scripts) from an interactive environment called IDLE. To start this, select · All Programs Python 3.1 IDLE (Python GUI) 3.1 · Up will pop

Vollmayr-Lee, Ben

275

Threat-Related Acoustical Differences in Alarm Calls by Wild Bonnet Macaques (Macaca radiata) Elicited by Python and  

E-print Network

) Elicited by Python and Leopard Models Richard G. Coss*, Brenda McCowan & Uma Ramakrishnanà * Department presentations of realistic models of spotted and dark leopards (Panthera pardus) and an Indian python (Python concealed views of the spotted morph. Four differ- ent forest troops were presented a slowly moving python

McCowan, Brenda

276

PYTHON PROGRAMMING FOR PHYSICISTS OUR FIRST item of business is to learn how to write computer programs in  

E-print Network

CHAPTER 2 PYTHON PROGRAMMING FOR PHYSICISTS OUR FIRST item of business is to learn how to write computer programs in the Python programming language. Python is easy to learn, simple to use or engineering in Python, surf the web or calculate your taxes, write words or write music, make a movie or make

Newman, Mark

277

Photodermatitis and photokeratoconjunctivitis in a ball python (Python regius) and a blue-tongue skink (Tiliqua spp.).  

PubMed

A male ball python (Python regius) and a female blue tongue skink (Tiliqua spp.) of unknown age were evaluated for anorexia, lethargy, excessive shedding, corneal opacity (python), and weight loss (skink) of approximately three weeks' duration. These animals represented the worst affected animals from a private herpetarium where many animals exhibited similar signs. At necropsy, the python had bilateral corneal opacity and scattered moderate dysecdysis. The skink had mild dysecdysis, poor body condition, moderate intestinal nematodiasis, and mild liver atrophy. Microscopic evaluation revealed epidermal erosion and ulceration, with severe epidermal basal cell degeneration and necrosis, and superficial dermatitis (python and skink). Severe bilateral ulcerative keratoconjunctivitis with bacterial colonization was noted in the ball python. Microscopic findings within the skin and eyes were suggestive of ultraviolet (UV) radiation damage or of photodermatitis and photokeratoconjunctivitis. Removal of the recently installed new lamps from the terrariums of the surviving reptiles resulted in resolution of clinical signs. Evaluation of a sample lamp of the type associated with these cases revealed an extremely high UV output, including very-short-wavelength UVB, neither found in natural sunlight nor emitted by several other UVB lamps unassociated with photokeratoconjunctivitis. Exposure to high-intensity and/or inappropriate wavelengths of UV radiation may be associated with significant morbidity, and even mortality, in reptiles. Veterinarians who are presented with reptiles with ocular and/or cutaneous disease of unapparent cause should fully evaluate the specifics of the vivarium light sources. Further research is needed to determine the characteristics of appropriate and of toxic UV light for reptiles kept in captivity. PMID:20063823

Gardiner, David W; Baines, Frances M; Pandher, Karamjeet

2009-12-01

278

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

279

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

280

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

281

PuLP: A Linear Programming Toolkit for Python  

E-print Network

Sep 5, 2011 ... are natural to the Python language, avoiding special syntax and keywords ... Several factors were considered in the design of PuLP and in the selection of .... AMPL and Pyomo, we need to do this before defining the model.

2011-09-05

282

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

283

Reticulated pythons in Sumatra: biology, harvesting and sustainability  

Microsoft Academic Search

Hundreds of thousands of giant snakes (Python reticulatus) are taken from the wild to be killed for their skins each year, raising doubts about the longterm sustainability of this offtake. We visited four locations in northern Sumatra (Medan, Seisuka, Rantauprapat and Cikampak) at four times of year and gathered information on the sizes, sexes, reproductive status and food habits of

Richard Shine; Ambariyanto; Peter S Harlow; Mumpuni

1999-01-01

284

Another breadth-first approach to CS I using python  

Microsoft Academic Search

In an effort to serve the needs of both majors and non-majors, the Computer Science Department at Centre College has restructured the CS I course so that it uses the language Python, devotes more attention to the Internet and the World Wide Web, addresses ethical and societal issues, and introduces students to programmable robots and an SQL database. This diverse

Christine Shannon

2003-01-01

285

Python robotics: an environment for exploring robotics beyond LEGOs  

Microsoft Academic Search

This paper describes Pyro, a robotics programming environment designed to allow inexperienced undergraduates to explore topics in advanced robotics. Pyro, which stands for Python Robotics, runs on a number of advanced robotics platforms. In addition, programs in Pyro can abstract away low-level details such that individual programs can work unchanged across very different robotics hardware. Results of using Pyro in

Douglas S. Blank; Lisa Meeden; Deepak Kumar

2003-01-01

286

FIRST IDENTIFICATION OF A RANAVIRUS FROM GREEN PYTHONS (CHONDROPYTHON VIRIDIS)  

Microsoft Academic Search

Ten juvenile green pythons (Chondropython viridis) died or were euthanized shortly after having been illegally imported into Australia from Indonesia in 1998. Histologic examination of two of the three snakes that died revealed moderately severe chronic ulceration of the nasal mucosa and focal or periacinar degeneration and necrosis of the liver. In addition there was severe necrotizing inflammation of the

A. D. Hyatt; M. Williamson; B. E. H. Coupar; D. Middleton; S. G. Hengstberger; A. R. Gould; P. Selleck; T. G. Wise; J. Kattenbelt; A. A. Cunningham; J. Lee

2002-01-01

287

Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications  

E-print Network

Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications Peter Bui, Dinesh Work Queue, a flexible master/- worker framework for building large scale scientific ensemble ap- plications that span many machines including clusters, grids, and clouds. In this paper, we describe Work

Thain, Douglas

288

Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese PythonPython molurus bivittatusManagement  

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

289

THE PHOTORECEPTORS AND VISUAL PIGMENTS IN THE RETINA OF A BOID SNAKE, THE BALL PYTHON (PYTHON REGIUS)  

Microsoft Academic Search

The photoreceptors and visual pigments of Python regius were studied using microspectrophotometry and scanning electron microscopy. The retina contains rods and cones, with rods constituting at least 90 % of the photoreceptor population. The rods are of a single type with long, narrow outer segments and are tightly packed. The wavelength of maximum absorbance (?max) of the visual pigment in

A. J. SILLMAN; J. K. CARVER; E. R. LOEW

1999-01-01

290

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

PubMed

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

Hunter, Margaret E; Hart, Kristen M

2013-01-01

291

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

292

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

293

Pharmacokinetics of a long-acting ceftiofur formulation (ceftiofur crystalline free acid) in the ball python (Python regius).  

PubMed

The objective of this study was to determine the pharmacokinetics of a long-acting formulation of ceftiofur crystalline-free acid (CCFA) following intramuscular injection in ball pythons (Python regius). Six adult ball pythons received an injection of CCFA (15 mg/kg) in the epaxial muscles. Blood samples were collected by cardiocentesis immediately prior to and at 0.5, 1, 2, 4, 8, 12, 18, 24, 48, 72, 96, 144, 192, 240, 288, 384, 480, 576, 720, and 864 hr after CCFA administration. Plasma ceftiofur concentrations were determined by high-performance liquid chromatography. A noncompartmental pharmacokinetic analysis was applied to the data. Maximum plasma concentration (Cmax) was 7.096 +/- 1.95 microg/ml and occurred at (Tmax) 2.17 +/- 0.98 hr. The area under the curve (0 to infinity) for ceftiofur was 74.59 +/- 13.05 microg x h/ml and the elimination half-life associated with the terminal slope of the concentration-time curve was 64.31 +/- 14.2 hr. Mean residence time (0 to infinity) was 46.85 +/- 13.53 hr. CCFA at 15 mg/kg was well tolerated in all the pythons. Minimum inhibitory concentration (MIC) data for bacterial isolates from snakes are not well established. For MIC values of < or =0.1 microg/ml, a single dose of CCFA (15 mg/kg) provides adequate plasma concentrations for at least 5 days in the ball python. For MICs > or =0.5 microg/ml, more frequent dosing or a higher dosage may be required. PMID:22950317

Adkesson, Michael J; Fernandez-Varon, Emilio; Cox, Sherry; Martn-Jimnez, Toms

2011-09-01

294

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

295

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

296

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

297

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

298

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

299

ViPEr, a Visual Programming Environment for Python  

Microsoft Academic Search

In this paper we describe a Python-and Tkinter-based visual-programming environment called ViPEr. This tool enables non-programmers to build computational and visualization networks interactively. Computational nodes can be placed onto a canvas and their input and output ports can be connected using the mouse. The connections between the nodes define a directed graph that will be used to propagate data and

Michel F. Sanner; Daniel. Stoffler; Arthur J. Olson

300

Extensible Message Passing Application Development and Debugging with Python  

Microsoft Academic Search

We describe how we have parallelized Python, an in- terpreted object oriented scripting language, and used it to build an extensible message-passing molecular dynam- ics application for the CM-5, Cray T3D, and Sun multi- processor servers running MPI. This allows us to interact with large-scale message-passing applications, rapidly pro- totype new features, and perform application specific de- bugging. It is

David M. Beazley; Peter S. Lomdahl

1997-01-01

301

GAiN: Distributed Array Computation with Python  

SciTech Connect

Scientific computing makes use of very large, multidimensional numerical arrays - typically, gigabytes to terabytes in size - much larger than can fit on even the largest single compute node. Such arrays must be distributed across a "cluster" of nodes. Global Arrays is a cluster-based software system from Battelle Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate these arrays. Written in and for the C and FORTRAN programming languages, it takes advantage of high-performance cluster interconnections to allow any node in the cluster to access data on any other node very rapidly. The "numpy" module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. numpy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, numpy is inherently serial. Our system, GAiN (Global Arrays in NumPy), is a parallel extension to Python that accesses Global Arrays through numpy. This allows parallel processing and/or larger problem sizes to be harnessed almost transparently within new or existing numpy programs.

Daily, Jeffrey A.

2009-04-24

302

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

303

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

2014-01-01

304

BioC implementations in Go, Perl, Python and Ruby.  

PubMed

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

2014-01-01

305

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

306

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

307

Rodents as intermediate hosts of Hepatozoon ayorgbor (Apicomplexa: Adeleina: Hepatozoidae) from the African ball python, Python regius?  

PubMed

Two experimental trials were performed to elucidate the role of rodents in the life cycle of Hepatozoon species using snakes as intermediate hosts. In one trial, two ball pythons, Python regius Shaw, 1802 were force fed livers of laboratory mice previously inoculated with sporocysts of Hepatozoon ayorgbor Sloboda, Kamler, Bulantov, Votpka et Modr, 2007. Transmission was successful in these experimentally infected snakes as evidenced by the appearance of intraerythrocytic gamonts, which persisted until the end of trial, 12 months after inoculation. Developmental stages of haemogregarines were not observed in histological sections from mice. In another experimental trial, a presence of haemogregarine DNA in mice inoculated with H. ayorgbor was demonstrated by PCR in the liver, lungs and spleen. PMID:18578163

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

2008-03-01

308

INSTALLING PYTHON 3.2.3 ON MAC OS X (10.6, 10.7, and 10.8) 1. Visit python.org/download/ and download the Mac installer. It will be called  

E-print Network

INSTALLING PYTHON 3.2.3 ON MAC OS X (10.6, 10.7, and 10.8) 1. Visit python.org/download/ and download the Mac installer. It will be called Python 3.2.3 Mac OS X 64-bit/32-bit x86-64/i386 Installer. 2 saved it to) and double-click to mount it. It will be named python-3.2.3-macosx10.6.dmg. The disk image

Stephenson, Ben

309

Life History Consequences of Nest-Site Variation in Tropical Pythons (Liasis fuscus)  

Microsoft Academic Search

We document and interpret microgeographic variation in life history traits of water pythons (Liasis fuscus) on the Adelaide River floodplain in tropical Australia. Subpopulations of pythons separated by ,2 km differ in reproductive timing, in survival rates at three different life history stages (adults, embryos, and hatchlings), in costs of reproduction, and in reproductive frequencies. Remarkably, these differences all seem

Thomas Madsen; Richard Shine

1999-01-01

310

The Molecular Modeling Toolkit: a case study of a large scientific application in Python  

Microsoft Academic Search

The Molecular Modeling Toolkit is a library of Python modules and C extension modules that provides an object-oriented description of molecular systems and an implementation of the most common modeling tech- niques. It is one of the first large scientific applica- tions implemented in Python. This article presents some aspects of its design and implementation that are typi- cal for

Konrad Hinsen

1997-01-01

311

Effects of temperature on the metabolic response to feeding in Python molurus  

Microsoft Academic Search

As ectothermic vertebrates, reptiles undergo diurnal and seasonal changes in body temperature, which affect many biological functions. In conjunction with a general review regarding the effects of temperature on digestion in reptiles, we describe the effects of various temperatures (2035 C) on the metabolic response to digestion in the Burmese python (Python molurus). The snakes were fed mice amounting to

Tobias Wang; Morten Zaar; Sine Arvedsen; Christina Vedel-Smith; Johannes Overgaard

2002-01-01

312

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

USGS Multimedia Gallery

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

2009-10-12

313

2012 M. Scott Shell 1/24 last modified 4/10/2012 Writing fast Fortran routines for Python  

E-print Network

© 2012 M. Scott Shell 1/24 last modified 4/10/2012 Writing fast Fortran routines for Python Table............................................................................................................................... 22 Importing and using f2py-compiled modules in Python ............................................................................................ 24 #12;© 2012 M. Scott Shell 2/24 last modified 4/10/2012 Overview Python, unfortunately, does

Shell, M. Scott

314

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 by the computer ·Toimporovefunctionalityandwork-flowofaGUIoriginallyde- signedinMATLABusingtheopen-sourcelanguage,Python ·To learn about the advantages of Python over MATLAB and best make use of its features to build a more

Barthelat, Francois

315

Bayes Blocks: A Python Toolbox for Variational Bayesian Antti Honkela, Markus Harva, Tapani Raiko, Harri Valpola, and Juha Karhunen  

E-print Network

Bayes Blocks: A Python Toolbox for Variational Bayesian Learning Antti Honkela, Markus Harva variables [2]. The underlying inference engine has been implemented in C++ with Python bindings to allow developing new models in Python. Version 1.0 of the software was released in July 2005 under the GNU GPL

Honkela, Antti

316

An OpenModelica Python Interface and its use in PySimulator Anand Kalaiarasi Ganeson1  

E-print Network

An OpenModelica Python Interface and its use in PySimulator Anand Kalaiarasi Ganeson1 , Peter.Pfeiffer@dlr.de Abstract How can Python users be empowered with the robust simulation, compilation and scripting abilities and simula- tion environment that would bridge the gap between the two agile programming languages Python

Zhao, Yuxiao

317

LASER STRIPPING COMPUTING WITH THE PYTHON ORBIT CODE  

SciTech Connect

The laser assisted hydrogen stripping becomes a widely discussed alternative for the existing stripping foil approach. The simulation tool for this new approach is presented. The created application is implemented in form of extension module to the Python ORBIT parallel code that is under development at the SNS. The physical model of the application deals with quantum theory and allows calculating evolution and ionization of hydrogen atoms and ions affected by superposition of electromagnetic and laser fields. The algorithm, structure, benchmark cases, and results of simulations for several future and existing accelerators are discussed.

Gorlov, Timofey V [ORNL] [ORNL; Shishlo, Andrei P [ORNL] [ORNL

2009-01-01

318

PyVO: Python access to the Virtual Observatory  

NASA Astrophysics Data System (ADS)

PyVO provides access to remote data and services of the Virtual observatory (VO) using Python. It allows archive searches for data of a particular type or related to a particular topic and query submissions to obtain data to a particular archive to download selected data products. PyVO supports querying the VAO registry; simple data access services (DAL) to access images (SIA), source catalog records (Cone Search), spectra (SSA), and spectral line emission/absorption data (SLAP); and object name resolution (for converting names of objects in the sky into positions). PyVO requires both AstroPy and NumPy.

Graham, Matthew; Plante, Ray; Tody, Doug; Fitzpatrick, Mike

2014-02-01

319

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

PubMed

The serum concentration of amikacin following intracardiac and i.m. administration of amikacin (3.48 mg/kg) in 12 ball pythons (Python regius) housed at 25 degrees C and 37 degrees C was studied. Blood samples were collected by cardiocentesis at intervals up to 144 hr after administration of amikacin. Drug concentration-versus-time curves following intracardiac administration at both temperatures best fit a two-compartment open model. For snakes housed at 37 degrees C, the extrapolated time 0 concentration (mean +/- SD) was 17.64 +/- 3.5 micrograms/ml with a median elimination half-life of 4.5 days. The maximum concentrations were 11.98 +/- 1.67 micrograms/ml and 13.87 +/- 2.61 micrograms/ml for snakes housed at 25 degrees C and 37 degrees C respectively. There were no significant pharmacokinetic differences among the snakes housed at 25 degrees C and 37 degrees C. Model-independent parameters were area under the curve, 69,900 +/- 0.011 micrograms.min/ml, apparent volume of distribution at steady state, 410 +/- 106 ml/kg, clearance, 0.036 +/- 0.009 ml/min/kg, and mean residence time, 3,530 +/- 273.7 minutes. Mean serum amikacin concentrations did not reach the recommended therapeutic peak concentrations for mammals (25 micrograms/ml). In addition, the amikacin serum concentration did not fall below the recommended therapeutic trough concentrations (2 micrograms/ml) by 6 days. The serum amikacin concentrations were efficacious based on the area under the curve. Therefore, amikacin (3.48 mg/kg) administered i.m. to ball pythons should produce maximum serum concentrations against most pathogenic bacteria. In this study, it would have taken another half-life, or 4.5 days, before trough concentrations of 2 micrograms/ml were achieved. To prevent accumulation, a one-time administration of amikacin may be appropriate. PMID:9226620

Johnson, J H; Jensen, J M; Brumbaugh, G W; Boothe, D M

1997-03-01

320

How to use python on the lab machines: -Log in to the system using your CoE account username and password.  

E-print Network

How to use python on the lab machines: - Log in to the system using it and go back to the terminal window - Type `python pa01.py'. This will compile your file. - Now type `python'. You will see the `>>>' python prompt. - Now

321

PyFACT: Python and FITS analysis for Cherenkov telescopes  

NASA Astrophysics Data System (ADS)

Ground-based very-high energy (VHE; E>100 GeV) gamma-ray astronomy is growing from being conducted by small teams in closed collaborations into a full-fledged branch of astronomy with open observatories. This is best illustrated by the number of known sources: it increased by one order of magnitude in the past ten years, from 10 in the year 2000 to more than 100 in 2010. It is expected that this trend will continue with the next-generation instrument Cherenkov Telescope Array (CTA). This transformation has a profound impact on the data format and analysis of Imaging Atmospheric Cherenkov Telescopes (IACTs). Up to now, IACT data analysis was an internal task performed by specialists with no public access to the data or software. In the future, a large community of VHE astronomers from different scientific topics should be enabled to work with the data. Ease of use, compatibility, and integration with existing astronomy standards and tools will be key. In this contribution, a collection of Python tools for the analysis of data in FITS format (PyFACT; Python and FITS Analysis for Cherenkov Telescopes) is presented, which connects with existing tools like xspec, sherpa, and ds9. The package is available as open source (https://github.com/mraue/pyfact, comments and contributions welcome). Advantages of the chosen ansatz are discussed and implications for future observatories and data archival are presented.

Raue, Martin; Deil, Christoph

2012-12-01

322

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

323

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

324

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

325

SClib, a hack for straightforward embedded C functions in Python  

E-print Network

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

Fuentes, Esteban

2014-01-01

326

Conservative constraints on early cosmology with MONTE PYTHON  

SciTech Connect

Models for the latest stages of the cosmological evolution rely on a less solid theoretical and observational ground than the description of earlier stages like BBN and recombination. As suggested in a previous work by Vonlanthen et al., it is possible to tweak the analysis of CMB data in such way to avoid making assumptions on the late evolution, and obtain robust constraints on ''early cosmology parameters''. We extend this method in order to marginalise the results over CMB lensing contamination, and present updated results based on recent CMB data. Our constraints on the minimal early cosmology model are weaker than in a standard ?CDM analysis, but do not conflict with this model. Besides, we obtain conservative bounds on the effective neutrino number and neutrino mass, showing no hints for extra relativistic degrees of freedom, and proving in a robust way that neutrinos experienced their non-relativistic transition after the time of photon decoupling. This analysis is also an occasion to describe the main features of the new parameter inference code MONTE PYTHON, that we release together with this paper. MONTE PYTHON is a user-friendly alternative to other public codes like COSMOMC, interfaced with the Boltzmann code CLASS.

Audren, Benjamin; Lesgourgues, Julien [Institut de Thorie des Phnomnes Physiques, cole Polytechnique Fdrale de Lausanne, CH-1015, Lausanne (Switzerland); Benabed, Karim; Prunet, Simon, E-mail: benjamin.audren@epfl.ch, E-mail: Julien.Lesgourgues@cern.ch, E-mail: benabed@iap.fr, E-mail: prunet@iap.fr [Institute d'Astrophysique de Paris, 98 Bd Arago, F-75014 Paris (France)

2013-02-01

327

Installing python software packages : the good, the bad and the ugly.  

SciTech Connect

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

Hart, William Eugene

2010-11-01

328

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators  

PubMed Central

Background Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. Results The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Conclusions Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/ PMID:21210978

2010-01-01

329

Somatosensory and visual correlation in the optic tectum of a python, Python regius: a horseradish peroxidase and Golgi study.  

PubMed

In snakes with infrared receptors the optic tectum receives infrared input in addition to visual and general somatosensory inputs. In order to observe their tectal termination patterns in ball pythons, Python regius, we injected horseradish peroxidase (HRP) into the nucleus of the lateral descending trigeminal tract (LTTD) which mediates infrared information, the optic nerve, and the nucleus of the trigeminal descending tract (TTD) which relays general somatosensory information. Fibers from LTTD were found in layers 5-13 of the contralateral optic tectum, and were especially dense in layers 7a-8. Optic nerve fibers terminated in layers 7a-13 of the contralateral tectum, and mainly in layers 12-13. TTD fibers were few, and could be seen in only the rostral half of the contralateral tectum. These fibers were found in layers 5-7b, but mainly in layers 6-7a. Among various types of neurons stained by the Golgi-Cox method, we focused on six types of neurons whose dendritic arborization overlapped with the distribution of the terminals of these sensory afferents described above. It is possible that these different sensory modalities converge on a single neuron of the various types. PMID:7478295

Kobayashi, S; Amemiya, F; Kishida, R; Goris, R C; Kusunoki, T; Ito, H

1995-06-01

330

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

331

AstroAsciiData: Table Handling in Python  

NASA Astrophysics Data System (ADS)

Tabulated character strings and numbers in text files are one of the most widespread data exchange format in astronomy and science in general. Presented here is version 1.0 of the Python module AstroAsciiData. This module is a lightweight framework that provides convenient access to table data and supports the common chore of writing scripts to read, manipulate and write the data. Well-formed tables are automatically parsed and transformed into objects, which allows a very convenient and intuitive data manipulation. Version 1.0 of the AstroAsciiData module uses metadata stored in the header of the ubiquitous SExtractor output catalogues and provides transformations to other data formats such as FITS or HTML.

Haase, J.; Kmmel, M.

2007-10-01

332

A pseudo-parallel Python environment for database curation  

E-print Network

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.

Eckhard Sutorius; Johann Bryant; Ross Collins; Nicholas Cross; Nigel Hambly; Mike Read

2007-11-13

333

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

334

PyORBIT: A Python Shell For ORBIT  

SciTech Connect

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

Jean-Francois Ostiguy; Jeffrey Holmes

2003-07-01

335

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

E-print Network

Safe Asynchronous Exceptions For Python #3; Williams College Technical Note 02-2002, Dec. 2002 Stephen N. Freund Mark P. Mitchell Department of Computer Science CodeSourcery, LLC Williams College 9978

Freund, Stephen N.

336

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit  

E-print Network

Abstract 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...

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

2008-03-09

337

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

USGS Publications Warehouse

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 2136 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.

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

2014-01-01

338

Obtaining and processing Daymet data using Python and ArcGIS  

USGS Publications Warehouse

This set of scripts was developed to automate the process of downloading and mosaicking daily Daymet data to a user defined extent using ArcGIS and Python programming language. The three steps are downloading the needed Daymet tiles for the study area extent, converting the netcdf file to a tif raster format, and mosaicking those rasters to one file. The set of scripts is intended for all levels of experience with Python programming language and requires no scripting by the user.

Bohms, Stefanie

2013-01-01

339

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

340

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

341

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

342

Python CS1 as Preparation for C++ CS2 Richard J. Enbody, William F. Punch, Mark McCullen  

E-print Network

Python CS1 as Preparation for C++ CS2 Richard J. Enbody, William F. Punch, Mark McCullen Department,punch,mccullen]@cse.msu.edu ABSTRACT How suitable is a Python-based CS1 course as preparation for a C++-based CS2 course? After fifteen changed the CS1 course to Python. This paper examines the impact of that change on the second course

343

AstroML: Python-powered Machine Learning for Astronomy  

NASA Astrophysics Data System (ADS)

As astronomical data sets grow in size and complexity, automated machine learning and data mining methods are becoming an increasingly fundamental component of research in the field. The astroML project (http://astroML.org) provides a common repository for practical examples of the data mining and machine learning tools used and developed by astronomical researchers, written in Python. The astroML module contains a host of general-purpose data analysis and machine learning routines, loaders for openly-available astronomical datasets, and fast implementations of specific computational methods often used in astronomy and astrophysics. The associated website features hundreds of examples of these routines being used for analysis of real astronomical datasets, while the associated textbook provides a curriculum resource for graduate-level courses focusing on practical statistics, machine learning, and data mining approaches within Astronomical research. This poster will highlight several of the more powerful and unique examples of analysis performed with astroML, all of which can be reproduced in their entirety on any computer with the proper packages installed.

Vander Plas, Jake; Connolly, A. J.; Ivezic, Z.

2014-01-01

344

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

345

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

346

Screening_mgmt: A Python Module for Managing Screening Data.  

PubMed

High-throughput screening is an established technique in drug discovery and, as such, has also found its way into academia. High-throughput screening generates a considerable amount of data, which is why specific software is used for its analysis and management. The commercially available software packages are often beyond the financial limits of small-scale academic laboratories and, furthermore, lack the flexibility to fulfill certain user-specific requirements. We have developed a Python module, screening_mgmt, which is a lightweight tool for flexible data retrieval, analysis, and storage for different screening assays in one central database. The module reads custom-made analysis scripts and plotting instructions, and it offers a graphical user interface to import, modify, and display the data in a uniform manner. During the test phase, we used this module for the management of 10,000 data points of various origins. It has provided a practical, user-friendly tool for sharing and exchanging information between researchers. PMID:25381290

Helfenstein, Andreas; Tammela, Pivi

2015-02-01

347

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

348

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

E-print Network

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

Revell, Liam

349

January 11, 2006 1. Write a python program to compute n! assuming n > 0 and print the result. Take the following as  

E-print Network

Exercise 1 CAO Shiqi January 11, 2006 1. Write a python program to compute n! assuming n > 0__ == "__main__": n = int(sys.argv[1]) #get command line argument and convert it to int Example output: > python fact.py 5 120 2. Write a python program to test if the input n is a primer number or not

Carette, Jacques

350

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

351

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

352

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

E-print Network

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

Souradeep, Tarun

353

[Transfer of exotic tick Aponomma latum (Koch, 1844) (Acari: Ixodida: Ixodidae) on ball pythons (Python regius Shaw, 1802) brought to Poland].  

PubMed

103 specimens of Python regius brought to Poland between October 2002 and March 2004 were examined. Occurrence of tick Aponomma latum was reported from 80.6% of the examined reptiles. 549 specimens of A. latum were collected including 341 males, 149 females and 59 nymphs at the various stage of engorgement. Tick A. latum is frequently transferred beyond its natural range of occurrence--Afrotropical region. PMID:16859046

Siuda, Krzysztof; Nowak, Magdalena; Kedryna, Mariusz

2004-01-01

354

Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom.  

PubMed

Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, including information from tissue-specific patterns of gene expression. We identified the orthologs of snake venom genes in the python genome, and conducted detailed analysis of gene expression of these venom homologs to identify patterns that differ between snake venom gene families and all other genes. We found that venom gene homologs in the python are expressed in many different tissues outside of oral glands, which illustrates the pitfalls of using transcriptomic data alone to define "venom toxins." We hypothesize that the python may represent an ancestral state prior to major venom development, which is supported by our finding that the expansion of venom gene families is largely restricted to highly venomous caenophidian snakes. Therefore, the python provides insight into biases in which genes were recruited for snake venom systems. Python venom homologs are generally expressed at lower levels, have higher variance among tissues, and are expressed in fewer organs compared with all other python genes. We propose a model for the evolution of snake venoms in which venom genes are recruited preferentially from genes with particular expression profile characteristics, which facilitate a nearly neutral transition toward specialized venom system expression. PMID:25338510

Reyes-Velasco, Jacobo; Card, Daren C; Andrew, Audra L; Shaney, Kyle J; Adams, Richard H; Schield, Drew R; Casewell, Nicholas R; Mackessy, Stephen P; Castoe, Todd A

2015-01-01

355

PyTrilinos: High-performance distributed-memory solvers for Python  

Microsoft Academic Search

PyTrilinos is a collection of Python modules that are useful for serial and parallel scientific computing. This collection contains modules that cover serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, domain decomposition and multilevel preconditioners, nonlinear solvers, and continuation algorithms. Also included are a variety of related utility functions and

Marzio Sala; William F. Spotz; Michael A. Heroux

2008-01-01

356

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

357

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

358

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

359

PyCOOL A Cosmological Object-Oriented Lattice code written in Python  

Microsoft Academic Search

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

J. Sainio

2012-01-01

360

Data management routines for reproducible research using the G-Node Python Client library.  

PubMed

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow. PMID:24634654

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J; Garbers, Christian; Rautenberg, Philipp L; Wachtler, Thomas

2014-01-01

361

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

USGS Multimedia Gallery

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

362

PyHelp - An automatic multi-output documentation generator for Python  

SciTech Connect

The DRACO code creates geometry and meshes through a command-line Python interface consisting of hundreds of classes and modules which must be accompanied by current documentation. The standard Python utility pydoc performs introspection on objects and prints their associated documentation strings verbatim. However, pydoc supports only very rudimentary formatting and cannot produce printable documentation. We decided to modify pydoc to process formatted ''docstrings'' and use the Doxygen tool to generate the needed forms of documentation. Codes with complex interfaces often require substantial effort to keep user documentation current with interface changes. The DRACO code creates geometry and meshes through a command-line Python interface consisting of hundreds of classes and thousands of functions. A previous attempt to write documentation manually quickly fell out of date, so the development team needed to find an alternative. The existing tools did not provide the flexibility we needed, and the team was already conversant in Doxygen, a C++ code-documenting utility with a simple tag-based markup. Python comes with a utility, pydoc, that performs introspection on objects and prints their docstrings verbatim. However, pydoc supports only very rudimentary formatting and cannot produce printable documentation. Thus we decided to create ''docstrings'' written in Doxygen syntax for each object and process them with a modified pydoc to generate the needed forms of documentation.

Nissen, W I

2005-02-10

363

Feeding Habits of the Diamond Python, Morelia s. spilota: Ambush Predation by a Boid Snake  

Microsoft Academic Search

Diamond pythons (Morelia s. spilota) are large (to 3 m) snakes of temperate-zone coastal eastern Australia. Foraging behavior was studied by observation of telemetered snakes, and diets deter- mined by dissection of museum specimens and collection of fecal samples from wild-caught snakes. Five adult snakes monitored in the field by radiotelemetry were found to be ambush foragers. In summer, telemetered

VID J. SLIP; RICHARD SHINE

364

GPAW - massively parallel electronic structure calculations with Python-based software.  

SciTech Connect

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used this approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.

Enkovaara, J.; Romero, N.; Shende, S.; Mortensen, J. (LCF)

2011-01-01

365

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

366

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

Microsoft Academic Search

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

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

2009-01-01

367

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity  

Microsoft Academic Search

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test

Lesley H. Rawlings; Stephen C. Donnellan

2003-01-01

368

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

369

Large snakes in a mosaic rural landscape: The ecology of carpet pythons Morelia spilota (serpentes: Pythonidae) in coastal eastern Australia  

Microsoft Academic Search

How can large pythons coexist with human beings in highly modified habitats throughout the eastern coastal region of Australia, when the same species has undergone rapid declines in other parts of the country? To investigate this question, we surgically implanted miniature temperature-sensitive radiotransmitters into 19 adult carpet pythons Morelia spilota (body lengths 1328 m; 1470 kg) from two study sites

R. Shine; M. Fitzgerald

1996-01-01

370

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

371

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

372

pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis  

E-print Network

Single molecule F\\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additio...

Murphy, Rebecca R; Klenerman, David

2014-01-01

373

BioServices: a common Python package to access biological Web Services programmatically  

PubMed Central

Motivation: Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. Results: BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming. Availability and implementation: BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license. Contact: cokelaer@ebi.ac.uk or bioservices@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24064416

Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M.; Serra-Musach, Jordi; Saez-Rodriguez, Julio

2013-01-01

374

PLACE: An Open-Source Python Package for Laboratory Automation, Control, and Experimentation.  

PubMed

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. PMID:25304874

Johnson, Jami L; Tom Wrden, Henrik; van Wijk, Kasper

2015-02-01

375

QuTiP 2: A Python framework for the dynamics of open quantum systems  

E-print Network

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [Comput. Phys. Comm. 183 (2012) 1760], we have introduced numerous new features, enhanced performance, made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version.

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

2012-11-28

376

ObsPy: A Python Toolbox for Seismology and Seismological Observatories  

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 extends 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 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 GPL/LGPLv3 open source licences. 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.

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

2013-04-01

377

An Object-Oriented Python Implementation of an Intermediate-Level Atmospheric Model  

NASA Astrophysics Data System (ADS)

The Neelin-Zeng Quasi-equilibrium Tropical Circulation Model (QTCM1) is a Fortran-based intermediate-level atmospheric model that includes simplified treatments of several physical processes, including a GCM-like convective scheme and a land-surface scheme with representations of different surface types, evaporation, and soil moisture. This model has been used in studies of the Madden-Julian oscillation, ENSO, and vegetation-atmosphere interaction effects on climate. Through the assumption of convective quasi-equilibrium in the troposphere, the QTCM1 is able to include full nonlinearity, resolve baroclinic disturbances, and generate a reasonable climatology, all at low computational cost. One year of simulation on a PC at 5.625 3.75 degree longitude-latitude resolution takes under three minutes of wall-clock time. The Python package qtcm implements the QTCM1 in a mixed-language environment that retains the speed of compiled Fortran while providing the benefits of Python's object-oriented framework and robust suite of utilities and datatypes. We describe key programming constructs used to create this modeling environment: the decomposition of model runs into Python objects, providing methods so visualization tools are attached to model runs, and the use of Python's mutable datatypes (lists and dictionaries) to implement the "run list" entity, which enables total runtime control of subroutine execution order and content. The result is an interactive modeling environment where the traditional sequence of "hypothesis ? modeling ? visualization and analysis" is opened up and made nonlinear and flexible. In this environment, science tasks such as parameter-space exploration and testing alternative parameterizations can be easily automated, without the need for multiple versions of the model code interacting with a bevy of makefiles and shell scripts. The environment also simplifies interfacing of the atmospheric model to other models (e.g., hydrologic models, statistical models) and analysis tools. The tools developed for this package can be adapted to create similar environments for hydrologic models.

Lin, J. W.

2008-12-01

378

Rain, rats and pythons: Climate-driven population dynamics of predators and prey in tropical Australia  

Microsoft Academic Search

All natural populations fluctuate in abundance and age structure through time; understanding why they do so is a critical step towards their effective management and conservation. However, the long-term data sets needed for such an understanding are rarely available, especially for tropical organisms. A 17-year capture- mark-recapture study yielded detailed information on the demography of water pythons (Liasis fuscus) and

THOMAS MADSEN; BEATA UJVARI; RICHARD SHINE; MATS OLSSON

2006-01-01

379

HTSeqa Python framework to work with high-throughput sequencing data  

PubMed Central

Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.de PMID:25260700

Anders, Simon; Pyl, Paul Theodor; Huber, Wolfgang

2015-01-01

380

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

381

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

382

The microvasculature of python pit organs: morphology and blood flow microkinetics.  

PubMed

Boid snakes have infrared sensing pits that resemble crotaline pits in electrophysiological function and ultrastructure, but differ in gross morphology, number, and location: boids have three or more simple pits in the labial scales vs a single facial pair with more complex morphology in the crotalines. We studied the morphology of the capillary bed and the microkinetics of blood flow in a boid snake, the ball python, Python regius, and compared them with the already known condition in crotalines. We used a Doppler blood flow recorder in conjunction with an electrocardiograph to measure blood flow and heartbeat, and resin casts, transmission electron microscopy, and laser confocal microscopy to study capillary morphology. Blood flow in response to infrared stimulus was virtually identical in the two taxa, but the morphology of the capillary bed differed drastically. In the ball python pits, the capillary bed consisted of a forest of vertically oriented loops with a characteristic dome at the top in contact with the receptor layer of the fundus. Immunohistochemical staining showed pericytes constricting the capillaries and domes with smooth muscle alpha-actin-labeled processes. Since latency of response was as short as 1 ms, the capillaries were apparently responding under local control to provide both nutrition and cooling to the heat-sensitive receptors. We concluded that mitochondria-filled receptors provided with a swiftly responding cooling system were nature's most efficient way of attaining infrared imaging. PMID:12711259

Goris, Richard C; Atobe, Yoshitoshi; Nakano, Masato; Hisajima, Tatsuya; Funakoshi, Kengo; Kadota, Tetsuo

2003-05-01

383

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

PubMed Central

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

384

Breakthrough Science at NERSC Harvey Wasserman  

E-print Network

Physics NP Nuclear Physics NERSC 2008 Allocations By DOE Office #12;Science View of Workload NERSC 2008...) 10 #12;Six Breakthrough Science Stories · Nuclear Physics · Geochemistry · Plasma Turbulence eigenvalues and eigenvectors using the Lanczos algorithm 12 Nuclear Physics (1 of 2) · I/O-dominated at high

385

Embedded Analytical Solutions Improve Accuracy in Convolution-Based Particle Tracking Models using Python  

NASA Astrophysics Data System (ADS)

Particle tracking often is used to generate particle-age distributions that are used as impulse-response functions in convolution. A typical application is to produce groundwater solute breakthrough curves (BTC) at endpoint receptors such as pumping wells or streams. The commonly used semi-analytical particle-tracking algorithm based on the assumption of linear velocity gradients between opposing cell faces is computationally very fast when used in combination with finite-difference models. However, large gradients near pumping wells in regional-scale groundwater-flow models often are not well represented because of cell-size limitations. This leads to inaccurate velocity fields, especially at weak sinks. Accurate analytical solutions for velocity near a pumping well are available, and various boundary conditions can be imposed using image-well theory. Python can be used to embed these solutions into existing semi-analytical particle-tracking codes, thereby maintaining the integrity and quality-assurance of the existing code. Python (and associated scientific computational packages NumPy, SciPy, and Matplotlib) is an effective tool because of its wide ranging capability. Python text processing allows complex and database-like manipulation of model input and output files, including binary and HDF5 files. High-level functions in the language include ODE solvers to solve first-order particle-location ODEs, Gaussian kernel density estimation to compute smooth particle-age distributions, and convolution. The highly vectorized nature of NumPy arrays and functions minimizes the need for computationally expensive loops. A modular Python code base has been developed to compute BTCs using embedded analytical solutions at pumping wells based on an existing well-documented finite-difference groundwater-flow simulation code (MODFLOW) and a semi-analytical particle-tracking code (MODPATH). The Python code base is tested by comparing BTCs with highly discretized synthetic steady-flow finite-difference transport simulations (MT3DMS). Results show more accurate simulation of pumping-well BTCs for a given grid cell size when using analytical solutions. The code base is extended to transient flow and BTCs are compared to results from MT3DMS simulations. Results show the particle-based solutions can resolve transient behavior using coarser model grids with far less computational effort than MT3DMS. The effect of simulation accuracy on parameter estimates (porosity) also is investigated. Porosity estimated using more accurate analytical solutions are less biased than in synthetic finite-difference transport simulations, which tend to be biased by coarseness of the grid. Eliminating the bias by using a finer grid comes at the expense of much larger computational effort. Finally, the code base was applied to an actual groundwater-flow model of Salt Lake Valley, Utah. Particle simulations using the Python code base compare well with finite-difference simulations, but with less computational effort, and have the added advantage of delineating flow paths, thus explicitly connecting solute source areas with receptors, and producing complete particle-age distributions. Knowledge of source areas and age distribution greatly enhances the analysis of dissolved solids data in Salt Lake Valley.

Starn, J. J.

2013-12-01

386

Functional morphology and patterns of blood flow in the heart of Python regius.  

PubMed

Brightness-modulated ultrasonography, continuous-wave Doppler, and pulsed-wave Doppler-echocardiography were used to analyze the functional morphology of the undisturbed heart of ball pythons. In particular, the action of the muscular ridge and the atrio-ventricular valves are key features to understand how patterns of blood flow emerge from structures directing blood into the various chambers of the heart. A step-by-step image analysis of echocardiographs shows that during ventricular diastole, the atrio-ventricular valves block the interventricular canals so that blood from the right atrium first fills the cavum venosum, and blood from the left atrium fills the cavum arteriosum. During diastole, blood from the cavum venosum crosses the muscular ridge into the cavum pulmonale. During middle to late systole the muscular ridge closes, thus prohibiting further blood flow into the cavum pulmonale. At the same time, the atrio-ventricular valves open the interventricular canal and allow blood from the cavum arteriosum to flow into the cavum venosum. In the late phase of ventricular systole, all blood from the cavum pulmonale is pressed into the pulmonary trunk; all blood from the cavum venosum is pressed into both aortas. Quantitative measures of blood flow volume showed that resting snakes bypass the pulmonary circulation and shunt about twice the blood volume into the systemic circulation as into the pulmonary circulation. When digesting, the oxygen demand of snakes increased tremendously. This is associated with shunting more blood into the pulmonary circulation. The results of this study allow the presentation of a detailed functional model of the python heart. They are also the basis for a functional hypothesis of how shunting is achieved. Further, it was shown that shunting is an active regulation process in response to changing demands of the organism (here, oxygen demand). Finally, the results of this study support earlier reports about a dual pressure circulation in Python regius. PMID:19097161

Starck, J Matthias

2009-06-01

387

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

E-print Network

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

Jani Sainio

2012-04-30

388

QuTiP 2: A Python framework for the dynamics of open quantum systems  

NASA Astrophysics Data System (ADS)

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Catalog identifier: AEMB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_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.: 33625 No. of bytes in distributed program, including test data, etc.: 410064 Distribution format: tar.gz Programming language: Python. Computer: i386, x86-64. Operating system: Linux, Mac OSX. RAM: 2+ Gigabytes Classification: 7. External routines: NumPy, SciPy, Matplotlib, Cython Catalog identifier of previous version: AEMB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760 Does the new version supercede the previous version?: Yes Nature of problem: Dynamics of open quantum systems Solution method: Numerical solutions to Lindblad, Floquet-Markov, and Bloch-Redfield master equations, as well as the Monte Carlo wave function method. Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Restrictions: Problems must meet the criteria for using the master equation in Lindblad, Floquet-Markov, or Bloch-Redfield form. Running time: A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.

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

2013-04-01

389

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

390

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

391

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

392

powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions  

PubMed Central

Power laws are theoretically interesting probability distributions that are also frequently used to describe empirical data. In recent years, effective statistical methods for fitting power laws have been developed, but appropriate use of these techniques requires significant programming and statistical insight. In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package. This software package provides easy commands for basic fitting and statistical analysis of distributions. Notably, it also seeks to support a variety of user needs by being exhaustive in the options available to the user. The source code is publicly available and easily extensible. PMID:24489671

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

393

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

394

SpacePy: Python-Based Tools for the Space Science Community  

NASA Astrophysics Data System (ADS)

SpacePy provides data analysis and visualization tools for the space science community. Written in Python, it builds on the capabilities of the NumPy and MatPlotLib packages to make basic data analysis, modeling and visualization easier. It contains modules for handling many complex time formats, obtaining data from the OMNI database, and accessing the powerful Onera library. It contains a library of commonly used empirical relationships, performs association analysis, coordinate transformations, radiation belt modeling, and CDF reading, and creates publication quality plots.

Morley, Steve; Koller, Josef; Welling, Dan; Larsen, Brian; Niehof, Jon

2014-01-01

395

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

USGS Publications Warehouse

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

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

2011-01-01

396

Pyff A Pythonic Framework for Feedback Applications and Stimulus Presentation in Neuroscience  

PubMed Central

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 braincomputer 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

397

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

PubMed Central

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

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

2009-01-01

398

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

399

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

400

Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit  

SciTech Connect

Global Arrays is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays. The NumPy module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. NumPy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, NumPy is inherently serial. Using a combination of Global Arrays and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Serial NumPy applications can become parallel, scalable GAiN applications with only minor source code changes. Scalability studies of several different GAiN applications will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Daily, Jeffrey A.; Lewis, Robert R.

2011-11-30

401

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

402

PlantGL: a Python-based geometric library for 3D plant modelling at different scales  

E-print Network

or plant parts, ranging from tissues and organs to plant populations. Based on a scene graph augmentedPlantGL: a Python-based geometric library for 3D plant modelling at different scales C. Pradal a 1 , F. Boudon a,1 , C. Nouguier a , J. Chopard b , C. Godin b aCIRAD, Virtual Plants INRIA Project

Paris-Sud XI, Université de

403

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

PubMed

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

Reed, Robert N

2005-06-01

404

SUPPRESSION OF BLOOD FEEDING BY OCHLEROTATUS DORSALIS AND OCHLEROTATUS MELANIMON (DIPTERA: CULICIDAE) ON CATTLE TREATED WITH PYTHON EAR TAGS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Adult mosquitoes were collected by drop traps to compare blood feeding rates between cattle treated with 2 Python ear tags (10% zeta cypermethrin and 20% piperonyl butoxide) per animal and animals that were untreated. Mosquitoes were collected both 2 and 4 weeks after application of the ear tags. ...

405

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

406

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

407

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

408

ABC-SysBioapproximate Bayesian computation in Python with GPU support  

PubMed Central

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

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

2010-01-01

409

PySP : modeling and solving stochastic mixed-integer programs in Python.  

SciTech Connect

Although stochastic programming is a powerful tool for modeling decision-making under uncertainty, various impediments have historically prevented its widespread use. One key factor involves the ability of non-specialists to easily express stochastic programming problems as extensions of deterministic models, which are often formulated first. A second key factor relates to the difficulty of solving stochastic programming models, particularly the general mixed-integer, multi-stage case. Intricate, configurable, and parallel decomposition strategies are frequently required to achieve tractable run-times. We simultaneously address both of these factors in our PySP software package, which is part of the COIN-OR Coopr open-source Python project for optimization. To formulate a stochastic program in PySP, the user specifies both the deterministic base model and the scenario tree with associated uncertain parameters in the Pyomo open-source algebraic modeling language. Given these two models, PySP provides two paths for solution of the corresponding stochastic program. The first alternative involves writing the extensive form and invoking a standard deterministic (mixed-integer) solver. For more complex stochastic programs, we provide an implementation of Rockafellar and Wets Progressive Hedging algorithm. Our particular focus is on the use of Progressive Hedging as an effective heuristic for approximating general multi-stage, mixed-integer stochastic programs. By leveraging the combination of a high-level programming language (Python) and the embedding of the base deterministic model in that language (Pyomo), we are able to provide completely generic and highly configurable solver implementations. PySP has been used by a number of research groups, including our own, to rapidly prototype and solve difficult stochastic programming problems.

Woodruff, David L. (University of California, Davis); Watson, Jean-Paul

2010-08-01

410

Team: Katherine Ahern Zachary Gillen  

E-print Network

Application View Sheriff Department Jail Ancillary System #12;Purpose of project Improve: Progress note entry STAND-ALONE SYSTEMS HL7 Based Messaging System Other Lab System Inpatient Pharmacy RADIOLOGY Medical Records Coding LABORATORY (GEN/BB/MICRO) Electronic Medical Record System CLINICALS Operating Room GI Lab

Militzer, Burkhard

411

Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.  

PubMed

In this article, we describe the use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes, including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis tasks, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral images of brain tissue surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels. Each channel consists of 6000 10,000 500 voxels with 16 bits/voxel, implying image sizes exceeding 250 GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analysis for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN) capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment. Our Python script enables efficient data storage and movement between computers and storage servers, logs all the processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries. PMID:24808857

Rey-Villamizar, Nicolas; Somasundar, Vinay; Megjhani, Murad; Xu, Yan; Lu, Yanbin; Padmanabhan, Raghav; Trett, Kristen; Shain, William; Roysam, Badri

2014-01-01

412

Fast prototyping of wavelet spatio-temporal RS fusion with Raingauge time series with GDAL and Python-DWT  

NASA Astrophysics Data System (ADS)

Availability of rainfall time-series is limited in many parts of the World, and the continuity of such records is variable. This research endeavors to extend actual daily rainfall observations to ungauged areas using vegetation response as witnessed by remote sensing data and taking into account rainfall event histograms as well as cumulative total daily rainfall, over a period of 11 years. Open Source code development permitted to gain on several aspects. The first one pertains to space, Python and its numerical part (NumPy) are scientifically concise, as a bonus to be expressive. The second is the availability of the Discrete Wavelet Transform (DWT) in Python already, which permitted to reduce the Wavelet Transform to a small set of instructions, clarifying and simplifying the understanding of the code once it reaches the Public Domain. GDAL interface permitted to load satellite imagery and write fused rainfall time-series in spatio-temporal dimensions. Other scientific tool from Numerical Python were also used in the process of developing the algorithm (scipy.stats.stats and scipy.interpolate.griddata). Due to the large amount of days (4019) and the kilometer based resolution of the vegetation RS data, it takes about a week for the code to resolve the fusion problem. An attempt at using an multicore interpolation implementation in Python (hpgl) which unfortunately was not an active project anymore, though certainly deserving interest. Results show that rainfall events histograms can be reconstructed, and that total cumulative rainfall is estimated with 85% accuracy, using a surrounding network of rain gauges at 30-50 km of distance from the point of study. This research can strengthen various types of research and applications such as ungauged basins research, regional climate modeling, agricultural insurance systems, etc. Further development aims at porting the code to distributed computing.

Chemin, Yann

2013-04-01

413

VarPy: A python library for volcanology and rock physics data analysis  

NASA Astrophysics Data System (ADS)

The increasing prevalence of digital instrumentation in volcanology and rock physics is leading to a wealth of data, which in turn is increasing the need for computational analyses and models. Today, these are largely developed by each individual or researcher. The introduction of a shared library that can be used for this purpose has several benefits: 1. when an existing function in the library meets a need recognised by a researcher it is usually much less effort than developing ones own code; 2. once functions are established and multiply used they become better tested, more reliable and eventually trusted by the community; 3. use of the same functions by different researchers makes it easier to compare results and to compare the skill of rival analysis and modelling methods; and 4. in the longer term the cost of maintaining these functions is shared over a wide community and they therefore have greater duration. Python is a high-level interpreted programming language, with capabilities for object-oriented programming. Often scientists choose this language to program their programs because of the increased productivity it provides. Although, there are many software tools available for interactive data analysis and development, there are not libraries designed specifically for volcanology and rock physics data. Therefore, we propose a new Python open-source toolbox called "VarPy" to facilitate rapid application development for rock physicists and volcanologists, which allow users to define their own workflows to develop models, analyses and visualisations. This proposal is triggered by our work on data assimilation in the NERC EFFORT (Earthquake and Failure Forecasting in Real Time) project, using data provided by the NERC CREEP 2 experimental project and volcanic experiments from INVG observatory Etna and IGN observatory Hierro as a test cases. In EFFORT project we are developing a scientist gateway which offers services for collecting and sharing volcanology and rock physics data with the intent of stimulating sharing, collaboration and comparison of methods among the practitioners in the two fields. As such, it offers facilities for running analyses and models either under a researcher's control or periodically as part of an experiment and to compare the skills of predictive methods. The gateway therefore runs code on behalf of volcanology and rock physics researchers. Varpy library is intended to make it much easier for those researchers to set up the code they need to run. The library also makes it easier to arrange that code is in a form suitable for running in the EFFORT computational services. Care has been taken to ensure that the library can also be used outside of EFFORT systems, e.g., on a researcher's own laptop, providing two variants of the library: the gateway version and developer's version, with many of the functions completely identical. The library must fulfill two purposes simultaneously: by providing a full repertoire of commonly required actions it must make it easy for volcanologist and rock physicists to write the python scripts they need to accomplish their work, and by wrapping operations it must enable the EFFORT gateway to maintain the integrity of its data. Notice that proposal of VarPy library does not attempt to replace the functions provided by other libraries, such as NumpY and ScipY. VarPy is complementary to them.

Filgueira, Rosa; Atkinson, Malcom; Bell, Andrew; Snelling, Brawen; Main, Ian

2014-05-01

414

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

NASA Astrophysics Data System (ADS)

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

lvarez-Gmez, Jos A.

2014-05-01

415

NIFTY - Numerical Information Field Theory. A versatile PYTHON library for signal inference  

NASA Astrophysics Data System (ADS)

NIFTy (Numerical Information Field Theory) is a software package designed to enable the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTy offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically without concerning the user. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and then apply the developed code in higher-dimensional settings of real world problems. The set of spaces on which NIFTy operates comprises point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those. The functionality and diversity of the package is demonstrated by a Wiener filter code example that successfully runs without modification regardless of the space on which the inference problem is defined. NIFTy homepage http://www.mpa-garching.mpg.de/ift/nifty/; Excerpts of this paper are part of the NIFTy source code and documentation.

Selig, M.; Bell, M. R.; Junklewitz, H.; Oppermann, N.; Reinecke, M.; Greiner, M.; Pachajoa, C.; Enlin, T. A.

2013-06-01

416

A Python Pipeline for the Mercury N-body Code With First-Order GR Effects  

NASA Astrophysics Data System (ADS)

We present a pipeline for use with the Mercury N-body code (Chambers 1999), which we make publicly available on github. We have modified the standard Mercury integrator to include first-order numerical relativistic effects and a smooth stellar potential for use in the near-Keplerian potential around a massive black hole. Python scripts generate the input files and perform analysis on hundreds of stars, including those in a disk around Sgr A* and in highly-eccentric remnants of disrupted binaries.We use this code to simulate the dynamical effects of an intermediate-mass black hole on the stars in the Galactic center. Preliminary results indicate significant effects on the semi-major axis and eccentricity distribution. Using the h-statistic (Madigan et al. 2014) as a proxy for eccentricity, this should be observable in current observational data, allowing us to constrain the remaining parameter space available to an intermediate-mass black hole in the Galactic center (Gualandris & Merritt, 2009).

Wieland, Christopher AM; Madigan, Ann-Marie

2015-01-01

417

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

418

A python module to normalize microarray data by the quantile adjustment method.  

PubMed

Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools. PMID:20970526

Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C; Sangar, Djibril; Doumbia, Seydou; Traor, Sekou F; Maiga, Mohamed S; Dembl, Doulaye

2011-06-01

419

A Python module to normalize microarray data by the quantile adjustment method  

PubMed Central

Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools. PMID:20970526

Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C.; Sangar, Djibril; Doumbia, Seydou; Traor, Sekou F.; Maiga, Mohamed S.; Dembl, Doulaye

2010-01-01

420

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

421

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

422

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

PubMed

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

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

2011-12-01

423

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

424

Development of the Brazilian Operational Ocean Forecast System with the OOF? Python engine for model ROMS  

NASA Astrophysics Data System (ADS)

The first implementation of an automatic operational ocean modeling system of the brazilian oceanic region was created and is under continuous development. The operational system is a joint effort between a group of institutions in a research and development consortium called Oceanographic Modelling and Research Network (with Portuguese acronym REMO). Among the objectives of this network is the contribution for a better understanding of the ocean, including mesoscale, shelf and tidal circulation, and to provide oceanographic forecasts for the Brazilian shelf/slope as support of the activities of the oil industry. The model underwent through a 9.5 years spinup being forced at the boundaries with climatological data from global simulations of the model OCCAM1-4, and at surface with data from NCEP (first 9 years) and GFS 1. The operational stage started at the 1st of July 2009 and is producing daily analysis and 5 days forecasts. Currently the model uses OCCAM1-12 boundary climatologies and GFS 0.5 surface forcings. The ocean model being used is the Regional Ocean Modeling System, ROMS, an advanced and robust rapidly evolving comunity-code model. ROMS has been applied in deterministic simulations in a wide range of space and time scales and oceanic systems types. In terms of technical operations, the task needed for the operational ocean model to run, like the creation of inputs files, extraction of atmospheric data, as well as the control of the successfulness of the simulations and all the operational flow, is done with OOF? (Operational Ocean Forecast Engine), a collection of Python modules prepared to perform all the work required for the operational modeling system, including data visualisation. Due to its design, OOF? requires almost no human intervention, and except for some initial refinements and performance issues, OOF? is now working in a totally automatic manner.

Marta-Almeida, Martinho; Cirano, Mauro; Pereira, Janini; Ruiz-Villarreal, Manuel

2010-05-01

425

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

426

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

427

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

428

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

USGS Publications Warehouse

Giant Constrictors: Biological and Management Profiles and an Establishment Risk Assessment for Nine Large Species of Pythons, Anacondas, and the Boa Constrictor, estimates the ecological risks associated with colonization of the United States by nine large constrictors. The nine include the world's four largest snake species (Green Anaconda, Eunectes murinus; Indian or Burmese Python, Python molurus; Northern African Python, Python sebae; and Reticulated Python, Broghammerus reticulatus), the Boa Constrictor (Boa constrictor), and four species that are ecologically or visually similar to one of the above (Southern African Python, Python natalensis; Yellow Anaconda, Eunectes notaeus; DeSchauensee's Anaconda, Eunectes deschauenseei; and Beni Anaconda, Eunectes beniensis). At present, the only probable pathway by which these species would become established in the United States is the pet trade. Although importation for the pet trade involves some risk that these animals could become established as exotic or invasive species, it does not guarantee such establishment. Federal regulators have the task of appraising the importation risks and balancing those risks against economic, social, and ecological benefits associated with the importation. The risk assessment quantifies only the ecological risks, recognizing that ecosystem processes are complex and only poorly understood. The risk assessment enumerates the types of economic impacts that may be experienced, but leaves quantification of economic costs to subsequent studies. Primary factors considered in judging the risk of establishment were: (1) history of establishment in other countries, (2) number of each species in commerce, (3) suitability of U.S. climates for each species, and (4) natural history traits, such as reproductive rate and dispersal ability, that influence the probability of establishment, spread, and impact. In addition, the risk assessment reviews all management tools for control of invasive giant constrictor populations. There is great uncertainty about many aspects of the risk assessment; the level of uncertainty is estimated separately for each risk component. Overall risk was judged to be high for five of the giant constrictors studied, and medium for the other four species. Because all nine species shared a large number of natural history traits that promote invasiveness or impede population control, none of the species was judged to be of low risk.

Reed, Robert N.; Rodda, Gordon H.

2009-01-01

429

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

PubMed Central

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

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

2014-01-01

430

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

431

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

432

Development of a 3D Potential Field Forward Modelling System in Python  

NASA Astrophysics Data System (ADS)

The collection of potential field data has long been a standard part of geophysical exploration. Specifically, airborne magnetic data is collected routinely in any brown-fields area, because of the low cost and fast acquisition rate compared to other geophysical techniques. However, the interpretation of such data can be a daunting task, especially when 3D models are becoming more necessary. The current trend in modelling software is to follow either the modelling of individual profiles, which are then "joined" up into 3D sections, or to model in a full 3D using polygonal based models (Singh and Guptasarma, 2001). Unfortunately, both techniques have disadvantages. When modelling in 2.5D the impact of other profiles is not truly available on your current profile being modelled, and vice versa. The problem is not present in 3D, but 3D polygonal models, while being easy to construct the initial model, are not as easy to make fast changes to. In some cases, the entire model must be recreated from scratch. The ability to easily change a model is the very basis of forward modelling. With this is mind, the objective of the project was to: 1) Develop software which was truly modelling in 3D 2) Create a system which would allow the rapid changing of the 3D model, without the need to recreate the model. The solution was to adopt a voxel based approach, rather than a polygonal approach. The solution for a cube (Blakely 1996) was used to calculate potential field for each voxel. The voxels are then summed over the entire volume. The language used was python, because of its huge capacity for scientific development. It enables full 3D visualisation as well as complex mathematical routines. Some properties worth noting are: 1) Although 200 rows by 200 columns by 200 layers would imply 8 million calculations, in reality, since the calculation for adjacent voxels produces the same result, only 200 calculations are necessary. 2) Changes to susceptibility and density do not affect the field shape, merely the amplitude of the anomaly. Therefore, it is not necessary to recalculate the entire field if one of these parameters is changed. The interface to the program works similar to a paint program. The model is simply drawn into the side views or top views of the volume of interest. Relevant voxels are either activated or deactivated in this way. The software has proved to be extremely successful. It has enabled faster modelling of anomalies in a non-complex manner - implying little or no training to prospective users. References Blakely, R.J., Potential Theory in Gravity and Magnetic Applications (1996), pp 200 - 201 Singh, B., Guptasarma, D., (2001). New method for fast computation of gravity and magnetic anomalies from arbitrary polyhedral, Geophysics, 66, pp. 521 - 526

Cole, P.

2012-12-01

433

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

E-print Network

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.

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

2011-11-22

434

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

435

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

436

Conservation genetics of Boelens python ( Morelia boeleni ) from New Guinea: reduced genetic diversity and divergence of captive and wild animals  

Microsoft Academic Search

Boelens python (Morelia boeleni) is a montane New Guinea endemic found in highlands above 1000m and below the tree line. The ecology, natural history, distribution,\\u000a population size, and conservation status of this species are largely unknown. It has a protected status in Papua New Guinea\\u000a but not in Indonesian Papua and several US and European zoos have active captive breeding

Christopher C. Austin; Marc Spataro; Stacy Peterson; Joshua Jordan; John D. McVay

2010-01-01

437

NERSC XT3/XT4 Benchmarking Harvey Wasserman  

E-print Network

of Energy under Contract No. DE-AC02-05CH11231. #12;NATIONAL ENERGY RESEARCH SCIENTIFIC COMPUTING CENTER COMPUTING CENTER Advertisement · SC07 submissions open March 12 · 2-part submission process for papers ENERGY RESEARCH SCIENTIFIC COMPUTING CENTER Science-Driven Computing Strategy · 3 Important Trends

438

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

439

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

440

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

441

Zachary Gagnon Hsueh-Chia Chang  

E-print Network

. A novel serpentine wire cap- able of sustaining a high voltage, up to 2500 VRMS, without causing excessive, such as micropumps, micromixers, microvalves, and microchannels, for an effective portable microfluidic kit. However

Chang, Hsueh-Chia

442

October 2012 981 by ZACHARY HUANG  

E-print Network

are forced to re- main phoretic if there is no brood, and this can last 5-6 months in cold climates. Mites their population. This oc- curs only under the capped brood cell. Ma- ture female mites are already mated when (viewed from the top of the cell). Mites have special appendages called "peretrimes" (es- sentially

Huang, Zachary

443

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.

444

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

445

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

446

Pancreatitis, very early compared with normal start of enteral feeding (PYTHON trial): design and rationale of a randomised controlled multicenter trial  

PubMed Central

Background In predicted severe acute pancreatitis, infections have a negative effect on clinical outcome. A start of enteral nutrition (EN) within 24 hours of onset may reduce the number of infections as compared to the current practice of starting an oral diet and EN if necessary at 3-4 days after admission. Methods/Design The PYTHON trial is a randomised controlled, parallel-group, superiority multicenter trial. Patients with predicted severe acute pancreatitis (Imrie-score ? 3 or APACHE-II score ? 8 or CRP > 150 mg/L) will be randomised to EN within 24 hours or an oral diet and EN if necessary, after 72 hours after hospital admission. During a 3-year period, 208 patients will be enrolled from 20 hospitals of the Dutch Pancreatitis Study Group. The primary endpoint is a composite of mortality or infections (bacteraemia, infected pancreatic or peripancreatic necrosis, pneumonia) during hospital stay or within 6 months following randomisation. Secondary endpoints include other major morbidity (e.g. new onset organ failure, need for intervention), intolerance of enteral feeding and total costs from a societal perspective. Discussion The PYTHON trial is designed to show that a very early (< 24 h) start of EN reduces the combined endpoint of mortality or infections as compared to the current practice of an oral diet and EN if necessary at around 72 hours after admission for predicted severe acute pancreatitis. Trial Registration ISRCTN: ISRCTN18170985 PMID:21392395

2011-01-01

447

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

448

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

449

The Effects of Fasting Duration on the Metabolic Response to Feeding in [ITAL]Python molurus[\\/ITAL]: An Evaluation of the Energetic Costs Associated with Gastrointestinal Growth and Upregulation  

Microsoft Academic Search

The oxygen uptake of Python molurus increases enormously following feeding, and the elevated metabolism coincides with rapid growth of the gastrointestinal organs. There are opposing views regarding the energetic costs of the gastrointestinal hy- pertrophy, and this study concerns the metabolic response to feeding after fasting periods of different duration. Since mass and function of the gastrointestinal organs remain elevated

Johannes Overgaard; Johnnie B. Andersen; Tobias Wang

2002-01-01

450

3-D Numerical Simulation and Analysis of Complex Fiber Geometry RaFC Materials with High Volume Fraction and High Aspect Ratio based on ABAQUS PYTHON  

NASA Astrophysics Data System (ADS)

Organic and inorganic fiber reinforced composites with innumerable fiber orientation distributions and fiber geometries are abundantly available in several natural and synthetic structures. Inorganic glass fiber composites have been introduced to numerous applications due to their economical fabrication and tailored structural properties. Numerical characterization of such composite material systems is necessitated due to their intrinsic statistical nature, which renders extensive experimentation prohibitively time consuming and costly. To predict various mechanical behavior and characterizations of Uni-Directional Fiber Composites (UDFC) and Random Fiber Composites (RaFC), we numerically developed Representative Volume Elements (RVE) with high accuracy and efficiency and with complex fiber geometric representations encountered in uni-directional and random fiber networks. In this thesis, the numerical simulations of unidirectional RaFC fiber strand RVE models (VF>70%) are first presented by programming in ABAQUS PYTHON. Secondly, when the cross sectional aspect ratios (AR) of the second phase fiber inclusions are not necessarily one, various types of RVE models with different cross sectional shape fibers are simulated and discussed. A modified random sequential absorption algorithm is applied to enhance the volume fraction number (VF) of the RVE, which the mechanical properties represents the composite material. Thirdly, based on a Spatial Segment Shortest Distance (SSSD) algorithm, a 3-Dimentional RaFC material RVE model is simulated in ABAQUS PYTHON with randomly oriented and distributed straight fibers of high fiber aspect ratio (AR=100:1) and volume fraction (VF=31.8%). Fourthly, the piecewise multi-segments fiber geometry is obtained in MATLAB environment by a modified SSSD algorithm. Finally, numerical methods including the polynomial curve fitting and piecewise quadratic and cubic B-spline interpolation are applied to optimize the RaFC fiber geometries. Based on the multi-segments fiber geometries and aforementioned techniques, smooth curved fiber geometries depicted by cubic B-spline polynomial interpolation are obtained and different types of RaFC RVEs with high fiber filament aspect ratio (AR>3000:1) and high RVE volume fraction (VF>40.29%) are simulated by ABAQUS scripting language PYTHON programming.

Jin, BoCheng

2011-12-01

451

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples  

PubMed Central

Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/. PMID:23311589

Boitard, Simon; Kofler, Robert; Franoise, Pierre; Robelin, David; Schltterer, Christian; Futschik, Andreas

2013-01-01

452

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

453

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

USGS Publications Warehouse

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

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

2011-01-01

454

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools  

PubMed Central

Background Gas chromatographymass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data tightly integrate data processing methods with graphical user interface facilitating interactive data processing. While interactive processing remains critically important in GC-MS applications, high-throughput studies increasingly dictate the need for command line tools, suitable for scripting of high-throughput, customized processing pipelines. Results PyMS comprises a library of functions for processing of instrument GC-MS data developed in Python. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX), noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. A novel common ion single quantitation algorithm allows automated, accurate quantitation of GC-MS electron impact (EI) fragmentation spectra when a large number of experiments are being analyzed. PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments. A set of specifically designed experiments was performed in-house and used to comparatively evaluate the performance of PyMS and three widely used software packages for GC-MS data processing (AMDIS, AnalyzerPro, and XCMS). Conclusions PyMS is a novel software package for the processing of raw GC-MS data, particularly suitable for scripting of customized processing pipelines and for data processing in batch mode. PyMS provides limited graphical capabilities and can be used both for routine data processing and interactive/exploratory data analysis. In real-life GC-MS data processing scenarios PyMS performs as well or better than leading software packages. We demonstrate data processing scenarios simple to implement in PyMS, yet difficult to achieve with many conventional GC-MS data processing software. Automated sample processing and quantitation with PyMS can provide substantial time savings compared to more traditional interactive software systems that tightly integrate data processing with the graphical user interface. PMID:22647087

2012-01-01

455

LN FN ADVISOR NAME Abbott Zachary Boucheron, Laura E.  

E-print Network

, Steven J. Hafez Ahmad Brahma, Sukumar Hall Tom Paz, Robert A. Hanson Nathan Borah, Deva K. Harris Ian Liu, Wenxin Hu Jennifer Boucheron, Laura E. Ives Jacob Ranade, Satishkuma J. Jenkins Stephen Deleon, Phi

Johnson, Eric E.

456

Zachary D. Barker: Final DHS HS-STEM Report  

SciTech Connect

Working at Lawrence Livermore National Laboratory (LLNL) this summer has provided a very unique and special experience for me. I feel that the research opportunities given to me have allowed me to significantly benefit my research group, the laboratory, the Department of Homeland Security, and the Department of Energy. The researchers in the Single Particle Aerosol Mass Spectrometry (SPAMS) group were very welcoming and clearly wanted me to get the most out of my time in Livermore. I feel that my research partner, Veena Venkatachalam of MIT, and I have been extremely productive in meeting our research goals throughout this summer, and have learned much about working in research at a national laboratory such as Lawrence Livermore. I have learned much about the technical aspects of research while working at LLNL, however I have also gained important experience and insight into how research groups at national laboratories function. I believe that this internship has given me valuable knowledge and experience which will certainly help my transition to graduate study and a career in engineering. My work with Veena Venkatachalam in the SPAMS group this summer has focused on two major projects. Initially, we were tasked with an analysis of data collected by the group this past spring in a large public environment. The SPAMS instrument was deployed for over two months, collecting information on many of the ambient air particles circulating through the area. Our analysis of the particle data collected during this deployment concerned several aspects, including finding groups, or clusters, of particles that seemed to appear more during certain times of day, analyzing the mass spectral data of clusters and comparing them with mass spectral data of known substances, and comparing the real-time detection capability of the SPAMS instrument with that of a commercially available biological detection instrument. This analysis was performed in support of a group report to the Department of Homeland Security on the results of the deployment. The analysis of the deployment data revealed some interesting applications of the SPAMS instrument to homeland security situations. Using software developed in-house by SPAMS group member Dr. Paul Steele, Veena and I were able to cluster a subset of data over a certain timeframe (ranging from a single hour to an entire week). The software used makes clusters based on the mass spectral characteristics of the each particle in the data set, as well as other parameters. By looking more closely at the characteristics of individual clusters, including the mass spectra, conclusions could be made about what these particles are. This was achieved partially through examination and discussion of the mass spectral data with the members of the SPAMS group, as well as through comparison with known mass spectra collected from substances tested in the laboratory. In many cases, broad conclusions could be drawn about the identity of a cluster of particles.

Barker, Z D

2008-08-14

457

Using Python for Pedigree Analysis  

Technology Transfer Automated Retrieval System (TEKTRAN)

A pedigree is a way of describing a population of people or animals in terms of genetic relationships among individuals. Pedigrees are of interest to many people, including scientists, animal and plant breeders, and genealogists. They are used to assess the diversity of populations, in combination ...

458

Design by Contract for Python  

Microsoft Academic Search

The idea of design by contract (DBC), realized in the statically typed object-oriented programming language Eiffel, can be viewed as a systematic approach to specifying and implementing object-oriented software systems. We believe that a statically typed programming language is not suitable in the analysis and design phase of a prototyping-oriented software life cycle. For this purpose, dynamically typed interpreted programming

Reinhold Plsch

1997-01-01

459

Compiling Little Languages in Python  

Microsoft Academic Search

"Little languages" such as configuration files orHTML documents are commonplace in computing.This paper divides the work of implementing a littlelanguage into four parts, and presents a frameworkwhich can be used to easily conquer the implementationof each. The pieces of the framework havethe unusual property that they may be extendedthrough normal object-oriented means, allowing featuresto be added to a little language

John Aycock

1998-01-01

460

HIERARCHICAL BAYESIAN ANALYSIS OF ARREST RATES Jacqueline Cohen, Daniel Nagin, Garrick Wallstrom and Larry Wasserman 1  

E-print Network

of past arrest records of all felons convicted of drug trafficking, drug possession, robbery, or burglary by incarceration of individuals convicted of drug offenses compared to those con­ victed of nondrug offenses. Two%. Since the mid­1980's increased incarceration of drug offenders has been a major contributing factor

461

STATISTICAL INFERENCE FOR A COMPUTATIONAL MODEL OF Randy Bruno, James McClelland and Larry Wasserman 1  

E-print Network

subjects before and after taking amphetamines. The hypothesis that the net captures the main features study we are concerned with, subjects performed the task before and after ingesting amphetamines. Two questions of interest are (i) how do we quantify the effect of the amphetamine and (ii) can this effect

462

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

E-print Network

upon Palestine undercut what had been Zionism's larger goal of a Jewish cultural revival. Since 1948, the commitment to Israel has drained attention, energies, and resources away from most other aspects of Jewish life in America. Too many American... centuries of American growth and cultural change. The topics covered are all innovative and im portant, even if the individual essays themselves are of uneven value. Among the livelier articles is a particularly welcome essay on the decline of the female...

Levine, Stuart

1976-01-01

463

PHDL : a Python Hardware Design framework  

E-print Network

is thesis presents PHDL, a new hardware design language (HDL). In PHDL digital hardware components can vary in input/output widths, target platform, and have optional inputs and outputs. PHDL enables developers to write ...

Mashtizadeh, Ali

2007-01-01

464

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.

465

Python Programming: Lecture 3 Lili Dworkin  

E-print Network

>>> foo(b='bean', a='apricot', c='cantaloupe') apricot bean cantaloupe >>> d = {'a': 'apricot', 'b': 'bean', 'c': 'cantaloupe'} >>> foo(**d) apricot bean cantaloupe #12;Args and Kwargs def foo(fruit1, fruit2

Plotkin, Joshua B.

466

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

467

Energy expenditure for parental care may be trivial for brooding pythons, Python regius  

Microsoft Academic Search

Intensive parental care improves reproductive success. Why, then, do most animal species not provide parental care to their progeny? Life history theory suggests that the costs must be too high unless they are balanced by considerable fitness benefits. The notion that intensive parental care necessarily entails major costs is based both on intuition and on abundant empirical data. We monitored

FABIEN AUBRET; X AVIER BONNET; R ICHARD SHINE; S TEPHANIE MAUMELAT

2005-01-01

468

Fuel switching and energy partitioning during the postprandial metabolic response in the ball python (Python regius).  

PubMed

Digestion, absorption and assimilation of the meal are active processes that require start-up energy before the energy contained in a meal can be utilized. The energetic costs associated with feeding (specific dynamic action, SDA) are high in sit-and-wait foraging snakes that tolerate long fasting periods. We used (13)C-labelled prey to partition between endogenous energy sources (i.e. snakes' own resources) and exogenous energy sources (i.e. prey). A linear mixing model was then applied to determine the portion of (13)C originating from the different sources. The snakes showed a normal and typical postprandial response. By four hours after feeding, the delta(13)C-values indicated fuel switching from endogenous to exogenous. From then on, fuel mixing continuously increased until, at 20 h after feeding, 75% of fuel was exogenous. Resource partitioning showed that throughout SDA, the amount of exogenous energy increased to approximately 60% of SDA, which was equivalent to approximately 4.5% of the energy contained in a meal. PMID:20348338

Waas, Stefan; Werner, Roland A; Starck, J Matthias

2010-04-01

469

Clutch size manipulation, hatching success and offspring phenotype in the ball python ( Python regius )  

Microsoft Academic Search

In a diverse array of avian and mammalian species, experimental manipulations of clutch size have tested the hypothesis that natural selection should adjust numbers of neonates produced so as to maximize the number of via- ble offspring at the end of the period of parental care. Reptiles have not been studied in this respect, probably because they rarely display parental

FABIEN AUBRET; XAVIER BONNET; RICHARD SHINE; STEPHANIE MAUMELAT

2003-01-01

470

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

E-print Network

is then fed to the display. A VR system is typically configured either as a head-mounted display (HMD concerned with the effects of these techniques on stereoscopic HTDs (Head-Tracked Display). In these systems the head is tracked but the display is stationary, attached to a desk, tabletop or wall. This paper

Wartell, Zachary

471

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

E-print Network

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

Smith, Scott F.

472

Lesion Resolution Following Exposure of Rat Lung to Pulsed Ultrasound James F. Zachary,1  

E-print Network

ultrasound-induced lung hemorrhage in mice, rats, rabbits, monkeys, and pigs. This study characterized). Rats were anes- thetized and the skin of the left thorax clipped and de- pilated. They were placed in right lateral recumbency and two black dots were positioned on the skin over the left intercostal spaces

Illinois at Urbana-Champaign, University of

473

The 2012 Sumatra great earthquake sequence Zacharie Duputel a,n  

E-print Network

magnitudes MwZ8.2, it consists of two of the largest strike-slip earthquakes ever recorded, and is among the largest intraplate earthquakes on instrumental records. Secondly, this unusual series of large intra. On 11 April 2012, this region was hit in a couple of hours by two of the largest strike-slip earthquakes

Tsai, Victor C.

474

In "Stochastic Networks: Theory and Applications", pages 339366 F. P. Kelly, S. Zachary and I.  

E-print Network

and engineering, and fractal models have been applied with with some success in areas, such as hydrology applications of fractal models in science and engineering have been based on empirical findings, they have. A fundamental feature of self­similar or fractal phenomena is that they en­ compass a wide range of time scales

Taqqu, Murad

475

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

E-print Network

of a human body to within a median of 10 to 13 cm in the x and y di- mensions, and 21 cm in the z dimension and occlusions, and human-computer interaction systems like Kinect, which can track a user without instrumenting the field of human-computer interaction by enabling 3D motion tracking without instrumenting the body

Polz, Martin

476

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

E-print Network

Japanese language and culture in the Asian Studies Program at Kansai University of Foreign Language Studies; graduated cum laude; Dean's List, 6 semesters ! President's Scholarship (four years; $40,000) ! studied Immersion. In preparation for ACM Transactions Computer-Human Interaction. JOURNAL ARTICLE 1. TOUPS, Z. O

Toups, Zach

477

STATE OF UTAH CONTRACT NUMBER: MA515 March 12, 2014 Revision number: Purchasing Agent: Zachary Derr  

E-print Network

Phone #: 801-538-3307 Email: zderr@utah.gov Item: Integrated Classroom which includes some or all of the following items: Sound System, Projectors, Document Cameras, White Boards, Student Response Systems/A Min shipment without charges: Other conditions: This is a new contract with the same vendor. RT14036

Capecchi, Mario R.

478

CONTRAST AGENT-INDUCED CARDIAC ARRHYTHMIAS IN RATS James F. Zachary  

E-print Network

in medical practice today [l]. To improve the imaging capabilities of diagnostic ultrasound systems - Although no known meaningful health risks have been reported following the use of microbubble ultrasound exposed to pulsed ultrasound following injection of contrast agent. A focused 5 1-mm-diameter, 3.1-MHz

Illinois at Urbana-Champaign, University of

479

Pooling of first-order inputs in second-order vision Zachary M. Westrick a,  

E-print Network

the first and second stages of filtering; if the first-stage filter consists of narrowband mechanisms tuned patterns has been characterized by a model that first filters the image to isolate one texture component-defined images (spatial-frequency- and orientation-tuned filters). This model, known as FRF for filter rectify

Landy, Michael S.

480

Fellowship Recipients By Discipline (past 3 years) Note: This list is as only complete as the information that gets submitted by departments or  

E-print Network

Historical Society, 2010 Kevin Doyle, John D. Rockefeller, Jr. Library, 2009 Sarah Feuer, American Institute Zachary Matusheski, George C. Marshall Foundation, Baruch Fellowship, 2011 Zachary Matusheski, Dwight D

Fraden, Seth

481

Temporal and Spatial Complexity of Maternal Thermoregulation in Tropical Pythons  

E-print Network

Stahlschmidt1,2, * Richard Shine3 Dale F. DeNardo1 1 School of Life Sciences, Arizona State University, Tempe quantity (size of clutch) and quality (develop- mental temperature). In nature, caregiving parents of all.g., clutch size; Wright et al. 1998), parent-offspring communica- tion (e.g., begging behavior in chicks

Denardo, Dale

482

Python-based Tools and Web Services for Structural  

E-print Network

Vis u VisBench project: client-server vis & analysis (RH at UIUC/NCSA '97-'03) Java Swing client CORBA://www.mutdb.org) MutDB provides structural annotations for disease-associated mutations and single nucleotide

Lumsdaine, Andrew

483

PySP: Modeling and Solving Stochastic Programs in Python  

E-print Network

Sep 6, 2010 ... The modeling of uncertainty is widely recognized as an integral ...... penalize the lack of implementability using a sub-gradient estimator for the non- ...... in PySP or are under active investigation include biofuel network design...

2010-09-07

484

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

485

Python Tools for Reproducible Research on Hyperbolic Problems  

E-print Network

of scholarship and a necessary component of the scientific method. Scientific and mathematical journals on reproducible research, the scientific method and style of presenting experiments in publications be examined to determine details of the method used. Some difficulties in achieving this goal are discussed

LeVeque, Randy

486

Python Tools for Reproducible Research on Hyperbolic Problems  

E-print Network

of scholarship and a necessary component of the scientific method. Scientific and mathematical journals on reproducible research, the scientific method and style of presenting experiments in publications, and can be examined to determine details of the method used. Some difficulties in achieving this goal

LeVeque, Randy

487

The Monty Python method for generating random variables  

Microsoft Academic Search

We suggest an interesting and fast method for generating normal, exponential, t, von Mises, and certain other important random variables used in Monte Carlo studies. The right half of a symmetric density is cut into pieces, then, using simple area-preserving transformations, reassembled into a rectangle from which the x-coordinateor a linear function of the x-coordinateof a random point provides the

George Marsaglia; Wai Wan Tsang

1998-01-01

488

Why Complicate Things? Introducing Programming in High School Using Python  

Microsoft Academic Search

Abstract: Deciding what to teach novices about programmingand what programming language to use is a commontopic for debate. Should an industry relevantprogramming language be taught, or should a languagedesigned for teaching novices be used? Typically,these questions are raised at university level,but in this paper we address them from a high schoolperspective.

Linda Grandell; Mia Peltomki; Ralph-johan Back; Tapio Salakoski

489

Respiratory consequences of feeding in the snake Python molorus  

Microsoft Academic Search

Snakes can ingest large meals and exhibit marked increases in metabolic rate during digestion. Because postprandial oxygen consumption in some snakes may surpass that attained during exercise, studies of digestion offers an alternative avenue to understand the cardio-respiratory responses to elevated metabolic rate in reptiles. The effects of feeding on metabolic rate, arterial oxygen levels, and arterial acidbase status in

Johannes Overgaard; Morten Busk; James W Hicks; Frank B Jensen; Tobias Wang

1999-01-01

490

Python: A Programming Language For Software Integration And Development  

Microsoft Academic Search

mational analysis, quantum mechanics, distance geometry, docking methods, ab-initio methods)is large and growing rapidly. Moreover, these programs come in many flavors and variations, using differentforce fields, search techniques, algorithmic details (e.g., continuous space vs. discrete, Cartesian vs.torsional). Each variation presents its own characteristic set of advantages and limitations. These programsalso tend to evolve rapidly and are usually not written as

M. F. Sanner

1999-01-01

491

Multi-Scale Investigation of Surface Topography of Ball Python ( Python regius ) Shed Skin in Comparison to Human Skin  

Microsoft Academic Search

A major concern in designing tribosystems is to minimize friction, save energy, and to reduce wear. Conventional philosophy\\u000a for design centers on mechanical and material considerations. In particular, designers pay more attention to material properties\\u000a and material choices based on mechanical properties rather than the design and shape of the contacting surfaces and the relation\\u000a of that surface to the

H. A. Abdel-Aal; M. El Mansori; S. Mezghani

2010-01-01

492

Multi Scale Investigation of Surface Topography of Ball Python (Python Regius) Shed Skin in Comparison to Human skin  

Microsoft Academic Search

Constructing a surface that is an integral part of the function of tribosystems (deterministic surface) is an intriguing goal. Inspirations for such surfaces come from studying natural systems and deducing design rules. The major attraction is that natural systems, while functionally complex, are, in general, of optimized shape and performance. It is further believed that functional complexity of natural systems

H. A. Abdel-Aal; M. El Mansori; S. Mezghani

2010-01-01

493

Python Regius (Ball Python) shed skin: Biomimetic analogue for function-targeted design of tribo-surfaces  

Microsoft Academic Search

A major concern in designing tribo-systems is to minimize friction, save energy, and to reduce wear. Satisfying these requirements depends on the integrity of the rubbing surface and its suitability to sliding conditions. As such, designers currently focus on constructing surfaces that are an integral part of the function of the tribo-system. Inspirations for such constructs come from studying natural

H. A. Abdel-Aal; M. El Mansori; I. C. Gebeshuber

2010-01-01

494

Python Regius (Ball Python) shed skin: Biomimetic analogue for function-targeted design of tribo-surfaces  

Microsoft Academic Search

A major concern in designing tribo-systems is to minimize friction, save\\u000aenergy, and to reduce wear. Satisfying these requirements depends on the\\u000aintegrity of the rubbing surface and its suitability to sliding conditions. As\\u000asuch, designers currently focus on constructing surfaces that are an integral\\u000apart of the function of the tribo-system. Inspirations for such constructs come\\u000afrom studying natural

H. A. Abdel-Aal; M. El Mansori; I. C. Gebeshuber

2010-01-01

495

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

E-print Network

, and improvements to wind turbine design and control can have a significant impact on energy sustainability a large impact on wind energy research. Pursuing this goal, in this paper we develop a small, fully, Russ Tedrake* Abstract-- Wind power represents one of the most promising sources of renewable energy

Jackson, Daniel

496

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 of this technique. INDEX TERMS: H.5.1 [Information Interfaces and Presentation]: Multimedia Information Systems

Wartell, Zachary

497

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

498

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

499

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

500

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

E-print Network

pipelines to minimize memory bandwidth using the architectural pattern of line-buffering, where all--Automatic Synthesis; I.3.1 [Computer Graphics]: Hardware Architecture-- Graphics Processors; I.3.6 [Computer Graphics for computational photography and computer vision. Researchers are developing ways to acquire better images

Stanford University