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1

A tribute to Zachary Fisk  

NASA Astrophysics Data System (ADS)

We pay tribute to Zachary Fisk's contributions to materials physics on the occasion of his 60th birthday. His theme of “new physics through new materials” was made possible by a love of chemistry, a thorough grasp of physics, and a life-long association with the best researchers in the field.

Hecker, Siegfried S.

2002-05-01

2

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

3

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....

4

Python Calculus  

NSDL National Science Digital Library

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

IMPART RET Program, College of Information Science & Technology,

5

Python Language Home Page  

NSDL National Science Digital Library

The Python Language Home Page is hosted by the Corporation for National Research Initiatives (CNRI), Reston, VA. Python is an "interpreted, interactive, object-oriented, extensible programming language." It is both clear and versatile, freely available, and it runs on Unix, PC, and many other systems. Python was developed in the early 1990s at CWI in Amsterdam (the Netherlands); it has seen continuing development and widespread use since then. The site contains the official Python source code distribution, binaries, documentation, and conference proceedings. It also hosts a collection of contributed code and contains links to organizations and mailing lists that provide technical support for Python users. There are links to various projects that are using Python as well as to a number of special interest group (SIG) mailing lists. The SIGs are working to extend and enhance Python.

1998-01-01

6

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,

7

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

8

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)....

9

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

10

NEURON and Python  

PubMed Central

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

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

2008-01-01

11

Developing Sherpa with Python  

NASA Astrophysics Data System (ADS)

Sherpa is the general purpose fitting and modeling application for CIAO, the Chandra Interactive Analysis of Observations system. We have modified the original design and implemented a new version in Python. This version will be part of the upcoming CIAO4.0 release. We have previously presented a modular, flexible design for CIAO4.0 with the goal of packaging many models, fitting methods and statistics for analysis of astronomical data. The new design promised to be more robust than the previous Sherpa, and more easily extensible with user-written scripts. (We already see some sign of this, in that there were 50,000 lines of code in the CIAO3.0 implementation; with our new, cleaner design, implemented in Python, only half that number of lines were required.) We present the latest updates to our design, and our progress developing Sherpa. A major feature of this work has been the use of Python to implement the data structures from our design. Each part of Sherpa---models, fitting methods, statistics, and so on---has been implemented as a Python module. We have also developed application code to bind together data, models, statistics, and fitting methods for performing fits to data, as well as a high-level UI that makes it simple for users to read in data, define models, and perform fits. Working in Python has been a great aid in speeding development of Sherpa. We expect that Python will also simplify extending and maintaining the Sherpa code base, as well as making it possible to interoperate with other Python-based astronomy packages. To make Sherpa fully accessible to S--Lang users, we use PySL, a new package that is an interface between Python and S--Lang. Users are now able to import other Python or S--Lang modules to extend Sherpa; in addition, users may write and use scripts of their own, written in either Python or S--Lang.

Doe, S.; Nguyen, D.; Stawarz, C.; Refsdal, B.; Siemiginowska, A.; Burke, D.; Evans, I.; Evans, J.; McDowell, J.; Houck, J.; Nowak, M.

2007-10-01

12

Monte Python: Monte Carlo Code for CLASS in Python  

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

13

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

14

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? (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

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

2005-01-01

15

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

16

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

17

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.

2012-03-26

18

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

19

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

20

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.

Bã¤cker, Arnd

2008-06-07

21

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

22

Humoral regulation of heart rate during digestion in pythons (Python molurus and Python regius).  

PubMed

Pythons exhibit a doubling of heart rate when metabolism increases several times during digestion. Pythons, therefore, represent a promising model organism to study autonomic cardiovascular regulation during the postprandial state, and previous studies show that the postprandial tachycardia is governed by a release of vagal tone as well as a pronounced stimulation from nonadrenergic, noncholinergic (NANC) factors. Here we show that infusion of plasma from digesting donor pythons elicit a marked tachycardia in fasting snakes, demonstrating that the NANC factor resides in the blood. Injections of the gastrin and cholecystokinin receptor antagonist proglumide had no effect on double-blocked heart rate or blood pressure. Histamine has been recognized as a NANC factor in the early postprandial period in pythons, but the mechanism of its release has not been identified. Mast cells represent the largest repository of histamine in vertebrates, and it has been speculated that mast cells release histamine during digestion. Treatment with the mast cell stabilizer cromolyn significantly reduced postprandial heart rate in pythons compared with an untreated group but did not affect double-blocked heart rate. While this study indicates that histamine induces postprandial tachycardia in pythons, its release during digestion is not stimulated by gastrin or cholecystokinin nor is its release from mast cells a stimulant of postprandial tachycardia. PMID:22422667

Enok, Sanne; Simonsen, Lasse Stærdal; Pedersen, Signe Vesterskov; Wang, Tobias; Skovgaard, Nini

2012-05-15

23

Steering object-oriented computations with Python.  

National Technical Information Service (NTIS)

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 ...

T. Y. B. Yang P. F. Dubois G. Furnish D. M. Beazley

1996-01-01

24

Python Programming for Astronomical Data Analysis  

NASA Astrophysics Data System (ADS)

The work is about using programming skills (Python programming in particular) for analyzing astronomical data. Some points about the importance of programming skills are presented. Some advantages of Python for astronomy research are also presented. Finally, an example of a Python code which solves an astronomical data analysis task is presented.

Vardanyan, V.

2012-05-01

25

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

26

Astropysics: Astrophysics utilities for python  

NASA Astrophysics Data System (ADS)

Astropysics is a library containing a variety of utilities and algorithms for reducing, analyzing, and visualizing astronomical data. Best of all, it encourages the user to leverage the existing capabilities of Python to make this quick, easy, and as painless as cutting-edge science can even actually be. There do exist other Python packages with some of the capabilities of this project, but the goal of this project is to integrate all these tools together and make them interact in the most straightforward ways possible.

Tollerud, Erik

2012-07-01

27

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

28

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.

29

Imagining a Stata / Python Combination  

NASA Technical Reports Server (NTRS)

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

Fiedler, James

2012-01-01

30

Advanced Python Scripting Using Sherpa  

NASA Astrophysics Data System (ADS)

Sherpa is a general purpose modeling and fitting application written in Python. The dynamism of Python allows Sherpa to be a powerful and extensible software package ready for the modern challenges of data analysis. Primarily developed for the Chandra Interactive Analysis of Observations (CIAO) package, it provides a flexible environment for resolving spectral and image properties, analyzing time series, and modeling generic types of data. Complex model expressions are supported using Sherpa's general purpose definition syntax. Sherpa's parameterized data modeling is achieved using robust optimization methods implementing the forward fitting technique. Sherpa includes functions to calculate goodness-of-fit and parameter confidence limits. CPU intensive routines are written in C++/FORTRAN. But since all other data structures are contained in Python modules, users can easily add their own data structures, models, statistics or optimization methods to Sherpa. We will introduce a scripted example that highlights Sherpa's ability to estimate energy and photon flux errors using simulations. The draws from these simulations, accessible as NumPy ndarrays, can be sampled from uni-variate and multi-variate normal distributions and can be binned and visualized with simple high level functions. We will demonstrate how Sherpa can be extended with user-defined model and statistic classes written in Python. Sherpa's open design even allows users to incorporate prior statistics derived from the source model.

Refsdal, R.; Doe, S.; Nguyen, D.; Siemiginowska, A.; Burke, D.; Evans, J.; Evans, I.

2011-07-01

31

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

32

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

33

PyFITS: Python FITS Module  

NASA Astrophysics Data System (ADS)

PyFITS provides an interface to FITS formatted files in the Python scripting language and PyRAF, the Python-based interface to IRAF. It is useful both for interactive data analysis and for writing analysis scripts in Python using FITS files as either input or output. PyFITS is a development project of the Science Software Branch at the Space Telescope Science Institute.

Barrett, Paul; Hsu, J. C.; Hanley, Chris; Taylor, James; Droettboom, Michael; Bray, Erik M.; Hack, Warren; Greenfield, Perry; Wyckoff, Eric; Jedrzejewski, Robert; De La Pena, Michele; Hodge, Phil

2012-07-01

34

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

35

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

USGS Publications Warehouse

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

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

2011-01-01

36

Astropy: Community Python library for astronomy  

NASA Astrophysics Data System (ADS)

Astropy provides a common framework, core package of code, and affiliated packages for astronomy in Python. Development is actively ongoing, with major packages such as PyFITS, PyWCS, vo, and asciitable already merged in. Astropy is intended to contain much of the core functionality and some common tools needed for performing astronomy and astrophysics with Python.

Greenfield, Perry; Robitaille, Thomas; Tollerud, Erik; Aldcroft, Tom; Barbary, Kyle; Barrett, Paul; Bray, Erik; Crighton, Neil; Conley, Alex; Conseil, Simon; Davis, Matt; Deil, Christoph; Dencheva, Nadia; Droettboom, Michael; Ferguson, Henry; Ginsburg, Adam; Grollier, Frédéric; Moritz Günther, Hans; Hanley, Chris; Hsu, J. C.; Kerzendorf, Wolfgang; Kramer, Roban; Lian Lim, Pey; Muna, Demitri; Nair, Prasanth; Price-Whelan, Adrian; Shiga, David; Singer, Leo; Taylor, James; Turner, James; Woillez, Julien; Zabalza, Victor

2013-04-01

37

Facility for creating Python extensions in C++.  

National Technical Information Service (NTIS)

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...

P. F. Dubois

1998-01-01

38

Grid Programming in Java and Python  

NSDL National Science Digital Library

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

Von Laszewski, Gregor; Jackson, Keith

39

Python-Based Applications for Hydrogeological Modeling  

NASA Astrophysics Data System (ADS)

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

Khambhammettu, P.

2013-12-01

40

PyMSES: Python modules for RAMSES  

NASA Astrophysics Data System (ADS)

PyMSES provides a python solution for getting data out of RAMSES (ascl:1011.007) astrophysical fluid dynamics simulations. It permits transparent manipulation of large simulations and interfaces with common Python libraries and existing code, and can serve as a post-processing toolbox for data analysis. It also does three-dimensional volume rendering with a specific algorithm optimized to work on RAMSES distributed data (Guillet et al. 2011 and Jones et a. 2011).

Guillet, Thomas; Chapon, Damien; Labadens, Marc

2013-10-01

41

PyRAF: Python alternative for IRAF  

NASA Astrophysics Data System (ADS)

PyRAF is a command language for running IRAF tasks that is based on the Python scripting language. It gives users the ability to run IRAF tasks in an environment that has all the power and flexibility of Python. PyRAF can be installed along with an existing IRAF installation; users can then choose to run either PyRAF or the IRAF CL.

Science Software Branch at STScI

2012-07-01

42

ParselTongue: AIPS Python Interface  

NASA Astrophysics Data System (ADS)

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

Kettenis, Mark; Sipior, Mike

2012-08-01

43

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 Lomé, 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; Stéphanie Maumelat

2005-01-01

44

Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus).  

PubMed

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

Huder, Jon B; Böni, Jürg; Hatt, Jean-Michel; Soldati, Guido; Lutz, Hans; Schüpbach, Jörg

2002-08-01

45

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

PubMed Central

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

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

2002-01-01

46

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

47

Python for Education: Computational Methods for Nonlinear Systems  

NSDL National Science Digital Library

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

Myers, Christopher; Sethna, James

2008-07-23

48

Change of cardiac function, but not form, in postprandial pythons  

Microsoft Academic Search

Pythons are renowned for a rapid and pronounced postprandial growth of the heart that coincides with a several-fold elevation of cardiac output that lasts for several days. Here we investigate whether ventricular morphology is affected by digestive state in two species of pythons (Python regius and Python molurus) and we determine the cardiac right-to-left shunt during the postprandial period in

Bjarke Jensen; Casper Kornbech Larsen; Jan Møller Nielsen; Lasse Stærdal Simonsen; Tobias Wang

2011-01-01

49

Web development with python and django (abstract only)  

Microsoft Academic Search

Many instructors have already discovered the joy of teaching programming using the Python programming language. Now it's time to take Python to the next level. This workshop will introduce Django, an open source Python web framework that saves you time and makes web development fun. It's aimed at Computer Science instructors who want to teach how to build elegant web

Ariel Ortiz

2012-01-01

50

Re-imagining a Stata/Python Combination.  

National Technical Information Service (NTIS)

At last year's Stata Conference, I presented some ideas for combining Stata and the Python programming language within a single interface. Two methods were presented: in one, Python was used to automate Stata; in the other, Python was used to send simulat...

J. Fiedler

2013-01-01

51

Charming Users into Scripting CIAO with Python  

NASA Astrophysics Data System (ADS)

The Science Data Systems group of the Chandra X-ray Center provides a number of scripts and Python modules that extend the capabilities of CIAO. Experience in converting the existing scripts—written in a variety of languages such as bash, csh/tcsh, Perl and S-Lang—to Python, and conversations with users, led to the development of the ciao_contrib.runtool module. This allows users to easily run CIAO tools from Python scripts, and utilizes the metadata provided by the parameter-file system to create an API that provides the flexibility and safety guarantees of the command-line. The module is provided to the user community and is being used within our group to create new scripts.

Burke, D. J.

2011-07-01

52

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

53

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

PubMed

Cover illustration. Snakes have no moveable eyelids. Instead, the eyelids remain fused in the embryonic state to create the spectacle, a transparent structure that covers and protects the eye. In this issue of the Journal of Morphology, Da Silva et al. (pp. 489-496 10.1002/jmor.20230) provide a detailed account on the histology and ultrastructure of the eye of ball pythons (Python regius). The cover image shows the head of a live ball python (image: J.M. Starck 2005). PMID:24723499

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

2014-05-01

54

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

USGS Publications Warehouse

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

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

2011-01-01

55

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

56

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

57

Python Bindings for the Common Pipeline Library  

NASA Astrophysics Data System (ADS)

The Common Pipeline Library is a set of routines written by ESO to provide a standard interface for VLT instrument data reduction tasks (“pipelines”). To control these pipelines from Python, we developed a wrapper called PYTHON-CPL that allows one to conveniently work interactively and to process data as part of an automated data reduction system. The package will be used to implement the MUSE pipeline in the AstroWISE data management system. We describe the features and design of the package.

Streicher, O.; Weilbacher, P. M.

2012-09-01

58

The zoonotic implications of pentastomiasis in the royal python (python regius).  

PubMed

Pentastomes are worm-like endoparasites of the phylum Pentastomida found principally in the respiratory tract of reptiles, birds, and mammals. They cause a zoonotic disease known as pentastomiasis in humans and other mammals. The autopsy of a Nigerian royal python (Python regius) revealed two yellowish-white parasites in the lungs, tissue necrosis and inflammatory lesions. The parasite was confirmed to be Armillifer spp (Pentastomid); this is the first recorded case of pentastomiasis in the royal python (Python regius) in Nigeria. This report may be an alert of the possibility of on-going zoonotic transmission of pentastomiasis from snake to man, especially in the sub-urban/rural areas of Nigeria and other West African countries where people consume snake meat. PMID:21327016

Ayinmode, Ab; Adedokun, Ao; Aina, A; Taiwo, V

2010-09-01

59

PyXNAT: XNAT in Python.  

PubMed

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

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

2012-01-01

60

Python Scripting in the Nengo Simulator  

PubMed Central

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

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

2008-01-01

61

PyXNAT: XNAT in Python  

PubMed Central

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

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

2012-01-01

62

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

63

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

USGS Publications Warehouse

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

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

2012-01-01

64

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

65

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.

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

2013-01-01

66

PyMidas: Interface from Python to Midas  

NASA Astrophysics Data System (ADS)

PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

Maisala, Sami; Oittinen, Tero

2014-01-01

67

Osteosarcoma in a woma python (Aspidites ramsayi).  

PubMed

Osteosarcoma of the axial skeleton in an 18-month-old woma python (Aspidites ramsayi) is described. A subcutaneous mass overlying the costal arches enlarged progressively over a period of 5 months and, in that time, became ulcerated and more invasive of surrounding tissues. A punch biopsy of the lesion under general anaesthesia provided tissue for histopathology and diagnosis of low-grade osteosarcoma. PMID:22103954

Cowan, M L; Monks, D J; Raidal, S R

2011-12-01

68

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

69

Re-imagining a Stata/Python Combination  

NASA Technical Reports Server (NTRS)

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

Fiedler, James

2013-01-01

70

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

71

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

72

Reptilian viruses: adenovirus-like agent isolated from royal python (Python regius).  

PubMed

An adenovirus-like agent was isolated from a moribund royal python (Python regius). The DNA containing virus replicated in IgH2-cells at 30 degrees C forming eosinophilic intranuclear inclusion bodies. The virus proved to be stabile to treatment with chloroform, pH3 und pH 12 but it was labile to heat (56 degrees C). Infected IgH2 cells revealed symmetric hexagonal virus particles measuring 67-79 nm in the nucleus. The isolate shared characteristics with the viruses of the family Adenoviridae. PMID:1337233

Ogawa, M; Ahne, W; Essbauer, S

1992-12-01

73

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

74

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

75

Python Test Framework with Jenkins Implementation in Software Automation Testing  

Microsoft Academic Search

The Python Test Framework is a test automation tool to manage and distribute the execution of web-based functional testing. This paper presents the introduction of Python Test Framework, Jenkins and implementation of the test automation tools integrated and managed by Jenkins, the continuous integration platform, to further improve the testing efficiency as well as minimizing the effort and risk in

Fakaruddin Fahmi Romli; Mohd Ariffudin Mohd Isa; Mohd Solehudin Abdullah; Sazianti Mohd Saad

76

PYTHON TEST FRAMEWORK WITH JENKINS IMPLEMENTATION IN SOFTWARE AUTOMATION TESTING  

Microsoft Academic Search

The Python Test Framework is a test automation tool to manage and distribute the execution of web-based functional testing. This paper presents the introduction of Python Test Framework, Jenkins and implementation of the test automation tools integrated and managed by Jenkins, the continuous integration platform, to further improve the testing efficiency as well as minimizing the effort and risk in

2012-01-01

77

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

78

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

79

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

2014-01-01

80

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.

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

2014-01-01

81

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

82

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, Bulantová, Votýpka et Modrý, 2007. Transmis- sion was successful in these

Michal Sloboda; Martin Kamler; Jana Bulantová; Jan Votýpka; David Modrý

83

Responses of python gastrointestinal regulatory peptides to feeding  

PubMed Central

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

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

2001-01-01

84

PyMOOSE: Interoperable Scripting in Python for MOOSE  

PubMed Central

Python is emerging as a common scripting language for simulators. This opens up many possibilities for interoperability in the form of analysis, interfaces, and communications between simulators. We report the integration of Python scripting with the Multi-scale Object Oriented Simulation Environment (MOOSE). MOOSE is a general-purpose simulation system for compartmental neuronal models and for models of signaling pathways based on chemical kinetics. We show how the Python-scripting version of MOOSE, PyMOOSE, combines the power of a compiled simulator with the versatility and ease of use of Python. We illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation. Finally, we build and run a composite neuronal/signaling model that uses both the NEURON and MOOSE numerical engines, and Python as a bridge between the two. Thus PyMOOSE has a high degree of interoperability with analysis routines, with graphical toolkits, and with other simulators.

Ray, Subhasis; Bhalla, Upinder S.

2008-01-01

85

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

PubMed

?-Hemolysin (HlyA) from Escherichia coli lyses mammalian erythrocytes by creating nonselective cation pores in the membrane. Pore insertion triggers ATP release and subsequent P2X receptor and pannexin channel activation. Blockage of either P2X receptors or pannexin channels reduces HlyA-induced hemolysis. We found that erythrocytes from Python regius and Python molurus are remarkably resistant to HlyA-induced hemolysis compared to human and Trachemys scripta erythrocytes. HlyA concentrations that induced maximal hemolysis of human erythrocytes did not affect python erythrocytes, but increasing the HlyA concentration 40-fold did induce hemolysis. Python erythrocytes were more resistant to osmotic stress than human erythrocytes, but osmotic stress tolerance per se did not confer HlyA resistance. Erythrocytes from T. scripta, which showed higher osmotic resistance than python erythrocytes, were as susceptible to HlyA as human erythrocytes. Therefore, we tested whether python erythrocytes lack the purinergic signalling known to amplify HlyA-induced hemolysis in human erythrocytes. P. regius erythrocytes increased intracellular Ca²? concentration and reduced cell volume when exposed to 3 mM ATP, indicating the presence of a P2X?-like receptor. In addition, scavenging extracellular ATP or blocking P2 receptors or pannexin channels reduced the HlyA-induced hemolysis. We tested whether the low HlyA sensitivity resulted from low affinity of HlyA to the python erythrocyte membrane. We found comparable incorporation of HlyA into human and python erythrocyte membranes. Taken together, the remarkable HlyA resistance of python erythrocytes was not explained by increased osmotic resistance, lack of purinergic hemolysis amplification, or differences in HlyA affinity. PMID:22064954

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

2011-12-01

86

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

87

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 11.9±5.0mm(3)g(-1). The volume fraction, i.e., the actual pulmonary exchange tissue per lung parenchyma, was 63.22±7.3%; the total respiratory surface was, on average, 0.214±0.129m(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 0.78±0.05?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 0.69±0.38ml 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

88

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

89

Reduction of blood oxygen levels enhances postprandial cardiac hypertrophy in Burmese python (Python bivittatus).  

PubMed

Physiological cardiac hypertrophy is characterized by reversible enlargement of cardiomyocytes and changes in chamber architecture, which increase stroke volume and via augmented convective oxygen transport. Cardiac hypertrophy is known to occur in response to repeated elevations of O2 demand and/or reduced O2 supply in several species of vertebrate ectotherms, including postprandial Burmese pythons (Python bivittatus). Recent data suggest postprandial cardiac hypertrophy in P. bivittatus is a facultative rather than obligatory response to digestion, though the triggers of this response are unknown. Here, we hypothesized that an O2 supply-demand mismatch stimulates postprandial cardiac enlargement in Burmese pythons. To test this hypothesis, we rendered animals anemic prior to feeding, essentially halving blood oxygen content during the postprandial period. Fed anemic animals had heart rates 126% higher than those of fasted controls, which, coupled with a 71% increase in mean arterial pressure, suggests fed anemic animals were experiencing significantly elevated cardiac work. We found significant cardiac hypertrophy in fed anemic animals, which exhibited ventricles 39% larger than those of fasted controls and 28% larger than in fed controls. These findings support our hypothesis that those animals with a greater magnitude of O2 supply-demand mismatch exhibit the largest hearts. The 'low O2 signal' stimulating postprandial cardiac hypertrophy is likely mediated by elevated ventricular wall stress associated with postprandial hemodynamics. PMID:24311803

Slay, Christopher E; Enok, Sanne; Hicks, James W; Wang, Tobias

2014-05-15

90

study Experimentally derived salinity tolerance hatchling Brems python (python mailers bivattatus) Everglades Florida (USA) authored USGS scientists christen M. Hart Pamela J. Schofield Denise R. Gregoire.  

EPA Pesticide Factsheets

Did you mean: study Experimentally derived salinity tolerance hatchling Brems python (python mailers bivattatus) Everglades Florida (USA) authored USGS scientists christen M. Hart Pamela J. Schofield Denise R. Gregoire. ?

91

study Experimentally derived salinity tolerance hatchling Brems python (python mailers bivattatus) Everglades Florida (USA) authored USGS scientists christen M. Hart Panola J. Schofield Denise R. Gregoire.  

EPA Pesticide Factsheets

Did you mean: study Experimentally derived salinity tolerance hatchling Brems python (python mailers bivattatus) Everglades Florida (USA) authored USGS scientists christen M. Hart Panola J. Schofield Denise R. Gregoire. ?

92

Status of NTCC Python Physics Server  

NASA Astrophysics Data System (ADS)

The National Transport Code Collaboration's Demonstration Project consists of a physics server, a graphical user interface (GUI) client, and a database server, each of which can run on a different computer. The Python-based physics server, PYNTD, is an object-oriented code that allows dynamic extension and configuration. It was originally written as a transport-model tester, advancing only ion and electron temperatures with all other fields prescribed. Recent developments include changes in the structure to accomodate an arbitrary number of fields, and implementation, specifically, of evolution equations for toroidal rotation. Also, interaction with the remote graphical-user-interface client, and with databases, has been enhanced in several ways, including in particular enabling the GUI to set the full set of ``settable'' parameters of any model. These advances will be described, as will the results of code validation activities and enhancements to the GUI client.

Cohen, R. H.; Jong, R.; Yang, T. B.; Cary, J.; Leutkemeyer, K.; Kinsey, J.; St. John, H.; Wiley, J.

1999-11-01

93

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

94

Multi-scale Analysis with Python  

NASA Astrophysics Data System (ADS)

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

Marvel, K. D.

2012-12-01

95

Using Python for Climate Model Intercomparison  

NASA Astrophysics Data System (ADS)

With the success of CMIP3, model intercomparison projects have become a core methodology for climate research. The nature of these projects requires users to sort through and download massive datasets, to work with arrays too large to fit into memory, and to handle a profusion of grids and other model-specific information in a flexible way. In this talk I will provide a climate scientist's perspective on using python to overcome these problems. I will share my experiences with server-side data reduction, automating data downloads, minimizing memory usage, parallel data processing, comparing and plotting data on differing (and perhaps irregular) grids, and using compiled (fortran) code to remove bottlenecks. Where possible, solution approaches will be illustrated with simple example code. Prepared by LLNL under Contract DE-AC52-07NA27344.

Caldwell, P.

2012-12-01

96

PyEphem: Astronomical Ephemeris for Python  

NASA Astrophysics Data System (ADS)

PyEphem provides scientific-grade astronomical computations for the Python programming language. Given a date and location on the Earth’s surface, it can compute the positions of the Sun and Moon, of the planets and their moons, and of any asteroids, comets, or earth satellites whose orbital elements the user can provide. Additional functions are provided to compute the angular separation between two objects in the sky, to determine the constellation in which an object lies, and to find the times at which an object rises, transits, and sets on a particular day.The numerical routines that lie behind PyEphem are those from the wonderful XEphem astronomy application, whose author, Elwood Downey, generously gave permission for us to use them as the basis for PyEphem.

Rhodes, Brandon Craig

2011-12-01

97

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

Microsoft Academic Search

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

Luca Luiselli; Francesco Maria Angelici

1998-01-01

98

MEG and EEG data analysis with MNE-Python  

PubMed Central

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

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

2013-01-01

99

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

100

Pythons metabolize prey to fuel the response to feeding.  

PubMed

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

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

2004-05-01

101

Pythons metabolize prey to fuel the response to feeding.  

PubMed Central

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

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

2004-01-01

102

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.

2011-01-01

103

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

104

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

105

PsychoPy--Psychophysics software in Python.  

PubMed

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

2007-05-15

106

PsychoPy--Psychophysics 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.

Peirce, Jonathan W.

2007-01-01

107

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

108

PyHelp-An Automatic Multi-Output Documentation Generator for Python.  

National Technical Information Service (NTIS)

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 pr...

W. I. Nissen

2005-01-01

109

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

110

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 µm in histological specimens and 108?±?13 µm 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. J. Morphol. 275:489-496, 2014. © 2013 Wiley Periodicals, Inc. PMID:24375578

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

2014-05-01

111

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

112

Benigní chondromy pr?dušnice u krajty královské (Python regius)  

Microsoft Academic Search

SUMMARY Hnízdo J., Hes O., Honsa V., Grégrová L. Benign tracheal chondromas in the ball python (Python regius). Veterinární 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. HNÍZDO; V. HONSA

113

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

114

Synthetic seismogram web service and Python tools  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

115

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

116

pyam: Python Implementation of YaM  

NASA Technical Reports Server (NTRS)

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

Myint, Steven; Jain, Abhinandan

2012-01-01

117

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.

Ibáñez, José-Miguel; García Segura, Antonio J.; Storz, Clemens; Fried, Josef W.; Fernández, Matilde; Rodríguez Gómez, Julio F.; Terrón, V.; Cárdenas, M. C.

2012-09-01

118

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.; Nuñez, Leroy P.; Mazzotti, Frank J.; Snow, Ray W.

2012-01-01

119

A parvovirus isolated from royal python (Python regius) is a member of the genus Dependovirus.  

PubMed

Parvoviruses were isolated from Python regius and Boa constrictor snakes and propagated in viper heart (VH-2) and iguana heart (IgH-2) cells. The full-length genome of a snake parvovirus was cloned and both strands were sequenced. The organization of the 4432-nt-long genome was found to be typical of parvoviruses. This genome was flanked by inverted terminal repeats (ITRs) of 154 nt, containing 122 nt terminal hairpins and contained two large open reading frames, encoding the non-structural and structural proteins. Genes of this new parvovirus were most similar to those from waterfowl parvoviruses and from adeno-associated viruses (AAVs), albeit to a relatively low degree and with some organizational differences. The structure of its ITRs also closely resembled those of AAVs. Based on these data, we propose to classify this virus, the first serpentine parvovirus to be identified, as serpentine adeno-associated virus (SAAV) in the genus Dependovirus. PMID:14993638

Farkas, Szilvia L; Zádori, Zoltán; Benko, Mária; Essbauer, Sandra; Harrach, Balázs; Tijssen, Peter

2004-03-01

120

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

121

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

PubMed

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

Jurica, Peter; van Leeuwen, Cees

2009-01-01

122

A crossed rubrobulbar projection in the snake Python regius.  

PubMed

In the present study a distinct crossed rubrobulbar projection has been demonstrated in the snake Python regius, a limbless vertebrate which lacks a rubrospinal tract. This rubrobulbar projection is presumably involved in the neural control of mastication. The red nucleus may relay cerebellar influence to the trigeminal and facial nuclei. PMID:6640341

Ten Donkelaar, H J; Bangma, G C

1983-11-21

123

Reticulospinal and vestibulospinal pathways in the snake Python regius  

Microsoft Academic Search

In the present HRP study extensive reticulospinal projections and more modestly developed vestibulospinal pathways have been demonstrated in the snake Python regius. The funicular trajectories of the main reticulospinal pathways have been shown: via the lateral funiculus pass spinal projections of the nucleus reticularis superior pars lateralis, the nucleus reticularis inferior and nucleus raphes inferior; via the ventral funiculus fibers

H. J. Donkelaar; G. C. Bangma; R. Boer-van Huizen

1983-01-01

124

SunPy: Python for Solar Physics Data Analysis  

NASA Astrophysics Data System (ADS)

In recent years, Python, a free cross platform general purpose high-level programming language, has seen widespread adoption among the scientific community resulting in the availability of wide range of software, from numerical computation and machine learning to spectral analysis and visualization. SunPy is a software suite specializing in providing the tools necessary to analyze solar and heliospheric datasets in Python. It provides a free and open-source alternative to the IDL-based SolarSoft (SSW) solar data analysis environment. We present the current capabilities of SunPy which include WCS-aware map objects that allow simple overplotting of data from multiple image FITS files; time-series objects that allow overplotting of multiple lightcurves, and integration with online services such as The Virtual Solar Observatory (VSO) and The Heliophysics Event Knowledgebase (HEK). SunPy also provides functionality that is not currently available in SSW such as advanced time series manipulation routines and support for working with solar data stored using JPEG 2000. 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 currently 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.

Hughitt, V. Keith; Christe, S.; Ireland, J.; Shih, A.; Mayer, F.; Earnshaw, M. D.; Young, C.; Perez-Suarez, D.; Schwartz, R.

2012-05-01

125

pynbody: N-Body/SPH analysis for python  

NASA Astrophysics Data System (ADS)

Pynbody is a lightweight, portable, format-transparent analysis package for astrophysical N-body and smooth particle hydrodynamic simulations supporting PKDGRAV/Gasoline, Gadget, N-Chilada, and RAMSES AMR outputs. Written in python, the core tools are accompanied by a library of publication-level analysis routines.

Pontzen, Andrew; Roskar, Rok; Stinson, Greg; Woods, Rory

2013-05-01

126

p3d - Python module for structural bioinformatics  

PubMed Central

Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

Fufezan, Christian; Specht, Michael

2009-01-01

127

ChiantiPy: Python package for the CHIANTI atomic database  

NASA Astrophysics Data System (ADS)

ChiantiPy is an object-orient Python package for calculating astrophysical spectra using the CHIANTI atomic database for astrophysical spectroscopy. It provides access to the database and the ability to calculate various physical quantities for the interpretation of astrophysical spectra.

Dere, Ken

2013-08-01

128

Teaching CS1 with Python GUI Game Programming  

NASA Astrophysics Data System (ADS)

Python is becoming a popular programming language in teaching freshman programming courses. The author designed a sequence of game programming labs using Pygame to further help engage students and to improve their programming skills. The class survey showed that the adoption of Pygame is successful.

Wang, Hong

2010-06-01

129

Change of cardiac function, but not form, in postprandial pythons.  

PubMed

Pythons are renowned for a rapid and pronounced postprandial growth of the heart that coincides with a several-fold elevation of cardiac output that lasts for several days. Here we investigate whether ventricular morphology is affected by digestive state in two species of pythons (Python regius and Python molurus) and we determine the cardiac right-to-left shunt during the postprandial period in P. regius. Both species experienced several-fold increases in metabolism and mass of the digestive organs by 24 and 48 h after ingestion of meals equivalent to 25% of body mass. Surprisingly there were no changes in ventricular mass or dimensions as we used a meal size and husbandry conditions similar to studies finding rapid and significant growth. Based on these data and literature we therefore suggest that postprandial cardiac growth should be regarded as a facultative rather than obligatory component of the renowned postprandial response. The cardiac right-to-left shunt, calculated on the basis of oxygen concentrations in the left and right atria and the dorsal aorta, was negligible in fasting P. regius, but increased to 10-15% during digestion. Such shunt levels are very low compared to other reptiles and does not support a recent proposal that shunts may facilitate digestion in reptiles. PMID:21605694

Jensen, Bjarke; Larsen, Casper Kornbech; Nielsen, Jan Møller; Simonsen, Lasse Stærdal; Wang, Tobias

2011-09-01

130

Building a programmable interface for physics codes using numeric python.  

National Technical Information Service (NTIS)

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...

T. Y. B. Yang P. F. Dubois Z. C. Motteler

1996-01-01

131

Comparison of cyclic correlation algorithm implemented in matlab and python  

NASA Astrophysics Data System (ADS)

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

Carr, Richard; Whitney, James

132

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

133

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; Martín-Jiménez, Tomás

2011-09-01

134

Expyriment: A Python library for cognitive and neuroscientific experiments.  

PubMed

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

Krause, Florian; Lindemann, Oliver

2014-06-01

135

Brian: A Simulator for Spiking Neural Networks in Python  

PubMed Central

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

Goodman, Dan; Brette, Romain

2008-01-01

136

AstroAsciiData: Table Handling in Python  

Microsoft Academic Search

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

J. Haase; M. Kümmel

2007-01-01

137

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

138

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

139

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

140

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/

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

2014-01-01

141

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

142

ACPYPE - AnteChamber PYthon Parser interfacE  

PubMed Central

Background ACPYPE (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 GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. Findings We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. Conclusions ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

2012-01-01

143

Python for Information Theoretic Analysis of Neural Data  

PubMed Central

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

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

2008-01-01

144

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

145

PyEEG: An Open Source Python Module for EEG/MEG Feature Extraction  

PubMed Central

Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As Python is gaining more ground in scientific computing, an open source Python module for extracting EEG features has the potential to save much time for computational neuroscientists. In this paper, we introduce PyEEG, an open source Python module for EEG feature extraction.

Bao, Forrest Sheng; Liu, Xin; Zhang, Christina

2011-01-01

146

PyEEG: an open source Python module for EEG/MEG feature extraction.  

PubMed

Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As Python is gaining more ground in scientific computing, an open source Python module for extracting EEG features has the potential to save much time for computational neuroscientists. In this paper, we introduce PyEEG, an open source Python module for EEG feature extraction. PMID:21512582

Bao, Forrest Sheng; Liu, Xin; Zhang, Christina

2011-01-01

147

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.

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

2011-01-01

148

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, Bulantová, Votýpka et Modrý, 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; Bulantová, Jana; Votýpka, Jan; Modrý, David

2008-03-01

149

Short Communication A parvovirus isolated from royal python (Python regius) is a member of the genus Dependovirus  

Microsoft Academic Search

Parvoviruses were isolated from Python regius and Boa constrictor snakes and propagated in viper heart (VH-2) and iguana heart (IgH-2) cells. The full-length genome of a snake parvovirus was cloned and both strands were sequenced. The organization of the 4432-nt-long genome was found to be typical of parvoviruses. This genome was flanked by inverted terminal repeats (ITRs) of 154 nt,

Szilvia L. Farkas; Maria Benko; Sandra Essbauer; Balazs Harrach; Peter Tijssen

150

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

PubMed

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

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

2012-01-15

151

What parts of the US mainland are climatically suitable for invasive alien pythons spreading from Everglades National Park?  

Microsoft Academic Search

The Burmese Python (Python molurus bivittatus) is now well established in southern Florida and spreading northward. The factors likely to limit this spread are unknown,\\u000a but presumably include climate or are correlated with climate. We compiled monthly rainfall and temperature statistics from\\u000a 149 stations located near the edge of the python’s native range in Asia (Pakistan east to China and

Gordon H. Rodda; Catherine S. Jarnevich; Robert N. Reed

2009-01-01

152

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

153

Embryonic development of Python sebae – I: Staging criteria and macroscopic skeletal morphogenesis of the head and limbs  

Microsoft Academic Search

This study explores the post-ovipositional craniofacial development of the African Rock Python (Python sebae). We first describe a staging system based on external characteristics and next use whole-mount skeletal staining supplemented with Computed tomography (CT) scanning to examine skeletal development. Our results show that python embryos are in early stages of organogenesis at the time of laying, with separate facial

Julia C. Boughner; Marcela Buchtová; Katherine Fu; Virginia Diewert; Benedikt Hallgrímsson; Joy M. Richman

2007-01-01

154

MTpy - Python Tools for Magnetotelluric Data Processing and Analysis  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

155

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics  

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

156

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

PubMed

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

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

2013-02-01

157

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit  

PubMed Central

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

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

2008-01-01

158

Amateur Image Pipeline Processing using Python plus PyRAF  

NASA Astrophysics Data System (ADS)

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

Green, Wayne

2012-05-01

159

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

160

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

161

CMCpy: Genetic Code-Message Coevolution Models in Python.  

PubMed

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

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

2013-01-01

162

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

163

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.

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

2013-01-01

164

Hardware-accelerated interactive data visualization for neuroscience in Python.  

PubMed

Large datasets are becoming more and more common in science, particularly in neuroscience where experimental techniques are rapidly evolving. Obtaining interpretable results from raw data can sometimes be done automatically; however, there are numerous situations where there is a need, at all processing stages, to visualize the data in an interactive way. This enables the scientist to gain intuition, discover unexpected patterns, and find guidance about subsequent analysis steps. Existing visualization tools mostly focus on static publication-quality figures and do not support interactive visualization of large datasets. While working on Python software for visualization of neurophysiological data, we developed techniques to leverage the computational power of modern graphics cards for high-performance interactive data visualization. We were able to achieve very high performance despite the interpreted and dynamic nature of Python, by using state-of-the-art, fast libraries such as NumPy, PyOpenGL, and PyTables. We present applications of these methods to visualization of neurophysiological data. We believe our tools will be useful in a broad range of domains, in neuroscience and beyond, where there is an increasing need for scalable and fast interactive visualization. PMID:24391582

Rossant, Cyrille; Harris, Kenneth D

2013-01-01

165

Programming biological models in Python using PySB.  

PubMed

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

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

2013-01-01

166

New Python-based methods for data processing.  

PubMed

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

2013-07-01

167

COBRApy: COnstraints-Based Reconstruction and Analysis for Python  

PubMed Central

Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software. Results Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes. Conclusion COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. Availability http://opencobra.sourceforge.net/

2013-01-01

168

SCoT: a Python toolbox for EEG source connectivity.  

PubMed

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

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

2014-01-01

169

CMCpy: Genetic Code-Message Coevolution Models in Python  

PubMed Central

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

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

2013-01-01

170

Temporal and spatial complexity of maternal thermoregulation in tropical pythons.  

PubMed

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

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

2012-01-01

171

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

172

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

173

Myiasis by Megaselia scalaris (Diptera: Phoridae) in a python affected by pulmonitis.  

PubMed

Myiases are caused by the presence of maggots in vertebrate tissues and organs. Myiases have been studied widely in humans, farm animals, and pets, whereas reports of myiasis in reptiles are scarce. We describe a case of myiasis caused by the Megaselia scalaris (Loew) in an Indian python (Python molurus bivittatus, Kuhl) (Ophida: Boidae). The python, 15 yr old, born and reared in a terrarium in the mainland of Venice (Italy), was affected by diffuse, purulent pneumonia caused by Burkholderia cepacia. The severe infestation of maggots found in the lungs during an autopsy indicated at a myiasis. PMID:23427672

Vanin, S; Mazzariol, S; Menandro, M L; Lafisca, A; Turchetto, M

2013-01-01

174

pNbody: A python parallelized N-body reduction toolbox  

NASA Astrophysics Data System (ADS)

pNbody is a parallelized python module toolbox designed to manipulate and interactively display very large N-body systems. It allows the user to perform complicated manipulations with only very few commands and to load an N-body system and explore it interactively using the python interpreter. pNbody may also be used in python scripts. pNbody contains graphical facilities for creating maps of physical values of the system, such as density, temperature, and velocities maps. Stereo capabilities are also implemented. pNbody is not limited by file format; the user may use a parameter file to redefine how to read a preferred format.

Revaz, Yves

2013-02-01

175

Benchmarking and Application of NTCC Python Physics Server  

NASA Astrophysics Data System (ADS)

The Python-based physics server, PYNTD, a component of the National Transport Code Collaboration's Demonstration Project, advances transport equations for any combination of electron and ion pressure, rotation, a turbulent energy density field, and (by the meeting date) density, with the remaining fields read in from a database. PYNTD has undergone benchmarking tests: simple analytic source and diffusivity models for which analytic solutions exist, as well as comparisons with other codes and experimental data for a selection of specific shots and anomalous transport models. In addition the code is being exercised to model experiments in DIII-D in which neon injection has been observed to facilitate transport barrier formation. Impurity effects on the turbulent transport, ExB velocity shear, and radiative cooling are modeled. Results from the benchmarks and impurity injection simulations will be presented, as well as a report on code status.

Cary, J. R.; Shasharina, S.; Cohen, R. H.; Jong, R.; Bateman, G.; Kinsey, J.; Kritz, A.; Houlberg, W.; Murakami, M.

2000-10-01

176

Python package for model STructure ANalysis (pySTAN)  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

177

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.; Kümmel, M.

2007-10-01

178

NIFTY: A versatile Python library for signal inference  

NASA Astrophysics Data System (ADS)

NIFTY (Numerical Information Field TheorY) is a versatile library enables 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. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTY permits rapid prototyping of algorithms in 1D and then the application of the developed code in higher-dimensional settings of real world problems. NIFTY operates on point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those.

Selig, Marco; Bell, Michael R.; Junklewitz, Henrik; Oppermann, Niels; Reinecke, Martin; Greiner, Maksim; Pachajoa, Carlos; Enßlin, Torsten A.

2013-02-01

179

One-dimensional statistical parametric mapping in Python.  

PubMed

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

Pataky, Todd C

2012-01-01

180

Multiple papillomas in a diamond python, Morelia spilota spilota.  

PubMed

A 4-yr-old male diamond python (Morelia spilota spilota) was evaluated for multiple black papillated exophytic skin proliferations and signs of pneumonia. The histopathologic structure of the skin biopsy specimens led to the diagnosis of a benign papilloma-like neoplasia. In this case, papillomavirus DNA could be amplified from a biopsy sample with a broad range polymerase chain reaction. Nested pan-herpes polymerase chain reaction was negative, and herpesvirus inclusion bodies were not found. Because of the histologically benign nature of the papilloma, the skin proliferations were left untreated. Ten mo after the first presentation, the skin lesions had regressed almost completely; 34 mo later, only scars from the biopsies were left. PMID:23272369

Gull, Jessica M; Lange, Christian E; Favrot, Claude; Dorrestein, Gerry M; Hatt, Jean-Michel

2012-12-01

181

PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python  

PubMed Central

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

Pecevski, Dejan; Natschlager, Thomas; Schuch, Klaus

2008-01-01

182

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

PubMed

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

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

2014-03-01

183

Shadowcopy: A Python-Based Shadow Volume Enumeration and Digest Tool.  

National Technical Information Service (NTIS)

This report presents shadowcopy, tool written in Python that extracts and deduplicates files from Microsoft NTFS Shadow copies using the Microsoft Volume Shadow Service (VSS), copies the files to an external volume, and prepares a report of each extracted...

M. Horn

2011-01-01

184

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

185

The photoreceptors and visual pigments in the retina of a boid snake, the ball python (Python regius)  

PubMed

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 ( &lgr; max) of the visual pigment in the rods is in the region of 494 nm. Two distinct types of cone are present. The most common cone, with a stout but stubby outer segment, contains a visual pigment with &lgr; max at approximately 551 nm. A relatively rare cone, with a long, slender outer segment, contains an ultraviolet-sensitive visual pigment with &lgr; max at approximately 360 nm. All the visual pigments have chromophores based on vitamin A1. The results are discussed in relation to the behavior of P. regius. PMID:10377274

Sillman; Carver; Loew

1999-07-01

186

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 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.

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

187

Python for hydrological modeling: interfacing C code with ctypes, dynamic typing and introspection  

NASA Astrophysics Data System (ADS)

The Python programming language has several features that make it an ideal front-end language for user-friendly numerical modelling of hydrological systems. In this presentation we will demonstrate this with a comprehensive hillslope hydrological modelling framework, where the following features are highlighted: •[Extensibility:] Often a low-level langage like C is better suited for the core functionality of numerical models, for instance because of the inherent higher computational speed, or the availability of specialized algorithms, like the well-known Numerical Recipes or the open source GNU Scientific Library. The now standard Python "ctypes" enables easy manipulation of the C functions and datastructures, provided the C code is compiled into a shared library. High-level Python wrapper functions or classes are easily constructed. •[Flexibility and introspection:] Python is strong but dynamically typed, meaning that variables can change type. This enables the construction of highly flexible functions that operate on a single model parameter, or a list of parameters, or a function that yields parameter values. Related to this, is the capacity of Python to inspect its own types and variables during runtime. So, depending on the actual type of a function argument (scalar, list, function) different actions are taken. Python classes are highly flexibly in the sense that member fields can be added to them during runtime. Python's introspection capacities enables finding out which member fields are actually present. This enables the construction of 'smart' functions that probe an object for the presence or absence of specified members (using their name), and then taking action. On example that will be worked out is a flexible parameter optimizer that takes a reference to a model object, and a list of a parameter names that are to be optimized.

Bogaart, P. W.

2008-12-01

188

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

PubMed Central

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

Ujvari, Beata; Madsen, Thomas

2009-01-01

189

Python framework for kinetic modeling of electronically excited reaction pathways  

NASA Astrophysics Data System (ADS)

The use of plasma energy to enhance and control the chemical reactions during combustion, a technology referred to as ``plasma assisted combustion'' (PAC), can result in a variety of beneficial effects: e.g. stable lean operation, pollution reduction, and wider range of p-T operating conditions. While experimental evidence abounds, theoretical understanding of PAC is at best incomplete, and numerical tools still lack in reliable predictive capabilities. In the context of a joint experimental-numerical effort at Michigan State University, we present here an open-source modular Python framework dedicated to the dynamic optimization of non-equilibrium PAC systems. Multiple sources of experimental reaction data, e.g. reaction rates, cross-sections and oscillator strengths, are used in order to quantify the effect of data uncertainty and limiting assumptions. A collisional-radiative model (CRM) is implemented to organize reactions by importance and as a potential means of measuring a non-Maxwellian electron energy distribution function (EEDF), when coupled to optical emission spectroscopy data. Finally, we explore scaling laws in PAC parameter space using a kinetic global model (KGM) accelerated with CRM optimized reaction sequences and sparse stiff integrators.

Verboncoeur, John; Parsey, Guy; Guclu, Yaman; Christlieb, Andrew

2012-10-01

190

Reticulospinal and vestibulospinal pathways in the snake Python regius.  

PubMed

In the present HRP study extensive reticulospinal projections and more modestly developed vestibulospinal pathways have been demonstrated in the snake Python regius. The funicular trajectories of the main reticulospinal pathways have been shown: via the lateral funiculus pass spinal projections of the nucleus reticularis superior pars lateralis, the nucleus reticularis inferior and nucleus raphes inferior; via the ventral funiculus fibers arising in the nucleus reticularis superior and nucleus reticularis medius. Spinal projections of the locus coeruleus and subcoeruleus area reach their targets via both the lateral and ventral funiculi. Two vestibulospinal pathways have been demonstrated: an ipsilateral tractus vestibulospinalis lateralis arising in the ventrolateral vestibular nucleus, and a contralateral tractus vestibulospinalis medialis from the descending and ventromedial vestibular nuclei. After HRP gel implants into the vestibular nuclear complex direct vestibulocollic projections to motoneurons in the rostral spinal cord were observed. Spinal projections from the ventral part of the nucleus reticularis inferior and the descending and ventromedial vestibular nuclei are mainly aimed at the thin "neck area" (approximately the first 50 spinal segments). This area is extensively used in such acts as orientation and prey-catching, requiring a rather delicate brain stem control. PMID:6606996

ten Donkelaar, H J; Bangma, G C; de Boer-van Huizen, R

1983-01-01

191

GOGrapher: A Python library for GO graph representation and analysis  

PubMed Central

Background The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs. Findings An object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation. Conclusion The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.

Muller, Brian; Richards, Adam J; Jin, Bo; Lu, Xinghua

2009-01-01

192

Paternal alleles enhance female reproductive success in tropical pythons.  

PubMed

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

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

2005-05-01

193

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

194

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

PubMed

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

Ujvari, Beata; Madsen, Thomas; Olsson, Mats

2004-06-01

195

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

196

PeptideBuilder: A simple Python library to generate model peptides  

PubMed Central

We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default.

Tien, Matthew Z.; Sydykova, Dariya K.; Meyer, Austin G.

2013-01-01

197

interPopula: a Python API to access the HapMap Project dataset  

PubMed Central

Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.

2010-01-01

198

PeptideBuilder: A simple Python library to generate model peptides.  

PubMed

We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default. PMID:23717802

Tien, Matthew Z; Sydykova, Dariya K; Meyer, Austin G; Wilke, Claus O

2013-01-01

199

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.

Chen, Weiliang; De Schutter, Erik

2014-01-01

200

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python  

PubMed Central

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code.

Wils, Stefan; Schutter, Erik De

2008-01-01

201

Python-based geometry preparation and simulation visualization toolkits for STEPS.  

PubMed

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

202

[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

203

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

NASA Astrophysics Data System (ADS)

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

Madsen, K.

2013-12-01

204

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

Microsoft Academic Search

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

Jussi Enkovaara; Nichols A. Romero; Sameer Shende; Jens J. Mortensen

2011-01-01

205

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 (2003–2012), 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

206

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

207

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

208

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

PubMed Central

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

Shah, Abhik; Woolf, Peter

2009-01-01

209

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

210

A high level interface to SCOP and ASTRAL implemented in Python  

PubMed Central

Background Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. Results We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. Conclusion The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

Casbon, James A; Crooks, Gavin E; Saqi, Mansoor AS

2006-01-01

211

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

212

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

213

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

214

A new giant python from the Pliocene Bluff Downs Local Fauna of northeastern Queensland  

Microsoft Academic Search

Liasis dubudingala n. sp., described on the basis of isolated vertebrae from the Early Pliocene Bluff Downs Local Fauna, is the largest snake known from Australia. Dependance of vertebral proportions on intracolumnar position indicates that the fossil taxon can be excluded from the Morelia\\/Python clade. High neural spines suggest possible affinity with Liasis olivacea, whereas a posterior dentary fragment with

John D. Scanlon; Brian S. Mackness

2001-01-01

215

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

PubMed

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

Madsen, Thomas; Ujvari, Beata; Olsson, Mats

2005-01-01

216

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.

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

2013-01-01

217

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

PubMed

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

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

2011-09-01

218

Pydoop: a Python MapReduce and HDFS API for Hadoop  

Microsoft Academic Search

MapReduce has become increasingly popular as a simple and efficient paradigm for large-scale data processing. One of the main reasons for its popularity is the availability of a production-level open source implementation, Hadoop, written in Java. There is considerable interest, however, in tools that enable Python programmers to access the framework, due to the language's high popularity. Here we present

Simone Leo; Gianluigi Zanetti

2010-01-01

219

Contractile properties of the functionally divided python heart: Two sides of the same matter  

Microsoft Academic Search

The heart of Python regius is functionally divided so that systemic blood pressure is much higher than pulmonary pressure (6.6±1.0 and 0.7±0.1 kPa, respectively). The present study shows that force production of cardiac strips from the cavum arteriosum and cavum pulmonale exhibits similar force production when stimulated in vitro. The high systemic blood pressure is caused, therefore, by a thicker ventricular

Morten Zaar; Johannes Overgaard; Hans Gesser; Tobias Wang

2007-01-01

220

Histamine induces postprandial tachycardia through a direct effect on cardiac H2-receptors in pythons.  

PubMed

The intrinsic heart rate of most vertebrates studied, including humans, is elevated during digestion, suggesting that a nonadrenergic-noncholinergic factor contributes to the postprandial tachycardia. The regulating factor, however, remains elusive and difficult to identify. Pythons can ingest very large meals, and digestion is associated with a marked rise in metabolism that is sustained for several days. The metabolic rise causes more than a doubling of heart rate and a fourfold rise in cardiac output. This makes the python an interesting model to investigate the postprandial tachycardia. We measured blood pressure and heart rate in fasting Python regius, and at 24 and 48 h after ingestion of a meal amounting to 25% of body wt. Digestion caused heart rate to increase from 25 to 56 min, whereas blood pressure was unchanged. The postprandial rise in heart rate was partially due to a doubling of intrinsic heart rate. The H(2)-antagonist did not affect heart rate of fasting snakes but decreased heart rate by 15-20 min at 24 h into digestion, whereas it had no effects at 48 h. Thus, the histaminergic tone on the heart rose from none to 30% at 24 h but vanished after 48 h. In anesthetized snakes, histamine caused a systemic vasodilatation and a marked increase in heart rate and cardiac output mediated through a direct effect on H(2)- receptors. Our study strongly indicates that histamine regulates heart rate during the initial phase of digestion in pythons. This study describes a novel regulation of the vertebrate heart. PMID:19091908

Skovgaard, Nini; Møller, Kate; Gesser, Hans; Wang, Tobias

2009-03-01

221

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

222

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

PubMed Central

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

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

2013-01-01

223

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

PubMed

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

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

2013-12-17

224

ObsPy: A Python Toolbox for Seismologists, Seismological Observatories and Data Centers  

NASA Astrophysics Data System (ADS)

Python combines 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. 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 the most common tasks in seismological analysis, b) provides read and write support for many common waveform and metadata file formats and c) enables access to various data centers, webservices and databases to retrieve waveform data and station/event metadata. In combination with widely used, 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 applications, output of modified/derived data and creating publication-quality figures. All functionality is extensively documented and the ObsPy Gallery/Tutorial give a good impression of the wide range of use cases. ObsPy is tested and running on Linux, MacOSX and Windows XP/Vista/7 and comes with installation routines for these systems. ObsPy is developed in a test-driven approach and is available under the GPL/LGPLv3 licences. Users are welcome to request help, report bugs or propose enhancements via the user mailing list or the Trac ticket system.

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

2012-04-01

225

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

226

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

227

A Python Analytical Pipeline to Identify Prohormone Precursors and Predict Prohormone Cleavage Sites  

PubMed Central

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

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

2008-01-01

228

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

229

Computed tomography of the lung of healthy snakes of the species Python regius, Boa constrictor, Python reticulatus, Morelia viridis, Epicrates cenchria, and Morelia spilota.  

PubMed

Thirty-nine healthy boid snakes representing six different species (Python regius, Boa constrictor, Python reticulatus, Morelia viridis, Epicrates cenchria, and Morelia spilota) were examined using computed tomography (CT) to characterize the normal appearance of the respiratory tissue. Assessment was done subjectively and densitometry was performed using a defined protocol. The length of the right lung was calculated to be 11.1% of the body length, without a significant difference between species. The length of the left lung in proportion to the right was dependent on the species examined. The most developed left lung was in P. regius (81.2%), whereas in B. constrictor, the left lung was vestigial or absent (24.7%). A median attenuation of -814.6 HU and a variability of 45.9 HU were calculated for all species with no significant difference between species. Within the species, a significantly higher attenuation was found for P. regius in the dorsal and cranial aspect of the lung compared with the ventral and caudal part. In B. constrictor, the reduced left lung was significantly hyperattenuating compared with the right lung. Results of this study emphasize the value of CT and provide basic reference data for assessment of the snake lung in these species. Veterinary Radiology & PMID:19788032

Pees, Michael; Kiefer, Ingmar; Thielebein, Jens; Oechtering, Gerhard; Krautwald-Junghanns, Maria-Elisabeth

2009-01-01

230

GMES: A Python package for solving Maxwell's equations using the FDTD method  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

231

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

232

The Python pit organ: imaging and immunocytochemical analysis of an extremely sensitive natural infrared detector.  

PubMed

The Python infrared-sensitive pit organ is a natural infrared imager that combines high sensitivity, ambient temperature function, microscopic dimensions, and self-repair. We are investigating the spectral sensitivity and signal transduction process in snake infrared-sensitive neurons, neither of which is understood. For example, it is unknown whether infrared receptor neurons function on a thermal or a photic mechanism. We imaged pit organs in living Python molurus and Python regius using infrared-sensitive digital video cameras. Pit organs were significantly more absorptive and/or emissive than surrounding tissues in both 3-5 microns and 8-12 microns wavelength ranges. Pit organs exhibited greater absorption/emissivity in the 8-12 microns range than in the 3-5 microns range. To directly test the relationship between photoreceptors and pit organ infrared-sensitive neurons, we performed immunocytochemistry using antisera directed against retinal photoreceptor opsins. Retinal photoreceptors were labeled with antisera specific for retinal opsins, but these antisera failed to label terminals of infrared-sensitive neurons in the pit organ. Infrared-receptive neurons were also distinguished from retinal photoreceptors on the basis of their calcium-binding protein content. These results indicate that the pit organ absorbs infrared radiation in two major atmospheric transmission windows, one of which (8-12 microns) matches emission of targeted prey, and that infrared receptors are biochemically distinct from retinal photoreceptors. These results also provide the first identification of prospective biochemical components of infrared signal transduction in pit organ receptor neurons. PMID:10028649

Grace, M S; Church, D R; Kelly, C T; Lynn, W F; Cooper, T M

1999-01-01

233

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

NASA Astrophysics Data System (ADS)

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

Hughes, J. D.; White, J.

2013-12-01

234

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

PubMed Central

Background Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. Methodology/Principal Findings Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. Conclusions/Significance The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species.

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

2008-01-01

235

Python-based framework for coupled MC-TH reactor calculations  

NASA Astrophysics Data System (ADS)

We develop a set of Python packages to provide a modern programming interface to codes used for analysis of nuclear reactors. Currently implemented interfaces to the Monte Carlo (MC) neutronics code MCNP and thermo-hydraulic (TH) code SCF allow efficient description of calculation models and provide a framework for coupled calculations. In this paper we illustrate how these interfaces can be used to describe a pin model, and report results of coupled MCNP-SCF calculations performed for a PWR fuel assembly, organized by means of the interfaces.

Travleev, Anton A.; Molitor, Richard; Sanchez, Victor

2014-06-01

236

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.

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

237

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

PubMed

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

Venthur, Bastian; Blankertz, Benjamin

2012-01-01

238

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

PubMed Central

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 macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.

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

2009-01-01

239

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

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

240

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

241

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

PubMed Central

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

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

242

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

243

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

244

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

PubMed

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

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

2012-07-01

245

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.

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

2009-01-01

246

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 Bulantová; Jan Votýpka; David Modrý

2007-01-01

247

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

PubMed

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

Dupoué, Andréaz; Angelier, Frédéric; Lourdais, Olivier; Bonnet, Xavier; Brischoux, François

2014-02-01

248

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

PubMed

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

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

2014-01-01

249

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

PubMed Central

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

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

2014-01-01

250

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

251

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

252

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

253

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

PubMed

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

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

2014-01-01

254

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

NASA Astrophysics Data System (ADS)

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

Lecocq, Thomas; Caudron, Corentin; Brenguier, Florent

2014-05-01

255

The adaptive significance of ontogenetic colour change in a tropical python.  

PubMed

Ontogenetic colour change is typically associated with changes in size, vulnerability or habitat, but assessment of its functional significance requires quantification of the colour signals from the receivers' perspective. The tropical python, Morelia viridis, is an ideal species to establish the functional significance of ontogenetic colour change. Neonates hatch either yellow or red and both the morphs change to green with age. Here, we show that colour change from red or yellow to green provides camouflage from visually oriented avian predators in the different habitats used by juveniles and adults. This reflects changes in foraging behaviour and vulnerability as individuals mature and provides a rare demonstration of the adaptive value of ontogenetic colour change. PMID:17443961

Wilson, David; Heinsohn, Robert; Endler, John A

2007-02-22

256

uPy: A Ubiquitous CG Python API with Biological-Modeling Applications.  

PubMed

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can simplify programming for many types of projects (not solely science applications) intended for multihost distribution. It's available at http://upy.scripps.edu. The first featured Web extra is a video that shows interactive analysis of a calcium dynamics simulation. YouTube URL: http://youtu.be/wvs-nWE6ypo. The second featured Web extra is a video that shows rotation of the HIV virus. YouTube URL: http://youtu.be/vEOybMaRoKc. PMID:24806987

Autin, L; Johnson, G; Hake, J; Olson, A; Sanner, M

2012-01-01

257

Modular Toolkit for Data Processing (MDP): A Python Data Processing Framework  

PubMed Central

Modular toolkit for Data Processing (MDP) is a data processing framework written in Python. From the user's perspective, MDP is a collection of supervised and unsupervised learning algorithms and other data processing units that can be combined into data processing sequences and more complex feed-forward network architectures. Computations are performed efficiently in terms of speed and memory requirements. From the scientific developer's perspective, MDP is a modular framework, which can easily be expanded. The implementation of new algorithms is easy and intuitive. The new implemented units are then automatically integrated with the rest of the library. MDP has been written in the context of theoretical research in neuroscience, but it has been designed to be helpful in any context where trainable data processing algorithms are used. Its simplicity on the user's side, the variety of readily available algorithms, and the reusability of the implemented units make it also a useful educational tool.

Zito, Tiziano; Wilbert, Niko; Wiskott, Laurenz; Berkes, Pietro

2008-01-01

258

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

PubMed Central

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

Hull, Michael J.; Willshaw, David J.

2014-01-01

259

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

PubMed

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

Hull, Michael J; Willshaw, David J

2013-01-01

260

A new species of Hepatozoon (Apicomplexa: Adeleorina) from Python regius (Serpentes: Pythonidae) and its experimental transmission by a mosquito vector.  

PubMed

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 Python regius by ingestion of infected mosquitoes, were performed to complete the life cycle. Similarly, transmission to different snake species (Boa constrictor and Lamprophis fuliginosus) and lizards (Lepidodactylus lugubris) was performed to assess the host specificity. Isolates were compared with Hepatozoon species from sub-Saharan reptiles and described as a new species based on the morphology, phylogenetic analysis, and a complete life cycle. PMID:18163356

Sloboda, Michal; Kamler, Martin; Bulantová, Jana; Votýpka, Jan; Modrý, David

2007-10-01

261

Optimizing python-based ROOT I/O with PyPy's tracing just-in-time compiler  

NASA Astrophysics Data System (ADS)

The Python programming language allows objects and classes to respond dynamically to the execution environment. Most of this, however, is made possible through language hooks which by definition can not be optimized and thus tend to be slow. The PyPy implementation of Python includes a tracing just in time compiler (JIT), which allows similar dynamic responses but at the interpreter-, rather than the application-level. Therefore, it is possible to fully remove the hooks, leaving only the dynamic response, in the optimization stage for hot loops, if the types of interest are opened up to the JIT. A general opening up of types to the JIT, based on reflection information, has already been developed (cppyy). The work described in this paper takes it one step further by customizing access to ROOT I/O to the JIT, allowing for fully automatic optimizations.

Tlp Lavrijsen, Wim

2012-12-01

262

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

PubMed

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

Jones, Hugh I; Mulder, Eridani

2007-03-01

263

Distribution of dopamine immunoreactivity in the forebrain and midbrain of the snake Python regius: a study with antibodies against dopamine.  

PubMed

The distribution of dopamine (DA) immunoreactivity in the forebrain and midbrain of the ball python, Python regius, was studied by using recently developed antibodies against DA. In order to determine general and species-specific features of the DA system in reptiles, we have selected the ball python as a representative of a reptilian radiation that hitherto has not been the subject of (immuno)histochemical studies. Dopamine-containing cell bodies were found around the glomeruli and in the external plexiform layer of both the main and accessory olfactory bulb, but not in the telencephalon proper. In the diencephalon, DA cells were observed in several parts of the periventricular hypothalamic nucleus, in the periventricular organ, the ependymal wall of the infundibular recess, the lateral hypothalamic area, the magnocellular ventrolateral thalamic nucleus, and the pretectal posterodorsal nucleus. In the midbrain, DA cells were found in the ventral tegmental area, the substantia nigra, and the presumed reptilian homologue of the mammalian A8 cell group. Dopaminergic fibers and varicosities were observed throughout the whole brain, particularly in the telencephalon and diencephalon. The nucleus accumbens, striatum, olfactory tubercle, and nucleus of the accessory olfactory tract appear to have the most dense innervation, but the lateral septal nucleus, the dorsal ventricular ridge, and the nucleus sphericus also show numerous DA-containing fibers and varicosities. Except for the lateral cortex, cortical areas are not densely innervated by DA fibers. The DA system of the snake Python regius shares many features with that of lizards and turtles as determined with the same antibodies. The taxonomically close relationship between lizards and snakes, which together constitute the Squamata, is reflected in a similar distribution of DA fibers and varicosities to the dorsal ventricular ridge and the lateral cortex, and in the limited number of CSF-contacting DA neurons in the hypothalamus. PMID:3385007

Smeets, W J

1988-05-01

264

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

265

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

PubMed Central

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.

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

2014-01-01

266

Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module.  

PubMed

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal. © 2012 Wiley Periodicals, Inc. PMID:22370965

Pool, René; Heringa, Jaap; Hoefling, Martin; Schulz, Roland; Smith, Jeremy C; Feenstra, K Anton

2012-02-28

267

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

268

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

NASA Astrophysics Data System (ADS)

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

Verkaik, J.

2013-12-01

269

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.

Álvarez-Gómez, José A.

2014-05-01

270

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.; Enßlin, T. A.

2013-06-01

271

Contractile properties of the functionally divided python heart: two sides of the same matter.  

PubMed

The heart of Python regius is functionally divided so that systemic blood pressure is much higher than pulmonary pressure (6.6+/-1.0 and 0.7+/-0.1 kPa, respectively). The present study shows that force production of cardiac strips from the cavum arteriosum and cavum pulmonale exhibits similar force production when stimulated in vitro. The high systemic blood pressure is caused, therefore, by a thicker ventricular wall surrounding the cavum arteriosum rather than differences in the intrinsic properties of the cardiac tissues. Similarly, there were no differences between the contractile properties of right and left atria. Force production was similar in atria and ventricle but the atria contracted and relaxed much faster than the ventricle. Graded hypoxia markedly reduced twitch force of all four cardiac tissues, and this was most pronounced when PO(2) was below 40 kPa. In contrast, the four cardiac tissues were insensitive to acidosis during normoxia although acidosis increased the sensitivity to hypoxia. Adrenergic stimulation increased twitch force of all cardiac tissues, while cholinergic stimulation only affected the atria and reduced twitch force markedly. In spite of the different oxygen availability of the two sides of the heart, the biochemical and functional properties are alike and the differences may instead be overcome by the coronary blood supply. PMID:17137816

Zaar, Morten; Overgaard, Johannes; Gesser, Hans; Wang, Tobias

2007-02-01

272

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

273

In the grip of the python: conflicts at the university-industry interface.  

PubMed

When the University of Toronto withdrew a contract it held with me in December 2000, it initiated a sequence of events that led to a public letter to the University from senior figures in the world psychopharmacology community protesting against the infringement of academic freedom involved and a first ever legal action, undertake by this author, seeking redress for a violation of academic freedom. The issues of academic freedom surrounding this case have been intertwined with a debate about the possibility that the selective serotonin reuptake inhibitor (SSRI) group of antidepressants have the potential to trigger suicidality in a subgroup of patients. Whether the SSRIs do trigger suicidality or not, exploration of this issue has given rise to a number of worrying sets of observations. First, in my view, there is evidence that pharmaceutical companies have miscoded raw data on suicidal acts and suicidal ideation. Second, this author also maintains that there is a growing body of examples of ghostwriting of articles in the therapeutics domain. Many of the tensions evident in this case, therefore, can be linked to company abilities to keep clinical trial data out of the public domain--this is the point at which the pharmaceutical python gets a grip on academia. PMID:12645230

Healy, David

2003-01-01

274

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

275

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

PubMed Central

Background The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. Findings To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. Conclusion ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL .

Armano, Giuliano; Manconi, Andrea

2009-01-01

276

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.

Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C.; Sangare, Djibril; Doumbia, Seydou; Traore, Sekou F.; Maiga, Mohamed S.; Dembele, Doulaye

2010-01-01

277

PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data  

PubMed Central

Background Cluster analysis is an important technique for the exploratory analysis of biological data. Such data is often high-dimensional, inherently noisy and contains outliers. This makes clustering challenging. Mixtures are versatile and powerful statistical models which perform robustly for clustering in the presence of noise and have been successfully applied in a wide range of applications. Results PyMix - the Python mixture package implements algorithms and data structures for clustering with basic and advanced mixture models. The advanced models include context-specific independence mixtures, mixtures of dependence trees and semi-supervised learning. PyMix is licenced under the GNU General Public licence (GPL). PyMix has been successfully used for the analysis of biological sequence, complex disease and gene expression data. Conclusions PyMix is a useful tool for cluster analysis of biological data. Due to the general nature of the framework, PyMix can be applied to a wide range of applications and data sets.

2010-01-01

278

A python-based docking program utilizing a receptor bound ligand shape: PythDock.  

PubMed

PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design. PMID:21975806

Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

2011-09-01

279

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; Sangaré, Djibril; Doumbia, Seydou; Traoré, Sekou F; Maiga, Mohamed S; Dembélé, Doulaye

2011-06-01

280

PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting  

PubMed Central

Structure-based virtual screening (SBVS) methods often rely on docking score. The docking score is an over-simplification of the actual ligand-target binding. Its capability to model and predict the actual binding reality is limited. Recently, interaction fingerprinting (IFP) has come and offered us an alternative way to model reality. IFP provides us an alternate way to examine protein-ligand interactions. The docking score indicates the approximate affinity and IFP shows the interaction specificity. IFP is a method to convert three dimensional (3D) protein-ligand interactions into one dimensional (1D) bitstrings. The bitstrings are subsequently employed to compare the protein-ligand interaction predicted by the docking tool against the reference ligand. These comparisons produce scores that can be used to enhance the quality of SBVS campaigns. However, some IFP tools are either proprietary or using a proprietary library, which limits the access to the tools and the development of customized IFP algorithm. Therefore, we have developed PyPLIF, a Python-based open source tool to analyze IFP. In this article, we describe PyPLIF and its application to enhance the quality of SBVS in order to identify antagonists for estrogen ? receptor (ER?). Availability PyPLIF is freely available at http://code.google.com/p/pyplif

Radifar, Muhammad; Yuniarti, Nunung; Istyastono, Enade Perdana

2013-01-01

281

A new algorithm to reduce noise in microscopy images implemented with a simple program in python.  

PubMed

All microscopical images contain noise, increasing when (e.g., transmission electron microscope or light microscope) approaching the resolution limit. Many methods are available to reduce noise. One of the most commonly used is image averaging. We propose here to use the mode of pixel values. Simple Python programs process a given number of images, recorded consecutively from the same subject. The programs calculate the mode of the pixel values in a given position (a, b). The result is a new image containing in (a, b) the mode of the values. Therefore, the final pixel value corresponds to that read in at least two of the pixels in position (a, b). The application of the program on a set of images obtained by applying salt and pepper noise and GIMP hurl noise with 10-90% standard deviation showed that the mode performs better than averaging with three-eight images. The data suggest that the mode would be more efficient (in the sense of a lower number of recorded images to process to reduce noise below a given limit) for lower number of total noisy pixels and high standard deviation (as impulse noise and salt and pepper noise), while averaging would be more efficient when the number of varying pixels is high, and the standard deviation is low, as in many cases of Gaussian noise affected images. The two methods may be used serially. PMID:21898664

Papini, Alessio

2012-03-01

282

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

PubMed

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

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

2014-01-01

283

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

284

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

285

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

PubMed Central

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

Madsen, T.; Shine, R.

1998-01-01

286

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

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

287

Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components  

PubMed Central

Many neural regions are arranged into two-dimensional topographic maps, such as the retinotopic maps in mammalian visual cortex. Computational simulations have led to valuable insights about how cortical topography develops and functions, but further progress has been hindered by the lack of appropriate tools. It has been particularly difficult to bridge across levels of detail, because simulators are typically geared to a specific level, while interfacing between simulators has been a major technical challenge. In this paper, we show that the Python-based Topographica simulator makes it straightforward to build systems that cross levels of analysis, as well as providing a common framework for evaluating and comparing models implemented in other simulators. These results rely on the general-purpose abstractions around which Topographica is designed, along with the Python interfaces becoming available for many simulators. In particular, we present a detailed, general-purpose example of how to wrap an external spiking PyNN/NEST simulation as a Topographica component using only a dozen lines of Python code, making it possible to use any of the extensive input presentation, analysis, and plotting tools of Topographica. Additional examples show how to interface easily with models in other types of simulators. Researchers simulating topographic maps externally should consider using Topographica's analysis tools (such as preference map, receptive field, or tuning curve measurement) to compare results consistently, and for connecting models at different levels. This seamless interoperability will help neuroscientists and computational scientists to work together to understand how neurons in topographic maps organize and operate.

Bednar, James A.

2008-01-01

288

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

289

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. Program summaryProgram title: QuTiP: The Quantum Toolbox in Python 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

290

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

291

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

PubMed

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

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

2003-09-01

292

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.

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

2011-01-01

293

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.  

PubMed

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

294

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

PubMed

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

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

2013-01-01

295

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

PubMed

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

296

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/

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

2013-01-01

297

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

PubMed

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

Schleip, Wulf D; O'Shea, Mark

2010-01-01

298

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

PubMed Central

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

Schleip, Wulf D.; O'Shea, Mark

2010-01-01

299

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

300

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.

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

2014-01-01

301

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

PubMed

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

302

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

303

Comparative Analysis of Vasotocin-Like Immunoreactivity in the Brain of the Turtle Pseudemys scripta elegan s and the Snake Python regius (Part 1 of 2)  

Microsoft Academic Search

The distribution of vasotocin in the brains of the turtle Pseudemys scripta elegans and the snake Python regius was studied with immunohistochemical methods. In both species, vasotocin-immunoreactive (VTi) cells were found in the supraoptic nucleus, the paraventricular nucleus and the bed nucleus of the stria terminalis. No VTi cell bodies were seen in the brainstem. Vasotocinergic fibers were found in

Wilhelmus J. A. J. Smeets; Janine J. Sevensma; Allert J. Jonker

1990-01-01

304

Comparative Analysis of Vasotocin-Like Immunoreactivity in the Brain of the Turtle Pseudemys scripta elegan s and the Snake Python regius (Part 2 of 2)  

Microsoft Academic Search

The distribution of vasotocin in the brains of the turtle Pseudemys scripta elegans and the snake Python regius was studied with immunohistochemical methods. In both species, vasotocin-immunoreactive (VTi) cells were found in the supraoptic nucleus, the paraventricular nucleus and the bed nucleus of the stria terminalis. No VTi cell bodies were seen in the brainstem. Vasotocinergic fibers were found in

Wilhelmus J. A. J. Smeets; Janine J. Sevensma; Allert J. Jonker

1990-01-01

305

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

306

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

307

CMB Anisotropy Constraints on Flat-Lambda and Open CDM Cosmogonies from DMR, UCSB South Pole, Python, Argo, Max, White Dish, OVRO, and SuZIE Data  

Microsoft Academic Search

We use joint likelihood analyses of combinations of fifteen cosmic microwave background (CMB) anisotropy data sets from the DMR, UCSB South Pole 1994, Python I III, ARGO, MAX 4 and 5, White Dish, OVRO, and SuZIE experiments to constrain cosmogonies. We consider open and spatially-flat-Lambda cold dark matter cosmogonies, with nonrelativistic-mass density parameter Omega0 in the range 0.1 1, baryonic-mass

Pia Mukherjee; Ken Ganga; Bharat Ratra; Graca Rocha; Tarun Souradeep; Naoshi Sugiyama; Krzysztof M. Gorski

2003-01-01

308

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

309

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

NASA Astrophysics Data System (ADS)

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

Yi, Guilian; Sui, Yunkang; Du, Jiazheng

2011-06-01

310

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, András

2014-09-01

311

PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis.  

PubMed

Cryo-electron tomography (CET) is a three-dimensional imaging technique for structural studies of macromolecules under close-to-native conditions. In-depth analysis of macromolecule populations depicted in tomograms requires identification of subtomograms corresponding to putative particles, averaging of subtomograms to enhance their signal, and classification to capture the structural variations among them. Here, we introduce the open-source platform PyTom that unifies standard tomogram processing steps in a python toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies. Furthermore, we present a novel stochastic classification method that yields significantly more accurate classification results than two deterministic approaches in simulations. We demonstrate that the PyTom workflow yields faithful results for alignment and classification of simulated and experimental subtomograms of ribosomes and GroEL(14)/GroEL(14)GroES(7), respectively, as well as for the analysis of ribosomal 60S subunits in yeast cell lysate. PyTom enables parallelized processing of large numbers of tomograms, but also provides a convenient, sustainable environment for algorithmic development. PMID:22193517

Hrabe, Thomas; Chen, Yuxiang; Pfeffer, Stefan; Cuellar, Luis Kuhn; Mangold, Ann-Victoria; Förster, Friedrich

2012-05-01

312

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

PubMed

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

Greaves, Mel

2009-01-01

313

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.  

PubMed

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations. PMID:23517329

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

314

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

PubMed

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

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

2013-05-01

315

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows  

PubMed Central

Summary: The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. Availability: The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. Contact: kiefer@micro.biol.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online.

Kiefer, Patrick; Schmitt, Uwe; Vorholt, Julia A.

2013-01-01

316

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

317

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

318

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

PubMed

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; Françoise, Pierre; Robelin, David; Schlötterer, Christian; Futschik, Andreas

2013-03-01

319

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/.

Boitard, Simon; Kofler, Robert; Francoise, Pierre; Robelin, David; Schlotterer, Christian; Futschik, Andreas

2013-01-01

320

Comparative analysis of vasotocin-like immunoreactivity in the brain of the turtle Pseudemys scripta elegans and the snake Python regius.  

PubMed

The distribution of vasotocin in the brains of the turtle Pseudemys scripta elegans and the snake Python regius was studied with immunohistochemical methods. In both species, vasotocin-immunoreactive (VTi) cells were found in the supraoptic nucleus, the paraventricular nucleus and the bed nucleus of the stria terminalis. No VTi cell bodies were seen in the brainstem. Vasotocinergic fibers were found in all major brain divisions. Intrahypothalamic VTi fibers were observed between the supraoptic and the paraventricular nuclei and in the median eminence. An extensive network of extrahypothalamic VTi fibers extends from the olfactory bulb to the spinal cord. Limbic structures, such as the nucleus accumbens, the septal area and the ventral amygdaloid nucleus, contain a moderate to dense VTi plexus. Other areas with a substantial number of VTi fibers are the lateral habenular nucleus, the ventral tegmental area, the substantia nigra, the locus coeruleus and the nucleus of the solitary tract. Sex-related differences in the density of the VTi fibers were observed in the lateral septal nucleus, the mid-brain periaqueductal gray and, to a lesser extent, in the ventral amygdaloid nucleus, the lateral habenular nucleus, the ventral tegmental area and the substantia nigra. In these areas, the density of VTi fibers is higher in males than in females. The distribution of vasotocin-like immunoreactivity in the brains of Pseudemys and Python resembles the pattern previously observed in the lizard Gekko gecko. However, among the three species several differences exist, the most remarkable one being the variation in number of liquor-contacting VTi cells in the paraventricular nucleus. PMID:2191754

Smeets, W J; Sevensma, J J; Jonker, A J

1990-01-01

321

Maternal influences on early development: preferred temperature prior to oviposition hastens embryogenesis and enhances offspring traits in the Children's python, Antaresia childreni.  

PubMed

Embryonic life is particularly sensitive to its surroundings, and the developmental environment can have long-lasting effects on offspring. In oviparous species, the impacts of the developmental environment on offspring traits are mostly examined during development within the egg. However, as more than 25% of the development of squamate reptiles can occur prior to oviposition, we explored the effect of thermal conditions on development prior to oviposition in an oviparous snake species, the Children's python (Antaresia childreni). We housed gravid female pythons under three thermal cycles: an optimal regime that reflected maternal preference in a non-constrained environment (constant preferred body temperature of gravid females, T(set)=31.5°C) and two mildly suboptimal regimes that shared the same mean temperature of 27.7°C, but differed in the duration at T(set). In one of the constraining regimes, females had access to T(set) for 4 h daily whereas in the other regime, females never reached T(set) (maximal temperature of 29.0°C). Thermal treatments were maintained throughout gravidity in all three groups, but, after oviposition, all eggs were incubated at T(set) until hatching. Compared with the optimal regime, the two suboptimal regimes had a longer duration of gravidity, which resulted in delayed hatching. Between the two suboptimal regimes, gravidity was significantly shorter in the treatment that included time at T(set). Furthermore, suboptimal regimes influenced offspring traits at hatching, including body morphology, antipredator behavior, strength and metabolism. However, partial access to maternal T(set) significantly enhanced several offspring traits, including performance. Our results demonstrate the importance of time at T(set) on early development and suggest an adaptive significance of maternal thermoregulation prior to oviposition. PMID:22442373

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

2012-04-15

322

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

NASA Astrophysics Data System (ADS)

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

Mayorga, E.

2013-12-01

323

The Python pit organ: imaging and immunocytochemical analysis of an extremely sensitive natural infrared detector 1 This paper was presented at the Fifth World Congress on Biosensors, Berlin, Germany, 3–5 June 1998. 1  

Microsoft Academic Search

The Python infrared-sensitive pit organ is a natural infrared imager that combines high sensitivity, ambient temperature function, microscopic dimensions, and self-repair. We are investigating the spectral sensitivity and signal transduction process in snake infrared-sensitive neurons, neither of which is understood. For example, it is unknown whether infrared receptor neurons function on a thermal or a photic mechanism. We imaged pit

Michael S Grace; Don R Church; Christopher T Kelly; William F Lynn; Thomas M Cooper

1999-01-01

324

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

325

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 chromatography–mass 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.

2012-01-01

326

Sunshine virus in Australian pythons.  

PubMed

Sunshine virus is a recently discovered novel paramyxovirus that is associated with illness in snakes. It does not phylogenetically cluster within either of the two currently accepted paramyxoviral subfamilies. It is therefore only distantly related to the only other known genus of reptilian paramyxoviruses, Ferlavirus, which clusters within the Paramyxovirinae subfamily. Clinical and diagnostic aspects associated with Sunshine virus are as yet undescribed. The objective of this paper was to report the clinical presentation, virus isolation, PCR testing and pathology associated with Sunshine virus infection. Clinical records and samples from naturally occurring cases were obtained from two captive snake collections and the archives of a veterinary diagnostic laboratory. The clinical signs that are associated with Sunshine virus infection are localised to the neurorespiratory systems or are non-specific (e.g. lethargy, inappetence). Out of 15 snakes that were infected with Sunshine virus (detected in any organ by either virus isolation or PCR), the virus was isolated from four out of ten (4/10) sampled brains, 3/10 sampled lungs and 2/7 pooled samples of kidney and liver. In these same 15 snakes, PCR was able to successfully detect Sunshine virus in fresh-frozen brain (11/11), kidney (7/8), lung (8/11) and liver (5/8); and various formalin-fixed paraffin-embedded tissues (7/8). During a natural outbreak of Sunshine virus in a collection of 32 snakes, the virus could be detected in five out of 39 combined oral-cloacal swabs that were collected from 23 of these snakes over a 105 day period. All snakes that were infected with Sunshine virus were negative for reovirus and ferlavirus by PCR. Snakes infected with Sunshine virus reliably exhibited hindbrain white matter spongiosis and gliosis with extension to the surrounding grey matter and neuronal necrosis evident in severe cases. Five out of eight infected snakes also exhibited mild bronchointerstitial pneumonia. Infection with Sunshine virus should be considered by veterinarians investigating disease outbreaks in snakes, particularly those that are associated with neurorespiratory disease. PMID:22883310

Hyndman, Timothy H; Shilton, Cathy M; Doneley, Robert J T; Nicholls, Philip K

2012-12-28

327

Parallel, Distributed Scripting with Python.  

National Technical Information Service (NTIS)

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 me...

P. Miller

2002-01-01

328

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

329

GaPP: Gaussian Processes in Python  

NASA Astrophysics Data System (ADS)

The algorithm Gaussian processes can reconstruct a function from a sample of data without assuming a parameterization of the function. The GaPP code can be used on any dataset to reconstruct a function. It handles individual error bars on the data and can be used to determine the derivatives of the reconstructed function. The data sample can consist of observations of the function and of its first derivative.

Seikel, Marina; Clarkson, Chris; Smith, Mathew

2013-03-01

330

SunPy: Python for Solar Physicists  

NASA Astrophysics Data System (ADS)

SunPy is a community-developed free and open-source software package for solar physics and is an alternative to the SolarSoft data analysis environment. SunPy provides data structures for representing the most common solar data types (images, lightcurves, and spectra) and integration with the Virtual Solar Observatory (VSO) and the Heliophysics Event Knowledgebase (HEK) for data acquisition.

SunPy development Team

2014-01-01

331

VisIt Python Interface Manual.  

National Technical Information Service (NTIS)

VisIt is a distributed, parallel, visualization tool for visualizing data defined on two and three-dimensional structured and unstructured meshes. VisIts distributed architecture allows it to leverage both the compute power of a large parallel computer an...

B. J. Whitlock

2005-01-01

332

PyDrizzle: Python version of Drizzle  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

333

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.

334

PyGFit: Python Galaxy Fitter  

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

335

Python Engine Installed in Altitude Wind Tunnel  

NASA Technical Reports Server (NTRS)

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

1949-01-01

336

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

337

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

338

Isolation of a reovirus from the snake, Python regius  

Microsoft Academic Search

Summary A reovirus isolated from a moribund snake was not neutralized by antisera against mammalian serotypes, did not agglutinate human 0 erythrocytes, and produced fusion of IgH 2 cells. The genome contained 10 segments of dsRNA.

W. Ahne; I. Thomsen; J. Winton

1987-01-01

339

Peristaltic pumping in an elastic tube: feeding the hungry python  

NASA Astrophysics Data System (ADS)

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

Takagi, Daisuke; Balmforth, Neil

2010-11-01

340

Comparison of the fork and PYTHON spent-fuel detectors  

SciTech Connect

Instruments to measure radiation from spent-fuel assemblies have been developed in the United States and in France. They have different objectives (safeguards and criticality safety) that have led to different designs, but are nevertheless sufficiently similar to compare and correlate. Small capsules of {sup 252}Cf and {sup 137}Cs were placed in a fuel pin and moved through a 17 {times} 17 array of pins. By raising the source pin, axial profiles were measured to help determine the total responses of the instruments to complete assemblies. The measurements show the relative contributions to the detectors' responses of neutrons and gamma rays from different pin locations. Sums of these measurements simulate total responses and how the instruments are correlated. Neutron absorbing pins containing gadolinium were inserted into the assembly to measure the dampening of the neutron count rates. These results will be useful in understanding the responses of spent fuel and fresh mixed-oxide fuel stored underwater with poison rods. 10 refs., 53 figs., 14 tabs.

Rinard, P.M. (Los Alamos National Lab., NM (USA)); Bignan, G.; Capsie, J.; Romeyer-Dherbey, J. (CEA Centre d'Etudes Nucleaires de Cadarache, 13 - Saint-Paul-lez-Durance (France). Service d'Exploitation et d'Experimentation de Rapsodie)

1990-07-01

341

Crates and Transform: Python Interfaces for Data Analysis  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

342

FiPy: Partial Differential Equations with Python  

Microsoft Academic Search

Many existing partial differential equation solver packages focus on the important, but arcane, task of numerically solving the linearized set of algebraic equations that result from discretizing a set of PDEs. Many researchers, however, need something higher level than that.

Jonathan E. Guyer; Daniel Wheeler; James A. Warren

2009-01-01

343

Preliminary Results from the PYTHON Microwave Background Anisotropy Experiment  

Microsoft Academic Search

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

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

1993-01-01

344

VisIt Python-Based Job Launching.  

National Technical Information Service (NTIS)

VisIt is a free interactive parallel visualization and graphical analysis tool that is commonly used at the U.S. Army Research Laboratory (ARL) for viewing scientific data on Linux, Windows, and OS X (Apple) workstations. An essential element for the succ...

R. C. Angelini

2013-01-01

345

Grief of Stepparents When a Child Dies  

MedlinePLUS

... sponsored by Georgia and Bruce Cockerham in loving memory of Zachary Owen Ward Read Zachary's Story The ... sponsored by Joan and Bill Campbell in loving memory of Lesley Michelle Campbell Read Lesley's Story Sponsor ...

346

Compassionate Friends  

MedlinePLUS

... sponsored by Georgia and Bruce Cockerham in loving memory of Zachary Owen Ward Read Zachary's Story The ... sponsored by Joan and Bill Campbell in loving memory of Lesley Michelle Campbell Read Lesley's Story Sponsor ...

347

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

348

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

349

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

350

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

351

Visual and infrared input to the same dendrite in the tectum opticum of the python, Python regius: electron-microscopic evidence.  

PubMed

In snakes with infrared receptors, the optic tectum receives input from both the visual and the infrared senses. We investigated the infrared and optic fiber terminations in the tectum with a combination of horseradish peroxidase and degeneration labeling. In addition to synapses by visual and infrared fibers onto individual neurons, we were able to observe for the first time visual and infrared synapses on one and the same dendrite. PMID:1473007

Kobayashi, S; Kishida, R; Goris, R C; Yoshimoto, M; Ito, H

1992-12-01

352

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

Microsoft Academic Search

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

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

2010-01-01

353

Maternal brooding in the children’s python (Antaresia childreni) promotes egg water balance  

Microsoft Academic Search

Parental care provides considerable benefits to offspring and is widespread among animals, yet it is relatively uncommon among\\u000a squamate reptiles (e.g., lizards and snakes). However, all pythonine snakes show extended maternal egg brooding with some\\u000a species being facultatively endothermic. While facultative endothermy provides thermal benefits, the presence of brooding\\u000a in non-endothermic species suggests other potential benefits of brooding. In this

Olivier Lourdais; Ty C. M. Hoffman; Dale F. DeNardo

2007-01-01

354

Isolation of a reovirus from the snake, Python regius. Brief report.  

PubMed

A reovirus isolated from a moribund snake was not neutralized by antisera against mammalian serotypes, did not agglutinate human O erythrocytes, and produced fusion of IgH 2 cells. The genome contained 10 segments of dsRNA. PMID:3579605

Ahne, W; Thomsen, I; Winton, J

1987-01-01

355

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

Microsoft Academic Search

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

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

2003-01-01

356

Web-Based Biobank System Infrastructure Monitoring Using Python, Perl, and PHP.  

PubMed

The establishment and maintenance of biobanks is only as worthwhile as the security and logging of the biobank contents. We have designed a monitoring system that continuously measures temperature and gas content, records the movement of samples in and out of the biobank, and also records the opening and closing of the freezers-storing the results and images in a database. We have also incorporated an early warning feature that sends out alerts, via SMS and email, to responsible persons if any measurement is recorded outside the acceptable limits, guaranteeing the integrity of biobanked samples, as well as reagents used in sample analysis. A surveillance system like this increases the value for any biobank as the initial investment is small and the value of having trustworthy samples for future research is high. PMID:24835365

Norling, Martin; Kihara, Absolomon; Kemp, Steve

2013-12-01

357

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

358

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

Microsoft Academic Search

Since 2003, the monitor and control software systems for the Robert C. Byrd Green Bank Telescope (GBT) have been substantially redesigned to make the telescope easier to use. The result is the release of the Astronomer's Integrated Desktop (Astrid), an observation management platform used to create and submit scheduling blocks, monitor their progress on the telescope, and provide a real

Nicole M. Radziwill; Amy L. Shelton

2006-01-01

359

[The organ topography of nonpoisonous snakes of the Boidae (boas and pythons) and Colubridae (adders) families].  

PubMed

In order to assist veterinarians with the diagnosis of diseases in snakes, the organ topography of 142 dissected snakes of 35 different species was analysed and examined in relation to body size and normal biotope. Apart from characteristic species specific differences, it was shown that there is a clear difference between arboreal and terrestrial snakes. It was recorded that nearly in all species the organs shifted along the body in relation to increase in growth. PMID:1481223

Keil, R; Wissdorf, H

1992-12-01

360

pySPACE-a signal processing and classification environment in Python.  

PubMed

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

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

2013-01-01

361

Programming an offline-analyzer of motor imagery signals via python language.  

PubMed

Brain Computer Interface (BCI) systems control the user's environment via his/her brain signals. Brain signals related to motor imagery (MI) have become a widespread method employed by the BCI community. Despite the large number of references describing the MI signal treatment, there is not enough information related to the available programming languages that could be suitable to develop a specific-purpose MI-based BCI. The present paper describes the development of an offline-analysis system based on MI-EEG signals via open-source programming languages, and the assessment of the system using electrical activity recorded from three subjects. The analyzer recognized at least 63% of the MI signals corresponding to three classes. The results of the offline analysis showed a promising performance considering that the subjects have never undergone MI trainings. PMID:22256162

Alonso-Valerdi, Luz María; Sepulveda, Francisco

2011-01-01

362

A comparison of spent fuel assembly control instruments: The Cadarache PYTHON and the Los Alamos Fork  

SciTech Connect

Devices to monitor spent fuel assemblies while stored under water with nondestructive assay methods, have been developed in France and in the United States. Both devices are designed to verify operator's declared values of exposures and cooling-time but the applications and thus the designs of the systems differ. A study, whose results are presented in this paper, has been conducted to compare the features and the performances of the two instruments. 4 refs., 9 figs.

Bignan, G.; Capsie, J.; Romeyer-Dherbey, J. (CEA Centre d'Etudes Nucleaires de Cadarache, 13 - Saint-Paul-lez-Durance (France). Direction des Reacteurs Nucleaires); Rinard, P. (Los Alamos National Lab., NM (United States))

1991-01-01

363

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

PubMed Central

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

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

2010-01-01

364

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

ERIC Educational Resources Information Center

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

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

2004-01-01

365

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

ERIC Educational Resources Information Center

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

Conner, David B.

1996-01-01

366

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

ERIC Educational Resources Information Center

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

Rockow, Michael

2007-01-01

367

Srimathi Kannan and Amy J. Schulz and Barbara A. Israel and Indira Ayra and Sheryl Weir and Timothy J. Dvonch and Zachary Rowe and Patricia Miller and Alison Benjamin - A Community-Based Participatory Approach to Personalized, Computer-Generated Nutrition Feedback Reports: The Healthy Environments Partnership - Progress in Community Health Partnerships: Research, Education, and Action 2:1  

Microsoft Academic Search

Background: Computer tailoring and personalizing recommendations for dietary health-promoting behaviors are in accordance with community-based participatory research (CBPR) principles, which emphasizes research that benefits the participants and community involved. Objective: To describe the CBPR process utilized to computer-generate and disseminate personalized nutrition feedback reports (NFRs) for Detroit Healthy Environments Partnership (HEP) study participants. Methods: The CBPR process included discussion and

Srimathi Kannan

2008-01-01

368

Exploratory trial to determine the efficacy of the PYthon and the PYthon Magnum slow-release insecticide ear tags for the control of midges (Culicoides spp.), attacking sheep and cattle and flies attacking cattle.  

PubMed

This study investigated the prophylactic action of the chemical combination zeta-cypermethrin and piperonyl butoxide, administered by means of slow-release insecticide-impregnated ear tags, against biting midges (Culicoides spp) attacking sheep and against midges, horn flies (Haematobia irritant), stable flies (Stomoxys calcitrans), and houseflies (Musca domestica) attacking cattle. Treated sheep and cattle were protected 100 percent against blood-feeding midges for two months and there was a clear reduction in the number of midges collected from treated animals. Three days after the ear tags were attached to cattle, the number of horn flies on the cattle was reduced to practically zero and remained at a low level until the end of the trial (day 85). There was also a strong reduction in the numbers of stable flies and houseflies counted. PMID:22930983

Goosen, H; de Vries, P J T; Fletcher, M G

2012-08-01

369

Weatherizing America  

ScienceCinema

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

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

2013-05-29

370

Weatherizing America  

ScienceCinema

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

371

Weatherizing America  

SciTech Connect

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

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

2009-01-01

372

76 FR 62442 - National Register of Historic Places; Notification of Pending Nominations and Related Actions  

Federal Register 2010, 2011, 2012, 2013

...Landmarks Program. ARIZONA Pima County Marist College Historic District...Florida Sts., Zachary, 11000761 MISSOURI Jackson County Milo Apartments, (Working-Class...Apartment Buildings in Kansas City, Missouri MPS), 1014-1020 W. 44th...

2011-10-07

373

Mitral Valve Models Reconstructor: a Python based GUI software in a HPC environment for patient-specific FEM structural analysis  

Microsoft Academic Search

\\u000a A new approach in the biomechanical analysis of the mitral valve (MV) focusing on patient-specific modelling has recently\\u000a been pursued. The aim is to provide a useful tool to be used in clinic for hypotheses testing in pre-operative surgical planning\\u000a and post-operative follow-up prediction. In particular, the integration of finite element models (FEMs) with 4D echocardiographic\\u000a advanced images processing seems

A. Arnoldi; A. Invernizzi; Raffaele Ponzini; E. Votta; Enrico G. Caiani; Alberto Redaelli

2008-01-01

374

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

PubMed

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

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

2012-01-01

375

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

SciTech Connect

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

Orndorff-Plunkett, Franklin

2011-05-01

376

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

Federal Register 2010, 2011, 2012, 2013

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

2010-08-19

377

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

Federal Register 2010, 2011, 2012, 2013

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

2011-02-04

378

CMISTARK: Python package for the Stark-effect calculation and symmetry classification of linear, symmetric and asymmetric top wavefunctions in dc electric fields  

NASA Astrophysics Data System (ADS)

The Controlled Molecule Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMISTARK software to calculate, view, and analyze the energy levels of adiabatic Stark energy curves of linear, symmetric top and asymmetric top molecules. The program exploits the symmetry of the Hamiltonian to generate fully labeled adiabatic Stark energy curves.

Chang, Yuan-Pin; Filsinger, Frank; Sartakov, Boris G.; Küpper, Jochen

2014-01-01

379

Cell-free protein synthesis: Search for the happy middle.  

PubMed

Cell-free protein synthesis (CFPS) is a versatile technique gaining popularity because it allows researchers access to on-demand production of proteins. This Commentary by Zachary Russ and John Dueber discusses the latest research article by Rui Gan and Michael Jewett, which reports a convenient and cost-effective methodology for the preparation of Saccharomyces cerevisiae-based CFPS reactions. PMID:24644248

Russ, Zachary N; Dueber, John E

2014-05-01

380

Making Colonial Subjects: Education in the Age of Empire  

ERIC Educational Resources Information Center

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

Hall, Catherine

2008-01-01

381

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

ERIC Educational Resources Information Center

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

National Multicultural Inst., Washington, DC.

382

Opening the Black Box of Social Cognitive Mapping  

ERIC Educational Resources Information Center

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

Neal, Zachary P.; Neal, Jennifer Watling

2013-01-01

383

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

ERIC Educational Resources Information Center

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

2002

384

77 FR 23666 - Information Collection; Submission for OMB Review, Comment Request  

Federal Register 2010, 2011, 2012, 2013

...by calling the Corporation for National and Community Service, Zachary Jackson, at (202) 606-6948 or email to zjackson@cns.gov. Individuals who use a telecommunications device for the deaf (TTY-TDD) may call 1-800-833-3722 between 8...

2012-04-20

385

Peer Mentoring and Action Learning  

ERIC Educational Resources Information Center

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

O'Neil, Judy; Marsick, Victoria J.

2009-01-01

386

Web Applications With Django  

Microsoft Academic Search

\\u000a Django is a modern Python web framework that redefined web development in the Python world. A fullstack approach, pragmatic\\u000a design, and superb documentation are some of the reasons for its success.

Josh Juneau; Jim Baker; Victor Ng; Leo Soto; Frank Wierzbicki

387

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

Federal Register 2010, 2011, 2012, 2013

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

2012-07-11

388

Cost engineering with quality function deployment  

Microsoft Academic Search

Conventional Quality Function Deployment (QFD) is technically one-sided. Prioritization of technical attributes, if carried out at all, attempts to maximize customer satisfaction without considering the costs incurred. However, product design is usually a techno-economic process, hence there is always a tradeoff between quality goals and limited budgets. Based on a prioritization method suggested by Wasserman [1], this paper integrates design

Jürgen Bode; Richard Y. K. Fung

1998-01-01

389

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

Federal Register 2010, 2011, 2012, 2013

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

2010-02-23

390

Transitivity and the path census in sociometry  

Microsoft Academic Search

This paper develops a method for calculating the tendency towards transitivity while keeping constant the number of choices which are made by each member of the group (Un(XI+) distribution) or the number of times each member is chosen (UN (X+J) distribution). Such a calculation was suggested by Wasserman, who used the triad census developed by Holland and Leinhardt. This work

Meir Fershtman

1985-01-01

391

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

Federal Register 2010, 2011, 2012, 2013

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

2011-02-16

392

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

ERIC Educational Resources Information Center

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

Schilling, Bernard N., Ed.

393

Pupil Dilation and Object Permanence in Infants  

ERIC Educational Resources Information Center

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

Sirois, Sylvain; Jackson, Iain R.

2012-01-01

394

A Green's Function Calculation of the dHvA Effective Mass in a Heavy Fermion Superconductor  

Microsoft Academic Search

We calculate the de Haas-van Alphen effective mass for a heavy fermion material in the superconducting vortex state. We use the field theoretic method of Wasserman and Springford, which is capable of incorporating the many-body interactions responsible for heaviness and superconductivity in these materials. The thermodynamic grand potential is calculated from an imaginary energy Green's matrix. From the potential we

Emily Townsend; Allen Wasserman

2004-01-01

395

Satiety and eating patterns in two species of constricting snakes  

Microsoft Academic Search

Satiety has been studied extensively in mammals, birds and fish but very little information exists on reptiles. Here we investigate time-dependent satiation in two species of constricting snakes, ball pythons (Python regius) and yellow anacondas (Eunectes notaeus). Satiation was shown to depend on both fasting time and prey size. In the ball pythons fed with mice of a relative prey

Torben P. Nielsen; Magnus W. Jacobsen; Tobias Wang

2011-01-01

396

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

PubMed

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

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

2009-05-01

397

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

NASA Technical Reports Server (NTRS)

Zachary Phys. Rev. A 29 (6), 3224 (1984) recently analyzed the instability of relativistic-electron helical trajectories in combined uniform axial and helical wiggler magnetic fields when the radial variation of the wiggler field is taken into account. It is shown here that the type 2 instability comprised of secular terms growing linearly in time, identified by Zachary and earlier by Diament Phys. Rev. A 23 (5), 2537 (1981), is an artifact of simple perturbation theory. A multiple-time-scale perturbation analysis reveals a nonsecular evolution on a slower time scale which accommodates an arbitrary initial perturbation. It is shown that, in the absence of exponential instability, the electron seeks a modified helical orbit more appropriate to its perturbed state and oscillates stably about it. Thus, the perturbed motion is oscillatory but nonsecular, and hence the helical orbits are stable.

Johnston, S.

1984-01-01

398

Fast method of detecting communities in complex networks  

Microsoft Academic Search

In this paper we introduce a novel method, LCDA, to identify the communities in large complex network based on ¿local community¿. Time complexity of our algorithm is O(n3 Ln(n) where is the mean degree and n is the number of vertices in the network. It is very useful in analyzing very larger complex network. By applying LCDA on Zachary club

Bin Liu; Jing Li

2009-01-01

399

Combinatorial Laplacian and entropy of simplicial complexes associated with complex networks  

NASA Astrophysics Data System (ADS)

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

Maleti?, S.; Rajkovi?, M.

2012-09-01

400

Contrasting Object-Based and Texture-Based Accounts of Same\\/Different Discrimination Learning With Trial-Unique Stimuli  

Microsoft Academic Search

Same\\/different discrimination is a classic task for investigating relational learning in animals. Recent research suggests that pigeons can learn a trial-unique same\\/different discrimination, which eliminates the opportunity to memorize the training items (Brooks & Wasserman, 2008). The authors conducted three tests to elucidate the role that item-based comparison plays in this trial-unique discrimination. In the first, the authors tested the

Daniel I. Brooks; Edward A. Wasserman

2010-01-01

401

Molecular Binding Energies from Partition Density Functional Theory  

SciTech Connect

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

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

2011-12-21

402

A Hensel lifting to replace factorization in list-decoding of algebraic-geometric and Reed-Solomon codes  

Microsoft Academic Search

This correspondence presents an algorithmic improvement to Sudan's list-decoding algorithm for Reed-Solomon codes and its gener- alization to algebraic-geometric codes from Shokrollahi and Wasserman. Instead of completely factoring the interpolation polynomial over the func- tion field of the curve, we compute sufficiently many coefficients of a Hensel development to reconstruct the functions that correspond to codewords. We prove that these

Daniel Augot; Lancelot Pecquet

2000-01-01

403

Chaotic self-similar wave maps coupled to gravity  

NASA Astrophysics Data System (ADS)

It was shown recently that the SU(2) sigma model coupled to gravity has periodic spherically symmetric self-similar solutions for small values of the coupling constant. In this article we extend the analysis of Bizo?, Szybka, and Wasserman to larger values of the coupling constant (??0.426) and present numerical evidence for the chaotic solution and the fractal threshold behavior. We explain this phenomenon in terms of horseshoelike dynamics and heteroclinic intersections.

Szybka, Sebastian J.

2004-04-01

404

Referral Web: combining social networks and collaborative filtering  

Microsoft Academic Search

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

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

1997-01-01

405

IK682, a tight binding inhibitor of TACE  

Microsoft Academic Search

TNF? converting enzyme (TACE) is the major metalloproteinase for the processing of TNF?, a key inflammatory cytokine. IK682, a hydroxamate compound, was reported to be a potent and specific TACE inhibitor [J.J. Duan, L. Chen, Z.R. Wasserman, Z. Lu, R.Q. Liu, M.B. Covington, M. Qian, K.D. Hardman, R.L. Magolda, R.C. Newton, D.D. Christ, R.R. Wexler, C.P. Decicco, J. Med. Chem.

Xiaoda Niu; Shelby Umland; Richard Ingram; Brian M. Beyer; Yan-Hui Liu; Jing Sun; Daniel Lundell; Peter Orth

2006-01-01

406

The nightly build and test system for LCG AA and LHCb software  

Microsoft Academic Search

The core software stack both from the LCG Application Area and LHCb consists of more than 25 C++\\/Fortran\\/Python projects build for about 20 different configurations on Linux, Windows and MacOSX. To these projects, one can also add about 70 external software packages (Boost, Python, Qt, CLHEP, ...) which have also to be build for the same configurations. It order to

K Kruzelecki; S Roiser; H Degaudenzi

2009-01-01

407

VPython  

NSDL National Science Digital Library

VPython is a 3D programming language developed at Carnegie Mellon University that is useful for presenting visualizations of physical phenomena. VPython is free and open-source. It includes: the Python programming language, an enhanced version of the Idle interactive development environment, and "Visual", a Python module that offers real-time 3D output, and is easily usable by novice programmers.

Scherer, David

2003-10-10

408

PyThinSearch: A Simple Web Search Engine  

Microsoft Academic Search

We describe a simple, functioning Web search engine for indexing and searching online documents using Python programming language. Python was chosen because it is an elegant language with simple syntax, is easy to learn and debug, and supports main operating systems almost evenly. The remarkable characteristics of this program are an adjustable search function that allows users to rank documents

Andri Mirzal

2009-01-01

409

Automatic generation of Feynman rules in the Schrödinger functional  

Microsoft Academic Search

We provide an algorithm to generate vertices for the Schrödinger functional with an abelian background gauge field. The background field has a non-trivial color structure, therefore we mainly focus on a manipulation of the color matrix part. We propose how to implement the algorithm especially in python code. By using python outputs produced by the code, we also show how

Shinji Takeda

2009-01-01

410

Lizards & Snakes: Alive! Coloring Book  

NSDL National Science Digital Library

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

411

Heider balance in human networks  

NASA Astrophysics Data System (ADS)

Recently, a continuous dynamics was proposed to simulate dynamics of interpersonal relations in a society represented by a fully connected graph. The final state of such a society was found to be identical with the so-called Heider balance (HB), where the society is divided into two mutually hostile groups. In the continuous model, a polarization of opinions was found in HB. Here we demonstrate that the polarization occurs also in Barabási-Albert networks, where the Heider balance is not necessarily present. In the second part of this work we demonstrate the results of our formalism, when applied to reference examples: the Southern women and the Zachary club.

Gawro?ski, P.; Ku?akowski, K.

2005-07-01

412

VPython  

NSDL National Science Digital Library

Python (from www.vpython.org) Python is a powerful object-oriented programming language initiated by Guido van Rossum in 1990. See the essay by van Rossum on "Programming for Everybody," www.python.org/cp4e. It is easy to start writing simple programs in Python, and even using classes and objects involves a relatively gentle learning curve. Python is cross-platform (Windows, Mac, Linux). It is open source (and therefore free) and supported by a sizable developer community. Python is a general-purpose programming language with significant numerical capabilities, though a common use of Python is managing servers, administering systems, etc. See the extensive web site, www.python.org. A good textbook is Learning Python by Mark Lutz and David Ascher, O'Reilly 1999. Realtime 3D Graphics: Visual Python itself does not provide graphics output. The Tk graphics library can be used to create 2D graphics, but it is difficult to use. In the spring of 2000, while a sophomore in computer science at Carnegie Mellon University, David Scherer created a 3D graphics module for Python, called "Visual," that is exceptionally easy to use. A program can create 3D objects (such as spheres, curves, etc.) and position them in 3D space. Visual, running in a separate thread, automatically updates a 3D scene many times per second, to reflect the current positions of the objects. The programmer does not need to deal with display management, but can focus on the computational aspects of the program. The user can navigate in the 3D scene by using the mouse to zoom and rotate while the program is running. Visual supports full vector algebra. Use in Classrooms Students in introductory physics courses have been using VPython to do computer modeling. VPython lets students focus on the physics computations without having to write explicit graphics statements yet obtain 3D visualization. Students can do true vector computations, which improves their understanding of the utility of vectors and vector notation. Platforms Supported The Python language itself is cross-platform. The Visual module, and the Idle integrated development environment, work with Python on Windows and Unix/Linux/MacOSX. Published Articles A journal article about VPython has been published: Scherer, D., Dubois, P., & Sherwood, B. (2000). VPython: 3D Interactive Scientific Graphics for Students, Computing in Science and Engineering, Sept./Oct. 2000, 82-88.

413

CyNEST: a maintainable Cython-based interface for the NEST simulator  

PubMed Central

NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, 2007). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., 1999). The introduction of PyNEST (Eppler et al., 2008), the Python interface for NEST, enabled users to control simulations using Python. As the majority of NEST users found PyNEST easier to use and to combine with other applications, it immediately displaced SLI as the default NEST interface. However, developing and maintaining PyNEST has become increasingly difficult over time. This is partly because adding new features requires writing low-level C++ code intermixed with calls to the Python/C API, which is unrewarding. Moreover, the Python/C API evolves with each new version of Python, which results in a proliferation of version-dependent code branches. In this contribution we present the re-implementation of PyNEST in the Cython language, a superset of Python that additionally supports the declaration of C/C++ types for variables and class attributes, and provides a convenient foreign function interface (FFI) for invoking C/C++ routines (Behnel et al., 2011). Code generation via Cython allows the production of smaller and more maintainable bindings, including increased compatibility with all supported Python releases without additional burden for NEST developers. Furthermore, this novel approach opens up the possibility to support alternative implementations of the Python language at no cost given a functional Cython back-end for the corresponding implementation, and also enables cross-compilation of Python bindings for embedded systems and supercomputers alike.

Zaytsev, Yury V.; Morrison, Abigail

2014-01-01

414

CyNEST: a maintainable Cython-based interface for the NEST simulator.  

PubMed

NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, 2007). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., 1999). The introduction of PyNEST (Eppler et al., 2008), the Python interface for NEST, enabled users to control simulations using Python. As the majority of NEST users found PyNEST easier to use and to combine with other applications, it immediately displaced SLI as the default NEST interface. However, developing and maintaining PyNEST has become increasingly difficult over time. This is partly because adding new features requires writing low-level C++ code intermixed with calls to the Python/C API, which is unrewarding. Moreover, the Python/C API evolves with each new version of Python, which results in a proliferation of version-dependent code branches. In this contribution we present the re-implementation of PyNEST in the Cython language, a superset of Python that additionally supports the declaration of C/C++ types for variables and class attributes, and provides a convenient foreign function interface (FFI) for invoking C/C++ routines (Behnel et al., 2011). Code generation via Cython allows the production of smaller and more maintainable bindings, including increased compatibility with all supported Python releases without additional burden for NEST developers. Furthermore, this novel approach opens up the possibility to support alternative implementations of the Python language at no cost given a functional Cython back-end for the corresponding implementation, and also enables cross-compilation of Python bindings for embedded systems and supercomputers alike. PMID:24672470

Zaytsev, Yury V; Morrison, Abigail

2014-01-01

415

Biophysics Course  

NSDL National Science Digital Library

An upper division biophysics course containing assignments that are suitable for teaching in an interdisciplinary manner. The assignments contain over 50 simulations written in SciPy/python. There are detailed instructions that come with the assignments.

Deutsch, John

2013-01-05

416

pyExtinction: Atmospheric extinction  

NASA Astrophysics Data System (ADS)

The Python script/package pyExtinction computes and plots total atmospheric extinction from decomposition into physical components (Rayleigh attenuation, ozone absorption, aerosol extinction). Its default extinction parameters are adapted to mean Mauna Kea summit conditions.

Buton, Clément; Copin, Yannick

2014-03-01

417

Lidar conversion tool script for ArcGIS 9.3  

NSDL National Science Digital Library

Chris Harding, Iowa State University Summary Python 2.5/2.6 script for converting .las Lidar data files inside a folder into one or more other data formats: ERDAS imagine raster file, TIN (full resolution and ...

Harding, Chris

418

77 FR 56821 - Privacy Act of 1974; System of Records  

Federal Register 2010, 2011, 2012, 2013

...Liaison Officer, Department of Defense. NM01500-13 System Name: Naval Postgraduate School Education Management System (PYTHON) (July 11, 2012, 77 FR 40865). Changes: * * * * * Exemptions claimed for the system: Delete entry and replace...

2012-09-14

419

OSP with Jython Web Start application - step-by-step guide  

NSDL National Science Digital Library

A description of how to build Java Web Start applications using the OSP library. Integrates the OpenSourcePhysics .jar library files and the Python classes generated by Jython during compiling time with jythonc.

2008-11-13

420

Problem Solving - Programming  

NSDL National Science Digital Library

Learn some basic math skills while at the same time learning some programming skills This short lesson focuses on solving simple math problem using computer programming. In this case, the examples given will be in Python (click on this link for more information: Official Tutorial for the Python programming language.). Computer programming can and has often been used to solve very complex mathematical problems along the lines of calculating ? ...

Kajigga

2009-09-23

421

Parallel Visualization using the Domain-Specific Interpreter Pattern  

Microsoft Academic Search

This paper concerns the software engineeering problem of de- ploying domain-specific optimisation. The work is motivated by experi- ence with parallelization and tiling in MayaVi, a 44,000-line visualisation application written in Python and VTK. To minimize disruption to MayaVi's open-source codebase, we do this by interposing a proxy between the Python client code, and the VTK library. The proxy delays

Karen Osmond; Olav Beckmann; Anthony J. Field; Paul H. J. Kelly

422

ReSP: A non-intrusive Transaction-Level Reflective MPSoC Simulation Platform for design space exploration  

Microsoft Academic Search

This paper presents ReSP (Reflective Simulation Platform), a Transaction-Level multi-processor simulation plat- form based on SystemC and Python; SystemC is a standard lan- guage for system modeling and verification, and Python provides the platform with reflective capabilities. These are employed to give the designer an easy way to specify the architecture of a system, simulate the given configuration and perform

Giovanni Beltrame; Cristiana Bolchini; Luca Fossati; Antonio Miele; Donatella Sciuto

2008-01-01

423

PyWiFeS: Wide Field Spectrograph data reduction pipeline  

NASA Astrophysics Data System (ADS)

PyWiFeS is a Python-based data reduction pipeline for the Wide Field Spectrograph (WiFeS). Its core data processing routines are built on standard scientific Python packages commonly used in astronomical applications. It includes an implementation of a global optical model of the spectrograph which provides wavelengths solutions accurate to ˜0.05 Å (RMS) across the entire detector. Through scripting, PyWiFeS can enable batch processing of large quantities of data.

Childress, Michael; Vogt, Frédéric; Nielsen, Jon; Sharp, Rob

2014-02-01

424

The morphology, crystallography, and chemistry of phases in as-cast nickel-aluminum bronze  

NASA Astrophysics Data System (ADS)

The morphology, crystallography, and composition of the phases present in as-cast nickel-aluminum bronze of nominal composition copper-10 wt pct aluminum-5 wt pct nickel-5 wt pct iron have been investigated using optical, electron optical, and microprobe analysis techniques. The as-cast microstructure consists of copper-rich ?, martensitic ?, and ?-phases based on Fe3Al and NiAl. The ?z precipitates have a dendritic morphology and are cored; the composition ranges from iron-rich solid solution to Fe3Al. The ?II and ?iv precipitates have, respectively, a dendritic and an equiaxed/dendritic morphology, and are based on Fe3Al, while ?III is a eutectoidal decomposition product of lamellar or globular morphology based on NiAl. The ?I, ?II, and ?III precipitates have the Kurdjumov-Sachs orientation relationship with ? matrix. Small ?IV precipitates exhibit the Nishiyama-Wasserman orientation relationship with the ? matrix, while large ?iv precipitates have an orientation relationship which lies between Kurdjumov-Sachs and Nishiyama-Wasserman.

Hasan, F.; Jahanafrooz, A.; Lorimer, G. W.; Ridley, N.

1982-08-01

425

Euthanasia attitude; A comparison of two scales  

PubMed Central

The main purposes of the present study were to see how the term “euthanasia” influences people’s support for or opposition to euthanasia; and to see how euthanasia attitude relates to religious orientation and personality factors. In this study two different euthanasia attitude scales were compared. 197 students were selected to fill out either the Euthanasia Attitude Scale (EAS) or Wasserman’s Attitude Towards Euthanasia scale (ATE scale). The former scale includes the term “euthanasia”, the latter does not. All participants filled out 50 items of International Personality Item Pool, 16 items of the the HEXACO openness, and 14 items of Religious Orientation Scale-Revised. Results indicated that even though the two groups were not different in terms of gender, age, education, religiosity and personality, mean score on the ATE scale was significantly higher than that of the EAS. Euthanasia attitude was negatively correlated with religiosity and conscientiousness and it was positively correlated with psychoticism and openness. It can be concluded that analyzing the attitude towards euthanasia with the use of EAS rather than the ATE scale results in lower levels of opposition against euthanasia. This study raises the question of whether euthanasia attitude scales should contain definitions and concepts of euthanasia or they should describe cases of it.

Aghababaei, Naser; Farahani, Hojjatollah; Hatami, Javad

2011-01-01

426

Book Review:  

NASA Astrophysics Data System (ADS)

I have had a love/hate relationship with this book ever since it first came out. On the one hand, this is an excellent introduction for mathematicians to the differential geometry underlying general relativity. On the other hand, this is definitely a book for mathematicians. The book's greatest strength is its clear, precise presentation of the basic ideas in differential geometry, combined with equally clear and precise applications to theoretical physics, notably general relativity. But the book's precision is also its greatest weakness; this is not an easy book to read for non-mathematicians, who may not appreciate the notational complexity, some of which is nonstandard. The present edition is very similar to the original, published in 1992. In addition to minor revisions and clarifications of the material, there is now a brief introduction to fibre bundles, and a (very) brief discussion of the gauge theory description of fundamental particles. The index to the symbols used is also a more complete than in the past, but without the descriptive material present in the previous edition. The bulk of the book consists of a careful introduction to tensors and their properties. Tensors are introduced first as linear maps on vector spaces, and only later generalized to tensor fields on manifolds. Th