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Sample records for zachary wasserman python

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

    E-print Network

    Denardo, Dale

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

  2. Sun-Sentinel Red hot email heats up Wasserman Schultz,

    E-print Network

    Fernandez, Eduardo

    on Wednesday, a day after their mutual dislike boiled over publicly. Many saw an element of entertainment on Wasserman Schultz. The lasting effect, though, may be limited, Wagner said. "It's good red meat for the base

  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. Simulation Programming with Python

    E-print Network

    Nelson, Barry L.

    for plotting (Matplotlib), GUI (WxPython, TKInter, PyQT, etc.), statistics (scipy.stats, statsmodelsChapter 4 Simulation Programming with Python This chapter shows how simulations of some of the examples in Chap. 3 can be programmed using Python and the SimPy simulation library[1]. The goals

  5. Eclipse Python Tutorial For Introduction to Programming Using Python

    E-print Network

    Liang, Y. Daniel

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

  6. 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)....

  7. Python to learn programming

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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.

  8. Peer-to-Peer Schema Mediation Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    Peer-to-Peer Schema Mediation Zachary G. Ives University of Pennsylvania CIS 650, Spring 2003 April))),(),,,,,1234,(.(: ),,ln,,,1234(:.(ln fnconcatnprDavisasexntghidPatientantghidTGHDB prsexpnfnPatientDavis

  9. All-in-One Python for Scientists

    E-print Network

    Delene, David J.

    to 3D Via scripting and GUI #12;Resources 2 Scientific Computing with Python - 2004 PythonPy4Science @ UND #12;#12;All-in-One Python for Scientists Enthought Python Distribution Open, NASA, NCAR, NOAA uses "Every pixel counts " #12;Resources 1 What is Python? by Wesley Chun Python 101

  10. Exploring Python as Matlab alternative A scientist view on python

    E-print Network

    Wardetzky, Max

    . ...... Exploring Python as Matlab alternative A scientist view on python Jochen Schulz Georg-August Universität Göttingen 1/61 #12;Aufbau ...1 Introduction ...2 Basic usage of python (Spyder) ...3 3D additional toolboxes (Symb. Math T., PDE T., Wavelet T.) mature and integrated GUI. . Disadvantages

  11. Repast for Python Scripting.

    SciTech Connect

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

    2005-01-01

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

  12. Biologists Remove Python from Everglades

    USGS Multimedia Gallery

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

  13. Python Data Visualization

    Energy Science and Technology Software Center (ESTSC)

    2011-08-15

    PDV is a Python module that reads in ULTRA data files and allows the user to perform data analysis and to create high-quality plots of the data. Features include the ability to perform integrals, take derivatives, perform arithmetic on data-sets, and to produce publication-quality plots. PDV is deliberaltely designed so that ULTRA users will be able to start running PDV with minimal training. PDV is easily customizable and extendible by anyone who knows a littlemore »Python.« less

  14. Python and computer vision

    SciTech Connect

    Doak, J. E.; Prasad, Lakshman

    2002-01-01

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

  15. Data Mining using Python --course introduction

    E-print Network

    Data Mining using Python -- course introduction Finn °Arup Nielsen DTU Compute Technical University of Denmark September 1, 2014 #12;Data Mining using Python -- course introduction Data Mining using Python DTU course 02819 Data mining using Python. Previously called DTU course 02820 Python programming (study admin

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

    E-print Network

    Mazzotti, Frank

    Invasive Species Distribution Notes Reproduction of the Burmese python (Python molurus bivittatus@flmnh.ufl.edu Key data: Python molurus bivittatus; Pythonidae; Burmese python; population; Everglades National Park.S., Mazzotti, F.J. (2007a): Python molurus bivattatus (Burmese Python). Nesting. Herpetol. Rev. 38: 93. Snow, R

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

    E-print Network

    van Geen, Alexander

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

  18. Integrating Network-Bound XML Data Zachary G. Ives

    E-print Network

    Integrating Network-Bound XML Data Zachary G. Ives Alon Y. Halevy Daniel S. Weld ¡ zives, alon, weld¢ @cs.washington.edu University of Washington Seattle, WA USA Abstract Although XML was originally not as a format for "materialized" or document data, but as a "wire protocol" for exchanging data through virtual

  19. Algorithms for Designing Pop-Up Cards Zachary Abel1

    E-print Network

    Demaine, Erik

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

  20. Symmetric Autocompensating Quantum Key Distribution Zachary D. Walton,

    E-print Network

    Teich, Malvin C.

    Symmetric Autocompensating Quantum Key Distribution Zachary D. Walton, Alexander V. Sergienko, Lev-2421 We present quantum key distribution schemes which are autocompensating (require no alignment.65.Ky Of all the capabilities afforded by quantum information science [1], quantum key distribution (QKD

  1. LN FN ADVISOR NAME Abbott Zachary Boucheron, Laura E.

    E-print Network

    Johnson, Eric E.

    LN FN ADVISOR NAME Abbott Zachary Boucheron, Laura E. Abotalebi Shayan Dawood, Muhammed Aguirre. Calzadillas Michael Ranade, Satishkuma J. Campolla Charles De Blassie, Richard D. Campos Luis Stochaj, Steven, Satishkuma J. Flores Kevin Furth, Paul M. Flores Arturo Ramirez-Angulo, Jaime Floyd Christopher Dawood

  2. Practical applications of Iterative Workload Distillation Zachary Kurmas

    E-print Network

    Kurmas, Zachary

    Practical applications of Iterative Workload Distillation Zachary Kurmas , Kimberly Keeton Abstract properties are "key" for a given workload and storage system. We have developed a tool, the Distiller, that automatically identifies the key properties for a given workload and storage system. The Distiller then uses

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

    USGS Publications Warehouse

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

    2011-01-01

    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.

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

    E-print Network

    Levine, Stuart

    1976-01-01

    to quibble, and much to be grateful for. # # * LIST (Library and Information Services Today): An International Registry of Re­ search and Innovation. Paul Wasserman et al., ed. Vol. 5. Detroit. Gale Research Co. 1975. $45.00. Professional librarians... to quibble, and much to be grateful for. # # * LIST (Library and Information Services Today): An International Registry of Re­ search and Innovation. Paul Wasserman et al., ed. Vol. 5. Detroit. Gale Research Co. 1975. $45.00. Professional librarians...

  5. Python programming --installation Finn Arup Nielsen

    E-print Network

    -oriented Python Distribution based on Qt and Spyder" containing Python, numpy, pip, matplotlib, PyQt4 (for GUI de development environments. Spyder espe- cially for numerical Python. idle -- Not so fancy GUI editor PyPython programming -- installation Finn °Arup Nielsen DTU Compute Technical University of Denmark

  6. Notes on clotting in a Burmese python (Python molurus bivittatus).

    PubMed

    Ratnoff, O D; Rosenberg, M J; Everson, B; Emanuelson, M; Tulodziecki, N

    1990-05-01

    Studies of the clotting mechanisms in the plasma of a Burmese python (Python molurus bivittatus) confirm earlier information that both extrinsic and intrinsic pathways of thrombin formation participate in reptilian hemostasis. Plasma fibrinogen was present at a concentration comparable to that in human plasma. Other assays were hampered by the need to use nonreptilian reagents. The activated partial thromboplastin time was shorter than was that of human plasma, thus implying the presence of prothrombin in python plasma; however, this protein could be demonstrated only in trace amounts. Similarly, only small amounts of Hageman factor (factor XII) and antihemophilic factor (factor VIII) were detected, and none of plasma prekallikrein, high-molecular-weight kininogen, and Christmas factor (factor IX). The prothrombin time was slower than that of human plasma. Factor VII was not detected, but both proaccelerin (factor V) and Stuart factor (factor X) were present. Python plasma inhibited bovine thrombin and human plasmin, but it was deficient in fibrinolytic capacity. PMID:2341766

  7. Pynamic: the Python Dynamic Benchmark

    SciTech Connect

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

    2007-07-10

    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.

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

    E-print Network

    Bennett, Albert F.

    182 The Effect of Meal Composition on Specific Dynamic Action in Burmese Pythons (Python molurus) M quantified the specific dynamic action (SDA) resulting from the ingestion of various meal types in Burmese pythons (Python molurus) at 30 C. Each snake was fed a series of experimental meals consisting of amino

  9. Extension Modules for the Python Interpretive language

    Energy Science and Technology Software Center (ESTSC)

    2006-12-29

    Python is an interpreted computer language, freely available to all, which may be extended by user developed "modules". These modules ay be written in a complied language such as 'C', and then linked into the Python program

  10. Algorithmic synthesis using Python compiler

    NASA Astrophysics Data System (ADS)

    Cieszewski, Radoslaw; Romaniuk, Ryszard; Pozniak, Krzysztof; Linczuk, Maciej

    2015-09-01

    This paper presents a python to VHDL compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and translate it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the programmed circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. This can be achieved by using many computational resources at the same time. Creating parallel programs implemented in FPGAs in pure HDL is difficult and time consuming. Using higher level of abstraction and High-Level Synthesis compiler implementation time can be reduced. The compiler has been implemented using the Python language. This article describes design, implementation and results of created tools.

  11. Python programming --GUI Finn Arup Nielsen

    E-print Network

    Python programming -- GUI Finn °Arup Nielsen Department of Informatics and Mathematical Modelling Technical University of Denmark October 1, 2012 #12;Python programming -- GUI Graphical user interface TkQT and PySide for Qt Finn °Arup Nielsen 1 October 1, 2012 #12;Python programming -- GUI Tkinter Hello world

  12. Python Examples C.1 FM Receiver

    E-print Network

    Kranakis, Evangelos

    Appendix C Python Examples C.1 FM Receiver File GCFMSDR.py 1 #!/usr/bin/env python 2 3 # Import self.BuildGui() 65 66 def BuildGui(self): 67 # GUI builder 68 # ----------- 69 # Use the "form APPENDIX C. PYTHON EXAMPLES D raft #12;Software Defined Radio © 2015 Michel Barbeau 89 # Add the box "radio

  13. Anatomy of the python heart.

    PubMed

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

    2010-12-01

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

  14. Python-ARM Radar Toolkit

    Energy Science and Technology Software Center (ESTSC)

    2013-03-17

    The Python-ARM Radar Toolkit (Py-ART) is a collection of radar quality control and retrieval codes which all work on two unifying Python objects: the PyRadar and PyGrid objects. By building ingests to several popular radar formats and then abstracting the interface Py-ART greatly simplifies data processing over several other available utilities. In addition Py-ART makes use of Numpy arrays as its primary storage mechanism enabling use of existing and extensive community software tools.

  15. Imagining a Stata / Python Combination

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2012-01-01

    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.

  16. Pybus -- A Python Software Bus

    SciTech Connect

    Lavrijsen, Wim T.L.P.

    2004-10-14

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

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

    E-print Network

    Chang, Hsueh-Chia

    Electrothermal ac electro-osmosis Zachary R. Gagnon and Hsueh-Chia Changa Center for MicrofluidicsHz for most conditions that scales as D/ l , where D is the ion diffusivity, is the Debye layer thickness

  18. Steering object-oriented computations with Python

    SciTech Connect

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

    1996-10-01

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

  19. Pyomo : Python Optimization Modeling Objects.

    SciTech Connect

    Siirola, John; Laird, Carl Damon; Hart, William Eugene; Watson, Jean-Paul

    2010-11-01

    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.

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

    USGS Multimedia Gallery

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

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

    PubMed

    Hedley, Joanna; Eatwell, Kevin; Schwarz, Tobias

    2014-01-01

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

  2. Evolution of Apache Open Source Software Haoran Wen, Raissa M. D'Souza, Zachary M. Saul, and Vladimir Filkov

    E-print Network

    D'Souza, Raissa

    Evolution of Apache Open Source Software Haoran Wen, Raissa M. D'Souza, Zachary M. Saul, and Vladimir Filkov University of California, Davis CA 95616, USA; hrwen@ucdavis.edu, rmdsouza. D'Souza, Zachary M. Saul, and Vladimir Filkov We analyze a series of fifty monthly snapshots

  3. 1 Compressive Optical Imaging: Architectures and Algorithms 1 Roummel F. Marcia, Rebecca M. Willett, and Zachary T. Harmany

    E-print Network

    Willett, Rebecca

    M. Willett, and Zachary T. Harmany 1.1 Introduction 1 1.2 Compressive Sensing 3 1.3 Architectures, Rebecca M. Willett, and Zachary T. Harmany 1) 1.1 Introduction Many traditional optical sensors of Natural Sciences, University of California, Merced. R. M. Willett and Z. T. Harmany, Department

  4. Python programming --databasing Finn Arup Nielsen

    E-print Network

    September 22, 2014 #12;Python programming -- databasing Overview Pickle -- simple format for persistence Key September 22, 2014 #12;Python programming -- databasing Persistence via pickle String representation of an object (Downey, 2008, section 14.7): >>> alist = [1, 2, 4] >>> import pickle >>> pickle

  5. Petite introduction Python pour le calcul scientifique

    E-print Network

    Goubet, Olivier

    Petite introduction NumPy SciPy Matplotlib Exemples Python pour le calcul scientifique Loïc Gouarin;Petite introduction NumPy SciPy Matplotlib Exemples Plan 1 Petite introduction 2 NumPy 3 SciPy 4 Matplotlib 5 Exemples Loïc Gouarin Python pour le calcul scientifique #12;Petite introduction NumPy Sci

  6. Python programming --Testing Finn Arup Nielsen

    E-print Network

    Python programming -- Testing Finn °Arup Nielsen DTU Compute Technical University of Denmark September 8, 2014 #12;Python testing Overview Testing frameworks: unittest, nose, py.test, doctest Coverage Testing of numerical computations GUI testing Web testing Test-driven development Finn °Arup Nielsen 1

  7. Python programming --Web serving Finn Arup Nielsen

    E-print Network

    (cgi) cherrypy django.view tornado.web Table 1: Web frameworks "LAMP": Linux, Apache, MySQL, Python (or-bar 0 No root access, e.g., to setup MySQL. Missing Python packages You own computer 0 May be difficult

  8. Einfuhrung Softwareentwicklungspraktikum "Python mit dem Raspberry Pi"

    E-print Network

    Einf¨uhrung Softwareentwicklungspraktikum "Python mit dem Raspberry Pi" (WiSe 2015/2016) Clemens Hauptprojekt 4 Zeitplan 5 Raspberry Pi 6 Python 2 / 16 #12;Organisation 1/4 Lernziele Programmieren-Vortr¨age zu Hauptprojekt 03.02.2016: Hauptprojekt Abnahme 11 / 16 #12;Raspberry Pi Offene Plattform

  9. Python programming --Pandas Finn Arup Nielsen

    E-print Network

    Python programming -- Pandas Finn °Arup Nielsen DTU Compute Technical University of Denmark October 5, 2013 #12;Pandas Overview Pandas? Reading data Summary statistics Indexing Merging, joining Group-by and cross-tabulation Statistical modeling Finn °Arup Nielsen 1 October 5, 2013 #12;Pandas Pandas? "Python

  10. Retroviral particles in neoplasms of Burmese pythons (Python molurus bivittatus).

    PubMed

    Chandra, A M; Jacobson, E R; Munn, R J

    2001-09-01

    Neoplastic diseases associated with retroviruses were diagnosed in four Burmese pythons (Python molurus bivattatus) from a single collection. Snake No. 1 was a 7-year-old female with recurrent undifferentiated mesenchymal round cell tumor (lymphosarcoma) of the oral cavity. At necropsy, similar neoplastic masses were evident in the uterus and ovary, and there was diffuse involvement of the spleen. Snake No. 2 was a 4.5-year-old female that was euthanatized because of complications following resection of a segmental colonic adenocarcinoma. Snake No. 3 was a 5-year-old female that was euthanatized because of a large transitional cell carcinoma of the right kidney. Snake No. 4 was a 19-year-old female that was euthanatized following recurrence of an intermandibular fibrosarcoma. Ultrastructural examination revealed few to numerous extracellular and intracellular (intravacuolar) type C-like retroviral particles in all tumors. Tumors were about 90-95 nm in diameter, with an electron-dense core and bilaminar external membrane. The relationship of the intraneoplastic viral particles to the etiology of the tumors is uncertain. PMID:11572567

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

    USGS Publications Warehouse

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

    2011-01-01

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

  12. Parallel, Distributed Scripting with Python

    SciTech Connect

    Miller, P J

    2002-05-24

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

  13. Development of hemipenes in the ball python snake Python regius.

    PubMed

    Leal, Francisca; Cohn, Martin J

    2015-01-01

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

  14. Reflection-Based Python-C++ Bindings

    SciTech Connect

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

    2004-10-14

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

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

    E-print Network

    Dukas, Reuven

    Effects of Early-Life Experience on Learning Ability in Fruit Flies Zachary Durisko & Reuven Dukas of their learning ability based on early-life cues of environmental complexity. We tested whether fruit fly larvae memory (Snell-Rood et al. 2009; Burns et al. 2011). Artificial selection experiments on fruit flies have

  16. A Human Study of Patch Maintainability Zachary P. Fry Bryan Landau Westley Weimer

    E-print Network

    Weimer, Westley

    A Human Study of Patch Maintainability Zachary P. Fry Bryan Landau Westley Weimer University and expensive part of the software lifecycle. Measuring the quality of bug-fixing patches is a difficult task interest in automatic patch generation makes a systematic understanding of patch maintainability

  17. Verifiable Audit Trails for a Versioning File System Randal Burns, Zachary Peterson, Giuseppe Ateniese, Stephen Bono

    E-print Network

    Ateniese, Giuseppe

    Verifiable Audit Trails for a Versioning File System Randal Burns, Zachary Peterson, Giuseppe constructs that create, manage, and verify dig- ital audit trails for versioning file systems. Based upon. Audit trails create an analog of the paper audit process for file data, helping to meet the requirements

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

    E-print Network

    Ferguson, Thomas S.

    OPTIMAL INVESTMENT POLICIES FOR THE HORSE RACE MODEL Thomas S. Ferguson and C. Zachary Gilstein on a winner in a horse race. It is assumed the investor knows for i = 1, . . . , m the probabilities pi, a situation referred to as the horse race in Baldwin [2]. The investor is given the opportunity to bet on m

  19. Using the Distiller to Direct the Development of Self-Configuration Software Zachary Kurmas

    E-print Network

    Kurmas, Zachary

    Using the Distiller to Direct the Development of Self-Configuration Software Zachary Kurmas College], we presented the design of the Distiller -- our tool that automates the process of finding a workload's key performance-affecting attributes. In this paper, we distill three production workloads and show

  20. Automated Incremental Design of Flexible Intrusion Detection Systems on Zachary K. Baker and Viktor K. Prasanna

    E-print Network

    Hwang, Kai

    Automated Incremental Design of Flexible Intrusion Detection Systems on FPGAs1 Zachary K. Baker a high-level, graph-based partition- ing methodology. We provide a library of performance- customized malicious packets. These techniques require significant compu- tational resources. However, using automated

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

    E-print Network

    Cosmides, Leda

    , Zachary L. Simmons Department of Psychology, University of California, Santa Barbara, CA 93106-9660, USA 2007 Abstract A growing body of research has shown that women express stronger attraction to more demonstrated that women express stronger attraction to higher testosterone men at different times in the cycle

  2. Approximating Hit Rate Curves using Streaming Zachary Drudi, Nicholas J. A. Harvey, Stephen Ingram, Andrew

    E-print Network

    Hutter, Frank

    Approximating Hit Rate Curves using Streaming Algorithms Zachary Drudi, Nicholas J. A. Harvey,nick,stephen,andy,jake}@cohodata.com Abstract A hit rate curve is a function that maps cache size to the proportion of requests that can be served from the cache. (The caching policy and sequence of requests are assumed to be fixed.) Hit rate

  3. Synthesizing Representative I/O Workloads Using Iterative Distillation Zachary Kurmas

    E-print Network

    Kurmas, Zachary

    Synthesizing Representative I/O Workloads Using Iterative Distillation Zachary Kurmas College proper- ties are "key" for a given workload and storage system. We have developed a tool, the Distiller, that automati- cally identifies the key properties ("attribute-values") of the workload. The Distiller then uses

  4. A Python Geospatial Language Toolkit

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

  5. Gist: A scientific graphics package for Python

    SciTech Connect

    Busby, L.E.

    1996-05-08

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

  6. SunPy—Python for solar physics

    NASA Astrophysics Data System (ADS)

    SunPy Community, The; Mumford, Stuart J.; Christe, Steven; Pérez-Suárez, David; Ireland, Jack; Shih, Albert Y.; Inglis, Andrew R.; Liedtke, Simon; Hewett, Russell J.; Mayer, Florian; Hughitt, Keith; Freij, Nabil; Meszaros, Tomas; Bennett, Samuel M.; Malocha, Michael; Evans, John; Agrawal, Ankit; Leonard, Andrew J.; Robitaille, Thomas P.; Mampaey, Benjamin; Iván Campos-Rozo, Jose; Kirk, Michael S.

    2015-01-01

    This paper presents SunPy (version 0.5), 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 visualization and plotting (matplotlib). SunPy is a data-analysis environment specializing in providing the software necessary to analyse solar and heliospheric data in Python. SunPy is open-source software (BSD licence) and has an open and transparent development workflow that anyone can contribute to. SunPy provides access to solar data through integration with the Virtual Solar Observatory (VSO), the Heliophysics Event Knowledgebase (HEK), and the HELiophysics Integrated Observatory (HELIO) webservices. It currently supports image data from major solar missions (e.g., SDO, SOHO, STEREO, and IRIS), time-series data from missions such as GOES, SDO/EVE, and PROBA2/LYRA, and radio spectra from e-Callisto and STEREO/SWAVES. We describe SunPy's functionality, provide examples of solar data analysis in SunPy, and show how Python-based solar data-analysis can leverage the many existing tools already available in Python. We discuss the future goals of the project and encourage interested users to become involved in the planning and development of SunPy.

  7. Measuring the Length of a Captured Burmese Python

    USGS Multimedia Gallery

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

  8. Starkiller : a static type inferencer and compiler for Python

    E-print Network

    Salib, Michael, 1978-

    2004-01-01

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

  9. Building a programmable interface for physics codes using numeric python

    SciTech Connect

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

    1996-04-16

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

  10. Type Ia Supernovae, Evolution, and the Cosmological Constant Persis S. Drell, 1 Thomas J. Loredo, 2 and Ira Wasserman 1;2

    E-print Network

    Loredo, Thomas J.

    predilection for or against evolution, is the odds ratio for these two classes of models. The resulting valuesType Ia Supernovae, Evolution, and the Cosmological Constant Persis S. Drell, 1 Thomas J. Loredo, 2 and Ira Wasserman 1;2 ABSTRACT We explore the possible role of evolution in the analysis of data on SNe Ia

  11. File Input and Output in Python Matt Huenerfauth

    E-print Network

    Rosenberg, Andrew

    , 2010 #12;Reading Command Line Arguments Thursday, October 7, 2010 #12;Two Ways to Use Python · GUIFile Input and Output in Python Matt Huenerfauth Guest Lecture: October 1, 2010 Methods in Thursday, October 7, 2010 #12;Asking the user for input · What if your Python program wants the user

  12. Environnement graphique Interface utilisateur graphique (GUI) en Python

    E-print Network

    Tichit, Laurent

    Environnement graphique Interface utilisateur graphique (GUI) en Python Cours_9_4 © L. Tichit, 26 Interface utilisateur graphique (GUI) en Python · Ce cours présentation de quelques généralités sur les le site du cours) · Références (également sur le site du cours) Tkinter reference : a GUI for Python

  13. Consumption of bird eggs by invasive Burmese Pythons in Florida

    USGS Publications Warehouse

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

    2012-01-01

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

  14. Implanting a Radio Transmitter in a Burmese Python

    USGS Multimedia Gallery

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

  16. Python Ephemeris Module for Radio Astronomy

    NASA Astrophysics Data System (ADS)

    Kuiper, T. B.

    2013-05-01

    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.

  17. Physiology: postprandial cardiac hypertrophy in pythons.

    PubMed

    Andersen, Johnnie B; Rourke, Bryan C; Caiozzo, Vincent J; Bennett, Albert F; Hicks, James W

    2005-03-01

    Oxygen consumption by carnivorous reptiles increases enormously after they have eaten a large meal in order to meet metabolic demands, and this places an extra load on the cardiovascular system. Here we show that there is an extraordinarily rapid 40% increase in ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding, which results from increased gene expression of muscle-contractile proteins. As this fully reversible hypertrophy occurs naturally, it could provide a useful model for investigating the mechanisms that lead to cardiac growth in other animals. PMID:15744290

  18. Introduction to Python Python is a great language for experimentation. It is an interpreted object-

    E-print Network

    Kranakis, Evangelos

    test.py, on Linux the mode is set as follows: chmod a+x test.py The execution of the script of the line. Python uses indentation to embed statements. Class A embeds a constructor. The constructor embeds

  19. Retained caseous yolk sac in a Burmese python (Python molurus bivittatus).

    PubMed

    Bodri, M S; Hendrick, M J; O'Brien, R T; Sadanaga, K K

    1990-10-01

    Retained yolk sacs are common in the domestic chicken and account for considerable morbidity and mortality during late embryonic development and within the first 10 days of life. What is believed to be the first recorded instance of a retained caseous yolk sac and its successful surgical removal from a Burmese python (Python molurus bivittatus) is reported. The snake experienced no post-operative complications and continues to be well 16 mo following surgery. PMID:2250338

  20. PyXNAT: XNAT in Python

    PubMed Central

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

    2012-01-01

    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

  1. Python for Scientific Gateways Development Randy Heiland

    E-print Network

    Lumsdaine, Andrew

    gateway is an interface that addresses some fundamental needs of a scientific community. This typically of their development and deployment costs yet empower scientific communities more than ever. Our approach should appeal immediately to scientific communities who are already using Python and thereby provide them with an economy

  2. Book Review Natural Language Processing with Python

    E-print Network

    Book Review Natural Language Processing with Python Steven Bird, Ewan Klein, and Edward Loper, xx+482 pp; paperbound, ISBN 978-0-596-51649-9, $44.99; on-line free of charge at nltk.org/book Reviewed by Michael Elhadad Ben-Gurion University This book comes with "batteries included" (a reference

  3. Py4Science 3 Python "names"

    E-print Network

    Delene, David J.

    Py4Science 3 @ UND 2009-06-18 #12;Python "names" In [1]: a=1 In [2]: id(a) Out[2]: memory-) # An empty generic dictionary to hold the variables 6-) # Read whole content of data and put into a ndarray 7

  4. Burmese Python Caught in the Everglades

    USGS Multimedia Gallery

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

  5. Python programming --exercises Finn Arup Nielsen

    E-print Network

    Google App Engine application up and running. Get a hello world Heroku up and running. Finn °Arup Nielsen __connection__ = 'mysql://root:@localhost/test' If you don't want to install MySQL try installing the simpler sqlite and its python support and then change the connection line. Finn °Arup Nielsen 5 October 10, 2013

  6. Data Mining using Python --exercises for installation

    E-print Network

    Install spyder Get a `Hello, World' program up and running on a cloud service up, either with Google App://root:@localhost/test' If you don't want to install MySQL try installing the simpler sqlite and its python support and then change the connection line to something like `sqlite:///home/user/the_data_base_file.db' Finn °Arup

  7. A Record-Breaking Invasive Burmese Python

    USGS Multimedia Gallery

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

  8. A Record-Breaking Invasive Burmese Python

    USGS Multimedia Gallery

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

  9. A Record-Breaking Invasive Burmese Python

    USGS Multimedia Gallery

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

  10. Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus.

    PubMed

    Falk, Bryan G; Reed, Robert N

    2015-01-01

    Molecular approaches to prey identification are increasingly useful in elucidating predator-prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons. PMID:26623196

  11. Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

    PubMed Central

    Reed, Robert N.

    2015-01-01

    Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons. PMID:26623196

  12. Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

    USGS Publications Warehouse

    Falk, Bryan; Reed, Robert

    2015-01-01

    Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

  13. PythonTeX: reproducible documents with LaTeX, Python, and more

    NASA Astrophysics Data System (ADS)

    Poore, Geoffrey M.

    2015-01-01

    PythonTeX is a LaTeX package that allows Python code in LaTeX documents to be executed and provides access to the output. This makes possible reproducible documents that combine results with the code required to generate them. Calculations and figures may be next to the code that created them. Since code is adjacent to its output in the document, editing may be more efficient. Since code output may be accessed programmatically in the document, copy-and-paste errors are avoided and output is always guaranteed to be in sync with the code that generated it. This paper provides an introduction to PythonTeX and an overview of major features, including performance optimizations, debugging tools, and dependency tracking. Several complete examples are presented. Finally, advanced features are summarized. Though PythonTeX was designed for Python, it may be extended to support additional languages; support for the Ruby and Julia languages is already included. PythonTeX contains a utility for converting documents into plain LaTeX, suitable for format conversion, sharing, and journal submission.

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

    E-print Network

    Liang, Y. Daniel

    (Python GUI) on Windows 7 or Vista, as shown in Figure 1. Click IDLE (Python GUI) to launch IDLE. You© Copyright Y. Daniel Liang, 2011 1 Using IDLE For Introduction to Programming Using Python By Y environment (IDE) for Python. It is 100% pure Python and developed using Tkinter. It has a text editor

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

    PubMed Central

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

    2014-01-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

  18. Matched regulation of gastrointestinal performance in the Burmese python, Python molurus.

    PubMed

    Cox, Christian L; Secor, Stephen M

    2008-04-01

    In Burmese pythons fasting and feeding cause dramatic regulation of gastric acid production and intestinal nutrient uptake. Predictably, other components of their gastrointestinal tract are similarly regulated with each meal. We therefore assessed the matched regulation of gastrointestinal performance by comparing the postprandial activities and capacities of gastric (pepsin), pancreatic (amylase and trypsin) and intestinal (aminopeptidase-N and maltase) enzymes, and intestinal nutrient uptake. Tissue samples were collected from pythons fasted and at 0.25, 0.5, 1, 2, 3, 4, 6, 10 and 15 days following their consumption of rodent meals equaling 25% of snake body mass. With feeding, pythons experience no significant change in stomach mass, whereas both the pancreas and small intestine doubled in mass. Feeding also triggered a depletion of gastric mucosal pepsinogen, a respective 5.7- and 20-fold increase in the peak activities of pancreatic trypsin and amylase, and a respective 2.3- and 5.5-fold increase in the peak activities of intestinal maltase and aminopeptidase-N. Enzyme activities peaked between 2 and 4 days postfeeding and returned to fasting levels by day 10. Independent of digestive stage, python intestine exhibited a proximal to distal decline in enzyme activity. For both sugars and proteins, intestinal capacities for enzyme activity were significantly correlated with nutrient uptake capacities. The concomitant postprandial upregulation of tissue morphology, intestinal nutrient transport rates and enzyme activities illustrate, for the python, the matched regulation of their gastrointestinal performance with each meal. PMID:18344488

  19. Ventilatory and cardiovascular responses of a python (Python molurus) to exercise and digestion.

    PubMed

    Secor, S M; Hicks, J W; Bennett, A F

    2000-08-01

    To investigate the potential limiting steps of peak metabolic rates, we examined gas exchange rates ( vdot (O2), vdot (CO2)), respiratory exchange ratio (RER), breathing frequency, tidal volume, minute ventilation volume (V.e) as well as the heart rate, systemic blood flow and stroke volume of Burmese pythons (Python molurus) while fasting at rest, exercising, digesting and exercising while digesting. All measured variables increased significantly during exercise (crawling at 0.4 km h(-)(1) and at vdot (O2max)), highlighted by a 17-fold increase in vdot (CO2) and a 24-fold increase in V.e. During the digestion of a meal equivalent to 25 % of the snake's body mass, pythons responded with increases in vdot (O2) and heart rate similar to those experienced during exercise, along with a 4.5-fold increase in systemic blood flow. Interestingly, pythons hyperventilated while exercising, whereas they hypoventilated during digestion. The combined demands of exercise and digestion resulted in significantly higher vdot (O2), vdot (CO2), breathing frequency and heart rate than during either exercise or digestion alone. Evidently, the capacities of the ventilatory and cardiovascular systems to transport oxygen to locomotor muscles are not a limiting factor in the attainment of peak metabolic rates during exercise in pythons PMID:10903159

  20. Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python (Python molurus).

    PubMed

    Astarita, Giuseppe; Rourke, Bryan C; Andersen, Johnnie B; Fu, Jin; Kim, Janet H; Bennett, Albert F; Hicks, James W; Piomelli, Daniele

    2006-05-01

    Oleoylethanolamide (OEA) is an endogenous lipid mediator that inhibits feeding in rats and mice by activating the nuclear receptor peroxisome proliferator-activated receptor-alpha (PPAR-alpha). In rodents, intestinal OEA levels increase about threefold upon refeeding, a response that may contribute to the induction of between-meal satiety. Here, we examined whether feeding-induced OEA mobilization also occurs in Burmese pythons (Python molurus), a species of ambush-hunting snakes that consume huge meals after months of fasting and undergo massive feeding-dependent changes in gastrointestinal hormonal release and gut morphology. Using liquid chromatography/mass spectrometry (LC/MS), we measured OEA levels in the gastrointestinal tract of fasted (28 days) and fed (48 h after feeding) pythons. We observed a nearly 300-fold increase in OEA levels in the small intestine of fed compared with fasted animals (322 +/- 121 vs. 1 +/- 1 pmol/mg protein, n = 3-4). In situ OEA biosynthesis was suggested by the concomitant increase of N-acyl phosphatidylethanolamine species that serve as potential biosynthetic precursors for OEA. Furthermore, we observed a concomitant increase in saturated, mono- and diunsaturated, but not polyunsaturated fatty-acid ethanolamides (FAE) in the small intestine of fed pythons. The identification of OEA and other FAEs in the gastrointestinal tract of Python molurus suggests that this class of lipid messengers may be widespread among vertebrate groups and may represent an evolutionarily ancient means of regulating energy intake. PMID:16373434

  1. Effect of feeding on circulating micronutrient concentrations in the Burmese python (Python molurus).

    PubMed

    Secor, S M; Nagy, T R; Johnston, K E; Tamura, T

    2001-06-01

    Burmese pythons (Python molurus) regulate digestive performance and metabolism with the ingestion of each meal. To explore the python's postprandial responses, we monitored the concentrations of blood micronutrients and homocysteine during fasting and for 15 days after feeding. Plasma folate concentrations peaked with a 270% increase over fasting levels 3 days after feeding, whereas plasma B-12 peaked with a 66% increase within 1 day. Erythrocyte folate concentrations were highest 15 days after feeding with a 44% increase. The major plasma folate was 5-methyltetrahydrofolate during fasting and was non-5-methyltetrahydrofolate during digestion, whereas erythrocytes contained polyglutamyl forms of non-5-methyltetrahydrofolate. Plasma homocysteine concentrations peaked with a 56% increase 3 days after feeding, and were markedly greater than those of mammals. Plasma zinc and copper did not change significantly. Plasma zinc concentrations were 20 times greater than plasma copper and approximately 30 times higher than those of mammals. Pythons showed a significant postprandial decline of 25% in hematocrit. Plasma pyridoxal 5'-phosphate (coenzyme form of vitamin B-6) was not detected probably due to its tight protein binding. Most micronutrient concentrations appear to plateau 3 days after feeding, suggesting that pythons have relatively rapid homeostasis of micronutrients despite the ingestion of large meals. PMID:11423336

  2. Meteor Shower Identification and Characterization with Python

    NASA Technical Reports Server (NTRS)

    Moorhead, Althea

    2015-01-01

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

  3. Python -die Alternative zu Matlab? Jochen Schulz

    E-print Network

    Wardetzky, Max

    . ...... Python - die Alternative zu Matlab? Jochen Schulz Georg-August Universität Göttingen 1 für alle Probleme 2/36 #12;MATLAB MATLAB steht für Matrix laboratory; ursprünglich speziell. Klare Code-Struktur. Ebenso viele Module für den nicht-wissenschaftlichen Gebrauch (nützlich z.B. für

  4. Py4Syn: Python for synchrotrons.

    PubMed

    Slepicka, H H; Canova, H F; Beniz, D B; Piton, J R

    2015-09-01

    In this report, Py4Syn, an open-source Python-based library for data acquisition, device manipulation, scan routines and other helper functions, is presented. Driven by easy-to-use and scalability ideals, Py4Syn offers control system agnostic solution and high customization level for scans and data output, covering distinct techniques and facilities. Here, most of the library functionalities are described, examples of use are shown and ideas for future implementations are presented. PMID:26289269

  5. Feeding a large-scale physics application to Python

    SciTech Connect

    Beazley, D.M.; Lomdahl, P.S.

    1997-10-01

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

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

    PubMed

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

    2015-01-01

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

  7. 75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

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

  8. Extensible message passing application development and debugging with Python

    SciTech Connect

    Beazley, D.M.; Lomdahl, P.S.

    1996-09-19

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

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

    SciTech Connect

    Gezahegne, A; Love, N S

    2007-12-10

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

  10. Re-imagining a Stata/Python Combination

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2013-01-01

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

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

    E-print Network

    Ras, Zbigniew W.

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

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

    E-print Network

    Sharp, Alexa

    Equilibria and Efficiency Loss in Games on Networks Joshua R. Davis, Zachary Goldman, Jacob Hilty played on social networks, where the network's nodes correspond to the game's players, have proven on a mathematical and general exploration of the relationship between 2-person strategic interactions (a "base game

  13. Multimode surface-wave analysis of near-surface data. Michel Cara, Zacharie Duputel, Luis A. Rivera and Georges Herquel

    E-print Network

    Duputel, Zacharie

    Multimode surface-wave analysis of near-surface data. Michel Cara, Zacharie Duputel, Luis A. Rivera to improve the dispersion measurements. The observed multimode dispersion data are then inverted in terms-c Diagrams Multi-mode signals recorded by an array of N sensors are stacked in order to reinforce

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

    E-print Network

    Choset, Howie

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

  15. Gastric function and its contribution to the postprandial metabolic response of the Burmese python Python molurus.

    PubMed

    Secor, Stephen M

    2003-05-01

    The large intact prey ingested by Burmese pythons require considerable processing by the stomach before passage into the small intestine. To investigate the function and cost of gastric digestion and its contribution to postprandial metabolic response for the Burmese python, I examined the rate of gastric digestion, the postprandial profile of gastric pH and the effects of decreasing gastric workload on the metabolic cost of digestion, referred to as specific dynamic action (SDA). Ingested meal mass (equivalent to 25% of snake body mass) was reduced by 18% within 1 day postfeeding, by which time intragastric pH had decreased from 7.5 to 2. Gastric pH was maintained at 1.5 for the next 5-7 days, after which it returned to 7.5. The SDA generated by digesting an intact rat meal was reduced by 9.1%, 26.0%, 56.5% and 66.8%, respectively, when pythons were fed steak, ground rat, liquid diet or ground rat directly infused into the small intestine. The production of HCl and enzymes and other gastric functions represent an estimated 55% of the python's SDA generated from the digestion of an intact rodent meal. Additional contributors to SDA include protein synthesis (estimated 26%), gastrointestinal upregulation (estimated 5%) and the activities of the pancreas, gallbladder, liver, kidneys and intestines during digestion (estimated 14%). Operating on a 'pay before pumping' principle, pythons must expend endogenous energy in order to initiate acid production and other digestive processes before ingested nutrients can be absorbed and channeled into metabolic pathways. PMID:12682094

  16. scikit-image: image processing in Python

    PubMed Central

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

    2014-01-01

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

  17. Rapid web development using AJAX and Python

    NASA Astrophysics Data System (ADS)

    Dolgert, A.; Gibbons, L.; Kuznetsov, V.

    2008-07-01

    We discuss the rapid development of a large scale data discovery service for the CMS experiment using modern AJAX techniques and the Python language. To implement a flexible interface capable of accommodating several different versions of the DBS database, we used a 'stack' approach. Asynchronous JavaScript and XML (AJAX) together with an SQL abstraction layer, template engine, code generation tool and dynamic queries provide powerful tools for constructing interactive interfaces to large amounts of data. We show how the use of these tools, with rapid development in a modern scripting language, improved the scalability and usability of the the search interface for different user communities.

  18. Python Program to Select HII Region Models

    NASA Astrophysics Data System (ADS)

    Miller, Clare; Lamarche, Cody; Vishwas, Amit; Stacey, Gordon J.

    2016-01-01

    HII regions are areas of singly ionized Hydrogen formed by the ionizing radiaiton of upper main sequence stars. The infrared fine-structure line emissions, particularly Oxygen, Nitrogen, and Neon, can give important information about HII regions including gas temperature and density, elemental abundances, and the effective temperature of the stars that form them. The processes involved in calculating this information from observational data are complex. Models, such as those provided in Rubin 1984 and those produced by Cloudy (Ferland et al, 2013) enable one to extract physical parameters from observational data. However, the multitude of search parameters can make sifting through models tedious. I digitized Rubin's models and wrote a Python program that is able to take observed line ratios and their uncertainties and find the Rubin or Cloudy model that best matches the observational data. By creating a Python script that is user friendly and able to quickly sort through models with a high level of accuracy, this work increases efficiency and reduces human error in matching HII region models to observational data.

  19. SunPy: Solar Physics in Python

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. 75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

    ... proposed rule (75 FR 11808) to list the Indian python (Python molurus, including Burmese python Python... proposed rule (75 FR 11808; March 12, 2010), draft economic analysis, draft environmental assessment, and U... comments, please refer to the March 12, 2010, proposed rule (75 FR 11808), available online at...

  1. Master 1 BBSG Python/Perl -MySQL Programmation Web Bases de Donnes

    E-print Network

    Tichit, Laurent

    Master 1 BBSG Python/Perl - MySQL Programmation Web Bases de Données Dans ce TP, vous devrez aller consulter de manière intensive la documentation http://dev.mysql.com/doc/connector-python/en/ 1. Tapez le script Python suivant et testez-le : #!/usr/bin/python3 import mysql.connector monServeur = "ensembldb

  2. New insights on facultative parthenogenesis in pythons WARREN BOOTH1,2,3

    E-print Network

    Castoe, Todd A.

    and triggering cell division. The deviating case involves a report of a captive Burmese python (Python bivittatus report of facultative parthenogenesis in the Burmese python and suggest an intriguing alternativeNew insights on facultative parthenogenesis in pythons WARREN BOOTH1,2,3 *, GORDON W. SCHUETT2

  3. Facultative thermogenesis during brooding is not the norm among pythons.

    PubMed

    Brashears, Jake; DeNardo, Dale F

    2015-08-01

    Facultative thermogenesis is often attributed to pythons in general despite limited comparative data available for the family. While all species within Pythonidae brood their eggs, only two species are known to produce heat to enhance embryonic thermal regulation. By contrast, a few python species have been reported to have insignificant thermogenic capabilities. To provide insight into potential phylogenetic, morphological, and ecological factors influencing thermogenic capability among pythons, we measured metabolic rates and clutch-environment temperature differentials at two environmental temperatures-python preferred brooding temperature (31.5 °C) and a sub-optimal temperature (25.5 °C)-in six species of pythons, including members of two major phylogenetic branches currently devoid of data on the subject. We found no evidence of facultative thermogenesis in five species: Aspidites melanocephalus, A. ramsayi, Morelia viridis, M. spilota cheynei, and Python regius. However, we found that Bothrochilus boa had a thermal metabolic sensitivity indicative of facultative thermogenesis (i.e., a higher metabolic rate at the lower temperature). However, its metabolic rate was quite low and technical challenges prevented us from measuring temperature differential to make conclusions about facultative endothermy in this species. Regardless, our data combined with existing literature demonstrate that facultative thermogenesis is not as widespread among pythons as previously thought. PMID:26113382

  4. An Extensible Python User Environment for Subsurface Modeling

    NASA Astrophysics Data System (ADS)

    Daily, J. A.

    2008-12-01

    We use the Python programming language to collect, organize, and present the multitude of data and provenance associated with running scientific application codes. Without a user environment, the inputs, outputs, analyses, and executables are muddled by arcane directory hierarchies, file names, and symbolic links. Our user environment emulates the ad hoc ways of the scientific application user while hiding the addling details of where files should go, which machines can run which application codes, and what steps it took to create their application study. We use the wxPython GUI toolkit to create a cross-platform GUI application that focuses on the task-oriented analysis process using a richly interactive graph as its main interface. Navigating the graph, users setup and launch their registered scientific applications and watch as the graph reacts in real-time to users' input and the output of their running processes. These processes reflect steps a user regularly takes and uses the tools and programs they are familiar with thanks to Python and wxPython's auto-discovery of system tools for file types, the extensibility of our registry for new or platform-dependent file types and installed tools, and the expressiveness and readability of the python language and the wxPython GUI toolkit. It is our interactive process graph and the seamless integration of user-familiar tools that makes our environment a novel example of Python for furthering and easing the use of scientific application codes.

  5. PyMOOSE: Interoperable Scripting in Python for MOOSE.

    PubMed

    Ray, Subhasis; Bhalla, Upinder S

    2008-01-01

    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. PMID:19129924

  6. PyMOOSE: Interoperable Scripting in Python for MOOSE

    PubMed Central

    Ray, Subhasis; Bhalla, Upinder S.

    2008-01-01

    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. PMID:19129924

  7. Responses of python gastrointestinal regulatory peptides to feeding.

    PubMed

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

    2001-11-20

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

  8. Ultrasonographic diagnosis of an endocarditis valvularis in a Burmese python (Python molurus bivittatus) with pneumonia.

    PubMed

    Schroff, Sandra; Schmidt, Volker; Kiefer, Ingmar; Krautwald-Junghanns, Maria-Elisabeth; Pees, Michael

    2010-12-01

    An 11-yr-old Burmese python (Python molurus bivittatus) was presented with a history of respiratory symptoms. Computed tomography and an endoscopic examination of the left lung were performed and revealed severe pneumonia. Microbiologic examination of a tracheal wash sample and an endoscopy-guided sample from the lung confirmed infection with Salmonella enterica ssp. IV, Enterobacter cloacae, and Klebsiella pneumoniae. Computed tomographic examination demonstrated a hyperattenuated structure within the heart. Echocardiographic examination revealed a hyperechoic mass at the pulmonic valve as well as a dilated truncus pulmonalis. As therapy for pneumonia was ineffective, the snake was euthanized. Postmortem examination confirmed pneumonia and infective endocarditis of the pulmonic valve caused by septicemia with Salmonella enterica ssp. IV. Focal arteriosclerosis of the pulmonary trunk was also diagnosed. The case presented here demonstrates the possible connection between respiratory and cardiovascular diseases in snakes. PMID:21370657

  9. Osteitis deformans (Paget's disease) in a Burmese python (Python molurus bivittatus)--a case report.

    PubMed

    Preziosi, Rosario; Diana, Alessia; Florio, Daniela; Gustinelli, Andrea; Nardini, Giordano

    2007-11-01

    Osteitis deformans (Paget's disease of bone) is a chronic focal disorder of bone remodelling characterized by an initial increase in osteoclast-mediated bone resorption, with subsequent compensatory increase in new bone formation, resulting in a disorganized mosaic of woven and lamellar bone. In the Burmese python (Python molurus bivittatus) of this report, multifocal gross swellings involving the proximal third of the vertebral spine were observed and associated with anorexia, a relative inability to move or to fully extend the body, and to strike at prey. Serum biochemistry revealed elevated alkaline-phosphatase activity. Radiographic changes (irregular bone proliferation along the vertebral margins), computed tomography scan results (abnormal mineral density), and histopathological features (generalized thickening of the bony trabeculae at the expense of the intertrabecular spaces and irregular patches of lamellar bone with a characteristic "mosaic" pattern) indicated osteitis deformans. PMID:17222574

  10. Use of the Wasserman equation in optimization of the duration of the power ramp in a cardiopulmonary exercise test: a study of Brazilian men

    PubMed Central

    Costa, D. C.; de Santi, G. L.; Crescêncio, J. C.; Seabra, L. P.; Carvalho, E. E. V.; Papa, V.; Marques, F.; Gallo, L.; Schmidt, A.

    2015-01-01

    This study aimed to analyze the agreement between measurements of unloaded oxygen uptake and peak oxygen uptake based on equations proposed by Wasserman and on real measurements directly obtained with the ergospirometry system. We performed an incremental cardiopulmonary exercise test (CPET), which was applied to two groups of sedentary male subjects: one apparently healthy group (HG, n=12) and the other had stable coronary artery disease (n=16). The mean age in the HG was 47±4 years and that in the coronary artery disease group (CG) was 57±8 years. Both groups performed CPET on a cycle ergometer with a ramp-type protocol at an intensity that was calculated according to the Wasserman equation. In the HG, there was no significant difference between measurements predicted by the formula and real measurements obtained in CPET in the unloaded condition. However, at peak effort, a significant difference was observed between oxygen uptake (V?O2)peak(predicted)and V?O2peak(real)(nonparametric Wilcoxon test). In the CG, there was a significant difference of 116.26 mL/min between the predicted values by the formula and the real values obtained in the unloaded condition. A significant difference in peak effort was found, where V?O2peak(real)was 40% lower than V?O2peak(predicted)(nonparametric Wilcoxon test). There was no agreement between the real and predicted measurements as analyzed by Lin’s coefficient or the Bland and Altman model. The Wasserman formula does not appear to be appropriate for prediction of functional capacity of volunteers. Therefore, this formula cannot precisely predict the increase in power in incremental CPET on a cycle ergometer. PMID:26397972

  11. Use of the Wasserman equation in optimization of the duration of the power ramp in a cardiopulmonary exercise test: a study of Brazilian men.

    PubMed

    Costa, D C; Santi, G L de; Crescêncio, J C; Seabra, L P; Carvalho, E E V; Papa, V; Marques, F; Gallo Junior, L; Schmidt, A

    2015-12-01

    This study aimed to analyze the agreement between measurements of unloaded oxygen uptake and peak oxygen uptake based on equations proposed by Wasserman and on real measurements directly obtained with the ergospirometry system. We performed an incremental cardiopulmonary exercise test (CPET), which was applied to two groups of sedentary male subjects: one apparently healthy group (HG, n=12) and the other had stable coronary artery disease (n=16). The mean age in the HG was 47±4 years and that in the coronary artery disease group (CG) was 57±8 years. Both groups performed CPET on a cycle ergometer with a ramp-type protocol at an intensity that was calculated according to the Wasserman equation. In the HG, there was no significant difference between measurements predicted by the formula and real measurements obtained in CPET in the unloaded condition. However, at peak effort, a significant difference was observed between oxygen uptake (V?O2)peak(predicted)and V?O2peak(real)(nonparametric Wilcoxon test). In the CG, there was a significant difference of 116.26 mL/min between the predicted values by the formula and the real values obtained in the unloaded condition. A significant difference in peak effort was found, where V?O2peak(real)was 40% lower than V?O2peak(predicted)(nonparametric Wilcoxon test). There was no agreement between the real and predicted measurements as analyzed by Lin's coefficient or the Bland and Altman model. The Wasserman formula does not appear to be appropriate for prediction of functional capacity of volunteers. Therefore, this formula cannot precisely predict the increase in power in incremental CPET on a cycle ergometer. PMID:26397972

  12. Postprandial morphological response of the intestinal epithelium of the Burmese python (Python molurus).

    PubMed

    Lignot, Jean-Hervé; Helmstetter, Cécile; Secor, Stephen M

    2005-07-01

    The postprandial morphological changes of the intestinal epithelium of Burmese pythons were examined using fasting pythons and at eight time points after feeding. In fasting pythons, tightly packed enterocytes possess very short microvilli and are arranged in a pseudostratified fashion. Enterocyte width increases by 23% within 24 h postfeeding, inducing significant increases in villus length and intestinal mass. By 6 days postfeeding, enterocyte volume had peaked, following as much as an 80% increase. Contributing to enterocyte hypertrophy is the cellular accumulation of lipid droplets at the tips and edges of the villi of the proximal and middle small intestine, but which were absent in the distal small intestine. At 3 days postfeeding, conventional and environmental scanning electron microscopy revealed cracks and lipid extrusion along the narrow edges of the villi and at the villus tips. Transmission electron microscopy demonstrated the rapid postprandial lengthening of enterocyte microvilli, increasing 4.8-fold in length within 24 h, and the maintaining of that length through digestion. Beginning at 24 h postfeeding, spherical particles were found embedded apically within enterocytes of the proximal and middle small intestine. These particles possessed an annular-like construction and were stained with the calcium-stain Alizarine red S suggesting that they were bone in origin. Following the completion of digestion, many of the postprandial responses were reversed, as observed by the atrophy of enterocytes, the shortening of villi, and the retraction of the microvilli. Further exploration of the python intestine will reveal the underlying mechanisms of these trophic responses and the origin and fate of the engulfed particles. PMID:16002308

  13. Implementation of quantum game theory simulations using Python

    NASA Astrophysics Data System (ADS)

    Madrid S., A.

    2013-05-01

    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.

  14. Effect of laser treatment on first-intention incisional wound healing in ball pythons (Python regius).

    PubMed

    Cole, Grayson L; Lux, Cassie N; Schumacher, Juergen P; Seibert, Rachel L; Sadler, Ryan A; Henderson, Andrea L; Odoi, Agricola; Newkirk, Kim M

    2015-10-01

    OBJECTIVE To evaluate effects of laser treatment on incisional wound healing in ball pythons (Python regius). ANIMALS 6 healthy adult ball pythons. PROCEDURES Snakes were sedated, a skin biopsy specimen was collected for histologic examination, and eight 2-cm skin incisions were made in each snake; each incision was closed with staples (day 0). Gross evaluation of all incision sites was performed daily for 30 days, and a wound score was assigned. Four incisions of each snake were treated (5 J/cm(2) and a wavelength of 980 nm on a continuous wave sequence) by use of a class 4 laser once daily for 7 consecutive days; the other 4 incisions were not treated. Two excisional skin biopsy specimens (1 control and 1 treatment) were collected from each snake on days 2, 7, 14, and 30 and evaluated microscopically. Scores were assigned for total inflammation, degree of fibrosis, and collagen maturity. Generalized linear models were used to investigate the effect of treatment on each variable. RESULTS Wound scores for laser-treated incisions were significantly better than scores for control incisions on day 2 but not at other time points. There were no significant differences in necrosis, fibroplasia, inflammation, granuloma formation, or bacterial contamination between control and treatment groups. Collagen maturity was significantly better for the laser-treated incisions on day 14. CONCLUSIONS AND CLINICAL RELEVANCE Laser treatment resulted in a significant increase in collagen maturity at day 14 but did not otherwise significantly improve healing of skin incisions. PMID:26413829

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

    PubMed

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

    2014-05-15

    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

  16. CIS192 Python Programming Generators Exceptions and IO

    E-print Network

    Plotkin, Joshua B.

    CIS192 Python Programming Generators Exceptions and IO Eric Kutschera University of Pennsylvania Exceptions and IO Generators Exceptions Input Output Context Managers Eric Kutschera (University Generators Exceptions and IO Generators Exceptions Input Output Context Managers Eric Kutschera (University

  17. PyMC: Bayesian Stochastic Modelling in Python

    PubMed Central

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

    2010-01-01

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

  18. Enrico: Python package to simplify Fermi-LAT analysis

    NASA Astrophysics Data System (ADS)

    Sanchez, David; Deil, Christoph

    2015-01-01

    Enrico analyzes Fermi data. It produces spectra (model fit and flux points), maps and lightcurves for a target by editing a config file and running a python script which executes the Fermi science tool chain.

  19. ORIGINAL PAPER Can invasive Burmese pythons inhabit temperate regions

    E-print Network

    Dorcas, Michael E.

    variety of avian and mammalian prey including wading birds, bobcats (Lynx rufus), and white-tailed deer, and behavior of Burmese pythons from South Florida in a semi-natural enclosure in South Carolina, where winters

  20. ORIGINAL PAPER Can invasive Burmese pythons inhabit temperate regions

    E-print Network

    Willson. J.D.

    wading birds, bobcats (Lynx rufus), and white-tailed deer (Odocoi- leus virginianus; Reed and Rodda 2009 United States. We examined survivorship, thermal biology, and behavior of Burmese pythons from South

  1. MEG and EEG data analysis with MNE-Python.

    PubMed

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

    2013-12-26

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

  2. Rapid Development of Interferometric Software Using MIRIAD and Python

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

  4. Using Python to Develop Graphical Interfaces to Scientific Data

    SciTech Connect

    MacFarland, L; Streletz, G J

    1999-09-24

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

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

    PubMed

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

    2012-09-01

    An invasive population of Burmese pythons (Python molurus bivittatus) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species. PMID:22938523

  6. Tachykinins (substance P, neurokinin A and neuropeptide gamma) and neurotensin from the intestine of the Burmese python, Python molurus.

    PubMed

    Conlon, J M; Adrian, T E; Secor, S M

    1997-01-01

    Peptides with substance P-like immunoreactivity, neurokinin A-like immunoreactivity and neurotensin-like immunoreactivity were isolated in pure form from an extract of the intestine of the Burmese python (Python molurus). The primary structure of python substance P (Arg-Pro-Arg-Pro-Gln-Gln-Phe-Tyr-Gly-Leu- Met-NH2) shows one amino acid substitution (Phe8-->Tyr) compared with chicken/alligator substance P and an additional substitution (Lys3-->Arg) as compared with mammalian substance P. The neurokinin A-like immunoreactivity was separated into two components. Python neuropeptide gamma (Asp-Ala-Gly-Tyr- Ser-Pro-Leu-Ser-His-Lys-Arg-His-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met-NH2 shows three substitutions (Gly5-->Ser, Gln6-->Pro and Ile7-->Leu) compared with alligator neuropeptide gamma and an additional substitution (His4-->Tyr) compared with mammalian neuropeptide gamma. Python neurokinin A (His-Lys-Thr-Asp-Ser-Phe-Val-Gly- Leu-Met.NH2) is identical to human/chicken/alligator neurokinin A. Python neurotensin (pGlu-Leu-Val-His-Asn-Lys-Ala-Arg-Pro-Tyr-Ile-Leu) is identical to chicken/alligator neurotensin. The data are indicative of differential evolutionary pressure to conserve the amino acid sequences of reptilian gastrointestinal peptides. PMID:9437709

  7. Renal plasticity in response to feeding in the Burmese python, Python molurus bivittatus.

    PubMed

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

    2015-10-01

    Burmese pythons are sit-and-wait predators that are well adapted to go long periods without food, yet subsequently consume and digest single meals that can exceed their body weight. These large feeding events result in a dramatic alkaline tide that is compensated by a hypoventilatory response that normalizes plasma pH; however, little is known regarding how plasma HCO3(-) is lowered in the days post-feeding. The current study demonstrated that Burmese pythons contain the cellular machinery for renal acid-base compensation and actively remodel the kidney to limit HCO3(-) reabsorption in the post-feeding period. After being fed a 25% body weight meal plasma total CO2 was elevated by 1.5-fold after 1 day, but returned to control concentrations by 4 days post-feeding (d pf). Gene expression analysis was used to verify the presence of carbonic anhydrase (CA) II, IV and XIII, Na(+) H(+) exchanger 3 (NHE3), the Na(+) HCO3(-) co-transporter (NBC) and V-type ATPase. CA IV expression was significantly down-regulated at 3 dpf versus fasted controls. This was supported by activity analysis that showed a significant decrease in the amount of GPI-linked CA activity in isolated kidney membranes at 3 dpf versus fasted controls. In addition, V-type ATPase activity was significantly up-regulated at 3 dpf; no change in gene expression was observed. Both CA II and NHE3 expression was up-regulated at 3 dpf, which may be related to post-prandial ion balance. These results suggest that Burmese pythons actively remodel their kidney after feeding, which would in part benefit renal HCO3(-) clearance. PMID:26123779

  8. Intracardiac flow separation in an in situ perfused heart from Burmese python Python molurus.

    PubMed

    Wang, Tobias; Altimiras, Jordi; Axelsson, Michael

    2002-09-01

    The heart of non-crocodilian reptiles has two separate atria that receive blood from the systemic and pulmonary circulations. The ventricle is not fully divided, but is compartmentalised into two chambers (cavum dorsale and cavum pulmonale) by a muscular ridge that runs from the apex to the base of the ventricle. The muscular ridge is small in turtles, but is well developed in varanid lizards and many species of snakes. These anatomical differences correlate with an effective blood flow separation in varanid lizards, whereas turtles can exhibit very large cardiac shunts. Very little is known about the cardiac shunt patterns in other groups of reptiles. Here we characterise cardiac performance and flow dynamics in the Burmese python (Python molurus) using an in situ perfused heart preparation. The pericardium remained intact and the two atria were perfused separately (Ringer solution), and the two systemic and the pulmonary outflows were independently cannulated. Right and left atrial filling pressures and ventricular outflow pressures of the pulmonary and systemic vessels could be manipulated independently, permitting the establishment of large experimental intraventricular pressure gradients across the muscular ridge. The maximal power output generated by the systemic side of the ventricle exceeded the maximal power output that was generated by the cavum pulmonale that perfuse the pulmonary circulation. Furthermore, systemic flow could be generated against a higher outflow pressure than pulmonary flow. Perfusate entering the right atrium was preferentially distributed into the pulmonary circulation, whereas perfusate into the left atrium was distributed to the systemic circulation. Our study indicates that the well-developed muscular ridge can separate the cavum systemic and pulmonary sides of the heart to prevent mixing of systemic and pulmonary flows. Therefore, the heart of Python appears to exhibit a large degree of ventricular flow separation as previously described for varanid lizards. We speculate that the ventricular separation has evolved in response to the need of maintaining high oxygen delivery while protecting the pulmonary circulation from oedema as result of high vascular pressures. PMID:12151377

  9. Functional changes with feeding in the gastro-intestinal epithelia of the Burmese python (Python molurus).

    PubMed

    Helmstetter, Cécile; Reix, Nathalie; T'Flachebba, Mathieu; Pope, Robert K; Secor, Stephen M; Le Maho, Yvon; Lignot, Jean-Hervé

    2009-09-01

    The morphology of the digestive system in fasting and refed Burmese pythons was determined, as well as the localization of the proton (H(+), K(+)-ATPase) and sodium (Na(+), K(+)-ATPase) pumps. In fasting pythons, oxyntopeptic cells located within the fundic glands are typically non-active, with a thick apical tubulovesicular system and numerous zymogen granules. They become active Immediately after feeding but return to a non-active state 3 days after the Ingestion of the prey. The proton pump, expressed throughout the different fasting/feeding states, is either sequestered in the tubulovesicular system in non-active cells or located along the apical digitations extending within the crypt lumen in active cells. The sodium pump is rapidly upregulated in fed animals and is classically located along the baso-lateral membranes of the gastric oxyntopeptic cells. In the Intestine, it is only expressed along the lateral membranes of the enterocytes, i.e., above the lateral spaces and not along the basal side of the cells. Thus, solute transport within the Intestinal lining is mainly achieved through the apical part of the cells and across the lateral spaces while absorbed fat massively crosses the entire height of the cells and flows into the Intercellular spaces. Therefore, in the Burmese python, the gastrointestinal cellular system quickly upregulates after feeding, due to Inexpensive cellular changes, passive mechanisms, and the progressive activation and synthesis of key enzymes such as the sodium pump. This cell plasticity also allows anticipation of the next fasting and feeding periods. PMID:19799514

  10. Introducing Python tools for magnetotellurics: MTpy

    NASA Astrophysics Data System (ADS)

    Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

    2013-12-01

    Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South Australia. Workflow of MT data processing. Within the structural diagram, the MTpy sub-packages are shown in red (time series data processing), green (handling of EDI files and impedance tensor data), yellow (connection to modelling/inversion algorithms), black (impedance tensor interpretation, e.g. by Phase Tensor calculations), and blue (generation of visual representations, e.g pseudo sections or resistivity models).

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  12. Python algorithms in particle tracking microrheology

    PubMed Central

    2012-01-01

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

  13. Bioinformatic pipelines in Python with Leaf

    PubMed Central

    2013-01-01

    Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum overhead for the programmer, thus providing a simple layer of software structuring. Results Leaf includes a formal language for the definition of pipelines with code that can be transparently inserted into the user’s Python code. Its syntax is designed to visually highlight dependencies in the pipeline structure it defines. While encouraging the developer to think in terms of bioinformatic pipelines, Leaf supports a number of automated features including data and session persistence, consistency checks between steps of the analysis, processing optimization and publication of the analytic protocol in the form of a hypertext. Conclusions Leaf offers a powerful balance between plan-driven and change-driven development environments in the design, management and communication of bioinformatic pipelines. Its unique features make it a valuable alternative to other related tools. PMID:23786315

  14. Python-Assisted MODFLOW Application and Code Development

    NASA Astrophysics Data System (ADS)

    Langevin, C.

    2013-12-01

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

  15. The effect of meal composition on specific dynamic action in burmese pythons (Python molurus).

    PubMed

    McCue, M D; Bennett, A F; Hicks, J W

    2005-01-01

    We quantified the specific dynamic action (SDA) resulting from the ingestion of various meal types in Burmese pythons (Python molurus) at 30 degrees C. Each snake was fed a series of experimental meals consisting of amino acid mixtures, simple proteins, simple or complex carbohydrates, or lipids as well as meals of whole animal tissue (chicken breast, beef suet, and mouse). Rates of oxygen consumption were measured for approximately 4 d after feeding, and the increment above standard metabolic rate was determined and compared to energy content of the meals. While food type (protein, carbohydrate, and lipid) had a general influence, SDA was highly dependent on meal composition (i.e., amino acid composition and carbohydrate structure). For chicken breast and simple carbohydrates, the SDA coefficient was approximately one-third the energetic content of the meal. Lard, suet, cellulose, and starch were not digested and did not produce measurable SDA. We conclude that the cost of de novo protein synthesis is an important component of SDA after ingestion of protein meals because (1) simple proteins, such as gelatin and collagen, did not stimulate levels of SDA attained after consumption of complete protein, (2) incomplete mixtures of amino acids failed to elicit the SDA of a complete mixture, and (3) the inhibition of de novo protein synthesis with the drug cycloheximide caused a more than 70% decrease in SDA. Stomach distension and mechanical digestion of intact prey did not cause measurable SDA. PMID:15778938

  16. Purification and characterization of islet hormones (insulin, glucagon, pancreatic, polypeptide and somatostatin) from the Burmese python, Python molurus.

    PubMed

    Conlon, J M; Secor, S M; Adrian, T E; Mynarcik, D C; Whittaker, J

    1997-08-29

    Insulin was purified from an extract of the pancreas of the Burmese python, Python molurus (Squamata:Serpentes) and its primary structure established as: A Chain: Gly-Ile-Val-Glu-Gln-Cys-Cys-Glu-Asn-Thr10-Cys-Ser-Leu-Tyr-Glu-Leu- Glu-Asn-Tyr-Cys20-Asn. B-Chain: Ala-Pro-Asn-Gln-His-Leu-Cys-Gly-Ser-His10-Leu-Val-Glu-Ala-Leu-Tyr- Leu-Val-Cys-Gly20-Asp-Arg-Gly-Phe-Tyr-Tyr-Ser-Pro-Arg-Ser30. With the exception of the conservative substitution Phe --> Tyr at position B25, those residues in human insulin that comprise the receptor-binding and those residues involved in dimer and hexamer formation are fully conserved in python insulin. Python insulin was slightly more potent (1.8-fold) than human insulin in inhibiting the binding of [125I-Tyr-A14] insulin to the soluble full-length recombinant human insulin receptor but was slightly less potent (1.5-fold) than human insulin for inhibiting binding to the secreted extracellular domain of the receptor. The primary structure of python glucagon contains only one amino acid substitution (Ser28 --> Asn) compared with turtle/duck glucagon and python somatostatin is identical to that of mammalian somatostatin-14. In contrast, python pancreatic polypeptide (Arg-Ile-Ala-Pro-Val-Phe-Pro-Gly-Lys-Asp10-Glu-Leu-Ala-Lys-Phe- Tyr20-Thr-Glu-Leu-Gln-Gln-Tyr-Leu-Asn-Ser-Ile30-Asn-Arg-Pro-Arg -Phe.NH2) contains only 35 instead of the customary 36 residues and the amino acid sequence of this peptide has been poorly conserved between reptiles and birds (18 substitutions compared with alligator and 20 substitutions compared with chicken). PMID:9350978

  17. A Python interface with Narcisse graphics

    SciTech Connect

    Motteler, Z.C.

    1996-04-15

    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.

  18. pyam: Python Implementation of YaM

    NASA Technical Reports Server (NTRS)

    Myint, Steven; Jain, Abhinandan

    2012-01-01

    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.

  19. Effects of meal size, clutch, and metabolism on the energy efficiencies of juvenile Burmese pythons, Python molurus.

    PubMed

    Cox, Christian L; Secor, Stephen M

    2007-12-01

    We explored meal size and clutch (i.e., genetic) effects on the relative proportion of ingested energy that is absorbed by the gut (apparent digestive efficiency), becomes available for metabolism and growth (apparent assimilation efficiency), and is used for growth (production efficiency) for juvenile Burmese pythons (Python molurus). Sibling pythons were fed rodent meals equaling 15%, 25%, and 35% of their body mass and individuals from five different clutches were fed rodent meals equaling 25% of their body mass. For each of 11-12 consecutive feeding trials, python body mass was recorded and feces and urate of each snake was collected, dried, and weighed. Energy contents of meals (mice and rats), feces, urate, and pythons were determined using bomb calorimetry. For siblings fed three different meal sizes, growth rate increased with larger meals, but there was no significant variation among the meal sizes for any of the calculated energy efficiencies. Among the three meal sizes, apparent digestive efficiency, apparent assimilation efficiency, and production efficiency averaged 91.0%, 84.7%, and 40.7%, respectively. In contrast, each of these energy efficiencies varied significantly among the five different clutches. Among these clutches production efficiency was negatively correlated with standard metabolic rate (SMR). Clutches containing individuals with low SMR were therefore able to allocate more of ingested energy into growth. PMID:17913527

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

    E-print Network

    Broschat, Shira Lynn

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

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

    SciTech Connect

    Kostka, Timothy D.

    2013-01-01

    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.

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

    E-print Network

    Ralphs, Ted

    IE 172 Laboratory 0: Setting Up Python and Eclipse Dr. T.K. Ralphs Due January 29, 2015 1 of an integrated development environment (IDE). 2. Understand how to install and use the Eclipse IDE with Python and the PyDev. 3. Understand how to develop a simple Python application using Eclipse from scratch. 4

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

    E-print Network

    Feschotte, Cedric

    The Burmese python genome reveals the molecular basis for extreme adaptation in snakes Todd A for vertebrate biology and med- icine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of ex- treme physiological and metabolic adaptation. We

  4. Adaptive regulation of digestive performance in the genus Python.

    PubMed

    Ott, Brian D; Secor, Stephen M

    2007-01-01

    The adaptive interplay between feeding habits and digestive physiology is demonstrated by the Burmese python, which in response to feeding infrequently has evolved the capacity to widely regulate gastrointestinal performance with feeding and fasting. To explore the generality of this physiological trait among pythons, we compared the postprandial responses of metabolism and both intestinal morphology and function among five members of the genus Python: P. brongersmai, P. molurus, P. regius, P. reticulatus and P. sebae. These infrequently feeding pythons inhabit Africa, southeast Asia and Indonesia and vary in body shape from short and stout (P. brongersmai) to long and slender (P. reticulatus). Following the consumption of rodent meals equaling 25% of snake body mass, metabolic rates of pythons peaked at 1.5 days at levels 9.9- to 14.5-fold of standard metabolic rates before returning to prefeeding rates by day 6-8. Specific dynamic action of these meals (317-347 kJ) did not differ among species and equaled 23-27% of the ingested energy. For each species, feeding triggered significant upregulation of intestinal nutrient transport and aminopeptidase-N activity. Concurrently, intestinal mass doubled on average for the five species, in part due to an 85% increase in mucosal thickness, itself a product of 27-59% increases in enterocyte volume. The integrative response of intestinal functional upregulation and tissue hypertrophy enables each of these five python species, regardless of body shape, to modulate intestinal performance to meet the demands of their large infrequent meals. PMID:17210969

  5. Effects of meal size on postprandial responses in juvenile Burmese pythons (Python molurus).

    PubMed

    Secor, S M; Diamond, J

    1997-03-01

    Pythons were reported previously to exhibit large changes in intestinal mass and transporter activities on consuming meals equal to 25% of the snake's body mass. This paper examines how those and other adaptive responses to feeding vary with meal size (5, 25, or 65% of body mass). Larger meals took longer to pass through the stomach and small intestine. After ingestion of a meal, O2 consumption rates rose to up to 32 times fasting levels and remained significantly elevated for up to 13 days. This specific dynamic action equaled 29-36% of ingested energy. After 25 and 65% size meals, plasma Cl- significantly dropped, whereas plasma CO2, glucose, creatinine, and urea nitrogen increased as much as a factor of 2.3-4.2. Within 1 day the intestinal mucosal mass more than doubled, and masses of the intestinal serosa, liver, stomach, pancreas, and kidneys also increased. Intestinal uptake rates of amino acids and of D-glucose increased by up to 43 times fasting levels, whereas uptake capacities increased by up to 59 times fasting levels. Magnitudes of many of these responses (O2 consumption rate, kidney hypertrophy, and D-glucose and L-lysine uptake) increased with meal size up to the largest meals studied; other responses (Na+-independent L-leucine uptake, plasma Cl-, and organ masses) plateaued at meals equal to 25% of the snake's body mass; and still other responses (nutrient uptake at day 1, passive glucose uptake, and plasma protein and alkaline phosphatase) were all-or-nothing, being independent of meal size between 5 and 65% of body mass. Pythons undergo a wide array of postprandial responses, many of which differ in their sensitivity to meal size. PMID:9087654

  6. Determinants of the postfeeding metabolic response of Burmese pythons, Python molurus.

    PubMed

    Secor, S M; Diamond, J

    1997-01-01

    The relatively large meal sizes consumed by sit-and-wait-foraging snake species make them favorable for investigating specific dynamic action, the rise in metabolic rate associated with digestion. Hence, we measured O2 consumption rates (VO2) before and up to 20 d after Burmese pythons (Python molurus) either had only constricted and killed rodent meals or had also been allowed to consume meals ranging in size from 5% to 111% of their body mass. Postprandial VO2 peaked within 2 d at a value that increased with meal size, up to 44 times standard metabolic rate for the largest meals. In addition to being the largest known magnitude of postprandial metabolic response, this also exceeds the factorial increase in VO2 during peak physical activity for all studied animals except perhaps racehorses. Specific dynamic action, calculated from the extra VO2 above standard metabolic rate over the duration of digestion, increased with meal size and equaled 32% of ingested meal energy. The allometric exponent for body mass was 0.68 for standard metabolic rate, 0.90 for peak postprandial VO2, and 1.01 for specific dynamic action. Specific dynamic action is higher, and standard metabolic rate is lower, in sit-and-wait-foraging snake species than in actively foraging snake species. This suggests that sit-and-wait-foraging snakes, which consume large meals at long and unpredictable intervals, reduce standard metabolic rate by allowing the energetically expensive small intestine and other associated organs to atrophy between meals but thereby incur a large specific dynamic action while rebuilding those organs upon feeding. PMID:9231393

  7. The big squeeze: scaling of constriction pressure in two of the world's largest snakes, Python reticulatus and Python molurus bivittatus.

    PubMed

    Penning, David A; Dartez, Schuyler F; Moon, Brad R

    2015-11-01

    Snakes are important predators that have radiated throughout many ecosystems, and constriction was important in their radiation. Constrictors immobilize and kill prey by using body loops to exert pressure on their prey. Despite its importance, little is known about constriction performance or its full effects on prey. We studied the scaling of constriction performance in two species of giant pythons (Python reticulatus and Python molurus bivittatus) and propose a new mechanism of prey death by constriction. In both species, peak constriction pressure increased significantly with snake diameter. These and other constrictors can exert pressures dramatically higher than their prey's blood pressure, suggesting that constriction can stop circulatory function and perhaps kill prey rapidly by over-pressurizing the brain and disrupting neural function. We propose the latter 'red-out effect' as another possible mechanism of prey death from constriction. These effects may be important to recognize and treat properly in rare cases when constrictors injure humans. PMID:26347553

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

    USGS Publications Warehouse

    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

    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.

  9. A novel Mycoplasma sp. associated with proliferative tracheitis and pneumonia in a Burmese python (Python molurus bivittatus).

    PubMed

    Penner, J D; Jacobson, E R; Brown, D R; Adams, H P; Besch-Williford, C L

    1997-10-01

    Proliferative lymphocytic tracheitis and pneumonia were observed histologically in the respiratory tract of a captive Burmese python (Python molurus bivittatus). A mycoplasma species was isolated from the respiratory tissue. Polymerase chain reaction analysis of the 16S rRNA gene sequence of the isolate showed 0.90 similarity to Mycoplasma agassizii, an organism previously shown to cause respiratory disease in reptiles. Based on these findings, a novel Mycoplasma species was suspected to be the causative agent of respiratory disease in this snake. PMID:9447490

  10. Double valvular insufficiency in a Burmese python (Python molurus bivittatus, Linnaeus, 1758) suffering from concomitant bacterial pneumonia.

    PubMed

    Schilliger, Lionel; Tréhiou-Sechi, Emilie; Petit, Amandine M P; Misbach, Charlotte; Chetboul, Valérie

    2010-12-01

    Ultrasonography, and, to a lesser extent, echocardiography are now well-established, noninvasive, and painless diagnostic tools in herpetologic medicine. Various cardiac lesions have been previously described in reptiles, but valvulopathy is rarely documented in these animals and, consequently, is poorly understood. In this report, sinoatrial and atrioventricular insufficiencies were diagnosed in a 5-yr-old captive dyspneic Burmese python (Python molurus bivittatus) on the basis of echocardiographic and Doppler examination. This case report is the first to document Doppler assessment of valvular regurgitations in a reptile. PMID:21370663

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

    E-print Network

    Vollmayr-Lee, Ben

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

  12. CIS192 Python Programming HTTP Requests and HTML Parsing

    E-print Network

    Plotkin, Joshua B.

    CIS192 Python Programming HTTP Requests and HTML Parsing Eric Kutschera University of Pennsylvania 1 Last Time os Queues itertools random datetime sys 2 HTTP Requests HTTP Requests 3 HTML Parsing HTML Beautiful Soup Eric Kutschera (University of Pennsylvania) CIS 192 February 27, 2015 2 / 33 #12;os

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

    E-print Network

    Thain, Douglas

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

  14. CIS192 Python Programming Web Servers and Web APIs

    E-print Network

    Plotkin, Joshua B.

    CIS192 Python Programming Web Servers and Web APIs Eric Kutschera University of Pennsylvania March 6, 2015 Eric Kutschera (University of Pennsylvania) CIS 192 March 6, 2015 1 / 22 #12;Outline 1 Web Servers Purpose of Web Servers Flask 2 Web APIs REST Encoding and Encryption Eric Kutschera (University

  15. Wyrm: A Brain-Computer Interface Toolbox in Python.

    PubMed

    Venthur, Bastian; Dähne, Sven; Höhne, Johannes; Heller, Hendrik; Blankertz, Benjamin

    2015-10-01

    In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm ( https://github.com/bbci/wyrm ), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm's software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python. PMID:26001643

  16. pyro: Python-based tutorial for computational methods for hydrodynamics

    NASA Astrophysics Data System (ADS)

    Zingale, Michael

    2015-07-01

    pyro is a simple python-based tutorial on computational methods for hydrodynamics. It includes 2-d solvers for advection, compressible, incompressible, and low Mach number hydrodynamics, diffusion, and multigrid. It is written with ease of understanding in mind. An extensive set of notes that is part of the Open Astrophysics Bookshelf project provides details of the algorithms.

  17. batman: BAsic Transit Model cAlculatioN in Python

    NASA Astrophysics Data System (ADS)

    Kreidberg, Laura

    2015-10-01

    batman provides fast calculation of exoplanet transit light curves and supports calculation of light curves for any radially symmetric stellar limb darkening law. It uses an integration algorithm for models that cannot be quickly calculated analytically, and in typical use, the batman Python package can calculate a million model light curves in well under ten minutes for any limb darkening profile.

  18. Rabacus: A Python package for analytic cosmological radiative transfer calculations

    NASA Astrophysics Data System (ADS)

    Altay, G.; Wise, J. H.

    2015-04-01

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

  19. PyKrige: Development of a Kriging Toolkit for Python

    NASA Astrophysics Data System (ADS)

    Murphy, B. S.

    2014-12-01

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

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

    PubMed Central

    Jurica, Peter; van Leeuwen, Cees

    2008-01-01

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

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

    E-print Network

    Blank, Douglas

    Python Robotics: An Environment for Exploring Robotics Beyond LEGOs Douglas Blank Computer Science to Handyboard-type, LEGO-based robots. The resulting system, called Pyro, was designed with the following goals Mawr, PA 19010 dkumar@cs.brynmawr.edu Abstract This paper describes Pyro, a robotics programming en

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

    USGS Publications Warehouse

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

    2011-01-01

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

  3. Emerge - A Python environment for the modeling of subsurface transfers

    NASA Astrophysics Data System (ADS)

    Lopez, S.; Smai, F.; Sochala, P.

    2014-12-01

    The simulation of subsurface mass and energy transfers often relies on specific codes that were mainly developed using compiled languages which usually ensure computational efficiency at the expense of relatively long development times and relatively rigid software. Even if a very detailed, possibly graphical, user-interface is developed the core numerical aspects are rarely accessible and the smallest modification will always need a compilation step. Thus, user-defined physical laws or alternative numerical schemes may be relatively difficult to use. Over the last decade, Python has emerged as a popular and widely used language in the scientific community. There already exist several libraries for the pre and post-treatment of input and output files for reservoir simulators (e.g. pytough). Development times in Python are considerably reduced compared to compiled languages, and programs can be easily interfaced with libraries written in compiled languages with several comprehensive numerical libraries that provide sequential and parallel solvers (e.g. PETSc, Trilinos…). The core objective of the Emerge project is to explore the possibility to develop a modeling environment in full Python. Consequently, we are developing an open python package with the classes/objects necessary to express, discretize and solve the physical problems encountered in the modeling of subsurface transfers. We heavily relied on Python to have a convenient and concise way of manipulating potentially complex concepts with a few lines of code and a high level of abstraction. Our result aims to be a friendly numerical environment targeting both numerical engineers and physicist or geoscientists with the possibility to quickly specify and handle geometries, arbitrary meshes, spatially or temporally varying properties, PDE formulations, boundary conditions…

  4. Postprandial remodeling of the gut microbiota in Burmese pythons.

    PubMed

    Costello, Elizabeth K; Gordon, Jeffrey I; Secor, Stephen M; Knight, Rob

    2010-11-01

    The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12?h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall 'species'-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships. PMID:20520652

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

    PubMed

    Hunter, Margaret E; Hart, Kristen M

    2013-01-01

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

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

    PubMed Central

    Hunter, Margaret E.; Hart, Kristen M.

    2013-01-01

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

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

    USGS Publications Warehouse

    Hunter, Margaret E.; Hart, Kristen M.

    2013-01-01

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

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

    PubMed

    Castoe, Todd A; de Koning, Jason A P; Hall, Kathryn T; Yokoyama, Ken D; Gu, Wanjun; Smith, Eric N; Feschotte, Cédric; Uetz, Peter; Ray, David A; Dobry, Jason; Bogden, Robert; Mackessy, Stephen P; Bronikowski, Anne M; Warren, Wesley C; Secor, Stephen M; Pollock, David D

    2011-01-01

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

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

    PubMed

    Groot, T V M; Bruins, E; Breeuwer, J A J

    2003-02-01

    Parthenogenesis among reptiles is rare. Only a few species have the ability to reproduce asexually. Most of these are obligate parthenogenetic species that consist (almost) entirely of females, which can reproduce solely through parthenogenesis. Rarer are sexual species that only sporadically reproduce through parthenogenesis. A female Python molurus bivittatus (Reptilia, Boidae) from the Artis Zoo, Amsterdam, produced eggs in five consecutive years that contained embryos while she was isolated from males. These eggs might be fertilized with stored sperm, or might be the product of parthenogenesis. Parthenogenesis has not been shown for the Boidae family before. We performed parentship analyses on the snake and seven of her embryos using microsatellites and AFLP. Four microsatellite loci developed for this species combined with three loci developed previously for different snake species revealed too little variation to discriminate between sperm retention and parthenogenesis. With AFLP we were able to confirm that the Artis Zoo female reproduced parthenogenetically. Because the offspring are genetically identical to their mother, whereas in previous studies on sporadic parthenogenesis in snakes a loss of genetic information was reported, we conclude that the meiotic pathways that produce the diploid egg cells are different. PMID:12634818

  10. PyRAT - python radiography analysis tool (u)

    SciTech Connect

    Temple, Brian A; Buescher, Kevin L; Armstrong, Jerawan C

    2011-01-14

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

  11. COOPR: A COmmon Optimization Python Repository v. 1.0

    Energy Science and Technology Software Center (ESTSC)

    2008-08-14

    Coopr integrates Python packages for defining optimizers, modeling optimization applications, and managing computational experiments. A major driver for Coopr development is the Pyomo package that can be used to define abstract problems, create concrete problem instances, and solve these instances with standard solvers. Other Coopr packages include EXACT, a framework for managing computational experiments, SUCASA, a tool for customizing integer programming solvers, and OPT, a generic optimization interface.

  12. Python as a Federation Tool for GENESIS 3.0

    PubMed Central

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

    2012-01-01

    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

  13. ObsPy: A Python Toolbox for Seismology

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed

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

    2015-09-01

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

  15. GAiN: Distributed Array Computation with Python

    SciTech Connect

    Daily, Jeffrey A.

    2009-04-24

    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.

  16. Python for Information Theoretic Analysis of Neural Data

    PubMed Central

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

    2008-01-01

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

  17. Parallel astronomical data processing with Python: Recipes for multicore machines

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

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

    PubMed

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

    2014-01-01

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

  19. ELLIPT2D: A Flexible Finite Element Code Written Python

    SciTech Connect

    Pletzer, A.; Mollis, J.C.

    2001-03-22

    The use of the Python scripting language for scientific applications and in particular to solve partial differential equations is explored. It is shown that Python's rich data structure and object-oriented features can be exploited to write programs that are not only significantly more concise than their counter parts written in Fortran, C or C++, but are also numerically efficient. To illustrate this, a two-dimensional finite element code (ELLIPT2D) has been written. ELLIPT2D provides a flexible and easy-to-use framework for solving a large class of second-order elliptic problems. The program allows for structured or unstructured meshes. All functions defining the elliptic operator are user supplied and so are the boundary conditions, which can be of Dirichlet, Neumann or Robbins type. ELLIPT2D makes extensive use of dictionaries (hash tables) as a way to represent sparse matrices.Other key features of the Python language that have been widely used include: operator over loading, error handling, array slicing, and the Tkinter module for building graphical use interfaces. As an example of the utility of ELLIPT2D, a nonlinear solution of the Grad-Shafranov equation is computed using a Newton iterative scheme. A second application focuses on a solution of the toroidal Laplace equation coupled to a magnetohydrodynamic stability code, a problem arising in the context of magnetic fusion research.

  20. Disposition of enrofloxacin and its metabolite ciprofloxacin after intramuscular injection in juvenile Burmese pythons (Python molurus bivittatus).

    PubMed

    Young, L A; Schumacher, J; Papich, M G; Jacobson, E R

    1997-03-01

    Eleven juvenile Burmese pythons (Python molurus bivittatus) weighing 0.75-1.75 kg were randomly divided into two groups. Blood samples were obtained through surgically placed anterior carotid artery cannulas. Six pythons received a single i.m. injection of enrofloxacin at 5 mg/kg. Blood samples were obtained at 0.5, 1, 3, 6, 12, 24, 48, 72, and 96 hr postinjection. A mean (+/- SD) maximal plasma concentration of 1.66 (+/- 0.42) micrograms/ml was measured at 5.75 hr postinjection. The harmonic mean half-life was calculated to be 6.37 hr. The second group of five snakes received enrofloxacin at 5 mg/kg i.m. s.i.d. for 5 days. Blood was collected immediately before each injection and at 6 hr after each injection. Over the 5-day period, there was a stepwise increase in mean trough plasma concentrations of enrofloxacin. Clinically effective peak plasma enrofloxacin concentrations were attained after the first injection but did not significantly increase during the sampling period. Pharmacokinetic data were assessed against minimum inhibitory concentrations of enrofloxacin for Pseudomonas ssp. isolates in snakes obtained from historical data at the Veterinary Medical Teaching Hospital, University of Florida. Enrofloxacin should be administered at 10 mg/kg i.m. every 48 hr when treating Pseudomonas ssp. infections in juvenile Burmese pythons. Treatment of infections of more enrofloxacin-sensitive gram-negative bacteria could be achieved with the administration of an initial i.m. dose of 10 mg/kg followed by 5 mg/kg every 48 hr. PMID:9226619

  1. Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades.

    PubMed

    McCleery, Robert A; Sovie, Adia; Reed, Robert N; Cunningham, Mark W; Hunter, Margaret E; Hart, Kristen M

    2015-04-22

    To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range. PMID:25788598

  2. Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades

    USGS Publications Warehouse

    McCleery, Robert A.; Sovie, Adia; Reed, Robert N.; Cunningham, Mark W.; Hunter, Margaret E.; Hart, Kristen M.

    2015-01-01

    To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range.

  3. 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...

  4. Cooperative Object-Oriented Programming in Python Department of Mathematics and Computer Science

    E-print Network

    Chan, Albert

    of object-oriented programming languages. On the other hand, there are some "add-on" features the object- oriented features of the Python programming language. Python supports encapsulation with limited is often advertised as a multi-paradigm programming language. It supports the imperative, object- oriented

  5. The fast azimuthal integration Python library: pyFAI

    PubMed Central

    Ashiotis, Giannis; Deschildre, Aurore; Nawaz, Zubair; Wright, Jonathan P.; Karkoulis, Dimitrios; Picca, Frédéric Emmanuel; Kieffer, Jérôme

    2015-01-01

    pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.1 PMID:25844080

  6. An object oriented Python interface for atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

    2016-01-01

    Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

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

    E-print Network

    Newman, Mark

    computer programs in the Python programming language. Python is easy to learn, simple to use computer screen that show the program you are working on and allow you to enter or edit lines of codeCHAPTER 2 PYTHON PROGRAMMING FOR PHYSICISTS OUR FIRST item of business is to learn how to write

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

    E-print Network

    Castoe, Todd A.

    in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding- dominant model species used to study such extreme responses has been the Burmese python because of the extreme nature of postfeed- ing response in this species. We analyzed the Burmese python intestine across

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  10. Fatty acids identified in the Burmese python promote beneficial cardiac growth.

    PubMed

    Riquelme, Cecilia A; Magida, Jason A; Harrison, Brooke C; Wall, Christopher E; Marr, Thomas G; Secor, Stephen M; Leinwand, Leslie A

    2011-10-28

    Burmese pythons display a marked increase in heart mass after a large meal. We investigated the molecular mechanisms of this physiological heart growth with the goal of applying this knowledge to the mammalian heart. We found that heart growth in pythons is characterized by myocyte hypertrophy in the absence of cell proliferation and by activation of physiological signal transduction pathways. Despite high levels of circulating lipids, the postprandial python heart does not accumulate triglycerides or fatty acids. Instead, there is robust activation of pathways of fatty acid transport and oxidation combined with increased expression and activity of superoxide dismutase, a cardioprotective enzyme. We also identified a combination of fatty acids in python plasma that promotes physiological heart growth when injected into either pythons or mice. PMID:22034436

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

    E-print Network

    Fuentes, Esteban

    2014-01-01

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

  12. New Python-based methods for data processing

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  14. Novel divergent nidovirus in a python with pneumonia.

    PubMed

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

    2014-11-01

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

  15. Pythran: enabling static optimization of scientific Python programs

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  16. New Python-based methods for data processing.

    PubMed

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

    2013-07-01

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

  17. Adaptive responses to feeding in Burmese pythons: pay before pumping.

    PubMed

    Secor, S M; Diamond, J

    1995-06-01

    Burmese pythons normally consume large meals after long intervals. We measured gut contents, O2 consumption rates, small intestinal brush-border uptake rates of amino acids and glucose, organ masses and blood chemistry in pythons during the 30 days following ingestion of meals equivalent to 25% of their body mass. Within 1-3 days after ingestion, O2 consumption rates, intestinal nutrient uptake rates and uptake capacities peaked at 17, 6-26 and 11-24 times fasting levels, respectively. Small intestinal mass doubled, and other organs also increased in mass. Changes in blood chemistry included a 78% decline in PO2 and a large 'alkaline tide' associated with gastric acid section (i.e. a rise in blood pH and HCO3- concentrations and a fall in Cl- concentration). All of these values returned to fasting levels by the time of defecation at 8-14 days. The response of O2 consumption (referred to as specific dynamic action, SDA) is the largest, and the upregulation of intestinal nutrient transporters the second largest, response reported for any vertebrate upon feeding. The SDA is a large as the factorial rise in O2 consumption measured in mammalian sprinters and is sustained for much longer. The extra energy expended for digestion is equivalent to 32% of the meal's energy yield, with much of it being measured before the prey energy was absorbed. PMID:7782719

  18. A Distributed Python HPC Framework: ODIN, PyTrilinos, & Seamless

    SciTech Connect

    Grant, Robert

    2015-11-23

    Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports the DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.

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

    SciTech Connect

    Hart, William Eugene

    2010-11-01

    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.

  20. A pseudo-parallel Python environment for database curation

    E-print Network

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

    2007-11-13

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

  1. A cross-validation package driving Netica with python

    USGS Publications Warehouse

    Fienen, Michael N.; Plant, Nathaniel G.

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Parviainen, Hannu

    2015-07-01

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

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

    PubMed

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

    2014-07-01

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

  4. PyORBIT: A Python Shell For ORBIT

    SciTech Connect

    Jean-Francois Ostiguy; Jeffrey Holmes

    2003-07-01

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

  5. PyRAT (python radiography analysis tool): overview

    SciTech Connect

    Armstrong, Jerawan C; Temple, Brian A; Buescher, Kevin L

    2011-01-14

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

  6. Python package for model STructure ANalysis (pySTAN)

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  7. Burmese Pythons in South Florida: Scientific Support for Invasive Species Management1

    E-print Network

    Mazzotti, Frank

    -- such as the common boa (Boa constrictor), green anaconda (Eunectes murinus), yellow anaconda (Eunectes notaeus pythons and common boas are known to be breeding. Boas have been breeding since approximately 1970

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

    PubMed

    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

    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

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

    USGS Publications Warehouse

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

    2014-01-01

    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.

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

    PubMed Central

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

    2014-01-01

    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

  11. Thermoregulation during gravidity in the children's python (Antaresia childreni): a test of the

    E-print Network

    Denardo, Dale

    Thermoregulation during gravidity in the children's python (Antaresia childreni): a test-existing maternal thermoregulatory behaviour. Despite its evolutionary relevance, thermoregulation during gravidity of reproductive status on thermoregulation. Reproductive females maintained higher and less variable body

  12. 6.189 A Gentle Introduction to Programming Using Python, January IAP 2010

    E-print Network

    Canelake, Sarina

    2010-01-01

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

  13. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  15. Obtaining and processing Daymet data using Python and ArcGIS

    USGS Publications Warehouse

    Bohms, Stefanie

    2013-01-01

    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.

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

    USGS Publications Warehouse

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

    2015-01-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

    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.

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

    PubMed

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

    2012-02-14

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

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

    PubMed

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

    2012-09-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. Gammapy - A Python package for {\\gamma}-ray astronomy

    E-print Network

    Donath, Axel; Arribas, Manuel P; King, Johannes; Owen, Ellis; Terrier, Régis; Reichardt, Ignasi; Harris, Jon; Bühler, Rolf; Klepser, Stefan

    2015-01-01

    In the past decade imaging atmospheric Cherenkov telescope arrays such as H.E.S.S., MAGIC, VERITAS, as well as the Fermi-LAT space telescope have provided us with detailed images and spectra of the {\\gamma}-ray universe for the first time. Currently the {\\gamma}-ray community is preparing to build the next-generation Cherenkov Telecope Array (CTA), which will be operated as an open observatory. Gammapy (available at https://github.com/gammapy/gammapy under the open-source BSD li- cense) is a new in-development Astropy affiliated package for high-level analysis and simulation of astronomical {\\gamma}-ray data. It is built on the scientific Python stack (Numpy, Scipy, matplotlib and scikit-image) and makes use of other open-source astronomy packages such as Astropy, Sherpa and Naima to provide a flexible set of tools for {\\gamma}-ray astronomers. We present an overview of the current Gammapy features and example analyses on real as well as simulated {\\gamma}-ray datasets. We would like Gammapy to become a commu...

  3. Python framework for kinetic modeling of electronically excited reaction pathways

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    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.

  4. SPOTting Model Parameters Using a Ready-Made Python Package

    PubMed Central

    Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

    2015-01-01

    The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function. PMID:26680783

  5. batman: BAsic Transit Model cAlculatioN in Python

    E-print Network

    Kreidberg, Laura

    2015-01-01

    I introduce batman, a Python package for modeling exoplanet transit light curves. The batman package supports calculation of light curves for any radially symmetric stellar limb darkening law, using a new integration algorithm for models that cannot be quickly calculated analytically. The code uses C extension modules to speed up model calculation and is parallelized with OpenMP. For a typical light curve with 100 data points in transit, batman can calculate one million quadratic limb-darkened models in 30 seconds with a single 1.7 GHz Intel Core i5 processor. The same calculation takes seven minutes using the four-parameter nonlinear limb darkening model (computed to 1 ppm accuracy). Maximum truncation error for integrated models is an input parameter that can be set as low as 0.001 ppm, ensuring that the community is prepared for the precise transit light curves we anticipate measuring with upcoming facilities. The batman package is open source and publicly available at https://github.com/lkreidberg/batman.

  6. Hyperopt: a Python library for model selection and hyperparameter optimization

    NASA Astrophysics Data System (ADS)

    Bergstra, James; Komer, Brent; Eliasmith, Chris; Yamins, Dan; Cox, David D.

    2015-01-01

    Sequential model-based optimization (also known as Bayesian optimization) is one of the most efficient methods (per function evaluation) of function minimization. This efficiency makes it appropriate for optimizing the hyperparameters of machine learning algorithms that are slow to train. The Hyperopt library provides algorithms and parallelization infrastructure for performing hyperparameter optimization (model selection) in Python. This paper presents an introductory tutorial on the usage of the Hyperopt library, including the description of search spaces, minimization (in serial and parallel), and the analysis of the results collected in the course of minimization. This paper also gives an overview of Hyperopt-Sklearn, a software project that provides automatic algorithm configuration of the Scikit-learn machine learning library. Following Auto-Weka, we take the view that the choice of classifier and even the choice of preprocessing module can be taken together to represent a single large hyperparameter optimization problem. We use Hyperopt to define a search space that encompasses many standard components (e.g. SVM, RF, KNN, PCA, TFIDF) and common patterns of composing them together. We demonstrate, using search algorithms in Hyperopt and standard benchmarking data sets (MNIST, 20-newsgroups, convex shapes), that searching this space is practical and effective. In particular, we improve on best-known scores for the model space for both MNIST and convex shapes. The paper closes with some discussion of ongoing and future work.

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

    PubMed

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

    2014-01-01

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

  8. BATMAN: BAsic Transit Model cAlculatioN in Python

    NASA Astrophysics Data System (ADS)

    Kreidberg, Laura

    2015-12-01

    I introduce BATMAN, a Python package for modeling exoplanet transit and eclipse light curves. The BATMAN package supports calculation of light curves for any radially symmetric stellar limb darkening law, using a new integration algorithm for models that cannot be quickly calculated analytically. The code uses C extension modules to speed up model calculation and is parallelized with OpenMP. For a typical light curve with 100 data points in transit, batman can calculate one million quadratic limb-darkened models in 30 s with a single 1.7 GHz Intel Core i5 processor. The same calculation takes seven minutes using the four-parameter nonlinear limb darkening model (computed to 1 ppm accuracy). Maximum truncation error for integrated models is an input parameter that can be set as low as 0.001 ppm, ensuring that the community is prepared for the precise transit light curves we anticipate measuring with upcoming facilities. The batman package is open source and publicly available at https://github.com/lkreidberg/batman.

  9. Oxygen transport is not compromised at high temperature in pythons.

    PubMed

    Fobian, Dannie; Overgaard, Johannes; Wang, Tobias

    2014-11-15

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

  10. Screening_mgmt: a Python module for managing screening data.

    PubMed

    Helfenstein, Andreas; Tammela, Päivi

    2015-02-01

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

  11. AstroML: Python-powered Machine Learning for Astronomy

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Bogaart, P. W.

    2008-12-01

    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.

  13. Prioritizing blood flow: cardiovascular performance in response to the competing demands of locomotion and digestion for the Burmese python, Python molurus.

    PubMed

    Secor, Stephen M; White, Scott E

    2010-01-01

    Individually, the metabolic demands of digestion or movement can be fully supported by elevations in cardiovascular performance, but when occurring simultaneously, vascular perfusion may have to be prioritized to either the gut or skeletal muscles. Burmese pythons (Python molurus) experience similar increases in metabolic rate during the digestion of a meal as they do while crawling, hence each would have an equal demand for vascular supply when these two actions are combined. To determine, for the Burmese python, whether blood flow is prioritized when snakes are digesting and moving, we examined changes in cardiac performance and blood flow in response to digestion, movement, and the combination of digestion and movement. We used perivascular blood flow probes to measure blood flow through the left carotid artery, dorsal aorta, superior mesenteric artery and hepatic portal vein, and to calculate cardiac output, heart rate and stroke volume. Fasted pythons while crawling experienced a 2.7- and 3.3-fold increase, respectively, in heart rate and cardiac output, and a 66% decrease in superior mesenteric flow. During the digestion of a rodent meal equaling in mass to 24.7% of the snake's body mass, heart rate and cardiac output increased by 3.3- and 4.4-fold, respectively. Digestion also resulted in respective 11.6- and 14.1-fold increases in superior mesenteric and hepatic portal flow. When crawling while digesting, cardiac output and dorsal aorta flow increased by only 21% and 9%, respectively, a modest increase compared with that when they start to crawl on an empty stomach. Crawling did triggered a significant reduction in blood flow to the digesting gut, decreasing superior mesenteric and hepatic portal flow by 81% and 47%, respectively. When faced with the dual demands of digestion and crawling, Burmese pythons prioritize blood flow, apparently diverting visceral supply to the axial muscles. PMID:20008365

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    E-print Network

    Revell, Liam

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed

    Yesylevskyy, Semen O

    2015-07-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  19. Enhancements to Ginga: a Python Package for Building Astronomical Data Viewers

    NASA Astrophysics Data System (ADS)

    Jeschke, E.; Inagaki, T.; Kackley, R.

    2015-09-01

    Ginga is a toolkit for building astronomical image viewers. The package is available under a BSD license at github.com and has undergone continuous development since its introduction at ADASS 2012. The package may may be of interest to software developers who are looking for a solution for integrating FITS or numpy-based data visualization into their python programs and end users interested in FITS viewers (via the example reference viewer). We present the updates and enhanced capabilities of the package, including: support for additional GUI toolkits, WCS-based image mosaicing, image overlays, customizable user interface bindings, support for python3 and more.

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

    NASA Astrophysics Data System (ADS)

    Houska, Tobias; Kraft, Philipp; Breuer, Lutz

    2015-04-01

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

  1. HOPE: A Python Just-In-Time compiler for astrophysical computations

    E-print Network

    Akeret, Joel; Amara, Adam; Refregier, Alexandre

    2014-01-01

    The Python programming language is becoming increasingly popular for scientific applications due to its simplicity, versatility, and the broad range of its libraries. A drawback of this dynamic language, however, is its low runtime performance which limits its applicability for large simulations and for the analysis of large data sets, as is common in astrophysics and cosmology. While various frameworks have been developed to address this limitation, most focus on covering the complete language set, and either force the user to alter the code or are not able to reach the full speed of an optimised native compiled language. In order to combine the ease of Python and the speed of C++, we developed HOPE, a specialised Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimisation on mathematical expressions at runtime. To enable the JIT compilation, the user only n...

  2. 77 FR 3329 - Injurious Wildlife Species; Listing Three Python Species and One Anaconda Species as Injurious...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-23

    ... inquiry in the Federal Register (73 FR 5784; January 31, 2008) soliciting available biological, economic..., 2010, we published a proposed rule in the Federal Register (75 FR 11808) to list Python molurus (which... (75 FR 38069; July 1, 2010). For the injurious wildlife evaluation in this final rule, in addition...

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

    SciTech Connect

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

    2010-11-29

    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.

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

    PubMed Central

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

    2014-01-01

    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

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

    USGS Multimedia Gallery

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

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

    ERIC Educational Resources Information Center

    Murrell, Elizabeth

    1998-01-01

    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)

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

    NASA Astrophysics Data System (ADS)

    Madsen, K.

    2013-12-01

    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.

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

    E-print Network

    Newman, Mark

    on the download link for your operating system (Windows or Mac), then download and install the appropriate file by its makers for free and is available for download on the Internet. To make best use of the book is as follows. 1. Open your web browser and go to www.python.org. Click on "down- load", and on the downloads

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

    E-print Network

    Castoe, Todd A.

    and organ physiology, regeneration, and regulation, with the most important example being the Burmese python tetrapods); 35 to 100% increases in the mass of the heart, liver, pancreas, small intestine, and kidneys of organ performance and regeneration. These animals are also readily obtained from commercial breeders

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

    PubMed Central

    Shah, Abhik; Woolf, Peter

    2009-01-01

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

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

    PubMed

    Shah, Abhik; Woolf, Peter

    2009-06-01

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

  12. Tomopy: A Python toolbox to perform X-Ray data proessing and image reconstruction.

    Energy Science and Technology Software Center (ESTSC)

    2014-01-30

    Tomopy is a Python toolbox to perform x-ray data processing, image reconstruction and data exchange tasks at synchrotron facilities. The dependencies of the software are currently as follows: -Python related python standard library (http://docs.python.org/2/library/) numpy (http://www.numpy.org/) scipy (http://scipy.org/) matplotlib (http://matplotlip.org/) sphinx (http://sphinx-doc.org) pil (http://www.pythonware.com/products/pil/) pyhdf (http://pysclint.sourceforge.net/pyhdf/) h5py (http://www.h5py.org) pywt (http://www.pybytes.com/pywavelets/) file.py (https://pyspec.svn.sourceforge.net/svnroot/pyspec/trunk/pyspec/ccd/files.py) -C/C++ related: gridec (anonymous?? C-code written back in 1997 that uses standard C library) fftw (http://www.fftw.org/) tomoRecon (multi-threaded C++ verion of gridrec. Author:more »Mark Rivers from APS. http://cars9.uchicago.edu/software/epics/tomoRecon.html) epics (http://www.aps.anl.gov/epics/)« less

  13. A MythTV Python API to complement the JustPlay Network

    E-print Network

    Deonier, Christian

    2008-01-01

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

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  15. Digestive physiology of the Burmese python: broad regulation of integrated performance.

    PubMed

    Secor, Stephen M

    2008-12-01

    As an apparent adaptation to predictably long episodes of fasting, the sit-and-wait foraging Burmese python experiences unprecedented regulation of gastrointestinal and cardiovascular performance with feeding and fasting. The ingestion of a meal signals the quiescent gut tissues to start secreting digestive acid and enzymes, to upregulate intestinal brush-border enzymes and nutrient transporters, and to grow. An integrated phenomenon, digestion is also characterized by increases in the mass, and presumably the function, of the heart, pancreas, liver and kidneys. Once digestion is complete, the python's stomach and small intestine rapidly downregulate performance. Much of the modulation of intestinal function can be explained by the 5-fold increase in microvillus length and apical surface area with feeding, and the subsequent shortening of the microvilli after digestion has finished. Digestion for the Burmese python is a relatively expensive endeavor, evident by the as much as a 44-fold increase in metabolic rate and equivalent in cost to as much as 37% of the meal's energy. Their large metabolic response is supported by substantial increases in ventilation and cardiac output and the apparent catabolism of glucose and lipids. Unmatched in the magnitude of its numerous physiological responses to feeding, the Burmese python is a very attractive model for examining the capacities and regulatory mechanisms of physiological performance. PMID:19043049

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

    USGS Publications Warehouse

    Reed, Robert N.; Snow, Ray W.

    2014-01-01

    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.

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  19. Molecular cloning and characterization of satellite DNA sequences from constitutive heterochromatin of the habu snake (Protobothrops flavoviridis, Viperidae) and the Burmese python (Python bivittatus, Pythonidae).

    PubMed

    Matsubara, Kazumi; Uno, Yoshinobu; Srikulnath, Kornsorn; Seki, Risako; Nishida, Chizuko; Matsuda, Yoichi

    2015-12-01

    Highly repetitive DNA sequences of the centromeric heterochromatin provide valuable molecular cytogenetic markers for the investigation of genomic compartmentalization in the macrochromosomes and microchromosomes of sauropsids. Here, the relationship between centromeric heterochromatin and karyotype evolution was examined using cloned repetitive DNA sequences from two snake species, the habu snake (Protobothrops flavoviridis, Crotalinae, Viperidae) and Burmese python (Python bivittatus, Pythonidae). Three satellite DNA (stDNA) families were isolated from the heterochromatin of these snakes: 168-bp PFL-MspI from P. flavoviridis and 196-bp PBI-DdeI and 174-bp PBI-MspI from P. bivittatus. The PFL-MspI and PBI-DdeI sequences were localized to the centromeric regions of most chromosomes in the respective species, suggesting that the two sequences were the major components of the centromeric heterochromatin in these organisms. The PBI-MspI sequence was localized to the pericentromeric region of four chromosome pairs. The PFL-MspI and the PBI-DdeI sequences were conserved only in the genome of closely related species, Gloydius blomhoffii (Crotalinae) and Python molurus, respectively, although their locations on the chromosomes were slightly different. In contrast, the PBI-MspI sequence was also in the genomes of P. molurus and Boa constrictor (Boidae), and additionally localized to the centromeric regions of eight chromosome pairs in B. constrictor, suggesting that this sequence originated in the genome of a common ancestor of Pythonidae and Boidae, approximately 86 million years ago. The three stDNA sequences showed no genomic compartmentalization between the macrochromosomes and microchromosomes, suggesting that homogenization of the centromeric and/or pericentromeric stDNA sequences occurred in the macrochromosomes and microchromosomes of these snakes. PMID:26205503

  20. Morphological Pulmonary Diffusion Capacity for Oxygen of Burmese Pythons (Python molurus): a Comparison of Animals in Healthy Condition and with Different Pulmonary Infections.

    PubMed

    Starck, J M; Weimer, I; Aupperle, H; Müller, K; Marschang, R E; Kiefer, I; Pees, M

    2015-11-01

    A qualitative and quantitative morphological study of the pulmonary exchange capacity of healthy and diseased Burmese pythons (Python molurus) was carried out in order to test the hypothesis that the high morphological excess capacity for oxygen exchange in the lungs of these snakes is one of the reasons why pathological processes extend throughout the lung parenchyma and impair major parts of the lungs before clinical signs of respiratory disease become apparent. Twenty-four Burmese pythons (12 healthy and 12 diseased) were included in the study. A stereology-based approach was used to quantify the lung parenchyma using computed tomography. Light microscopy was used to quantify tissue compartments and the respiratory exchange surface, and transmission electron microscopy was used to measure the thickness of the diffusion barrier. The morphological diffusion capacity for oxygen of the lungs and the anatomical diffusion factor were calculated. The calculated anatomical diffusion capacity was compared with published values for oxygen consumption of healthy snakes, and the degree to which the exchange capacity can be obstructed before normal physiological function is impaired was estimated. Heterogeneous pulmonary infections result in graded morphological transformations of pulmonary parenchyma involving lymphocyte migration into the connective tissue and thickening of the septal connective tissue, increasing thickness of the diffusion barrier and increasing transformation of the pulmonary epithelium into a columnar pseudostratified or stratified epithelium. The transformed epithelium developed by hyperplasia of ciliated cells arising from the tip of the faveolar septa and by hyperplasia of type II pneumocytes. These results support the idea that the lungs have a remarkable overcapacity for oxygen consumption and that the development of pulmonary disease continuously reduces the capacity for oxygen consumption. However, due to the overcapacity of the lungs, this reduction does not result in clinical signs and disease can progress unrecognized for an extended period. PMID:26410400

  1. Selected regulation of gastrointestinal acid-base secretion and tissue metabolism for the diamondback water snake and Burmese python.

    PubMed

    Secor, Stephen M; Taylor, Josi R; Grosell, Martin

    2012-01-01

    Snakes exhibit an apparent dichotomy in the regulation of gastrointestinal (GI) performance with feeding and fasting; frequently feeding species modestly regulate intestinal function whereas infrequently feeding species rapidly upregulate and downregulate intestinal function with the start and completion of each meal, respectively. The downregulatory response with fasting for infrequently feeding snakes is hypothesized to be a selective attribute that reduces energy expenditure between meals. To ascertain the links between feeding habit, whole-animal metabolism, and GI function and metabolism, we measured preprandial and postprandial metabolic rates and gastric and intestinal acid-base secretion, epithelial conductance and oxygen consumption for the frequently feeding diamondback water snake (Nerodia rhombifer) and the infrequently feeding Burmese python (Python molurus). Independent of body mass, Burmese pythons possess a significantly lower standard metabolic rate and respond to feeding with a much larger metabolic response compared with water snakes. While fasting, pythons cease gastric acid and intestinal base secretion, both of which are stimulated with feeding. In contrast, fasted water snakes secreted gastric acid and intestinal base at rates similar to those of digesting snakes. We observed no difference between fasted and fed individuals for either species in gastric or intestinal transepithelial potential and conductance, with the exception of a significantly greater gastric transepithelial potential for fed pythons at the start of titration. Water snakes experienced no significant change in gastric or intestinal metabolism with feeding. Fed pythons, in contrast, experienced a near-doubling of gastric metabolism and a tripling of intestinal metabolic rate. For fasted individuals, the metabolic rate of the stomach and small intestine was significantly lower for pythons than for water snakes. The fasting downregulation of digestive function for pythons is manifested in a depressed gastric and intestinal metabolism, which selectively serves to reduce basal metabolism and hence promote survival between infrequent meals. By maintaining elevated GI performance between meals, fasted water snakes incur the additional cost of tissue activity, which is expressed in a higher standard metabolic rate. PMID:22162867

  2. ExoData: A python package to handle large exoplanet catalogue data

    E-print Network

    Varley, Ryan

    2015-01-01

    Exoplanet science often involves using the system parameters of real exoplanets for tasks such as simulations, fitting routines, and target selection for proposals. Software that bridges the barrier between the catalogues and code enables users to improve the specific repeatability of results by facilitating the retrieval of exact system parameters used in an articles results along with unifying the equations and software used. As exoplanet science moves towards large data, gone are the days where researchers can recall the current population from memory. An interface able to query the population now becomes invaluable for target selection and population analysis. ExoData is a python interface and exploratory analysis tool for the Open Exoplanet Catalogue. It allows the loading of exoplanet systems into python as objects (Planet, Star, Binary etc) from which common orbital and system equations can be calculated and measured parameters retrieved. This allows researchers to use tested code of the common equatio...

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

    NASA Technical Reports Server (NTRS)

    Lang, Timothy J.

    2015-01-01

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

  4. Two-dimensional echocardiographic anatomy of the snake heart (Python molurus bivittatus).

    PubMed

    Snyder, P S; Shaw, N G; Heard, D J

    1999-01-01

    Two-dimensional echocardiography was performed on Burmese pythons (Python molurus bivittatus) to determine an optimal echocardiographic imaging technique for snakes and to describe the echocardiographic anatomy of the snake heart. Five snakes immobilized with tiletamine/zolazepam and maintained on isoflurane in oxygen were imaged in dorsal recumbency. The portion of the snake's body containing the heart was submerged in warm water to reduce the artifact created by air trapped between and under the scales. Imaging in sagittal planes demonstrated the caudal vena cava, sinus venous valve, right atrium, various portions of the ventricle, horizontal septum, the left aortic arch, and pulmonary artery. Transverse imaging depicted the spatial relationship of the left and right aortic arches and pulmonary artery and the horizontal septum. Basic knowledge of cardiac blood flow in the reptile was necessary to understand the echocardiographic anatomy. PMID:10023997

  5. Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1:Fortran, C, and Python Editions

    NASA Astrophysics Data System (ADS)

    Kaplan, G. H.; Bangert, J. A.; Barron, E. G.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

    2012-08-01

    The Naval Observatory Vector Astrometry Software (NOVAS) is a source - code library that provides common astrometric quantities and transformations to high precision. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS is used for a wide variety of applications, including the U.S. portions of The Astronomical Almanac and a number of telescope control systems. NOVAS uses IAU recommended models for Earth orientation, including the IAU 2006 precession theory, the IAU 2000A and 2000B nutation series, and diurnal rotation based on the celestial and terrestrial intermediate origins. Equinox - based quantities, such as sidereal time, are also supported. NOVAS Earth orientation calculations match those from SOFA at the sub - microarcsecond level for comparable transformations. NOVAS algorithms for aberration an d gravitational light deflection are equivalent, at the microarcsecond level, to those inherent in the current consensus VLBI delay algorithm. NOVAS can be easily connected to the JPL planetary/lunar ephemerides (e.g., DE405), and connections to IMCCE and IAA planetary ephemerides are planned. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and currently mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to exploit the object - oriented features of Python. In the Version 3.1 C edition, the ephemeris - access functions have been revised for use on 64 - bit systems and for improved performance in general. NOVAS source code, auxiliary files, and documentation are available from the USNO website (http://aa.usno.navy.mil/software/novas/novas_info.php).

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

    PubMed Central

    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.; Yandell, Mark; Warren, Wesley C.; Secor, Stephen M.; Pollock, David D.

    2013-01-01

    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

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

    PubMed

    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

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Lin, J. W.

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    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.

  11. ObsPy: A Python Toolbox for Seismology and Seismological Observatories

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    Python combines the power of a full-blown programming language with the flexibility and accessibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. ObsPy 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.

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

    PubMed Central

    Pecevski, Dejan; Kappel, David; Jonke, Zeno

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  14. Structural flexibility of the intestine of Burmese python in response to feeding.

    PubMed

    Starck, J M; Beese, K

    2001-01-01

    The small intestine of Burmese pythons, Python molurus bivittatus, undergoes a remarkable size increase shortly after feeding. We studied the dynamics, reversibility and repeatability of organ size changes using noninvasive imaging techniques. We employed light and electron microscopy, flow cytometry and immunohistology to study the cytological mechanisms that drive the size changes of the small intestine. Within 2 days of feeding, the size of the small intestine increased to up to three times the fasting value. The size changes were fully reversible and could be elicited repeatedly by feeding. These enormous size changes were possible because the mucosal epithelium of the small intestine is a transitional epithelium that allows for considerable size changes without cell proliferation. Histological evidence suggested that a fluid pressure-pump system (lymphatic, blood pressure) was the driving force that inflated the intestinal villi. The rates of cell proliferation were not elevated immediately after feeding but peaked 1 week later when small intestine size was already declining. In contrast to the current paradigm, we suggest that the small intestine is not part of the previously proposed 'pay-before-pumping' model. Instead, the size of the python's small intestine may be upregulated without major metabolic investment. It can occur even if the individual is energetically exhausted. An evolutionary perspective of the transitional epithelium mechanism suggests superior functionality compared with the pay-before-pumping model because it allows for long periods of fasting and depletion of energy reserves, while still enabling the snake to digest prey and absorb nutrients. PMID:11136618

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

    PubMed Central

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

    2008-01-01

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

  16. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

    PubMed

    Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

    2014-01-01

    pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). PMID:24420968

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

    NASA Astrophysics Data System (ADS)

    Starn, J. J.

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Hughes, J. D.; White, J.

    2013-12-01

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

  1. ? Scope: python based scientific workbench with visualization tool for MDSplus data

    NASA Astrophysics Data System (ADS)

    Shiraiwa, S.

    2014-10-01

    ? Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. ?Scope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on ?Scope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

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

    SciTech Connect

    Sainio, J.

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Schreier, Franz; García, Sebastián Gimeno

    2013-05-01

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

  4. Powerlaw: a Python package for analysis of heavy-tailed distributions.

    PubMed

    Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Catalog identifier: AEMB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 33625 No. of bytes in distributed program, including test data, etc.: 410064 Distribution format: tar.gz Programming language: Python. Computer: i386, x86-64. Operating system: Linux, Mac OSX. RAM: 2+ Gigabytes Classification: 7. External routines: NumPy, SciPy, Matplotlib, Cython Catalog identifier of previous version: AEMB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760 Does the new version supercede the previous version?: Yes Nature of problem: Dynamics of open quantum systems Solution method: Numerical solutions to Lindblad, Floquet-Markov, and Bloch-Redfield master equations, as well as the Monte Carlo wave function method. Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Restrictions: Problems must meet the criteria for using the master equation in Lindblad, Floquet-Markov, or Bloch-Redfield form. Running time: A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.

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

    PubMed Central

    Wiseman, Richard; Watt, Caroline

    2015-01-01

    Perceptual science has frequently benefited from studying illusions created outside of academia. Here, we describe a striking, but little-known, example of inattentional blindness from the British comedy series “Monty Python's Flying Circus.” Viewers fail to attend to several highly incongruous characters in the sketch, despite these characters being clearly visible onscreen. The sketch has the potential to be a valuable research and teaching resource, as well as providing a vivid illustration of how people often fail to see something completely different. PMID:26034570

  7. PySLHA: a Pythonic interface to SUSY Les Houches Accord data

    E-print Network

    Andy Buckley

    2015-07-28

    This paper describes the PySLHA package, a Python language module and program collection for reading, writing and visualising SUSY model data in the SLHA format. PySLHA can read and write SLHA data in a very general way, including the official SLHA2 extension and user customisations, and with arbitrarily deep indexing of data block entries and a dedicated, intuitive interface for particle data and decay information. PySLHA can additionally read and write the legacy ISAWIG model format, and provides format conversion scripts. The draft SLHA3 XSECTION feature is also fully supported. A publication-quality mass spectrum & decay chain plotting tool, slhaplot, is also included.

  8. A Python-based GUI Software to Calculate Times of Maximum and Minimum: Xtrema

    NASA Astrophysics Data System (ADS)

    Bahar, E.; Šenavc?, H. V.; Ba?türk, Ö.

    2015-07-01

    We develop a python-based GUI code, Xtrema, that can be used for calculating the times of minimum for eclipsing binary systems as well as the maxima of pulsating stars. Xtrema performs minimum/maximum time determination from multi-cycle light curves (i.e., 1000) such as from Kepler/CoRoT data, using different methods, and also provides error estimates. Despite the coarse sampling rate of the long cadence Kepler data, Xtrema can be used to determine reliable times of minimum/maximum by combining successive minimum/maximum profiles as defined by the user.

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  16. Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit

    SciTech Connect

    Daily, Jeffrey A.; Lewis, Robert R.

    2011-11-30

    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.

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

    PubMed

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

    2014-09-01

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

  18. PylotDB - A Database Management, Graphing, and Analysis Tool Written in Python

    Energy Science and Technology Software Center (ESTSC)

    2012-01-04

    PylotDB, written completely in Python, provides a user interface (UI) with which to interact with, analyze, graph data from, and manage open source databases such as MySQL. The UI mitigates the user having to know in-depth knowledge of the database application programming interface (API). PylotDB allows the user to generate various kinds of plots from user-selected data; generate statistical information on text as well as numerical fields; backup and restore databases; compare database tables acrossmore »different databases as well as across different servers; extract information from any field to create new fields; generate, edit, and delete databases, tables, and fields; generate or read into a table CSV data; and similar operations. Since much of the database information is brought under control of the Python computer language, PylotDB is not intended for huge databases for which MySQL and Oracle, for example, are better suited. PylotDB is better suited for smaller databases that might be typically needed in a small research group situation. PylotDB can also be used as a learning tool for database applications in general.« less

  19. PylotDB - A Database Management, Graphing, and Analysis Tool Written in Python

    SciTech Connect

    2012-01-04

    PylotDB, written completely in Python, provides a user interface (UI) with which to interact with, analyze, graph data from, and manage open source databases such as MySQL. The UI mitigates the user having to know in-depth knowledge of the database application programming interface (API). PylotDB allows the user to generate various kinds of plots from user-selected data; generate statistical information on text as well as numerical fields; backup and restore databases; compare database tables across different databases as well as across different servers; extract information from any field to create new fields; generate, edit, and delete databases, tables, and fields; generate or read into a table CSV data; and similar operations. Since much of the database information is brought under control of the Python computer language, PylotDB is not intended for huge databases for which MySQL and Oracle, for example, are better suited. PylotDB is better suited for smaller databases that might be typically needed in a small research group situation. PylotDB can also be used as a learning tool for database applications in general.

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

    PubMed

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

    2002-11-01

    As ectothermic vertebrates, reptiles undergo diurnal and seasonal changes in body temperature, which affect many biological functions. In conjunction with a general review regarding the effects of temperature on digestion in reptiles, we describe the effects of various temperatures (20-35 degrees C) on the metabolic response to digestion in the Burmese python (Python molurus). The snakes were fed mice amounting to 20% of their body weight and gas exchange (oxygen uptake and CO(2) production) were measured until digestion had ended and gas exchange returned to fasting levels. Elevated temperature was associated with a faster and larger metabolic increase after ingestion, and the time required to return to fasting levels was markedly longer at low temperature. The factorial increase between fasting oxygen consumption (VO(2)) and maximal VO(2) during digestion was, however, similar at all temperatures studied. Furthermore, the integrated SDA response was not affected by temperature suggesting the costs associated with digestion are temperature-independent. Other studies on reptiles show that digestive efficiency is only marginally affected by temperature and we conclude that selection of higher body temperatures during digestion (postprandial thermophilic response) primarily reduces the time required for digestion. PMID:12443910

  1. PyCon 2008: Presentation Proposal Using Python To Teach Object-Oriented Programming in CS1

    E-print Network

    Goldwasser, Michael

    PyCon 2008: Presentation Proposal Using Python To Teach Object-Oriented Programming in CS1 Michael students to grasp, and that teaching those principles takes time away from the basics that are needed in CS often introduced with a pro- cedural paradigm. For those teaching object orientation in CS1, Java

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

    E-print Network

    Castoe, Todd A.

    for the Evolution of Snake Venom Jacobo Reyes-Velasco,1 Daren C. Card,1 Audra L. Andrew,1 Kyle J. Shaney,1 Richard H diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging compared with all other python genes. We propose a model for the evolution of snake venoms in which venom

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  4. Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation.

    PubMed

    Wall, Christopher E; Cozza, Steven; Riquelme, Cecilia A; McCombie, W Richard; Heimiller, Joseph K; Marr, Thomas G; Leinwand, Leslie A

    2011-01-01

    The infrequently feeding Burmese python (Python molurus) experiences significant and rapid postprandial cardiac hypertrophy followed by regression as digestion is completed. To begin to explore the molecular mechanisms of this response, we have sequenced and assembled the fasted and postfed Burmese python heart transcriptomes with Illumina technology using the chicken (Gallus gallus) genome as a reference. In addition, we have used RNA-seq analysis to identify differences in the expression of biological processes and signaling pathways between fasted, 1 day postfed (DPF), and 3 DPF hearts. Out of a combined transcriptome of ?2,800 mRNAs, 464 genes were differentially expressed. Genes showing differential expression at 1 DPF compared with fasted were enriched for biological processes involved in metabolism and energetics, while genes showing differential expression at 3 DPF compared with fasted were enriched for processes involved in biogenesis, structural remodeling, and organization. Moreover, we present evidence for the activation of physiological and not pathological signaling pathways in this rapid, novel model of cardiac growth in pythons. Together, our data provide the first comprehensive gene expression profile for a reptile heart. PMID:21045117

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

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

    SciTech Connect

    Morley, Steven K; Welling, Daniel T; Koller, Josef; Larsen, Brian A; Henderson, Michael G

    2010-01-01

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

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

    PubMed Central

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

    2014-01-01

    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

  9. Python based integration of GEM detector electronics with JET data acquisition system

    NASA Astrophysics Data System (ADS)

    Zabo?otny, Wojciech M.; Byszuk, Adrian; Chernyshova, Maryna; Cieszewski, Rados?aw; Czarski, Tomasz; Dalley, Simon; Hogben, Colin; Jakubowska, Katarzyna L.; Kasprowicz, Grzegorz; Po?niak, Krzysztof; Rzadkiewicz, Jacek; Scholz, Marek; Shumack, Amy

    2014-11-01

    This paper presents the system integrating the dedicated measurement and control electronic systems for Gas Electron Multiplier (GEM) detectors with the Control and Data Acquisition system (CODAS) in the JET facility in Culham, England. The presented system performs the high level procedures necessary to calibrate the GEM detector and to protect it against possible malfunctions or dangerous changes in operating conditions. The system also allows control of the GEM detectors from CODAS, setting of their parameters, checking their state, starting the plasma measurement and to reading the results. The system has been implemented using the Python language, using the advanced libraries for implementation of network communication protocols, for object based hardware management and for data processing.

  10. PySLHA: a Pythonic interface to SUSY Les Houches Accord data

    NASA Astrophysics Data System (ADS)

    Buckley, Andy

    2015-10-01

    This paper describes the PySLHA package, a Python language module and program collection for reading, writing and visualising SUSY model data in the SLHA format. PySLHA can read and write SLHA data in a very general way, including the official SLHA2 extension and user customisations, and with arbitrarily deep indexing of data block entries and a dedicated, intuitive interface for particle data and decay information. The draft SLHA3 XSECTION feature is also fully supported. PySLHA can additionally read and write the legacy ISAWIG model format, and provides format conversion scripts. A publication-quality mass spectrum and decay chain plotting tool, slhaplot, is included in the package.

  11. uPy: a ubiquitous computer graphics Python API with Biological Modeling Applications

    PubMed Central

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

    2015-01-01

    In this paper we describe uPy, an extension module for the Python programming language that provides a uniform abstraction of the APIs of several 3D computer graphics programs called hosts, including: Blender, Maya, Cinema4D, and DejaVu. A plugin written with uPy is a unique piece of code that will run in all uPy-supported hosts. We demonstrate the creation of complex plug-ins for molecular/cellular modeling and visualization and discuss how uPy can more generally simplify programming for many types of projects (not solely science applications) intended for multi-host distribution. uPy is available at http://upy.scripps.edu PMID:24806987

  12. naima: a Python package for inference of relativistic particle energy distributions from observed nonthermal spectra

    E-print Network

    Zabalza, Víctor

    2015-01-01

    The ultimate goal of the observation of nonthermal emission from astrophysical sources is to understand the underlying particle acceleration and evolution processes, and few tools are publicly available to infer the particle distribution properties from the observed photon spectra from X-ray to VHE gamma rays. Here I present naima, an open source Python package that provides models for nonthermal radiative emission from homogeneous distribution of relativistic electrons and protons. Contributions from synchrotron, inverse Compton, nonthermal bremsstrahlung, and neutral-pion decay can be computed for a series of functional shapes of the particle energy distributions, with the possibility of using user-defined particle distribution functions. In addition, naima provides a set of functions that allow to use these models to fit observed nonthermal spectra through an MCMC procedure, obtaining probability distribution functions for the particle distribution parameters. Here I present the models and methods availabl...

  13. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

    PubMed Central

    Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen; Pandurangan, Arun Prasad; Sahota, Harpal; Topf, Maya

    2015-01-01

    Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists. PMID:26306092

  14. uPy: a ubiquitous CG Python API with biological-modeling applications.

    PubMed

    Autin, Ludovic; Johnson, Graham; Hake, Johan; Olson, Arthur; Sanner, Michel

    2012-01-01

    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

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

    PubMed

    Hull, Michael J; Willshaw, David J

    2013-01-01

    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

  16. Heavy Analysis and Light Virtualization of Water Use Data with Python

    NASA Astrophysics Data System (ADS)

    Kim, H.; Bijoor, N.; Famiglietti, J. S.

    2014-12-01

    Water utilities possess a large amount of water data that could be used to inform urban ecohydrology, management decisions, and conservation policies, but such data are rarely analyzed owing to difficulty in analyzation, visualization, and interpretion. We have developed a high performance computing resource for this purpose. We partnered with 6 water agencies in Orange County who provided 10 years of parcel-level monthly water use billing data for a pilot study. The first challenge that we overcame was to refine all human errors and unify the many different formats of data over all agencies. Second, we tested and applied experimental approaches to the data, including complex calculations, with high efficiency. Third, we developed a method to refine the data so it can be browsed along a time series index and/or geo-spatial queries with high efficiency, no matter how large the data. Python scientific libraries were the best match to handle arbitrary data sets in our environment. Further milestones include agency entry, sets of formulae, and maintaining 15M rows X 70 columns of data with high performance of cpu-bound processes. To deal with billions of rows, we performed an analysis virtualization stack by leveraging iPython parallel computing. With this architecture, one agency could be considered one computing node or virtual machine that maintains its own data sets respectively. For example, a big agency could use a large node, and a small agency could use a micro node. Under the minimum required raw data specs, more agencies could be analyzed. The program developed in this study simplifies data analysis, visualization, and interpretation of large water datasets, and can be used to analyze large data volumes from water agencies nationally or worldwide.

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

    SciTech Connect

    Woodruff, David L.; Watson, Jean-Paul

    2010-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Tlp Lavrijsen, Wim

    2012-12-01

    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.

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

    USGS Publications Warehouse

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

    2009-01-01

    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, but presumably include climate or are correlated with climate. We compiled monthly rainfall and temperature statistics from 149 stations located near the edge of the python's native range in Asia (Pakistan east to China and south to Indonesia). The southern and eastern native range limits extend to saltwater, leaving unresolved the species' climatic tolerances in those areas. The northern and western limits are associated with cold and aridity respectively. We plotted mean monthly rainfall against mean monthly temperature for the 149 native range weather stations to identify the climate conditions inhabited by pythons in their native range, and mapped areas of the coterminous United States with the same climate today and projected for the year 2100. We accounted for both dry-season aestivation and winter hibernation (under two scenarios of hibernation duration). The potential distribution was relatively insensitive to choice of scenario for hibernation duration. US areas climatically matched at present ranged up the coasts and across the south from Delaware to Oregon, and included most of California, Texas, Oklahoma, Arkansas, Louisiana, Mississippi, Alabama, Florida, Georgia, and South and North Carolina. By the year 2100, projected areas of potential suitable climate extend northward beyond the current limit to include parts of the states of Washington, Colorado, Illinois, Indiana, Ohio, West Virginia, Pennsylvania, New Jersey, and New York. Thus a substantial portion of the mainland US is potentially vulnerable to this ostensibly tropical invader. ?? 2008 Springer Science+Business Media B.V.

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

    PubMed

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

    2014-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Verkaik, J.

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Peterschmitt, Jean-Yves; Doutriaux, Charles

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Álvarez-Gómez, José A.

    2014-05-01

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

  5. Increased blood oxygen affinity during digestion in the snake Python molurus.

    PubMed

    Overgaard, Johannes; Wang, Tobias

    2002-11-01

    Many snakes exhibit large increases in metabolic rate during digestion that place extensive demands on efficient oxygen transport. In the present study, we describe blood oxygen affinity following three weeks of fasting and 48 h after feeding in the Burmese python (Python molurus). We also report simultaneous measurements of arterial blood gases and haematological parameters. Arterial blood was obtained from chronically implanted catheters, and blood oxygen-dissociation curves were constructed from oxygen content measurements at known oxygen partial pressure (P(O(2))) values at 2% and 5% CO(2). Arterial pH remained constant at approximately 7.6 after feeding, but digestion was associated with an approximately 6 mmol l(-1) increase in [HCO(3)(-)], while CO(2) partial pressure (P(CO(2))) increased from 2.21+/-0.13 kPa in fasted animals to 2.89+/-0.17 kPa at 48 h after feeding. Blood oxygen affinity in vivo was predicted on the basis of pH in vivo and the blood oxygen-dissociation curves obtained in vitro. The blood oxygen affinity in vivo increased during digestion, with P(50) values decreasing from 4.58+/-0.11 kPa to 3.53+/-0.24 kPa. This increase was associated with a significant decrease in the red blood cell [NTP]/[Hb(4)] ratio (relationship between the concentrations of organic phosphates and total haemoglobin) and a significant decrease in mean cellular haemoglobin content, which is indicative of swelling of the red blood cells. Our data for blood oxygen affinity and arterial oxygen levels, together with previously published values of oxygen uptake and blood flows, allow for a quantitative evaluation of oxygen transport during digestion. This analysis shows that a large part of the increased metabolism during digestion is supported by an increased venous extraction, while arterial P(O(2)) (Pa(O(2))) and haemoglobin saturation do not vary with digestive status. Thus, we predict that venous P(O(2)) (Pv(O(2))) is reduced from a fasting value of 5.2 kPa to 1.6 kPa during digestion. PMID:12324542

  6. Python tools for rapid development, calibration, and analysis of generalized groundwater-flow models

    NASA Astrophysics Data System (ADS)

    Starn, J. J.; Belitz, K.

    2014-12-01

    National-scale water-quality data sets for the United States have been available for several decades; however, groundwater models to interpret these data are available for only a small percentage of the country. Generalized models may be adequate to explain and project groundwater-quality trends at the national scale by using regional scale models (defined as watersheds at or between the HUC-6 and HUC-8 levels). Coast-to-coast data such as the National Hydrologic Dataset Plus (NHD+) make it possible to extract the basic building blocks for a model anywhere in the country. IPython notebooks have been developed to automate the creation of generalized groundwater-flow models from the NHD+. The notebook format allows rapid testing of methods for model creation, calibration, and analysis. Capabilities within the Python ecosystem greatly speed up the development and testing of algorithms. GeoPandas is used for very efficient geospatial processing. Raster processing includes the Geospatial Data Abstraction Library and image processing tools. Model creation is made possible through Flopy, a versatile input and output writer for several MODFLOW-based flow and transport model codes. Interpolation, integration, and map plotting included in the standard Python tool stack also are used, making the notebook a comprehensive platform within on to build and evaluate general models. Models with alternative boundary conditions, number of layers, and cell spacing can be tested against one another and evaluated by using water-quality data. Novel calibration criteria were developed by comparing modeled heads to land-surface and surface-water elevations. Information, such as predicted age distributions, can be extracted from general models and tested for its ability to explain water-quality trends. Groundwater ages then can be correlated with horizontal and vertical hydrologic position, a relation that can be used for statistical assessment of likely groundwater-quality conditions. Convolution with age distributions can be used to quickly ascertain likely future water-quality conditions. Although these models are admittedly very general and are still being tested, the hope is that they will be useful for answering questions related to water quality at the regional scale.

  7. pyAudioAnalysis: An Open-Source Python Library for Audio Signal Analysis

    PubMed Central

    Giannakopoulos, Theodoros

    2015-01-01

    Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal analysis (e.g. audio-visual analysis of online videos for content-based recommendation), etc. This paper presents pyAudioAnalysis, an open-source Python library that provides a wide range of audio analysis procedures including: feature extraction, classification of audio signals, supervised and unsupervised segmentation and content visualization. pyAudioAnalysis is licensed under the Apache License and is available at GitHub (https://github.com/tyiannak/pyAudioAnalysis/). Here we present the theoretical background behind the wide range of the implemented methodologies, along with evaluation metrics for some of the methods. pyAudioAnalysis has been already used in several audio analysis research applications: smart-home functionalities through audio event detection, speech emotion recognition, depression classification based on audio-visual features, music segmentation, multimodal content-based movie recommendation and health applications (e.g. monitoring eating habits). The feedback provided from all these particular audio applications has led to practical enhancement of the library. PMID:26656189

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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.

  9. Publishing Earth Science Data with Python: A Case Study with Regional Climate Model Output

    NASA Astrophysics Data System (ADS)

    Green, G. M.; Tedesco, M.; Alexander, P. M.; Fettweis, X.; Datta, R.

    2014-12-01

    As datasets become larger, with the increasing spatial and temporal resolution of both observed and modeled data, the need to provide a service that makes them more accessible to the scientific community is increasing. At the same time, open-source tools are making more options available, but it can be difficult to determine what the viable alternatives are. In this presentation, we discuss a software architecture and data distribution model that was adopted to distribute the outputs of the regional climate model Modèle Atmosphérique Régional (MAR). This involved summarizing a large static dataset for ad-hoc query and data download in a web-based application called "MAR Explorer", and making the application available using a cloud-based Amazon server. The application was built using open-source Python tools, and is available at cryocity.org. We discuss the web application development tools and data processing methods used to distribute the above mentioned dataset, with the goal of making these methods more easily accessible to others needing to distribute similar data.

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

    SciTech Connect

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

    2011-11-01

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

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

    PubMed Central

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

    2014-01-01

    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

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

    SciTech Connect

    Turk, M.; /KIPAC, Menlo Park

    2008-09-30

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

  13. pyAudioAnalysis: An Open-Source Python Library for Audio Signal Analysis.

    PubMed

    Giannakopoulos, Theodoros

    2015-01-01

    Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal analysis (e.g. audio-visual analysis of online videos for content-based recommendation), etc. This paper presents pyAudioAnalysis, an open-source Python library that provides a wide range of audio analysis procedures including: feature extraction, classification of audio signals, supervised and unsupervised segmentation and content visualization. pyAudioAnalysis is licensed under the Apache License and is available at GitHub (https://github.com/tyiannak/pyAudioAnalysis/). Here we present the theoretical background behind the wide range of the implemented methodologies, along with evaluation metrics for some of the methods. pyAudioAnalysis has been already used in several audio analysis research applications: smart-home functionalities through audio event detection, speech emotion recognition, depression classification based on audio-visual features, music segmentation, multimodal content-based movie recommendation and health applications (e.g. monitoring eating habits). The feedback provided from all these particular audio applications has led to practical enhancement of the library. PMID:26656189

  14. Magnetic resonance imaging volumetry for noninvasive measures of phenotypic flexibility during digestion in Burmese pythons.

    PubMed

    Hansen, Kasper; Pedersen, Pil Birkefeldt Møller; Pedersen, Michael; Wang, Tobias

    2013-01-01

    Pythons are renowned for the profound phenotypical flexibility of their visceral organs in response to ingestion of large meals following prolonged fasting. Traditionally, the phenotypic changes are studied by determining organ mass of snakes killed at different times during digestion. Here we evaluate the use of magnetic resonance imaging (MRI) for in vivo measurements of the visceral organs in fasting and digesting snakes. Twelve snakes were MRI scanned immediately before the organs were removed and weighed to provide direct comparison of the two methods. Both methods provided similar estimates for the mass of liver, gallbladder, and pancreas, whereas MRI overestimated the size of the heart and small intestine, probably because blood and digesta contributed to the volume determined by MRI. The correlations were used to derive wet organ mass from MRI-based volumes to evaluate the mass development through repeated MRI scans of five digesting snakes. MRI was performed at fasting and 24, 48, 72, 132, and 500 h after eating a meal corresponding to 25% of body mass. This observation period revealed a reversible volume upregulation of the visceral organs, supporting the view that successive MRI facilitates in vivo investigations of structural changes accompanied by digestion. PMID:23303329

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed

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

    2013-01-01

    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

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

    PubMed

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

    2014-10-01

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

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

    PubMed Central

    Schleip, Wulf D.; O’Shea, Mark

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Campbell, Carl E

    1951-01-01

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

  20. 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

    Reed, Robert N.; Rodda, Gordon H.

    2009-01-01

    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.

  1. CellLab-CTS 2015: a Python library for continuous-time stochastic cellular automaton modeling using Landlab

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state-code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS model. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.

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

    PubMed

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

    2015-05-01

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

  3. Novel phospholipase A2 inhibitors from python serum are potent peptide antibiotics.

    PubMed

    Samy, Ramar Perumal; Thwin, Maung Maung; Stiles, Brad G; Satyanarayana-Jois, Seetharama; Chinnathambi, Arunachalam; Zayed, M E; Alharbi, Sulaiman Ali; Siveen, Kodappully Sivaraman; Sikka, Sakshi; Kumar, Alan Prem; Sethi, Gautam; Lim, Lina Hsiu Kim

    2015-04-01

    Antimicrobial peptides (AMPs) play a vital role in defense against resistant bacteria. In this study, eight different AMPs synthesized from Python reticulatus serum protein were tested for bactericidal activity against various Gram-positive and Gram-negative bacteria (Staphylococcus aureus, Burkholderia pseudomallei (KHW and TES strains), and Proteus vulgaris) using a disc-diffusion method (20 ?g/disc). Among the tested peptides, phospholipase A2 inhibitory peptide (PIP)-18[59-76], ?-Asp65-PIP[59-67], D-Ala66-PNT.II, and D60,65E-PIP[59-67] displayed the most potent bactericidal activity against all tested pathogens in a dose-dependent manner (100-6.8 ?g/ml), with a remarkable activity noted against S. aureus at 6.8 ?g/ml dose within 6 h of incubation. Determination of minimum inhibitory concentrations (MICs) by a micro-broth dilution method at 100-3.125 ?g/ml revealed that PIP-18[59-76], ?-Asp65-PIP[59-67] and D-Ala66-PNT.II peptides exerted a potent inhibitory effect against S. aureus and B. pseudomallei (KHW) (MICs 3.125 ?g/ml), while a much less inhibitory potency (MICs 12.5 ?g/ml) was noted for ?-Asp65-PIP[59-67] and D-Ala66-PNT.II peptides against B. pseudomallei (TES). Higher doses of peptides had no effect on the other two strains (i.e., Klebsiella pneumoniae and Streptococcus pneumoniae). Overall, PIP-18[59-76] possessed higher antimicrobial activity than that of chloramphenicol (CHL), ceftazidime (CF) and streptomycin (ST) (30 ?g/disc). When the two most active peptides, PIP-18[59-76] and ?-Asp65-PIP[59-67], were applied topically at a 150 mg/kg dose for testing wound healing activity in a mouse model of S. aureus infection, the former accelerates faster wound healing than the latter peptide at 14 days post-treatment. The western blot data suggest that the topical application of peptides (PIP-18[59-67] and ?-Asp65-PIP[59-67]) modulates NF-kB mediated wound repair in mice with relatively little haemolytic (100-1.56 ?g/ml) and cytotoxic (1000-3.125 ?g/ml) effects evident on human cells in vitro. PMID:25583073

  4. Short Sage history Status Viability? Freedom! Python Interfaces SageTEX Combinatorics Sage-Combinat Sage: a free open-source

    E-print Network

    Goubet, Olivier

    1/49 Short Sage history Status Viability? Freedom! Python Interfaces SageTEX Combinatorics Sage-Combinat Sage: a free open-source general purpose mathematics software system Nicolas M. Thiéry Laboratoire de, William Stein, ... Rencontres Mondiales du Logiciel Libre, July 9th of 2013 #12;2/49 Short Sage history

  5. 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

    McFalls, Joseph A.; And Others

    1986-01-01

    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.…

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

    NASA Astrophysics Data System (ADS)

    Cole, P.

    2012-12-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  9. Documentation and Instructions for Running Two Python Scripts that Aid in Setting up 3D Measurements using the Polytec 3D Scanning Laser Doppler Vibrometer.

    SciTech Connect

    Rohe, Daniel Peter

    2015-08-24

    Sandia National Laboratories has recently purchased a Polytec 3D Scanning Laser Doppler Vibrometer for vibration measurement. This device has proven to be a very nice tool for making vibration measurements, and has a number of advantages over traditional sensors such as accelerometers. The non-contact nature of the laser vibrometer means there is no mass loading due to measuring the response. Additionally, the laser scanning heads can position the laser spot much more quickly and accurately than placing an accelerometer or performing a roving hammer impact. The disadvantage of the system is that a significant amount of time must be invested to align the lasers with each other and the part so that the laser spots can be accurately positioned. The Polytec software includes a number of nice tools to aid in this procedure; however, certain portions are still tedious. Luckily, the Polytec software is readily extensible by programming macros for the system, so tedious portions of the procedure can be made easier by automating the process. The Polytec Software includes a WinWrap (similar to Visual Basic) editor and interface to run macros written in that programming language. The author, however, is much more proficient in Python, and the latter also has a much larger set of libraries that can be used to create very complex macros, while taking advantage of Python’s inherent readability and maintainability.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Yi, Guilian; Sui, Yunkang; Du, Jiazheng

    2011-06-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Sandner, Raimar; Vukics, András

    2014-09-01

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

  13. Tribological analysis of the ventral scale structure in a Python regius in relation to laser textured surfaces

    NASA Astrophysics Data System (ADS)

    Abdel-Aal, H. A.; El Mansori, M.

    2013-09-01

    Laser texturing is one of the leading technologies applied to modify surface topography. To date, however, a standardized procedure to generate deterministic textures is virtually non-existent. In nature, especially in squamata, there are many examples of deterministic structured textures that allow species to control friction and condition their tribological response for efficient function. In this work, we draw a comparison between industrial surfaces and reptilian surfaces. We chose the Python regius species as a bio-analogue with a deterministic surface. We first study the structural make up of the ventral scales of the snake (both construction and metrology). We further compare the metrological features of the ventral scales to experimentally recommended performance indicators of industrial surfaces extracted from open literature. The results indicate the feasibility of engineering a laser textured surface based on the reptilian ornamentation constructs. It is shown that the metrological features, key to efficient function of a rubbing deterministic surface, are already optimized in the reptile. We further show that optimization in reptilian surfaces is based on synchronizing surface form, textures and aspects to condition the frictional response. Mimicking reptilian surfaces, we argue, may form a design methodology potentially capable of generating advanced deterministic surface constructs capable of efficient tribological function.

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

    PubMed

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  17. Molecular evolution of peptide tyrosine--tyrosine: primary structure of PYY from the lampreys Geotria australis and Lampetra fluviatilis, bichir, python and desert tortoise.

    PubMed

    Wang, Y; Nielsen, P F; Youson, J H; Potter, I C; Lance, V A; Conlon, J M

    1999-02-01

    Peptide tyrosine-tyrosine (PYY) has been isolated from the intestines of two species of reptile, the desert tortoise Gopherus agassizii (Testudines) and the Burmese python Python molurus (Squamata), from the primitive Actinopterygian fish, the bichir Polypterus senegalis (Polypteriformes) and from two agnathans, the Southern-hemisphere lamprey Geotria australis (Geotriidae) and the holarctic lamprey Lampetra fluviatilis (Petromyzontidae). The primary structure of bichir PYY is identical to the proposed ancestral sequence of gnathostome PYY (YPPKPENPGE10/DAPPEELAKY20/YSALR HYINL30/ITRQRY). Tortoise and python PYY differ by six and seven residues, respectively, from the ancestral sequence consistent with the traditional view that the Testudines represent an earlier divergence from the primitive reptilian stock than the Squamates. The current views of agnathan phylogeny favor the hypothesis that the Southern-hemisphere lampreys and the holarctic lampreys arose from a common ancestral stock but their divergence is of a relatively ancient (pre-Tertiary) origin. The Geotria PYY-related peptide shows only two amino acid substitutions (Pro10-->Gln and Leu22-->Ser) compared with PYY from the holarctic lamprey Petromyzon marinus. This result was unexpected as Petromyzon PYY differs from Lampetra PYY deduced from the nucleotide sequence of a cDNA (Söderberg et al. J. Neurosci. Res. 1994;37:633-640) by 10 residues. However, a re-examination of an extract of Lampetra intestine revealed the presence of a PYY that differed in primary structure from Petromyzon PYY by only one amino acid residue (Pro10-->Ser). This result suggests that the structure of PYY has been strongly conserved during the evolution of Agnatha and that at least two genes encoding PYY-related peptides are expressed in Lampetra tissues. PMID:10100922

  18. Scalable, Example-Based Refactorings with Refaster Louis Wasserman

    E-print Network

    Cortes, Corinna

    , syn- tax tree, error-prone, OpenJDK, Guava, refactoring 1. Problem The Java Core Libraries Team (JCLT utilities. Many of these libraries are open-sourced as the popular Guava project. [1] A large proportion

  19. Tutorial on Nonparametric Chad Schafer and Larry Wasserman

    E-print Network

    Masci, Frank

    ;Regression Methods: Binning Local averaging Kernels Local polynomials Splines Wavelets Tutorial General Concepts of Smoothing, Bias-Variance Tradeoff Linear Smoothers Cross Validation Local Polynomial parameter h. For a histogram, h = binwidth. Consider the regression estimator based on local averaging: f

  20. MAGNETIC FUSION ENERGY Zachary S Hartwig

    E-print Network

    of thermonuclear fusion plasmas, beginning with electrodynamics as a foundation and developing single particle physics, plasma parameters, plasma models, plasma trans- port, plasma waves, and nuclear physics. Chapters derived from an original source, such as peer-reviewed literature, evaluated nuclear data tables

  1. Building Adaptivity into Execution Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    , execution step completes, ... § ... trigger the rules § Test conditions Memory free, tuples read, operator leverage conventional/distributed DB technology #12;3 It's Not as Easy as It Sounds... § How do we optimize join (invented for parallel DBs), but invent ways to handle memory constraints #12;6 Tukwila

  2. Introduction to Computer Security Peterson, Zachary

    E-print Network

    techniques, including trojan horses, viruses, and worms. 6. Be able to describe fundamental principles Machines, Implantable Medical Devices, Security Theatre, Hardware Security 1 Identity and Authentication Software Security, Malware, and Mitigation Social Engineering, Trojan Horses, Viruses, Worms, Logic Bombs

  3. Wilson-Cowan Model Zachary P. Kilpatrick*

    E-print Network

    Kilpatrick, Zachary P.

    motion of particles to a mean ensemble motion of a whole fluid or gas (Reichl and Prigogine 1980). Thus time at instant t. Thus, ae,i(t) ¼ 0 corresponds to a low-activity resting state. Excitatory;Thus, the activity variables ae,i(t) obey first-order kinetics with timescales te,i, tracking

  4. Data Integration Systems Zachary G. Ives

    E-print Network

    Ives, Zachary G.

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

  5. 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)

    Meyer, Carl L; Johnson, Lavern A

    1952-01-01

    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.

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

    PubMed

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

    2014-03-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed Central

    2012-01-01

    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. PMID:22647087

  11. Python Crash Course Day 2

    E-print Network

    Daume III, Hal

    a dictionary with ('apple':2,'orange':5) Add/change a value in the dictionary fruit = {'apple':2, 'orange':5} fruit = dict([('apple',2), ('orange',5)]) fruit = dict(apple=2, orange=5) fruit['banana']=3 => {'apple':2, 'orange':5, 'banana':3} fruit['apple']=3 => {'apple':3, 'orange':3, 'banana':3} #12;Dictionary

  12. Introduction into Python Daniel Polani

    E-print Network

    Polani, Daniel

    >>> 7/-3 -3 >>> 7.0 / 2 # floating point is recognized dynamically 3.5 >>> width = 20 >>> height = 5 * 9 >>> width * height 900 >>> x = y = z = 0 Daniel Polani: Introduction into Pyth Strings >>> 'spam eggs' 'spam eggs' >>> 'doesn\\'t' "doesn't" >>> "doesn't" "doesn't" >>> '"Yes," he said.' '"Yes," he said

  13. Using Python for Pedigree Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  15. Syntax of the Finite Model Property Zachary Ernst

    E-print Network

    Veroff, Robert

    Evaluation (1) Figure: 1 CCppp Cpp p p p p CpCCppp (1,0) (1,0) (1,0) (1,0) 2 1 1 2 Left Child Child 2 Child > Right Child 1 2 1 1 2 22 2 2 1 1 CCppp Cpp p p p CpCCpppInitial State: 1 Initial Counter: 0 U-Formula: Cpp States: {1,2} +: Increment -: Set to zero (1,1) 1 (1,0) p (2,0) Left child counter is greater #12

  16. Minimizing Movement in Mobile Facility Location Problems Zachary Friggstad

    E-print Network

    Salavatipour, Mohammad R.

    . in SODA 2007 [11] where a simple 2- approximation was proposed for the minimum maximum movement mobile. There is a company with some manufacturing plants. There are also several retail stores (with different demands possibility is to send the products to each retailer from its closest manufacturing plant. Another possibility

  17. Adaptive Query Processing for Internet Applications Zachary G. Ives

    E-print Network

    @cs.washington.edu Alon Y. Levy University of Washington alon@cs.washington.edu Daniel S. Weld University of Washington weld@cs.washington.edu Daniela Florescu INRIA Rocquencourt Daniela.Florescu@inria.fr Marc Friedman, and heterogeneous, the query optimizer will often not have histograms or any other quality statistics. Moreover

  18. Development of Prototype UrbanSim Models Zachary Patterson

    E-print Network

    Bierlaire, Michel

    TRANSP-OR 080814 Transport and Mobility Laboratory School of Architecture, Civil and Environmental in Switzerland), this paper describes a procedure to develop a prototype UrbanSim model and how to use section describes the two case studies. The fifth section describes a procedure to develop prototype Urban

  19. Zachary D. Barker: Final DHS HS-STEM Report

    SciTech Connect

    Barker, Z D

    2008-08-14

    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.

  20. Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1

    E-print Network

    . The authors also thank Dan Handley, Clark Glymour, Peter Spirtes, Richard Scheines, Greg Cooper and the other are grateful to David Peters and Rob O'Doherty for allowing them to use the data from the fat cell experiment

  1. Clustering After Transformation and Smoothing Nicoleta Serban and Larry Wasserman1

    E-print Network

    Serban, Nicoleta

    , NSF Grant DMS-98-03433 and NSF Grant DMS-0104016. The authors are grateful to David Peters and Rob O'Doherty for allowing them to use the data from the fat cell ex- periment, Dan Handley, Clark Glymour, Peter Spirtes Since our goal is to cluster the curves, we need a measure of the efficacy of a set of clusters. Let C

  2. Programming with Python Unit code: MATH20622

    E-print Network

    Sidorov, Nikita

    .). 10. Basics of testing and debugging. File I/O. Study hours Lectures - 11 hours Practical classes of presenting and solving mathematical problems in a form understandable by a computer, with the practical work

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

    E-print Network

    Chou, Ling

    1997-01-01

    Bjarne Stroustrup invented the C++ programming language at AT&T and published his first book on it in 1985. Because of its excellent performance and vast application domains, C++ stood as the dominate OOP language for a decade. During which, a lot...

  4. CIS192 Python Programming More Webservers

    E-print Network

    Plotkin, Joshua B.

    app = Flask(__name__) @app.route('/', methods=['GET']) def home_page(): return 'Hello World' if __name_headers=[('X-Powered-By', 'WSGI')]) @app.route('/', methods=['GET']) def home_page(): return 'Hello World' if __name__ == '__main all have received feedback from me on your proposal You don't need to respond (but feel free) Get

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

    ERIC Educational Resources Information Center

    Jehle, Dorothy M.

    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…

  6. Python Engine Installed in Altitude Wind Tunnel

    NASA Technical Reports Server (NTRS)

    1949-01-01

    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.

  7. PyCS : Python Curve Shifting

    NASA Astrophysics Data System (ADS)

    Tewes, Malte

    2015-09-01

    PyCS is a software toolbox to estimate time delays between multiple images of strongly lensed quasars, from resolved light curves such as obtained by the COSMOGRAIL monitoring program. The pycs package defines a collection of classes and high level functions, that you can script in a flexible way. PyCS makes it easy to compare different point estimators (including your own) without much code integration. The package heavily depends on numpy, scipy, and matplotlib.

  8. PHDL : a Python Hardware Design framework

    E-print Network

    Mashtizadeh, Ali

    2007-01-01

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

  9. MTpy: A Python toolbox for magnetotellurics

    USGS Publications Warehouse

    Krieger, Lars; Peacock, Jared R.

    2014-01-01

    In this paper, we introduce the structure and concept of MTpy  . Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

  10. 1999 Macmillan Magazines Ltd 12. Wasserman, E., Stixrude, L. & Cohen, R. E. Thermal properties of iron at high pressures and

    E-print Network

    Rasmussen, Joseph

    ., Holmes, N. C., Ross, M., Webb, D. J. & Pike, C. Shock temperatures and melting of iron at Earth core.nature.com ................................................................. Stable isotope evidence for the food web consequences of species invasions in lakes M. Jake Vander Zanden

  11. False Discovery Control With P-Value Weighting Christopher R. Genovese, Kathryn Roeder and Larry Wasserman1

    E-print Network

    False Discovery Exceedance. 1 Introduction Data from DNA microarray experiments, genetic epidemiologyFalse Discovery Control With P-Value Weighting Christopher R. Genovese, Kathryn Roeder and Larry for multiple hypothesis testing that maintains control of the False Discovery Rate while incorporating prior

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

    E-print Network

    Rose, Mark P.; Williams, David L.

    2014-06-09

    of atypical color/pattern variants, little research has been conducted, to date, into genetic variants of reptiles, relative to common domestic (e.g., dogs, cats). This work aims to raise awareness among the animal welfare science community of the potential...

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

    E-print Network

    Zhu, Jianwen

    our own def print_lyrics() : print "I am a lumberjack, and I am OK." print "I sleep all night and I! (if indented anyway for readibility, why the waste?) >>> print print_lyrics lyrics at 0xb8e99e9c> >>> print type(print_lyrics) >>> print_lyrics() · Function can call

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

    E-print Network

    Smith, Scott F.

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

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

    E-print Network

    Dixon, Michael

    a good composition, and adjusts the camera until a "good" composition is found. At this point the robot al [1]. For more information on the quality of interaction Fig. 1. The robot and cameras. between B21r mobile robot, with two cameras, mounted on a Directed Perception pan/tilt unit (see figure 1

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

    E-print Network

    Illinois at Urbana-Champaign, University of

    echogenic contrast imaging agents (MUECIA) in the United States, premature ventricular contractions have including heart disease and cancer. Premature ventricular contractions/complexes have been reported

  17. Dynamic In-hand Sliding Manipulation Jian Shi, J. Zachary Woodruff, and Kevin M. Lynch

    E-print Network

    MacIver, Malcolm A.

    -- This paper presents a framework for planning the motion of an n-fingered robot hand to create an inertial robot manipulation tasks involve controlling motion of the object relative to the manip- ulator, tapping, and kicking. Even in pick-carry-place manipulation, where the carry portion of the task keeps

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

    E-print Network

    Illinois at Urbana-Champaign, University of

    ). Rats were anes- thetized and the skin of the left thorax clipped and de- pilated. They were placed in right lateral recumbency and two black dots were positioned on the skin over the left intercostal spaces of pigment was substantially decreased. By 16 dpe the lung area with lesions had returned to a near normal

  19. Control of an Affordable Hand and Wrist Prosthesis Zachary Abraham Dong Bien Kwon

    E-print Network

    Muzzio, Fernando J.

    for implementation.1 In this study, a three dimensional (3D) printed prosthesis for below-the-elbow amputees, which to manufacture prostheses has been introduced. 3D printing allows for the development of lighter prostheses. In this study, a working and cost-effective prosthetic hand and wrist was developed using 3D printing and a Myo

  20. A GENERAL INVESTMENT MODEL Thomas S. Ferguson and C. Zachary Gilstein

    E-print Network

    Ferguson, Thomas S.

    , it is assumed that his distribution of future events is independent of his current and past choices on knowledge of the probability distributions of possible investment re- turns (future market events) and of informative dependent variables (future world events). General conditions on these distributions are given

  1. An Adaptive Query Execution System for Data Integration Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    @cs.washington.edu Daniel S. Weld University of Washington weld@cs.washington.edu Abstract Query processing in data optimization and execution techniques for three reasons: there is an absence of quality statistics about

  2. An Adaptive Query Execution System for Data Integration Zachary G. Ives

    E-print Network

    @cs.washington.edu Daniel S. Weld University of Washington weld@cs.washington.edu Abstract Query processing in data optimization andexecution techniques for three reasons: there is an absence of quality statistics about

  3. Making Research Tools Accessible for All AI Students Zachary Dodds, Christine Alvarado, and Sara Owsley Sood

    E-print Network

    Bustamante, Fabián E.

    (ref), robot control libraries and computer vision infrastructures (Carmen, Player/Stage, OpenCV), user Foundation, a fundamental resource for investigating pen-based computing and user interfaces. · OpenCV We also outline an introduction to the OpenCV library of computer vision routines through

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

    E-print Network

    Dukas, Reuven

    Mubasher1 , Reuven Dukas1 1 Animal Behaviour Group, Department of Psychology, Neuroscience & Behaviour, Mc in this social burrowing were also identified [13,14]. Recently, it has been shown that larvae are attracted instar larvae indicated that focal larvae are attracted to groups of other foraging larvae and learn

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

    E-print Network

    Blumstein, Daniel T.

    , Daniel T. Blumstein Department of Ecology and Evolutionary Biology, University of California, 621 Young Non-lethal deterrents Marine mammals Depredation Conservation behavior Fear conditioning a b s t r a c applied to marine mammals to mitigate conflict with fisheries and suggest that fear conditioning could

  6. Wrap-Up: Data Sharing and the Web Zachary G. Ives

    E-print Network

    Ives, Zachary G.

    -QL § Difference-based models: Y Change detection in semistructured data Y Heraclitus Y Harmony § Semantic Web § Groupware § Matching schemas and data #12;7 How Much Real-World Impact? I § Data integration: § Systems Real-World Impact? II § Publish-subscribe: § Not too much use (exception: RSS, available from Netscape

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

    E-print Network

    Gordon, Arnold L.

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

  8. Shape Replication through Self-Assembly and RNase Enzymes Zachary Abel

    E-print Network

    Demaine, Erik

    a specific number of copies, or an unbounded number of copies. Motivated by practical DNA implementations of Wang tiles, we consider a model in which tiles consisting of DNA or RNA can be dynamically added, Cambridge, MA 02138, USA, {zabel,kominers}@fas.harvard.edu. MIT Computer Science and Artificial Intelligence

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

    E-print Network

    Ras, Zbigniew W.

    -automated, or manual techniques are used to reconstruct the urban model. In the latter case, users may use 3D design dynamics. Military applications for urban combat zones, for example, must consider sudden damageVisual Analysis of Urban Terrain Dynamics Thomas Butkiewicz, Remco Chang, William Ribarsky

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

    E-print Network

    Wartell, Zachary

    -automated, or manual techniques are used to reconstruct the urban model. In the latter case, users may use 3D design with significantly faster dynamics. Military applications for urban combat zones, for example, must consider sudden1 Visual Analysis of Urban Terrain Dynamics Thomas Butkiewicz, Remco Chang, William Ribarsky

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

    E-print Network

    Toups, Zach

    .M.S.P. ! developing geographic information sensemaking visualizations to support military planning and training TEES Japanese language and culture in the Asian Studies Program at Kansai University of Foreign Language Studies-09-27­2013-10-13. PEER-REVIEWED, ARCHIVAL PUBLICATIO

  12. Gully measurement strategies in a pixel using python

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  13. Pages de variables Document = Apprendre programmer avec Python

    E-print Network

    Tichit, Laurent

    to think like a computer scientist de Allen B. Downey, Jeffrey Elkner & Chris Meyers disponible sur : http'entre eux. #12;Grace Hopper, inventeur du compilateur : « Pour moi, la programmation est plus qu'un art

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

    ERIC Educational Resources Information Center

    Sullivan, Rick; Green, David

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

  15. Sample Syllabus (Python) CSCI 1301 Introduction to Programming Principles

    E-print Network

    Liang, Y. Daniel

    Covered Hours Reference in the Text SP History History of computers, programming languages, Internet, Web 0.75 Chapter 1 PL Language Translation Interpretation vs. compiling 0.25 Chapter 1 PL Basic Type.daniel.liang@gmail.com Office Hours: MWF 8:00 ­ 9:00 a.m., 2:00 ­ 3:00 p.m., or by appointment Text: Introduction to Programming

  16. ORIGINAL PAPER Cold-induced mortality of invasive Burmese pythons

    E-print Network

    Dorcas, Michael E.

    College, P.O. Box 7118, Davidson, NC 28035, USA R. N. Reed US Geological Survey, Fort Collins Science Ave., Davie, FL 33314, USA e-mail: fjma@ufl.edu K. M. Hart US Geological Survey, Southeast Ecological

  17. Lambda Functions For Introduction to Programming Using Python

    E-print Network

    Liang, Y. Daniel

    for a student. For example, students = [("John", "Smith", 96), ("Susan", "King", 76), ("Kim", "Yao", 99. For example, >>> sorted(students) [('John', 'Smith', 96), ('Kim', 'Yao', 99), ('Susan', 'King', 76: >>> sorted(students, key = lambda t: (t[1])) [('Susan', 'King', 76), ('John', 'Smith', 96), ('Kim', 'Yao', 99

  18. Introduction to Python Part 1: Basic types and control flow

    E-print Network

    North Carolina at Chapel Hill, University of

    -9, and _ · not start with a number · not be a keyword # Okay variable names: banana i_am_awesome student Also, don't use __stuff__, this could show up in future versions. # Okay variable names: banana i_am_awesome

  19. DiffPy-CMI-Python libraries for Complex Modeling Initiative

    Energy Science and Technology Software Center (ESTSC)

    2014-02-01

    Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

  20. Multi-Receiver Vector Tracking Based on a Python Platform

    E-print Network

    Gao, Grace Xingxin

    Tracking (MRVT) architecture for the joint tracking of multiple GPS receivers to determine the reference attenuation and multipath. The MRVT architecture is implemented using a Software Defined Radio (SDR) written variables of each individual receiver to a single reference position on the rigid body and the attitude

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

    E-print Network

    Johnson, James Harvey

    1995-01-01

    . For snakes housed at 37'C the Co, or extrapolated time zero concentration, was 17.64+3.52 ug/ml with a median elimination half-life of 6,604.5 minutes (4.5 days). The Cmax was 11.98+1.67 ug/ml and 13.87 + 2.61 ug/ml for snakes housed at 25'C and 37'C...

  2. Outlier Detection and False Discovery Rates for Whole-Genome DNA Matching Author(s): Jung-Ying Tzeng, William Byerley, B. Devlin, Kathryn Roeder, Larry Wasserman

    E-print Network

    Roeder, Kathryn

    Outlier Detection and False Discovery Rates for Whole-Genome DNA Matching Author(s): Jung Discovery Rates for Whole-GenomeDNA Matching Jung-YingTZENG,WilliamBYERLEY,B. DEVLIN,KathrynROEDER,and Larry the discovery and use of these resources. For more information about JSTOR, please contact support

  3. Integrated AC electrokinetic cell separation in a closed-loop device Zachary Gagnon, Jill Mazur and Hsueh-Chia Chang*

    E-print Network

    Chang, Hsueh-Chia

    Article on the web 4th January 2010 DOI: 10.1039/b917220c We integrate electrothermally induced micro-pumps and dielectrophoretic (DEP) traps into micro- circulating fluidic channel loops for yeast cell concentration and cellular manipulation. From a detailed study into the frequency dependent DEP behavior of viable (live

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

    E-print Network

    Rogers, John A.

    Organic light-emitting devices with laminated top contacts Daniel A. Bernards, Tomasz Biegala; accepted 22 March 2004; published online 20 April 2004 We demonstrate the fabrication of organic light the quality of the lamination process. © 2004 American Institute of Physics. DOI: 10.1063/1.1739270 Organic

  5. Cloud Security Auditing based on Behavioral Modeling Zachary Birnbaum, Bingwei Liu, Andrey Dolgikh, Yu Chen, Victor Skormin

    E-print Network

    Chen, Yu

    of the most attractive features of cloud computing, which provides significant benefits to both clients. However, this architecture also introduces additional security implications. Client Virtual Machine (VM the behaviors of client VMs and to detect suspicious processes on the highest semantic level. Our preliminary

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

    E-print Network

    Kotz, David

    of pervasive wearable devices, whether for health monitoring, personal assistance, entertainment, or home), or to monitor their physiology (e.g., a cardiac patient concerned about heart arrhythmia or a diabetic managing a method to achieve the latter, that is, for a wearable device to identify the wearer, allowing sensor data

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

    E-print Network

    Smart, William

    and conference receptions. The robot, Lewis, navigates through the environment, opportunistically taking photography system mounted on a mobile robot. The robot navigates around social events, such as wedding. The cameras are mounted on top of the robot on a Directed Perception pan/tilt unit. All computation is done on

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

    E-print Network

    Dixon, Michael

    and conference receptions. The robot, Lewis, navigates through the environment, opportunistically taking photography system mounted on a mobile robot. The robot navigates around social events, such as wedding- ameter. The cameras are mounted on top of the robot on a Directed Perception pan/tilt unit. All

  9. WordPlay Baton Rouge on the Web Trey Miller, Thomas Gary, Eric Totte, Bridget Kovacs, Zachary Dever

    E-print Network

    Kundu, Sukhamay

    for the kids to learn and use. There will be an Admin account to police content generated by the users to keep to display their work in a positive environment, allowing members to interact outside of WordPlay events. The information on the website will be maintained by the kids involved with Word- Play, so a simple user interface

  10. Organometallics Roundtable 2011 John A. Gladysz,* Zachary T. Ball, Guy Bertrand, Suzanne A. Blum, Vy M. Dong, Reto Dorta,

    E-print Network

    Jones, William D.

    change in academic, industrial, and government-based research worldwide, and navigating these rough, as well as from industry. We were fortunate that so many busy experts could take the time to spend with us in obtaining acrylic acid esters from ethylene and CO2 using nickel-based complexes. My wish would

  11. SMARTx: An Embedded Proximity Detection System for Reducing Collisions Clinton Beasley* Joshua S. Williams* Zachary Brasuell* Sunho Lim Michael Shin

    E-print Network

    Lim, Sunho

    to reducecollisions significantly. Antenna (nRF905) Arduino GPS Bluetooth Receiver Side Antenna (nRF905) GPS Arduino and developed an embedded proximity detection system using Arduino and its communication components. Proposed

  12. A review of "Image Government: Monarchical Metamorphoses in English Literature and Art." by T. R. Langley 

    E-print Network

    Stephen Gleissner

    2005-01-01

    generation ago: E. R. Wasserman?s ?Nature Moralized: Divine Analogy in the Eighteenth Century,? EHL, 20, 1953 and Edgar Wind?s ?Julian the Apos- tate at Hampton Court,? Journal of the Warburg and Courtauld Institutes, vol. 3, 1939-40. Wasserman asserted...

  13. Endogeneity in the Environmental Kuznets Curve: An Instrumental Variables Approach1

    E-print Network

    Lin, C.-Y. Cynthia

    of California at Davis, and a member of the Giannini Foundation of Agricultural Economics. Zachary Liscow Lin Zachary D. Liscow The effects of increasing income on environmental quality is an issue that has

  14. A Trade Space Model for Robotic Lunar Exploration

    E-print Network

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

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

    ERIC Educational Resources Information Center

    Cummins, Lauren

    2004-01-01

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

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

    E-print Network

    Murray, Richard M.

    ! 1! Protein degradation in a TX-TL cell-free expression system using ClpXP protease AUTHORS as an alternative prototyping environment to the cell for synthetic circuits [1-5]. Basic circuit elements]. Circuits can also be prototyped from basic parts within 8 hours, avoiding cloning and transformation steps

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

    SciTech Connect

    1980-05-01

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

  18. Accepted Manuscript (to appear) IEEE 10th Symp. on 3D User Interfaces, March 2015 Cite as: Jialei Li, Isaac Cho, Zachary Wartell.

    E-print Network

    Ras, Zbigniew W.

    , not many studies address cur- sor offset techniques for multi-display virtual environments, such as a Cave Automatic Virtual Environment (CAVE), which require different directions of the cursor offset for different, cursor offset, input devices, CAVE, virtual environments Index Terms: H.5.2 [Information interfaces

  19. Improving the Durability of Coastal Bridges with CFRP Prestressed Cored Slabs Griffith Shapack, Zachary Van Brunt, Rudolf Seracino, Gregory Lucier, Sami Rizkalla, Mohammad Pour-Ghaz

    E-print Network

    prestressed cored slab superstructures are a common structural system for multi-span bridges in coastal North earned his PhD from North Carolina State University in 2012. He studies large-scale structural systems is a member of ACI Committee 444, Structural Health Monitoring and Instrumentation as well as ACI Committee

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

    E-print Network

    logistics plan and construction timeline constructed on MS Project The cost estimation of the Greenhouse for presentation purposes The structural system of the building will be a combination of steel and wood truss system in RISA 2D The structural gravity design system for the Greenhouse Café The environmental

  1. Prot-2S: a new python web tool for protein secondary structure studies.

    PubMed

    Munteanu, Cristian R; Magalhães, Alexandre L

    2009-01-01

    Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S applications showing its usefulness in protein research and as an e-learning tool as well. PMID:19640828

  2. 75 FR 11808 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ... South Florida. The Service published a notice of inquiry in the Federal Register (73 FR 5784; January 31... habitat from lowland tropical rainforest (Indonesia and Southeast Asia) to thorn-scrub desert (Pakistan... Amazon River, and several drainages in French Guiana. DeSchauensee's anaconda is known from a...

  3. 75 FR 11808 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ... South Florida. The Service published a notice of inquiry in the Federal Register (73 FR 5784; January 31... exhibit among the broadest diet range of any snake, including ectotherms (lizards, crocodilians, turtles... consume fish. Green anacondas consume a wide variety of endotherms and ectotherms from higher...

  4. 75 FR 11808 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ...maturation, rapid growth, longevity, and...or reduce large populations, or recover ecosystems...maturation, rapid growth, longevity, and...or reduce large populations, or recover ecosystems...or reduce large populations; control spread...maturation, rapid growth, longevity,...

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

    PubMed Central

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

    2008-01-01

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

  6. SkData: data sets and algorithm evaluation protocols in Python

    NASA Astrophysics Data System (ADS)

    Bergstra, James; Pinto, Nicolas; Cox, David D.

    2015-01-01

    Machine learning benchmark data sets come in all shapes and sizes, whereas classification algorithms assume sanitized input, such as (x, y) pairs with vector-valued input x and integer class label y. Researchers and practitioners know all too well how tedious it can be to get from the URL of a new data set to a NumPy ndarray suitable for e.g. pandas or sklearn. The SkData library handles that work for a growing number of benchmark data sets (small and large) so that one-off in-house scripts for downloading and parsing data sets can be replaced with library code that is reliable, community-tested, and documented. The SkData library also introduces an open-ended formalization of training and testing protocols that facilitates direct comparison with published research. This paper describes the usage and architecture of the SkData library.

  7. The python project: a unique model for extending research opportunities to undergraduate students.

    PubMed

    Harvey, Pamela A; Wall, Christopher; Luckey, Stephen W; Langer, Stephen; Leinwand, Leslie A

    2014-01-01

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

  8. 77 FR 3329 - Injurious Wildlife Species; Listing Three Python Species and One Anaconda Species as Injurious...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-23

    ...highest mean monthly air temperatures identified for...fairly temperate climate range, including...with suitable climates for its establishment...that their body temperature adjusts to be...the surrounding air temperature is. Thus,...

  9. pySPACE—a signal processing and classification environment in Python

    PubMed Central

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

    2013-01-01

    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

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

    ERIC Educational Resources Information Center

    Conner, David B.

    1996-01-01

    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)

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

    ERIC Educational Resources Information Center

    Rockow, Michael

    2007-01-01

    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…

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    Undergraduate science education curricula are traditionally composed of didactic instruction with a small number of laboratory courses that provide introductory training in research techniques. Research on learning methodologies suggests this model is relatively ineffective, whereas participation in independent research projects promotes enhanced…

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

    ERIC Educational Resources Information Center

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

    2004-01-01

    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…

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

    E-print Network

    Hopkins, William A.

    in the frequency of raccoon observations, decreases of 98.9% and 87.5% for opossum and bobcat observa- tions, such as raccoons and bobcats, bode poorly for species of conservation concern, which often are more difficult

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

    PubMed Central

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

    2014-01-01

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

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

    E-print Network

    Langmead, Christopher James

    Joint CMU-Pitt Program in Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA]. A recent and widely acknowledged belief is that local dynamics (local changes to hydrogen bonds and hy

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

    SciTech Connect

    Bignan, G.; Capsie, J.; Romeyer-Dherbey, J. . Direction des Reacteurs Nucleaires); Rinard, P. )

    1991-01-01

    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.

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

    E-print Network

    Blank, Douglas

    , inexpensive robots (such as the Handyboard and LEGO Mindstorms) were introduced and their use proliferated for Teaching Robotics DOUGLAS BLANK Bryn Mawr College DEEPAK KUMAR Bryn Mawr College LISA MEEDEN Swarthmore called Pyro which provides a set of abstractions that allows students to write platformindependent robot

  19. Introduc)on to Compu)ng Using Python Impera've Programming

    E-print Network

    -in func'on input() first = input('Enter your first name: ') last = input('Enter your last name: ') line1 = input('Enter your name: ') Enter your name: Michael >>> name 'Michael' >>> ========= RESTART ============= >>> Enter your first name: Michael Enter your last name: Jordan Hello Michael Jordan... Welcome to the world

  20. Statically Typed String Sanitation Inside a Python Nathan Fulton Cyrus Omar Jonathan Aldrich

    E-print Network

    Aldrich, Jonathan

    constructed using string concatenation exposes a SQL injection vulnerability: 'SELECT * FROM users WHERE name-encode special characters, which would head off both SQL injection attacks and cross-site scripting attacks sanitized user input can as a result be a vector for command injection attacks. In this paper, we introduce

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

    E-print Network

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

    2014-01-01

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

  2. Grundlagen II: Variablen, Werte, Typen, Strukturen Softwareentwicklungspraktikum "Python mit dem Raspberry Pi"

    E-print Network

    Raspberry Pi" (WiSe 2015/2016) Clemens Schefels Lehr- und Forschungseinheit f¨ur Programmier- und;Dictionary Beispiele f¨ur Schl¨ussel/Wert Paare 1 >>> abkuerzung = {"Raspi" : "Raspberry Pi", 2 "S2: 2 print("Hallo Raspberry") 20 / 37 #12;Schleifen ­ Programmbeispiel Programm-Beispiel Beispiel

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

    NASA Astrophysics Data System (ADS)

    Radziwill, Nicole M.; Shelton, Amy L.

    2006-06-01

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

  4. PythonBiogeme 2.4: estimating a first model Michel Bierlaire

    E-print Network

    Bierlaire, Michel

    _TRAIN, ASC_SM, ASC_CAR from data. Consequently, ASC_SM is normalized to 0. The availability of an alternative.4. 1 The data file Biogeme assumes that the data file contains in its first line a list of labels corresponding to the available data, and that each subsequent line contains the exact same number of numerical

  5. Colorsims: A python package for evolving linguistic color naming conventions within a

    E-print Network

    White, Douglas R.

    evolution of linguistic color naming conventions. Several previous studies [8, 10, 2] were based on early, 4, 3, 6, 7] Email: stauber@uci.edu 1 MBS Technical Report 15-01 #12;about the evolution the literature on the evolution of color naming conventions [8, 5, 4, 3, 6, 7]. In this section I outline

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

    SciTech Connect

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

    2009-01-01

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

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

    E-print Network

    Bringsjord, Selmer

    o Not happy - Made of wood o Likes - Burning not permitted/not desired o Dislikes - Burning's permission to burn her. King Arthur has just rode into the village and is watching the scene from a distance - boundary 1 #12; o Tet - Non-human o Happy - Not made of wood

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

    E-print Network

    Bringsjord, Selmer

    is a witch. They would like Sir Bedevere's permission to burn her. King Arthur has just rode into the village ­ boundary 1 #12; ffl Tet ­ Non­human ffl Happy ­ Not made of wood ffl Not happy ­ Made of wood ffl Likes ­ Burning not permitted/not desired ffl Dislikes ­ Burning permitted/desired 3 Given Information ffl F

  9. 76 FR 40082 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-07

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

  10. 77 FR 7968 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-13

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

  11. Invasion Ecology Definitions & Stages

    E-print Network

    Schweik, Charles M.

    · Nov 20, 25 & Dec 2 (presentation) #12;Species of the day: Burmese python (Python molurus bivittatus) #12;Species of the day: Burmese python (Python molurus bivittatus) #12;Burmese pythons eat everything Great blue heron Alligator (fail) Sheep #12;Python removal from the everglades #12;Dorcas et al., 2012

  12. Efficient multi-objective calibration of a computationally intensive hydrologic model with parallel computing software in Python

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With enhanced data availability, distributed watershed models for large areas with high spatial and temporal resolution are increasingly used to understand water budgets and examine effects of human activities and climate change/variability on water resources. Developing parallel computing software...

  13. Modeling Multiphase Coastal and Hydraulic Processes in an Interactive Python Environment with the Open Source Proteus Toolkit

    NASA Astrophysics Data System (ADS)

    Kees, C. E.; Farthing, M. W.; Ahmadia, A. J.; Bakhtyar, R.; Miller, C. T.

    2014-12-01

    Hydrology is dominated by multiphase flow processes, due to the importance of capturing water's interaction with soil and air phases. Unfortunately, many different mathematical model formulations are required to model particular processes and scales of interest, and each formulation often requires specialized numerical methods. The Proteus toolkit is a software package for research on models for coastal and hydraulic processes and improvements in numerics, particularly 3D multiphase processes and parallel numerics. The models considered include multiphase flow, shallow water flow, turbulent free surface flow, and various flow-driven processes. We will discuss the objectives of Proteus and recent evolution of the toolkit's design as well as present examples of how it has been used used to construct computational models of multiphase flows for the US Army Corps of Engineers. Proteus is also an open source toolkit authored primarily within the US Army Corps of Engineers, and used, developed, and maintained by a small community of researchers in both theoretical modeling and computational methods research. We will discuss how open source and community development practices have played a role in the creation of Proteus.

  14. March 1, 2012 Computers are really good at doing repetitive tasks. Everything we have asked of Python so far have

    E-print Network

    Lega, Joceline

    Loops Sarah Mann March 1, 2012 Computers are really good at doing repetitive tasks. Everything we'll learn how to make them do repetitive tasks by using loops. We'll discuss loops together in class, so I

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

    PubMed

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

    2012-01-01

    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

  16. PyLDTk: Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients for arbitrary filters

    NASA Astrophysics Data System (ADS)

    Parviainen, Hannu

    2015-10-01

    PyLDTk automates the calculation of custom stellar limb darkening (LD) profiles and model-specific limb darkening coefficients (LDC) using the library of PHOENIX-generated specific intensity spectra by Husser et al. (2013). It facilitates exoplanet transit light curve modeling, especially transmission spectroscopy where the modeling is carried out for custom narrow passbands. PyLDTk construct model-specific priors on the limb darkening coefficients prior to the transit light curve modeling. It can also be directly integrated into the log posterior computation of any pre-existing transit modeling code with minimal modifications to constrain the LD model parameter space directly by the LD profile, allowing for the marginalization over the whole parameter space that can explain the profile without the need to approximate this constraint by a prior distribution. This is useful when using a high-order limb darkening model where the coefficients are often correlated, and the priors estimated from the tabulated values usually fail to include these correlations.

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

    SciTech Connect

    Orndorff-Plunkett, Franklin

    2011-05-01

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

  18. Aligning social welfare and agent preferences to alleviate traffic congestion

    E-print Network

    Tumer, Kagan

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

  19. Minima and Saddles in the MLS Surface Definition Nina Amenta

    E-print Network

    Amenta, Nina

    and Zachary Abel (a Harvard undergrad) point out (personal communication) a problem in the proof of Claim 1 direction is true. A point of the MLS surface does indeed satisfy Equation (1), but as Shlomo and Zachary be a maximum, so it has to be either a saddle or a minimum. Dept. of CS, U. of California, Davis, CA 95616

  20. NPS Master Curriculum Chart Length PO APC JPME Dept Ph D. Committee ChairAcademic Associate Program OfficerDepartment ChairSchool / Curriculum / Degree Convenes Refresher P_Codes

    E-print Network

    Harold A. Trinkunas Zachary Shore James A. McMullinFall / Winter / Spring / SummerMA Security Studies Hemisphere) 2103P 684 - Europe and Eurasia 18 38 265 JPME NS Harold A. Trinkunas Zachary Shore James A. Mc/DoD Identity Management Professional Edu 6 32 0 CS Thomas W. Otani Duane T. DavisPeter J. DenningFall / Winter