ライフサイエンスコーパス: Python

1 ogramming languages (e.g., C++, Fortran, and Python).

2 SD license, with bindings for C++, C, R, and Python.

3 The algorithm is implemented in MATLAB and Python.

4 teractive data science software ecosystem in Python.

5 thVisioRPC functionalities using examples in Python.

6 tistical analysis and visualization tools in Python.

7 med in scripting languages like R, Perl, and Python.

8 of programming languages such as Perl, R or Python.

9 It is implemented in C and Python.

10 insights into the extreme phenotypes of the python.

11 provides efficient access to tabular data in Python.

12 nalysis, BitSeq, has been written in C++ and Python.

13 ol as well as a library in C, Java, Perl and Python.

14 ity and implementation: Ruffus is written in python.

15 need for a multivariate analysis toolbox in Python.

16 the popular open-source programming language Python.

17 INTEGRATE-Neo is implemented in C ++ and Python.

18 y available at www.github.com/briney/clonify-python.

19 d survived predation attempts by reticulated pythons.

20 HangOut is implemented in Python 2.3 and runs on all Unix-compatible platforms.

21 Python 2.6+ and virtualenv are required.

22 It requires Python 2.7 and several freely available Python packages.

23 pen source (MIT license) and executable with Python 2.7 or iPython notebook, and available on GitHub.

24 The software implemented in Python 2.7 programming language is available from reques

25 This package works with Python 2.7, 3.4, and 3.5 on MacOS, Linux and Windows.

26 ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical u

27 Therefore, we introduce a python (2.7) based package, PyLDM, to address this need.

28 FQC is implemented in Python 3 and Javascript, and is maintained under an MIT

29 PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibil

30 Because ParamAP is implemented in Python 3, it is also highly customizable and extensible.

31 Code in Java and Python along with instructions to download the reads and

32 Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation a

33 windows installer that configures MR-Tandem, Python and all necessary packages are available at this

34 ilitating data access and manipulation using Python and any other programming language that implement

35 mplementation: Allerdictor is implemented in Python and available as standalone and web server versio

36 The program is implemented in Python and C and licensed under the GNU Public License.

37 com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.

38 Reference implementation in Python and C components available at http://noble.gs.was

39 Python and C source code are available upon request from

40 kr computational package (in MATLAB, Octave, Python and C) for the Linux and Mac platforms is availab

41 The software was written in Python and C++ and is available under an open-source lic

42 It is implemented in Python and C++.

43 at http://wiki.chasmsoftware.org, Source in Python and C++.

44 RSeQC is written in Python and C.

45 MaryGold has been written in C++ and Python and can be downloaded from http://bioinformatics.

46 PyRadiomics is implemented in Python and can be used standalone or using 3D Slicer.

47 within a user-friendly implementation using Python and Docker.

48 Software is written in Python and freely available at http://www.dereneaton.com

49 axy Data Manager framework is implemented in Python and has been integrated as part of the core Galax

50 This open-source toolset was implemented in Python and has been integrated into the online data anal

51 This open-source toolset was implemented in Python and has been integrated into the online data anal

52 MAT is developed in open-source Python and is available at http://chip.dfci.harvard.edu/

53 Enrich is implemented in Python and is available under a FreeBSD license at http:

54 OMAAT is written in Python and is integrated with OpenMSI, a platform for st

55 The PyLOH package is written in Python and is publicly available at https://github.com/u

56 SplicePlot is implemented in Python and is supported on Linux and Mac OS.

57 lociNGS is written in Python and is supported on MacOSX and Unix; it is distri

58 We compare the python and king cobra genomes along with genomic samples

59 Python and MATLAB implementations of our method are avai

60 e and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the D

61 ntroduction of a library, libChEBI, in Java, Python and Matlab.

62 Site implemented in Python and MySQL, with all major browsers supported.

63 ed kruX, an algorithm implemented in Matlab, Python and R that uses matrix multiplications to simulta

64 thub.com/jsh58/DMRfinder ); it is written in Python and R, and is supported on Linux.

65 GIM(3)E has been implemented in Python and requires a COBRApy 0.2.x.

66 r programming languages, such as Java, Perl, Python and Ruby.

67 ATSHAP is embedded in a toolkit developed in Python and supports genomics datasets in standard file f

68 has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak

69 application programming interface in C++ and Python and through standardized open data formats.

70 orthologues from pit-bearing snakes (vipers, pythons and boas) are the most heat-sensitive vertebrate

71 Among vertebrates, only vampire bats, boas, pythons and pit vipers are capable of detecting infrared

72 eloped in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML

73 he application was developed using Pearl and Python, and is available at the following URL: http://us

74 r offers a basic introduction to coding, via Python, and it includes concrete examples and exercises

75 nd translated into differential equations in Python, and Python code is automatically generated to so

76 The analysis was implemented in R and Python, and source code can be found in Supplementary Da

77 TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux pl

78 trast, HOXD digit enhancers are conserved in pythons, and HOXD gene expression in the hindlimb buds p

79 ecades, despite no evidence of this in boas, pythons, and their relatives.

80 d pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocall

81 des a Python command line interface (CLI), a Python application programming interface (API) and an iP

82 Its Python Application Programming Interface (API) is simila

83 both a suite of command line utilities and a Python application programming interface.

84 lear and consistent abstractions through its Python application programming interface.

85 #, and integration instructions for Perl and Python are provided.

86 his difference matches previous reports that pythons are more susceptible to IBD than boas and could

87 is an open-source software and is written in Python as both a suite of command line utilities and a P

88 Agta ate pythons as well as deer, wild pigs, and monkeys, which a

89 freely available as an extension package for Python based eMZed2, an open source framework built for

90 ircularLogo is implemented in JavaScript and Python based on the Django web framework.

91 ary and interoperable scientific software in Python based upon SciPy.

92 spector, the Unipept web application and the Python-based BioServices package.

93 Python-based code for non-commercial use and test data a

94 rary presented here provides an open-source, Python-based framework for modeling internal metabolic f

95 density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xt

96 We present PyIgClassify (for Python-based immunoglobulin classification), a database

97 PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular mod

98 A Python-based library implementing our approach is availa

99 a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework.

100 hat may facilitate the development of future python-based programs that require the manipulation of m

101 troduce new methods for sector analysis in a python-based software package (pySCA).

102 PyRosetta contains Python bindings to libraries that define Rosetta functio

103 trate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, ba

104 rofiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced super

105 mation was associated with infection in ball pythons but not in boa constrictors.

106 We infected boa constrictors and ball pythons by cardiac injection of purified virus.

107 Python code and command-line utilities implementing CROC

108 The web-based tools and Python code are available at: http://bioserver.cs.rice.e

109 Python code for implementing the automated threshold sel

110 d into differential equations in Python, and Python code is automatically generated to solve the syst

111 rithm is implemented in platform-independent Python code.

112 are produced by executing the auto-generated Python code.

113 t are read by Pycellerator, which includes a Python command line interface (CLI), a Python applicatio

114 We have developed a new Python command line tool, which is compatible with the w

115 multiple genomic data formats into standard Python data structures and allows flexible, customized m

116 dentify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independe

117 orm in a small package that requires minimal python dependencies to function.

118 and "loop" records represented as individual Python dictionary data structures).

119 .1 formatted files, parsing them into usable Python dictionary- and list-based data structures, makin

120 Burmese pythons display a marked increase in heart mass after a

121 n interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and t

122 report that hindlimb development arrests in python embryos as a result of mutations that abolish ess

123 Ball pythons fell ill within 2 months of infection and displa

124 Python files will be available for download at http://ty

125 The server is implemented using Python, Flask, NumPy and SciPy.

126 Pythoscape is a framework implemented in Python for processing large protein similarity networks

127 ied by a support library, written in C++ and Python, for reading and writing the VDJML file format.

128 BioServices is a comprehensive Python framework that provides programmatic access to ma

129 Burmese pythons, giant constricting snakes native to Asia, now a

130 vanced data-mining of ASAP II with Pygr (the Python Graph Database Framework for Bioinformatics) incl

131 We used Pygr (The Python Graph Database Framework for Bioinformatics) to q

132 Python has become a popular programming language in the

133 onal pipeline using the programming language Python has been developed and applied to maize full leng

134 These findings suggest that predation by pythons has resulted in dramatic declines in mammals wit

135 these species are more common in areas where pythons have been discovered only recently and are most

136 Pythons have increased dramatically in both abundance an

137 vels of circulating lipids, the postprandial python heart does not accumulate triglycerides or fatty

138 In the Python heart, we found a corresponding progressive decli

139 Python hindlimb buds then develop transitory pre-chondro

140 , SHH transcription is weak and transient in python hindlimb buds, leading to early termination of a

141 The Python implementation is available at http://www.stats.o

142 variation.Availability and implementation: A Python implementation is freely available at https://bit

143 A C++ and Python implementation of the method demonstrated in this

144 A Python implementation of the proposed method is availabl

145 ally and spatially with the proliferation of pythons in ENP.

146 Ball pythons infected with Golden Gate virus (GoGV) and with

147 implement and works on any platform that has python installed.

148 sting tools with similar goals is the use of Python instead of a specifically constructed language, p

149 It provides an intuitive Python interface that extends upon the popular BEDTools

150 ng workflows, facilitated by a comprehensive Python interface to solvers implemented in C++.

151 Kit , an open source, modular and extensible Python interface which allows facile conversion between

152 nd C bindings, and interactively through its Python interface.

153 MethylCoder requires only a python interpreter and a C compiler to run.

154 Python is the only dependency, and our web site provides

155 We found that heart growth in pythons is characterized by myocyte hypertrophy in the a

156 ehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access

157 aboration of volunteer developers, providing Python libraries for a wide range of bioinformatics prob

158 ed our software to three currently available Python libraries for parsing NMR-STAR formatted files: P

159 everal programming languages and a reference Python library (phconvert), to create new Photon-HDF5 fi

160 We introduce cyvcf2 , a Python library and software package for fast parsing and

161 e LCA* has been implemented as a stand-alone Python library compatible with the MetaPathways pipeline

162 We introduce Pycellerator, a Python library for reading Cellerator arrow notation fro

163 d pydna, an extensible, free and open source Python library for simulating basic molecular biology DN

164 Here we present COSMOS, a Python library for workflow management that allows forma

165 is work, we aim at providing a comprehensive Python library implementing conditional random fields (C

166 ere we report an open-source and easy-to-use Python library that facilitates the parsing, manipulatio

167 comb-p is a command-line tool and a python library that manipulates BED files of possibly ir

168 lable as a web-based tool and an open-source Python library.

169 Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locall

170 Fedora Core 8,10,11 and Ubuntu 10), 2.5*</= Python <3.0*, MySQL server >5.0, 60 GB available hard di

171 multiple SNPrank implementations, including Python, Matlab and Java as well as CPU versus GPU implem

172 ow-protein diet improved cardiac function in Python mice.

173 ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image

174 esent GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genom

175 A python module implementing our algorithm is available fr

176 ww.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from Py

177 oth as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-

178 sion of this algorithm as a freely available Python module.

179 allows for rapid extension using a range of Python modules and is part of the growing amount of comp

180 The implementation as python modules offers flexibility, which has already all

181 ble for academic use as a set of open source Python modules under a GNU General Public License from h

182 rce implementation of the method as a set of Python modules using the computational framework OpenStr

183 g the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiolog

184 ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding, which res

185 The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell

186 lar sequelae leading to heart failure in the Python monogenic dilated cardiomyopathy model.

187 namin-related protein 1 (Drp1) underlies the Python mouse model of monogenic dilated cardiomyopathy.

188 Web site implemented with PHP, Python, MySQL and Apache, with all major browsers suppor

189 Python Nearest Alignment Space Termination (PyNAST) is a

190 By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone

191 xperimental workflow as a single, serialized Python object containing explicit provenance and environ

192 gical heart growth when injected into either pythons or mice.

193 d documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

194 ves and metrics are available at http://pypi.python.org/pypi/CROC/

195 Package available at http://pypi.python.org/pypi/ercs.

196 e on the Python Package Index at http://pypi.python.org/pypi/pybedtools.

197 pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX pac

198 Our method is implemented in a Python package called Popcorn.

199 dies of DNAs and nucleotides, we developed a Python package called representations of DNAs (repDNA) f

200 er design code is available as a stand-alone Python package for broader applications.

201 Here, we present Assocplots, a Python package for viewing and exploring GWAS results no

202 We introduce the caspo toolbox, a python package implementing a workflow for reasoning on

203 sion 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manag

204 s well as documentation are available on the Python Package Index at http://pypi.python.org/pypi/pybe

205 nload and automated installation through the Python Package Index site, while the active development

206 nestly can be installed from the Python Package Index via pip; it is open source (MIT lic

207 rent stable build can be downloaded from the python package index with development builds available o

208 ConKit is available via the Python Package Index.

209 The repDNA Python package is freely accessible to the public at htt

210 The BINOCh open source Python package is freely available at http://liulab.dfci

211 The CEAS Python package is publicly available at http://liulab.df

212 ely available and can be installed using the Python package management system pip.

213 from the Python Package Index (PyPI) using a Python package manager such as pip.

214 : We present Goldilocks: a Python package providing functionality for collecting su

215 Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation

216 Here we describe Mackinac, a Python package that combines ModelSEED's ability to auto

217 software environment, ABC-SysBio, which is a Python package that runs on Linux and Mac OS X systems a

218 We present nestly, a Python package to facilitate running tools with nested c

219 Here we present a Python package, ABC-SysBio, that implements parameter in

220 We present a Python package, cuda-sim, that provides highly paralleli

221 We developed a Python package, ProDy, for structure-based analysis of p

222 d GC content, which we have developed into a python package.

223 PyBamView is available as a standard python package.

224 , cross platform application and open source Python package.

225 DGW is available as an open source Python package.

226 Python packages are available at PyPI.

227 Here we report a set of Python packages that can automatically generate ISA-Tab

228 ires Python 2.7 and several freely available Python packages.

229 source code and unit tests are available in Python, Perl and Java.

230 MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at w

231 piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source softwar

232 des language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many featu

233 The Python pickle file generated in the process is used by t

234 independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive we

235 o identified a combination of fatty acids in python plasma that promotes physiological heart growth w

236 r incorporation of other data types, modular Python plugins enable users to compute and fit data from

237 reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5].

238 ython regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7].

239 genetic algorithm has been implemented as a Python program called Frnakenstein.

240 pen source and freely available as a C++ and Python program running on all Unix-compatible platforms.

241 pen source and freely available as a C++ and Python program running on all Unix-compatible platforms.

242 We present an updated version of the popular Python program StrAuto, to streamline population structu

243 es and structures, and we provide an example Python program to demonstrate how easily Opal-based web

244 We have created a Python programming interface for the RCSB Protein Data B

245 DendroPy is a cross-platform library for the Python programming language that provides for object-ori

246 n-source implementation of this algorithm in Python programming language with user instructions can b

247 Additionally, the source code written in the Python programming language, is available under the Gene

248 of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records rep

249 uitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR forma

250 e demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromos

251 ogy using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme p

252 and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and py

253 crease in ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding,

254 analysis methods in common languages such as Python, R, and SQL; to using an interactive web applicat

255 ex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons po

256 y recently and are most abundant outside the python's current introduced range.

257 within WormBase, and can be downloaded using Python's standard pip installer.

258 FunGAP is written in Python script and is available in GitHub.

259 elationships between DWTPs and WWTPs, with a python script designed to perform a network analysis by

260 treatment by MZmine 2 followed by a homemade Python script freely available to the community that cle

261 The MR-Tandem Python script is Apache licensed and available as part o

262 e provide a freely available and open source python script that can be used to analyze raw read data

263 ghtly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amaz

264 ghtly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amaz

265 ed with new ones easily added via a provided Python script.

266 a computational string search with a custom Python script.

267 ne graphical user interface (GUI), using the Python scripting language.

268 , using iPython and (ii) script-based, using Python scripting.

269 Source code and accompanying Python scripts are available at http://shendurelab.githu

270 Source code, compiled code and R and Python scripts are available from http://thebrain.bwh.ha

271 The MALTAB and Python scripts are available in the Supplementary Materi

272 fying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines.

273 It is a set of Python scripts that integrate freely available specializ

274 Python Sequence Labeling (PySeqLab) is an open source pa

275 pybedtools is a flexible Python software library for manipulating and exploring g

276 We built a Python software library for working with phylogenetic da

277 SSuMMo is GPLv3 open source Python software, available at http://code.google.com/p/s

278 Our proposal has been implemented using Python software.

279 fferential equations, generating stand-alone Python solvers, and optionally running and plotting the

280 The C source code for compete and Python source code for MCMC-based inference are availabl

281 ry package for 64-bit Linux computers and as python source-code.

282 axy workflow system accelerated with MPI and Python threading on compute clusters.

283 m (CERES) with a PV performance model (PVLIB-Python) to calculate the impact of aerosols and clouds o

284 Here, we present the L.U.St package, a python tool for approximate maximum likelihood supertree

285 We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of t

286 method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gen

287 TRFolder is a command-line Python toolkit for TR-specific structure prediction.

288 Our Python tools are freely available at www.cs.hmc.edu/ app

289 ver and utilize the complete set of standard Python tools.

290 by creating custom XML requests from native Python types, allowing extensibility and straightforward

291 The software is implemented in Python using the Django web framework, and runs on elast

292 The Decombinator package is implemented in Python (v2.6) and is freely available at https://github.

293 is application note we describe PyPanda, the Python version of PANDA.

294 miTRATA is implemented in Python (version 3) and employs parallel processing modul

295 A custom program written in Python was used to determine single nucleotide polymorph

296 oduce metaseq, a software library written in Python, which enables loading multiple genomic data form

297 The software relax is written in Python with C modules and is released under the GPLv3+ l

298 We now implement this computational tool in Python with increased usability and the capability of pe

299 We infected boa constrictors and ball pythons with purified reptarenavirus.

300 Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) anal