ライフサイエンスコーパス: Python

1 platform independent and written in Java and Python.

2 It is functional with built-in Perl and Python.

3 m interpreted languages including MATLAB and Python.

4 and graphical user interface tool written in Python.

5 arily in bash with helper scripts written in python.

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

7 the popular open-source programming language Python.

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

9 The algorithm is implemented in MATLAB and Python.

10 teractive data science software ecosystem in Python.

11 is a free and open source program written in Python.

12 d with the classification of this dataset in Python.

13 roducibility, we prototyped the method using Python.

14 familiar with basic programming in MATLAB or Python.

15 ing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public

16 CharGer is implemented in Python 2.7 and is supported on Unix-based operating syst

17 DISPOT is implemented in Python 2.7 and packaged as an open-source tool.

18 package manager and is compatible with both Python 2.7 and Python 3.6.

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

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

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

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

23 Squiggle is written in Python 3 and freely available under the permissive MIT l

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

25 svist4get is implemented in Python 3 and runs on Linux.

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

27 or programming languages, namely, C++, Java, Python 3, and R to kick-start adoption and integration.

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

29 a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions.

30 Based on Python 3.5, MixONat analyses a {(1)H}-(13)C NMR spectrum

31 spectrum_utils is available for Python 3.6+, includes extensive online documentation and

32 r and is compatible with both Python 2.7 and Python 3.6.

33 multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux

34 language system responses to code written in Python, a text-based programming language (Experiment 1)

35 rkflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing.

36 ners; the core algorithms were written in R, Python, Ada and C++.

37 mming and analysis through scripting in R or Python, allowing the trainer to cover more ground in the

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

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

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

41 Its pipeline was written using Python and C++ languages.

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

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

44 VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS

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

46 atomium is implemented in Python and its performance is equivalent to the existing

47 to enable DrawGlycan-SNFG implementation in Python and Java.

48 n in several programming languages (Java, R, Python and Javascript) and (iv) a web service for progra

49 The workflow described leverages Python and Kepler-Python actor for plotting and pre/post

50 abseqs is an open-source tool implemented in Python and licensed under the MIT license.

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

52 ive improvement from existing solutions like Python and MongoDB, by utilizing a domain-specific langu

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

54 The tool is implemented using the Python and R programming languages, and is supported on

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

56 The SCGid package is implemented in python and R.

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

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

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

60 ATLAS is written in Python and the workflow implemented in Snakemake; it ope

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

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

63 BEAN-counter is open source, written in Python, and freely available for academic use.

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

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

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

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

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

69 A Python/Answer Set Programming implementation can be acce

70 Here we introduce Logomaker, a Python API for creating publication-quality sequence log

71 chromosome simulations using GPUs via OpenMM Python API, called Open-MiChroM.

72 is possible through configuration files and Python API.

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

74 ed and monitored using local commands or the Python Application Programming Interface (API) and cloud

75 Its Python Application Programming Interface (API) is simila

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

77 to integrate the obtained results into other Python applications and pipelines.

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

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

80 We developed JUDI on top of DoIt, a Python based WMS, to systematically handle parameter set

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

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

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

84 PrimedRPA is a python-based package that automates the creation and fil

85 esent CRIS.py, a simple and highly versatile python-based program which concurrently analyzes next-ge

86 "Brian" is a popular Python-based simulator for spiking neural networks, comm

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

88 resent iLearn, a comprehensive and versatile Python-based toolkit, integrating the functionality of f

89 WAVES was developed with Django, a Python-based web framework.

90 The use of C++ lambda functions and Python bindings provide extensive flexibility for analys

91 is the Lemon framework, a C++11 library with Python bindings, which provides a consistent workflow me

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

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

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

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

96 It is written in Python, C, AWK, and Bash.

97 reprocessing of methylation array data using Python can accelerate data preparation for downstream me

98 h a Python front-end, any user familiar with Python can specify a genome and simulate gene expression

99 thon implementation of the algorithm and the Python code developed for this study on Github.

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

101 re produced using video recording and custom Python code.

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

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

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

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

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

107 chunking for large sequence files, JSON and Python dictionary output, and built-in sequence filterin

108 .1 formatted files, parsing them into usable Python dictionary- and list-based data structures, makin

109 approach, termed Differential Expression in Python (DiffExPy), that uniquely combines discrete, diff

110 is the foundation upon which the scientific Python ecosystem is constructed.

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

112 d was used to trigger column switching using Python-enabled two-way communication with the standard U

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

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

115 tical and easy to use toolkit implemented in Python for extracting various features from proteins, DN

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

117 limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sor

118 Here, we present Glycosylator, a Python framework for the identification, modeling and mo

119 Written in C++ with a Python front-end, any user familiar with Python can spec

120 framework as an open-source software, called Python Geneset Network Analysis (PyGNA).

121 stering technique, VOCCluster, prototyped in Python, handles features of deconvolved GC/MS breath dat

122 Python has become a popular programming language in the

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

124 Python hindlimb buds then develop transitory pre-chondro

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

126 lore gene family history encoded in HOGs and python HOG analysis method, a python library for program

127 We provide a Python implementation of the algorithm and the Python co

128 Here, we present a python implementation of the Epigenetic Pacemaker (EPM),

129 eper and NormFinder with respect to previous Python implementation.

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

131 It is fully portable, as only a Python installation is required to run Django.

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

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

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

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

136 comprehensive description of all MATLAB and Python interfaces and user documents are provided.

137 c mutation enrichment that is implemented in Python, is freely available, can be efficiently parallel

138 AOGP is developed in Python, is fully open-sourced, and is equipped with a us

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

140 CYPminer was developed in the Python language to facilitate rapid, comprehensive analy

141 he primary array programming library for the Python language.

142 the use of new programming languages (e.g., Python), learning how to apply machine-learning methods

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

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

145 ooler is based on HDF5 and is supported by a Python library and command line suite to create, read, i

146 ScaffoldGraph (SG) is an open-source Python library and command-line tool for the generation

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

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

149 e we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB,

150 ed in HOGs and python HOG analysis method, a python library for programmatic processing of genes fami

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

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

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

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

155 We developed Epiviz File Server, a Python library that implements an in situ data query sys

156 s resource is available as a well-documented python library with a simple command-line interface.

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

158 vised SugarPy, a glycan database independent Python module, and validated it on the glycoproteome of

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

160 s provided as an open-source and easy-to-use python module, GeneNet.

161 aLAFFA according to common practices while a Python module-based configuration system provides advanc

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

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

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

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

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

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

168 ML, COMBINE archive, MATLAB, Mathematica, R, Python or C++.

169 eker.pythonanywhere.com) and a user-friendly Python package (github.com/gussow/seeker) allowing resea

170 cellHarmony is implemented as a python package and as an integrated workflow within the

171 popular spike sorting codes are wrapped in a Python package and evaluated on a compute cluster using

172 We present hypercluster, a python package and SnakeMake pipeline for flexible and p

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

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

175 PyIOmica is an open-source Python package focusing on integrating longitudinal mult

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

177 fully integrated open-source application and Python package for coevolutionary analysis.

178 We developed FactorialHMM, a Python package for fast exact inference in Factorial HMM

179 to facilitate this task, spectrum_utils is a Python package for mass spectrometry data processing and

180 However, the existing Python package for operating on coverage files is not op

181 data analysis, we present scedar, a scalable Python package for scRNA-seq exploratory data analysis.

182 ipcoal is a free and open source Python package for simulating and analyzing genealogies

183 SAGA-optimize is a useful Python package for solving boundary-value inverse proble

184 software ecosystem, we implemented BOFdat, a Python package for the definition of a Biomass Objective

185 Here, we present Medusa, a Python package for the generation and analysis of ensemb

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

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

188 Software is also distributed through the Python Package Index (PyPI) repository.

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

190 , BSD-licensed and can be installed from the Python package index or the bioconda repository.

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

192 s available through Bioconda, GitHub and the Python Package Index.

193 s are freely available on GitHub and via the Python Package Index.

194 rom github.com/Lab41/squiggle as well as the Python Package Index.

195 ConKit is available via the Python Package Index.

196 CRNT4SBML is available via the Python Package Index.

197 and line interface and an underlying modular Python package makes the full power of coevolutionary an

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

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

200 This new tool was implemented as a Python package named eCAMI.

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

202 e implemented the resulting methodology in a python package specially designed to efficiently impute

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

204 eloped CoMut, a stand-alone, object-oriented Python package that creates comutation plots from arbitr

205 Keras R-CNN is a Python package that performs automated cell identificati

206 PyCellBase is an open-source Python package that provides an efficient access to hete

207 In this work we present PyCellBase, a Python package that provides programmatic access to the

208 -performance data analysis pipelines or as a Python package to implement new tests and analyses.

209 We developed pyBedGraph, a Python package to quickly obtain summary statistics for

210 amplimap is available as a free Python package under the open-source Apache 2.0 License.

211 Finally, we demonstrated the utility of the Python package using Staphylococcus aureus strains that

212 le both as a command line interface and as a Python package with an application programming interface

213 ratio (NVR) feature selection approach as a Python package with substantial improvements in performa

214 d package documentation are provided in the 'Python package' section of the website.

215 lipidomics data, we developed an open-source Python package, LiPydomics, which enables performing sta

216 using either the web-interface, a dedicated Python package, or custom remote clients.

217 Implemented as an open source Python package, our framework can be extended by the com

218 e provide an updated toolbox, developed as a Python package, that includes new features such as graph

219 , cross platform application and open source Python package.

220 DGW is available as an open source Python package.

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

222 lysis software is available as the protaccel Python package.

223 putationally efficient techniques with other Python packages (e.g., Nilearn, Scikit-learn) for file h

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

225 ires Python 2.7 and several freely available Python packages.

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

227 implemented in C++ (computational core) and Python (pipelining scripting wrapper, >=3.6.1).

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

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

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

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

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

233 developmental version that is a stand-alone Python program.

234 generate and customize such logos within the Python programming environment.

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

236 Although the Python programming language counts many Bioinformatics a

237 -source scientific computing library for the Python programming language.

238 icense, with bindings for the C++, C, R, and Python programming languages.

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

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

241 MS scan and MS/MS of PB products assisted by Python programs.

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

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

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

245 ly productive workflow systems, for example, Python/R in Jupyter/RStudio.

246 Independent projects to create and publish Python/R native CA interface libraries have reached an a

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

248 XDream is implemented in Python, released under the MIT License, and works on Lin

249 and reading ribo files in the R (RiboR) and Python (RiboPy) environments.

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

251 Additional optimization methods from the Python scipy library are utilized as well.

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

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

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

255 ein structure that can be used directly in a Python script through its application programming interf

256 We provide a user-friendly Python script to apply this strategy to real datasets.

257 al records was performed using a proprietary python script to identify any mention of QT prolongation

258 Therefore, we also include a Python script to quickly (ca. 132 000 molecules/min) cal

259 zed in three levels) and is searchable via a python script.

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

261 and combine optimization specifications via Python scripts or Genbank annotations.

262 The Python scripts that implement the SNP2SIM workflow are a

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

264 DP, have been implemented in the open-source Python software FRAPOSA, available at github.com/davidda

265 Analysis and Classifier Toolkit (PACT) is a Python software package that marries the fitness metric

266 oped BrainIAK (brainiak.org), an open-source Python software package that seamlessly integrates sever

267 Our proposal has been implemented using Python software.

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

269 into the growing scientific/cheminformatics Python stack, increasing the flexibility and extendibili

270 open-source and modular pipeline written in Python that introduces a novel method of assessing probe

271 ehavior analysis pipelines using interactive Python that researchers with no prior programming experi

272 BSA-Seq data analysis and implemented it in Python; the program was named PyBSASeq.

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

274 we present two different libraries in R and Python to facilitate the development of tools that can p

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

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

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

278 Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 fo

279 Here, we present Tensorpac, an open-source Python toolbox dedicated to PAC analysis of neurophysiol

280 We developed a python toolkit AnnoGen, which at the first time, allows

281 This lightweight python toolkit efficiently identifies clusters within a

282 We present ProteoClade, a Python toolkit that performs taxa-specific peptide assig

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

284 ndividuals who participated in ten 45-minute Python training sessions.

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

286 CpGtools is written in Python under the open-source GPL license.

287 SequelTools is implemented in bash, R, and Python using only standard libraries and packages and is

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

289 It is implemented in Python using the Flask-RESTful framework for the API, an

290 ChaperISM is implemented in Python version 3.

291 The EPM is compatible with python version 3.6 and above.

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

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

294 MAP is a suit of programs written in C++ and Python, where each program can be run separately, or an

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

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

297 dard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousand

298 The Python workflow utilizes molecular dynamics software (NA

299 We have developed PyIR, a Python wrapper and library for IgBLAST, which offers a m

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