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

P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, M. J. L. de Hoon
2009 Bioinformatics  
Availability: Biopython is freely available, with documentation and source code, at www.biopython.org under the Biopython license.  ...  The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems.  ...  The many Biopython contributors over the years are warmly thanked, a list too long to be reproduced here.  ... 
doi:10.1093/bioinformatics/btp163 pmid:19304878 pmcid:PMC2682512 fatcat:boemypxobfh5dm3zdfynibw46e

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

Eric Talevich, Brandon M Invergo, Peter JA Cock, Brad A Chapman
2012 BMC Bioinformatics  
Results: We built a Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology.  ...  Bio.Phylo is included with Biopython, available through the Biopython website, http://biopython.org.  ...  We also thank the Biopython community and Open Bioinformatics Foundation for ongoing advice and support.  ... 
doi:10.1186/1471-2105-13-209 pmid:22909249 pmcid:PMC3468381 fatcat:252rrkv2tvbdrdmc5pidepesfq

Diary

2000 Briefings in Bioinformatics  
BioCoRE, 11 a Biological Collaborative Research Environment for Structural Biology, is a web-based collection of tools that is freely available.  ...  Another area is in scripting, where biologically focused scripting libraries such as BioPerl and BioPython have become extremely popular tools for writing quick queries to the numerous publicly available  ... 
doi:10.1093/bib/1.4.421 fatcat:3bpgbivypjbvzdqkdslqikausu

News section

D. S. Gonzalez
2002 Briefings in Bioinformatics  
BioCoRE, 11 a Biological Collaborative Research Environment for Structural Biology, is a web-based collection of tools that is freely available.  ...  Another area is in scripting, where biologically focused scripting libraries such as BioPerl and BioPython have become extremely popular tools for writing quick queries to the numerous publicly available  ... 
doi:10.1093/bib/3.4.421 fatcat:dzo5pxx3bbff7nqov7oasn2rwi

Biotite: a unifying open source computational biology framework in Python

Patrick Kunzmann, Kay Hamacher
2018 BMC Bioinformatics  
We have developed the Python package Biotite: a general computational biology framework, that represents sequence and structure data based on NumPyndarrays.  ...  As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising.  ...  Availability of data and materials The Biotite source code is hosted at https://github.com/biotite-dev/biotite and its official documentation at https://www.biotite-python.org/.  ... 
doi:10.1186/s12859-018-2367-z pmid:30285630 pmcid:PMC6167853 fatcat:5gy5ujsacvfohm4yrekjdqrdbu

Pise: Software for building bioinformatics webs

D. Gilbert
2002 Briefings in Bioinformatics  
It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services  ...  Pise is interface construction software for bioinformatics applications that run by commandline operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses.  ...  Pise-python provides similar integration with BioPython and the Python programming environment.  ... 
doi:10.1093/bib/3.4.405 pmid:12511068 fatcat:dw77hayqnzcobig656h7glgjbe

Bio-Stamp: Simple Tool for Routine Biological Data Analysis

Peter Tharwat Habib, Alsamman Mahmoud Alsamman, Aladdin Hamwieh
2018 Annals of Clinical and Laboratory Research  
The massive extension in biological data induced a need for user-friendly bioinformatics tools could be used for routine biological data manipulation.  ...  These tools accept common biological data formats and produce humanreadable output files could be stored on local computer machines.  ...  Bio-Stamp source code and freely available, where its code could be modified, extended or integrated in different bioinformatics pipelines.  ... 
doi:10.21767/2386-5180.100265 fatcat:uczghwutyfeurckm5bxonynl2a

RCytoscape: tools for exploratory network analysis

Paul T Shannon, Mark Grimes, Burak Kutlu, Jan J Bot, David J Galas
2013 BMC Bioinformatics  
Conclusions: Progress in bioinformatics and computational biology depends upon exploratory and confirmatory data analysis, upon inference, and upon modeling.  ...  Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and quantities of data available  ...  Acknowledgements The authors thank their colleagues at their respective institutions, especially Vésteinn Þórsson and Vangelis Simeonidis of the Institute for Systems Biology, and Alexander Skupin of the  ... 
doi:10.1186/1471-2105-14-217 pmid:23837656 pmcid:PMC3751905 fatcat:3d2vq5didrbrtejzfdwoikuhe4

PyElph - a software tool for gel images analysis and phylogenetics

Ana Brânduşa Pavel, Cristian Ioan Vasile
2012 BMC Bioinformatics  
Results: PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community.  ...  Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface  ...  ABP provided the biological expertise and had a significant contribution to the back-work of the program: lane and band detection, weight computation, band matching and phylogenetic tree generation.  ... 
doi:10.1186/1471-2105-13-9 pmid:22244131 pmcid:PMC3299638 fatcat:62dmculvifebziuauryznmscji

pdb-tools: a swiss army knife for molecular structures

João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
2018 F1000Research  
The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI.  ...  The pdb-tools are a collection of Python scripts for working with molecular structure data in the Protein Data Bank (PDB) format.  ...  Acknowledgments The authors acknowledge the members of the Bonvin group for fruitful discussions and suggestions of new tools over the years.  ... 
doi:10.12688/f1000research.17456.1 pmid:30705752 pmcid:PMC6343223 fatcat:zozzlxplefgxzlobqi4v2gqpfu

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces

Elishai Ezra Tsur
2017 BioData Mining  
Databases are imperative for research in bioinformatics and computational biology.  ...  It is currently evident that fields such as computational biology and bioinformatics are practically fueled by the increasing computational resources available and the development of software encapsulation  ...  Consent for publication Not applicable. Ethics approval and consent to participate Not applicable.  ... 
doi:10.1186/s13040-017-0130-z pmid:28293298 pmcid:PMC5346198 fatcat:dmipmvs3xjdp3fs2a7vkqdkfte

Workflow and web application for annotating NCBI BioProject transcriptome data

Roberto Vera Alvarez, Newton Medeiros Vidal, Gina A. Garzón-Martínez, Luz S. Barrero, David Landsman, Leonardo Mariño-Ramírez
2017 Database: The Journal of Biological Databases and Curation  
They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities.  ...  Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data.  ...  Acknowledgements We thank Richa Agarwala for transcriptome assembly, Mark Johnson for his help and advice about Django, Anatoliy Kuznetsov and Victor Joukov for the support and contribution to integrate  ... 
doi:10.1093/database/bax008 pmid:28605765 pmcid:PMC5467576 fatcat:voiub6j2uree7jy5gud3xmujkq

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen, Dong-Sheng Cao
2018 Journal of Cheminformatics  
, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions.  ...  PyBioMed is freely available at http:// projects.scbdd.com/pybiomed.html.  ...  Conclusion PyBioMed provides a freely available and ease-to-use python library to calculate various features of biological molecules and complex interaction samples conveniently.  ... 
doi:10.1186/s13321-018-0270-2 pmid:29556758 pmcid:PMC5861255 fatcat:ss76y77rcrbn5ayrondsyql77q

EggLib: processing, analysis and simulation tools for population genetics and genomics

Stéphane De Mita, Mathieu Siol
2012 BMC Genetics  
Results: In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C ++/Python software package providing efficient and easy to use computational tools for  ...  With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity.  ...  Acknowledgements The authors would like to thank Sylvain Glémin, Julien Dutheil, Stephen Wright, Joëlle Ronfort, François Sabot and three reviewers for comments on the manuscript and Gerben Bijl for discussions  ... 
doi:10.1186/1471-2156-13-27 pmid:22494792 pmcid:PMC3350404 fatcat:ue2z2dh37baonmeock6ghhyelq

G-language System as a platform for large-scale analysis of high-throughput omics data

Kazuharu Arakawa, Masaru Tomita
2006 Journal of pesticide science  
The G-language software suite provides a comprehensive workbench for large-scale omics research and systems biology.  ...  The suite includes a bioinformatics research framework G-language Genome Analysis Environment, which contains a Gene Prediction Accuracy Classification benchmarking tool for the quantification of the sensitivity  ...  Acknowledgments This research was supported in part by the Japan Society for the Promotion of Science (JSPS), and CREST of JST (Japan Science and Technology).  ... 
doi:10.1584/jpestics.31.282 fatcat:miwfmcb34bcbtcmyre5t7sgbhi
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