PyPedia
| Autor: | Joël Kuiper, Morris A. Swertz, George Potamias, Alexandros Kanterakis |
|---|---|
| Přispěvatelé: | Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI) |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Open science
Information Systems and Management Computer science PYTHON LIBRARY CODE Health Informatics SOFTWARE Reuse computer.software_genre Crowdsourcing Bioinformatics World Wide Web Dissemination computer.programming_language Web services Wiki business.industry PLATFORM Python (programming language) Data science Computer Science Applications WEB BIOLOGISTS Crowd sourcing Web service business computer Information Systems Coding (social sciences) Python |
| Zdroj: | Source code for biology and medicine, 10:14. BioMed Central Ltd. Source Code for Biology and Medicine |
| ISSN: | 1751-0473 |
| Popis: | Background Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. Results We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. Conclusions PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. Availability PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License. Electronic supplementary material The online version of this article (doi:10.1186/s13029-015-0042-6) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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