PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols

Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
2015 Source Code for Biology and Medicine  
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
more » ... n 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.
doi:10.1186/s13029-015-0042-6 pmid:26587054 pmcid:PMC4652372 fatcat:tw7dzq6jazc37l4nqy7gzmd7aq