title: PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.
abstract: 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.
  
  
  BACKGROUND
  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.
authors.affiliation: University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Postbus 30 001, Groningen, 9700 RB The Netherlands ; Institute of Computer Science, Foundation for Research and Technology Hellas (FORTH), Nikolaou Plastira 100, Heraklion, 71110 Greece.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Kanterakis
authors.affiliation: University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Postbus 30 001, Groningen, 9700 RB The Netherlands.
authors.forename: Joël
authors.initials: J
authors.lastname: Kuiper
authors.affiliation: Institute of Computer Science, Foundation for Research and Technology Hellas (FORTH), Nikolaou Plastira 100, Heraklion, 71110 Greece.
authors.forename: George
authors.initials: G
authors.lastname: Potamias
authors.affiliation: University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Postbus 30 001, Groningen, 9700 RB The Netherlands.
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
keywords: Crowdsourcing; Open science; Python; Web services; Wiki