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

Area of Science:

• Bioinformatics
• Computational Biology
• Life Sciences

Background:

• Numerous open-source bioinformatics protocols exist, but few maximize reuse and reproducibility.
• The wiki model, successful for information dissemination and collaboration, has not been widely applied to bioinformatics protocols.

Purpose of the Study:

• To explore the applicability of the wiki paradigm for bioinformatics protocols.
• To develop a platform that facilitates collaborative development, sharing, and execution of bioinformatics protocols.

Main Methods:

• PyPedia, a wiki-based platform, was developed where each article serves as both implementation and documentation for Python-based bioinformatics protocols.
• Hyperlinks enable the composition of complex workflows and promote protocol reuse.
• A RESTful API allows for external code execution.

Main Results:

• PyPedia integrates protocol implementation and documentation within a collaborative wiki environment.
• The platform supports the creation of complex workflows through inter-article linking.
• Initial content includes protocols for population statistics, format conversion, and genotype imputation.
• The user-friendly wiki syntax lowers the barrier for researchers with varying programming expertise.

Conclusions:

• PyPedia offers a collaborative environment for developing, sharing, and executing bioinformatics protocols.
• It complements existing resources and is suitable for both local and multi-center research teams.
• The platform promotes reproducible science and enhances collaboration among biologists and bioinformaticians.