The Jupyter notebook bioinformatics-help-wanted.ipynb searches the GitHub API for repositories matching search terms, and for open issues within those repositories matching an issue label. For example, use this code to find a list of all repositories matching the search term "bioinformatics", written in languages of your choice, with issues labeled "help wanted".
pip install -r requirements.txt
A GitHub account and associated OAuth token are required to run this notebook. See these instructions to create a token.
Simply modify the "Parameters" section with your GitHub credentials and desired search terms.
# GitHub credentials
gh_username = 'pamelarussell'
gh_oauth_file = 'gh_oauth_token.txt'
# GitHub search terms
topics = ['bioinformatics']
languages = ['scala', 'java']
issue_label = 'help wanted'
The running notebook will print a summary of repos and open issues matching your search terms.
Example results:
Repo: hail-is/hail
Description: Scalable genomic data analysis.
Language: Scala
URL: https://github.com/hail-is/hail
Open issues with label "help wanted":
- Improve nCubeOfVolumeAtMost (https://github.com/hail-is/hail/issues/1998)
- Hail's Matrix Multiply Should Perform Better When Massively Reducing Size (https://github.com/hail-is/hail/issues/1975)
Repo: biojava/biojava
Description: :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Language: Java
URL: https://github.com/biojava/biojava
Open issues with label "help wanted":
- Extend dssp implementation to also support the promotif standard (https://github.com/biojava/biojava/issues/764)
- Use Protonation Variants Companion Dictionary (https://github.com/biojava/biojava/issues/686)
- Secondary structure assignment could be done taking all symmetry partners into account (https://github.com/biojava/biojava/issues/454)
- Add Bird parsing functionality (https://github.com/biojava/biojava/issues/436)
- Add support for parsing secondary structure in mmCIFF (https://github.com/biojava/biojava/issues/333)
- New StructuralAlignment Algorithms (https://github.com/biojava/biojava/issues/307)
- Introduction of semiglobal alignments (https://github.com/biojava/biojava/issues/243)
- Add ability to create a Profile from a multiple sequence alignment file (https://github.com/biojava/biojava/issues/223)
- MrBayes Parser (https://github.com/biojava/biojava/issues/123)
- Balibase (https://github.com/biojava/biojava/issues/119)
- Add a SCOP2 parser (https://github.com/biojava/biojava/issues/82)
Repo: openwdl/wdl
Description: Workflow Description Language - Specification and Implementations
Language: Java
URL: https://github.com/openwdl/wdl
Open issues with label "help wanted":
- map contains_key() function (https://github.com/openwdl/wdl/issues/305)
- Allow passthrough of inputs from the `inputs.json` to a subworkflow (https://github.com/openwdl/wdl/issues/262)
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