Tools for keeping track of biogems
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The following information describes the steps to getting your biogem registered on If you are looking to generate the website instead: read! tracks interesting Ruby gems for bioinformatics.

To get your gem listed, simply create a gem named 'bio-mygem', i.e. start the name with bio dash, and push it onto You can use the biogem tool to create the plumbing, if you like. If you wish to name your gem differently, or host the gem elsewhere, it can still be listed. Either add a project description to /etc/biogems/name.yaml, or add an issue to the github tracker at

Gem settings

The settings displayed, on, are the ones you specify for a gem. In particular = "bio-gem"
gem.homepage = ""
gem.license = "MIT"
gem.summary = %Q{BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package}
gem.description = %Q{BioGem is a scaffold generator for those
  ... } = ""
gem.authors = ["Raoul J.P. Bonnal"]

This is the information pushed to when releasing a gem. harvests this information, with the download statistics.

Additional settings

Information, not available through gems, is captured through overriding settings. These are stored in this source repository, under ./etc/biogems/. These files add information, such as doi references, and the status of a gem (core, stable, test), but also potentially override gem settings, such as the summary field(!)

For example in ./etc/biogems/bio.yaml

# Additional BioRuby settings
:doi: 10.1093/bioinformatics/btq475
:status: core

It is also possible the overriding gemname.yaml is in your github repository(!) Just tell us where it resides through

GitHub API access limits

Without using authentication, the GitHub API allows only 60 requests per hour from a single IP address. But during the data collection phase of generating the website, the script currently needs to make around 200 requests to this API to fetch the number of issues and stargazers for each gem.

To get around this, go to the applications tab on your GitHub settings page and generate a new “Personal API access token”. Then copy that token (but not into the repository!), and before running the ./ script, set the GITHUB_API_TOKEN environment variable like this:

export GITHUB_API_TOKEN="copy-here-the-token-string-from-github"

That lets the script make 5000 requests per hour, which should be more then enough.

Website source

This repository on github contains the source code for the website. is an initiative by the BioRuby developers Copyright (C) 2011,2012,2013,2014 Pjotr Prins <>