Tools for keeping track of biogems through
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Latest commit 367adb9 Mar 1, 2016 @pjotrp Merge pull request #86 from yeban/ncbi-blast-dbs
Add ncbi-blast-dbs gem.
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bin Fetch rubygems Oct 25, 2015
doc formatting Apr 2, 2015
etc Add ncbi-blast-dbs gem. Mar 1, 2016
features Revamping biogems Oct 24, 2015
html Proceeding with middleman Oct 25, 2015
lib Fixing Oct 25, 2015
scripts Fetch rubygems Oct 25, 2015
source Meta tags Jan 17, 2014
test/data Rename YAML Dec 30, 2013
.gitignore Revamping biogems Oct 24, 2015
Gemfile Revamping biogems Oct 24, 2015
Gemfile.lock Generating site Oct 24, 2015 Moving stuff Oct 26, 2015 Revamping biogems Oct 24, 2015
Rakefile Revamping biogems Oct 24, 2015
config.rb Rewrite website from staticmatic to middleman Dec 7, 2013 tracks interesting Ruby gems for bioinformatics.

The following information describes the steps to getting your biogem registered on If you are looking to generate the website instead: read!

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

Displayed gem information

The settings displayed, on, are the ones you specify in your 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

Website source

This repository on github contains the source code for the website. is an initiative by the BioRuby developers Copyright (C) 2011-2015 Pjotr Prins