interface layered on top of rserve-client gem for interacting with R

you should check out rsruby first. This is a very low-tech way to run R. It does have the advantage of being able to run R code essentially unchanged.

uses a simple YAML format to store bibliographies. Then modifies citations in openoffice and outputs a bibliography (in different forms) for inclusion in the document

does high pairwise alignment of sequencing reads with a template using bioruby and clustalw. gives template-centric output.

uses pymol

basic, shared functionality for mspire libraries.

aids for creating and calculating error rates using target-decoy searches and sample validation.

provides programmatic access to fasta files

mspire library for working with mzIdentML, pepxml, and related.

peptide fragmentation and protein digestion

quantitation of mass spectrometry datasets (proteomic, metabolomic/lipidomic). Not related to MSQuant

reads .SRF, .SQT and supports conversions