Interfaces to PeptideAtlas: a case study of standard data access systems.

Access to public data sets is important to the scientific community as a resource to develop new experiments or validate new data. Projects such as the PeptideAtlas, Ensembl and The Cancer Genome Atlas (TCGA) offer both access to public data and a repository to share their own data. Access to these data sets is often provided through a web page form and a web service API.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

Background: High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.

Results: Existing software solutions provide static and well-established algorithms in a restrictive package.

mspecLINE: bridging knowledge of human disease with the proteome.

Background: Public proteomics databases such as PeptideAtlas contain peptides and proteins identified in mass spectrometry experiments. However, these databases lack information about human disease for researchers studying disease-related proteins. We have developed mspecLINE, a tool that combines knowledge about human disease in MEDLINE with empirical data about the detectable human proteome in PeptideAtlas.