a MOLGENIS based Platform for Proteomics

Summary

Developers	​GeorgeByelas, JoeriVanDerVelde?, ​MorrisSwertz
Status	Design, components development, test-cases identification

Abstract:

High-throughput proteomics research is complex and requires the combination of multiple experimental approaches each producing large amounts of diverse data. The analysis and evaluation of these data are equally complex requiring specific integrations of various software tools into complex workflows. The programming and configuration efforts to create and run tools as pipelines, and their deployment on clusters, grids, fileservers and databases, is complicated and time consuming.
We use the novel approach of ‘domain specific models’ to efficiently describe what tools and pipelines are needed. Then from these models we automatically produce all the software code needed for a ‘dynamic software infrastructures’ that enables biologist to focus on answering biological questions instead of informatics.
The result is a software suite to easily add new proteomics analysis tools to a shared infrastructure and automatically generate suitable web user interfaces for biologists and programmatic-interfaces in SOAP and Java, which can be deployed in a 'cloud' computing infrastructure for proteomics researchers to run their pipelines.

Project Major Deliverables:

• Tool and pipeline description languages
• Proteomics Platform software
• Independent software components (including web-services and individual software packages)

Current prototype architecture