WORKSHOP: DATA MANAGEMENT FOR SYSTEMS BIOLOGY AND THE LIFE SCIENCES
MAY 5-6, 2011, BIOQUANT HEIDELBERG
Authors: Ela Hunt, Peter Kunszt and Bernd Rinn
Affiliation: ETH Zurich
SystemsX.ch is a large national initiative for Systems Biology in Switzerland. Currently 14 large distributed projects are underway as well as many inderdisciplinary PhD projects and some joint projects with industry. SyBIT delivers the needed computational solutions for SystemsX.ch, particularly for large-scale data analysis and management. Priority areas are proteomics, next generation sequencing, high content screening, metabolomics and novel techniques for microscopy-based studies.
With SyBIT we provide and support large scale data and computing infrastructures (hierarchical file systems, cluster computing, security), common databases (openBIS and B-Fabric), common workflow solutions (P-GRADE, iBRAIN2, Galaxy); visualization and modeling solutions (GDV, XuvTools and MorphoGraphX). SyBIT enables collaborations with community developments like CellProfiler, and maintains several targeted short duration software projects to address a particular scientific question or to package new tools, providing visibility to the groups developing the algorithms. SyBIT also supports project processes and communications, lowering cross-organizational barriers for the distributed projects in SystemsX.ch. A shared wiki infrastructure, software, data and publication repositories are maintained. SyBIT's goal is to enable scientific collaboration and exchange, publications with high impact and documentation of data and methods for reproducibility.
In order to scale to very large data volumes, it is essential to decouple the low-level management of IT storage infrastructure from the end-user. With the openBIS framework we have developed and deployed a solution to this abstraction. The users see and manage their data through openBIS, which provides both a Web-UI as well as command line tools and is integrated with the tools people use daily, like Matlab. OpenBIS keeps track of the data on the storage arrays, which can be changed and managed independently of what the users see. Other tools in SyBIT integrate also with openBIS, like the workflow and process management tools.