SyBIT Tools for SystemsX.ch Ela Hunt and Peter Kunszt, SyBIT, SystemsX.ch, ETH Zurich

{ela.hunt, peter.kunszt}@systemsx.ch

SystemsX.ch is a consortium encompassing nine universities and three research institutions. It is funded with a federal budget of CHF 100 Mio for the period of 2008 – 2011, matched by the same amount by the partners receiving funds. SystemsX.ch supports about 750 researchers from 250

research groups in 62 projects. https://wiki.systemsx.ch/display/SYBIT/, http://ww.sybit.net

The portal administrators together with the advanced users develop and publish workflow (WF) templates. The scientific users access the workflows via a friendly interface and focus on the results.

WORKFLOWS AND CLOUDS FOR PROTEOMICS AND NGSWORKFLOWS AND CLOUDS FOR PROTEOMICS AND NGS iBRAIN2 AND openBIS FOR HCSiBRAIN2 AND openBIS FOR HCS

P-GRADEP-GRADE

OpenBISOpenBISComputingClusters

ComputingClusters

ConfigureWF

ADMIN

Choose data+WF

SCIENTIST

Results

Step 1: the workflow processes the inputs in parallel using X!Tandem, OMSSA and Mascot. Step 2: the workflow combines the results from each parameter set using ProteinProphet and Spectrast. The results are exported into OpenBIS.

OpenBISDataStoreServer

iBRAIN2Workflow Manager

OpenBISWeb Application

iBRAIN2Status Monitor Cluster + Cluster FS

Acquire data

managestoreddata

request data store results

browse data

monitor workflowsretrieve data

stage data

iBRAIN2 together with openBIS support high content screening (HCS). HCS experiments produce TB-sized data. Images are compressed, transferred to a database, sent to a computing cluster for analysis, and the results are brought back to the database. The software replicates the functionality of iBRAIN, http://www.imsb.ethz.ch/researchgroup/plucas/Software/iBRAIN, in a portable and reconfigurable Java and DB-based platform.

openBIS FOR HCS, NGS, PROTEOMICS AND METABOLOMICSopenBIS FOR HCS, NGS, PROTEOMICS AND METABOLOMICS

Merged channelsCy3DAPIGFP

http://www.cisd.ethz.ch/software/openBIS provides high volume image and metadata storage and search functions and supports image and data analysis for HCS, NGS, proteomics and metabolomics in the lab via a range of visualisation options. Video material on openBIS is available.

Ela Hunt Peter Kunszt

PS 281

IBM Cloud Data Centers

IMSB CloudBroker IBM

PlatformClient

…

Rosetta InstancesStorage Instance

input filedownloadresult fileupload

numbercrunching

job steeringInstance allocation and

deallocation

Clientrequest

result file downloadInput file upload

Strep pneumoniae protein 3D modelling: the CloudBroker Platform manages the data placement and steers Rosetta instance allocations and deallocations

FMI NGS pipeline. SyBIT Team

Recent publications1. P Kunszt, L Espona Pernas, A Quandt, E Schmid, E Hunt, L Malmstrom (2011). The Swiss Grid Proteomics Portal. PARENG'11. Civil-Comp Press, Stirlingshire, UK, Paper 81, 2011.2. K Kozak, A Bauch, T Pylak, B Rinn (2010). Towards a comprehensive open source platform for management and analysis of High Content Screening data. European Pharmaceutical Review, 4:34-38.3. R Murri, P Kunszt, S Maffioletti, V Tschopp. GridCertLib: a Single Sign-on Solution for Grid Web Portals, to appear in Journal of Grid Computing.