Katy Wolstencroft @ Systems Biology Task Force - Wed 18th April at 11AM EDT - TODAY!

Dear All,

Please join me tomorrow at the Systems Biology Task force, where Katherine
Wolstencroft will give us an overview of SEEK.

*PLEASE NOTE:* Like last time, we will attempt to use webex for slide
sharing, so I will share the webex link on IRC at 11AM EDT today.

*

SEEK: An e-Laboratory for Systems Biology in Europe
Franco B. Du Preez(1), Stuart Owen(2), Katherine Wolstencroft(2), Olga
Krebs(3), Quyen Nguyen(3), Wolfgang Müller(3), Carole Goble(2) & Jacky L.
Snoep(4)

The SEEK is an open-source, web-based platform for the management and
exchange of Systems Biology data, models and processes. It was originally
developed in the SysMO-DB project (http://www.sysmodb.org) for the
pan-European SysMO consortia (Systems Biology of Micro Organisms). However,
it is now also being adopted by a large number of other consortia across
Europe, for example, the Virtual Liver, EviMalar and Unicellsys.

The SEEK is an e-Laboratory. In addition to providing a registry and
repository of Systems Biology data, it provides facilities for model
simulation, data exploration and is a gateway to other useful resources,
such as JWS Online, BioModels and the BioPortal. Taverna workflows will
also be available for discovering and running through SEEK, giving SEEK
users access to a collection of complex Systems Biology analysis methods
and data integration protocols (http://www.myexperiment.org/packs/47.html)

Underlying the SEEK is the JERM (Just Enough Results Model), which is a
minimum information model describing the relationships between SEEK assets.
The JERM incorporates the ISA structure (Investigation, Study, Assay) to
associate data with the assays that generated them, and to allow the
aggregation of assays into wider studies and investigations. JERM data
compliance is managed by the distribution of JERM spreadsheet templates,
which can be semantically enabled with RightField, a tool that embeds
collections of ontology terms into specific spreadsheet cells. Ongoing work
is exploring extracting, storing and querying collected data and metadata
in RDF.
1.Manchester Interdisciplinary Biocentre, University of Manchester, UK
2.School of Computer Science, University of Manchester, UK
3.Heidelberg Institute for Theoretical Studies (Hits), gGmbH, Germany
4.Department of Biochemistry, Stellenbosch University, South Africa

Katy Wolstencroft

I am a Research Fellow at the University of Manchester and a visiting
researcher at the Vrije Universiteit in Amsterdam. I am a member of the
SysMO-DB project and the myGrid consortium. My background is in
bioinformatics and my work focuses on data integration, semantic data
integration and scientific workflows.

Stuart Owen is a Software Architect at the University of Manchester. He is
a member of the SysMO-DB project and the myGrid consortium. He has a long
background in Software Engineering, with a particular focus on Knowledge
Management.
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*Conference Details
*Systems Biology
http://www.w3.org/wiki/HCLSIG/SysBio

 Date of Call: Wednesday April 18 2012
 Time of Call: 11:00am - 12:00pm EDT
 Dial-In #: +1.617.761.6200 (Cambridge, MA)
 Dial-In #: +33.4.26.46.79.03 (Paris, France)
 Dial-In #: +44.203.318.0479 (London, UK)
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see [
http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [
http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
 Mibbit quick start: Click on [
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit]
for instant IRC access
 Duration: 1h
 Convener: Helena F Deus

*Agenda
** Katy's talk
* Ideas about next invited speakers
* Volunteers to start looking at systems biology models



-- 
Helena F. Deus
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/