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

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 18 Apr 2012 10:15:14 -0700
Message-ID: <c8ec955d4658a81ccec41db11971061a@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Laleh.Kazemzadeh@deri.org, Joanne Luciano <jluciano@gmail.com>
hi lena,

here's the reference to pubcrawl: https://www.systemsbiology.org/pubcrawl

there's a link to the google code site from there.



Michael Miller

Software Engineer

Institute for Systems Biology

*From:* Joanne Luciano [mailto:jluciano@gmail.com]
*Sent:* Wednesday, April 18, 2012 9:47 AM
*To:* M. Scott Marshall
*Cc:* Helena Deus; W3C HCLSIG hcls; <Laleh.Kazemzadeh@deri.org>
*Subject:* Re: Katy Wolstencroft @ Systems Biology Task Force - Wed 18th
April at 11AM EDT - TODAY!


Or another time?

I signed on, but couldn't stay had to catch a train (FYI - highly recommend
the train to/from Rensselaer / NY city. Beautiful ride along the east bank
of the Hudson river (2.5 hrs for planning purposes))

Sorry to miss you Katy!

Also, in case any of you have not seem Katy's earlier work on classifying
phosphotases check it out.  It is a beautiful straightforward example of
using defined classes in OWL and reasoners to do science. I have used that
example many times.

Katy- were you able to get the wet lab experiment done to look for the
unclassified phosphate?


Sent from my iPhone

On Apr 18, 2012, at 10:58 AM, "M. Scott Marshall" <mscottmarshall@gmail.com>

Regrets. Any chance of a webex recording?


On Apr 18, 2012 12:42 PM, "Helena Deus" <helenadeus@gmail.com> wrote:

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.


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

*Conference Details**
*Systems Biology

 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 #: + (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

** 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

Received on Wednesday, 18 April 2012 17:15:47 UTC

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