Hi Jun and all,
Apologies, I can't join you today, but it is an interesting topic.
On the subject of aligning related models, there is some nice work from
Edda Klipp's group that you might want to look at (the makers of
Semantic SBML)
BMC Bioinformatics. <http://www.ncbi.nlm.nih.gov/pubmed/22289386#> 2012
Jan 30;13:18.
Propagating semantic information in biochemical network models.
Schulz M
<http://www.ncbi.nlm.nih.gov/pubmed?term=Schulz%20M%5BAuthor%5D&cauthor=true&cauthor_uid=22289386>,
Klipp E
<http://www.ncbi.nlm.nih.gov/pubmed?term=Klipp%20E%5BAuthor%5D&cauthor=true&cauthor_uid=22289386>,
Liebermeister W
<http://www.ncbi.nlm.nih.gov/pubmed?term=Liebermeister%20W%5BAuthor%5D&cauthor=true&cauthor_uid=22289386>.
Genome Inform. <http://www.ncbi.nlm.nih.gov/pubmed/17503356#>
2006;17(1):62-71.
SBMLmerge, a system for combining biochemical network models.
Schulz M
<http://www.ncbi.nlm.nih.gov/pubmed?term=Schulz%20M%5BAuthor%5D&cauthor=true&cauthor_uid=17503356>,
Uhlendorf J
<http://www.ncbi.nlm.nih.gov/pubmed?term=Uhlendorf%20J%5BAuthor%5D&cauthor=true&cauthor_uid=17503356>,
Klipp E
<http://www.ncbi.nlm.nih.gov/pubmed?term=Klipp%20E%5BAuthor%5D&cauthor=true&cauthor_uid=17503356>,
Liebermeister W
<http://www.ncbi.nlm.nih.gov/pubmed?term=Liebermeister%20W%5BAuthor%5D&cauthor=true&cauthor_uid=17503356>.
Annotation and *merging* of *SBML* models with semanticSBML.
<http://www.ncbi.nlm.nih.gov/pubmed/19933161>
Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.
Bioinformatics. 2010 Feb 1;26(3):421-2. Epub 2009 Nov 17.
Best wishes,
Katy
On 22/05/2012 17:53, Mark wrote:
Excellent! Looking forward to it!
M
On Tue, 22 May 2012 15:27:12 +0200, Jun Zhao <jun.z...@zoo.ox.ac.uk>
wrote:
Dear all,
I am helping Lena to chair tomorrow's call because she is tied up
with travel plans.
Tomorrow we are planning to learn more about the MAPK pathway by
looking into the BioModels database, and how to align related models
using approaches like Semantic SBML or others.
Agenda below:
Meeting: HCLS System Biology
Date: May 23, 2012
Frequency: Every other Wednesday
Convener: Jun Zhao
Dial-In #: +1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS
IRC Web: http://goo.gl/A6WZn
Agenda
* (Semantic) alignment of SysBio Model related to MAPK pathways
* See also:
** BioModels Database: http://www.ebi.ac.uk/biomodels-main/
** Semantic SBML: http://semanticsbml.org/semanticSBML/simple/index
* AOB
Hope to see as many of you as possible. Come to help!
Cheers,
Jun
--
Dr. Katy Wolstencroft
Research Fellow
School of Computer Science
1.17 Kilburn Building
University of Manchester
Manchester
M13 9PL
