Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

Hi Oliver,

Thank you for the paragraph, with your permission I would like to add it to
the wiki; and great to hear that you are interested in participating.

Best,
Lena

On Fri, Feb 24, 2012 at 4:55 PM, Oliver Ruebenacker <curoli@gmail.com>wrote:

>     Hello Helena, All,
>
>  I'm interested in joining the Systems Biology Taskforce. Sorry I
> could not make the initial call. My interest is turning biological
> knowledge into mathematical models, automatically. A brief description
> is below.
>
>  Thanks!
>
>     Take care
>     Oliver
>
>  Living organisms are so enormously complex that we need computer
> simulations to understand the consequences of their vast biochemical
> reaction networks. As we uncover an increasing part of these networks,
> our established knowledge is increasingly stored in free web databases
> and available for query and download in machine-readable formats,
> especially in the RDF/OWL-based community standard Biological Pathways
> Exchange (BioPAX) [1]. The available data is massive and growing, e.g.
> Pathway Commons [2] stores 1,700 pathways, 414 organisms, 440,000
> interactions and 86,000 substances. This data is fully linked with
> open controlled terminologies such as gene ontology (e.g. anatomical
> features) [3] and other free online databases such as ChEBI
> (chemicals) [4], KEGG (genes a.o.) [5], UniProt (proteins) [6] and
> PubMed (publications) [7].
>
>  Automatic use of this knowledge for computer simulations of
> biological organisms has been an ongoing challenge [8,9,10]. Now,
> Systems Biology Pathway Exchange (SBPAX) [11], a BioPAX extension,
> allows the inclusion of quantitative data and systems biology terms,
> especially the Systems Biology Ontology (SBO) [12]. SBPAX support has
> been implemented by the Virtual Cell [13], Signaling Gateway Molecule
> Pages [14] and System for the Analysis of Biochemical Pathways -
> Reaction Kinetics (SABIO-RK) [15]. For the first time, a mathematical
> model can be automatically built and fully annotated from a pathway of
> interest.
>
>  Citations:
>
>  [1] Biological Pathway Exchange (BioPAX), www.biopax.org
>  [2] Pathway Commons, www.pathwaycommons.org
>  [3] Gene Ontology (GO), www.geneontology.org/
>  [4] Chemical Entities of Biological Interest (ChEBI),
> www.ebi.ac.uk/chebi/
>  [5] Kyoto Encyclopedia of Genes and Genomes (KEGG), wwww.genome.jp/kegg/
>  [6] UniProt, www.uniprot.org
>  [7] PubMed, www.ncbi.nlm.nih.gov/pubmed/
>  [8] Modeling without Borders: Creating and Annotating VCell Models
> Using the Web, Michael L. Blinov, Oliver Ruebenacker, James C. Schaff
> and Ion I. Moraru,  Lecture Notes in Computer Science, 2010, Volume
> 6053 (2010).
>  [9] Using views of Systems Biology Cloud: application for model
> building, Oliver Ruebenacker, Michael Blinov, Theory in Biosciences,
> Volume 130, Number 1, 45-54 (2010).
>  [10] Integrating BioPAX pathway knowledge with SBML models, Michael
> L Blinov, Oliver Ruebenacker, Ion I Moraru, IET Syst. Biol., 2009,
> Vol. 3, Iss. 5, pp. 317-328 (2009).
>  [11] Systems Biology Pathway Exchange (SBPAX), www.sbpax.org
>  [12] Systems Biology Ontology, www.ebi.ac.uk/sbo/main/
>  [13] Virtual Cell, http://vcell.org
>  [14] Signaling Gateway Molecule Pages,
> www.signaling-gateway.org/molecule/
>  [15] System for the Analysis of Biological Pathways – Reaction
> Kinetics (SABIO-RK), http://sabio.villa-bosch.de/
>
> On Tue, Feb 21, 2012 at 4:32 PM, Helena Deus <helenadeus@gmail.com> wrote:
> > Dear All,
> >
> > Please join me tomorrow for the kick-off telco of the Systems Biology
> Task
> > Force. Systems Biology is about looking at biological systems from an
> > integrated perspective and to use that perspective to understand
> disease. We
> > will be discussing the general goals, strategy and structure of the task
> > force.
> >
> > Please see http://www.w3.org/wiki/HCLSIG/SysBio for an initial
> motivation,
> > and description, of what this task will be focused on (with due
> flexibility
> > according to participants input).
> >
> >
> > * Date of Call: Tuesday February 21, 2012
> > * Time of Call: 11:00am Eastern Daylight Time (EDT)
> > * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> > * [Note: limited access to European dial in numbers below]
> > * Dial-In #: +33.4.26.46.79.03 (Nice, France)
> > * Dial-In #: +44.203.318.0479 (Bristol, UK)
> > * Participant Access Code: 4257 ("HCLS").
> > * IRC Channel: irc.w3.org port 6665 channel #HCLS
> > For instant IRC access:
> > 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]), Quick Start:
> Click
> > on
> > [http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
>  mibbit]
> >
> > * Duration: ~1h
> > * Convener: Helena
> > * Scribe: TBD
> >
> > Kind regards,
> > Helena
>
>
>
> --
> Oliver Ruebenacker, Computational Cell Biologist
> Virtual Cell (http://vcell.org)
> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
> http://www.oliver.curiousworld.org
>



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