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

Me too - I was sorry not to be able to make the initial meeting, and I am
very interested in participating. My group is researching large scale data
mining of drug discovery datasets, including development of the
Chem2Bio2RDF repository and various algorithms (more information at
http://djwild.info)

Thanks and best wishes

David
____________________________________________________

Dr. David J. Wild, djwild@indiana.edu, http://djwild.info
Assistant Professor of Informatics & Computing
Director, Cheminformatics & Chemogenomics Research Group
Indiana University School of Informatics and Computing
150 S. Woodlawn Rm 330B, Bloomington, IN 47405
Tel. +1 812 856 1848



On Fri, Feb 24, 2012 at 12:10 PM, Helena Deus <helenadeus@gmail.com> wrote:

> 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/
>
>