BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Talks.cam//talks.cam.ac.uk// X-WR-CALNAME:Talks.cam BEGIN:VEVENT SUMMARY:Towards large scale models of biochemical networks - James Faeder (University of Pittsburgh) DTSTART:20160404T091500Z DTEND:20160404T100000Z UID:TALK65290@talks.cam.ac.uk CONTACT:INI IT DESCRIPTION:Co-authors: Jose Juan Tapia (University of Pittsburgh)\, John Sekar (University of Pittsburgh)

In this talk I will a ddress some of the challenges faced in developing detailed models of bioch emical networks\, which encompass large numbers of interacting components. Although simpler coarse-grained models are often useful for gaining insig ht into biological mechanisms\, such detailed models are necessary to unde rstand how molecular components work in the network context and essential to developing the ability to manipulate such networks for practical benefi ts. The rule-based modeling (RBM) approach\, in which biological molecules can be represented as structured objects whose interactions are governed by rules that describe their biochemical interactions\, is the basis for a ddressing multiple scaling issues that arise in the development of large s cale models. Currently available software tools for RBM\, such as BioNetGe n\, Kappa\, and Simmune\, enable the specification and simulation of large scale models\, and these tools are in widespread use by the modeling comm unity. I will re view some of the developments that gave rise to those cap abilities\, and then I will describe our current efforts broaden the appea l of these tools as well as to better enable collaborative development of models through re-use of existing models and improving visual representati ons of models.

Related Links LOCATION:Seminar Room 1\, Newton Institute END:VEVENT END:VCALENDAR