11/10/00SC2000 Panel, Convergence at the Extremes1 Convergence at the Extremes How are we doing?  Electronic circuits: A (cheating)  The weather: B+ (grade inflation)  Cells: I (Extenuating Circumstances)  Its really hard (lots of fine structure, mixed modes)  Experimental outcome data is highly abstract We can’t say that we understand a system until we can write a simulator that predicts behavior. (Necessary Condition)

11/10/00SC2000 Panel, Convergence at the Extremes2 Virtual Cell Geometric/Physical Modeling Virtual Cell D.G. Shin, L. Liu, J. Schaff, L. Loew, (1998) "Virtual Cell: A General Framework for Simulating and Visualizing Cellular Physiology," Proc. of 4th IFIP 2.6 Working Conference on Visual Database Systems, L'Aquila, Italy, May calcium wave in neuroblastoma mitochondrial respiration

11/10/00SC2000 Panel, Convergence at the Extremes3 ECELL: Gene Networks ECELL: software environment for whole-cell simulation Bioinformatics, Vol 15, 72-84, Copyright © 1999 by Oxford University Press Substances, Genes and reaction rules 120 Genes selected from Mycoplasma genitalium quantities and rates gene Expression levels

11/10/00SC2000 Panel, Convergence at the Extremes4 Cell Model Building machine Code (mining, sim) homogenize analyze treat the data is aggregate and static the meta-data is complex! low volume real-time Self-describing stimulus/response

11/10/00SC2000 Panel, Convergence at the Extremes5 Capturing the Meta-data

11/10/00SC2000 Panel, Convergence at the Extremes6 Convergence at the Extremes events

11/10/00SC2000 Panel, Convergence at the Extremes7 Software Infrastructure Event by event re-composition – instead of static connections Interpretation Subscription User Association User Association

11/10/00SC2000 Panel, Convergence at the Extremes8 Take Home Integration of the Small w/ the Big (Convergence)  Demands new kinds of software  Dynamic composition of services  Mobility of code, data, devices, and users  Careful attention to use of state to keep things running  Domain specific abstractions: interact w/ a domain appropriate interface, not a file system  Requires certain capabilities from domain specific devices  Basic communication skills  Basic adaptability  Will have a huge payoff in many fields and applications