BioPathways SIG: Nicolas Le Novére "The Systems... - ISMB/ECCB Stockholm 2009

supposedly biologist-friendly pathway maps are completely unintelligible - Ruchira S. Datta

by contrast, electric circuit diagrams, even very complex ones, can be understood by high school students - Ruchira S. Datta

Systems Biology Graphical Notation http://sbgn.org a limited number of well-defined symbols for biochemical and cellular events - Ruchira S. Datta

3 languages: process diagrams, entity relationships, and activity flow - Ruchira S. Datta

Thanks for updating us - I'm reading with interest from the DAM SIG room in between talks! - Allyson Lister

process diagrams: biochemistry; entity relationships: molecular biology; activity flow: physiology/genetics - Ruchira S. Datta

we're "projecting" the biological process onto different dimensions (the different languages) - Ruchira S. Datta

process diagrams: entity pool nodes (things that can be counted): containers, and process nodes: pipes - Ruchira S. Datta

also connecting arcs, which connect the various nodes w/ logical operators - Ruchira S. Datta

syntactic rules define what can connect with what, and diagram rules show how to render well-formed expressions - Ruchira S. Datta

can contract large diagrams into small ones - Ruchira S. Datta

color is strictly insignificant, so can photocopy diagrams - Ruchira S. Datta

entity relationships can be viewed as rules - Ruchira S. Datta

a process diagram representation of the same process would result in combinatorial explosion; the rule expresses this much more compactly - Ruchira S. Datta

activity flow never represents molecules, only the activities of those molecules - Ruchira S. Datta

have also annotations (not strictly part of SBGN), e.g., GO annotations - Ruchira S. Datta

SBGN is supported by many tools - Ruchira S. Datta

new version is about to be released - Ruchira S. Datta

have upcoming fora and hackathons - Ruchira S. Datta

it is compatible with BioPAX - Ruchira S. Datta

SBGN is more concerned about the graphic representation, so you can import BioPax pathways and visualize them with SBGN - Michael Kuhn

Science Daily summary of the August 8 Nature Biotechnology article: http://www.sciencedaily.com/release... reshared from Jenny Morman http://ff.im/6uWIo - Ruchira S. Datta