BioPathways at ISMB 2004

6^th BioPathways Meeting

July 29th-30^th, 2004 – Glasgow , Scotland

Scottish Exhibition and Convention Centre - Boisdale Room

A satellite of ISMB/EECB'04 (www.iscb.org/ismbeccb2004/)

Conference Program and Abstract (Booklet .pdf)

Conference Program (Schedule)

The 6th BioPathways meeting held on July 29th and 30th, in Glasgow, Scotland is organized by the BioPathways Consortium (www.biopathways.org), an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological networks.

The meeting includes plenary sessions, presenting invited talks on various aspects of computational pathway biology such as systems scale analysis of molecular networks, reconstruction of pathways from heterogenous types of high throughout data, the evolution of molecular pathways, and the representation and visualization of pathway data.

Joanne Luciano
Aviv Regev
Vincent Schachter

Invited Talks

Jeffery Chuang	Functional Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome
Debra Goldberg	Topology classification for biological networks using maximum likelihood estimation and model selection
Ruth Hershberg	Chromosomal organization is shaped by the transcription of transcription regulatory network
Tommy Kaplan	Ab initio prediction of transcription factor targets using structural knowledge
Peter Kharchenko	Gap-filling in metabolic networks using expression information
Manuel Middendorf	Prediction Of Genetic Regulatory Response Using Classification
Csaba Pál	Adaptive and reductive evolution of metabolic networks
David Reiss	Predicting protein-protein interactions via a network-based motif sampler
Tomer Shlomi	Constraint-based modeling of perturbated organisms: ROOM with a View
Sarah Teichmann	Evolution and Dynamics of Transcriptional Regulatory Networks

Contributed Talks

BioGraphNet Frank Gibbons
BioPAX BioPAX Workgroup (Gary Bader)
Cytoscape Gary Bader
KGML Kawashima Shuichi
metapathhunter Ron Pinter
Oracle10g Susie Stephens
PATIKA – Ugur Dogrusoz, Emik Demir, Ozgun Babur
P-tools – Peter Karp, Michele Green
Reactome – Geeta Johni-Tope
SBML – Mike Hucka
STRING - Lars Juhl Jensen
VisANT - Joe Mellor

Contributed Abstracts

BiGCaT Rachel van Haaften
BioUML Fedor Kolpakov
ELM Rune Linding
Forst Christian Forst
GenMAPP Kam Dahlquist
GEST Ken Fukuda
IBM Barbara A Eckman
LacplantCyc Frank H.J. van Enckevort
metaSHARK John Pinney
ROSPath -백은옥 Paek - Choi
SME – Susan Wilson, H. Booth

6^th BioPathways Meeting Program

Day I - July 29 th

9:00-9:15	Vincent Schachter Genoscope & BioPathways Consortium	Opening remarks
Plenary Session I: Network evolution
9:15-10:00	Sarah Teichmann Cambridge University	Evolution and Dynamics of Transcriptional Regulatory Networks
10:00-10:30	Coffee break
10:30-11:15	Csaba Pal Eötvös, Loránd University Budapest	Adaptive and reductive evolution of metabolic networks
11:15-12:00	Jeffrey Chuang University of California, San Francisco	Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome
12:00-13:00	Lunch (Montrose)
Plenary Session II: Regulatory networks
13:00-13:45	Ruthy Hershberg Hebrew University, Jerusalem	Chromosomal organization is shaped by the transcription regulatory network
13:45-14:30	Tommy Kaplan Hebrew University, Jerusalem	ab initio prediction of transcription factor targets using structural knowledge
14:30-15:00	Coffee break
15:00-15:45	Manuel Middendorf Columbia University	Prediction of genetic regulatory response using classification
15:45-16:30	Open discussion: Network evolution and regulatory networks
Contributed Session I: Network Visualization
16:30-17:00	Gary Bader Memorial Sloan Kettering Cancer Center, NYC	Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
17:00-17:30	Frank Gibbons Harvard University	BioGraphNet: A distributed Forum for Heterogeneous Biological Networks
17:30-18:00	Joe Mellor Boston University	The VisANT Network and Pathway Workbench
18:00-19:00	Open discussion: Visualization of biological networks

Day II - July 30 th

Plenary Session III & Contributed Session II: Metabolic networks
9:00-9:20	Michele Green SRI	Pathway Tools Software for Creation and Analysis of Pathway/Genome Databases
9:20-9:40	Lars Juhl Jensen EMBL, Heidelberg	STRING: Predicting novel metabolic pathways through the integration of diverse genome-scale data
9:40-10:00	Ron Pinter Technion, Haifa	A New Tool for the Alignment of Metabolic Pathways
10:00-10:30	Coffee break
10:30-11:15	Tomer Shlomi Tel Aviv University	Constraint-based modeling of perturbed organisms : ROOM with a view
11:15-12:00	Peter Kharchenko Harvard University	Gap-filling in metabolic networks using expression information
12:00-13:00	Lunch (Dunkeld)
Contributed/Plenary Session II: Protein-protein interactions
13:00-13:45	Debra Goldberg Harvard University	Topology classification for biological networks using maximum likelihood estimation and model selection
13:45-14:30	David Reiss Institute for Systems Biology	Predicting protein-protein interactions via a network-based motif sampler
14:30-15:00	Coffee break
15:00-15:30	Open discussion: Metabolic and protein-protein interaction networks
Contributed Session III: Database and exchange languages
15:30-15:50	Michael Hucka California Institute of Technology	Software Infrastructure for SBML, from SBML.org (A Roundup of Software Tools for SBML)
15:50-16:10	Gary Bader Memorial Sloan Kettering Cancer Center, NYC	BioPAX - Biological Pathway Data Exchange Format
16:10-16:30	Geeta Joshi-Tope Cold Spring Harbor Laboratory	The Reactome Project
16:30-16:50	Ugur Dogrusoz Bilkent University, Ankara, Turkey	The PATIKA Project
16:50-17:10	Susie Stephens Oracle Corp.	Graph Modeling and Analysis in Oracle DBs
17:10-17:30	Kawashima Shuichi Kyoto University	KGML (KEGG Markup Language) for Exchanging the KEGG Graph Objects
17:30-19:00	Panel discussion: Sharing and integration of pathway information