ISMB 2008でのワークショップとユーザーミーティング

Cytoscape Retreatは、ISMBの前に行なわれますが、ISMBの中でも、ユーザーミーティングとワークショップが開催されます。

Sunday, July 20

Cytoscape User Group

Leader: Gary Bader

Sunday, July 20 – 12:45 p.m. – 2:00 p.m.

Room: 701B

Cytoscape is free, open-source software for network visualization and
analysis. Users and plugin developers are invited to join core
developers for Cytoscape discussion.

Workshop 2: Cytoscape

Wednesday, July 23 - 10:45 a.m. – 12:40 p.m.

Room 715

Presenters: Various

Cytoscape: An Open-Source Platform for Network Analysis and Visualisation

Allan Kuchinsky, Piet Molenaar, Scooter Morris, Alex Pico, Yeyejide Adeleye, David States, Gary Bader

Cytoscape (
is an open-source software package for the visualisation and analysis
of biological networks and the integration of molecular state data.
Cytoscape provides functionality to layout and search networks; to
visually integrate networks with expression profiles, phenotypes, and
other molecular states; and to link to databases of functional
annotations. In this demo we will provide an introduction to the core
functionality of Cytoscape and network-based analysis that will be of
relevance to researchers with an interest in the analysis of biological
data in the context of biological networks and pathways. Various
plugins will also be demonstrated, such as MiMI (Poster K15) and
Pathway Commons (Poster R66)

GenePro: a Cytoscape Plug-in for Advanced Visualization and Analysis of Interaction Networks

Jim Vlasblom, Shuye Pu, and Shoshana J. Wodak. Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto Canada.

features a set of versatile tools that greatly facilitates the
visualization and analysis of protein networks derived from high
throughput interactions data and the validation of various methods for
parsing these networks into meaningful functional modules. Availability:
The GenePro plugin is available for download at:

Interactive analysis of metabolic pathways, their enzymes and metabolites

Brian Turner, Steve Constable, Zahrah Kahlid, Koji Ogata and Shoshana J. Wodak

Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto Canada.

We will demonstrate new Plug-in enabling interactive analyses of metabolic
pathways. Pathways imported using the BioPax format are displayed and
interactively queried for information on metabolites (chemical
structure and 3D conformation), and enzymes (Go annotations, domain
structure and architecture, sequences information, homologs, 3D
structure (PDB), SCOP classification etc.). Information on enzymes is
obtained from the iProClass database using XML-based query tools.



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