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Workshop: April 30, 2008 Institut Curie (Paris).
Organizers: Andrei Zinovyev (Institut Curie), Laurence Calzone (Institut Curie), Emmanuel Barillot (Institut Curie), Igor Ulitsky (Tel Aviv University), Ron Shamir (Tel Aviv University)
This workshop will introduce six software packages for drawing, analysing biological pathways and integrating data.
The first two systems (CellDesigner and Cytoscape) recently gathered the largest user community
and became standards de facto for biological pathway analysis (see this paper,
for example). To adapt Cytoscape for the needs of systems biology, we
developed BiNoM plugin, extending basic Cytoscape features.
They will be presented by Andrei Zinovyev and Laurence Calzone:
- CellDesigner (1 hour)
- BiNoM (1,5 hour)
More specifically, during this workshop we will introduce:
* Basic notions on Systems Biology Graphical Notation standard
* Basic notions on BioPAX pathway description standard
* Basic notions on Systems Biology Markup Language standard
* Basic skills with CellDesigner v4.0
* A case study for a pathway charting
* Working with BiNoM for pathway structural analysis
* Working with BiNoM for querying pathway database
The other packages will be presented by Igor Ulitsky:
- Expander (45 minutes) - microarray analysis
- Amadeus (45 minutes) -
de-novo motif finding in promoters and 3' UTRs
- Spike (30 minutes) -
signaling pathway knowledgebase
- Matisse (30 minutes) - joint analysis of
network and expression data
The following links and references can be useful in undestanding better the content of the tutorial:
SBGN
(Systems Biology Graphical Notation) is a format for representing
graphically biological interactions e.g. protein-protein interactions,
gene regulatory networks, etc. http://www.sbgn.org/
BioPAX (Biological Pathway Exchange) is a format for storing biological data. http://www.biopax.org/
SBML (Systems Biology Markup Language is a format for representing models of biochemical reaction networks. http://www.sbml.org
BioModels: Database of numerical models: http://www.ebi.ac.uk/biomodels/
Session 1: CellDesigner Basic Skills
CellDesigner is a structured diagram editor for drawing gene-regulatory
and biochemical networks that uses standard formats. We will introduce
the basic features of the software.
CellDesigner offers an
« easy-to-use » and standard graphical
representation of a network; facilitates exchange of models developed
by different groups, using a standard language (SBML: Systems Biology
Markup Language); allows to annotate the reactions, proteins, genes,
etc.; proposes links to other databases (PubMed, IHOP, BioModels,
KEGG, etc.); organizes a lot of information in a unique diagram; allows
an exchange with other modeling tools; offers the possibility to
simulate numerical models; etc
You can find a written support here [doc] and the presentation here [ppt].
Session 2: BiNoM Introduction
BiNoM is a Cytoscape plugin,
developed to facilitate the manipulation of biological networks
represented in standard systems biology formats and to carry out
studies on the network structure. BiNoM provides the user with a
complete interface for the analysis of biological networks in
Cytoscape environment.
Very good tutorial on Cytoscape environment can be found in this paper from Nature Protocols
The first version of the BiNoM software supports the following functions:
- Import of BioPAX, SBML and CellDesigner formats
- Export to BioPAX, SBML and CellDesigner formats after user manipulations
- Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
- Full support of BioPAX information (reaction network, interaction network, pathway structure, references),
concept of BioPAX index and network interfaces
- Browsing, editing, extracting parts, merging BioPAX files with network graph interface
- Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
- Support of generating network modular view
- BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
- Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)
You can find the presentation here [ppt].
Session 3: Expander (microarray analysis)
The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]
Session 4: Amadeus (de-novo motif finding in promoters and 3' UTRs)
The powerpoint presentation can be found here [ppt].
Session 5: Spike (signaling pathway knowledgebase)
The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]
Session 6: Matisse (joint analysis of
network and expression data)
The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]
Material:
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