Standards and formats in systems biology

Slides:



Advertisements
Similar presentations
BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech.
Advertisements

BiNoM, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats Eric Bonnet Computational Systems Biology of Cancer.
Look for other standards: - BioPAX (composition) - CellML (aggregation) - Other SBML L3 extensions (modules - rule-based modeling)
Pathway Knowledge Base: A Public Repository for Searching Biological Pathways Nikesh Kotecha 1, Kyle Bruck 1, William Lu 1 and Nigam Shah 1 1 Department.
Network biology Wang Jie Shanghai Institutes of Biological Sciences.
David PA Cohen 1,2,3, Laurence Calzone 1,2,3, I Kuperstein 1,2,3, M Chanrion 1,, C Barrière 1, F El-Marjou 1, D Vignjevic 1, L Stimmer 1, I Bieche 1, S.
CellDesigner Tutorial Laurence Calzone, Andrei Zinovyev UMR U900 INSERM/Institut Curie/Ecole des Mines de Paris Wednesday, April 30th.
A Comprehensive Map of Molecular Interactions in RB Pathway Laurence Calzone (1), Amélie Gelay (1), Andrei Zinovyev (1), François Radvanyi (2), Emmanuel.
BiNoM Tutorial Andrei Zinovyev, Laurence Calzone UMR U900 INSERM/Institut Curie/Ecole des Mines de Paris Wednesday, April 30th.
The Computable Plant Claire Schulkey Kiri Hamaker California Institute of Technology Dr. Bruce E. Shapiro.
Biological networks Tutorial 12. Protein-Protein interactions –STRING Protein and genetic interactions –BioGRID Signaling pathways –SPIKE Network visualization.
341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London
Ch10. Intermolecular Interactions and Biological Pathways
Cytoscape A powerful bioinformatic tool Mathieu Michaud
Review of Ondex Bernice Rogowitz G2P Visualization and Visual Analytics Team March 18, 2010.
Lecture 3: Pathway Generation Tool I: CellDesigner: A modeling tool of biochemical networks Y.Z. Chen Department of Pharmacy National University of Singapore.
Copyright OpenHelix. No use or reproduction without express written consent1.
Detection of structural variants and copy number alterations in cancer: from computational strategies to the discovery of chromothripsis in neuroblastoma.
Comprehensive model for formalized description, visualization and simulation of biological systems Fedor A. Kolpakov Biosoft.Ru,
BioUML integrated platform for building virtual cell and virtual physiological human Fedor Kolpakov Institute of Systems Biology Laboratory of Bioinformatics,
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands 1 François Moreews SIGENAE, INRA, Rennes Cytoscape.
Copyright OpenHelix. No use or reproduction without express written consent1.
Virtual Cell and CellML The Virtual Cell Group Center for Cell Analysis and Modeling University of Connecticut Health Center Farmington, CT – USA.
BIological NetwOrk Manager Cytoscape plugin Andrei Zinovyev Institut Curie/INSERM/Ecole de Mines, UMR 900 “Computational Systems Biology of Cancer”
Ewing tumor as a model for systems biology Andrei Zinovyev Service Bioinformatique, Institut Curie.
Aggregation Connector: A Tool for Building Large Molecular Network Models from Components Thomas C. Jones Jr 1, Clifford A. Shaffer 1, Alida Palmisano.
Chapter 5: Business Intelligence: Data Warehousing, Data Acquisition, Data Mining, Business Analytics, and Visualization DECISION SUPPORT SYSTEMS AND BUSINESS.
Sharing Models. How Can I Exchange Models? SBML (Systems Biology Markup Language): de facto standard for representing cellular networks. A large number.
CellDesigner and Virtual Cell Leang Chhun and Chanchala Kaddi Georgia Institute of Technology 29 June, 2006.
Microarrays.
PROGNOCHIP-BASE, FORTH-ICS 1 PrognoChip-BASE: An Information System for the Management of Spotted DNA MicroArray Experiments Extension of BASE v
W e present BiNoM [1,2], a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats.
BBN Technologies Copyright 2009 Slide 1 The S*QL Plugin for Cytoscape Visual Analytics on the Web of Linked Data Rusty (Robert J.) Bobrow Jeff Berliner,
A curated database of biological pathways.
Types of Cellular Networks. Gene Regulatory Networks
341- INTRODUCTION TO BIOINFORMATICS Overview of the Course Material 1.
Kaifeng Chen Institute for Theoretical Physics Synthetic Biology with Engineering Tools 1 Francis Chen.
Introduction and Applications of Microarray Databases Chen-hsiung Chan Department of Computer Science and Information Engineering National Taiwan University.
INFSO-RI Enabling Grids for E-sciencE Construction of a Mathematical Model of a Cell as a Challenge for Science in the 21 Century.
Modeling the cell cycle regulation by the RB/E2F pathway Laurence Calzone Service de Bioinformatique U900 Inserm / Ecoles de Mines / Institut Curie Collaborative.
CSC, Dec.15-16,2005. Cytoscape Team Trey Ideker Mark Anderson Nerius Landys Ryan Kelley Chris Workman Past contributors: Nada Amin Owen Ozier Jonathan.
Biological Networks. Can a biologist fix a radio? Lazebnik, Cancer Cell, 2002.
Dynamical Dimension Flat dimension : by Karhunen-Loève expansion (PCA) Limit Simplifications A modular technique : a)define modules : set of intermediate.
Ontology Driven Data Collection for EuPathDB Jie Zheng, Omar Harb, Chris Stoeckert Center for Bioinformatics, University of Pennsylvania.
High throughput biology data management and data intensive computing drivers George Michaels.
BiNoM: a Cytoscape plugin for using and analyzing biological networks Andrei Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot Institut Curie /
Selection of genes: Choose threshold on fit score to include known EWS/FLI1-induced genes. Model-based approach for analysis of transcriptome perturbation.
Algorithms and Computational Biology Lab, Department of Computer Science and & Information Engineering, National Taiwan University, Taiwan Network Biology.
GPML Plugin for Cytoscape Thomas Kelder Maastricht University
IGEM 2009 Tutorial Modelling. What? Model A model in science is a symplified physical, mathematical, or logical representation of a system of entities,
Reactome pathway knowledgebase Connecting pathways, networks, and disease Robin Haw, PhD Project Manager and Outreach Coordinator Ontario Institute for.
a Cytoscape plugin to assess enrichment of
Why Create a PGDB? Perform pathway analyses as part of a genome project Analyze omics data Create a central public information resource for the organism,
KnowEnG: A SCALABLE KNOWLEDGE ENGINE FOR LARGE SCALE GENOMIC DATA
Cell Designer Sarah Killcoyne.
Themes of Biology Chapter 1
Tutorial 12 Biological networks.
Pathway Visualization
Community detection in graphs
BioGateway: an RDF store for supporting Systems Biology
Gene Expression Analysis and Proteins
Overview Gene Ontology Introduction Biological network data
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
CCO: concept & current status
Nicole Anguiano and Anu Varshneya
Network biology An introduction to STRING and Cytoscape
Pathway Visualization
Analyzing Massive Graphs - ParT I
Biologic processes necessary for survival after alkylation damage are conserved and when compiled generate a cross-species functionome. Biologic processes.
Anthony N. Imbalzano, Stephen N. Jones  Cancer Cell 
Presentation transcript:

Standards and formats in systems biology Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech http://sysbio.curie.fr Seminar Mathematics and Biology of Cancer Institut Curie 12/06/2013 1

A B 1500 1000 500 250 225 200 er tumor

Pathway databases

Why do we need standards? Evil. Yes, we can.

Systems Biology standard formats Open access. Dynamic, community-driven development. Promote development and use of software libraries. SBML Community organization SBML Forum (propositions) SBML Editors (evaluation, reconciliation) SBML Team (funding, material) SBML SAB (guidance)

BiNoM Structure analysis BiNoM BioPAX Utilities BiNoM, a Biological Network Manager BiNoM Utilities BiNoM Structure analysis BiNoM BioPAX Query BiNoM I/O BiNoM BioPAX Utilities BiNoM Modules Cytoscape plugin. Supports standard systems biology formats (BioPAX, CellDesigner, etc.). Facilitates the visualization and manipulation of biological networks. Help the user to analyze, extract and condense network information. http://binom.curie.fr

Modular representation Cell Cycle regulation RB / E2F network, 70+ proteins, 150+ genes, 200 species, 160+ reactions Modular representation Graph pruning, extracting strongly connected components, decomposition into cycles, finding shortest, subpotimal, all paths, clustering subgraphs, export to SBML

Acknowledgements Laurence Calzone Daniel Rovera Gautier Stoll Paola Vera-Licona Emmanuel Barillot Eric Viara Andrei Zinovyev

Feedback: Privacy Policy Feedback
Do Not Sell My Personal Information
About project: SlidePlayer Terms of Service

© 2024 SlidePlayer.com. Inc. All rights reserved.