binom and navicell: tools for navigation, curation, maintenance and analysis of complex molecular...

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BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech - Institut Curie Biocuration 2013 – Cambridge, UK

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Page 1: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular

interaction maps

David CohenU900 INSERM - Mines ParisTech - Institut Curie

Biocuration 2013 – Cambridge, UK

Page 2: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

NAVICELL

Page 3: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

What is NaviCell

Web based environment for navigation, curation and maintenance of biochemical

reaction networks

Page 4: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech
Page 5: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Based on Google Maps

Semantic zoom

Page 6: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Pop-up Bubble

Blog Module

Page 7: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Blog view

Module view

Page 8: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Summary

http://navicell.curie.frVideo Tutorial: https://navicell.curie.fr/pages/tutorial.html

• Navigation• Blog system feedback and maintenance• Semantic zoom levels

http://arxiv.org/abs/1301.7618.http://goo.gl/BF34R

Page 9: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

BINOMPlug-in for Cytoscape

Bonnet et al. BMC Systems Biology 2013 7:18

Page 10: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

BiNoM, a Biological Network Manager

• Facilitates the visualization and manipulation of biological networks.• Supports standard systems biology formats (BioPAX, CellDesigner, etc.).• Assists the user in the analysis of networks.• Extracts specific information from databases such as Reactome.

Page 11: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

New Features

• BioPAX level 3• Cytoscape 2.8• CellDesigner 4.3 • Pathway Influence Quantification• Minimal Cut Set• Creation of interactive molecular maps

Page 12: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

New BioPAX specifications

gene regulatory network

Genetic interaction

Page 13: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Pathway Influence Quantificattion

α: activity of path of the starting node

σ: sign of path

λ: length of path

q: number of paths

Page 14: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Example PIQUANT

Page 15: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Minimal Cut SetsI1 -> B -> C -> O1

I1 -> E -> C -> O1

I2 -> E -> C -> O1

Cut Set: {B,E}, {I1,I2], {C}

Defining novel drug targets

Page 16: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Colouring data

Page 17: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Staining background

Page 18: BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps David Cohen U900 INSERM - Mines ParisTech

Acknowledgements

Computational Systems Biology of Cancer*

*Equipe labellisée par la Ligue Nationale Contre le Cancer

Daniel RoveraGautier StollPaula Vera-LiconaStuart PookHien Anh NguyenAndrei Zinovyev

Emmanuel BarillotEric BonnetLaurence CalzoneDavid CohenSimon FourquetInna Kuperstein

navicell.curie.fr binom.curie.fr

Poster 104