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BioNetVisA 2015 workshop

From biological network reconstruction to data visualization and analysis in molecular biology and medicine

25 November 2015


Yong Loo Lin School of Medicine

National University of Singapore (NUS)



ICSB 2015



Program and abstracts booklet 2015             Presentation slides 2015 

BioNetVisA workshop brings together different actors of network biology from database providers, networks creators, computational biologists, biotech companies involved in data analysis and modeling to experimental biologists, clinicians that use systems biology approaches. The participants are exposed to the different paradigms of network biology and the latest achievements in the field.



The goal of BioNetVisA workshop is to build a discussion around various approaches for biological knowledge formalisation, data integration and analysis; compatibility between different methods and biological networks resources available the field; applicability for concrete research and clinical projects depending on scientific question and type of high-throughput data.


The BioNetVisA workshop aims at identifying bottlenecks and proposing short- and long-term objectives for the community as discussing questions about accessibility of available tools for wide range of user in every-day standalone application in biological and clinical labs. In addition, the possibilities for collective efforts by academic researchers, clinicians, biotech companies and future development directions in the field will be discussed during the round table panel.




Graphical representation of biological knowledge

Molecular interaction and pathway databases

Comprehensive signalling networks

Networks annotation and curation

High-throughput data visualisation, analysis and interpretation in the context of networks

Network modelling

Basic research and clinical application of network biology



Development, curation and maintenance of biological network databases

Data models from interaction to pathway and network, available tools for the integration of new discoveries into existing signalling diagrams. Discussion of curation models from map manager-oriented to community-based update using web-tools and forums.


Cell signalling knowledge representation paradigms

From interaction to single pathways representation to comprehensive signalling networks: discussion of modes of biological processes representation; granularity, coverage, sources of information, annotation modes, cross-citations between different signalling networks resources, etc. Standard data formats, graphical representation standards.


Visualization of data through networks

Paradigms of visualization of different types of high-throughput data on a network map. Data integration with a map. Methods compatibility with different paradigms of signalling networks reconstruction in various databases and resources.


Analytical tools for network biology

Tools for network analysis and manipulation, network modeling, network-based statistics. Studying network activation and inhibition, feedbacks and compensations, synthetic interactions, clinical treatment response and resistance.




The registration has to be performed via ICSB site



Session 1

Development of biological network databases and platforms



Garuda Platform and Its Applications in Biomedical Research

Yukiko Matsuoka (Systems Biology Institute, Tokyo, Japan)

Abstract Slides



PhysioDesigner: A versatile platform for multilevel modeling of physiological   systems network

Yoshiyuki Asai (The Okinawa Institute of Science and Technology, Okinawa, Japan) Abstract Slides



Studying cancer biology big data with Google Maps: NaviCell Web Service and Atlas of Cancer Signaling Network

Andrei Zinovyev (Institut Curie, Paris, France)

Abstract Slides


10.30-10.45 Break



SIGNOR: a database of causal relationships between biological entities

          Livia Perfetto (University of Rome Tor Vergata, Rome, Italy)

Abstract Slides



Keynote lecture

Molecular networks as determinants of response and outcome

Lodewyk Wessels (Netherlands Cancer Institute, Amsterdam, Netherlands)



12.00-13.30 Lunch


Session 2

Data visualisation and analysis in the context of biological networks in research and medicine



NetLand: A comprehensive tool for simulation and visualization of transcriptional network kinetics

Jie Zheng (Nanyang Technological University, Singapore)

Abstract Slides



Significant prognostic gene and interconnection network enrichment (SPGINE) analysis stratifies breast cancers into three reproducible subclasses determined by novel genetic grading signatures

          Vladimir Kuznetsov (Bioinformatics Institute, Singapore)




Prediction of sensitivity to genotoxic drug by modeling cancer cell lines and

patient omics data in the context of comprehensive DNA repair signaling network

Inna Kuperstein (Institut Curie, Paris, France)

Abstract Slides



Communities and Disease Comorbidities from Multiplex Biological Networks

Anaïs Baudot (CNRS-AMU, Marseilles, France)

Abstract Slides


14.50-15.00 Break



Modelling of biological networks



Predictive logical modelling of cell fate decision networks

Denis Thieffry (IBENS, Ecole Normale Supérieure, Paris, France)

Abstract Slides



Computing Life: Blue-print modelling and domino approach in design principle studies of Reactive Oxygen Species management

          Alexey Kolodkin (University of Luxembourg, Luxembourg)

Abstract Slides



Multiscale model to recapitulate breast cancer invasion phenotypes

Arnau Montagud (Institut Curie, Paris, France)

Abstract Slides



Keynote lecture

Data-based modeling of signal-transcription network for cell fate control

Mariko Okada (RIKEN Center for Integrative Medical Sciences Yokohama, Japan)

Abstract Slides


17.00-17.10 Break



Round table discussion





Block MD7, Seminar Room M9

Yong Loo Lin School of Medicine

National University of Singapore (NUS)


The nearest train station: Kent Ridge Station on the Circle line


Organising Committee


Inna Kuperstein (Institut Curie, France)

Emmanuel Barillot (Institut Curie, France)

Andrei Zinovyev (Institut Curie, France)

Hiroaki Kitano (Okinawa Institute of Science and Technology Graduate University, RIKEN Center for Integrative Medical Sciences, Japan)

Nicolas Le Novère (Babraham Institute, UK)

Robin Haw (Ontario Institute for Cancer Research, Canada)

Alfonso Valencia (Spanish National Bioinformatics Institute, Madrid, Stain)


Link to BIoNetVisA 2014


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