BioNetVisA 2017 workshop

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

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12 September 2017

University of Basel

Basel, Switzerland



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.

BioNetVisA program


Session 1

Signaling and metabolic network databases



Stephan Gebel (University of Luxembourg, Luxembourg)

A comprehensive map of signalling in Parkinson’s disease



Ronan Fleming (University of Luxembourg, Luxembourg)

                       MitoMap: an aesthetic mitochondrial biochemical network map



Konstantinos Sidiropoulos (EMBL-EBI, Hinxton, UK)

Reactome: New features for enhanced pathway visualisation



Falk Schreiber (University of Konstanz, Konstanz, Germany)

From static visualisation to immersive analytics of biological networks



Björn Sommer (Monash University, Melbourne, Australia)

Multiscale Modeling and 3D Visualization of spatially-embedded Cytological Networks



10.30-11.00 Coffee break


Session 2

Platforms and method for analysis of complex biological networks



EMBO keynote lecture

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

         Networks and Co-evolution in the Interpretation of Epigenetic Regulation



            Andrei Zinovyev (Institut Curie, Paris, France)

Application of the reduced Google Matrix approach for the analysis of directed biological networks



Ugur Dogrusoz (Bilkent University, Ankara, Turkey)

Interactive web based curation of biological pathways with advanced layout and complexity management support



Aura Ileana Moreno-Vega (Institut Curie, Paris, France)

Characterization of the FGFR3 regulatory network in bladder tumors



12.30-13.30 Lunch


Session 3

Biological networks in drug discovery and toxicology studies



Keynote lecture

Minoru Kanehisa (Institute for Chemical Research, Kyoto University)

From gene variants to network variants: a new database for understanding diseases and drugs



Mark Ibberson (Swiss Institute of Bioinformatics)

Biomarker discovery in diabetes: A network-based approach



Barry Hardy (Douglas Connect GmbH, Basel, Switzerland)

Integrated Modelling and Testing Strategies supporting Systems Toxicology and

Evidence-based Safety Assessment



Justyna Szostak (Philip Morris International group, Neuchâtel, Switzerland)

Detect Liver Toxicity through Causal Biological Network Model and Computational Algorithm



15.00-15.30 Coffee break


Session 4

Biological networks modelling in medicine



Gregory Batt (Institut Pasteur, Paris, France)

                     A multi-scale model for investigating TRAIL resistance in multi-cellular tumor spheroids



Patrick Kemmeren (Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands)

Exhaustive Petri net modeling to infer mechanisms of genetic interactions



Valeriya Malysheva (Université de Strasbourg, Illkirch, France)

Integration of chromatin structure dynamics in the regulatory network governing cell fate acquisition 



Matteo Barberis (University of Amsterdam, Amsterdam, The Netherlands)

GEMMER: GEnome-wide software for Multi-scale Modeling data Extraction and Representation 



Closing remarks and discussion


Important dates


August 2

Late abstract submission deadline (for posters only) Submit now!

August 5

Notification of accepted late abstracts (for posters only)

August 12

Early bird registration deadline Register here

August 28

Registration deadline Register here

September 12

BioNetVisA workshop

August 13-15

BC2 main conference


Abstract submission instructions

Late abstract submission for posters only is possible till August 1st 2017


Number of poster abstracts will be selected for flash poster presentations (3 minutes of topic advertisement).


Abstract format:


List of author (the first author is a presenting author)


Abstract text in unstructured format (maximum 300 words)


Submission process:

The link below will take you to the EasyChair submission page. Once logged, click on the 'Submission' tab to start the submission process. Enter authors, title without HTML elements, abstract up to 300 words, keywords, and select up to three relevant topic sessions.


To assist us with creating the abstract booklet, please upload the same abstract as a word document in the section called "Upload Paper" using this TEMPLATE


When the form is adequately filled out, press the 'Submit' button. You will receive an email from the conference "EasyChair". This email is solely a notification that EasyChair for BioNetVisA2014 has received the abstract.


Submit your abstract here

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)

Minoru Kanehisa (Institute for Chemical Research, Kyoto University, Japan)

Samik Ghosh (Systems Biology Institute, Tokyo, Japan)

Nicolas Le Novère (Babraham Institute, UK)

Robin Haw (Ontario Institute for Cancer Research, Canada)

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

Lodewyk Wessels (Netherlands Cancer Institute, Amsterdam, Netherlands)

Patrick Kemmeren (Princess Maxima Center for Pediatric Oncology, Utrecht, Netherands)



University of Basel

Room t.b.a.

Link to BIoNetVisA 2014

Link to BIoNetVisA 2015

Link to BIoNetVisA 2016



Program and abstracts booklet 2014               Presentations 2014

Program and abstracts booklet 2015               Presentations 2015

Program and abstracts booklet 2016               Presentations 2016


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