The 3rd Disease Maps Community Meeting (DMCM2018) is hosted by the Computational Systems Biology of Cancer group, Institut Curie.
The programme and the abstract booklet are available here
To download the presentations, follow this link
Photos from the meeting are available at CurieSysBio Instagram
Objectives
The objective of the 3rd DMCM is to consolidate efforts around the disease map projects and extend the Disease Maps Community. The 3rd DMCM will expose progress of the projects from the Disease Maps Community and beyond. The representative examples of network maps generation, their applications for disease data analysis, disease comorbidity, drug response prediction, advances in tools development and modelling approaches will be presented.
Topics
Among others, the following topics will be discussed: biocuration of prior knowledge related to different human diseases; creation and maintenance of disease network maps following common standards; sharing sub-maps with mechanisms implemented into different human diseases; providing technical solutions for network maps complexity management, mathematical modelling of maps and web-tools for explorations in maps. Topic-specific roundtable discussions will be organised to identify bottleneck problems and ways to overcome them.
Hands-on tutorials
Part of the meeting will be dedicated to demos and hands-on tutorials on major tools supporting the disease maps. The downloadable materials are available at the tutorial description in the meeting programme.
Programme
21 June
Amphithéâtre BDD
| 08:30 - 09:00 Arrival and registration |
| 09:00 - 09:05 Opening session and welcome Emmanuel Barillot, Institute Curie, Paris, France Reinhard Schneider, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg |
| 09:05 - 09:15 Aims and perspectives of the DMCM2018 meeting Alexander Mazein, European Institute for Systems Biology and Medicine, Lyon, France Inna Kuperstein, Institute Curie, Paris, France |
Session 1: Disease maps resources
| 09:15 - 09:30 Integrating disease maps using a graph database approach Irina Balaur, European Institute for Systems Biology and Medicine, Lyon, France Abstract |
| 09:30 - 09:45 A disease map for the blood pressure and glomerular filtration regulatory network on which antihypertensive and analgesic drugs act Francisco J. Lopez Hernandez, University of Salamanca, Salamanca, Spain Abstract |
| 09:45 - 10:00 Towards a molecular map of cystic fibrosis mechanisms Catarina Pereira and Andre Falcao, University of Lisbon, Lisbon, Portugal Abstract |
10:00 - 10:30 Coffee break at BDD Hall
Session 2: Disease maps resources II
| 10:30 - 10:45 The AsthmaMap: computational representation of disease mechanisms using domain expert knowledge Alexander Mazein, European Institute for Systems Biology and Medicine, Lyon, France Abstract |
| 10:45 - 11:00 A multiscale signalling network map of immune response in cancer reveals signatures of cell heterogeneity and functional polarization Maria Kondratova, Institute Curie, Paris, France Abstract |
| 11:00 - 11:15 Parkinson's disease map facilitated gene expression analysis reveals new insights in PD pathogenesis Stephan Gebel, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg Abstract |
| 11:15 - 11:30 Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model Anna Niarakis, Universite d' Evry Val d' Essonne, Evry Val d' Essonne, France Abstract |
| 11:30 - 12:30 Invited talk: WikiPathways: curation, visualization and analysis of biological pathways Martina-Summer Kutmon Maastricht University, Maastricht, the Netherlands Abstract |
12:30 - 13:30 Lunch and collaborations discussion at BDD Hall
13:30 - 15:00 Hands-on tutorials: parallel sessions
| Time/Place | Amphi BDD | Annexes 1-3 BDD |
| 13:30 - 14:10 | Tutorial 1 | Tutorial 3 |
| 14:10 - 14:15 | Break | Break |
| 14:15 - 14:55 | Tutorial 2 | Tutorial 4 |
| Tutorial 1: Constructing and visualizing pathways with web-based SBGN editor Newt Ugur Dogrusoz, Bilkent University, Ankara, Turkey Abstract |
| Tutorial 2: MINERVA for visualization of disease maps Piotr Gawron, Marek Ostaszewski, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg Abstract Requirements and downloads: To follow this tutorial, is recommended to install CellDesigner. All tutorial files are available here. Additionally, all files will be available on LCSB’s ownCloud (Password: DMCM2018) |
| Tutorial 3: rROMA, a tool for module activity calculation from omics data and networks Luca Albergante, Urszula Czerwinska, Andrei Zinovyev, Loredana Martignetti, Institute Curie, Paris, France Abstract Requirements and downloads: To follow this tutorial, is recommended to install R or R Studio and to download these files |
| Tutorial 4: COBRA toolbox for visualisation and map manipulation through CellDesigner and MatLab environment Jennifer Modamio, Ronan Fleming, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg Nicolas Sompairac, Andrei Zinovyev, Inna Kuperstein, Institute Curie, Paris, France Abstract Requirements and downloads: To follow this tutorial, is recommended to install MATLAB (Paying license needed), CellDesigner and the COBRAToolBox . The files for the tutorial can be downloaded here |
Session 3:Maps of biological processes and disease
| 15:00 - 15:10 The adult neurogenesis map Rupert Overall, German Center for Neurodegenerative Diseases, Dresden, Germany Abstract |
| 15:10 - 15:20 The Ras/Raf/Mek/Erk Signaling Pathway - Attention to Details Maria Dost, Humboldt-Universität zu Berlin, Berlin, Germany Abstract |
| 15:20 - 15:30 Is cellular senescence a prerequisite for tumor invasion? Mathieu Boissan, Centre de recherche St-Antoine, Paris, France Abstract |
15:30 - 16:00 Coffee break at BDD Hall
Session 4: Maps for drug assessment and disease comorbidity
| 16:00 - 16:10 Comprehensive signaling network of regulated cell death: comparison of cell death modes in Alzheimer's neurodegenerative disease and cancer Cristobal Monraz, Institute Curie, Paris, France Abstract |
| 16:10 - 16:20 Predicting personal activation potential of CD4 T cells Feng He, Luxembourg Institute of Health, Luxembourg, Luxembourg Abstract |
| 16:20 - 16:30 Reconstruction of integrated maps for drug efficacy assessment Tatiana Serebriyskaya, Moscow Institute of Physics and Technology, Moscow, Russia Abstract |
| 16:30- 16:40 Metabolic and signalling network map integration: application to cross-talk studies and omics data analysis in cancer Nicolas Sompairac, Institute Curie, Paris, France Abstract |
16:45- 17:00 Group photo
17:00 - 18:15 Marie Curie museum and garden visit
http://musee.curie.fr
22 June
Amphithéâtre BDD
Session 5:Methods resources and models
| 09:00 - 09:15 Access and Discover Biological Pathway Information from Pathway Commons Augustin Luna, Dana-Farber Cancer Institute/Harvard University, Boston, United States Abstract |
| 09:15 - 09:30 Community resources connecting chemistry and toxicity knowledge to environmental observations Emma Schymanski, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg Antony Williams, National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Durham,USA Abstract |
| 09:30 - 09:45 Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models Joaquin Dopazo, Fundación Progreso y Salud, Sevilla, Spain Abstract |
| 09:45 - 10:00 A computational model of the circadian clock and its application to understanding renal disease
Tom Freeman, The University of Edinburgh, Edinburgh, United Kingdom Abstract |
10:00 - 10:30 Coffee break at BDD Hall
Session 6: Large Reconstructions and integrations
| 10:30 - 10:45 Status report: parameter estimation of a large-scale mechanistic model for mast cells in asthma Thomas S. Ligon, Ludwig-Maximilians-Universitat, Munich, Germany Jan Hasenauer, Helmholtz Zentrum Munchen, Munich, Germany Abstract |
| 10:45 - 11:00 Application of disease maps to rare diseases: as muscular dystrophies Cecilia Jimenez Mallebrera, Hospital Sant Joan de Deu, Barcelona, Spain Abstract |
| 11:00 - 11:15 Maps of influence and interactions of infectious and cancer diseases from Wikipedia networks Dima Shepelyansky, Laboratoire de Physique Theorique CNRS, Universite Paul Sabatier, Toulouse, France Abstract |
| 11:15 - 11:30 Integrating ontological representation and reasoning into a disease map: application to Alzheimer’s disease Vincent Henry, ICM Brain and Spine Institute, Paris, France Abstract |
| 11:30 - 12:30 Invited talk: Reactome multi-scale pathway visualization Henning Hermjakob, Molecular Systems services EMBL-EBI, Cambridge, United Kingdom Abstract |
12:30 - 13:30 Lunch and collaborations discussion at BDD Hall
13:30 - 15:00 Hands-on tutorials: parallel sessions
| Time/Place | Amphi BDD | Annexes 1-3 BDD |
| 13:30 - 14:10 | Tutorial 5 | Tutorial 7 |
| 14:10 - 14:15 | Break | Break |
| 14:15 - 14:55 | Tutorial 6 |
| Tutorial 5: From interaction maps to dynamical models with Cell Collective: a hands-on tutorial Tomas Helikar, University of Nebraska-Lincoln, Lincoln, United States Abstract Requirements and downloads: To follow this tutorial, is recommended to create a free acount on the Cell Colective website |
| Tutorial 6: mEPN and yEd: a graphical and computational modelling platform for biological pathways Tom C. Freeman, University of Edinburgh, Edinburgh, UK Abstract Requirements and downloads: To follow this tutorial, is recommended to download and install yEd and Graphia Professional |
| Tutorial 7: A tutorial of hipathia, a mechanistic model of pathway activity Martha R Hidalgo, Centro de Investigación Principe Felipe, Valencia, Spain Joaquin Dopazo, Fundación Progreso y Salud, Sevilla, Spain Abstract |
| 15:00 - 15:30 Invited talk: Share FAIR – Data management and standards for Systems Medicine Martin Golebiewski, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Abstract |
15:30 - 16:00 Coffee break at BDD Hall
Session 7: Visualization and modeling frameworks
| 16:00 - 16:10 Instantiation of patient-specific network-based logical models with multi-omics data allows clinical stratification of patients Jonas Beal, Institute Curie, Paris, France Abstract |
| 16:10 - 16:20 Visual analytics of biological networks using VANTED and its SBGN-ED add-on Hanna Borlinghaus, University of Konstanz, Konstanz, Germany Abstract |
| 16:20 - 16:30 MINERVA API and plugin architecture: new data visualization interfaces for disease maps Piotr Gawron, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg Abstract |
| 16:40 - 17:15 Thematic discussion groups (suggested topics): Integration of maps in a shared repository Tools for maps generation Applications of disease maps in research and clinics: what is missing to close the gap? Maps to models: curation standards to allow easy transformation of networks into executable models Maps' complexity management approaches Disease pathways vs. healthy pathways: how different are they? |
| 17:15 - 17:30 Conclusions and closing session Emmanuel Barillot, Institute Curie, Paris, France Reinhard Schneider, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg |
Abstract submission
Submit abstracts (up to 400 words) via the submission link for oral presentations and/or posters. Indicate 4 keywords to allocate it into the suitable session.
Registration
The registration is free but mandatory. Fill in the registration form here.
Location
Batiment de biologie du developpement et cancer (BDD building)
11 rue Pierre et Marie Curie
75005, Paris
France
Accommodation
Recommended hotels:
Les Jardins Du Luxembourg
5 Impasse Royer-Collard, 75005 Paris, France
Hotel Elysa-Luxembourg
6 Rue Gay Lussac, 75005 Paris, France
Hotel du Brésil
10 rue Le Goff, 75005 Paris, France
Hotel Michelet Odeon
6 Place De L Odeon, 75006 Paris, France
Hotel de l'Avenir
65 rue Madame, 75006 Paris, France
Hôtel Des Mines
125 Bd Saint Michel, 75005 Paris, France
Contact
disease-maps-coord@googlegroups.com
Organisers
Computational Systems Biology of Cancer group, Institut Curie:
Emmanuel Barillot
Maria Kondratova
Inna Kuperstein
Cristobal Monraz
Andrei Zinovyev
Irina Balaur
Disease Maps Project Coordinators
Alexander Mazein
Marek Ostaszewski
Inna Kuperstein
Andrei Zinovyev
Reinhard Schneider
Emmanuel Barillot
Rudi Balling
Charles Auffray