COMBINE 2017 Schedule v2
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ABCDE
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COMBINE 2017 Schedule
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DayTitle/topic & speakerTopicRoomSlot
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Monday
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9:00Registration and breakfastAtrium
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Session 1 (Marco Antoniotti)
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10:30Welcome (UNIMIB)Martini (U6-04)
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10:45James Faeder - Toward integrated models of cell behavior: How rule-based modeling can contributeMartini (U6-04)
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11:30Martin Golebiewski - Don’t be lost in the jungle of standards: Cataloguing, harmonizing and application of modelling standards Martini (U6-04)
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12:15LunchFree
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Session 2 (Martin Golebiewski)
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13:45Marco Nobile - Turning uncertainty and lack of quantitative data into dynamic models with fuzzy logicMartini (U6-04)
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14:30Carlos Lopez - Reaction flux and information flow in the COX-2 reaction networkMartini (U6-04)
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15:15Dirk Drasdo - Multi-scale/multi-level challenges in multicellular systems biology, systems medicine and systems toxicology: example from liverMartini (U6-04)
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16:00BreakAtrium
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Session 3 (David Nickerson)
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16:30Padraig Gleeson - The Open Source Brain Initiative, enabling collaborative model development in computational neuroscienceMartini (U6-04)
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17:15Shailesh AppukuttanMartini (U6-04)
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Tuesday
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8:30Breakfast
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Session 4 (Claudine Chaouiya)
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9:00Rahuman Sheriff, Varun B Kothamachu, Tung Nguyen, Mihai Glont, Sarala Wimalaratne, Sarah Keating, Nicolas Rodriguez, Nick Juty, Vijayalakshmi Chelliah, Nicolas Le Novère and Henning Hermjakob - Resources for semantic enrichment and sharing of models in standard formatsModel SharingMartini (U6-04)1
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9:15Mihai Glont, Tung Nguyen, Raza Ali, Rahuman Sheriff, Nick Juty, Camille Laibe, Vijayalakshmi Chelliah, Nicolas Le Novere and Henning Hermjakob - Towards a new infrastructure for BioModelsModel SharingMartini (U6-04)2
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9:30Varun B Kothamachu, Rahuman Sheriff, Mihai Glont, Nguyen Tung, Vijayalakshmi Chelliah, Nicolas Le Novère and Henning Hermjakob - BioModels: Sharing computational models of biological processesModel SharingMartini (U6-04)3
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9:45Vasundra Tourè, Åsmund Flobak, Astrid Lægreid and Martin Kuiper - Extraction and representation of causal statements: Creating a model building resource for Systems BiologyModel SharingMartini (U6-04)4
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10:00Jacky Snoep, Martin Peters, Kathleen Green, Carla Louw, Carl Christensen, Natalie Stanford, Stuart Owen, Carole Goble, Dagmar Waltemath and Dawie van Niekerk - The JWS Simulation Database: How linking experimental data and mathematical models enables publication of reproducible model-based resultsModel SharingMartini (U6-04)29
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10:15Discussion
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10:45BreakAtrium
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Session 5 (Anil Wipat)
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11:15Mirco Tribastone - Reduction of ordinary differential equations with ERODEModelingMartini (U6-04)5
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11:30Claudine Chaouiya, Laurence Calzone, Tomas Helikar, Céline Hernandez, Pedro Monteiro, Aurélien Naldi, Denis Thieffry and Dagmar Waltemath - Standardisation effort from the Consortium for Logical Models and Tools (CoLoMoTo)ModelingMartini (U6-04)6
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11:45Fengkai Zhang and Martin Meier-Schellersheim - Release of SBML Multi — A milestone in addressing rule-based modeling interoperability challengesModelingMartini (U6-04)8
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12:00Nicolas Rodriguez, Thomas M. Hamm, Roman Schulte, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Chris J. Myers, Akira Funahashi, Nicolas Le Novère, Michael Hucka and Andreas Dräger - The JSBML project: a fully featured Java API for working with systems biological modelsModelingMartini (U6-04)9
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12:15Andra Waagmeester, Sarah Keating, Alexander Pico, Henning Hermjakob and Andrew Su - Standardizing Pathway Entries to WikidataModelingMartini (U6-04)20
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12:30Discussion
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13:00LunchFree
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14:00Parallel Breakouts 1 2 3
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SBML/CellML/Sed-ML: Multicellular/Agent-based modelling (Dirk Drasdo)Martini (U6-04)
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SBOL Visual Specification Writing
Statistica 1 (2062 U7)
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SBGN Specification Writing
Statistica 2 (4026 U7)
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15:30BreakAtrium
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16:00Parallel Brekouts 4 5 6
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Cross-standard: Annotations (Martin Golebiewski, David Nickerson)Martini (U6-04)
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SBOL Visual Specification Writing
Statistica 1 (2062 U7)
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SBGN Specification Writing
Statistica 2 (4026 U7)
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17:30Daily Wrap-upMartini (U6-04)
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Wednesday
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8:30BreakfastAtrium
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Session 6 (Augustin Luna)
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9:00Bryan Bartley, Herbert Sauro and John Gennari - Automated Coupling of Circuit and Chassis for Synthetic BiologySBOLMartini (U6-04)12
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9:15James Alastair McLaughlin, Göksel Mısırlı and Anil Wipat - Standards for Data Integration in Synthetic BiologySBOLMartini (U6-04)10
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9:30Alasdair Humphries, James Alastair McLaughlin and Anil Wipat - Encoding recipes for experimental implementation in SBOLSBOLMartini (U6-04)11
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9:45Bryan Bartley, Jacob Beal, John Gennari, Angel Goni-Moreno, Raik Gruenberg, Maciej Holowko, Ali Humphries, Vishwesh Kulkarni, Curtis Madsen, James McLaughlin, Göksel Mısırlı, Chris Myers, Tramy Nguyen, Ernst Oberortner, Matthew Pocock, Nicholas Roehner, Meher Samineni, Herbert Sauro, James Skelton, Leandro Watanabe and Anil Wipat - Representing the Design-Build-Test-Learn Cycle with the Synthetic Biology Open LanguageSBOLMartini (U6-04)27
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10:00Zach Zundel, James McLaughlin, Chris Myers and Anil Wipat - Recent Updates to the SynBioHub Data RepositorySBOLMartini (U6-04)15
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10:15Discussion
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10:45BreakAtrium
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Session 7 (Andreas Dräger)
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11:15Miguel de Alba, Carolina Plaza Rodríguez and Matthias Filter - Extensible model metadata in FSK-ML — A Standard for annotation and exchange of executable script based modelsAnnotationMartini (U6-04)16
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11:30Karam Kim, Reza Kalbasi, Koray Atalag, David Nickerson and John Gennari - Linking Clinical Data with Computational Physiology Models Using Semantic AnnotationsAnnotationMartini (U6-04)17
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11:45Matej Troják, David Šafránek, Jakub Šalagovič, Františka Romanovská and Matej Hajnal - Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological ProcessesAnnotationsMartini (U6-04)18
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12:00Discussion
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12:30LunchFree
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14:00Parallel Breakouts 7 8 9
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SED-ML L1V3 wrapup + L1V4 plans (Matthias, David)Martini (U6-04)
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SBOL: Encoding design-build-test
Statistica 1 (2062 U7)
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NeuroML/Neuroscience
Statistica 2 (4026 U7)
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15:30BreakAtrium
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16:00Parallel Breakouts 10 11 12
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SBML/SED-ML: Test suite, model curation and logical models (Lucian Smith)Martini (U6-04)
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SBOL: Encoding design-build-test
Starisitca 1 (2062 U7)
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SBGN Specification Writing
Statistica 2 (4026 U7)
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17:30Daily Wrap-upMartini (U6-04)
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Thursday
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8:30Breakfast
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Session 8 (Chris Myers) [CHARME]
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9:00Ugur Sezerman - Identification of disease  related pathways in complex diseases   via ssystem Biology based analysis of omics dataMartini (U6-04)
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9:45Chris EveloMartini (U6-04)
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10:30BreakAtrium
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Session 9 (Nicolas Rodriguez)
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11:00Igor Rodchenkov, Augustin Luna, Emek Demir, Özgün Babur, Jeffrey Wong, Chris Sander and Gary Bader - Access and Discover Biological Pathway Information from Pathway Commons and BioPAXBioPax/PathwaysMartini (U6-04)19
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11:15Zaynab Hammoud and Frank Kramer - Implementing a multilayer framework for pathway data integration, analysis and visualizationBioPax/PathwaysMartini (U6-04)21
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11:30Augustin Luna, Alexander Mazein, Ugur Dogrusoz, Robin Haw, Tobias Czauderna and Vasundra Toure - Introduction and Current Status of the Systems Biology Graphical Notation (SBGN)SBGNMartini (U6-04)22
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11:45Adrien Rougny and Christine Froidevaux - SBGNLog: a translation of SBGN PD and SBGN AF into first-order logic to reason on molecular networksSBGNMartini (U6-04)23
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12:00Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis and Bernhard O. Palsson - Visualization and Creation of Biochemical Networks with EscherSBGNMartini (U6-04)24
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12:15Discussion
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12:45LunchFree
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14:00Parallel Breakouts 13 14 15
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CHARME WGde Lillo
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SBML/SED-ML/CellML/NeuroML using data (NuML, CSV, HDF5...)Martini (U6-04)
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SBOL: Combinatorial Design Specification and Library Hacking
Statistica 1 (2062 U7)
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