Attendees at COMBINE 2010
on 2011-2-24. The following presents a list of registered attendees. The project descriptions were provided by the individuals when filling out the registration form.
| Name | Institution | Project(s) |
|---|---|---|
| Tariq Abdulla | Loughborough University, UK | Project Fallot |
| Multiscale modelling of heart development, initially using Compucell 3D, and interested in combining this with tools such as SBW. | ||
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| Richard Adams | University of Edinburgh, UK | libSED-ML on SourceForge |
| Developing a native Java library, jlibsedml, to support level 1 of the SED-ML specification, in collaboration with Ion Moraru and Anu Lakshminarayana. The library supports creation, manipulation and verification of SED-ML documents, including evaluation of MathML statements. | ||
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| Kira Anthony | Nature Publishing Group | NCI-Nature PID |
| NCI-Nature Pathway Interaction Database, a resource for cell signaling and gene regulatory pathways. | ||
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| Nadia Anwar | Memorial Sloan Kettering Cancer Center, USA | BioPAX |
| Yoshiyuki Asai | Okinawa Institute of Science and Technology (OIST), Open Biology Unit, JP | [1] |
| We are developing insilicoML: an XML-based model descriptive language, insilicoIDE: a platform for model construction and simulation. | ||
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| Gary Bader | University of Toronto, Canada | BioPAX, Pathway Commons, Cytoscape, GeneMANIA |
| BioPAX, Pathway Commons, Cytoscape, GeneMANIA | ||
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| Frank Bergmann | University of Washington, USA | sys-bio, RoadRunner on SourceForge, SBML Layout, SbwSimTool on SourceForge, libSED-ML on SourceForge, SBML |
| The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms – to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. | ||
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| Bernard de Bono | EMBL-EBI, UK | Ricordo Project |
| The RICORDO project is developing metadata strategies for biomedically-related models and data, as well as a graphical notation for anatomy-scale physiology models. | ||
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| Michael Blinov | University of Connecticut Health Center, USA | BioNetGen Systems Biology Linker (SyBiL) |
| BioNetGen - rule-based modeling software for generating models - relevant to SBML L3 multi and SBGN ER. SyBiL - Systems Biology Linker - retrieves data in BioPAX into Vcell - relevant to BioPAX, SBGN ER and SBML L3 multi | ||
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| Robert Cannon | Textensor Limited, UK | NeuroML, NeuroML user defined types proposal |
| NeuroML, and support for user defined types therein. Specifically, declarative specifications for minimally redundant hierarchical models - the type of thing you would construct if you wanted the cleanest and most reusable expression of a particular class of models.
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| Vijayalakshmi Chelliah | EMBL-EBI, UK | BioModels Database |
| I am one of the curator of BioModels Database
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| David Croft | EMBL-EBI, UK | Reactome |
| REACTOME is a free, online, open-source, open access, curated pathway database encompassing many areas of human biology. Information is authored by expert biological researchers, maintained by the Reactome editorial staff and cross-referenced to a wide range of standard biological databases. These include NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and GO. The curated human data are used to infer orthologous events in 22 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, two plants and E.coli. Tools for pathway analysis include Skypainter and Biomart. Pathway data can be exported in SBML and BioPAX formats. A description of Reactome has been published in Genome Biology and Nucleic Acids Research. | ||
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| Tobias Czauderna | Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany | SBGN-ED |
| SBGN-ED, libSBGN | ||
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| Joseph Olufemi Dada | Universiy of Manchester | SBRML |
| Systems Biology Results Markup Language (SBRML) is a software-neutral language intended to allow any type of systems biology results to be represented. SBRML associates a model with several data sets. Each data set consists of a series of values associated with model variables, and their corresponding parameter values. It provides a flexible way of indexing both simulation results and experimental data to model parameter values which supports both spreadsheet-like data or multidimensional data cubes. | ||
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| Emek Demir | Memorial Sloan Kettering Cancer Center, USA | BioPAX, Pathway Commons |
| BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. | ||
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| Andreas Draeger | Eberhard Karls University Tuebingen, Germany | SBMLsqueezer |
| My special interest is the computational modeling of biochemical systems. I want to investigate and understand the complex mutual influences within living systems and believe that methods from engineering such as simulation and model construction can help to reach this goal. | ||
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| Jurgen Eils | DKFZ (German Cancer Research Center), Germany | |
| Reimplementation of BioModels Database | ||
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| Lukas Endler | EMBL-EBI, UK | BioModels Database |
| I am a curator of BioModels Database, a open and free repository of curated, quantitative models of biological processes described in the peer reviewed literature. BioModels Database is part of the BioModels.net effort and tries to propagate open formats and standards for model representation and annotation. | ||
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| Andrew Finney | Ansys, UK | Ansys |
| I'm developing (actually mostly debugging) software for the integration of multiphysics simulation technology for a wide range of applications. See project URL for more details. | ||
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| Tom Freeman | Ansys, UK | mEPN, BioLayout |
| I have an interest in pathway modeling being an author and supporter of SBGN, whilst also developing our own approach to the graphical depiction and computational modeling of pathway systems in particular with respect to our interest in macrophage biology. I also lead the development of the network analysis tool BioLayout Express3D. | ||
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| Akira Funahashi | Keio University, Japan | CellDesigner |
| CellDesigner: A modeling tool of biochemical networks. | ||
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| Alan Garny | University of Oxford, UK | CellML, OpenCell, Cellular Open Resource (COR) |
| CellML, OpenCell and COR (this one is in maintenance mode now though). | ||
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| Ralph Gauges | University of Heidelberg, Germany | COPASI, SBML Layout Extension |
| I am one of the authors of the COPASI simulation software as well as one of the authors of the SBML layout and render extension. | ||
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| Padraig Gleeson | UCL, UK | NeuroML, neuroConstruct |
| One of main developers of NeuroML, involved in development of NeuroML version 2.0 which will feature greater interaction with other XML languages, including SBML and CellML. Also implementer of neuroConstruct, which has extensive NeuroML support with SBML support in development. | ||
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| Martin Golebiewski | Heidelberg Institute for Theoretical Studies (HITS gGmbH), Germany | SABIO-RK |
| SABIO-RK is a curated database system bundling data referring to biochemical reactions and their kinetics. It offers data for metabolic pathways and as a novelty also for signaling reactions. The database model comprises the description of reactions with their kinetic laws and corresponding parameters and metadata in a structured and standardised format applying controlled vocabulary, as well as annotations to external resources complying with the MIRIAM standard (Minimum Information Required In the Annotation of Models). The data in SABIO-RK can be accessed either manually via a web-based user interface or automated via web-services, both supporting the export of the data together with its annotations in SBML (Systems Biology Markup Language). | ||
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| Martin Goodfellow | University of Strathclyde, UK | Personal Homepage, BioNessie, GeneGram, ViP2P |
| I am interested in the composition and decomposition of SBML networks. I have developed software for the composition of SBML models. I also have an interest in graph matching and composition in general within the biological area. However, my current focus is on SBML. | ||
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| Neil Hanlon | Centre for Systems Biology at Edinburgh, UK | SBSI |
| Systems Biology Software Infrastructure, or SBSI, a numerics framework for parallel optimisation of systems biology models on hpc clusters and a GUI on top. | ||
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| Ron Henkel | University of Rostock, Germany | BioModels Database Demo |
| The increasing number of computational models of biological systems demands a better support for search facilities. One improvement is to enable ranked retrieval of models based on existing model annotation and the evaluation of ontological knowledge. We believe that ranked search results help users to find models relevant to their work. | ||
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| Henning Hermjakob | EMBL-EBI, UK | Reactome, IntAct |
| REACTOME is a free, online, open-source, curated pathway database encompassing many areas of human biology. Information is authored by expert biological researchers, maintained by the Reactome editorial staff and cross-referenced to a wide range of standard biological databases. IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. | ||
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| Michael Hoehl | DKFZ (German Cancer Research Center) | COPASI |
| Reimplementation of BioModels Database | ||
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| Stefan Hoops | VBI | COPASI |
| COPASI and alumi SBML editor. | ||
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| Michael Hucka | California Institute of Technology, USA | SBML |
| I have been working primarily on SBML, and a little bit on SBGN and MIRIAM. | ||
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| Peter Hunter | University of Auckland, New Zealand | CellML |
| VPH/Physiome Project | ||
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| Martijn van Iersel | BiGCaT Bioinformatics, Holland | PathVisio, WikiPathways, BridgeDB, libSBGN on SourceForge |
| WikiPathways: collaborative pathway repository (now BioPAX compatible); PathVisio: pathway editor + multi-omics data visualization; BridgeDb: identifier mapping framework (MIRIAM compatible); involved in LibSBGN | ||
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| Dragana Jovanovska | INRIA - Rocquencourt Paris, FR | BIOCHAM |
| BIOCHAM - BioChemical Abstract Machine is an environment for modeling biological systems and formalizing experimental knowledge. The current release has a SBGN compliant reaction graph editor for drawing biochemical networks. | ||
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| Nick Juty | EMBL-EBI, UK | MIRIAM, SBO |
| MIRIAM and SBO curator | ||
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| Sarah Keating | EMBL-EBI, UK | libSBML, SBMLToolbox |
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| Yoshiyuki Kido | Osaka University, JP | [2] |
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| Christian Knuepfer | University of Jena, Germany | TEDDY, Sembiotics |
| TEDDY: The TErminology for the Description of DYnamics. Sembiotics: Formal Semantics of Bio-Models. | ||
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| Fedor Kolpakov | Institute of Systems Biology, Russia | BioUML |
| BioUML is open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript), embedded genome browser and workflow support it provides powerful possibilities for analyses of high-throughput data. Plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins. BioUML supports main standards in systems biology: SBML, SBGN, BioPAX, CellML, PSI-MI, OBO, MIRIAM. As far as I know BioUML is the only simulator that passed all tests from SBML test suite version 2.0 (SBML L1v2, L2v1-4, L3v1). | ||
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| Tina Kutmon | BiGCaT Bioinformatics, Holland | PathVisio |
| I have worked on a BioPAX-based Stem Cell knowledge base. I was present at the BioPAX workshop in 2009 New York. I just started as a PhD student in Maastricht, working on the PathVisio pathway editor. | ||
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| Camille Laibe | EMBL-EBI, UK | BioModels.net |
| BioModels.net tools and services | ||
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| Nicolas Le Novère | EMBL-EBI, UK | Group Homepage |
| SBML, SBGN, SED-ML, SBO, MIRIAM | ||
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| Wolfram Liebermeister | Humboldt University Berlin, Germany | semanticSBML |
| SemanticSBML: software for model annotation, comparison, and merging | ||
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| Catherine Lloyd | Auckland Bioengineering Institute, New Zealand | CellML Model Repository |
| CellML model curation. | ||
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| Augustin Luna | National Cancer Institute and Bioinformatics Department, USA | Molecular Interactions Maos (MIM) |
| The Molecular Interactions Map (MIM) notation is a precursor to SBGN and a parallel project directed towards standardized notations in biology. Software related to MIMs is being developed centered on a machine readable format for MIM diagrams for the translation to and from other formats; the related projects include a diagram editor, a syntactically and semantically clear specification, and an application programming interface for a MIM data model. I personally am interested and involved in the development of SBGN, libSBGN, and BioPAX. | ||
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| Curtis Madsen | University of Utah, USA | iBioSim |
| iBioSim is a tool that has been developed for the analysis of biochemical reaction network models. While the primary target of iBioSim is models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. | ||
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| Rainer Machne | University of Vienna, AT | SBMLodeSolver |
| SBML ODE Solver, a C library for ODE construction and numerical integration from SBML models. | ||
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| Yukiko Matsuoka | The Systems Biology Institute, Japan | CellDesigner, Payao |
| CellDesigner Payao | ||
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| Alexander Mazein | University of Edinburgh, UK | Ghazal group, Payao |
| Metabolic and signal transduction pathways reconstruction, biological knowledge organization and visualisation, visual notation development. Using SBGN for large biological networks representation: signalling, gene regulation, metabolic and metabolism regulation pathways. Logic-based modelling. Current project: INF-gamma-induced TNF-alpha gene expression. | ||
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| Chris McEwan | UPMC, France | Immunology Immunopathology Immunotherapy (i3) |
| Working with immunologists to develop a UML-like modelling language to aid the study of T-Cells. | ||
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| Huaiyu Mi | SRI International, USA | PANTHER |
| PANTHER Pathway | ||
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| Stuart Moodie | University of Edinburgh, UK | Edinburgh Pathway Editor, SBGN |
| SBGN Editor, Edinburgh Pathway Editor | ||
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| Ion I. Moraru | University of Connecticut Health Center, USA | VCell, JlibSEDML, BioNetGen, BioPAX at VCell |
| jlibSEDML VCell, including BNG@VCell and BioPAX@VCell | ||
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| Robert Muetzelfeldt | Simulistics Ltd, UK | Simulistics |
| We have developed Simile, a continuous-systems modelling environment with advanced capabilities for representing complex, disaggregated systems. A model can represent a large number (105+) of objects, with associations (e.g. 'is_next_to') between them, making it suitable for modelling discretised spatial systems and cell populations, with arbitrary hierarchical organisation. Although originally developed for ecological and environmental modelling, its capabilities apply equally to Systems Biology, and a paper describing its potential for handling various proposed SBML L3 extension packages is available at [3]. | ||
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| Chris Myers | University of Utah, USA | iBioSim |
| We are developing iBioSim for modeling, analysis, and design of genetic circuits. | ||
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| David Nickerson | Auckland Bioengineering Institute, New Zealand | CellML |
| CellML, SED-ML, and model annotation. | ||
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| Poul Nielsen | Auckland Bioengineering Institute, New Zealand | CellML, FieldML |
| I am one of the principal organisers of the CellML and FieldML projects. | ||
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| Brett Olivier | VU University Amsterdam, Holland | PySCeS on SourceForge, MEMSA |
| My current project involves modelling microbial interactions with the environment using genome scale reconstructions. As part of this project I have developed a contraint based modelling extension to the PySCeS simulation software and am interested in developing in the use of SBML that allows for the exchange of genome scale stoichiometric models. | ||
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| Jean-Baptiste Pettit | EMBL-EBI, UK | SBML Converters |
| Creation of a general converter between several modeling format such as SBML, BioPAX and also Octave and XPP conversion. | ||
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| Nicolas Rodriguez | EMBL-EBI, UK | jsbml on SourceForge, BioModels Database, SBMLeditor, SBML converters |
| JSBML - The JSBML project's aim is to provide an pure java SBML parser. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions. Biomodels DB - BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. SBMLeditor - a low level SBML editor SBML Converters - a set of converters from SBML to other formats, like BioPax, CellML, XPP, SBGN/SVG. | ||
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| Andrey Rzhetsky | University of Chicago, USA | |
| Mining biomedical interactions from text, representing complex molecular networks | ||
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| Julio Saez-Rodriguez | EMBL-EBI, UK | Group Homepage |
| Interested in signal network modeling, using logic and mechanistic formalisms in combination with high-throughput biochemical data to study mammalian signaling. | ||
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| Sven Sahle | University of Heidelberg, Germany | COPASI |
| Copasi is a software tool for modeling biochemical reaction networks. | ||
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| Herbert Sauro | University of Washington, USA | sys-bio |
| SBML, SBGN, SEDML, Synthetic Biology etc | ||
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| Jim Schaff | University of Connecticut Health Center, USA | VCell vfrap |
| I'm the lead developer of VCell (vcell.org), a current SBML editor, and am working on the SBML Level 3 spatial extension. Our group is also involved in SEDML. | ||
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| Falk Schreiber | IPK Gatersleben & University of Halle, Germany | SBGN-ED, VANTED, MetaCrop, RIMAS |
| SBML, SBGN, SEDML, Synthetic Biology etc | ||
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| Evangelos Simeonidis | Manchester Centre for Integrative Systems Biology, UK | Group Homepage |
| The MCISB's goal is to combine modelling techniques with biological experimentation to investigate how the proteins in Saccharomyces cerevisiae behave in a coherent fashion. Protein and metabolite data, together with the enzyme kinetic parameters, are introduced into an SBML-based model for calibration and testing. SBML-compliant software packages, such as MATLAB, Mathematica and COPASI, are used to create a comprehensive quantitative kinetic model of yeast metabolism. The construction and validation of the yeast model is intended to be iterative, with models being continually improved as new data are being generated from more discriminating experiments, which in turn are designed based on model predictions. | ||
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| James Sluka | Indiana University Bloomington, USA | CompuCell 3D |
| Ontology development for multi-cell simulations, Multi-cell simulations in cancer and toxicology. | ||
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| Kieran Smallbone | Manchester Centre for Integrative Systems Biology, UK | Group Homepage U+003F Blogsite |
| We create mathematical models of cellular processes, with a focus on metabolism. Through adhering to and developing systems biology standards, we ensure portability of our models. | ||
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| Lucian Smith | University of Washington, USA | Antimony |
| SBML editor -creator/developer of Antimony, a modular human-readable, human-writeable model definition language -Worked on translation of Antimony to and from SBML and CellML. | ||
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| Anatoly Sorokin | University of Edinburgh, UK | Edinburgh Pathway Editor |
| Edinburgh Pathway Editor | ||
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| Andrea Splendiani | Rothamsted Research, UK | BioPAX |
| I'm working on BioPAX and, in the specific, in aspects that relates to its integration in semantic web knowledge bases: - how to improve the definition of the format so that it can support queries across heterogenous knowledge bases - how BioPAX tools can benefit from tools developed within the Semantic Web - how to develop query, analysis and visualization strategies which can leverage on the RDF/Ontology features of BioPAX. | ||
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| Natalie Stanford | Manchester Centre for Integrative Systems Biology, UK | Group Homepage |
| MCSIB | ||
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| Neil Swainston | Manchester Centre for Integrative Systems Biology, UK | Group Homepage |
| The Manchester Centre for Integrative Systems Biology concerns itself with large-scale kinetic modelling, initially of yeast. In addition to this, the centre is interested in the generation of genome-scale metabolic reconstructions, and has led the development of networks in yeast and human. In doing so, much work has been performed in the area of application of MIRIAM-compliant, semantic annotations to SBML models. This work has been developed further with the ongoing work in proposing a new Level 3 package focussed on extending the current recommendations for semantic annotations in SBML. | ||
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| Alice C. Villeger | University of Manchester, UK | Arcadia, libSBGN |
| Main project: Arcadia (displays SBML files as SBGN diagrams) Also involved in: LibSBGN (electronic exchange, conversion and validation of SBGN maps) | ||
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| Katja Wegner | Albstadt-Sigmaringen University, Germany | Apostrophe |
| We develop the tool NetBuilder' that supports the modeling and simulation of genetic networks involving SBML and SBGN. | ||
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| Darren Wilkinson | Newcastle University, UK | SBML, CaliBayes, SBML-shorthand |
| SBML Editor | ||
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| Sarala Wimalaratne | EMBL-EBI, UK | RICORDO |
| A meta-data framework for annotating VPH data and models. | ||
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| Andrei Zinovyev | Institut Curie, France | BiNoM, retinablastoma project, Group Homepage |
| At the "Computational Systems Biology of Cancer" group, we are constructing several comprehensive maps of pathways involved in cancer, we develop software allowing to deal with sysbio standards (BiNoM cytoscape plugin), we participate in defining SBGN and we participate in several EU projects where we promote SBML, BioPAX and SBGN | ||
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