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Abstracts for projects represented at the 2009 Hackathon

(Image:Updated.gif 2009-03-20.) The following are abstracts for posters that were presented during the 2009 SBML Hackathon.

Title Presenter Abstract
SBW Frank Bergmann Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW, ) is a software framework that allows heterogeneous application components to communicate and re­use each others' capabilities. SBW is a simple, high performance, open­source software infrastructure which is easy to implement and understand. SBW is also a collection of tools for Systems Biology encompassing the areas of modeling, simulation and visualization of biochemical networks. Main applications include: Jarnac, JDesigner for modeling and analysis and roadRunner for high performance simulations.
SBML2LaTeX Andreas Dräger The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication, and interchange of models in systems biology. As a machine­ readable format, XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e. g., unit declarations, complex kinetic equations, or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTeX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTeX, and PDF, and provides many settings for customization. Source code, documentation, and a web service are freely available at .
SBMLsqueezer Andreas Dräger The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the ongoing development of the human­ readable diagrammatic representation SBGN (Systems Biology Graphical Notation). The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws often requires manual assembly and specific knowledge of kinetic equations. SBMLsqueezer facilitates this modeling step via automated equation generation, overcoming the highly error­prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the type of participating species, and the kind of regulatory relations of the SBGN diagram. Such information allows distinctions between different kinds of state transitions. The types of kinetics considered are numerous, for instance generalized mass action, Hill, convenience and several other enzyme kinetics, each including activation and inhibition. SBMLsqueezer covers metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format. SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for each reaction, only applicable kinetic formulas are considered. This modeling scheme creates kinetics in accordance with the diagrammatic representation. Additional material and the source code can be found at
SABIO-RK Martin Golebiewski SABIO-­RK is a database system offering comprehensive information about biochemical reactions and corresponding kinetic data. It not only describes par ticipating or modifying molecules and kinetic parameters of reactions, but also provides the kinetic rate equations and the environmental conditions. It can be accessed manually by a web ­interface or programmatically by web ser vices. The collected data is standardized to a uniform format and structure. This comprises the usage and development of controlled vocabularies and algorithms to unify the data. Entities and expressions in SABIO-­RK are annotated to other resources and biological ontologies. The data can be expor ted in SBML together with the annotations to shared identifiers complying with the MIRIAM standard. (
KiSAO, TEDDY Christian Knüpfer Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of models. For this purpose we propose two ontologies: The Kinetic Simulation Algorithm Ontology (KiSAO) and the TErminology for the Description of DYnamics (TEDDY). KiSAO covers algorithms used for simulation of computational models. The ontology classifies and puts into context existing simulation algorithms. For the classification, it uses several criteria such as deterministic/stochastic or spatial/non-spatial. The aim of TEDDY is to provide terms for describing and characterising dynamical behaviours, observable dynamical phenomena, and control elements of biological models and biological systems in Systems Biology and Synthetic Biology. ( and
semanticSBML Wolfram Liebermeister semanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format abstract: Semantic annotations in SBML desribe the meaning of model elements and enable computer programs to check and process models based on their biochemical meaning. This is key for model merging, a key step towards the construction of large­scale kinetic models. The program semanticSBML helps users to check and edit semantic annotations and SBO terms in SBML models. Using a large collection of biochemical names and database identifiers, it supports modellers in finding the right annotations. Lists of biochemical reactions can be translated into new annotated SBML models. Finally, semanticSBML allows users to merge models. Conflicts between model elements are detected automatically, but the user can also control all details of the merged model. (
BioModels Database Chen Li 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. (
Saint Allyson Lister The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time­-intensive manual process. Modellers need to know and understand both the systems they are modelling and the intricacies of SBML. However, the amount of relevant data for even a relatively small and well­-scoped model is over whelming. Saint, an automated SBML annotation integration ( environment, aims to aid the modeller and reduce development time by providing extra information about any given SBML model in an easy­ to­use interface. Saint accepts SBML­-formatted files and integrates information from multiple databases automatically. Any new information that the user agrees with is then automatically added to the SBML model. (
SyBiL Ion Moraru SyBiL is short for Systems Biology Linker. Biological pathways, reaction and signaling networks are made publicly availabel in formats standardized to the Biological Pathway eXchange format (BioPAX). Simulation tools for biological pathways are standardized to other Markup languages such as Systems Biology Markup Language (SBML) and Virtual Cell Markup Language (VCML). To take full advantage of scientific advances requires the mapping and integration of simulation markup languages with BioPAX. Sybil is developed to convert models between BioPAX and SBML/VCML. (
PySCeS Brett Olivier PySCeS, the Python Simulator for Cellular Systems (
BioModels Database,
and SBML converters
Nicolas Rodriguez SBMLeditor (

BioModels Database (
SBML converters (

COPASI Sven Sahle COPASI: a software tool for the modeling of biochemical reaction networks (
SBW Herbert Sauro Frank Bergmann does most of the work but it involves SBW, using the various ontologies, considering other areas for standardization including synthetic biology (Deepak Chandran) and multicellular systems.
Antimony Lucian Smith Antimony: A human-readable, human-writable model definition language. Features include modularity, conversion to and from SBML, and a novel method of modeling genetic circuits. (
libAnnotationSBML Neil Swainston Bridging the gap between libSBML and MIRIAM: A library for exploiting SBML annotations.

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