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Tools


 

  • SBOS

    SBOS

    SBOS (Systems Biology Operational Software) is a Linux live DVD designed to fit the needs of systems biologists. It features a collection of up-to-date free software tools and kinetic models installed in a Linux environment. SB.OS is based on the popular Linux distribution Ubuntu 20.04 and ready to use for all non-commercial purposes.

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  • SBtab

    SBtab

    SBtab is a set of conventions for data tables, facilitating data exchange in Systems Biology. Its aim is to simplify data processing by a standardized syntax and names. This includes, among other things, prescriptions for column names, semantic annotations, and physical units. On our website, we also offer tools for the processing of SBtab files: Their syntax can be validated online and SBtab files can be converted to SBML files (and vice versa).

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  • Parameter balancing

    Parameter balancing

    Parameter balancing is a method to determine consistent parameter sets for kinetic metabolic models. Experimentally measured values, when directly inserted into a model, are likely to yield incomplete and inconsistent parameter sets. Balanced parameter sets, which are complete and consistent, are computed from kinetic constants and other data collected from experiments or the literature, based on constraints between biochemical quantities and assumptions about typical ranges, represented by prior values and bounds. On our website, users can employ an online interface of the parameter balancing tool. This requires mainly a metabolic model in either the SBML or the SBtab format.

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  • Annotate your model

    Annotate your model

    In Systems Biology models are created in various formats. So far only few formats (like SBML) allow the annotation of the biological context of a model. This service will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.

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  • rxncon

    rxncon

    The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modeling. In this project, we develop a new way to describe these networks that minimizes the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models. The development has been driven in collaboration with the Systems Biology Institute in Tokyo and partners at Linköping University and the University of Gothenburg.

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  • Biographer

    Biographer

    Biological network layout and visualization

    biographer is a biological network layout and visualization tool which has been developed at the Theoretical Biophysics Group in Berlin as part of the Google Summer of Code 2011.

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  • SemanticSBML

    SemanticSBML

    semanticSBML  is collection of online services within the semanticSBML project.
    SemanticSBML provides methods to process biochemical network models in SBML format and the semantic annotations therein.

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  • CeLinEx

    CeLinEx

    CeLinEx is a comprehensiv Experiment Database that stores and grants acces to cell line specific Results. to prevent conflicting Data.

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  • PPODB

    PPODB

    Plant-Phenological Online Database offers access to plant-phenological observations in Central Europe mainly Germany, from about 9000 stations, covering 130 years (1880-2009), comprising over 16 millions observations.
    The PPODB offers a unique data source, where, for the first time, plant-phenological observations from 129 years are brought together in one consistent database. Moreover, sophisticated outlier detection methods and quality checks are applied.

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  • YCMDB

    YCMDB

    Curated yeast data for mathematical modeling
    YCMDB collects, annotates and categorizes published data on yeast physiology along with its experimental context to provide a quantitative resource for cellular modelling.

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Humboldt-Universität zu Berlin, Institute of Biology,
Theoretical Biophysics, 10099 Berlin, Germany