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Bachmann_Archive

This public repository is a collaborative effort of participants of the module "Bioinformatik und Systembiologie" in the Master Program BIDS, organized by the Graduate School Rhein-Neckar in cooperation with MIRACUM, a consortium of the Medizininformatik-Initiative.

Our goal is to provide the Bachmann Model as a fully-featured COMBINE archive, a standardized container for data files related to biological simulation studies described by Scharm & Waltemath ([1]).

Contents

This COMBINE archive is a preliminary representation of a study by Bachmann et al. on JAK2/STAT5 signaling from 2011 ([2]).

Structure

The files are organized into folders as follows:

  • documentation: files describing the model and its characteristics, e.g. the original publication by Bachmann et al..
  • model: files describing and encoding the biological system, e.g. the model in SBML format or graphic representations.
  • experiment: files describing and encoding the experimental setup, e.g. SED-ML simulation descriptions.
  • result: files obtained from running in silico experiments, including plots and tables.

Explore the COMBINE archive

This COMBINE Archive is available here: https://cat.bio.informatik.uni-rostock.de/rest/share/6b507398-c103-4b92-9c90-d6b105ff1372

You can clone this repository or download the latest version of this archive.

References in our project

[1] Scharm, M. and Waltemath, D. A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5, 2421 (2016). https://doi.org/10.12688/f1000research.9379.1

[2] Bachmann, J., Raue, A., Schilling, M. et al. Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range. Molecular Systems Biology 7, 516 (2011). https://doi.org/10.1038/msb.2011.50

[3] Schölzel, C., Blesius, V., Ernst, G. et al. Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. npj Syst Biol Appl 7, 27 (2021). https://doi.org/10.1038/s41540-021-00182-w

[4] Novère, N., Hucka, M., Mi, H. et al. The Systems Biology Graphical Notation. Nat Biotechnol 27, 735–741 (2009). https://doi.org/10.1038/nbt.1558

[5] Rougny, A., Touré, V., Moodie, S. et al. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 16, 20190022 (2019). https://doi.org/10.1515/jib-2019-0022

[6] Le Novère, N. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet 16, 146–158 (2015). https://doi.org/10.1038/nrg3885

[7] Touré, V., Le Novère, N., Waltemath, D. & Wolkenhauer, O. Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput Biol 14, e1005740 (2018). https://doi.org/10.1371/journal.pcbi.1005740.g001

[8] Vogt, T., Czauderna, T. & Schreiber, F. Translation of SBGN maps: Process Description to Activity Flow. BMC Syst Biol 7, 115 (2013). https://doi.org/10.1186/1752-0509-7-115

[9] Balci, H. et al. Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinformatics 37, 1475–1477 (2021). https://doi.org/10.1093/bioinformatics/btaa850

[10] Sari, M. et al. SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PLoS ONE 10, e0128985 (2015). https://doi.org/10.1371/journal.pone.0128985

[11] Rohn, H., Junker, A., Hartmann, A. et al. VANTED v2: a framework for systems biology applications. BMC Syst Biol 6, 139 (2012). https://doi.org/10.1186/1752-0509-6-139

[12] Junker, B.H., Klukas, C. & Schreiber, F. VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109 (2006). https://doi.org/10.1186/1471-2105-7-109

[13] Czauderna, T., Klukas, C. & Schreiber, F. Editing, validating and translating of SBGN maps. Bioinformatics 26, 2340–2341 (2010). https://doi.org/10.1093/bioinformatics/btq407

[14] Rougny, A., Froidevaux, C., Calzone, L. et al. Qualitative dynamics semantics for SBGN process description. BMC Syst Biol 10, 42 (2016). https://doi.org/10.1186/s12918-016-0285-0

[15] Bergmann, F. T. et al. Systems biology graphical notation markup language (SBGNML) version 0.3. Journal of Integrative Bioinformatics 17, 20200016 (2020). https://doi.org/10.1515/jib-2020-0016

[16] van Iersel, M.P., Villéger, A. C., Czauderna, T. et al. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28, 2016-2021 (2012). https://doi.org/10.1093/bioinformatics/bts270