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The SYMBIONT project: symbolic methods for biological networks

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Andreas WeberAuthors Info & Claims

ACM Communications in Computer Algebra, Volume 52, Issue 3

Pages 67 - 70

https://doi.org/10.1145/3313880.3313885

Published: 16 February 2019 Publication History

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Abstract

The international interdisciplinary SYMBIONT project ranges from mathematics via computer science to systems biology, with a balanced team of researchers from those fields. At the present stage the project has a clear focus on fundamental research on mathematical methods, and prototypes in software. Results are systematically benchmarked against models from computational biology databases. We summarize the motivation and aims for the project, and report on existing results by the consortium and first activities. The project website can be found at www.symbiont-project.org.

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H. Errami, M. Eiswirth, D. Grigoriev, W. Seiler, T. Sturm, and A. Weber. Detection of Hopf bifurcations in chemical reaction networks using convex coordinates. J Comput Phys, 291:279--302, 2015.

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Bradford RDavenport JEngland MSadeghimanesh AUncu A(2022)The DEWCAD projectACM Communications in Computer Algebra10.1145/3511528.351153855:3(107-111)Online publication date: 12-Jan-2022
https://dl.acm.org/doi/10.1145/3511528.3511538
Lüders CSturm TRadulescu O(2022)ODEbase: a repository of ODE systems for systems biologyBioinformatics Advances10.1093/bioadv/vbac0272:1Online publication date: 26-Apr-2022
https://doi.org/10.1093/bioadv/vbac027
Kruff NLüders CRadulescu OSturm TWalcher S(2021)Algorithmic Reduction of Biological Networks with Multiple Time ScalesMathematics in Computer Science10.1007/s11786-021-00515-2Online publication date: 8-Jul-2021
https://doi.org/10.1007/s11786-021-00515-2
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The SYMBIONT project: symbolic methods for biological networks
1. Applied computing
  1. Life and medical sciences

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cover image ACM Communications in Computer Algebra

ACM Communications in Computer Algebra Volume 52, Issue 3

September 2018

67 pages

ISSN:1932-2232

EISSN:1932-2240

DOI:10.1145/3313880

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Association for Computing Machinery

New York, NY, United States

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Published: 16 February 2019

Published in SIGSAM-CCA Volume 52, Issue 3

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Bradford RDavenport JEngland MSadeghimanesh AUncu A(2022)The DEWCAD projectACM Communications in Computer Algebra10.1145/3511528.351153855:3(107-111)Online publication date: 12-Jan-2022
https://dl.acm.org/doi/10.1145/3511528.3511538
Lüders CSturm TRadulescu O(2022)ODEbase: a repository of ODE systems for systems biologyBioinformatics Advances10.1093/bioadv/vbac0272:1Online publication date: 26-Apr-2022
https://doi.org/10.1093/bioadv/vbac027
Kruff NLüders CRadulescu OSturm TWalcher S(2021)Algorithmic Reduction of Biological Networks with Multiple Time ScalesMathematics in Computer Science10.1007/s11786-021-00515-2Online publication date: 8-Jul-2021
https://doi.org/10.1007/s11786-021-00515-2
Rahkooy HSturm T(2021)Testing Binomiality of Chemical Reaction Networks Using Comprehensive Gröbner SystemsComputer Algebra in Scientific Computing10.1007/978-3-030-85165-1_19(334-352)Online publication date: 13-Sep-2021
https://dl.acm.org/doi/10.1007/978-3-030-85165-1_19
Rahkooy HSturm T(2021)Parametric Toricity of Steady State Varieties of Reaction NetworksComputer Algebra in Scientific Computing10.1007/978-3-030-85165-1_18(314-333)Online publication date: 13-Sep-2021
https://dl.acm.org/doi/10.1007/978-3-030-85165-1_18
Rahkooy HMontero C(2020)A Graph Theoretical Approach for Testing Binomiality of Reversible Chemical Reaction Networks2020 22nd International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC)10.1109/SYNASC51798.2020.00027(101-108)Online publication date: Sep-2020
https://doi.org/10.1109/SYNASC51798.2020.00027
Grigoriev DIosif ARahkooy HSturm TWeber A(2020)Efficiently and Effectively Recognizing Toricity of Steady State VarietiesMathematics in Computer Science10.1007/s11786-020-00479-9Online publication date: 21-Jul-2020
https://doi.org/10.1007/s11786-020-00479-9
Rahkooy HSturm T(2020)First-Order Tests for ToricityComputer Algebra in Scientific Computing10.1007/978-3-030-60026-6_30(510-527)Online publication date: 14-Sep-2020
https://dl.acm.org/doi/10.1007/978-3-030-60026-6_30
Rahkooy HRadulescu OSturm T(2020)A Linear Algebra Approach for Detecting Binomiality of Steady State Ideals of Reversible Chemical Reaction NetworksComputer Algebra in Scientific Computing10.1007/978-3-030-60026-6_29(492-509)Online publication date: 14-Sep-2020
https://dl.acm.org/doi/10.1007/978-3-030-60026-6_29
Radulescu O(2020)Tropical Geometry of Biological Systems (Invited Talk)Computer Algebra in Scientific Computing10.1007/978-3-030-60026-6_1(1-13)Online publication date: 14-Sep-2020
https://dl.acm.org/doi/10.1007/978-3-030-60026-6_1

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