Computer Algebra Applications in the Life Sciences

Screenshot of a computation done by Singular, computing a Comprehensive Grobner System of the steady state ideal of the 2-site phosphorylation network. Creater: AmirHosein Sadeghimanesh.
Photo of working in a biology lab, a 96-well plate and a pipette. Photographer: Patporn Chankong.
Screenshot of a computation done by Maple, decomposing the parameter space with respect to the number of steady states that a population model attains. Creater: AmirHosein Sadeghimanesh.

ACA 2022 Special Session

15-19 August 2022, Istanbul-Gebze, Turkey


Confirmed Speakers

Aims and Scope

Initially one would think that doing symbolic computation with a computer would be a hard task, but later through the advent of new algebraic objects such as Gröbner basis invented by Bruno Buchberger in 1965 or Cylindrical Algebraic Decomposition by George Collins in 1975, things started to look different. Now thanks to rapid developments in computer algebra, instead of studying bifurcation events of a biological model for only a specific value of the parameters, one can decompose the whole parameter space according to the types of bifurcations that the model can exhibit. This emphasizes the strength of a symbolic approach which lets us treat free parameters in contrast with using numerical and simulations. However, still many of algebraic algorithms have high complexity and there is still a long path ahead to the point where one can use these tools for realistic examples in biology or chemistry with more than a few parameters and variables.

This special session is focused on three main aspects of computational algebra with application in biology and chemistry:

  • how to model questions from the realm of biology and chemistry using algebra,

  • algorithms that can be used to answer questions of interest of experimentalists about the models,

  • implementations of developed algorithms effectively in computer algebra systems.

We would like to assemble a diverse group of researchers from (experimental and theoretic) biology and chemistry, mathematics, computer science, etc. We hope that diverse backgrounds coming together within the frame of shared interests will lead to future collaborations.

Topics of interests include, but are not limited to the developments and applications in the following:

  • Modelling biological/chemical questions using algebra

  • Cylindrical algebraic decomposition

  • Quantifier elimination theory

  • Comprehensive Gröbner basis

  • Chemical reaction network theory

  • Computer algebra packages for real algebraic geometry

  • Parametric system of polynomial equations


Our session is scheduled for the first three days of ACA, 15th-17th August. Below you can see which talk is in-person and which is online plus the title of the talks. You can see the abstract of each talk by clicking on its title. The talks are ordered alphabetically by the last name of the speaker. Some of the speakers gave permission to share their slides which you can access by clicking on "<slides>" in front of title of their talks.

The exact time of the talks can be found in the following table (in Turkey time zone GMT+03:00). We will have CASinLife group photos in each day a few minutes before the start of the session or a few minutes after the end of the session.

Photos of the session

For the photos of the session click on "Photo gallery" at top right side of the page. Thanks to Fatih Yilmaz, the professional photographer of ACA.

Call for Contributions

If you are interested in presenting your recent work in this session, please send your title and abstract to one of the session organizers, no later than May 30, 2022. Please use the LaTeX template for your submission.

Images at the top of the page: The photo in the middle is taken by Patporn Chankong, the two other images are created by AmirHosein Sadeghimanesh.
For permission to use these images out of this page, contact the corresponding creator.