2023-07-27 –, 32-D463 (Star)
The Scientific Machine Learning (SciML) ecosystem is rapidly gaining momentum within the field of systems biology. With this birds of feather discussion we want to bring the international community of systems biology tool developers and users at one table to (a) brainstorm promising routes for future developments, and (b) facilitate collaborative projects.
Purpose: The Scientific Machine Learning (SciML) ecosystem in Julia holds great potential for applications in the field of systems biology. Much of this potential can be attributed to fast ODE solvers and parameter estimation packages, and convenient interface with neural differential equations and systems biology standards/formats. While an increasing number of systems biology groups are starting to use Julia to address biological questions, many existing systems biology tools are not yet available in Julia.
In this Birds of Feather discussion we want to address the following questions:
1. What are the community needs, plans and visions?
2. Which existing systems biology tools hold great potential for faster implementations if ported to Julia?
3. Which new tools are enabled by the features of the SciML ecosystem.
4. Where can we find synergies and common interests for joining efforts on systems biology tool development?
5. (How) can we improve on the existing communication channels to facilitate coordinated and collaborative tool development.
Significance: Bringing key players in the field of open-source systems biology tool development at one table to discuss the above questions will facilitate a flourishing ecosystem of systems biology tools and pipelines in Julia, and increase the uptake of the language by the community as a consequence.
Agenda: the following points will be on the agenda.
- ~5 min: Introduction by Paul Lang or Anand Jain
- ~15 min: Every participant briefly addresses question (1) from above from their perspective
- ~50 min: Participants are split up into 2-5 groups to discuss questions (2)-(5) from above.
- ~15 min: One member of each group summarizes the main points from the group discussion for the other groups.
- ~5 min: Closing remarks by Paul Lang and Anand Jain
- (Optional if time is left: Talking to people from other discussion groups and unguided networking.)
A short document summarizing the Birds of Feather discussion may be published on Twitter, Discourse and the sysbio-sciml Slack channel on the Julia workspace for the broader community by the end of August.
Moderators: Paul Lang and Anand Jain
Paul Lang works in developing comprehensive models of biochemical reaction systems and
supporting software tools. He obtained a BSc degree in Molecular Biology at the University of
Graz (Austria) and an MSc degree in Molecular Health Sciences at ETH Zurich (Switzerland). He
then switched from experimental to computational research. During his PhD at the University of
Oxford (UK), Paul developed a rule-based cell cycle model that explains location and dynamics
of 16 observables in RPE1 cells. As visiting scholar at the Icahn School of Medicine at Mount
Sinai in New York (USA), he co-developed BpForms, a toolkit for concretely describing non-
canonical polymers to enable the construction of whole-cell models. Paul also co-developed SBMLToolkit.jl, which imports SBML models into the SciML ecosystem. Currently, Paul works for JuliaHub on developing a parameter optimization tool for quantitative systems pharmacology. He also helps clients to translate their models to ModelingToolkit.jl ODESystems.
At JuliaHub, Dr. Roesch shares her knowledge of the impact of Julia and JuliaHub products on Quantitative Systems Pharmacology. She earned her PhD in Theoretical Systems Biology from the University of Melbourne, Australia. She has researched and published about the use of the Julia programming language in Systems Biology.