SciML / SciML/JumpProcesses.jl
network free solvers
Nobody has claimed this yet.
- Dominant language
- Julia
- Stars
- 150
- Forks
- 41
- Avg merge
- 1d 9h
- Merged PRs (30d)
- 28
Description
@TorkelE pointed out that on a multisite phosphorylation benchmark where species can have many phosphorylation states, we are starting to lose performance relative to network-free methods as the number of sites increases (NF methods track individual molecules and their states). It would be worth thinking about how to include such solvers / representations here too, especially in ways that can exploit our current SSA infrastructure.
@TorkelE when you are able to share, could you link the network files and sources?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files or tests are named. Start by obtaining the network files and sources from TorkelE, then study the existing SSA infrastructure and the multisite phosphorylation benchmark; done requires an agreed and implemented network-free solver or representation with benchmark evidence.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- julia
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100