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**Project description**
AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the prote…
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https://github.com/SciML/JumpProcesses.jl/pull/351 adds a default algorithm, but we should follow up and benchmark / examine existing benchmarks to better determine where the switch points between met…
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I discovered a relatively innocuous bug where KroneckerBio falsely warns of duplicate reactions. When finalizing a mass action model, if two reactions have the same stoichiometry, use the same rate pa…
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**Background**
* [SBML](https://synonym.caltech.edu) and [CellML](https://www.cellml.org) are now widely adopted for defining and sharing models of subcellular biological processes.
* @MauriceHendri…
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We've decided to try applying the sharing of input/output instances between reaction activities to Reactome GO-CAM models. This was already applied for YeastPathways models in #258. Referencing https:…
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Bug description: In FBACell.run, the upper bound on the biomass reaction is set to be equivalent to the rate that would fill the current cell. This overrides the limit set in the model file, which we …
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**Motivation**
In the multi-channel exchange model, inter-channel transfer along different channels is currently handled within the unit in CADET-Core.
In the future it would be useful to have diffe…
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Currently the material models have to compute viscosity, various other parameters, and the variables that define the equation of state, all in one class. Magali Billen suggested that, long term, these…
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Models that expand to large numbers of species and/or reactions have a very high memory footprint (one model with ~4K species and ~50K reactions used almost 4GB on a 64-bit python). I think the bloat …
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= Description =
- Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical reactions are central to the SBML language; it shou…