Analyze enzyme regulation with metabolome data.
License: MIT License
Hi there 👋. I'm a microbial ecologist studying the human gut microbiome. 🦠+💻 = 💓
Our lab GitHub can be found here.
Most of my work takes place in other Github organizations.
Obviously important, also necessary for bioconductor in the future.
Allow passing a set of fluxes for each measurement that will be used. Also clarify what actually happens for type = "bias".
Vertex enumeration in its current form can not handle larger models (>100 reactions) in reasonable time. Some alternative methods would be better. As a first step porting LRS to R could help...
Could be nicer. An import option would be good.
Using table based formats with "array cells" might be a nicer option.
Right now dycone uses asolver already contained in the rcdd package. However, it is based on converting everything to fractions and using an exact solver based on rational arithmetic. This is great for numeric stability but also slow. A better option would be to enable several backends for float-based solvers, peferably CLP and CPLEX/GUROBI. FVA should also be converted to the "fast" version using warm starts.
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