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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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adding Aspergillus niger SBMLs and updating Fungal_Models.xlsx #168

Closed jplfaria closed 4 years ago

jplfaria commented 4 years ago

Adding "JDZ836_nc12v7.xml": There are no changes to the biochemistry, this is a version of the model updated to the latest version of the reference genome of Neurospora Crassa I got directly from the author Jeremy Zucker (@djinnome). Additional notes from Jeremy on the biochemistry unique to the model: "As you know, many of the pathways in MetaCyc include generic reactions that contain compound classes, For example, during ceramide biosynthesis, sphinganine combines with a long-chain acyl-CoA to form a dihydroceramide, and this dihydroceramide is desaturated to become a sphingosine-containing ceramide. Note that the length and saturation of the long-chain acyl-CoA is not specified.

When we had Neurospora-specific information about the instances of those compound classes, we created them. For example, according to Figure 6.5 on page 100 of (Davis 2000) in Neurospora crassa the fatty acyl group is composed mainly of OH-18:0, OH-18:1, and OH-24:0, so we created CPD2T-88, CPD2T-89, and CPD2T-90, which correspond to the OH-18:0, OH-18:1, and OH-24:0 forms of the dihydroceramide. We then also created CPD2T-92, CPD2T-91 and CPD2T-93, which corresponds to the OH-18:0, OH-18:1, and OH-24:0 forms of sphingosine-containing ceramides.

samseaver commented 4 years ago

If he specifically says "there's no changes to the biochemistry", then there's no point in integrating both models, I'll integrate this one as its the latest, and ignore the previous one.