Greg Medlock

I like the concept of scoring, but fear that scores that are too general may lead to meaningless comparison between reconstructions, or misguided curation efforts (e.g. curating to achieve a...

Looks like the most efficient method to do this would be the /identifers/validate/{id} service described here: http://identifiers.org/restws I'm not familiar enough with REST/associated internet protocols to know whether having users...

To get the discussion going about what this will look like for cobrapy and memote, how do you envision cobrapy users interacting with SBO terms? There are many cases that...

Not sure how others think here, but I think the application is a bit too narrow given how straightforward the process is to warrant a new function to maintain. There...

Maybe we could steer users in the right direction with a function that checks SBML compliance prior to writing, so that what we end up putting in documentation is more...

@cdiener agreed--I should have been more specific. The proposed function would only check compliance for SBML aspects that are already checked when writing the file via libSBML (e.g., IDs). The...

I think sorting on SBML output is the best option if we wanted to solve this, but SBML is also not intended to be human readable. Most software for reading/writing...

Sounds good to me. While we're at it, reaction.genes is currently a set as well... I frequently find myself trying to access genes within a reaction, e.g. `reaction.genes[0]`, which doesn't...

PR #927 looks good to me, but I'm not sure whether it's also worth breaking backwards compatibility in reaction.genes *yet*, since there is a desire to improve handling of GPRs,...

I think the main implementation concern is being careful with circular references as much as possible so that deletion and addition of objects doesn't mangle group membership. This is probably...