Thomas Pfau

Did you test, whether your bound changes made the model infeasible? This could be a reason for gapFill to fail as it requires a feasible model as input.

Hi, The example file is just for for the headers. Yes, this file does not load since it is missing Metabolites, and thus the model cannot be created properly, but...

I know, but at some point carrying extremely old things along becomes a burden. In particular since any old script would still work with the cobra version tagged 3.0, and...

Thanks for the quick response. This still causes the same error message. ``` Exception in thread "main" java.util.ServiceConfigurationError: io.vertx.core.spi.VerticleFactory: io.reactiverse.es4x.impl.JSVerticleFactory Unable to get public no-arg constructor ``` Interestingly, when I...

@pmlopes are there any examples using vert.x 4 with es4x combining Java and Javascript verticles using maven as a build tool? The only example I have found that actually combined...

Hi, Coming back to this: I managed to get the js verticle to work. What I needed to add were dependencies for graalvm: ``` org.graalvm.sdk graal-sdk 22.0.0.2 org.graalvm.js js 22.0.0.2...

I doubt that SBO terms exist for those, and I highly doubt, that most models do contain this information. One additional check you could do besides GPR as @draeger pointed...

I would: 1. Check for GPR Rule 2. Check for EC-Number Potentially: Check other annotations (e.g. a Uniprot link, would indicate enzymatic reaction). 3. Check SBO Term - With additional...

The problem with confidenceScores is that they are barely existent for anything thats not a model organism, as we often enough just "dont know". About SBOTerms: Yes, you have to...

@draeger Essentially, two items in the SBML would indicate that they are identified by the same external object. And, in contrast to the current situation, it would be necessary to...