Rodrigo Santibáñez-Palominos

Hello sanger-pathogens team, I installed roary from the repository (ubuntu 18.04) and performed the test using `dzil test`. However, it seems some tests failed and I don't know what to...

Hello, as_matrix() was deprecated (https://pandas.pydata.org/pandas-docs/version/0.25.2/reference/api/pandas.DataFrame.as_matrix.html) and values() won't work as expected following the pandas' dev suggestion. Instead, to_numpy() works and produce simulations with cupsoda (https://pandas.pydata.org/pandas-docs/version/0.25.2/reference/api/pandas.DataFrame.to_numpy.html#pandas.DataFrame.to_numpy) (I made a mistake in...

Allows exporting to kappa when rules refer to only one compartment

1

Hello everyone, I did a workaround for models with one compartment or many but with rules only referring to one compartment. For instance, I took the model MODEL1608100000 from Biomodels....

error importing SBML model

3

Hello everyone, I found a problem trying to import an SBML model (https://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1608100001). It seems the SBML file has something invalid `SyntaxError: invalid syntax (, line 1)` for PySB. However,...

Incongruity between kappa.run_simulation() and bng.run_ssa() outputs

3

Hello, I found that kappa.run_simulation() and bng.run_ssa() report their results in differente formats. For example: input: bng.run_ssa(model, ...) output: array([( 0., 2., 100., 1., 0., 2., 100.), ( 10., 2.,...

Hello, cameo works fine with cobrapy 0.24.0 Best,

Reconstruct models from protein fasta

2

Dear @jotech, Thank you for developing gapseq. I tried it, however, I have only protein fasta files which I think are incompatible right now. Do you plan to add support...

# Description of the issue The name should be L-idonate 5-dehydrogenase (NADP) # Page http://bigg.ucsd.edu/models/iLF82_1304/reactions/IDOND2 # Browser Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:88.0) Gecko/20100101 Firefox/88.0

Hello, Is there a plan to update pyDNAse to an updated version of matplotlib? `ERROR: pydnase 0.3.0 has requirement matplotlib

docker problems

6

Hello, I found the following error when trying the example pipeline with `nextflow run . -profile docker` ``` N E X T F L O W ~ version 19.08.1-edge Launching...