Rodrigo Santibáñez-Palominos
Rodrigo Santibáñez-Palominos
I used `numpy.reshape` to format the kappa.run_simulation(...) output as in bng.run_ssa(...). Best regards.
Hi Alex, I didn't know what I need to do until I search Google and found numpy.shape and reshape. That was pure luck!
As far I know, it is possible to observe a variable. However, your request is more like "observe a rule" or "count how many time the rule fired at the...
Sure. I agree with you. I also wanted to measure the flow of the rules along with the agent quantities. Anything that reduces the amount of effort to write down...
I'm open to help and collaborate. We could talk later and formally with our groups about how to parameterize kappa models. And how to implement other useful analysis. Best!
I call KaSim using python multiprocessing and then averaging (and also calculating the standard deviation) the outputs files using pandas dataframes. ``` multiprocessing.Pool(multiprocessing.cpu_count()-1).map(run_kasim_precompiled, range(0, 1000)) ```
Maybe this is related https://github.com/soedinglab/MMseqs2/issues/384#issuecomment-742564711
I think "--target-cov" was changed to "-c" List matches above this fraction of aligned (covered) residues (see --cov-mode) [0.000]
I think "--max-seqs" doesn't exist anymore. I tracked changes in the code (src/commons/Parameters.cpp) and the option disappeared. I removed it from the script.
Also, I have the bin folder in the path, so I can't understand why the script can't found the truncate_header.lua