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Handle more Biomodels models #7
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Thanks Lucian. New PySCeS release is currently waiting on a bug fix in |
Quoting @luciansmith from #6 here
This is most definitely a wrapper issue. There have been major changes and fixes to the way PySCeS deals with assignment rules in version 1.1.1, and also on 1.2.0 and 1.2.1 there have been fixes to this functionality (the latter mainly having to do with substring matching). The wrapper in all eventuality predates this. The data are there: >>>mod = pysces.model('BIOMD0000000297_url.xml.psc', '.')
>>>mod.__settings__['cvode_return_event_timepoints'] = False
>>>mod.doSim(end=140, points=200)
>>>mod.sim.columns
Index(['Time', 'Trim', 'Sic', 'Clb', 'PTrim', 'PClb', 'SBF', 'IE', 'Cdc20a',
'Cdc20', 'Cdh1', 'Swe1', 'Swe1M', 'PSwe1', 'PSwe1M', 'Mih1a', 'Mcm',
'BE', 'Cln', 'mass', 'R1', 'R2', 'R3', 'R4', 'R5', 'R6', 'R7', 'R8',
'R9', 'R10', 'R11', 'R12', 'R13', 'R14', 'R15', 'R16', 'R18', 'R19',
'R20', 'R21', 'R22', 'R23', 'R24', 'R25', 'R26', 'R27', 'R28', 'R29',
'R30', 'R31', 'R32', 'R33', 'R34', 'R35', 'R36', 'R37', 'R38', 'R39',
'R40', 'R41', 'R42', 'R43', 'R44', 'R45', 'R46', 'R47', 'R48', 'R49',
'R50', 'R51', 'R52', 'kswe', 'kmih', 'SBFin', 'IEin', 'Cdh1in', 'Mih1',
'Mcmin', 'Swe1T'],
dtype='object')
I played no part in writing the wrapper for PySCeS, so would not really be able to help there unless I get into the code from scratch. But perhaps this info is sufficient to easily update the wrapper. Perhaps this should go into a new issue? |
Thanks for the info! And yes, let's maybe use this issue (#7) to find particular problems and file those as different smaller-chunk issues? The problem with the wrappers is that the person who wrote all the wrappers (Jonathan Karr) left to go work for industry, so we've been very slowly building back up wrapper expertise as we go. I can certainly take a look; hopefully the fix will be straightforward. |
Continued in #5 as that issue pertains to the present bug. |
So! PySCeS version 1.2.2 is now up and running on biosimulators.org. I have not yet tackled the issue of exporting variables from assignment rules, but it finally looks like I can do that, and hopefully it'll be a relatively straightforward fix? Even before that, though, I ran all the biomodels through 1.2.2, and got successful runs for 345 models, where before I only succeeded on 241. Progress! Thanks again for all your help. |
Here's a new list of successes and failures with PySCeS. 711 now successfully run! |
Great, thanks for your efforts! 😄 |
Here's links to all the biomodels that currently fail when running PySCeS:
pysces_failures.csv
(Many of these are probably due to #6; putting this here so I don't forget to update it when that gets fixed.)
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