These are chat archives for opencobra/cobrapy

8th
Mar 2017
Henning Redestig
@hredestig
Mar 08 2017 08:29
Hey guys, I'm just making 0.6.0a1 release, all future pull requests are to go against devel as devel-2 is no more
Peter St. John
@pstjohn
Mar 08 2017 14:57
Awesome!
Christian Diener
@cdiener
Mar 08 2017 15:00
:+1:
Christian Diener
@cdiener
Mar 08 2017 16:46
I think it would be cool if we can make 0.6.0a1 a Github release as well ("Draft release" button) so it shows up on badges etc.
Henning Redestig
@hredestig
Mar 08 2017 16:58
Done, should add this to travis plan as well...
Christian Diener
@cdiener
Mar 08 2017 16:59
Cool will add a badge and section to the website as well.
Henning Redestig
@hredestig
Mar 08 2017 17:02
Fantastic, cheers!
Christian Diener
@cdiener
Mar 08 2017 22:24
@Midnigher Finally got to testing model.metabolites.fdp_c.summary(fva=0.99) but it works fine for me. Only requires solving the model before or ti gives an error (which is informative).
In [9]: model.metabolites.fdp_c.summary(fva=0.99)
PRODUCING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)
----------------------------------------------------------
%       FLUX  RANGE           RXN ID    REACTION
----  ------  --------------  --------  -------------------------------------
100%    7.48  [-6.17, -8.92]  PFK       atp_c + f6p_c --> adp_c + fdp_c + h_c

CONSUMING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)
----------------------------------------------------------
%       FLUX  RANGE           RXN ID    REACTION
----  ------  --------------  --------  -------------------------------------
100%    7.48  [6.17, 8.92]    FBA       fdp_c <=> dhap_c + g3p_c
0%      0     [6.17, 8.92]    FBP       fdp_c + h2o_c --> f6p_c + pi_c
Peter St. John
@pstjohn
Mar 08 2017 22:26
:thumbsup:
Speaking of summary methods, any other opinions on #441? I’m not sure whether the niche (?) case of multiple imports per boundary species is worth re-casting the summary in terms of reactions over metabolites. If that’s something we think we’ll see often though I’m happy to reconsider
Christian Diener
@cdiener
Mar 08 2017 22:39
Or just throw an error that metabolite summary does not allow more than one exchange per metabolite... In the long run a "model best pactices/recommendations" could be worthwhile for the docs.