opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

https://opencobra.github.io/cobratoolbox

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Pan models #1498

Open PejmanS opened 5 years ago

PejmanS commented 5 years ago

Hi I tried to create pan models in family level, but the result of model test shows me it has leak. what could i do? Is there anyway i test it completely and solve model problems? I hereby confirm that I have:

[x] Tried to solve the issue on my own
[x] Retried to run my code with the latest version of The COBRA Toolbox
[x] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

PejmanS commented 5 years ago

@almut-heinken @rmtfleming

almut-heinken commented 5 years ago

Hello @PejmanS , sorry for the late response. Unfortunately, such futile cycles resulting in unrealistic ATP production can only be identified manually. Try constraining all reactions in the pan-models to zero flux one by one while maximizing ATP demand on Western diet. Multiple transporters for the same compound are often the cause. Have a look at line 204-265 in the createPanModels function and add any fixes you find to the reactionsToReplace variable. I hope that helps, best Almut

PejmanS commented 5 years ago

@almut-heinken Thanks! As it has written in tutorials, Pan models in Genus level are stable and tested? Is it ok in AGORA 1.03?

almut-heinken commented 5 years ago

Hello @PejmanS yes, they are tested on genus level. However, I get a different error due to recent changes in the COBRA Toolbox: readCbModel crashes on a certain model. Please give me some time to fix this.

PejmanS commented 5 years ago

Have you tested AGORA 1.03?

On Mon, Sep 16, 2019, 10:53 PM almut-heinken notifications@github.com wrote:

Hello @PejmanS https://github.com/PejmanS yes, they are tested on genus level. However, I get a different error due to recent changes in the COBRA Toolbox: readCbModel crashes on a certain model. Please give me some time to fix this.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1498?email_source=notifications&email_token=AKYJQYXESMJ4O7PPGYTJ4VLQJ7FK5A5CNFSM4IK2JD4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD62B3TQ#issuecomment-531897806, or mute the thread https://github.com/notifications/unsubscribe-auth/AKYJQYRLZN2OFVG7QXILHNDQJ7FK5ANCNFSM4IK2JD4A .

almut-heinken commented 5 years ago

1511

PejmanS commented 5 years ago

@almut-heinken Thanks. Should i download AGORA from vmh again now? has it changed?

almut-heinken commented 5 years ago

Hi @PejmanS not yet, it still needs to be replaced. You can use the previous one, but then you have to temporarily replace all instances of readCbModel with load.

PejmanS commented 4 years ago

@almut-heinken Hi Almut what is this error for? Index exceeds matrix dimensions.

Error in createPanModels (line 251) modelTest = addReaction(modelTest, reactionsToReplace{j, 3}, RxForm{1, 1});

I'm using #1511 pull and changed file. This error occurs for species and genus level.

almut-heinken commented 4 years ago

Hi @PejmanS I just submitted a pull request to COBRA.papers that I think should fix this. Best, Almut