cdanielmachado / transcript2flux Goto Github PK

Hi, I have problems executing the code, my setup is

MAC OSX
opencobra 7e6385f
Gurobi7
Matlab R2012a

I get the following error output when I run main.m:

MException

Properties:
identifier: ''
message: [1x54 char]
cause: {0x1 cell}
stack: [6x1 struct]

Methods

MException

Properties:
identifier: ''
message: [1x54 char]
cause: {0x1 cell}
stack: [6x1 struct]

Methods

86 exchange_rates = fluxes_exp(exchange_idxs_data);
K>> fluxes_exp(exchange_idxs_data)
Index exceeds matrix dimensions.

Index exceeds matrix dimensions.

Error in evaluate_method (line 86)
exchange_rates = fluxes_exp(exchange_idxs_data);

Error in benchmark_method (line 31)
result = evaluate_method(model, dataset, method, condition,
ref_condition, options);

Error in main (line 49)
benchmark_method(methods{i}, model, dataset, options);

Wonder if you could help me find the error, from what I see the error comes from the function

fluxes_exp = fit_fluxes_to_model(model, dataset.reactions, fluxes_exp_old);

which returns an empty object instead of the fitted fluxes(as required I presume),

Thank you and best regards.

This is mainly a reminder for me or someone else to hopefully add this feature if given time.

Currently an older version of gurobi is required for the version of MADE included in transcript2flux; it would be good to have the same version of gurobi used in all tests (if nothing else this simplifies installation greatly) MADE is now part of the TIGER toolbox (bitbucket.org/csbl/tiger), which supports Gurobi5 as of version 1.3.

See https://bitbucket.org/paj2s/made/issue/1/cmpi-doesnt-support-gurobi5 for more details.

consider the following example
A AND B AND C OR D AND E
With a precedence of AND over OR this should be evaluated as

((A AND B) AND C) OR (D AND E)

It is now evaluated as

((A AND B) AND (C OR D)) AND E

Which clearly gives a different result.

Hi,

I have noticed that the instructions for installing the required software may be outdated, as the link for the MADE package is currently not working.

I am interested in comparing the results of your study with my own, so I kindly request your assistance in obtaining the necessary resources to replicate your programming environment. Alternatively, I would appreciate any suggestions for obtaining the prediction and error values.

Thanks