MINERVA Tutorial Troubleshooting

[Claire Velikonja]

Hey guys,

I'm looking to use Minerva to visualize a pathway and I had a couple questions about the application. 

1. Can it be used to visualize metabolic reconstructions other than ReconMap? I'm currently interested in visualized pathways in the Harvey Harvetta model, is this possible using Minerva?

2. When I currently try to look at ReconMaps at the VMH website (ex. https://www.vmh.life/#reconmaps/peroxisome), it tells me that either the website is currently down, or the website has been moved. Is this a software issue on my end/is there anything I can do to still see the pathways?

3. When I currently try to follow the tutorial online about visualization using ReconMap 2, I get the following error:

{"error" : "Query server error.","reason":"lcsb.mapviewer.commands.CommandExecutionException: At least two rows try to set color to reaction: R_4ABUTtm"}

Overlay NOT generated successfully. curl post size in MB:0.01153

serverResponse =

    'Overlay NOT generated successfully. curl post size in MB:0.01153'

The script that I used was: 

load('minerva.mat')

minerva.minervaURL = 'http://www.vmh.life/minerva/index.xhtml';

minerva.map = 'ReconMap-3';

  

minerva.login = 'user-name';

minerva.password = 'user-password';

minerva.googleLicenseConsent = 'true';

%initialize the cobra toolbox

% changeCobraSolver('ibm_cplex','QP');

% changeCobraSolver('ibm_cplex', 'LP')

% model = readCbModel('Recon2.v04.mat');

model = load('Recon2.v04.mat');

model = model.modelR204;

formula = printRxnFormula(model, 'ATPS4m');

model_atp_production = model;

model_atp_production = changeObjective(model_atp_production, 'ATPS4m');

solution_atp_prod_max_regularised = optimizeCbModel(model_atp_production, 'max',1e-6);

solution_atp_prod_max_sparse = optimizeCbModel(model_atp_production, 'max','zero');

formula = printRxnFormula(model, 'r0603');

nnz(solution_atp_prod_max_regularised.v)

solution_atp_prod_max_regularised.v(strcmp(model.rxns,'r0603'))

nnz(solution_atp_prod_max_sparse.v)

solution_atp_prod_max_sparse.v(strcmp(model.rxns,'r0603'))

solution_atp_prod_max_regularised.v(solution_atp_prod_max_regularised.v~=0)=1;

solution_atp_prod_max_sparse.v(solution_atp_prod_max_sparse.v~=0)=1;

serverResponse = buildFluxDistLayout(minerva, model, solution_atp_prod_max_sparse, 'atp_prod_max_sparse_2020','#6617B5')

serverResponse = buildFluxDistLayout(minerva, model, solution_atp_prod_max_sparse, 'atp_prod_max_sparse_2020','#6617B5')

I was wondering if I am using the minerva structure wrong, or if I need to be loading a Recon3 to use Minerva? I'm not sure where to currently download it at the moment.

Thank you so much for your help and assistance! Help on any of these three questions would be greatly appreciated!

Thanks,

Claire

[Ronan M.T. Fleming]

Dear Claire,

we fixed some bugs in the code and also updated the tutorials. Please
update your cobra toolbox using
updateCobraToolbox()

Note that function is only for use when you are not also developing
cobra toolbox code. If the latter then see
https://opencobra.github.io/cobratoolbox/stable/faq.html#i-cannot-update-the-cobra-toolbox-using-updatecobratoolbox-why
and
https://opencobra.github.io/cobratoolbox/latest/contributing.html

More generally, thanks a lot for helping us to maintain the cobra
toolbox tutorials. At the moment, we do not automatically test them,
but with sufficient person-power we would be as it needs to be done.

Regards,

Ronan

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[Claire Velikonja]

Thanks Professor Fleming!

I'm able to now run the command " serverResponse = buildFluxDistLayout(minerva, model, solution_atp_prod_max_sparse, 'atp_prod_max_sparse4', [],'#6617B5')

without issue. However, when I try to submit the "solution_atp_prod_max_regularised" server request in the tutorial, I receive the following error:

Error using postMINERVArequest (line 40)

The command is too long to execute.

Error in buildFluxDistLayout (line 78)

serverResponse = postMINERVArequest(login, password, map, googleLicenseContent, identifier, content);

Error in Recon_Map_Visualization_Test (line 42)

serverResponse = buildFluxDistLayout(minerva, model, solution_atp_prod_max_regularised, 'atp_prod_max_regularised',

[],'#6617B5')

I was wondering if you've encountered this issue before, and if there was a fix for it?

Thank you so much for your help!

Claire

[Ronan M.T. Fleming]

Hi Claire,
I'm afraid, I dont know the solution to that. We have been advised by
the MINERVA developers to update the version we are using, but we
would need to find a student to do that. It seems like its something
to do with the number of reactions to be highlighted. I am not sure
what the limit is.
Regards,
Ronan

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[Ines Thiele]

Hi Claire

1. You will need to replace the organ descriptor at the beginning of the reaction abbr with R_ (e.g., Lung_ has to be replaced with R_)

2. https://www.vmh.life/#reconmaps/peroxisome. With safari this link works for me.

3. Ronan and I run the visualisation yesterday successfully. I do not remember how many reactions I visualised however it worked for Harvetta's lung.

Best Ines

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Principal Investigator, Ryan Institute

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National University of Ireland, Galway
School of Medicine
School of Natural Science | Discipline of Microbiology, Orbsen Building | Galway, Ireland

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On Sun, 14 Mar 2021 at 19:58, Claire Velikonja <claire.v...@mail.utoronto.ca> wrote:

[Claire Velikonja]

Hey Professor Thiele,

Thanks for the help, it's awesome that Minerva can be used to visualize Harvey/Harvetta!

I'm a little bit confused about where I should be replacing the organ descriptor in the visualization code with R_. My main goal is to be able to visualize the cholesterol metabolism subsystem in the Harvey model. The current way that I've been trying to visualize the subsystem is:

load('minerva.mat')

minerva.minervaURL = 'http://www.vmh.life/minerva/index.xhtml';

minerva.map = 'ReconMap-3';

  

minerva.login = 'user-name';

minerva.password = 'password';

minerva.googleLicenseConsent = 'true';

model = load('HarveyHarvetta.mat');

model = model.male;

model_HMG_CoA = model;

% ObjRxns = {'Liver_r0488', 'Liver_LDL_HSSYN', 'Liver_HDL_HSDEG', 'Liver_r1050'};

% ObjCoeff = [1, 1, 1, -1];

% model_HMG_CoA = changeObjective(model_HMG_CoA, ObjRxns, ObjCoeff);

% FBAsolution = solveCobraLPCPLEX(model_HMG_CoA, 0, 0, 0, [], 0,'ILOGcomplex');

% fluxData = FBAsolution.full;

% FBAsolution.v = FBAsolution.full;

generateSubsytemsLayout(minerva, model_HMG_CoA, 'Cholesterol metabolism', '#6617B5');

When I currently run this script, it does tell me the overlay is successfully generated and it does appear as generated in my ReconMap account; however, when I click view an overlay doesn't appear. Is there a minerva.map that I should be referencing in the third line if I want to visualize pathways in Harvey? I was also unsure if I needed to run the HH model if I wanted to generate a subsystem layout, as the function just passes in the model and the subsystem name. 

Thank you both so much for your help with this! I'm sorry for the continuous questions, I've really appreciated your help with the software.

Best,

Claire

[Mike Sportiello]

Hi,

I'm having pretty much the exact same issue, but I successfully replaced my reaction names with "R_" in the beginning (for example, one reaction is "'R_EX_acthr__L_e'".

Could you give more details on what you might think might be going on? When I go to my layouts and "download" the layout, it's just a txt file with the only contents being "name" and that's it. any help would be appreciated. thanks.

mike