Data Extraction from SimBiology Simulations

What is the BEST way to get the simulation data out of simbiology and into excel or some other program?

I have found a brief explanation on how to export to Matlab area and then convert to XLS but its not working terrible well

[Anh-Dung Le]

I have matlab 2020a now and the simbiology that comes with it is slightly different 2018. However, you can export it to Matlab file and then view the data from there. My problem is the data size isn't large enough and I don't know to increase it. It gives me 70x1 (ie. 70 time units) and the simulations should give alot more if I'm going to export it into excel and use it another graphing platform. Does anyone know how to increase the data size for the simulation?

Answer 1

[Sietse Braakman]

Hi Andrew,

Assuming you are using the SimBiology app, you can do this by right-clicking on the simulation plot and selecting 'Export Data':

Then you can select to export directly to .xls:

If you want to export the data from a SimData object in the MATLAB workspace, you could use code along the lines of:

% make datanames suitable for use as variable names (replace all spaces by underscores)
datanames = tobj.DataNames;
datanames = replace(datanames,' ','_');
%create table from data array
dataTable = array2table(tobj.Data,'VariableNames',datanames);
% create table from time array
timeTable = array2table(tobj.Time,'VariableNames',{'Time'});
% concatenate time and data tables
exportTable = [timeTable dataTable];
% export to .xls file
writetable(exportTable,'exportData.xls')

Let me know how you get on.

[Andrew Heitman]

I actually dont have that third option to export directly to XLS

I am using Matlab 2018B -

UPDATE: Added screenshot of what I see when right-clicking on plot. I am using a mac

[Sietse Braakman]

Thanks for letting me know. Do you mean the third option in the right-click drop down ("Export Data...") or the third option to export to Excel in the dialog box ("Save data to Excel file:")?

[Andrew Heitman]

I updated with a screenshot - I mean the the third option in the dialog box

Answer 2

[Sietse Braakman]

It looks like you are on Mac OS - the export to Excel uses the function xlswrite, which unfortunately only works on Windows.

https://www.mathworks.com/matlabcentral/answers/20058-help-with-xlswrite

So alas, you'll have to use some code to achieve this. You can use/adopt the code I wrote above. Whenever you simulate a model in your SimBiology task editor, the simulation data will be present in the MATLAB workspace and will be called 'tobj'. You should be able to use that code to write the tobj to an excel. Note that this code uses the writetable function, rather than xlswrite.

[micronaut]

doesn't work on R2018a running on Windows 10. No export to workspace or Excel.

[Sietse Braakman]

Could you give me more detail on what doesn't work? Is it the writing to excel with xlsread/writetable not working or is the 'Export data' functionality not working in the SimBiology task editor?

[Gary Gorman]

Hello Sietse. I have Ro22a on MacOS Big Sur 11.6.5.

I cannot find any way to get Simbiology simulation data out of Simbiology and into the Matlab workspace.

1) Simbiology simulation results do NOT automatically appear in the Matlab workspace. Perhaps the Matlab workspace needs to be linked to the Simbiology Model Analyzer by simply opening the Model Builder from the Matlab window?

2) Right click on plot in Simbiology Model analyzer does NOT have an "Export Data" selection. Only "Export Plot" is available. "Export Plot" does indeed export a plot but there is no data with the plot.

[Fulden Buyukozturk]

The interface in 22a is different than described above.

• To export results to MATLAB workspace, right-click on LastRun under the program of interest in Model Analyzer and choose "Export Data to MATLAB Workspace"
• To export results to Excel, add a new Datasheet in Model Analyzer and drag results of the LastRun to the empty datasheet you just created. Right-click anywhere on the Datasheet and choose "Export Datasheet"

To automatically have the results in Workspace after a run in SimBiology, go to Model Analyzer>SimBiology Preferences>Programs, check the box "Export data when program completes executing".

Hope this helps.

Fulden

[Milagros Riquelme]

@Fulden Buyukozturk Thank you. I was looking for an updated answer

[Shakir Atoyebi]

@Fulden Buyukozturk & @Sietse Braakman

Hi, I just started using R2023b (I was using R2019a). Thanks for the answers provided above on exporting dat to Excel. Currently, I am able to export results to Excel via "Export Data to MATLAB Workspace". However, all the exported results comes under 1 single sheet "Sheet1" in the exported spreadsheet, even for multiple scan samples. I am hoping there might be a way to export my results into multiple Excel "sheets" like the older version (R2019a).

using R2023b, can simulated data for 50 samples be automatically exported into 50 individual sheets within a single Excel spreadsheet as common for R2019a? Thank you

[Fulden Buyukozturk]

Hi Shakir,

You can write to different sheets using:

% let's say your exported simdata containing scan results is called results
A = arrayfun(@(x) array2table(x.Data,'VariableNames', x.DataNames),results,UniformOutput=false);
for i=1:length(A)
writetable(A{i}, 'myresults.xlsx', 'Sheet',['Run' num2str(i)])
end

Fulden

[Shakir Atoyebi]

Hi Fulden,

Thanks for your kind response. It worked! I was able to use the code you shared to export the results into multiple sheets on Excel.

One more thing, how might I modify the code to get the 'time' values exported alongside the other data within the results? Thank you.

Shakir

[Fulden Buyukozturk]

Hi Shakir - I missed your follow up question, sorry. To add time data along with state data, you can do:

A = arrayfun(@(x) array2table([x.Time, x.Data],'VariableNames', ['Time'; x.DataNames]),results,UniformOutput=false);

Fulden

[Shakir Atoyebi]

@Fulden Buyukozturk, Please, is there an update to this code. It is no longer working for me even with R2023b. Thank you.

[Jeremy Huard]

@Shakir Atoyebi : Can you share the error message you get?

[Shakir Atoyebi]

@Jeremy Huard, I tried to code again to get the error message. Strangely, it worked now. Thank you.