how can i export the model in way i can include it in my thesis?

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Tejal Odedra

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Jun 1, 2022, 2:22:07 PMJun 1
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how can i export the model in way i can include it in my thesis?

I am trying to export my model and put the code into my paper but when i try exporting it it says there is no author. 

König, Matthias

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Jun 2, 2022, 3:31:24 AMJun 2
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Hi Tejal,

I would export the model as SBML and store the CPS COPASI files in addition.
What I am doing is to
- create a github repository for the model (which allows for versioning and tracking of model changes. Here you put the CPS and SBML files)
- connect the repository with zenodo, so the model can be cited via a unique DOI
- link the SBML files with sbml4humans for a simple online report for reviewers

See for instance the following repository
https://github.com/matthiaskoenig/pravastatin-model
which you can then cite via the zenodo entry
https://zenodo.org/record/6481380

SBML is the exchangable format between tools.
In addition I can recommend to upload your model to a dedicated model repository after publication such as biomodels.

By adding an author to your model the export should work.
Hope this helps.

Best Matthias

________________________________
Matthias König, PhD.
Junior Group Leader Systems Medicine of the Liver Lab
Humboldt-Universität zu Berlin, Institute for Biology, Institute for Theoretical Biology
Philippstraße 13, Haus 20, 10115 Berlin
koen...@hu-berlin.de
+49 30 2093 98435
https://livermetabolism.com
https://twitter.com/konigmatt
https://github.com/matthiaskoenig

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Von: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com> im Auftrag von Tejal Odedra <sugar...@gmail.com>
Gesendet: Mittwoch, 1. Juni 2022 20:22:07
An: COPASI User Forum
Betreff: [ext] [copasi-user-forum] how can i export the model in way i can include it in my thesis?

how can i export the model in way i can include it in my thesis?

I am trying to export my model and put the code into my paper but when i try exporting it it says there is no author.

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Frank Bergmann

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Jun 2, 2022, 4:30:12 AMJun 2
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Hello Tejal, 

just to add to what matthias said. You received a warning message, that no author was specified. This just means that some meta information cannot be added until you do so. The model will still be exported as SBML file. Still it is a good idea to add that information. To set this up easily, go to the COPASI preferences, (in Tools\References) and add your user information (like shown in the first picture). From then on when editing the model annotations (by clicking on the Annotation tab on the model) you can click 'add me' and your author information will automatically added. 

Alternatively you can manually specify your information there. For more information see also: 


best
Frank
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