It is rather common for Cytoscape users to save the whole session they are working with as a .cys file by simply clicking on File > Save Session As... and giving a name to their session.
In the current MGG implementation, if you save your microbetag-annotated network as a session, then you most probably will not be able to parse the seed and pathway complementarities once you re-open the session.
We already work on supporting saving the session feature of Cytoscape.
Until then, one can save a microbetag-annotated network as described here, in order to have all the MGG features once they re-open it:
- Click on
File > Export >Network to File.. - From the list of File Formats, select the
CX JSON (*.cx)one - Give a name to your
microbetag-annotated network and pressOK.
Remember that in this way, you only save the specific network and not all the networks you may have opened in your session!
You can always save your session normally, export the microbetag-annotated network as described above and when you want to open your session as it used to be, then you first load the session and from there you import the .cx file you exported. This will be equivalent with saving the whole original session.
Now you can re-open the microbetag-annotated network as descrobed here.