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iVis-at-Bilkent / newt

A web application to visualize and edit pathway models
http://newteditor.org
GNU Lesser General Public License v3.0
53 stars 27 forks source link

Prepare a legend for SBML #696

Closed ugurdogrusoz closed 3 months ago

ugurdogrusoz commented 1 year ago

@SelbiEreshova Can you tell me where to find this information? Which node can connect to which type of node via what kind of edge?

SelbiEreshova commented 1 year ago

@ugurdogrusoz The legend for SBML is similar to CellDesigner's: https://www.celldesigner.org/help/images/components42.png Also, you can see the exact rules in the GSoC report: https://docs.google.com/document/d/17Yp1YPOVLc3PJYNRKO9FeCiH_bzyK8rVv08jGs3ilyQ/edit?usp=sharing

ugurdogrusoz commented 3 months ago

@umut-er Other Legends (see under Legend menu) have been prepared using Inkscape and used in .svg format. Please use the same format/style and create one for SBML (now that Newt 4 supports an SBML palette).

ugurdogrusoz commented 3 months ago

Looks good thanks. One minor improvement: can we increase the width of the window so that the title fits in a single line?

umut-er commented 3 months ago

This worked on my local computer. Next deployment is at 19.30. If it doesn't work on the server I can change it again.

SelbiEresh commented 3 months ago

@umut-er There seems to some minor mistakes in the notation:

  1. Translation consumption and translation production. Notice that the line contain . instead of .. Otherwise there is no difference between translation and transcription.
  2. The edge 'negative influence'
  3. The edge 'unknown reduced stimulation '

Please refer to cell designer's legend for correct notation : https://www.celldesigner.org/help/images/components42.png

umut-er commented 3 months ago

Hey, thanks for the review! It should be fixed now. We can close this issue.

ugurdogrusoz commented 3 months ago

Please confirm @SelbiEreshova here

SelbiEresh commented 3 months ago

Yes, it looks correct now. Thank you @umut-er!