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## Background
Metabolic pathways are series of chemical reactions that start with a substrate and finish with an end product.
These pathways are being displayed as certain kind of infographics, of…
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During HARMONY we noticed, that the conversion of SBGN file to SBML with layout / render is currently not working in the deployed newteditor. Error messages come from the minerva API calls:
```
[…
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This issue here is created from https://github.com/iVis-at-Bilkent/newt/issues/724
Example:
```
curl -X 'GET' \
'https://www.pathwaycommons.org/pc2/graph?source=BRCA1&source=BRCA2&limit=1&fo…
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The spec says that a ? can be used to represent unspecified stoichiometry. This conflicts with fact that cardinality is always defined for an EPN and the stoichiometric process should be balanced. The…
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- [x] When I click on "Errors" download button when no file is uploaded, it throws an error in the console. It doesn't prevent the program from running, but let's fix it anyway.
- [x] After I resolve…
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In V1.3, phenotype, that is a process, could be cloned.
Now that processes have instance identity (voted), phenotype should not be cloned.
Should we enforce this? Make an exception?
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Currently, we have maps of these types: SBGN: PD, AF, PD+AF, SIF, SBML, and All. One can see the map type under Map Properties:
- Similar result wh…
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Upon my testing of the current unstable branch of newt, I have encountered the following issues:
- [x] 1. [@okg21] Color scheme not being properly loaded for sample maps.
- [x] ~~2. [@NoorMuhammad…
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In the SBGN PD1.1 spec, it says phenotype can be cloned.
Cloning is only allowed for EPNs, isn't it?
If Phenotype is a Process Node, why can it have connections attached?
It would be helpful to have …