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Currently, when an error is encountered, sometimes the server will crash not gracefully handling the problem so, let's rectify these situations. A generic error that pops up saying "Invalid map or uns…
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We've been running into an issue around abstraction levels, with different groups representing interactions at different levels of detail. None of these is more "right" than the others, since one legi…
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In sample 2, when we resolve errors and separate empty set (source and sink) nodes and then download the resulting SBGNML file, empty set nodes don't have coordinates. If we load it to Newt, we cannot…
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### Background
A biological pathway is a network consisting of interactions between biological molecules (e.g. proteins and chemicals) in a cell that lead to a certain product or a change. Research…
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Normally, we can add specified node groups by using SBGN Bricks (Edit -> Add Using SBGN Bricks...) if the map type involves PD. If map type doesn't involve PD, we do nothing. However, currently we can…
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Irina was noting that the maven build on her machine failed with:
```
vn install
[INFO] Scanning for projects...
[INFO]
[INFO] ---------------------< com.github.libsbgn:libsbgn >-------------…
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#### Problem description
> With the memote API it would be quite simple to integrate memote into a pipeline that automatically addresses erroneous test results. There is a plethora of tools availab…
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In the past, the SBGN editors decided that drawing catalysis of reversible reactions was not permissible, as it can often be hardly distinguished which direction is favored by the catalysis. As it sta…
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I guess it's a new issue - has to do with SBGN format only...
```
curl -X 'GET' 'https://www.pathwaycommons.org/pc2/graph?source=ANK1&source=PTEN&limit=1&format=SBGN&kind=NEIGHBORHOO…
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- [x] 1. Load PD sample "PolyQ ..." and then export as "SBGN-ML Plain". Exports fine but on loading the exported file we get "Incorrect File Format". This works fine with some other samples.
- [x] …