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When we try to export SBGN maps as GPML, we lost some edges during MINERVA conversion. Here is an example:
When we import WP554 pathway [WP554.gpml.txt](https://github.com/user-attachments/files/1…
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We'll be able to validate the below map without issues but trying to resolve the errors will yield an error:
[new_file.sbgn.txt](https://github.com/user-attachments/files/16255894/new_file.sbgn.t…
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State variables are not loaded properly from SBGN-ML when the element inside the state variable element is prefixed (e.g., ). The state variable is represented but it has no text inside (the value a…
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Current export menu is implemented for exporting SBGNML maps to other formats such as SBML, SIF etc. and they should be working well. However, when we added other formats, SIF and SBML, we didn't put …
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I discovered two issues in the Node connectivity section (3.4.1)
\* I believe that modulation (influence, stimulation, ...) should be allowed to point to the assoc / dissoc node. This is in fact the …
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Section 3.5.2.1, page 43:
"5. The EPNs that make up the LHS of the process should be consistent with the RHS, i.e. the process should constitute a balanced biochemical reaction."
What is meant by that…
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Poor performance in a complex PHP file.
PHP-fpm: 80qps
Nginx +unit or Unit：60
A simple PHP file, unit is more quickly than php-fpm, but a complex PHP file is more worse than php-fpm.
A complex P…
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How can the casualpath jar be run from Cytoscape? Via a commandline call like "java -jar ..." or by calling a function in the jar? The best would be if it can be run calling Java functions, but I do …
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As identified as part of #19, when a logical operator does not have ports, we seem to incorrectly take it as a sign of source/target issue, etc. To allow maps where ports are not in use, we should rel…
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We used to perform **incremental** layout during **Resolve Errors**; now it's back to non-incremental.