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iVis-at-Bilkent
A web application to visualize and edit pathway models
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...
state variables glyphs are not loaded properly from SBGN-ML when their state sub-element is prefixed
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...
Before Newt 4 can be tested and released the new SBML feature needs to be merged into the unstable branch as it was developed on this separate branch. But we...
There have been many new features/improvements in the unstable branch over the last couple of years. These will be part of Newt 4.0. Let's test this Newt to make sure...
As Reactome content is available in BioPAX format and we already have the necessary modules to make graph-based queries (e.g. paths between, common targets/regulators, etc.) on data in BioPAX format...
Previously when SBML was imported, we created a map of type SBGN PD. Now we create a map of type SBGN PD. The service/module that we used previously now could...
Make sure we store any annotation information in .sbml files both when a map of type SBML is created from scratch and also when SBML is imported (both to SBGN...
When we export an sbml file and try to save it as a nwt file, it gives error which can be seen in the developer console. Edit: When I try...
@SelbiEreshova Can you tell me where to find this information? Which node can connect to which type of node via what kind of edge?
Looks like when checking whether or not each process has at least one substrate and one product we only check the regular processes, not associations, etc. For a map like...
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A web application to visualize and edit pathway models