Doing a bit more digging, it’s using cytoscape[0] which is similar to graphviz. If you search your favorite search engine with “Cytoscape Session Viewer”, you’ll find many websites displaying the same type of graphs (select layout: circle). FYI, circo doesn’t always output a circle. I recently created https://github.com/MegaManSec/SSH-Snake/blob/main/tools/SSH-Snake-dot-circo.png.

– Source: Hacker News
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9 months ago

The YAML files are then parsed, and a CYJS file produced, which is a graph model. This is used directly in the web app, but can also be opened in the Cytoscape desktop app , and imported into Neo4j if desired. I can add additional “export” steps to the automated build process, so e.g. GraphML (yEd, Gephi) or DOT files (GraphViz, mermaid, etc) can be used for whatever purpose needed.

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over 1 year ago

Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I’d recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to…

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almost 2 years ago

Two common GUI tools for analysis and editing of graph data are Gephi and Cytoscape. An older alternative starting with a P is Pajek, but I’ve never used it.

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about 2 years ago

I’ve been thinking that Gephi is getting long in the tooth. Has anybody tried Cytoscape? (https://cytoscape.org/) (DNS is SERVFAILing at the moment.) I use it for a combination of “no K” clustering (general exploration) and what’s referred to in threat intelligence by the term of art “pivoting”.

– Source: Hacker News
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over 2 years ago

The formatting stuff was all in Cytoscape, which is a pretty sick program for graph stuff.

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over 2 years ago

Protein interaction networks: Cytoscape.

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almost 3 years ago

Have you had a look at Cytoscape? I think this could work for what you’re doing. It has a lot of layout options https://cytoscape.org.

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about 3 years ago

Also if you don’t need to embed it in a webpage you can just use cytoscape.

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about 3 years ago

What about this one? https://cytoscape.org/.

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over 3 years ago

Hi! I’m looking for software that can map biological pathways and from several posts I found on ReasearchGate and Biostars, it seems like Cytoscape and PathVisio are the major players here. So I want to know what is the differences and which might be better for my need. PathVisio claimed that these are very different programs and it also mentioned that “PathVisio sees pathways as drawings, not as graphs. This…

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over 3 years ago