Based on our record, Graphviz should be more popular than Cytoscape. It has been mentiond 79 times since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.
Thoughtful post, thanks. However, this tripped me up: "our GPU graph viz server" -- I couldn't understand how you a) scale graphviz[1] on a GPU and b) make money hosting graphviz. Quick read of your web site cleared that up :) [1] https://graphviz.org/. - Source: Hacker News / 3 months ago
Tracing flows: breakdown complex UDP/TCP ECMP traces into individual flows (i.e. Common network path); render a chart of flows in GraphViz DOT format (example). Source: 5 months ago
It has the look of graphviz about it, which is an excellent tool. Often helpful in debugging anything related to graphs. https://graphviz.org/. - Source: Hacker News / 8 months ago
If you are talking about making visualisations for other people it would depend if you want to make them interactive, static, or a mix of the two. I’m not really sure what to recommend given I don’t know - but here are a few places to start: - Python tutor - manim - processing - graphviz - simple but good - draw.io. Source: 11 months ago
It sounds like you're looking for a web-hosted tool - if you're interested in self-hosted text-based tools, graphviz can make flowcharts, and if integration with LaTeX is desirable, so can TikZ. Source: 11 months ago
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 / 4 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. Source: 12 months 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... Source: over 1 year 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. Source: almost 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 / about 2 years ago
PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
draw.io - Online diagramming application
KeyLines - The JavaScript toolkit for graph visualization
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.
UCINET - UCINET for Windows is a software package for the analysis of social network data.