Graphviz VS Cytoscape

Graphviz Reviews

Cytoscape Reviews

Graphviz mentions (79)

• Should I Open Source my Company?

  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

• Trippy 0.9.0 Release

  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

• Calculate the difference and intersection of any two regexes

  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

• What are some tools to help in visualizing concepts

  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

• Good graphic FlowChart drawing tool ?

  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

Cytoscape mentions (11)

• A Canadian payroll dependency chart

  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

• Budō Lineage Tree: a community-driven database and interactive explorer

  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: 11 months ago

• Any advice on a community detection algorithm?

  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

• Lost interactive graph (as in nodes + edges) editing tool

  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

• Gephi – The Open Graph Viz Platform

  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