What is Reddit's opinion of Cytoscape?

From 3.5 billion Reddit comments

Have you looked at http://www.cytoscape.org I think you can garner more interest if you target an area which needs attention, or you can contribute to one of the many existing open-source bioinformatics tools!

I use Cytoscape for work, and I'm considering keeping a network going for my campaign for kicks. I'm not sure what kind of relationship mapping you want to display, so that tool may be a bit much.

Coworker is a big fan of Neo4j, though I don't have much experience with it. It's mostly for databases, though I'm sure you could hook it up with a spreadsheet. Does require scripting, however.

A program with a GUI that may help is Cytoscape. This program is used in the bioinformatics community, where the very complex interaction networks in biology are explored. You can use it for networks or graphs more generally though and create very nice visualizations and perform certain analysis of a given topology to find central nodes, clusters etc. Advanced simulations on the network don't fit that easily though, then the already recommended Python library is more flexible.

Hi!

If I understand your question correctly, this is indeed a graph you are describing. If you can reduce your problem to a dataset with the interacting metabolites it should be very easy to handle.

There are tools that can deal with biological data like this, the most commonly used is Cytoscape. It's pretty simple to use, here's the manual.

I'm doing my PhD on network/systems biology, let me know if you have any questions about it, this is my main tool in the day to day work

Real-Time is more theoretical than an actual thing that happens, I find for most software out there that caters to the "real-time" aspirers.

For me this concept of "real-time" is more of a best-effort thing than a hard requirement of when data should be displayed/updated. I don't really have a problem if it's only able to update every minute or 2 minutes when at peak loads, but in general I would like for a solution that attempts to achieve "real-time".

To elaborate further on my requirements, I can refer you to an open-source project that pretty much displays the information in the way I would want this solution to: http://www.cytoscape.org/

A little late to the party, but if you're still interested, you can parse your igraph object (g) into Cytoscape (a fantastic, free, Java-based network visualisation GUI) using the CytoscapeRPC plug-in. You can then manipulate the object in there quite easily using the in-built Vizmapper. Can provide examples if needed.

Data source: Web of Science Tools: For network analysis: Network Workbench For network visualization: Cytoscape Update: changed the layout (names are now easier to read) and added a .png

In addition to Gephi, which is excellent, you may want to check out Cytoscape. To me, Cytoscape feels a bit more heavy weight for many uses, but its extension ecosystem is a bit more robust than Gephi's. It also provides interesting mechanisms for interactive exploration of very large graphs - including the pretty awesome AllegroLayout plugin that makes visualizations of large graphs absolutely fly on a machine with a good GPU (check out the videos of the layout engine in action).

When I see "visualizations with annotation data" and etc, I think networks. Cytoscape is one example and here is the link (since you didn't post anything in specific you're doing) and check out the plug ins/apps. http://www.cytoscape.org/

Cytoscape is used for visualization of networks, it's free, open source. R's iGraph package with other bioconductor libraries can also parse these types of data.