The BioFabric Demo

[Todd Detwiler]

Please help me understand the relationship between the web demo and the BioFabric available for download. Is the web demo a re-implementation in Javascript (with D3)? I am interested in the Javascript API, if there is one, but don't see it in the downloads or in GitHub. Is it available anywhere?

[Bill Longabaugh]

Todd:

Thanks for you interest in BioFabric.

At the moment, the web version is really just a demo. The JavaScript source code is all contained directly in the one file, so you should be able to rip out all the animation bits and have it just display the final product with a little bit of refactoring of the code. But note that as-is it is likely to have problems with features like duplicate links or singleton nodes, and if I recall there are some really inefficient implementations which worked OK just because the demo network was small.

If that's something that you would be happy to tackle, I'd love to have a production-quality BioFabric D3 version available on GitHub. If not, I'll try to make it a priority to get something like that done (it has been on my to-do list for some time now), but it will take awhile.

Thanks,

Bill

[Bill Longabaugh]

To better describe the relationship between the demo and the download, I should also note that the JavaScript demo is just the network renderer, while the Java-based program for download has all the bells and whistles of search, navigation, alternate layouts, selection with sub-network generation, multi-threaded rendering using image tiles for huge networks, and the like. Those features are necessary for handling the very large networks that arise in a biological context.

Bill

[Todd Detwiler]

Thanks Bill. I've forwarded your response to my principle investigator. It is possible that he will want me to try and hack together a visualization from the code in the demo. If I do so, I'll let you know. It is unlikely, however, that I can help with the production quality release. I have only a few weeks left on this particular visualization project.

Thanks again,
Todd

On Thursday, September 11, 2014 11:01:50 AM UTC-7, Bill Longabaugh wrote:

[William Longabaugh]

Nothing like having a potential user to kick me into action! I have
hacked away at the Super-Quick demo to create a simple, standalone,
bare-bones version of the BioFabric D3 renderer. It's been posted at:

https://github.com/wjrl/D3BioFabric

Big networks? Forget it! Multiple component networks? Forget that too!
But it is good for simple demos. Just convert your network to the format
used in the data/miserablesSimple.json example file, and you're on your way.

Hope somebody finds this useful. I'll be happy to consider any pull
requests if anybody wants to make it more robust.

Bill

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