BioGPS extensibility

So far, we’ve introduced the simple BioGPS plugin interface, and shown how this interface was used to construct an extensive plugin library.

Browsing the BioGPS plugin library, you’ll undoubtedly note that the vast majority of plugins we’ve hooked up go to established third-party standalone websites — sites like STRING, MGI, WikiPathways, and OMIM. Importantly, we didn’t need to ask any of those site administrators to implement any new protocol to be included as BioGPS plugins — the web interface they’ve already implemented is exactly the same interface that BioGPS uses.

The data content providers and website developers out there will quickly see the advantages of this simple setup. Do what you’d do anyway to display your data to the world, and hooking it up to BioGPS will likely take five minutes or less. Take advantage of the existing BioGPS user base to draw more eyeballs to your data and your site.

Technically speaking, BioGPS “plugins” are not plugins in the typical computer science sense. We don’t host any of your code, and we don’t interact directly with any of your content. BioGPS plugins are rendered in IFRAMEs, which are simply browsers within your browser.

To summarize, gene report layouts allow for customizability, and the simple HTML interface allows for easy extensibility.


  1. Anonymous

    Hi Andrew,
    Can you open ‘general discussion forum’ on BioGPS blog? Would be easier to discuss general problems/issues.

  2. Anonymous

    Hi Andrew
    Below, you find a copy of my comment to one of your previous post (to easier found your answer):
    I like the Exon array Gene Atlas plugin but a utility of it is limited due to lack of links to probes/probesets description. You wrote “Data from our exon array Gene Atlas”, therefore is it possible to get information about the probes used in the arrays? Additionally, can you add a new plugin links to a web-page of EBI ( on Alternative Splicing Database Project? Linking the data from two resources would be advantages.
    I like the expression feature from SymAtlas too, especially possibility of combining results (union with previous/ intersect with previous). Please do not retire SymAtlas yet. Now your both pages seems to be complementary. All the best,

  3. Hi Chris, thanks for your comments.

    Regarding the exon atlas, it’s been high on our list (and with ever comment like yours growing higher) to provide better annotation for all of our expression data sets and plugins. Briefly, these data are from the Affy Exon array chip (4 probes per exon) across many diverse tissues. More to come…

    Regarding the EBI ASD site, I can definitely add it as a BioGPS plugin. The unannounced news (as of last week) is that so can any registered user! If you can figure out the URL syntax to deep-link to the page on their site, then BioGPS allows any user to add and share plugins. You must have a BioGPS account and log in, and then go to the “Plugin library” to “Add a new plugin”. (I’m currently on vacation, but if I don’t see the ASD plugin pop up next week, I’ll look into adding it…)

    Finally, regarding the general discussion forum, I can’t see where in the settings to configure this. More info? Also, another unannounced addition is the BioGPS Google Groups. To be officially unveiled soon, but you’re welcome to use it now!

    Thanks again for your comments…

  4. Anonymous

    Hi Andrew, thank you for quick replay.

    Regarding adding new plugin by end-user, usually “Server Error (500)” message appear.

    Have a nice holidays

  5. Hi, Chris, this issue should be fixed now. Please try again.

  6. Anonymous

    Hi, Can you tell me how to remove unnecessary layouts from ‘my layouts’, please.

  7. Hi Chris, unfortunately, our “layout manager” is not yet live, so for the moment there is no good way for you to delete your layouts. Look for that feature to arrive soon. In the mean time, feel free to email us the names of the layouts you’d like to delete (or keep) and we’ll help you out with that. Thanks for using BioGPS!

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