The retirement of SymAtlas

Although SymAtlas has served us well over the years, it’s finally time for its graceful retirement. We’ve been keeping it running on life support for quite some time now (with varying degrees of success).

We’ve tried to make the transition from SymAtlas to BioGPS a gradual one. In BioGPS’s early stages, we had them running in parallel, and we purposely modeled the BioGPS gene report after the SymAtlas design. In August 2008, we posted a prominent link from SymAtlas to BioGPS, noting our plans for the future. In March 2009, we then actively started redirecting traffic from the SymAtlas home page to BioGPS, while leaving users a “backdoor” to access the old site. A couple months ago, we started redirecting “deep links” to specific SymAtlas pages to the corresponding BioGPS pages (again, leaving a “backdoor” for resistant users). At that time, we also forced users from the SymAtlas front page to go to BioGPS (a move that in retrospect I wish we’d delayed).

Starting shortly after the Thanksgiving holiday, this transition will be complete. We will force all traffic from SymAtlas to BioGPS with no exceptions. If you had a bookmarked link or were following a link to specific SymAtlas page, we’ll try to get you to the right page in BioGPS. If you’ve been resistant to migrate to BioGPS, you should know that acceptance by the majority of our the community has been phenomenal. Moreover, over 80% of users who were given the choice between continuing to BioGPS and going back to SymAtlas chose the “right option”.

If there are still loyal SymAtlas hold outs, please let us know why you haven’t migrated over to BioGPS. We’ll do our best to satisfy your needs. But overall, we strongly believe that BioGPS offers a brighter future with more and better features.


12 Comments

  1. howard petrie

    Well for our specific purposes, we found both SymAtlas and BioGPS to be extremely useful BUT…one advantage of SA (for us) was that 'thymus' was represented as a tissue, while now you have only purified lymphoid components of the thymus (meaning that the stromal elements that constitute the stable thymic organ are absent). Thus, many genes expressed in thymus are no longer found. Fortunately, we have downloaded the data from SA, but it's certainly not as convenient as a browser interface, and it's sad that this data will no longer be readily accessible.

  2. Hi!

    An extremely useful feature in SymAtlas was to search for tissue specific genes, i.e. set thresholds for up/downregulation and the get lists of genes fulfilling the threshold criteria.

    I don't see this functionality anywhere – can you consider putting it in?

    Overall the interface have been much improved, what I think is missing (granted, from a brief look) are methods to access the data that makes sense for bioinformaticians – e.g. the feature mentioned above, the ability to upload lists of genes, regions etc.

    Regards,
    Erik

  3. Howard, I think the data set you're referring to is still available within BioGPS. I think the issue is that the default data set shown has changed. The current mouse default is called "GeneAtlas MOE430, gcrma" and has the purified cell populations you mention. If you change the data set to "GeneAtlas GNF1M, gcrma", you will see the older data set that was the default for SymAtlas. Does that help? (If anything is not clear, please follow up at our BioGPS google group so I can include image attachments in the reply.)

    Cheers,
    -andrew

  4. Erik, you are correct, the "search by expression" feature on SymAtlas has not been ported to BioGPS. There is a more detailed explanation in this recent question on the BioGPS google group, but the short answer is that you now need to use the correlation search function. Which means you need to start with a "seed gene" whose pattern you're interested in. We're hoping that this feature will satisfy most users' needs, but we're certainly open to feedback from users if it doesn't.

    On your second issue, we have most of our data available for download on our downloads page. If you have specific use cases for web services that we should expose for bioinformaticians, please let us know and we can work together on it.

    Cheers,
    -andrew

  5. howard petrie

    Hi Andrew: I still don't see "thymus" as a tissue. I see only thymocytes (purified) of various types.

  6. Howard, after changing the species selector to "mouse", you should be able to change the data set to "GeneAtlas GNF1M, gcrma" to see the thymus sample.

    "GeneAtlas GNF1M, gcrma" is the older data set that was the default on SymAtlas. "GeneAtlas MOE430, gcrma" is the newer mouse data set that is the default on BioGPS.

  7. Is there a way to download the mapping of the Affymetrix Custom Arrays (Novartis) for Mouse and Human?
    This used to be available on http://wombat.gnf.org/index.html, but this link does not work anymore…
    Thanks for your help
    Julien

  8. Hi Julien,

    The new link is http://biogps.gnf.org/downloads/. Sorry about the change — I'll see if we can put in an automatic redirection.

    Cheers,
    -andrew

  9. Hi,

    I looking for mas5 version of the dataset. Do you know where are they?

    Thanks

    yuhong

  10. Hi Yuhong,

    We no longer post the MAS5 versions of our data. If those are important for your work, then you can generate these results yourself. On our Downloads page under the Chip Annotation section, we post links to the GEO page where you can download the relevant library files. Let us know if you have any problems…

    Cheers,
    -andrew

  11. Anonymous

    Hi,

    I can't seem to find out what strain of mouse tissues you used for generating the GNF1M or MOE430 data. Please advice. Thanks!

  12. Hello Anonymous,

    Apologies for the late reply. The mouse tissues were all generated from C57BL6/J mice, as described in this paper.

    Cheers,
    -andrew

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