Welcome SymAtlas users


As of today, users who visit http://symatlas.gnf.org will be redirected to BioGPS.

Many of you are probably reading this blog for the first time because of this new feature, and believe me, it’s not a change we take lightly. SymAtlas has a very loyal user base, and one that we value highly.

We’ve foreshadowed this change previously, and we’ve posted annoying red banners on SymAtlas encouraging people to give BioGPS a try. But we think it’s finally that time when 90% of SymAtlas users will have a better user experience over at BioGPS, and this is another gentle (but firm) nudge in that direction.

Why should you transition over to BioGPS? First, we’ve largely kept the same user interface, so the learning curve should be minimal. Second, and more importantly, BioGPS is a more powerful and useful research tool. There are more reference gene expression data sets, more annotation data sources to choose from, more up-to-date information, and a more customizable user interface. Check out the screencasts or past blog posts (linked at the right) for more information.

This step also points to the eventual and inevitable retirement of SymAtlas. We’re making this transition slowly to give all of our users sufficient time to get accustomed to BioGPS. Even with the SymAtlas redirection announced here, users will have a backdoor to access SymAtlas. But even that will eventually go away.

If there are still reasons that you’re continuing to use SymAtlas instead of BioGPS (aside from inertia), then please let us know now! Correlation search is the only distinguishing feature on SymAtlas, and due to user feedback we’ll be adding it to BioGPS shortly. Other than that, we strongly believe BioGPS will be a more productive tool for you in your research.

Welcome to the BioGPS community!


16 Comments

  1. I cannot say that I am happy about this move, although it had been announced a while ago.
    I have been using both symatlas and BioGPS simultaneously. Obviously, BioGPS looks nicer and has much more features. However, there is one key feature in Symatlas which is lacking from BioGPS: the possibility to start from one gene (expression profile) and search for other genes with a similar expression profile.

    Will it be possible to implement something similar for BioGPS, or will the new expression data be made available for download (so that these calculations can be done locally)? Both would be great!

  2. Hi suicyte,

    Thanks for your feedback. You give us a good opportunity to highlight two things. First, as I mentioned in the post (but perhaps under-emphasized), the ability to search by correlation will absolutely be added to BioGPS before SymAtlas is phased out completely. In fact, it’s our goal to implement every SymAtlas feature that people rely on in BioGPS. No promises that we’ll hit 100%, but the correlation search has definitely made the cut. Again, if there are any other features which are keeping you at the SymAtlas site, speak now or forever hold your peace!

    Second, we’ve always had a strong belief in releasing as much raw data as we possibly can, exactly for the reason that you suggest — so that people can do any analysis they want themselves. At wombat.gnf.org, you’ll find many files available for download, and GEO accession numbers under the “Raw Dataset Requests” link. If there’s something that you think is missing, just email us and we’ll do our best to get you what you need.

    Thanks again for your feedback!

    Cheers,
    -andrew

  3. Hi Andrew,

    many thanks for the clarification, this is good news indeed! Also, thanks for offering the data for downloading.
    Maybe it would be useful if you could indicate somewhere which of the downloadable data files correspond to which BioGPD name (e.g. GeneAtlas MOE430 gcrma)

    All the Best,
    -kay

    Cheers,

  4. You point to another important issue on our to-do list — better annotation of the data sets we display. We hope to get to that one soon (though admittedly it’s a lower priority than some of the cool new features we have planned). In the mean time, the answer is just an email (or in this case, a blog comment) away. The “GeneAtlas MOE430 gcrma” data set is referenced here as the “Mouse GeneAtlas V3 data set”, which can be found at GEO under the accession GSE10246.

    Any other feedback is welcome and appreciated…

    Cheers,
    -andrew

  5. Anonymous

    The new website looks good but does not seem to work very well. I want to search by expression (e.g. >3x in heart) and then intersect that search with another e.g. by genome interval. I could do that before, is it still possible? BTW the help videos are not very helpful and crashed my computer.

  6. Hello, thanks for your feedback. You’re right, BioGPS doesn’t currently have a “search by expression” or “search by correlation” function. As noted in my response to suicyte above, implementing search by correlation is high on our list of upcoming features, mostly due to the overwhelming response by our users. So look for that feature to be added in the future.

    You’re also right that we don’t yet have the capability to do set operations on searches. Look for that feature in the future too, and for the moment, you should continue to use SymAtlas for those use cases.

    I’m sorry to hear the videos crashed your computer. If anyone else is having problems viewing them, please let us know. We’ve tested on a variety of operating systems and browsers and have not been able to reproduce the problem.

    Cheers,
    -andrew

  7. Anonymous

    Thanks Andrew. Is the intersection of searches still working on the old website? I tried it there but either had forgotten how to do it, or it has been disabled. The computer I was using to view the tutorial was clapped out, so that probably explains it.

    Sorry for the somewhat intemperate words, I think in general your site provides a great resource.

  8. Hi there again… Hmmm, you’re right, I can’t seem to do the sequential search over at SymAtlas either. Thanks for pointing that out. I can’t promise we’ll be able to restore that functionality at SymAtlas, but if not, it definitely increases the priority of that item (and a better gene list management tool overall) over at BioGPS.

    Please keep the feedback coming…

    Cheers,
    -andrew

  9. Christopher

    Hi,
    I would like to add my 2 cents worth – the addition of tissue expression level searching is something that is absolutely necessary as this is easily done on other platforms. Is this still available on the symatlas? How can I log on to the old platform?
    thanks

  10. I’d like to compliment you on all the nice looking features. I do agree with many other bloggers that the feature of looking for genes which are 3x higher in one tissue and 5x lower in another tissue is key. I used this to define and work out my work in the past which lead to a nature paper. Hopefully this feature will be back online.

  11. Anonymous

    hi, i wish that the ability to look at genes all similarly expressed in different tissues was available. this was the best thing about symatlas…

  12. Christopher, you can still reach SymAtlas at http://symatlas.gnf.org. But I’m not sure we’re talking about the same thing, because I’m not aware of other tools that allow searching by expression. Can you elaborate?

    Yo and anonymous, duly noted.

    Thanks to all of you for your comments and suggestions…

    Cheers,
    -andrew

  13. Anonymous

    Hi,

    I would like to download all gene-expression datasets in biogps, is it possible? Please let me know what is the procedure.

    Thanks a lot!

  14. Hello Anonymous,

    Yes, you can download the expression data found in BioGPS. Please see http://wombat.gnf.org and http://wombat.gnf.org/suppl.html. Let us know if you have any problems.

    Cheers,
    -andrew

  15. I’m trying to finish a manuscript for publication and need access to the “search by expression” feature available on the old Symatlas webpage. Unfortunately, when following the link: http://symatlas.gnf.org
    I am no longer able to access the old Symatlas page, instead I just get the automatic redirect to BioGPS. I thought old Symatlas features were supposed to be available on BioGPS BEFORE Symatlas was shut down completely. Any help you could offer would be greatly appreciated. Thanks.

  16. Joseph, thanks for letting us know about the SymAtlas outage. Unfortunately, the hardware that hosts SymAtlas is getting a bit long in the tooth, but we are experiencing periodic outages. Thankfully, restoring service is an easy fix, so please let us know whenever you notice that the site is not behaving normally.

    And rest assured, BioGPS will have search by correlation before we retire SymAtlas, as promised… And, you can expect an official notice on the blog and mailing list.

    Cheers,
    -andrew

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