Archive for April, 2016

MG-RAST newsletter, May 2016

Tuesday, April 12th, 2016

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  1. MG-RAST hits 100 Terabasepairs
  2. Funding update
  3. Policy change: We will enforce data publication
  4. Beta version of next generation user interface

1. MG-RAST hits 100 Terabasepairs and 20,000 data submitters
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MG-RAST has finished processing 100 Tbp threshold (terabasepairs or 100 x 10^12) earlier in April 2016. A total of over 240,000 data sets containing over 800 billion (800 * 10^9) sequences have been processed.

The MG-RAST systems continues to be popular with scientists, MG-RAST now has over 20,000 data submitters, in 2015 the web site and API had over 45,000 individual data consumers.

2. Funding update
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MG-RAST has been fortunate to receive two awards recently, allowing us to continue operating. To our delight one of the awards will strengthen our collaboration with our friends from the EBI’s MG-Portal team. Resources remain tight but we are working hard to provide updates and good service to our users.

3. Policy change: We will enforce data publication
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You will be no doubt aware that priority for processing in MG-RAST depends on your stated intention to release the data to the public. Many of you  have chosen to publish their data, subsequently received priority processing and have not released their data. On top of that we are receiving several help desk tickets per month for data that has been published in journals and not actually public on MG-RAST.

Therefore the new user interface will include reminders if data is overdue for publication.

In addition we will have the technical means to disable future submission for individual users if data release commitments have not been met.

4. Beta version of next generation user interface
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MG-RAST’s popularity has led to some major load issues with our backend server infrastructure. Fortunately with the recent developments of web technologies and the progress in computing in general, we have the option of restructuring the user interaction. While retaining the graphical UI and adding a lot of functions, we are off-loading a lot of the load from the server to your desktop machines. This is done in a way that empowers the users and does not overwhelm current desktop machines. With the new MG-RAST client, you can download data sets from MG-RAST and prepare analyses using a graphical interface.

 

The beta version is available for testing at:

http://v4-web.metagenomics.anl.gov

The new interface:

  • has significantly better optics and is faster
  • works with any modern browser (goodbye Firefox only requirement)
  • provides submission receipts with details on all user provided parameters
  • has a project editor that allows among other things moving non public metagenomes between projects
  • contains a processing receipt with details on the processing
  • significantly updated metadata dialogues

Upcoming features:

  • google spreadsheet editor for metadata
  • offline analyses of metagenomes including slice & dice
  • project page editor

Our plan is to collect feedback on the new user interface and update the production version after June 1st 2016.