MG-RAST API Release of Version 1

September 17th, 2013 by folker

Hi everyone, we’ve updated our API to point to Version 1. If you need to access the previous version of our API, you can do so by going to:

http://api.metagenomics.anl.gov/beta/

It’s always a good idea to reference a version of the API in your code and in your publications, so you know where your data came from. Version 1 can now be reached at either the base API URL or by explicitly including the version number:

http://api.metagenomics.anl.gov/
http://api.metagenomics.anl.gov/1/

To help guide you when using the API, links to documentation are provided on http://api.metagenomics.anl.gov/api.html

Thanks,
The MG-RAST Team

MG-RAST 3.3 release notes [December 12, 2012]

December 13th, 2012 by mark

New database:
The database underlying the MG-RAST analyses has been completely revamped and now uses a completely new schema running on new hardware.
The analyses results for all existing metagenomes in MG-RAST were ported to the new database and all code was modified to use the new schema.

Upload/Submission:
Changed to remove confusing text and simplify the interface.  Also, removed processing from Upload page and pushed it off to the compute cluster so that the Upload page should hang less and user’s will be informed more quickly what is happening.

Overview page:
We added a ‘delete’ button on the overview page which will delete a metagenome from MG-RAST completely. This button will be displayed to some users only, usually the owner of a metagenome. In addition, datasets which have been made public can not be deleted. Please be careful when using this function, once a dataset has been deleted it can not be recovered.

Miscellaneous:
Misc. changes and bug fixes

Upcoming change to MG-RAST upload (early August 2015)

July 28th, 2015 by folker

In the week of August 3rd, we will change the upload mechanism for MG-RAST to a new, improved platform.

This will improve the end-user experience by providing:

  •  automatic MD5 checking on client and server side (for most files) to ensure that files are received correctly by MG-RAST
  •  faster upload and the ability to resume stopped uploads
  •  pre-upload file checking for content and naming scheme compliance
  •  de-multiplexing for Illumina barcoded data
  •  pre-upload metadata validation
  •  auto-decompression

In addition to the web browser based upload we will also provide a python based upload script that end users can either use as is or adapt to their needs.

We will be discontinuing the use of the existing, slow and disk-space limited upload system and retiring that system. As a result we ask that users submit all the data in their Inbox ASAP and not wait with submission. Immediately before the switch over we will put a warning up on the MG-RAST homepage to inform users.

For any data remaining in old upload system, we will migrate that to the new system IF the files are less than 72 hours at the time of transition.

July 28th, 2015

 

MG-RAST API available

January 15th, 2015 by folker

A long time in the making the application programmers interface (API) for MG-RAST has now left beta status.

By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects.

Our paper describing the API in PLoS Computational Biology is here.

The API entry point is: http://api.metagenomics.anl.gov/api.html

Before you embark on a journey exploring the new capabilities, we’d like to mention:

  • we are fully committed to this API, it is what powers the web interface and will be the basis of any future development.
  • we note that programming skills are required to utilize the API, while we’d like to we cannot write the code to implement your analysis or query. We will however provide examples via github.
  • the API is versioned
  • we expect users to adhere to our terms of service.

Finally we’d like to thank the dozens of beta testers for their patience and helpful comments.

MG-RAST newsletter, September 2014

September 17th, 2014 by mark

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Request for letter of support/testimonials
************************************************
The MG-RAST team is applying for funding to support continued development on MG-RAST and to improve several aspects of the system. In particular, we need to update and improve the underlying data integration which has not changed significantly in the last five years. The funding will also be used to develop and upgrade the user interface.

We are requesting you as a member of our user community to help us by providing a letter of support that addresses the potential for the project, along with a testimonial as to the value MG-RAST has brought to your research. Your opinion is very important to us, we would like to include testimonials from the entire spectrum of MG-RAST users.

Your letter of support should be addressed to Dr. Folker Meyer at folker at anl.gov and include your name, position and organization, it will need to be received before September 30, 2014 for inclusion in our proposal.

Click here to start

Thank you for your help,
Folker Meyer and the MG-RAST team

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Recent highlights
************************************************

– More server stability (new backend technology)

You may or may not have noticed several hardware related outages recently. Several of our servers are getting rather old and instead of replacing in kind (which is hard at our budget levels) we chose to move to newer more flexible technologies. Over the past 12 months, we have re-written the entire MG-RAST storage subsystem to rely on an object management system [SHOCK (https://github.com/MG-RAST/Shock)] rather than a traditional file system.

Used together with the AWE resource management software, SHOCK allows the execution of the MG-RAST (and other) pipelines on a wide array of computational platforms. We have already provided cloud (aka Amazon EC2) machine images to a number of groups interested in providing their own computational resources for their data while analyzing the data with MG-RAST.

– More security

MG-RAST now supports encryption for your passwords. We note that the MG-RAST system does not offer secure connections (due to the increased hardware cost that would create).

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Analysis Pipeline slowdown
************************************************

You may have noticed that jobs submitted since June are taking longer to be processed. There are many contributing reasons — multiple hardware problems, move to the new Magellan cluster configuration, and preparing for the move to the SHOCK/AWE pipeline. In addition, there were some kinks in the new pipeline which are being worked out. The net result has been a large backlog in the compute queue and an increase in analysis time. Most of these issues have been resolved and we are working on resolving the last technical hurdles as quickly as we can.

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Metadata issue
************************************************

MG-RAST uses a controlled vocabulary for the metadata entries biome, feature, and material. This ontology, which was created and is controlled by EnvO (Environment Ontology), is available on the BioPortal site. Some terms from the latest EnvO version do not validate correctly on the MG-RAST website, resulting in an error message. We are revising our internal metadata validation process and until this is completed, you will need to select from compatible metadata terms from the list at:
http://api.metagenomics.anl.gov/1/metadata/cv?label=biome (or label=feature or label=material)
The list is returned as a JSON structure, use a viewer, e.g. FireFox + JSONView, to format it in a human-readable manner.

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Publishing MG-RAST IDs
************************************************

If you cite a MG-RAST ID in a publication you are responsible for making the data public on the MG-RAST site — all data in MG-RAST is private by default and has to be made public by explicit action of the owner. The declaration made during the submission process of the intention to make data public is only used to assign priority for the compute queue, your data will not be made public automatically based on the date entered.

The MG-RAST manual (ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf and linked from the front page) has more information in Section 4.11.

If you provide links to public datasets in a publication, use the linkin.cgi mechanism, not the URL displayed by the browser.
For example for the public dataset with MG-RAST ID 4440283.3 the linkin URL is:
http://metagenomics.anl.gov/linkin.cgi?metagenome=4440283.3
and for the public project with project ID 128 the linkin URL is:
http://metagenomics.anl.gov/linkin.cgi?project=128
These URLs provide a stable method to link to public datasets in MG-RAST.

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Citing MG-RAST
************************************************

If you use our service for analysis or to make your data public, please cite:
The Metagenomics RAST server — A public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer, D. Paarmann, M. D’Souza, R. Olson , E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, and R. A. Edwards
BMC Bioinformatics 2008, 9:386
http://www.biomedcentral.com/1471-2105/9/386

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UI Changes/Bug fixes
************************************************

FireFox v30 problems: upload broken, minor visual glitches
metadata file validation error for metadata files with integer metagenome names
collections removed from cacheing
fix missing list for jobs in progress
visual updates to job progress

Regards,
Folker Meyer
and the MG-RAST team

MG-RAST data migration, September 2, 2014

September 2nd, 2014 by mark

MG-RAST is moving from using a traditional file system to store data to an object management system SHOCK (https://github.com/MG-RAST/Shock). The data involved includes but is not limited to sequence files, intermediate analyses pipeline outputs and annotation products.

The change will take place in the backend and the website should not be impacted, all webpages and analyses should work normally. However, if you do notice a problem with the website please let us know as soon as possible with all relevant details.

This change will have an impact on the MG-RAST ftp site. While most public datasets will remain available in the short term, projects which have been made public recently will not be accessible at all. We are working on a permanent long-term solution to this problem and should have it in place shortly.

We thank you for your patience and understanding.

— the MG-RAST team

MG-RAST Newsletter, June 2014

June 18th, 2014 by mark

MG-RAST Newsletter, June 2014

Recent highlight
MG-RAST has crossed the 400 billion sequences annotated threshold, that is
400×10^9 sequences. The estimated BLAST cost for this would have exceeded
100 million US dollars on Amazon’s EC2 cloud*.

* Following the calculations in Angiuoli et al, BMC Bioinformatics 2011
(DOI 10.1186/1471-2105-12-356) and Wilkening et al, IEEE Cluster 2009
(DOI: 10.1109/CLUSTR.2009.5289187).


User manual [NEW FEATURE]
We are transitioning our user help documentation from the blog system currently used
to a user manual in PDF format, mirrored by a “traditional” web site.
The PDF is ready today at:
ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf
We will keep updating and revising the user manual without changing this URL.
Dangers of account sharing [WARNING]
We are experiencing issues caused by multiple individuals sharing a single account.
Please note we cannot tell who the legitimate owner of an account is in cases like
this. If you share your password with another person, they can change it, thus taking
away access to your account and your data. The built-in sharing feature is a better way
to share data with someone. The metagenome overview and project pages have
‘share’ buttons, just type in a valid email address for the person you want to share with
(it does not matter if they have an MG-RAST account or not) to grant access to your
data. The user manual (linked above) has more details in section 4.11.
API [NEW FEATURE]
As part of the next version of MG-RAST we have created a REST application programmers’
interface. The API provides access to all public and private data in MG-RAST in many
programming languages, the access to private data requires authentication.
Check out details at: http://api.metagenomics.anl.gov/api.html

New version of MG-RAST [UPDATE]

As some of you may have heard, we are working hard on a new version of MG-RAST to
be released later this year. It will include a number of new features, including better
support for metatranscriptomics, a browser independent user interface, and updated
annotations — we will update old jobs AND archive existing results. With this new version
we will also start automatic rolling updates of annotations for all jobs.
UI Changes/Bug fixes [UPDATE]
– fixed database issues caused by sequence file names containing unacceptable characters by modifying the file name filtering step,
– removed size restrictions for the clustering stage, allowing more efficient handling of extremely large datasets,
– several minor bug fixes improving the stability of the existing pipeline
– resolved several minor issues to improve usability of the UI

Regards,
Folker Meyer
and the MG-RAST team

MG-RAST 3.3.6 release notes (API changes and new Search implementation) [July 2013]

July 31st, 2013 by folker

User documentation and tech report available

We have made a PDF with a manual and tech report available describing MG-RAST in detail.

New search function

As many users have no doubt noticed the search function prior to version 3.3.6 was overwhelmed by the amount of data in the system. We have implemented a new search function that replaces the old capabilities but is significantly faster than prior to 3.3.6.

Creation of collections from search results

To create a collection from search results first select the metagenomes with the checkboxes and then click the “create collection” button. The collections created are displayed in the metagenome selection widget on the analysis page where they can be used for comparison, either as individual metagenomes or as a group.

Anonymous reviewer access

To grant reviewers access to a project while preserving their anonymity we added a ‘Create Reviewer Access Token’ button on the project page which is visible when you click on the ‘Share Project’ link. This generates a token that can be sent to the publisher to pass on to reviewers who can use the included link to get anonymous access to the project. The number of reviewers who have accessed the project will be displayed to the owner in the list of users the project is shared with, but the identity of the reviewers is not disclosed. The owner of the project can revoke the token at any time to disable access.

Some changes to the programmers interface (API) [still beta]

We have made some changes to the programmers interface that will affect existing deployed clients and third party tools. We will notify all known API users separately.

Misc. changes and bug fixes

Many miscellaneous changes and bug fixes have been implemented, see the github pages for details. See here: https://github.com/MG-RAST/MG-RAST/pull/391

MG-RAST v3 tech-report and manual available

June 19th, 2013 by folker

The tech-report and manual for MG-RAST version 3.3 is available for download.

MG-RAST 3.2.5 release notes [November 2, 2012]

November 14th, 2012 by mark

Analysis page:
High resolution images are now being displayed scaled to 800×800 pixels, the raw image size has not been changed
LCA — tree dsplay modified for display when multiple datasets selected.

Upload/Submission:
Metadata template updated
MetaZen made available. MetaZen is web-based tool for entering metadata into a spreadsheet and is an alternative to downloading and filling in the metadata template. It requires you to enter the metadata through a webpage and returns the data formatted in a metadata spreadsheet which can be edited further if necessary and then uploaded to MG-RAST.

Download:
The download page was modified to make it simpler to use and the download mechanism was changed to make downloads of large files more efficient.

Miscellaneous
Misc. changes and bug fixes