Qiita 0.1.0: alpha release

We are pleased to announce the first alpha release of Qiita (:feet: try it out now 🐾), thanks to our contributors and active users of the system. We’ve come a long way since our pre-alpha release, the following is a quick summary of the major changes that occurred during this development cycle:

Metadata constraints have now been relaxed

When you upload a sample and a prep template, you are required to include only the minimal information needed for processing. This allows users to quickly get from sequence to preliminary results. As always, we recommend that you standardize your metadata to be compliant with the GSC ontologies where possible. Processing of some tasks is disabled if needed information is not supplied by the user, so pay close attention to messages from the system regarding your metadata. For example, raw sequences cannot be demultiplexed if your prep template does not contain a “barcode” column. Please see a full description here.

Improved analysis pipeline

Finding the samples you want to use in a new analysis is now more intuitive. You can browse your studies in a single view, search by sample or study metadata, and add samples to analyses using a familiar “shopping cart”-like interface (see the animated GIF below):

Revamped study management interface

You can now update metadata columns and values or even add new samples to an existing sample template. We’ve also added the ability to delete existing studies and their different components (processed data, preprocessed data, sample template, etc.).

We have improved study privacy settings

You can now change the privacy status of your study's files on a per-processed data basis (a processed data for a 16S analysis is typically an OTU table). A processed data (and the study, by extension) can have one of four possible states: sandboxed, awaiting approval, private, and public. A sandboxed processed data is only visible to the owner and other users with whom the processed data is shared but can be combined with other data available to those users in analyses as usual. Once the user is satisfied with the state of the processed data, he or she can ask for approval from the Qiita admins (QA) to make it private, in which case the processed data changes to the awaiting approval state. To move to a private state, the QA will check that all metadata is MiMARKs compliant and that it processed correctly. In this state the sequence data can be submitted to EBI. The processed data (and hence the study) becomes public when the user explicitly makes the processed data public.

Miscellaneous

• Based on your feedback we have improved the error messages shown on screen so they are more informative.
• Browser compatibility has been improved.
• Quality control, demultiplexing, and OTU picking are now parameterized so you can select from a variety of parameters. Make sure you let us know if you would like to see new parameters.
• Qiita is powered by QIIME v1.9.0.
• The deployment of Qiita maintained by the Knight lab has now officially moved to the University of California, San Diego. Our new DNS is: http://qiita.microbio.me and you should use this URL if you want to reference the central system.
• As always we encourage you to participate in the development of Qiita by:
  • Reporting a bug or feature request in our issue tracker.
  • Submitting a new feature (if you are curious please review our development guidelines).
  • Adding your study to the system, which should not only facilitate its analysis but will allow you to combine it with other public studies or even share it with other users.