Qiita 0.0.1: pre-alpha release

The qiita-dev-team is delighted to let you know that qiita.colorado.edu is up for public initial testing. The goal of this pre-alpha release is to get feedback from users, and attract new developers.

In the current system, you will be able to create new accounts and manage them. Additionally, you will be able to create studies, add sample and prep templates, and upload raw sequences. Note that the templates must follow the MIMARKS standard, and that we currently only support raw (without pre-demultiplexing) FASTQ sequences as initial input.

Qiita relies on the concept of studies, where each study has one sample template (metadata about the samples), and multiple raw data files (e.g. different sequencing runs) where each run has a different preparation (prep) templates (run information). This structure allows us to support diverse sequencing strategies, like having different preparations (e.g. ITS and 16S on the same samples) in a single sequencing run.

Once a sample and prep template are uploaded and added to the database, you can visualize summaries of each one of them, redownload them, and get a valid QIIME mapping file for further analysis. Additionally, you can download the post-demultiplexing raw sequence files generated by the system. For those studies, where we have preprocessed these sequences using the new tools that will be available in QIIME 1.9.0, more below, you will be able to also download the processed data, also know as the close reference biom table.

A test subset of the Earth Microbiome Project studies (around 100) have been processed using the new pipelines that will be available in QIIME 1.9.0, release due on December 3rd, 2014. Meta-analyses (beta, alpha, and taxonomy analysis of single or combined studies) can be tested on the live system. Note that the demultiplexed sequences for these studies are not available yet, but should be available within the next couple of weeks. Also, the system still does not support automatic creation of processed data (e.g. otu picking), although again this will be done soon.

This new system is capable of automatically submitting pre-processed sequences, for example those produced after quality control and demultiplexing, to the European Bioinformatics Institute. During this pre-alpha phase, we only submit sequences processed within the system and by requesting an admin to do it. The submission is per prep template.

Another new feature in the system is that you can share your study with other registered users. This new feature allows collaboration and addresses cases where the raw files exist at a different site.

As noted in the text qiita.colorado.edu will reflect the current status of our master development branch, meaning that as improvements come along they will be proactively deployed. To ensure no data is lost throughout this development phase we have setup an internal replication system of the database.

If you want to try out Qiita in your own system see our installation notes.

Finally, remember that this is a pre-release, so please be patient and if you have some spare time, we need help both on finding issues and on fixing existing ones. If you find new issues with the live system, have suggestions or possible improvements, add them to the issue tracker. In the next week we will be adding more documentation so local installs and testing is easier.