connecting tutorials to CMI

qiita_pet/support_files/doc/source/index.rst

@@ -16,6 +16,9 @@ standards as described by this documentation.  Easily interface with the EBI
 repository for automated deposition. Query and interact with Qiita data
 programmatically.
 
+The latests tutorials can be found in:
+`CMI Qiita/GNPS workshop pages <http://cmi-workshop.readthedocs.io/en/latest/>`__.
+
 If you intend to use Qiita at the `central deployment
 <http://qiita.microbio.me>`__ we recommend that you have a look at the
 following documents:

qiita_pet/support_files/doc/source/qiita-philosophy/index.rst

@@ -69,6 +69,77 @@ public, both in Qiita and the permanent repository, Figure 2.
    study listing page.
 
 
+Qiita allows for complex study designs
+--------------------------------------
+
+As seen in Figure 1 studies are the  main source of data for Qiita, and studies
+can contain only one set of samples but can also contain multiple sets, each of
+which can have a different preparations.
+
+The traditional study design includes a single sample and a single preparation
+information file. However as technology improves, study designs become more
+complex where a study with a defined set of collected samples can have subsets
+prepared in different ways so we can answer different questions. For example,
+let's imagine a study looking at how different `microbial communities changes
+during mammalian corpse decomposition
+<https://www.ncbi.nlm.nih.gov/pubmed/26657285>`__; thus, your full study design
+is to collect a set of samples, which you will then process with 16S, 18S and
+ITS primers. This will result in 1 sample and 3 preparation information files,
+`see it in Qiita <https://qiita.ucsd.edu/study/description/10141>`__.
+
+Now, let's imagine other more complex example:
+
+1. All of the samples were prepped for 16S and sequenced in two separate
+   MiSeq runs
+
+2. 50 of the samples were prepped for 18S and ITS, and sequenced in a single
+   MiSeq run
+
+3. 50 of the samples were prepped for WGS and sequenced on a single
+   HiSeq run
+
+4. 30 of the samples have metabolomic profiles
+
+To represent this project in Qiita, you will need to create a single
+study with a single sample information file that contains all 100 of the
+samples. Separately, you will need to create four prep information files that
+describe the preparations for the corresponding samples. All raw data
+uploaded will need to correspond to a specific preparation (prep) information
+file. For instance, the data sets described above would require the following
+data and prep information:
+
+1. All of the samples prepped for 16S and sequenced in two separate
+   MiSeq runs
+
+   a) 1 prep information file describing the two MiSeq runs (use a
+      run\_prefix column to differentiate between the two MiSeq runs, more
+      on metadata below) where the 100 samples are represented
+   b) the 4-6 fastq raw data files without demultiplexing (i.e., the
+      forward, reverse (optional), and barcodes for each run)
+
+2. 50 of the samples prepped for 18S and ITS, and sequenced in a single
+   MiSeq run
+
+   a) prep information files, one describing the 18S and the other describing the
+      ITS preparations
+   b) the 2-3 fastq raw data files (forward, reverse (optional), and
+      barcodes)
+
+3. 50 of the samples prepped for WGS and sequenced on a single HiSeq run
+
+   a) 1 prep information files describing how the samples were multiplexed
+   b) the 2-3 fastq raw data files (forward, reverse (optional), and
+      barcodes).
+   c) NOTE: We currently do not have a processing pipeline for WGS but
+      should soon.
+
+4. 30 of the samples with metabolomic profiles
+
+   a) 1 prep information file. the raw data file(s) from the metabolomic
+      characterization.
+   b) NOTE: We currently do not have a processing pipeline for metabolomics but
+      should soon.
+
 Portals
 -------