Merge pull request #144 from tripal/revise_experimental_design_form

Revise experimental design form

README.md

@@ -13,10 +13,10 @@ New documentation for the new data loaders and module structure is under develop
 3. [Module Features](#features)
 4. [Loading Biosamples](#loading-biosamples)
 5. [Loading Expression Data](#loading-expression-data)
-6. [Protocols](#protocols)
-7. [Viewing Data](#viewing-and-downloading-data)
-9. [Administrative Pages](#administrative-pages)
-10. [Example Files](#example-files)
+6. [Viewing Data](#viewing-and-downloading-data)
+7. [Administrative Pages](#administrative-pages)
+8. [Protocols](#protocols)
+9. [Example Files](#example-files)
 
 # Introduction 
 Tripal Analysis: Expression is a [Drupal](https://www.drupal.org/) module built to extend the functionality of the [Tripal](http://tripal.info/) toolset.
@@ -180,42 +180,14 @@ The biosample name will be taken as the name of the file minus the file extensio
 * **Regex for End of Data** - If the expression file has a footer, use this field to capture teh line that occurs after the end of expression data. This line of text and all text following will be ignored.
 
 #### Experimental Design Fields
-The "Experimental Design" fields allow a complete description of the experimental design by implementing the [Chado MAGE design schema](http://gmod.org/wiki/Chado_Mage_Module).  The Chado MAGE module uses the arraydesign, assay, quantification, and acquisition tables to describe an experiment. This is reflected in the following fields available to describe an experiment.
+The "Experimental Design" fields allow a complete description of the experimental design by implementing the [Chado MAGE design schema](http://gmod.org/wiki/Chado_Mage_Module).  The Chado MAGE module uses the arraydesign, assay, quantification, and acquisition tables to describe an experiment. The Tripal Analysis Expression creates generic instances of all these for you.
 
-* **Biomaterial Provider** - The person or organization responsible for collecting the biosample.
 * **Array Design** - This is only applicable for microarray expression data. This may be left blank for experiments that do not utilize an array (ie next generation sequencing). 
-
-#### Acquisition Details
-This represents the quantification technique. In the case of a microarray, it is scanning, in the case of a sequencer, it is sequencing. The output of this process is a digitial image of an array for a microarray or a set of digital images or nucleotide base calls for a sequencer.
-
- * **Acquisition URI** - A web address to a page that describes the acquisition process.
- * **Date Acquisition Run** - The date the acquisition was run. 
- * **Acquisition Protocol** - The acquisition protocol used in the experiment. (See protocol description below).
-
-#### Quantification Details
-
 * **Units** - The units associated with the loaded values, such as FPKM.  You may also update the units of your experiments using the **Quantification Units** admin page.
- * **Date Quantification Run** - The date the quantification was run. 
- * **Quantification URI** - A web address to a page that describes the quantification process.
- * **Quantification Operator** - The person or organization that ran the quantification.
- * **Quantification Protocol** - The quantification protocol used in the experiment. (See protocol description below).
-
-![Experimental Design Fields](https://cloud.githubusercontent.com/assets/14822959/12991557/a4b0228e-d0dd-11e5-93de-2f206be6d5fe.png)
-![Data Loader Fields](https://cloud.githubusercontent.com/assets/14822959/12991553/a4ade58c-d0dd-11e5-97d2-1096d78bb189.png)
-
-
-# Protocols
-
-Acquisition, Quantification, Array Design, and Assays all utilize protocols to describe them.  Think of protocols as the **experimental design**, and Acquisitions, Quantifications, Array Designs, and Assays as the experiment following that experimental design.
 
-**Protocol Descripton** - The protocol content types can be created by navigating to **Add Tripal Content->Protocol**. A protocol can be used to add extra detail to an experimental design. A protocol can be used to describe the assay, acquisition, and quantification steps of the experiment design. A protocol can also be used to further describe the array design content type. The fields of a protocol are:
-* **Protocol Name (must be unique - required)**
-* **Protocol Link (Required)** - A web address to a page that describes the protocol.
-* **Protocol Description** - A description of the protocol.
-* **Hardware Description** - A description of the wardware used in the protocol.
-* **Software Description** - A description of the software used in the protocol.
-* **Protocol Type (required)** - The protocol type can acquisition, array design, assay, or quantification. The user can also create new protocol types by inserting new CVterms into the protocol type CV.
-* **Publication** - A publication that describes the protocol.
+>![file information portion of expression loader](example_files/doc_images/expression_loader_file_info.png)
+>![experimental design portion of expression loader](example_files/doc_images/expression_loader_experimental_design.png)
+> The expression loader accepts parameters describing your file, as well as some experimental design parameters.
 
 # Viewing and Downloading Data
 
@@ -272,6 +244,24 @@ You can also assign quantification units to **all unitless quantifications** usi
 
 
 
+
+# Protocols
+
+Acquisition, Quantification, Array Design, and Assays all utilize protocols to describe them.  Think of protocols as the **experimental design**, and Acquisitions, Quantifications, Array Designs, and Assays as the experiment following that experimental design.
+
+There is currently no support for inputting, or displaying, acquisitions, quantifications, or assays.  The Expression module creates generic instances of these entities.
+
+**Protocol Descripton** - The protocol content types can be created by navigating to **Add Tripal Content->Protocol**. A protocol can be used to add extra detail to an experimental design. A protocol can be used to describe the assay, acquisition, and quantification steps of the experiment design. A protocol can also be used to further describe the array design content type. The fields of a protocol are:
+* **Protocol Name (must be unique - required)**
+* **Protocol Link (Required)** - A web address to a page that describes the protocol.
+* **Protocol Description** - A description of the protocol.
+* **Hardware Description** - A description of the wardware used in the protocol.
+* **Software Description** - A description of the software used in the protocol.
+* **Protocol Type (required)** - The protocol type can acquisition, array design, assay, or quantification. The user can also create new protocol types by inserting new CVterms into the protocol type CV.
+* **Publication** - A publication that describes the protocol.
+
+
+
 # Example Files
 
 ### Biomaterial Loader