README.md - Update documentation, point to new installation instructi…

…ons.

README.md

@@ -1,19 +1,26 @@
-Proxl
-=====================
-Proxl is a web application for analyzing, visualizing, and sharing protein cross-linking mass spectrometry data. It supports data generated by any software pipeline and does not depend on FASTA files created from particular databases.
+# Proxl
+Proxl is a web application for analyzing, visualizing, and sharing protein cross-linking mass spectrometry data.
+It supports data generated by any software pipeline and does not depend on FASTA files created from particular
+databases.
 
-More Information
-------------------
+## More Information
 * You can learn more about proxl's features at http://proxl-ms.org/.
 * Comprehensive documentation for proxl can be found at http://www.yeastrc.org/proxl_docs/.
 * The proxl publication can be found at [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/?term=27302480).
 
-Demo Site
----------------
+## Using Proxl
+A server has been set up at https://www.yeastrc.org/proxl_public/ for general use. Anyone can make
+an account, upload data, and view their cross-linking results. Note that your data are not public
+unless you make them public.
+
+## Install Proxl Yourself
+You may run your own instance of proxl on your own computer.
+Please follow our [installation documentation](https://proxl-web-app.readthedocs.io/en/latest/install/intro.html).
+
+## Demo Site
 We have set up a demo website to demonstrate many of proxl features. Please visit http://yeastrc.org/proxl_demo/.
 
-Proxl XML and Importing Data
--------------------------------------
+## Proxl XML and Importing Data
 To simplify support for as many software pipelines as possible, we have developed a XML specification
 dubbed Proxl XML for describing the cross-linking proteomics results from any software pipeline.
 Data imported into proxl must first be converted to Proxl XML. To learn more about Proxl XML and the import process,
@@ -23,6 +30,7 @@ Converters for several major protein cross-linking mass spectrometry pipelines h
 For your convenience, links to the respective importers are provided below. Please be sure to review
 the [import documentation](http://proxl-web-app.readthedocs.io/en/latest/using/upload_data.html) for more information.
 
+* [Trans Proteomics Pipeline or TPP](https://github.com/yeastrc/proxl-import-iprophet)
 * [Kojak](https://github.com/yeastrc/proxl-import-kojak)
 * [Crux](https://github.com/yeastrc/proxl-import-crux)
 * [pLink 1.x](https://github.com/yeastrc/proxl-import-plink) [pLink 2.x](https://github.com/yeastrc/proxl-import-plink2)