EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing

This repository contains the full EpiExplorer source code that is being used by EpiExplorer at MPI: http://epiexplorer.mpi-inf.mpg.de

• The Frontend folder contains the files that make the EpiExplorer front end as deployed on http://epiexplorer.mpi-inf.mpg.de
• The Backend folder contains the backend files responsible for preprocessing annotations, processing custom datasets and answering user queries
• The Datasets contain the information about genomic and epigenomic annotations used by EpiExplorer

CompleteSearch provides native support for advanced search features such as query autocompletion and database-style JOIN operations, and it has been shown to outperform more standard approaches based on inverted indices

• Linux or Mac Os X
• Python 2.6
• C++ Compiler
• CompleteSearch (See above)
• BedTools

1. Install CompleteSearch http://ad-wiki.informatik.uni-freiburg.de/completesearch

2. Install bedtools https://github.com/arq5x/bedtools2

3. Checkout EpiExplorer source code https://github.com/MPIIComputationalEpigeNetics/EpiExplorer

   • UserInterface/ contains all userinterface files and is not relevant for this task.
   • GDM/ contains all backend sources
   • Datasets/ contains all dataset initialization settings

4. The backend sources have 3 main entry points:

   • GDM/CGSDatasetServer.py is the main dataset annotation server
   • GDM/CGSQueryServer.py is responsible for answering user queries and starting and stopping CompleteSearch instances
   • GDM/CGSServer.py is the main server used only to forward requests from the Userinterface

5. Set up EpiExplorer configuration file /Cosgen/GDM/settings.py

   • Set up EpiExplorer path
   • Set up Bedtools path
   • Set up servers location addresses and ports
   • Set up completesearch path
   • Set up temporary files path

6. Start CGSDatasetServer.py

7. Process the default region sets:

   • The GDM/Tests/testServer.py has the code of how to process the default regions

8. Start CGSQueryServer.py and CGSServer.py

1. Apache HTTP server with mod_python
2. Install Apache Httpd Server with PHP and mod_python
3. Configure Httpd server for handling the python files (.py) of the directory UserInterface/cgi-bin with the mod_python module
4. Configure Httpd server for handling the PHP files (.php) of the directory UserInterface/www/pub
5. Configure the $rpc_server and $rpc_port variables inside the file UserInterface/www/pub/settings.php for pointing to CGSServer.py address and port

Upon starting the dataset server (CGSDatasetServer.py) performs the following actions:

1. Reads the available genome from the settings.py
2. For every genome, tries to read its basic initialization file
   1. These files are named unix_.ini and are located in the Datasets folder.
   2. Each line of this file is formed =
      1. Every dataset initialization file is of similar format =
      2. The most important properties of each dataset initialization files are:
         • genome the genome assembly for the dataset
         • datasetSimpleName simple name for the dataset
         • datasetWordName name for the dataset used in words, it should be the same for similar properties across genomes
         • datasetPythonClass the class that handles similar types of data
         • hasFeatures if the dataset encodes features or not, for ex
         • hasGenomicRegions if the dataset encodes regions or not. For example the DNA sequence dataset has features, but does not have regions, while genome-wide tiling regions have regions, but do not have any annotation properties associated with them
         • These are only the common ones, for every specific dataset type there are other properties that are expected from the python classes for full customization
3. If a dataset requires downloading external resource, it is downloaded
4. If a dataset requires preprocessing, it is preprocessed
5. Some datasets should be downloaded before

Tutorials are available at the supplementary material page

Halachev, K., Bast, H., Albrecht, F., Lengauer, T. & Bock, C. EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol. 13, R96 (2012).

The paper is freely available at http://genomebiology.com/2012/13/10/r96

Bast H, Weber I: The CompleteSearch engine: interactive, efficient, and towards IR & DB integration. CIDR 2007, Third Biennial Conference on Innovative Data Systems Research: 7-10 January 2007; Asilomar, CA, USA 2007, 88-95, [proceedings](http://www.cidrdb.org/ 2007Proceedings.zip). pdf