#Biomolecular simulation repository

iBIOMES - Integrated Biomolecular Simulations

Copyright (C) 2014 Julien Thibault, University of Utah

This project provides logical and data models to prototype a repository for biomolecular simulations. Scripts are available to build a MySQL DB, along with the Java API to interact with the database (through Hibernate).

A set of dictionaries (including basis sets, force-fields, and computational methods) was also created to define terms that are commonly used in the field of biomolecular simulation, whether it it is in the literature or in the input/output files used to run the simulations. All the dictionaries are stored as simple CSV (Comma-Separated Value) files. A Java API was created to wrap these dictionaries into Apache Lucene indexes. The API can be used within a program to query elements based on their name or description. A set of SQL scripts is also provided to use these dictionaries as database tables. The scripts create a database schema and populate the new tables with the CSV data.

Directory structure

This folder (we will call it $BIOSIM_REPO_HOME) contains the following sub-directories:

• [config] Configuration files to edit before API use. These files specify the SQL connection parameters and the Lucene-related parameters)
• [data/csv] CSV files containing the dictionary data
• [lucene] Java API to build and use the Lucene-based dictionaries
• [lucene/scripts] Scripts to build and test the Lucene indexes.
• [sql] Hibernate mappings (Java/SQL) for the database
• [sql/scripts] Scripts to create and populate the SQL tables
• [uml] UML logical (Java) and physical (MySQL) models
• [web] Web interface for the Lucene-based dictionaries

Creating the database

Prerequisites

• MySQL server 5+
• Java 1.5+
• Apache Maven 2

Installation

Copy the CSV files to the /tmp directory so that MySQL can read files:

cp -f $BIOSIM_REPO_HOME/data/csv/* /tmp/

To create the tables and populate the data, source 'db_all.sql' in MySQL. First go to the scripts directory:

cd $BIOSIM_REPO_HOME/sql/scripts/

Then source the SQL script with something like:

mysql -u SQL_USERNAME -D MY_DATABASE -p < db_all.sql

If you only want to create the dictionary tables, source 'biosim_dict_all.sql':

mysql -u SQL_USERNAME -D MY_DATABASE -p < biosim_dict_all.sql

To compile the Java API (Hibernate mappings):

cd $BIOSIM_REPO_HOME/sql
mvn install

Creating the Lucene-based dictionaries

Prerequisites

• Java 1.5+
• Apache Maven 2

Installation

To compile the Java API:

cd $BIOSIM_REPO_HOME/lucene
mvn package

A JAR file containing all the compiled classes should be created in $BIOSIM_REPO_HOME/lucene/target/biosim-dictionary-lucene-api.jar

To build the Lucene indexes:

cd $BIOSIM_REPO_HOME/lucene
./scripts/lucene-build-dictionaries.sh <csv-dir> <output-dir>

	<csv-dir> path to the folder containg all the CSV files representing the dictionary data
	<output-dir>: path to the directory where all the Lucene indexes will be created

To test the dictionary lookups:

cd $BIOSIM_REPO_HOME/lucene
./scripts/lucene-lookup.sh [options]

Options: lookup -i <index-path> -t <term> [-f <lookup-field>] [-n <max-hits>]
         list   -i <index-path>

lookup: lookup a term in the Lucene index at in a particular field . list: list all the entries in the Lucene index at .

Dictionary web interface

Prerequisites

• Java 1.5+
• Apache Maven 2
• Java container (e.g. Apache Tomcat, JBoss)

Installation

To compile the Java API and package into WAR file:

cd $BIOSIM_REPO_HOME/web
mvn install

This will create a WAR file into the target/ directory. To install:

• Build the Lucene-based dictionary (see above)

• Set the $BIOSIM_REPO_HOME environment variable

• Edit the $BIOSIM_REPO_HOME/config/biosim-dictionaries-lucene.properties to provide the absolute path of the Lucene index.

• Copy the WAR file into your web container, for example with Tomcat:

  cp $BIOSIM_REPO_HOME/web/target/biosim-dictionary-web.war $CATALINA_HOME/webapps/

Restart tyour web server if necessary.

Building everything

Make sure you read the previous sections first. To compile:

cd $BIOSIM_REPO_HOME
mvn install