About QuickLoad

Introduction

QuickLoad is a simple system for users to distribute data for visualization in IGB.

A QuickLoad site is very simple - it contains annotation files and/or sequence files for one or more genomes together with some simple meta-data files describing those genomes.  You can set up a QuickLoad site on your local computer or on a Web server.

To view an example, see the demonstration BioViz QuickLoad site.

How to Set Up a QuickLoad Site

Setting up a QuickLoad site is easy, but you will need to create a few simple files that IGB will read before it displays your data.  These files contain information about the genomes your site supports, your data files, and other information that IGB needs in order to add your site's information to the IGB Data Access Panel.

Step One: Create a QuickLoad root directory.

For this, create a folder on your local computer or on a Web server.  This folder will contain your genome directories and a "meta-data" file called "contents.txt."

Tip: If you are hosting a QuickLoad site using the Apache Web server, you can configure QuickLoad to demand a user name and password from anyone who accesses the data. This is useful if you want to share your data with colleagues but are not yet ready to make the data publicly-available.  To do this, you can created and add an .htaccess file to your top-level QuickLoad folder.  If the .htaccess file contains password directives, then IGB will prompt users for a user name and password before allowing them to view files and access your site.  

(Here is some documentation from the Apache Web site to help you get started: http://httpd.apache.org/docs/2.0/howto/auth.html.)

Step Two: Create contents.txt file.

Create a file called "contents.txt" and add it the top-level directory.  This file should be a plain text, tab-delimited file.  (You can create one using Notepad or by using the "save as text" options in word processing software.)

The first column in the contents.txt file should list the name of the directory containing each genome you want to support.  The second column is optional - it contains text IGB will display on the title bar when you open IGB.

For example, here is a sample contents.txt file from the BioViz QuickLoad site:

Note: The two columns should be separated by a tab character!

Optional Step: Create a synonyms.txt file.

This is a list of synonyms for genomes and chromosomes.  Each line contains any number of synonyms for an individual sequence, separated by tabs.  This file helps IGB recognize identical sequences that have different names on different DAS servers or QuickLoad sites.

Step Three: Create one or more genome directories.

Next create genome directories for each of the genome versions you want to make available via QuickLoad.  The names of these directories should match the names you used in the first column of your contents.txt file.

Note: You can include other directories and other files in your QuickLoad site.  IGB will simply ignore anything that isn't listed in your contents.txt file.

For example, here is a directory listing for the BioViz QuickLoad directory:

Tip: If you set up your QuickLoad site in the Web directories of an Apache server, you can modify and fine-tune how files are displayed by adding directives to the .htacess file in that directory.  You can configure Apache to allow users to view the contents of your QuickLoad directory and include a short description of each file.

For example, the BioViz QuickLoad .htacess file allows users to view the contents of the directory in a Web browser and directs the browser to show short descriptions for each file:

Step Four: Create mod_chromInfo.txt files.

For each genome directory, create a mod_chromInfo.txt file that lists all the chromosomes in your genome, together with their sizes.  As with the contents.txt file, it should be tab delimited.  The first column lists the chromosome names and the second column lists their sizes.  IGB uses this file to create the sequence selection table under the Data Access Panel.  

Here is an example of a mod_chomInfo.txt file from the BioViz QuickLoad site:

Optional Step: Create liftall.lft file.

This describes how contigs are assembled into chromosomes.  If you do not have this information available, you may use a "mod_chromInfo.txt" file instead.  Each line contains: CONTIG_START tab CONTIG_NAME tab CONTIG_LENGTH tab CHROMOSOME_NAME tab CHROMOSOME_LENGTH

Step Five: Create annots.xml files.

If you have any annotations for your genomes, you can make it possible for IGB to display them in the Data Access Panel by listing them in the annots.xml file.

Here is a simple example from the TAIR9 (A_thaliana_Jun_2009) genome:

An annots.xml file contains one or more file tags, enclosed in a files element. The file tag has four attributes:

Step Six: Add your annotation files.

Place your annotations into the appropriate genome sub-directories. They can be "gzipped" or not depending on your preference. You should be able to use any of the many formats IGB supports.  For annotation files, BED format is the most commonly used.

Step Seven: Add your sequence data files.

You may not need to do this if you are working with a genome that other QuickLoad or DAS2 sites support. That is, IGB may be able to retrieve sequence data for your genome from other sites if it can recognize that your annotations belong to the same genome version as the other data providers it gets data from.  However, if you are working with a newly sequenced genome or don't want to use other groups' servers, you can support IGB's sequence visualization functionality by setting up your own sequences to distribute.

To do this, you will need to obtain sequence files and convert them to one of two specialized compressed binary formats (bnib or 2bit) that allow IGB to quickly obtain the sequence data when users press Get Sequence buttons. For more information on how to do this, see Converting FASTA to BNIB. Be sure that you name your files using the same names you listed in your mod_chromInfo.txt file.

Step Eight: Add your new QuickLoad site to IGB.

Select the Data Access Panel tab and click the button labeled Configure.  You should see a window that looks something like this:

To add your server, click Add.

Use the menu to select QuickLoad.

Enter a user-friendly name for your site in the top text box.  Next, either enter a URL Web address in the lower textbox, or click the button to choose a local directory.

For example:

If everything is configured correctly, IGB will list your new QuickLoad site and data sets when you choose a species and/or genome version your QuickLoad site contains data for.  If IGB can figure out what species your genome belongs to, it will list your genome under the Species menu.

Getting Help

If you have problems, you may be able to diagnose the problem by reading status and error messages IGB prints to the Console. To view the messages, choose the Show Console option under the Help menu.

And of course, you can always post a question to the IGB Help Forum.