The ALEXA platform is implemented as a pipeline of Perl and R scripts (mostly Perl) which interact with a mySQL relational database. Most of these scripts interact with the database via a simple API consisting of a small number of Perl modules. This pipeline was developed in a Linux/UNIX environment and most of the bioinformatic tools used by the pipeline are designed primarily for Linux/UNIX. Each script can be run without options for a brief description and usage intructions. For further details on installing and running the ALEXA platform refer to the ALEXA User Manual. We have used this platform to create and test several array designs. These designs were created by the package described below but the arrays themselves were manufactured by NimbleGen Systems Inc. using the design files we provided them. We also used NimbleGen's hybridization service but you can also order the arrays and conduct the hybridizations in house as well.
Before using the ALEXA platform, you will need to download and install either the ALEXA platform or the
source code (see below). Once this is done you can either create an array from one of our pre-computed
ALEXA designs or you can create an entirely new design.
Creating a custom array from a pre-computed ALEXA design
The simplest use of ALEXA is simply to create a custom array from one of our pre-computed designs described in the Design section. Once you have installed the virtual machine or source code, download the MYSQL tables corresponding to the design of interest from our FTP server, install them, and create a custom array as follows (using ALEXA_cf_42_2 as an example):
1.) Log into mysql and create a target database. (e.g. mysql; CREATE DATABASE ALEXA_cf_42_2; exit)
2.) cp -r ALEXA_template ALEXA_cf_42_2
3.) mv ALEXA_cf_42_2.tables.tar.gz ALEXA_cf_42_2/database_backup
4.) cd ALEXA_cf_42_2/database_backup
5.) gunzip ALEXA_cf_42_2.tables.tar.gz
6.) tar -xvf ALEXA_cf_42_2.tables.tar
Creating a new design
If none of the pre-computed designs available meet your needs, you may wish to create a new design. For example, we may not have a pre-computed design for your species of interest or you may want to create an updated version of one of our pre-computed designs. To create a new design, follow the instructions in the ALEXA User Manual.
Download the ALEXA Platform as a Virtual Machine Appliance
What is a virtual machine?
A 'virtual machine appliance' is a complete operating system that you can run WITHIN your operating system. Software created by VMware and others allows the user to safely create a 'virtual' computer within their operating system. This 'virtual' computer has hard drives, memory, etc. which exist as a discrete set of files on your 'actual' computer. Once a virtual machine is created it can be passed to other users who can then use this machine by loading it in a 'player'. Since the VMware player is free and available for Mac, Linux and PC, this allows us to makes the ALEXA platform available for any operating system.
Description of the ALEXA Virtual Machine Appliance
The ALEXA virtual machine is a complete operating system pre-configured with all of the source code and tools needed to create array designs. To test it we used it to generate the C. elegans design described in the designs section. The virtual machine itself is a striped down installation of Fedora Linux 7. It was created with VMware Workstation 6.
Download the ALEXA virtual machine
To use the ALEXA virtual machine you will first need to download and install the free VMware player for your operating system. If you already own VMware workstation, that will work as well. Once the player is installed download the ALEXA virtual machine, unpack it it and load it in the player. For more details, refer to the ALEXA User Manual.
Download as a Gzipped tar archive: ALEXA_VM_v1.1.tar.gz
Download as a WinRAR archive: ALEXA_VM_v1.1.rar
Version history: VersionLog.txt
Download only the source code
The ALEXA platform is also available as an archive. Download: ALEXA_package_v1.1.zip
Version history: VersionLog.txt
The ALEXA package contains all materials needed for the creation of custom microarray designs for the study
of alternative transcription events (alternative splicing, transcription initiation and polyadenylation). A
brief description of the contents of this package follows:
|/ALEXA_User_Manual.pdf||Complete user manual for running the ALEXA pipeline|
|/alexa/||Top directory for ALEXA code|
|/alexa/Array_design||Main directory of Perl scripts for the creation of designs|
|/alexa/Array_design/utilities||Perl modules used by these scripts|
|/alexa/Array_design/R_bin||R scripts used by the pipeline|
|/alexa/perldocs||Perldocs for Perl modules in html format|
|/alexa/sql||Complete SQL database schema and scripts for creating or restoring DB backups|
|/ALEXA_template||A template for the directory file structure of an ALEXA design. Consists of empty directories of names and arrangement expected by the pipeline of scripts|