This document describes the tools you
will need to run a TMAJ server.
Note that a TMAJ client can be
run from just about anywhere; all you need is the Java 6 Runtime
Array Slide Scanning Machine
You will need a way of getting a gif/jpeg image from each coordinate
(spot) on an arraySlide.
As long as you can get 1 individual image (a jpeg, gif, etc) for
each coordinate (spot) on an array-slide, you will be able to use TMAJ.
One couldn't just give TMAJ one massive image representing an entire
ArraySlide with every coordinate on it; every spot must be its own
Please click here for more
details on array-slide scanning machines
You must have a database up and running for TMAJ to store its
MySQL is recommended, because it is open source and free.
Currently TMAJ supports any of four databases:
MySQL is an open-source database and is available for free.
We have tested TMAJ with the following versions:
- Oracle 8i Enterprise Edition
- Oracle Database 10g
- MySQL 5.0
- Sybase ASA
- Sybase ASA version 8
- Sybase ASA version 9
- Microsoft SQL Server 2005
Free Software Required
- Java 6
(or later) Development Kit (JDK) Java is available at no cost
Microsystems. Note that TMAJ requires Java 6 or later, and is not
compatible with Java 1.4 or Java 5.
- Apache Tomcat
is free software, and made available by the Apache Software Foundation.
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- TMAJ is written in Java, so a server can be installed on any
machine that supports Apache Tomcat and Java. This includes both
Windows and Linux machines. It might be possible to install a
TMAJ server on a Macintosh, but this has not been attempted. (We
have however installed TMAJ clients on Macs)
- TMAJ is not
processor or memory intensive. Some users have installed it on
their personal desktops and have had no performance problems.
- A limiting factor worth mentioning is hard drive space. The
produced by a scanning machine can take up a great deal of space.
Compressing the images will help out a great deal with this, however
you should choose a hard drive with ample space.
* The JHU TMAJ database is the Sybase
(ASA) database engine, which is part of the "SQL Anywhere Studio"
This is NOT the same as Sybase "Adaptive Server
Enterprise". Adaptive Server Enterprise (ASE), also called
"Sybase ASE" was formally called "Sybase SQL Server", but the name was
changed to ASE after version 11.5 in 1995 to avoid confusion with
Microsoft's product, Microsoft SQL Server). ASE
is the "true" Sybase database. ASA is actually a product Sybase
acquired when they bought a company called PowerBuilder.