PubArray Installer

PubArray is a database and web application that allows researchers to explore and share thier analized microarray data. Unlike similar web applications PubArray is not intended to be a centeral repository for microarray data. Rather, any researcher can host thier own instances of PubArray. This key difference makes PubArray a good option for the following use cases:

Because researchers will be creating thier own instances of PubArray we have spent effort automating and simplifying as many of the technical steps as possible. In fact, we have tried to make it so simple that you can regard an instance of PubArray as disposible: If you don't like something about how your instance is configured, throw it out and start over. If a new version of PubArray is released and you want to upgrade, throw it out and start over. If your analysis has progressed and you want to publish the updated results ...

Experiment Overview

The experiment overview panel allows you to name and describe the experiment that you are publishing with PubArray.

Overview Panel

The input fields for this panel work as follows:

Load Design File

This panel allows you to load the experiment's design file. The column headers for the design file should match the design factors that describe your experiment and each row in the design file (excluding the header row) describes the values for a single array. As a point of reference, this is the same design file format that is accepted by the R/maanova program. After you select the design file for your experiment you will be shown a preview of the file's contents as shown below.

load design panel

The input fields for the "Load Design File" panel:

Load Data File

The "Load Data File" panel allows you to load your microarray intensity data. The data file's leftmost column must contain unique probeset/gene identifiers. The other columns contain intensity values for each of the microarrays that are a part of your experiment. Note that the column count in the data file (ignoring the probeset ID column) should match the row count in the design file (ignoring the design files header row).

load data panel

The input fields for the "Load Data File" panel work pretty much the same as the fields for the "Load Design File" panel.

Load Annotation and Statistics

The "Load Annotations and Statistics" panel allows you to upload probeset/gene statistic and annotation files. The structure of these files is similar to th structure of the data file. The rightmost column must contain unique probeset/gene identifiers which match the identifiers in the data file. The column identifiers should describe the annotation or statistics for that column. The data can be either numeric data or text data.

load annotations and statistics panel

Load Per-Gene Image Directories

The "Load Per-Gene Images Directories" panel can be used to load any custom graphs that you have generated for the probesets/genes in your microarray experiment. If you do not have any such graphs you can skip this step using the "Next" button.

The directories that you select must contain images where the file name will exactly match one of the probeset/gene IDs in your data file and the file extension can be one of ".jpg", ".jpeg", ".gif" or ".png". So, for example if our experement uses gene ID's: "gene1", "gene2" and "gene3" we might add a "Liver" directory containing images like:

Load Per-Gene Image Directories Panel

Create WAR File

The final panel allows you to create the WAR file that you will deploy for your web application. A default file is chosen for you but you can change it to whatever filename you like as long as you keep the ".war" file extension.

create WAR file panel

Deploying the WAR File

Once you have created this file you can deploy it using the latest version of the tomcat application server (the WAR file is completely self-contained so no other files need to be uploaded to tomcat). The only other thing that you may need to pay attention to is the memory limit used for tomcat. Since PubArray instances typically contain a lot of data it is recommended that you allocate more than the default amount of memory to the tomcat server. This step may not be necessary if your experiment's dataset is relatively small. Here is an example of launching tomcat on Mac or Linux with a memory limit of 1 GB (this assumes your working directory is the tomcat home directory and that you are using a bash shell).
JAVA_OPTS="-Xmx1024m" ./bin/startup.sh
That should do it. You should now have a working instance of PubArray for your experiment.