Citing ermineJ

If you use ermineJ in your published work please cite:

• Lee H.K., Braynen W., Keshav K. and Pavlidis P. (2005) ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6:269. (Download a PDF or view the abstract).

The original work that led to the development of ermineJ is described here:

• Pavlidis, Lewis and Noble, Proceedings of the Pacific Symposium on Biocomputing 7. pp 474-485, 2002. (Download a reprint) .

Contact information

Contact Anton Zoubarev or Paul Pavlidis with bug reports, feature requests, and questions.

Before reporting a problem:

• Please confirm that you are using the latest version of ermineJ. If you found a bug, it might already have been fixed and updated. To keep informed about updates, please subscribe to the ermineJ announcement mailing list (see below).
• Read the FAQ and the manual, your question may already be addressed.

When writing us with questions about ermineJ, please include the following information:

• Your operating system and amount of memory (e.g. "Windows XP with 256 MB RAM").
• The version of ermineJ you are using (found using the "Help-->About ermineJ" menu item).
• The version of java you are running. Under windows this can usually be found in the Control Panel called "Java" by clicking on "About" in the "General" tab, or by typing java -version at a command line.
• The contents of your ermineJ log file (found using "Help-->View log" menu item or in your home directory).

In some situations sending the results of a saved analysis or your input data files will be helpful, but don't send those items unless we ask for them or your question is about those files in particular.

Mailing list

If you use ermineJ, we urge you to subscribe to the ermineJ announcement mailing list. This serves two purposes. First, it will allow you to automatically receive information on updates to ermineJ. Second, it helps us track how many people use ermineJ. This is especially important when we try to obtain support for ermineJ development.

Credits

The software was written by Paul Pavlidis, Homin Lee, William Braynen, Kiran Keshav and Kelsey Hamer. Some code is based on an earlier version of the software written by Shahmil Merchant and Edward Chen, based in turn on a Perl implementation by Paul Pavlidis. Our Gene Ontology annotations were obtained through the Gene Ontology Consortium web site.