ARRAYPIPE version 1.0 README ---------------------------- TABLE OF CONTENTS OVERVIEW DESCRIPTION INSTALLATION BUG REPORTING COPYRIGHT AND LICENCE AUTHOR INFORMATION ACKNOWLEDGEMENTS 1) OVERVIEW Please cite the following publication if you use ArrayPipe in your research: Hokamp K, Roche FM, Acab M, Rousseau ME, Kuo B, Goode D, Aeschliman D, Bryan J, Babiuk LA, Hancock RE, Brinkman FS (2004) ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Research 32:W457-459 The standalone version of ArrayPipe is distributed under the Perl Artistic Licence (see the LICENSE.txt file included in the download) by the Brinkman Laboratory, Simon Fraser University, Burnaby, B.C., Canada. This standalone version of ArrayPipe has initially been developed for the Linux environment. This document gives an overview of the ArrayPipe package you have downloaded. For installation instructions, please read the INSTALL.txt file included with the package. For further information, please contact arraypipe-REMOVECAPSemail@sfu.ca. 2) DESCRIPTION ArrayPipe is a Perl program that can be run through the Web or from the command line. It consists of functions and filters that can be arranged into a pipeline to process and analyze microarray data. The Brinkman Laboratory headed development of ArrayPipe for the Genome Canada Pathogenomics project (www.pathogenomics.ca). A manuscript describing the ArrayPipe Web Server has been accepted for publication in the Web Server edition 2004 of Nucleic Acid Research. Please refer to http://www.pathogenomics.ca/arraypipe for more information. To read about the latest updates, see the Changes.txt file included in the downloadable version of ArrayPipe. The author invites feedback on ArrayPipe. If you find a bug, please send the information described in the BUGS section below. 3) INSTALLATION For installation and configuration of the program (either as a stand-alone version or as a Web server), please refer to the document INSTALL.txt, which is part of the download package. 4) BUG REPORTING If you find a bug, please report it to arraypipe-REMOVECAPSemail@sfu.ca along with the following information: - version of Perl (output of 'perl -V' is best) - operating system type and version - exact text of error message or description of problem - example files/data being processed If we don't have access to a system similar to yours, you may be asked to insert some debugging lines and report back on the results. The more help and information you can provide, the better. 5) COPYRIGHT AND LICENCE The program and the modules distributed with ArrayPipe are Copyright (C) 2004 Karsten Hokamp and Fiona Brinkman. All rights reserved. This program is distributed under the Perl Artistic License. Please see the included LICENSE.txt file for details of what this entails. 6) AUTHOR INFORMATION The main development of ArrayPipe has been carried out by Karsten Hokamp of the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada: http://www.pathogenomics.sfu.ca/brinkman Some code has been provided by collaborators in the Pathogenomics project. These are (in alphabetical order): - Dana Aeschliman (Statistics, University of British Columbia, Vancouver, BC, Canada) - Jenny Bryan (Statistics, University of British Columbia, Vancouver, BC, Canada) - David Goode (Finlay Lab, University of British Columbia, Vancouver, BC, Canada) - Byron Kuo (Inimex Pharmaceuticals, Inc., Vancouver, BC, Canada) - Marc-Etienne Rousseau (Inimex Pharmaceuticals, Inc., Vancouver, BC, Canada) Annotation information accessed by ArrayPipe has been assembled by Fiona Roche and Michael Acab (both at the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada). 7) ACKNOWLEDGEMENTS Thanks go to all the members of the SFU Brinkman Laboratory for being particularly helpful during the development process of this package.