Ingeneue 0.93b README File Updated January 2008 Kerry J. Kim This file contains important last minute information and installation instructions. Install instructions are available online at http://ingeneue.com 1. Installation: Unzip the package: First you need to unzip the Ingeneue.zip files to the directory of your choice. On Linux systems this may be done at the command line by using the unzip command: prompt> unzip Ingeneue.zip On Windows systems right-click on the Ingeneue.zip file and choose extract all. Most Mac systems will automatically unzip the package when you double-click on it. If not open a terminal window and use the unzip command as for Linux. 2. To run Ingeneue: To run Ingeneue you need Java version 1.4.2 or higher. Look for the the latest Java Standard Edition (J2SE) on sun's website http://java.sun.com/j2se/downloads.html and download and install either the JDK (Java Developers Kit) or JRE (Java Runtime System). The JRE is smaller and all that is needed if you just want to run Ingeneue. After unzipping (see above), start Ingeneue as follows: * Windows: Double click on the IngeneueWin.bat file in the Ingeneue directory. * Mac: Double click on the IngeneueMac.command file in the Ingeneue directory. * On *nix machines (or if you are using a mac/win machine and the above 2 steps do not work), Ingeneue can be launched by typing the following command from Ingeneue's home directory: java main.GeneNet 3. Organization of directories: All directories contain the source code for Ingeneue except the following: * networks: Contains the input files for the segment polarity, neurogenic, and other networks. Both network files and iterators can be found here * doc: Documentation & help files. The documentation for the affectors is included here, and contains detailed information on the mathematical formula for each affector and how to use it in net files. * manual: The Ingeneue manual. Open the manual.html file in your web browser for easy printing (the manual as one long page). Otherwise, click on the manual00toc.html for the navigation-friendly version. Can also be viewed from Ingeneue's help menu. * output: Initially empty; this is the default location for Ingeneue's output files resulting from parameter searches run by iterators. * tutorials: Walkthroughs for various features in Ingeneue. Can be viewed from Ingeneue's help menu. 4. Additional information: The latest version of Ingeneue is available from http://www.ingeneue.com or http://celldynamics.org Please check there for the latest updates, tutorials, models, and information on Ingeneue. If you find a bug or have a question, please contact the authors of Ingeneue at the email addresses listed on the Ingeneue web pages mentioned above. 5. Gnu Public license This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . You must cite one of the following papers by the above authors in any published work which makes use of Ingeneue: von Dassow, G., E. Meir, E. Munro, G. M. Odell. 2000. The segment polarity network is a robust developmental module. Nature 406: 188 - 92. and/or Meir, E., G. von Dassow, E. Munro, G. M. Odell. 2002. Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the Segment Polarity Network. J. Experimental Zoology 294: 216-251.