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Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)
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This directory is the main directory for software developed by Stephen Ramsey at the Institute for Systems Biology. 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 Lesser Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Copyright Stephen Ramsey, Institute for Systems Biology ---------------------------------------------------------------- The following subdirectories can be found in this directory: apps: Contains all of the applications in this source tree. Generally does not contain any Java source code, just application build and config files, and other resources. Broken out by project (e.g., apps/Dizzy) For more information, read the "apps/README.txt" file. config: Configuration data that is not specific to a particular application, is placed in this directory. For more information, read the "config/README.txt" file. docs: Documentation that is not specific to a particular application, is placed in this directory. For more information, read the "docs/README.txt" file. images: image files used for the project website java: The java source tree. All Java code is contained in this tree. For more information, read the "java/README.txt" file. tools: For software tools that aren't really an integrated "application". Temporary directories that are created in the build tree: classes: Contains compiled java classes (created by build system) build: Temporary directory created by build system, to hold things like built Jar files, Web content, etc. The build system used underneath this directory tree is "Ant" (http://ant.apache.org). Invoking "Ant" is just like invoking the "make" program familiar from Unix operating systems, as shown here: ant <target> where "<target>" is the name of the target to be invoked. NOTE: All Ant invocations should be made in the top-level directory for this project; attempting to invoke Ant from a lower-level subdirectory will likely result in an error and a failed build. Supported targets are: clean: remove (most) build files (java class files are not removed, but remain under the "classes" directory) distclean: remove all temporary build files, including the java class files build: compile all java classes and perform other "build" functions, resulting in a JAR file being placed in the "build" subdirectory, along with a source tarball buildWeb: Build all web content, including HTML documentation, PDF manuals, and InstallAnywhere web installers, into the "build/web" subdirectory. (NOTE: this requires quite a bit of software to be carefully installed on the build machine; make sure you read the WebPagesManagementManual.html document, which is contained in the "docs/private" subdirectory.) buildHTML: Build all HTMl web content, including Javadoc API documentation, into the "build/web" subdirectory PDF documentation and InstallAnywhere installers are not generated. You must have first run the "build" task. buildPDF: Build the PDF documentation (you must have first run the "buildHTML" task), into "build/web" subdirectory. (NOTE: This requires special software to be installed on your computer; please read the WebPagesManagementManual.xml document, which is contained in the "docs/private" subdirectory.) buildInstallers: Build the InstallAnywhere installers and store them under the "build/web" subdirectory. This requires that the InstallAnywhere program be installed on your computer. uploadWeb: upload the built web content tree to the web server; only the part of the web content tree that has been built (with buildWeb target), will be uploaded to the web server. test: Compile all test code (eventually, compile and run unit tests) IMPORTANT: Using the build system requires special software to be installed on your computer, as described here: * In order to use the "uploadWeb" target, you will need to have a version of "Ant" installed that understands the "<ftp>" target. This means that your version of "Ant" should have been built with the external "NetComponents.jar" library in the CLASSPATH (see the WebPagesManagementManual.html document for more info). * In order to use the "buildPDF" target, you will need additional software installed (please read the docs/private/WebPagesManagementManual.xml document). * You can run most of the above targets from within an individual project directory (e.g., "apps/Dizzy" or "apps/Mogul"). However, the "buildWeb" and "uploadWeb" targets may only be run in the top-level directory. To build only the HTML for a given sub-project, change to the project's directory and run the "ant buildHTML" command. -Stephen Ramsey