Open2Dprot Pipeline Modules Downloads

Open2Dprot Pipeline Modules Downloads

Combined binary distribution of all released pipeline modules

All of the stable beta-level released modules may be downloaded in a combined binary distribution in one Zip file. A distribution includes demonstration data as well as executable module .jar files, Windows .exe files (used instead of the module .jar files), Windows .bat and Unix (or MacOS-X) shell .sh startup scripts, and some documentation. The distribution Zip file contents is listed below. As new pipeline modules are released, we will make them available for download. [The old download method is no longer used and is deprecated.]

You may also download individual module distributions. These distributions include the Java source code for that module. The modules are named <module-name>-dist-<Version nbr>.zip. E.g., Seg2Dgel-dist-V0.5.11.zip. Note tha the source code is also available from the SourceForge CVS server - however it may not be as stable as the officially released distributions. Individual source code files may be viewed on the CVS browser.

In all cases, select the file to download with the highest version number if there is more than one distribution file with the same prefix name.

1. Installation procedure

Download page for the latest Open2Dprot-bin-dist-versionNbr.zip distribution file from the SourceForge Files Mirror download area. This is listed under the Open2Dprot package and Open2Dprot combined binary release files.
Create an installation directory (E.g, on Windows this might be C:\Open2Dprot\, or C:\Program Files\Open2Dprot\, etc.) where you want to installOpen2Dprot. If you are using Unix or MacOS-X, create a directory to put the installation.
Unzip the downloaded .zip file into the installation directory.If you are getting a more recent release and want to use the same directory, just overwrite the files when you unzip the new distribution .Zip file.
To run the pipeline modules as stand-alone programs, just run the appropriate startup demo-<module-name> .bat or .sh script or the <module-name>.jar files. If you are on Microsoft Windows, there are <module-name>.exe files that you can run or make "Short-cuts".

You can read the individual subproject reference manuals on-line as HTML or as PDFs by accessing the Documentation or PDFs in the Modules list. The full manual PDFs are also included in the distribution in the PDFs/ directory.

When the main Open2Dprot scheduler program is released, all of these modules can be run through this one program and will be released in one distribution).

If you are installing Open2Dprot on a Microsoft Windows system, no system registry entries are used. The paradigm is similar to that used in the open source eclipse.org program. This results in smaller installer footprint and better use of the SourceForge Files mirror.

2. Contents of the Zip distribution file(s)

The Zip files containing the following files and directories. The format is the same for the combined binary distribution and for individual modules except that the latter also has the Java source code in a src/ directory.

<module-name>.jar (the main Jar file(s) for the module(s)),
<module-name>.exe (MS Windows executable program packaged with a program launcher for the main jar file(s)). Just click on the file to start the program,
Other library jars required (including: O2Plib.jar, SUN's Java Advanced Imaging (jai_codec.jar, jai_core.jar), Apache XML (xercesImpl.jar, xml_apis.jar), and others),
demo Windows .bat and Unix .sh startup scripts demo-<module-name>.bat (Windows) and demo-<module-name>.sh (Unix, MacOS-X) which run the modules in batch (or GUI in the case of Accession or Landmark). GUI versions are supplied if the module could be run both ways and are named demo-<module-name>-GUI.bat (Windows) demo-<module-name>-GUI.sh (Unix, MacOS-X),
a demo/ demonstration data directory with four sample images, accession database, landmark database, and related files,
a PDF/ directory with the full modules documentation as PDF files,
a license/ directory with the the open source license,
a src/ directory with the source code (not in binary distribution). If you don't care about the source code, just delete the src/ directory.

3. Documentation

See the reference manuals for the individual applications for details on running the programs. You can get to the table of links to module documents (both HTML and PDF) either through the Open2Dprot web site Module List The full reference PDF documents for the applications are in the distribution in the PDF/ directory.

4. Demonstration data set

This distribution includes a four sample (2D gels) demonstration data set in directory demo/ (see list of demonstrations in the documentation list for further descriptions of the dataset). Currently, the applications default to this dataset. See the reference manuals (in that same list) for each application to see how to use it on other data.

5. Running the separate module applications

On Windows, you can start any of the applications by using either the .exe programs or the demo-<module-name>.bat or demo-<module-name>-GUI.bat programs. See the reference manuals for details. You can make short-cuts to either the .exe or .bat files to make it easier to start the applications.

On Unix and MacOS-X, use the demo-<module-name>.sh or demo-<module-name>-GUI.sh programs. See the reference manuals for details.

If your software environment is set up to automatically run .jar files using the java virtual machine program (that was previously installed), you can just click on a module .jar file to start it. However, be aware that you can not adjust runtime parameters such as names of samples, or the amount of memory to use when running the program. You mus supply this information via the java interpreter command-line such as is done in the demo- scripts. You could use scripts as a model for scripts specific for your needs and data.

6. Downloading source code

You can download source code several different ways. One is to download the individual released module .zip files. If you have CVS, then you can download the most recent (not necessarily the most stable) source code using the SourceForge CVS server for Open2Dprot.

Revised 12/09/2005