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Computational representation of developmental genetic regulatory networks. If you run into any issues with getting Tomcat analysis j k baxter to run on your computer that you cannot resolve, or have a program crash, please send a report to biotapestry at systemsbiology dot org or post a message on the BioTapestry-users Google group so we can address your problem.
Browsing the Google group is a good way of finding out about any recently identified compatibilty issues and what workarounds have been developed to addess them. If problems arise due to the version of Java installed on your computer, see the section below to learn about obtaining a supported version of Java.
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Starting with Version 7. If you have previous BioTapestry files that are not loading into the current version correctly, or run into any other show-stopping bugs with the new version, the previous versions e.
If you encounter problems with a particular version of Java, please let us know about it; switching to a different version should solve any version-related problems.
The JRE can be downloaded from here click the "Free Java Download" button or here if you want to select from a wide variety of versions. BioTapestry for Gaggle Beginning with Version 7. Instructions and the final release Version 7.
There are example plugins in the source code tree see below that can serve as a starting point. If you need any guidance on building plugins, feel free to contact us.
BioTapestry can be called in batch mode from within another Java program to generate images from a comma-separated-value specification coming from a provided InputStream.
A small example is provided in the source code tree see below in the org. The BioTapestry Viewer can be embedded as a visualization component inside another Java program. An example of how to do this is shown in the class org. EmbeddedViewerPanelTestWrapper in the source code.
Source Code A tar file of the current version of the source code is available here. There are separate repositories; one for the Java codebase and another for the new browser-based Viewer Web Application code. We now support a new way of hosting a Viewer embedded in the web browser that does not require the user to have Java installed on their computer.
This change requires that the web server hosting the Viewer supports Java Servlets e. Apache Tomcat Version 6. We provide a page with detailed instructions on how to get a Viewer installation up and running.
You can also contact us using the resources listed in the Feedback section if you are having problems. If your deployment is on a publically available web site, please let us know about it. Even if you prefer not to be linked to, we appreciate being able to keep track of viewer deployments. Send Feedback We are eager to receive any feedback you wish to send us, such as questions, bug reports, feature requests, and usability issues.
The best place to do this is in the BioTapestry-users Google group. However, you can also email us privately at: The group home page is: The orginal contributors were: Suzanne Paquette Kalle Leinonen Also: Mac executable is bundled with the appbundler code provided by Oracle and Infinite Kind.
Code is available on BitBucket. The content of this web site is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
A copy of the license agreement is available online here. The downloadable Mac executable is bundled with the appbundler code that is copyright Oracle, and is licensed under the GNU General Public License version 2 with "Classpath" exception.
BioTapestry is under continual development, and despite our best efforts there are bugs in the software. Please be advised that, as stated in the license agreement, the Institute for Systems Biology and the authors disclaim any liability stemming from the use of this software.
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