Team:Berkeley Software/Downloads

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Clotho Design Environment - [[http://sourceforge.net/projects/clothocad/ Code], Documentation]

Clotho Design Environment

The code link (above) connects to [http://sourceforge.net sourceforge] (an open source code distribution website) where the "download now" button on the project main page provides a build of the Clotho core framework. This is the standalone version of Clotho and should be downloaded by the majority of Clotho users. In this form Clotho comes packaged along with the following Clotho tools:

  • Algorithm Manager - tool for running assembly algorithms to create efficient composite device assemblies.
  • Enzyme Library - mechanism for highlighting and locating enzymes in DNA sequences.
  • Features Library - library of user defined annotations for DNA sequences.
  • Notepad - basic text editing utility which acts as a virtual lab notebook.
  • Parts Manager - parts browser and manager.
  • Sequence View - DNA sequence editor and viewer.
  • Spectacles - visual editing environment for device construction.

The download is an executable jar file which you can run from your computer. You can also get the source code there as well. The source code itself is available here as well. This allows advanced users to build Clotho with only the tools they want as well as incorporate the Clotho RMI tool which is available there as well.

Eugene Domain Specific Language - [[http://sourceforge.net/projects/eugene/ Code], Documentation]

Kepler/Clotho Integration - [[http://sourceforge.net/projects/keplerclotho/ Code], Documentation]

Java 6

Clotho and all its tools along with the Eugene interpreter all require Java 6. You can get it here. Also there are a number of issues regarding using Java 6 on Macs. More information on getting Clotho to run on Macs is available here.

Netbeans

Clotho is developed using the Netbeans Integrated Development Environment. We highly recommend you use Netbeans to avoid any potential difficulties. In particular Netbean's GUI builder creates .form files which allow for the creation of Java Swing based GUI elements.

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