Team:Berkeley Software/Downloads




On this page we provide links that access all the code and documentation for the tools that we have written. Clotho, Eugene, Spectacles, and Kepler (workflows and actors) are the four major software projects and all represent a substantial amount of effort. For example in the Clotho project alone there are over 200 files and 250,000 lines of code. Therefore in addition to the source code and documentation, we highly recommend the use of an integrated development environment (Netbeans for example; info below) as well as the use of a revision control system (SVN for example; info below). Our code is all open source under a general BSD license and the majority of the code (99%) is written in Java.

Contact Information

For general information or to contribute: clothodevelopment AT googlegroups DOT com

For emails regarding any bugs: clothobugs AT googlegroups DOT com

For emails regarding any desired features: clothofeatures AT googlegroups DOT com

Clotho Design Environment - [Executable, Code, Documentation]

Clotho Design Environment Splashscreen (Courtesy of Christine Tsin)

The links (above) connect to 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.
  • Database Manager - tool for modifying entries in the active database connection.
  • 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. The source code itself is available here as well. This allows advanced users to build Clotho with only the tools they want. In addition you can incorporate the Clotho Remote Method Invocation (RMI) tool which is available there (used to connect with Kepler). Also available is the alpha version of the SPAM (Sequence Packaging And Manipulation) tool and Clotho "Classic" Beta (the older version of Clotho).

Eugene Domain Specific Language - [Executable, Code, Documentation]

Eugene Domain Specific Language

Here the Eugene programming language interpreter is available. Eugene's interpreter was written with ANTLR. Also included are example files and information on how to run the tool. We provide both an executable jar which one can run graphically as well as support for command line operation. We strongly recommend you read the comprehensive README file that comes bundled with the download. In addition syntax highlighting support is available in the download for Notepad++.

Eugene Command Line Operation
Eugene GUI Operation
Eugene Syntax Highlighting

Kepler/Clotho Integration - [Code, Documentation]

Kepler Actors and Workflows

We have created a number of workflows and actors for Kepler which are available here. These are available as source code only and require advanced knowledge of not only Java but also the process of building complex Java projects. Much of this project also requires advanced knowledge of Kepler. The actors and workflows available are:

Oligo Construction File Manipulation Workflow
  • Assembly Automation Workflow
  • Oligo Construction File Manipulation Workflow
  • Clotho Connection Actor: Opens a connection to Clotho via RMI
  • Data Retrieval Actors: Get tool data through RMI connection
  • DialogOption Actor: Allow workflows to retrieve user options at runtime
  • Assembly Actors: Special actors for the automation flow
  • Reaction Plate Actor: Combines 3 spreadsheets to produce a single sheet for parts, oligos, and plates for each reaction.

We hope to continue to add documentation and tutorials to the sourceforge page in the future and make it easier for those wishing to get involved at a very high level to do so.

Supporting Tools

Clotho and all its tools along with the Eugene interpreter all require Java 6. You can get it here. In general we recommend that you have the latest version of Java installed on whatever machine you run Clotho on. 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. We have gotten Clotho to run on many Mac configurations. Please don't give up and please contact us if you have further questions.

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. You will need to create a new project with the source code you download as well as add the libraries needed. Many of these libraries are available with the Clotho download while others come with Netbeans. You will need to augment your Netbeans project with these libraries. Please see the documentation for more information on how to build Clotho as a new project.

Finally, in order to get our code from sourceforge it may be necessary to download Subversion (SVN) software. You can get this here. In particular we recommend Tortoise SVN for interactive use as well as Slik SVN for a command line version (to use with Netbeans for example).