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Sigmoid Model Explorer

Sigmoid Model Explorer (SME) is a Graphical User Interface of the Sigmoid Project. It is a front end that provides access to the web services of the pathway databases and Cellerator, the module responsible for simulations. Some of SME's features are:

  • Query and retrieval of Cellerator Models in Sigmoid Database via web service
  • Graphical view of Cellerator Models with customizable icons
  • Custom selection and editing of model parameters
  • Remote simulation of customized models in Cellerator via web service

SME as well as all the others modules of the Sigmoid project is open source. The development efforts of our team are supported by the project management software provided by sourceforge.net. If you are interested in:

  1. internal details of Sigmoid implementation you should visit http://sigmoid.sourceforge.net which is the development website hosting all of the Sigmoid source code.
  2. using SME, the next section of the web page provides directions on how to install and use SME

 

How to Install SME

SME was tested on Windows, Linux, and MacOS X. Ideally, it should run on any platform that has Java 1.4 or better installed. If you don't have Java 1.4+ installed or if your Java Virtual Machine is older than 1.4, you can download it for free from http://java.sun.com/j2se/. You can download either J2SE Development Kit (JDK) or J2SE Java Runtime Environment (JRE). JDK incudes JRE and, therefore, is considerably bigger. SME does not need extra functionality provided by JDK.

Current version is 1.8.

There are two ways to start SME:

  1. you can download a zip file (click here), uncompress it, and start SME
    • for Windows users: unzip the file (you can use Winzip for that), open the SME folder and click on sme.jar;
    • for Linux users: unzip the file to the disk (you can use unzip command for that), in a command prompt switch to the SME folder, and type "java -jar sme.jar";
    • for MaxOS X users: unzip the file, open the SME folder, and click on sme.jar;
  2. you can launch the application via WebStart, for that you need only to click HERE:

    ,no other configuration is necessary. WebStart will download all the needed files and will start the application for you.

 

How to use SME

The tutorial on how to use SME will be published soon.

 

Statistics of Sigmoid Web Services

Check out the usage statistics of Sigmoid web services

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