README

If you can not download our software,you can use the github command:git fetch [remote-name] .

1 Description

BiArkit is a versatile toolkit that integrates different modules together and helps researchers approach information on synthetic biology. The first kit is GenomeBrowser, which visualizes the genomes of some model microorganisms, locates the genes on the genome and makes it easy to study the genomes. Secondly, Biobrick from the registry are transformed into the localized search tool. Thirdly, Riboswitch and SiRNA assist the design of regulatory elements. Fourthly, we have developed MetaNetwork to optimize the methods of scanning and output of the existing database of pathways. Fifthly, to analyze the dynamic change in various metabolic networks, we present the Simulator that help researchers analyze the network in silico. Sixthly, G-Circle is designed to illustrate the expression level of different genomes under the given environment. Further, to make it more convenient, the software is localized; that is to say, all functions mentioned above can be achieved without linkage to Internet.

All the functional modules have been successfully added to the Clotho Frame.

2 Directory Structure

src - including source code of BiArkit, including the seven application and rjava package.

BiArkit Project.rar - including open source code of BiArkit, which is provided for the advanced development and improvement by other programmers. It can be opened by Netbeans. Notice: you should open the folder “BiArkit\Rjava” by eclipse and make sure your R’s path is set correctly.

install.txt - including the guides for users to install BiArkit.

BiArkit_windows_1_05.exe - including Setup of BiArkit.

clothoBiArkitApp.zip - including open source code and Setup of BiArkit integrated into Clotho frame.

eugene - an expansion tool for Eugene platform for processing texture file.

Tutorial - including the guides for using BiArkit.

3 Compiling the code

Announcement: You just need to click on the Setup to install BiArkit and if you want to refine the codes, you can open BiArkitProject.rar by Netbeans.

More information about our BiArkit software system: http://2012.igem.org/Team:SYSU-Software

Contant us:

       You can speak Chinese if you can...
       Any question about the software please contact :1036479561@qq.com;whenjonny@gmail.com
       Any question about our team:jiang2@mail2.sysu.edu.cn or shanjiang-2008@163.com