Team:SYSU-Software

       We are developing a multifunctional toolbox biArkit, which integrates different modules together and help researchers approach information they need. Firstly, we consider the Genome Browser, which visualizes the genomes of several microorganisms, locates the genes on the genome and make it easy to study the characteristics of the genome. Secondly, we develop a Regulator Designer, to help the design of regulatory elements, mainly non-coding RNA, a thriving method applied in biological research. Thirdly, to meet the need of systems and synthetics researches, we optimize the methods of scanning and output of the existing database of pathways. Fourthly, to analyze the dynamic change in various metabolic networks, we present a simulator that help the researchers analyze the network in silico, in method of flux balance analysis (FBA). 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.

      With this Genome Browser, users are able to search Biobricks, plasmids and genomes of model microorganisms; at the same time, gene annotations and information of GenBank are presented. The primary protein sequence is also presented according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need.

      This part of the software focus on the design of regulatory elements of metabolic networks, mainly non-coding RNAs including SiRNA and Riboswitch. When a certain gene or protein is given, the Designer would generate the elements. What’s more, the primary and secondary structure can be predicted and presented in the Designer. The function of structure prediction can be also applied in other non-coding RNAs, for instance, microRNAs.

      Relying on the KEGG Pathway database, the Illustrator exports the optimized relevant pathway map of a gene or transcription factor the user interests in.

      Simulator is a tool to analyze target metabolic network in method of flux balance analysis (FBA). The Simulator would help researchers rebuild the metabolic network and search key genes in the network, in order to simplify the synthesis design. Relying on the KEGG Pathway database, a novel rFBA model is formed when regulation-relevant conditions are added into the primitive FBA model, which would help the researchers observe the dynamic change in the metabolic system. Moreover, unlike the mainstream of FBA, the analysis of the Simulator is not based on Matlab and is more convenient for researchers to use.