Team:SYSU-Software

      Faced with the emergency of bio-information in recent years, we are motivated to consider how to exploit them and integrate them into biological researches. In order to design and engineer artificial organisms, Synthetic Biology has much more requirements to the understanding of the information comprehensively as its final goal is to assemble and construct the systems under the standard criteria. BiArkit, a multifunctional tool box, assists synthetic biology researchers to further comprehend bio-information from sequences and parts to the whole systems. Besides, it provides medium for users to generate desired information in experiments.

      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 is the section for parts information. It can facilitate researchers to search features and functions of Biobricks documented in the Registry of Standard Biological Parts. All of the relevant operations can be completed without connecting with the Internet.

      This is the section for generating parts information. It can assist researchers to design the sequences and structures of potential riboswitches according to their inputs and choices of aptamers. Both of the up-regulation and down-regulation riboswiches can be provided by this kit.

      This is the section for generating parts information. It can design another regulator in engineering biological systems – siRNA. According to the input sequences, it can figure out the potential siRNA automatically.

      This is the section for system information. Given the friendly interface, researchers can explore and acquire their interested gene’s relevant pathways and networks in one map. Users can even drag every graphic element in the maps to check the information conveniently and effectively.

      This is the section for generating system information. Based on the reconstruction of genome-scale models, researcher can use this kit to edit the existent models according to their needs. Then, they can choose different combination of analysis to predict effect from a intended loss-of –function mutation, find necessary and basic genes maintaining the whole system, predict phenotypic behavior under the given environmental conditions and interpret the coupled reaction activities.

      This is the section for sequence information. It can illustrate the given genome and the expression level of genes within it under different environment in one graph. In addition, we have developed it as one app and integrated it into Clotho.

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