Introduction

Synthetic Biology, depending on interdisplinary knowledge and experience , cooperates wet and dry experiments to create artificial biological systems . Our team has developed a novel software system, BiArkit, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop GenomeBrowser and G-Circle for researchers. Besides, Biobrick is localized and transformed into searching kit for users to get comprehensive information conveniently. Further, Riboswitch and SiRNA are designed to compute out potential regulatory parts for engineering systems. For processing data from system level, MetaNetwork can illustrate information of various biological pathways on the graphical and user-friendly interface. And Simulator is intended for modifying and simulating genome-scale metabolic models, which involves many kinds of analyses to predict possible results of conditional changes in experiments. All the functional modules have been successfully added to the Clotho Frame.

GenomeBrowser

This is the section for sequences information. With this browser, researchers can surf for genomes from the typical model organisms. Users can locate the interested genes in terms of the input items, including name, product or coordinate. In addition, new genomes data will be saved on our website as downloadable contents.

Biobrick

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.

Riboswitch

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.

SiRNA

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.  

MetaNetwork

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.

Simulator

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.

G-Circle

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.  

Clotho

Clotho assists researchers to engineer synthetic biological systems and manage the data which is used to create them. It has been developed as the App environment that anyone can create and share new tools in it. These tools facilitate synthetic biologists to arrange their researches under the computer-based and automated- designed environment. Thus, to advanced develop the Clotho frame, we have successfully transfer the seven parts of our software, BiArkit, into Apps. Users can choose to employ our software through the Clotho media.            Click to get detailed introduction