Team:SYSU-Software/Project
![]( https://static.igem.org/mediawiki/2012/6/6d/Little-boy.png)
Our Project
Contents |
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 which has been added to the Clotho frame 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.
GenomeBrowsero:p>
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.