Team:SYSU-Software/Project
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Our Project
Contents |
Introduction
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.
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.
MetaNewtwork
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.