Team:SYSU-Software/SecondEdition
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Second Edition
Contents |
Overall
The first version of
BiArkit is now completed and released. The second version,
BiArkit 2.0, has been proposed and designed to be more competent to
fulfill the needs of synthetic biology researchers.
BiArkit 2.0 will still concentrate on how to deeply exploit
bio-information for researchers to design and execute their further experiments.
First, every kit will be optimized functionally and ameliorated to be more
user-friendly. Second, the explosion of second generation sequencing motivates
us to involve the next generation sequencing data to BiArkit
2.0.
Third, for more information coming from biological systems, including
reconstruction networks, molecular interactions, and artificial networks, we
will make standards and integrate them into one section to provide the
comprehensive prospects for researchers to employ. Fourth, as
BiArkit was coden by JAVA, we plan to make this
software run not only on
Win but also on the platform of
Mac
and
Linux.
GenomeBrowser
The updated GenoneBrowser will incorporate bio-information out of RNA-Seq,
ChIP-Seq and tiling-array to illustrate the genome expression level under given
conditions and locate molecular that interact with the genomes. With the known
annotation, the genomes can be divided according to the products they
transcribed. Besides, for make this kit more user friendly, we are going to
refine it and allow researchers to screen their interested genomes graphically
only by pasting the relevant web links to the interface. After pasting the
links, this kit will download the xml or fasta from the original web
automatically.
Biobrick
The updated Biobrick section will focus on three parts to be optimized. First,
we will specifically classify the known biobricks. As lots of accomplishments by
using biobricks have come out, some bricks have been tested to be adjustable to
the specific kinds of researches. For example, a kind of biobricks are always
used to implement the cell signals transportation and another kind are always
applied to the cell colony communication etc. This
research-oriented
classification facilitate researchers get the useful information they need
conveniently and efficiently. Second, we will refine the codes to make this kit
updated immediately according to the official website. Third, we will try to
improve the ways of restoring the data by documenting more graph and credit
identification information for each biobricks.
Regulator Designer
Apart from Riboswitch and SiRNA, some other kinds of
regulator will also be considered in the next version of the kit. One of the
most common used in synthetic biology is transcriptional factors (TFs). We will
develop a TFs matcher for researchers to find their desired TFs according to the
experimental requirements. The selection process is executed based on the
existent TFs database and previous common used TFs in synthetic biology. And our
ultimate goal is to add the regulator designer, including riboswitch, siRNA, TFs
and others to the
Clotho
frame for sharing among all the researchers.
Simulator
The advanced version of Simulator will be improved
from three prospects.
(1)
One focuses on ameliorating the Algorithms of the original one.
The next version of Simulator, other methods
for simulating will combined into this part according to the completeness of the
information necessary for certain kind of analysis provided by the SBML files.
In the first version, we use the
constraint-based FBA
but in the next version algorithm with both constraint and kinetic approaches will be applied to enhance the reliability and
sensitivity of simulation.
For program code To realize FBA analysis, the original version is realized based
on Package ‘abcdeFBA’ of R. While in the second version of this part,
programming will be supported directly by JAVA or C++, which will not only
reduce the size of the software but also accelerate computation.
(2)
One focuses on improving the user experiencing.
Firstly, for model used in simulation, users will not only use SBML files
documented in released database like Biomodels but also can edit and save the
SBML in a user-friendly way. Information necessary for FBA including reactions
and metabolites will be showed clearly and in the interface where user can
revise model . The new model can be saved in a revised SBML file. Secondly, the
metabolic network can be visualized in the interface. Users can drag the
pathways joint to a right place in the screen like playing the building block
game, which can add to the fun of this simulation.
(3)
Inspired by the recent whole-cell model in
predicting phenotype and giving insights in some undiscovered cellular
behaviors, we plan to expand our models and simulation not only concentrating on
metabolome information but also should involve genome annotation, transcriptome
, proteome and molecular interaction into consideration. As cell processes have
been divided into 28 submodels and synthetic biology have developed many typical
artificial systems recent years, we hope to give out a new standard for
documenting these cellular process and relevant bioinformation mentioned above
in one file. Thus, researchers just need to edit such kinds of files, such as
adding metabolites or deleting one interaction between two molecular, to
simulate their designed systems before experiments. And the mentioned
comprehensive bio-information can be applied to offset the difference between
prediction and experiments, which often motivate the discovery of unobserved
cellular process.
Trans-platform Realization