Description

Background

As iGEM requires, Software teams should create a novel software tool that supports some aspect of synthetic biology. Since recent years our team were committed to software development which may contribute little to synthetic biology or relating works, we want to develop something more "biology" this year.
After talking with our PI, we learned about Flux balance analysis (FBA). FBA is a method for analyzing the flow of metabolites through a metabolic network. FBA can calculate the flow of it and make it possible to "foresee" the growth rate of an organism or a biotechnologically significant metabolite.

Inspiration

iGEMers and biological factories frequently complain it repeated and troublesome to improve a genetic circuit and implement genome-scale metabolic network reconstructions when they dissatisfy the productivity of the organism, as we investigated. Factories regularly do such work simply based on experience or maybe just by random attempt. Labs may use some mathematical methods. Just as mentioned, the FBA and its further study have been proved useful in physiological studies, gap-filling efforts and genome-scale synthetic biology. However, using such methods doesn't mean that failure would not occur, and plenty of experiments, namely, plenty waste of time may still be demanded. For sure, there are several software that are made for such modeling, yet they do have several defects. Meanwhile, considering that both factories and iGEMers may specialize in biology but be quite unfamiliar with computer software, those command-prompt-only software are not perfect.
Obviously, current tools cannot satisfy the need. Thus, here comes "ForeSyn", the software born to solve the problem.

Project

Foresyn is a user-friendly platform that was designed specifically for synthetic biologists to solve such issues above. Just like its name, Foresyn can foresee the targeted improvements to the users' experiment, give advise and therefore increase productivity, literally by the neoteric workflow management based on our customized database.
By using our software, labs and factories can alter the bounds on certain reactions to simulate the growth on different media or of bacteria with multiple gene knockouts. Despite this, users can select their own object function, and our software can output the optimal solution of it.
Of course, users don't need to recite so many command codes. All you need may be a single mouse. Moreover, our software performs a better user experience by presenting supreme graphical result display.
Through this things, Foresyn can literally predict, I mean, foresee the likely result or trend of an experiment conducted by a synthetic biologist. Particularly, what it sees immediately transforms into what you see.

Features

Lessen Your Needless Works
What You See Is What You Get
No Command Prompt Using Need
Comprehensive Customized Database

Comparison

Comparing our project with the software we can get from online now, we find that our project has some significant features that distinguish it from the others. Firstly, we do some research on the cobra. Undoubtedly, it's a powerful software when it comes to simulation and calculation. However, it bases on the Matlab and requires a relatively long time to learn how to use it. And it’s hard to compare two model with each other.
After that, we do some more detailed researches on several types of software based on cobra, and most of them have some significant defects. For example, you have to download the whole MatLab to use some of the software. And some of them like CellNetAnalyzer are more friendly for Linux and cannot function well in Windows, which will cause a lot of troubles.

	CellNetAnalyzer	Cobra	BioSPICE MOMA	MetaFluxNet	PathFluxNet	Fbatool
Graphical	✔	✘	✘	✔	✘	✘
Operating System	Windows	Windows	Windows Linux	Windows	Linux UNIX	Corona
Algorithm	MFA SNA	FBA MOMA DFBA FVA	FBA MOMA	MFA	FBA MOMA	FBA

The GUI of CellNetAnalyzer

And we have also done some researches on simbiology, a tool in Matlab referred by Yonghao Liang, a senior student in our school. It turns out that it can predict how the concentration of metabolites will change as time goes on. But it can only deal with a few reactions at one time, which can not meet our needs to edit a whole model.

One simulation by simbiology

Our tool is more user-friendly because you can use it directly online, and you don't need to learn a new programming language. Just a few inputs are required, but you can get a complete analysis!

Slogan

Foresyn has foreseen the experiments, that helps synthetic biologists see further.
Foresyn foresees the synthetic biological experiments, and makes you see further.
Foresyn makes the experiments foreseen, and makes you see further.
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