Difference between revisions of "Team:USTC-Software/Description"

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           <h3>Background</h3>
 
           <h3>Background</h3>
 
           <div class="passage">
 
           <div class="passage">
−
             As iGEM requires, Software teams should create a novel software tool that supports some aspect of synthetic biology.  
+
             As iGEM requires, Software teams should create a novel software tool that supports some aspect of synthetic
−
             Since recent years our team were committed to software development which may contribute little to synthetic biology or relating works,  
+
            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.
 
             we want to develop something more "biology" this year.
 
             <br>
 
             <br>
−
             After talking with our PI, we learned about Flux balance analysis (FBA). FBA is a method for analyzing the flow of metabolites through  
+
             After talking with our PI, we learned about Flux balance analysis (FBA). FBA is a method for analyzing the
−
             a metabolic network. FBA can calculate the flow of it and make it possible to "foresee" the growth rate of an organism or a  
+
            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.
 
             biotechnologically significant metabolite.
 
           </div>
 
           </div>
 
           <h3>Inspiration</h3>
 
           <h3>Inspiration</h3>
 
           <div class="passage">
 
           <div class="passage">
−
             iGEMers and biological factories frequently complain it repeated and troublesome to improve a genetic circuit and  
+
             iGEMers and biological factories frequently complain it repeated and troublesome to improve a genetic
−
             implement genome-scale metabolic network reconstructions when they dissatisfy the productivity of the organism, as we investigated.  
+
            circuit and
−
             Factories regularly do such work simply based on experience or maybe just by random attempt. Labs may use some mathematical methods.  
+
             implement genome-scale metabolic network reconstructions when they dissatisfy the productivity of the
−
             Just as mentioned, the FBA and its further study have been proved useful in physiological studies, gap-filling efforts and genome-scale  
+
            organism, as we investigated.
−
             synthetic biology. However, using such methods doesn't mean that failure would not occur, and plenty of experiments, namely, plenty waste  
+
             Factories regularly do such work simply based on experience or maybe just by random attempt. Labs may use
−
             of time may still be demanded. For sure, there are several software that are made for such modeling, yet they do have several defects.  
+
            some mathematical methods.
−
             Meanwhile, considering that both factories and iGEMers may specialize in biology but be quite unfamiliar with computer software,  
+
             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.
 
             those command-prompt-only software are not perfect.
 
             <br>
 
             <br>
−
             Obviously, current tools cannot satisfy the need. Thus, here comes "ForeSyn", the software born to solve the problem.
+
             Obviously, current tools cannot satisfy the need. Thus, here comes "ForeSyn", the software born to solve the
 +
            problem.
 
           </div>
 
           </div>
 
           <h3>Project</h3>
 
           <h3>Project</h3>
 
           <div class="passage">
 
           <div class="passage">
−
             Foresyn is a user-friendly platform that was designed specifically for synthetic biologists to solve such issues above.  
+
             Foresyn is a user-friendly platform that was designed specifically for synthetic biologists to solve such
−
             Just like its name, Foresyn can foresee the targeted improvements to the users' experiment, give advise and therefore  
+
            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.
 
             increase productivity, literally by the neoteric workflow management based on our customized database.
 
             <br>
 
             <br>
−
             By using our software, labs and factories can alter the bounds on certain reactions to simulate the growth on different  
+
             By using our software, labs and factories can alter the bounds on certain reactions to simulate the growth
−
             media or of bacteria with multiple gene knockouts. Despite this, users can select their own object function, and our  
+
            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.
 
             software can output the optimal solution of it.
 
             <br>
 
             <br>
−
             Of course, users don't need to recite so many command codes. All you need may be a single mouse. Moreover,  
+
             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.
 
             our software performs a better user experience by presenting supreme graphical result display.
 
             <br>
 
             <br>
−
             Through this things, Foresyn can literally predict, I mean, foresee the likely result or trend of an experiment conducted  
+
             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.
 
             by a synthetic biologist. Particularly, what it sees immediately transforms into what you see.
 
           </div>
 
           </div>
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           <h3>Comparison</h3>
 
           <h3>Comparison</h3>
 
           <div class="passage">
 
           <div class="passage">
−
             Still Unfinished.
+
             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.
 +
            <br>
 +
            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.
 +
            <br>
 +
            <div class="table_show">
 +
              <table class="table table-striped table-hover text-center table-bordered">
 +
                <thead>
 +
                <tr>
 +
                  <td></td>
 +
                  <td>CellNetAnalyzer</td>
 +
                  <td>Cobra</td>
 +
                  <td>BioSPICE MOMA</td>
 +
                  <td>MetaFluxNet</td>
 +
                  <td>PathFluxNet</td>
 +
                  <td>Fbatool</td>
 +
                </tr>
 +
                </thead>
 +
                <tbody>
 +
                <tr>
 +
                  <td>Graphical</td>
 +
                  <td>&#x2714;</td>
 +
                  <td>&#x2718;</td>
 +
                  <td>&#x2718;</td>
 +
                  <td>&#x2714;</td>
 +
                  <td>&#x2718;</td>
 +
                  <td>&#x2718;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>Operating System</td>
 +
                  <td>Windows</td>
 +
                  <td>Windows</td>
 +
                  <td>Windows Linux</td>
 +
                  <td>Windows</td>
 +
                  <td>Linux UNIX</td>
 +
                  <td>Corona</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>Algorithm</td>
 +
                  <td>MFA SNA</td>
 +
                  <td>FBA MOMA DFBA FVA</td>
 +
                  <td>FBA MOMA</td>
 +
                  <td>MFA</td>
 +
                  <td>FBA MOMA</td>
 +
                  <td>FBA</td>
 +
                </tr>
 +
                </tbody>
 +
              </table>
 +
            </div>
 +
            <br>
 +
            <div class="psgImg">
 +
              <img alt="" src="undefined">
 +
              <p>The GUI of CellNetAnalyzer</p>
 +
            </div>
 +
            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.
 +
            <br>
 +
            <div class="psgImg">
 +
              <img alt="" src="undefined">
 +
              <p>One simulation by simbiology</p>
 +
            </div>
 +
            <br>
 +
            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!
 
           </div>
 
           </div>
 
           <h3>Slogan</h3>
 
           <h3>Slogan</h3>
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Revision as of 04:25, 20 October 2019

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.
...