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

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          <h1 class="text-center">Description</h1>
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          <h3>Background</h3>
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          <div class="passage">
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            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.
 +
            <br>
 +
            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.
 +
          </div>
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          <h3>Inspiration</h3>
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          <div class="passage">
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            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.
 +
            <br>
 +
            Obviously, current tools cannot satisfy the need. Thus, here comes "ForeSyn", the software born to solve the problem.
 +
          </div>
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          <h3>Project</h3>
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          <div class="passage">
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            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.
 +
            <br>
 +
            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.
 +
            <br>
 +
            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.
 +
            <br>
 +
            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.
 +
          </div>
 +
          <h3>Features</h3>
 +
          <div class="passage">
 +
            Lessen Your Needless Works
 +
            <br>
 +
            What You See Is What You Get
 +
            <br>
 +
            No Command Prompt Using Need
 +
            <br>
 +
            Comprehensive Customized Database
 +
          </div>
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          <h3>Comparison</h3>
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          <div class="passage">
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            I don't know what to write.
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          </div>
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          <h3>Slogan</h3>
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          <div class="passage">
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            Foresyn has foreseen the experiments, that helps synthetic biologists see further.
 +
            <br>
 +
            Foresyn foresees the synthetic biological experiments, and makes you see further.
 +
            <br>
 +
            Foresyn makes the experiments foreseen, and makes you see further.
 +
            <br>
 +
            ...
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          </div>
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        </div>
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    <h1>ForeSYN</h1>
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    <p>A Metabolic network software based on gene expression and meabolic network modeling </p>
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    <h3>Inspiration</h3>
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    <p>Since we’ve been doing the similar projects with even same names, we want to have a change this year. Not only
+
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        doing same things is quite boring, but we wish to do something that is really in need. After visited a synthetic
+
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        biologist in our school, chatted a lot, we came up with an idea. Our professor mention that a software can help
+
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        him a lot is one can tell him what changes will happen to the various ingredients after he changes the metabolic
+
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        pathway, especially the coenzymes. Considering it’s absolute more interesting than making a search engine, we
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        set our project as it.</p>
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    <p>Generally, our project focuses on the proportion of the coenzymes after adjusting the metabolic pathway. Giving
+
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        the variation range of the concentration of the coenzymes will greatly lessen the pressure of synthetic
+
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        biologists while doing experiments and reduce the time or money cost of many trials.</p>
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    <h3>Project</h3>
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    <h4>1.Method</h4>
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    <p>This is method description.</p>
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            <li>
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                By analyzing and modeling the gene expression and metabolic network, our software can get the range of
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                the concentration or proportion of the intermediate reactant after changing or adjusting a metabolic
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                pathway.
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            <li>
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                Compared with other metabolic prediction software, we more consider whether the concentration of
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                coenzymes, for example NADH/NAD+ is in the best range.
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            </li>
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            <li>
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                Even included some data visualization work so that it’s convenient for the experimenter to analyze the
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                bacteria and optimize the experimental design.
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            </li>
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            <li>
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+
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                Recognizing the database of metabolic network or packages of the prediction tools are still not robust
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                or complete for us to use, we first do several work of database integrations.
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            </li>
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            <li>
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                To make our software more usable, we design a set of algorithms, creating a recommendation system.
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            </li>
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            <li>
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                We managed to create a platform where the synthetic biologist can easily share their ideas and issue
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                their results.
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Revision as of 13:07, 16 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

I don't know what to write.

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.
...