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

 
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      <div class="card page-content" style="background: rgba(255, 255, 255, 0.6);">
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          <h1 class="text-center">Description</h1>
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<div class="text-center psgImg">
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              <img src="https://static.igem.org/mediawiki/2019/d/d4/T--USTC-Software--design.png" alt="" style="max-height:120%">
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            </div>
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          <h3>Background</h3>
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          <div class="passage">
 +
            Since we wanted to develop the software that indeed solve wet-lab problems using our software solutions, we went to collaborate with Team USTC in our school, doing experiments for a period in their lab. During our learning at the lab, we found some problems, I mean, some needless and superfluous issues which may be reduced by our good software. Also, we learned a lot from our PI, got a better understanding of synthetic biology.
 +
            <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 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>
 +
          <h3>Inspiration</h3>
 +
          <div class="passage">
 +
Before we went to Huaheng Biotech, the company in the leading position around the world in the field of alanine products producing using microbiological fermentation methods, actually, we were still confused about which kind of project we should do. During this trip, their technical backbone kept complaining about the inconvenience and unreliability of their research. We talked a lot with the leader about what we have seen. Naturally, we had such thoughts below and gradually came up with our project idea.<br><br>
  
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<div class="column full_size">
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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>
 +
            <br>
 +
            Obviously, current tools cannot satisfy the need. Thus, here comes "ForeSyn", the software born to solve the problem.
 +
          </div>
 +
          <h3>Project</h3>
 +
          <div class="passage">
 +
            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>
 +
            <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. Meanwhile, our biobricks recommendation system can greatly reduce the experimenters' needless searching time.
 +
            <br>
 +
            <br>
 +
            Generally, the workflow can be described as follows. First and foremost, by using our simple GUI, the user can easily select or upload a base model and choose to edit it with our accurate recommendation and precise prediction. Then, the user gets his/her customized model. Users can add it to favorite, get biobricks recommendation and share it out to get comment and rank. In addition, users can get the view of their history, making it much more user-friendly. Last, Foresyn will use many efficient and reliable methods to analysis your model and give a bright output.
 +
            <br><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>
 +
            <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>Breakthrough</h3>
 +
            <div class="passage">
 +
              Probably you know that currently there are plenty of pathway or network prediction software tools already
 +
              existed, and may regard our project a repeated work. It's a <b>total misunderstanding</b>.
 +
              <br>
 +
              <br>
 +
              We made a breakthrough in both in-silico designing and system and synthetic biology. Our project is the
 +
              first and presently the only one that successfully applies regulatory flux balance analysis (rFBA) in our
 +
              in-silico models. Compared with those simple network analysis tools, our Foresyn can consider the
 +
              regulatory network, and add constraints based on FBA, which compresses the solution space and makes the
 +
              result more exact and credible. It's a bold choice to combine the metabolic network with transcription
 +
              regulation, but we made it. Such improvement also urged us to integrate a more comprehensive database and
 +
              ensure the use of biobricks.
 +
              <br>
 +
              <br>
 +
              Therefore, by adding rFBA as a function, we made our project useful from beginning to the end. We have a
 +
              marvelous biobricks recommendation, while we have an amazingly cool graphical UI to present the result. Of
 +
              course, the adoption of rFBA network guarantees us software can fit all kinds of conditions and makes the
 +
              Foresyn's solutions more authentic.
 +
            </div>
 +
          <h3>Features</h3>
 +
            <div class="passage"><b>
 +
              Lessen Your Needless Works
 +
              </b><br>
 +
              <br>
 +
              <div style="display: flex; justify-content: space-around">
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                <div style="width: 500px;">
 +
                  Foresyn can show you the exact thing you want. You will no longer suffer from needless searching.
 +
                </div>
 +
                <img src="https://static.igem.org/mediawiki/2019/a/af/T--USTC-Software--des_feature_lesson.svg" alt="" style="max-width: 500px;">
 +
              </div>
 +
              <br><b>
 +
              What You See Is What You Get
 +
              </b><br>
 +
              <br>
 +
              <div style="display: flex; justify-content: space-around">
 +
                <div style="width: 500px;">
 +
                    Foresyn is extraordinarily smooth and beautiful. You can get wonderful information from it without delay.
 +
                </div>
 +
                <img src="https://static.igem.org/mediawiki/2019/b/b0/T--USTC-Software--des_feature_whatyousee.svg" alt="" style="max-width: 500px;">
 +
              </div>
 +
              <br><b>
 +
              No Command Prompt Using Need
 +
              </b><br>
 +
              <br>
 +
              <div style="display: flex; justify-content: space-around">
 +
                <div style="width: 500px;">
 +
                    Foresyn has a splendid graphical UI. You can use it with ease, and you don't need to study the command prompt.
 +
                </div>
 +
                <img src="https://static.igem.org/mediawiki/2019/0/0c/T--USTC-Software--des_feature_nocmd.svg" alt="" style="max-width: 500px;">
 +
              </div>
 +
              <br><b>
 +
              Comprehensive Customized Database
 +
              </b><br>
 +
              <br>
 +
              <div style="display: flex; justify-content: space-around">
 +
                <div style="width: 500px;">
 +
                    Foresyn integrates a fabulous database. You can get all kinds of information and get your personal one.
 +
                </div>
 +
                <img src="https://static.igem.org/mediawiki/2019/1/1a/T--USTC-Software--des_feature_database.svg" alt="" style="max-width: 500px;">
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              </div>
 +
              <br>
 +
            </div>
 +
          <h3>Comparison</h3>
 +
          <div class="passage">
 +
            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
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            and calculation. However, it bases on the Matlab and requires a relatively long time to learn how to use it.
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            And it’s hard to compare two model with each other.
 +
            <br>
 +
            <br>
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            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
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            Windows, which will cause a lot of troubles.
 +
            <br>
 +
            <div class="table_show">
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              <table class="table table-striped table-hover text-center table-bordered">
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                <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>✔</td>
 +
                  <td>✘</td>
 +
                  <td>✘</td>
 +
                  <td>✔</td>
 +
                  <td>✘</td>
 +
                  <td>✘</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>Operating System</td>
 +
                  <td>Windows</td>
 +
                  <td>Windows</td>
 +
                  <td>Windows Linux</td>
 +
                  <td>Windows</td>
 +
                  <td>Linux UNIX</td>
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                  <td>Corona</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>Algorithm</td>
 +
                  <td>MFA SNA</td>
 +
                  <td>FBA MOMA DFBA FVA</td>
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                  <td>FBA MOMA</td>
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                  <td>MFA</td>
 +
                  <td>FBA MOMA</td>
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                  <td>FBA</td>
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                </tr>
 +
                </tbody>
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              </table>
 +
            </div>
 +
            <br>
 +
            <div class="psgImg">
 +
              <img alt="" src="https://static.igem.org/mediawiki/2019/b/b2/T--USTC-Software--des_compari_2.png">
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              <p>The GUI of CellNetAnalyzer</p>
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            </div>
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            And we have also done some researches on simbiology, a tool in Matlab referred by Yonghao Liang, a senior
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            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
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            whole model.
 +
            <br>
 +
            <div class="psgImg">
 +
              <img alt="" src="https://static.igem.org/mediawiki/2019/8/85/T--USTC-Software--des_compari_3.png">
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              <p>One simulation by simbiology</p>
 +
            </div>
 +
            <br>
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            Our tool is more user-friendly because you can use it directly online, and you don't need to learn a new
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            programming language. Just a few inputs are required, but you can get a complete analysis!
 +
          </div>
 +
          <h3>Slogan</h3>
 +
          <div class="passage">
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            Foresyn foresees the synthetic biological experiments, and makes you see further.
 +
          </div>
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          <h2 class="ref">References</h2>
 +
            <div class="ref-list">
 +
              <ul>
 +
                <li>Covert M W, Palsson B Ø. Transcriptional regulation in constraints-based metabolic models of
 +
                  Escherichia coli[J]. Journal of Biological Chemistry, 2002, 277(31): 28058-28064.</li>
 +
              </ul>
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            </div>
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        </div>
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      </div>
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    </div>
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  </div>
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    <h1>Metpredictor</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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    <h4>2.Fuction</h4>
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        <ol>
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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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                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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                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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                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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                To make our software more usable, we design a set of algorithms, creating a recommendation system.
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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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Latest revision as of 22:41, 21 October 2019

Description

Background

Since we wanted to develop the software that indeed solve wet-lab problems using our software solutions, we went to collaborate with Team USTC in our school, doing experiments for a period in their lab. During our learning at the lab, we found some problems, I mean, some needless and superfluous issues which may be reduced by our good software. Also, we learned a lot from our PI, got a better understanding of synthetic biology.

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

Before we went to Huaheng Biotech, the company in the leading position around the world in the field of alanine products producing using microbiological fermentation methods, actually, we were still confused about which kind of project we should do. During this trip, their technical backbone kept complaining about the inconvenience and unreliability of their research. We talked a lot with the leader about what we have seen. Naturally, we had such thoughts below and gradually came up with our project idea.

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. Meanwhile, our biobricks recommendation system can greatly reduce the experimenters' needless searching time.

Generally, the workflow can be described as follows. First and foremost, by using our simple GUI, the user can easily select or upload a base model and choose to edit it with our accurate recommendation and precise prediction. Then, the user gets his/her customized model. Users can add it to favorite, get biobricks recommendation and share it out to get comment and rank. In addition, users can get the view of their history, making it much more user-friendly. Last, Foresyn will use many efficient and reliable methods to analysis your model and give a bright output.

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.

Breakthrough

Probably you know that currently there are plenty of pathway or network prediction software tools already existed, and may regard our project a repeated work. It's a total misunderstanding.

We made a breakthrough in both in-silico designing and system and synthetic biology. Our project is the first and presently the only one that successfully applies regulatory flux balance analysis (rFBA) in our in-silico models. Compared with those simple network analysis tools, our Foresyn can consider the regulatory network, and add constraints based on FBA, which compresses the solution space and makes the result more exact and credible. It's a bold choice to combine the metabolic network with transcription regulation, but we made it. Such improvement also urged us to integrate a more comprehensive database and ensure the use of biobricks.

Therefore, by adding rFBA as a function, we made our project useful from beginning to the end. We have a marvelous biobricks recommendation, while we have an amazingly cool graphical UI to present the result. Of course, the adoption of rFBA network guarantees us software can fit all kinds of conditions and makes the Foresyn's solutions more authentic.

Features

Lessen Your Needless Works

Foresyn can show you the exact thing you want. You will no longer suffer from needless searching.

What You See Is What You Get

Foresyn is extraordinarily smooth and beautiful. You can get wonderful information from it without delay.

No Command Prompt Using Need

Foresyn has a splendid graphical UI. You can use it with ease, and you don't need to study the command prompt.

Comprehensive Customized Database

Foresyn integrates a fabulous database. You can get all kinds of information and get your personal one.

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 foresees the synthetic biological experiments, and makes you see further.

References

  • Covert M W, Palsson B Ø. Transcriptional regulation in constraints-based metabolic models of Escherichia coli[J]. Journal of Biological Chemistry, 2002, 277(31): 28058-28064.