Difference between revisions of "Team:USTC-Software"

 
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−
                        <img id="ustcsoftware" src="USTC-Software-ustcsoftware.svg" />
+
<img id="ustcsoftware" src="/wiki/images/e/ed/USTC-Software-ustcsoftware.svg">
  
−
                        <!--iGEM logo-->
+
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                        <img id="igem_logo" src="USTC-Software-igem_logo.png" style="" />
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<img id="igem_logo" src="/wiki/images/7/7e/USTC-Software-Igem_logo.png">
  
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                        <!--goto-->
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<!--goto-->
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                        <a id="goto" href="http://ustc.software">
+
<a id="goto" href="https://ustc.software">
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                            <img src="USTC-Software-biobless_logo.png" />
+
    <img src="/wiki/images/0/0c/USTC-Software-Biobless_logo.png">
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                            <p>GoTo</p>                           
+
    <p>GoTo</p>                           
−
                        </a>
+
</a>
−
                       
+
  
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                        <!--code for "BioBLESS"-->
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<!--code for "BioBLESS"-->
−
                        <div id="biobless">
+
<div id="biobless">
−
                            <div id="bio" class="bio">
+
    <div id="bio" class="bio">
−
                                <i>Bio</i>
+
        <i>Bio</i>
−
                            </div>
+
    </div>
−
                            <div id="bless_1" class="bless" style="">B</div>
+
    <div id="bless_1" class="bless">B</div>
−
                            <div id="bless_2" class="bless" style="">L</div>
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    <div id="bless_2" class="bless">L</div>
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                            <div id="bless_3" class="bless" style="">E</div>
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    <div id="bless_3" class="bless">E</div>
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                            <div id="bless_4" class="bless" style="">S</div>
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    <div id="bless_4" class="bless">S</div>
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                            <div id="bless_5" class="bless" style="">S</div>
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    <div id="bless_5" class="bless">S</div>
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</div>
  
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                        <img id="feature_4" src="USTC-Software-feature_4.svg" />
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 +
<img id="globe" src="/wiki/images/c/c4/USTC-Software-globe.svg">
  
 +
<!--five paragraphs for features-->
 +
<h2 id="hd_1" class="para" style="left:67.19%;top:19.02%;">
 +
    Logic<br>From a truth table to abstract logic circuits
 +
</h2>
 +
<p id="para_1" class="para" style="left:67.19%;top:20.30%;">
 +
  In BioBLESS, a truth table dialog box will be displayed for users to input<br>
 +
Boolean numbers 0/1. All you need to do is to click Boolean buttons and <br>
 +
then “Create”. The corresponding designed logic circuits with different <br>
 +
predicted performances will be automatically generated and displayed <br>
 +
in order. You can immediately and clearly see the configuration of a <br>
 +
designed logic circuit, which in most cases is supposed to be a compli-<br>
 +
cated multi-input circuit. Besides the function above, gates list will <br>
 +
provide many Boolean gates, and users can drag them freely to our <br>
 +
canvas to design logic circuits.
 +
</p>
 +
<h2 id="hd_2" class="para" style="left:2.03%;top:30.00%;">
 +
    Gene Network<br>See the detailed structure of a designed gene circuit
 +
</h2>
 +
<p id="para_2" class="para" style="left:2.03%;top:31.20%;">
 +
    A simple click on “Gene network” button will lead you to<br>
 +
another tab where the detailed structure of your designed <br>
 +
gene circuit is shown. When a gene circuit consists of many <br>
 +
Boolean gates, it is crucial to understand the internal sub-<br>
 +
stances and mechanisms. In this tab, you can see how <br>
 +
substances react with each other clearly, such as inhibition <br>
 +
and activation in or between Boolean gates.
 +
</p>
 +
<h2 id="hd_3" class="para" style="left:67.00%;top:46.00%;">
 +
    SIMULATION<br>Get concentration-time simulation results
 +
</h2>
 +
<p id="para_3" class="para" style="left:67.00%;top:47.20%;">
 +
    Given a designed gene circuit, such as a simple serial circuit composed of<br>
 +
an AND gate and an OR gate, you can use our default parameters and <br>
 +
change initial concentration of reactants to get simulation results. If you <br>
 +
want to get different results, you just need to change system parameters <br>
 +
such as the rate of reactions, namely, to fill constants into the dialog <br>
 +
boxes on our canvas. What’s more, simulation time slot is necessary as well to give
 +
concentration-time figures of the inputs and outputs of a given gene circuit.
 +
You are free to see the concentration-time evolution of every substance in
 +
designed gene circuits individually.
 +
</p>
 +
<h2 id="hd_4" class="para" style="left:1.00%;top:57%;">
 +
    ANALYSIS<br>Get robustness and sensitivity analysis
 +
</h2>
 +
<p id="para_4" class="para" style="left:1.00%;top:58.2%;">
 +
    While offering various functions, BioBLESS also serves as an <br>
 +
analysis tool for designed gene circuits. Having designed a gene <br>
 +
circuit, you can click the “Analysis” button to reset parameters of <br>
 +
initial concentrations and reaction rates. Meanwhile, BioBLESS <br>
 +
will set simulation slots and carry the simulation task <br>
 +
automatically. According to the perturbation ratio you <br>
 +
input, such as 20% or 30%, the concentration-time <br>
 +
curves of inputs and outputs will be shown toge-<br>
 +
ther to shed light on the robustness of a designed<br>
 +
gene circuit. Moreover, data processing and<br>
 +
demonstration will help users to better<br>
 +
understand the robustness of<br>
 +
designed gene circuits.
 +
</p>
 +
<h2 id="hd_5" class="para" style="left:65.00%;top:69.80%;">
 +
    DNA<br>Get the DNA sequence!
 +
</h2>
 +
<p id="para_5" class="para" style="left:65.00%;top:71.00%;">
 +
    Users have the freedom to drag specific BioBricks on our canvas and<br>
 +
    combine them into a functional gene circuit. Then the DNA sequence<br>
 +
    and other information of the designed circuit are available for users<br>
 +
    to check and download. Wet lab protocols are partly incorporated into<br>
 +
    our DNA sequences which may make the design better and applicable in<br>
 +
    laboratories.
 +
</p>
  
−
                       
+
<!--attributions, copyrights and address-->
 +
<p id="ustc_address">
 +
    University of Science and Technology of China<br>
 +
    No.96, Jinzhai Road, Hefei, Anhui, P.R.China<br>
 +
    USTC-Software 2015
 +
</p>
 +
<p id="ustc">
 +
    University of Science and Technology of China
 +
</p>
 +
<p id="copyright">
 +
    &copy;2015 USTC-Software, University of Science and Technology of China. All rights reserved.
 +
</p>
 +
<div id="contact">                       
 +
    <p>We are here for you</p>
 +
    <img id="via_facebook" class="contact" src="/wiki/images/f/f1/USTC-Software-Facebook_logo.png">
 +
    <img id="via_twitter" class="contact" src="/wiki/images/5/55/USTC-Software-Twitter_logo.png">
 +
    <img id="via_gmail" class="contact" src="/wiki/images/3/3b/USTC-Software-Gmail_logo.png">
 +
    <img id="via_github" class="contact" src="/wiki/images/d/dc/USTC-Software-Github_logo.png">
 +
</div>
 +
<div id="sponseror">                   
 +
    <p>Sponsered by</p>                     
 +
    <img id="dbsc_white" src="/wiki/images/b/b2/USTC-Software-Dbsc_white.png">
 +
</div>
 +
<script>
 +
$(function() {
 +
    USTC.load_css_wiki("style/Home");
 +
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 +
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 +
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                        <!--code for svg#globe-->
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−
 
+
−
                        <!--five paragraphs for features-->
+
−
                        <h2 id="hd_1" class="para" style="left:67.19%;top:19.02%;">
+
−
                            BRIDGE<br />From a truth table to abstract logic circuits
+
−
                        </h2>
+
−
                        <p id="para_1" class="para" style="left:67.19%;top:20.30%;">
+
−
                            In BioBLESS, a truth table dialog box will be displayed to get inputted<br />
+
−
                            Boolean numbers 0/1 by. You just need to input 0/1 and click “Create”,<br />
+
−
                            then the gene circuit corresponding to the truth table will be displayed.<br />
+
−
                            Truth table will be automatically transformed into gene circuit, you can<br />
+
−
                            see the configuration of a designed gene circuit immediately and clearly,
+
−
                            such as a NOR gate.
+
−
                        </p>
+
−
                        <h2 id="hd_2" class="para" style="left:2.03%;top:30.00%;">
+
−
                            GENE CIRCUIT<br />See the detailed structure of a designed gene circuit
+
−
                        </h2>
+
−
                        <p id="para_2" class="para" style="left:2.03%;top:31.20%;">
+
−
                            A single click on “?” button will bring you to another tab<br />
+
−
                            where the detailed structure of your designed gene circuit<br />
+
−
                            is shown. If you want to see the abstract structure, just<br />
+
−
                            click “?” button and you will see configuration of every<br />
+
−
                            Boolean gate hidden behind gate symbols.
+
−
                        </p>
+
−
                        <h2 id="hd_3" class="para" style="left:67.00%;top:46.00%;">
+
−
                            SIMULATION<br />Get concentration-time simulation results
+
−
                        </h2>
+
−
                        <p id="para_3" class="para" style="left:67.00%;top:47.20%;">
+
−
                            Given a designed gene circuit, such as a simple serial circuit<br />
+
−
                            composed of an AND gate and a OR gate, you only need to input<br />
+
−
                            parameters to confirm the initial concentration of reactants<br />
+
−
                            and the rate of reactions, namely, to fill constant into the<br />
+
−
                            dialog boxes corresponding to designed gene circuits on our<br />
+
−
                            canvas. Simulation time slot is needed as well to give<br />
+
−
                            concentration-time figures of the inputs and outputs of a<br />
+
−
                            given gene circuit.
+
−
                        </p>
+
−
                        <h2 id="hd_4" class="para" style="left:1.00%;top:57%;">
+
−
                            ANALYSIS<br />Get robustness and sensitivity analysis
+
−
                        </h2>
+
−
                        <p id="para_4" class="para" style="left:1.00%;top:58.2%;">
+
−
                            While offering various functions, BioBLESS also serves as<br />
+
−
                            analysis tool for designed gene circuit. When you have<br />
+
−
                            designed a gene circuit, you can click the “analysis”<br />
+
−
                            button to reset robustness analysis parameters. Meanwhile,<br />
+
−
                            BioBLESS will set simulation slots and carry the simulation<br />
+
−
                            task automatically. According to the<br />
+
−
                            perturbation-to-background ratio you input, such as 20%<br />
+
−
                            or 30%, the concentration-time curves of inputs and<br />
+
−
                            outputs will be shown together to give<br />
+
−
                            a visualized intuition on the robustness<br />
+
−
                            of a designed gene circuit.
+
−
                        </p>
+
−
                        <h2 id="hd_5" class="para" style="left:65.00%;top:69.80%;">
+
−
                            DNA<br />Get the DNA sequence!
+
−
                        </h2>
+
−
                        <p id="para_5" class="para" style="left:65.00%;top:71.00%;">
+
−
                            Users have the freedom to drag specific BioBricks on our canvas and<br />
+
−
                            combine them into a functional gene circuit. Then the DNA sequence<br />
+
−
                            and other information of the designed circuit are available for users<br />
+
−
                            to check and download. Wet lab protocols are partly incorporated into<br />
+
−
                            our DNA sequences which may make the design better and applicable in<br />
+
−
                            laboratories.
+
−
                        </p>
+
−
                       
+
−
                       
+
−
                        <!--attributions, copyrights and address-->
+
−
                        <p id="ustc_address">
+
−
                            Unversity of Science and Technology of China<br />
+
−
                            No.96, Jinzhai Road, Hefei, Anhui, P.R.China<br />
+
−
                            USTC-Software 2015
+
−
                        </p>
+
−
                        <p id="ustc">
+
−
                            Unversity of Science and Technology of China
+
−
                        </p>
+
−
                        <p id="copyright">
+
−
                            &copy;2015 USTC-Software, Unversity of Science and Technology of China. All rights reserved.
+
−
                        </p>
+
−
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+
−
                            <p>We are here for you</p>
+
−
                            <img id="via_facebook" class="contact" src="USTC-Software-facebook_logo.png" />
+
−
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+
−
                            <img id="via_gmail" class="contact" src="USTC-Software-gmail_logo.png" />
+
−
                            <img id="via_github" class="contact" src="USTC-Software-github_logo.png" />
+
−
                        </div>
+
−
                        <div id="sponseror">                   
+
−
                            <p>Sponsered by</p>                     
+
−
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+
−
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Latest revision as of 01:17, 19 September 2015

GoTo
Bio
B
L
E
S
S

Logic
From a truth table to abstract logic circuits

In BioBLESS, a truth table dialog box will be displayed for users to input
Boolean numbers 0/1. All you need to do is to click Boolean buttons and
then “Create”. The corresponding designed logic circuits with different
predicted performances will be automatically generated and displayed
in order. You can immediately and clearly see the configuration of a
designed logic circuit, which in most cases is supposed to be a compli-
cated multi-input circuit. Besides the function above, gates list will
provide many Boolean gates, and users can drag them freely to our
canvas to design logic circuits.

Gene Network
See the detailed structure of a designed gene circuit

A simple click on “Gene network” button will lead you to
another tab where the detailed structure of your designed
gene circuit is shown. When a gene circuit consists of many
Boolean gates, it is crucial to understand the internal sub-
stances and mechanisms. In this tab, you can see how
substances react with each other clearly, such as inhibition
and activation in or between Boolean gates.

SIMULATION
Get concentration-time simulation results

Given a designed gene circuit, such as a simple serial circuit composed of
an AND gate and an OR gate, you can use our default parameters and
change initial concentration of reactants to get simulation results. If you
want to get different results, you just need to change system parameters
such as the rate of reactions, namely, to fill constants into the dialog
boxes on our canvas. What’s more, simulation time slot is necessary as well to give concentration-time figures of the inputs and outputs of a given gene circuit. You are free to see the concentration-time evolution of every substance in designed gene circuits individually.

ANALYSIS
Get robustness and sensitivity analysis

While offering various functions, BioBLESS also serves as an
analysis tool for designed gene circuits. Having designed a gene
circuit, you can click the “Analysis” button to reset parameters of
initial concentrations and reaction rates. Meanwhile, BioBLESS
will set simulation slots and carry the simulation task
automatically. According to the perturbation ratio you
input, such as 20% or 30%, the concentration-time
curves of inputs and outputs will be shown toge-
ther to shed light on the robustness of a designed
gene circuit. Moreover, data processing and
demonstration will help users to better
understand the robustness of
designed gene circuits.

DNA
Get the DNA sequence!

Users have the freedom to drag specific BioBricks on our canvas and
combine them into a functional gene circuit. Then the DNA sequence
and other information of the designed circuit are available for users
to check and download. Wet lab protocols are partly incorporated into
our DNA sequences which may make the design better and applicable in
laboratories.

University of Science and Technology of China
No.96, Jinzhai Road, Hefei, Anhui, P.R.China
USTC-Software 2015

University of Science and Technology of China

We are here for you

Sponsered by

University of Science and Technology of China
No.96, Jinzhai Road, Hefei, Anhui, P.R.China
USTC-Software 2015

University of Science and Technology of China

We are here for you

Sponsered by