Difference between revisions of "Team:TJUSLS China/Software"

 
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.</p>
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            <a class="toggleMenu" href="">Menu</a>
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                <script>
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<h5> Inspiration </h5>
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<p>
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Here are a few examples from previous teams:
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<ul>
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<li><a href="https://2013.igem.org/Team:TU-Munich/Results/Software">TU Munich 2013</a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li>
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</ul>
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                </script>
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                <li onmouseover="getHover(0)"><a href="https://2016.igem.org/Team:TJUSLS_China">TJUSLS</a></li>
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                <li onmouseover="getHover(1)" class=""><a href="" class="root">project</a>
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                    <ul>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Description">Description</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Design">Design</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Experiments">Experiments</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Proof">Proof of Concept</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Demonstrate">Demonstrate</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Notebook">Notebook</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Results">Results</a></li>
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                    </ul>
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                </li>
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                <li onmouseover="getHover(2)" class=""><a href="https://2016.igem.org/Team:TJUSLS_China/Parts">PARTS</a>
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                    <ul>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Basic_Part">Basic Parts</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Composite_Part">Composite Parts</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Part_Collection">Part Collection</a></li>
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                    </ul>
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                <li class="active" onmouseover="getHover(3)"><a class="active" href="https://2016.igem.org/Team:TJUSLS_China/Safety">SAFETY</a></li>
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                <li onmouseover="getHover(4)" class=""><a href="https://2016.igem.org/Team:TJUSLS_China/Attributions">ATTRIBUTIONS</a>
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                </li>
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                <li onmouseover="getHover(5)" class=""><a href="https://2016.igem.org/Team:TJUSLS_China/Human_Practices">HUMAN PRACTICES</a>
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                    <ul>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/HP/Silver">Silver</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/HP/Gold">Gold</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Integrated_Practices">Integrated Practices</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Engagement">Engagement</a></li>
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                    </ul>
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                </li>
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                <li onmouseover="getHover(6)" class=""><a href="https://2016.igem.org/Team:TJUSLS_China/Modeling">MODELING</a>
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                    <ul>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Modeling">Modeling</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Software">Software</a></li>
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                    </ul>
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                </li>
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                <li onmouseover="getHover(7)" class=""><a href="https://2016.igem.org/Team:TJUSLS_China/Team">TEAM</a>
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                    <ul>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Team">Team</a></li>
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                        <li><a href="https://2016.igem.org/Team:TJUSLS_China/Collaborations">Collaborations</a></li>
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                    </ul>
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                </li>
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            </ul>
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        <img class="sec-menu-close" src="https://static.igem.org/mediawiki/2016/b/b5/T--TJUSLS_China--sec-menu-close.png"/>
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        <ul>
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            <li><a href="#part1">Introduction</a></li>
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            <li><a href="#part2">Run the Software</a></li>
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            <li><a href="#part3">Operation</a></li>
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            <li><a href="#part4">Code</a></li>
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        </ul>
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    Software
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        <div class="fengmian">
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            <h2>Operation Guide Book of Calculate Software</h2>
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            <br><br><br>
 +
            <h4>TJUSLS_China Modeling Group</h4>
 +
        </div>
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        <h3 id="part1">Introduction</h3>
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        <div class="sec-wenzi-content">We utilize High Performance Liquid Chromatography (HPLC) in gaining the production. Our experiment needs a mass of HPLC data. However, it is not convenient to use the integrating software of HPLC apparatus. So we developed a software to process HPLC data using the MATLAB GUI module.
 +
            <br>Our software can calculate peak area of any substance by the raw data of HPLC conveniently and accurately. It can display the image details saved at any period of time. It also can automatically identify substance peak and calculate the area. In addition, we can manually select the range of the area calculated. What’s more, in order to facilitate the analysis, it can store the results of calculations in a same file which contains the filename of the HPLC data.
 +
        </div>
  
 +
        <h3 id="part2">Run the Software</h3>
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        <div class="sec-wenzi-content">The software must run in MATLAB GUI environment.
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        <br>Open the MATLAB program in your computer, input “guide” on the “command window”, then press “enter” on the keyboard.
 +
</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/b/b5/T--TJUSLS_China--software_new1.png">
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        <div class="sec-wenzi-content">On the pop-up window “GUIDE Quick Start”, choose the “Open Existing GUI”, click “Browse” button. Find the software downloaded and open it. (<a href="https://2016.igem.org/File:T--TJUSLS_China--user.zip">Download link</a>) </div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/a/a0/T--TJUSLS_China--software_new2.png">
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        <img src="https://static.igem.org/mediawiki/2016/a/a7/T--TJUSLS_China--software_new3.png">
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 +
        <div class="sec-wenzi-content">Finally, click “▶” (Run Figure) button on the “fig” window. The software is open.
 +
        </div>
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        <img src="https://static.igem.org/mediawiki/2016/d/dc/T--TJUSLS_China--software_new4.png">
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        <div class="sec-wenzi-content">
 +
            If the GUIDE window pop-up, click the “Change Folder” button.</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/b/b4/T--TJUSLS_China--software_new5.png">
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        <h3 id="part3">Operation</h3>
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        <div class="sec-wenzi-list">Names and Functions of Parts</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/6/67/T--TJUSLS_China--software_new6.png">
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        <div class="sec-wenzi-content"><p style="text-align: center">Picture 1: interface of the software</p></div>
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        <div class="sec-wenzi-content"><b>Menu bar</b>: The functions of opening a new data file and close the window are available here in menu format.
 +
 +
            <br><b>Filename display bar</b>: Display the opened filename.
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            <br><b>Image display field</b>: Display the HPLC data image entirely or partly.
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            <br><b>Operation field</b>: When a data is input, process setting and calculate method can be selected using the mouse and the function keys located here.
 +
        </div>
 +
        <div class="sec-wenzi-list">Basic Operation</div>
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        <div class="sec-wenzi-content">Open a data file</div>
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        <div class="sec-wenzi-content">Verify the data file type before open it.
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            <br> Pure data file is as picture 2; data file with text is as picture 3.
 +
        </div>
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        <img src="https://static.igem.org/mediawiki/2016/d/d1/T--TJUSLS_China--software_new7.png">
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        <div class="sec-wenzi-content"><p style="text-align: center">Picture 2: pure data file</p></div>
 +
        <img src="https://static.igem.org/mediawiki/2016/2/2a/T--TJUSLS_China--software_new8.png">
 +
        <div class="sec-wenzi-content"><p style="text-align: center">Picture 3: data file with text</p></div>
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        <div class="sec-wenzi-content">If the data file is with text, ensure the radio button (Data file with text) in “Setting” is selected.
 +
            <br>If the data file is pure data, ensure it is unselected.
 +
        </div>
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        <img src="https://static.igem.org/mediawiki/2016/8/8b/T--TJUSLS_China--software_new9.png">
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        <div class="sec-wenzi-content">Click the menu bar “File-open”, data file can be opened in this window.</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/e/e6/T--TJUSLS_China--software_new10.png">
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 +
        <div class="sec-wenzi-content">When the filename is displayed, this file is opened successfully.</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/4/49/T--TJUSLS_China--software_new11.png">
 +
 +
        <div class="sec-wenzi-list"> Plot the data image </div>
 +
        <div class="sec-wenzi-content">
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            Click the “Plot All” button, the entire data image will be displayed.</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/e/ed/T--TJUSLS_China--software_new12.png">
 +
 +
        <div class="sec-wenzi-content">The detail of the image can be displayed when the “Plot Part” button is clicked.</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/9/92/T--TJUSLS_China--software_new13.png">
 +
        <div class="sec-wenzi-content">Its default range is 21min~22min for our objective peak is in this range.
 +
            This range can also be changed by inputting appropriate numbers in the textbox of “tmin” and “tmax”, then click the “Plot All” button, a new image can be displayed.</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/7/79/T--TJUSLS_China--software_new14.png">
 +
 +
        <div class="sec-wenzi-list">Calculate the peak area</div>
 +
 +
        <div class="sec-wenzi-content">If there is only one clear peak in this window, the peak area can be identified and calculated automatically by click the “Auto Calculate” button.</div>
 +
        <img src="https://static.igem.org/mediawiki/2016/d/d2/T--TJUSLS_China--software_new15.png">
 +
 +
        <div class="sec-wenzi-content">But when there are several peaks or the peak is unclear, it can’t be identified exactly. Then the manual calculate function can be used.
 +
            <br> First, click the “Manual Select” button, there will be a focus point. The range can be selected by clicking the image window.
 +
        </div>
 +
        <img src="https://static.igem.org/mediawiki/2016/3/3a/T--TJUSLS_China--software_new16.png">
 +
        <div class="sec-wenzi-content">Then click the “Manual Calculate” button, peak area of the range selected can be calculated.</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/7/7f/T--TJUSLS_China--software_new17.png">
 +
 +
        <div class="sec-wenzi-list">Output the peak area</div>
 +
        <div class="sec-wenzi-content">Click the “Save area” button, the filename of the HPLC data and the peak area will be save into a file whose name is “Peak_area”.</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/b/b6/T--TJUSLS_China--software_new18.png">
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/3/30/T--TJUSLS_China--software_new19.png">
 +
        <div class="sec-wenzi-content">Every time you click the “Save area” button, there will be one line data saved into this file.</div>
 +
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/0/06/T--TJUSLS_China--software_new20.png">
 +
 +
        <h3 id="part4">Code</h3>
 +
        <div class="sec-wenzi-list">Here is our program code:</div>
 +
 +
        <img src="https://static.igem.org/mediawiki/2016/b/be/T--TJUSLS_China--software_code1.png">
 +
        <br><img src="https://static.igem.org/mediawiki/2016/4/40/T--TJUSLS_China--software_code2.png">
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        <br><img src="https://static.igem.org/mediawiki/2016/5/53/T--TJUSLS_China--software_code3.png">
 +
        <br><img src="https://static.igem.org/mediawiki/2016/5/51/T--TJUSLS_China--software_code4.png">
 +
        <br><img src="https://static.igem.org/mediawiki/2016/6/6c/T--TJUSLS_China--software_code5.png">
 +
        <br><img src="https://static.igem.org/mediawiki/2016/4/42/T--TJUSLS_China--software_code6.png">
 +
        <br><img src="https://static.igem.org/mediawiki/2016/8/8a/T--TJUSLS_China--software_code7.png">
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Latest revision as of 12:34, 19 October 2016

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Software

Operation Guide Book of Calculate Software




TJUSLS_China Modeling Group

Introduction

We utilize High Performance Liquid Chromatography (HPLC) in gaining the production. Our experiment needs a mass of HPLC data. However, it is not convenient to use the integrating software of HPLC apparatus. So we developed a software to process HPLC data using the MATLAB GUI module.
Our software can calculate peak area of any substance by the raw data of HPLC conveniently and accurately. It can display the image details saved at any period of time. It also can automatically identify substance peak and calculate the area. In addition, we can manually select the range of the area calculated. What’s more, in order to facilitate the analysis, it can store the results of calculations in a same file which contains the filename of the HPLC data.

Run the Software

The software must run in MATLAB GUI environment.
Open the MATLAB program in your computer, input “guide” on the “command window”, then press “enter” on the keyboard.
On the pop-up window “GUIDE Quick Start”, choose the “Open Existing GUI”, click “Browse” button. Find the software downloaded and open it. (Download link)
Finally, click “▶” (Run Figure) button on the “fig” window. The software is open.
If the GUIDE window pop-up, click the “Change Folder” button.

Operation

Names and Functions of Parts

Picture 1: interface of the software

Menu bar: The functions of opening a new data file and close the window are available here in menu format.
Filename display bar: Display the opened filename.
Image display field: Display the HPLC data image entirely or partly.
Operation field: When a data is input, process setting and calculate method can be selected using the mouse and the function keys located here.
Basic Operation
Open a data file
Verify the data file type before open it.
Pure data file is as picture 2; data file with text is as picture 3.

Picture 2: pure data file

Picture 3: data file with text

If the data file is with text, ensure the radio button (Data file with text) in “Setting” is selected.
If the data file is pure data, ensure it is unselected.
Click the menu bar “File-open”, data file can be opened in this window.
When the filename is displayed, this file is opened successfully.
Plot the data image
Click the “Plot All” button, the entire data image will be displayed.
The detail of the image can be displayed when the “Plot Part” button is clicked.
Its default range is 21min~22min for our objective peak is in this range. This range can also be changed by inputting appropriate numbers in the textbox of “tmin” and “tmax”, then click the “Plot All” button, a new image can be displayed.
Calculate the peak area
If there is only one clear peak in this window, the peak area can be identified and calculated automatically by click the “Auto Calculate” button.
But when there are several peaks or the peak is unclear, it can’t be identified exactly. Then the manual calculate function can be used.
First, click the “Manual Select” button, there will be a focus point. The range can be selected by clicking the image window.
Then click the “Manual Calculate” button, peak area of the range selected can be calculated.
Output the peak area
Click the “Save area” button, the filename of the HPLC data and the peak area will be save into a file whose name is “Peak_area”.
Every time you click the “Save area” button, there will be one line data saved into this file.

Code

Here is our program code:






Copyright 2016 TJUSLS