Difference between revisions of "Team:TecCEM/Software"

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    <img src="https://static.igem.org/mediawiki/2018/a/aa/T--TecCEM--Cells.gif" alt="Cell Gif">
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    <h1>Software</h1>
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<h1>Software</h1>
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<div class="wrapper">
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<h3>Best Software Tool Special Prize</h3>
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    <nav class="sidebar-index">
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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.
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        <div class="sidebar-header">
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            <h3>Software</h3>
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        </div>
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        <a href="#softwareSubmenu" data-toggle="collapse" aria-expanded="false" data-change="sidemenu">
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            <span data-change="el" class="d-inline-block open"></span>
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            Index
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        </a>
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        <ul class="collapse list-unstyled" id="softwareSubmenu">
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            <li class="active">
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                <a data-target="#introduction">Introduction</a>
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            </li>
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            <li class="active">
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                <a data-target="#activity">Activity Log</a>
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            </li>
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            <li class="active">
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                <a data-target="#cellcount">Cell Count</a>
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            </li>
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        </ul>
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    </nav>
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    <div class="content">
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        <div class="container my-3" id="description">
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            <div class="row" id="introduction">
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                <div class="col">
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                    <p class="lead">For this year’s software, we developed a web application with three main
 +
                        functionalities, a cell counter, a BioBrick builder and an activity log for our hardware. Up
 +
                        next, we will explain each one of them!</p>
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                </div>
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            </div>
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            <div class="row" id="activity">
 +
                <div class="col">
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                    <h1>Activity Log</h1>
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                    <p>The activity log is a really simple piece of software but nevertheless very important. This part
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                        of the web application is where the software and the hardware converge into a single solution.
 +
                        The user interface is really basic and minimalistic and shows the data obtained from the
 +
                        hardware as a table and as a graph.</p>
 +
                    <p>To distinguish between all the different projects from different people we use a login.
 +
                        First-time users need to register into the platform which will create an account for them. Once
 +
                        this is done, the person can register different projects. </p>
 +
                    <figure class="figure text-center">
 +
                        <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/b/ba/T--TecCEM---sof1.png"
 +
                            alt="signup activity-log">
 +
                        <figcaption class="figure-caption text-xs-right">Figure 1. Sign up </figcaption>
 +
                    </figure>
 +
                    <p>The project signup is a bit more complex because we need a way to link the automation system
 +
                        (hardware) with the platform. First of all, it is necessary to have BoB, its automation system
 +
                        and a computer with Arduino installed on it. </p>
 +
                    <p>Once we have this two things ready, open the arduino code called “auto.ino” - you can get the
 +
                        code from this repository <a class="text-project" href="https://github.com/SantiagoMille/BoB_Automation">Github
 +
                            Link</a>
 +
                        - and set up your
 +
                        local wifi network as shown in <strong>Figure 2.</strong>:</p>
 +
                    <figure class="figure text-center w-100">
 +
                        <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/2/29/T--TecCEM---sof2.png"
 +
                            alt="configuration activity-log">
 +
                        <figcaption class="figure-caption text-xs-right">Figure 2. Code configuration. </figcaption>
 +
                    </figure>
 +
                    <p>Then, we need to connect our NodeMCU board to the computer, load the program and open the serial
 +
                        monitor. In this monitor a token will be displayed, we need to copy and paste it in the Project
 +
                        Code input as shown in <strong>Figure 3</strong></p>
 +
                    <figure class="figure text-center w-100">
 +
                        <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/d/d5/T--TecCEM---sof3.png"
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                            alt="Adding Project activity-log">
 +
                        <figcaption class="figure-caption text-xs-right">Figure 3. Adding a new project. </figcaption>
 +
                    </figure>
 +
                    <p>Once we have an account and a project set, we can visualize the data sensed from Bob. The data
 +
                        can be filtered depending on the date selected. The default setup shows all the data obtained
 +
                        throughout the projects time. </p>
 +
                    <div class="row">
 +
                        <div class="col">
 +
                            <figure class="figure text-center w-100">
 +
                                <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/e/e9/T--TecCEM---sof4.png"
 +
                                    alt="Default data activity-log">
 +
                                <figcaption class="figure-caption text-xs-right">Figure 4. All data of default project.
 +
                                </figcaption>
 +
                            </figure>
 +
                        </div>
 +
                        <div class="col">
 +
                            <figure class="figure text-center w-100">
 +
                                <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/4/41/T--TecCEM---sof5.png"
 +
                                    alt="Default data with filter activity-log 2">
 +
                                <figcaption class="figure-caption text-xs-right">Figure 5. All data of default project
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                                    filtered by month.
 +
                                </figcaption>
 +
                            </figure>
 +
                        </div>
 +
                    </div>
 +
                    <p>The advantages of this application are the following; firstly it keeps track and displays it in
 +
                        form of a plot with the most relevant data of the experiments done inside BoB. For example, it
 +
                        could be possible to watch how is it that the color of the medium is changing and after some
 +
                        time relate this plots to the cell proliferation or the time it takes for some cell colonies to
 +
                        grow.
 +
                    </p>
 +
                    <p>
 +
                        It also displays the CO2 and temperature which are extremely important variables of an
 +
                        incubator, the improvement we are seeking for our hardware.
 +
                    </p>
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                </div>
  
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            </div>
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<br><br>
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            <div class="row" id="cellcount">
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
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                <div class="col">
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<br><br>
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                    <h1>Cell Count</h1>
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You must also delete the message box on the top of this page to be eligible for this prize.
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                    <p>The cell count software is a beta version image processing program that takes an input image and
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</p>
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                        outputs a close estimate of the number of cells in the picture. The main reasons of it to still
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                        be a beta is because we would like to perform more tests on it, and once it’s done, that will
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                        return the proliferation percentage.
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</div>
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                    </p>
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                    <p>
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<div class="column third_size">
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                        This software works for two kinds of cell colonies. To use it, it is necessary to access the
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<div class="highlight decoration_A_full">
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                        web application and go to the section of Cell Count found on the top left hand. Upload your
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<h3> Inspiration </h3>
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                        picture and wait for the results.
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<p>
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                    </p>
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Here are a few examples from previous teams:
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                    <figure class="figure text-center">
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</p>
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                        <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/e/ea/T--TecCEM---sof6.png"
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<ul>
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                            alt="cell selection cellcount">
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<li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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                        <figcaption class="figure-caption text-xs-right">Figure 6. Cell Selection Cell Count
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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                        </figcaption>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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                    </figure>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">2014 Aachen</a></li>
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                    <div class="row">
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</ul>
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                        <div class="col">
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</div>
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                            <figure class="figure text-center">
 +
                                <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/4/46/T--TecCEM---sof7.png"
 +
                                    alt="result 1 cellcount">
 +
                                <figcaption class="figure-caption text-xs-right">Figure 7. Result Test 1 Cell Count
 +
                                </figcaption>
 +
                            </figure>
 +
                        </div>
 +
                        <div class="col">
 +
                            <figure class="figure text-center">
 +
                                <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/0/0a/T--TecCEM---sof8.png"
 +
                                    alt="result 2 cellcount">
 +
                                <figcaption class="figure-caption text-xs-right">Figure 8. Result Test 2 Cell Count
 +
                                </figcaption>
 +
                            </figure>
 +
                        </div>
 +
                    </div>
 +
                    <p>This software is planned to be a relief for a lot of researchers that make this process the hard
 +
                        way. This will optimize time, effort and resources letting the scientists do more science and
 +
                        less counting.</p>
 +
                </div>
 +
            </div>
 +
        </div>
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    </div>
 
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Revision as of 12:40, 17 October 2018

Cell Gif

Software

For this year’s software, we developed a web application with three main functionalities, a cell counter, a BioBrick builder and an activity log for our hardware. Up next, we will explain each one of them!

Activity Log

The activity log is a really simple piece of software but nevertheless very important. This part of the web application is where the software and the hardware converge into a single solution. The user interface is really basic and minimalistic and shows the data obtained from the hardware as a table and as a graph.

To distinguish between all the different projects from different people we use a login. First-time users need to register into the platform which will create an account for them. Once this is done, the person can register different projects.

signup activity-log
Figure 1. Sign up

The project signup is a bit more complex because we need a way to link the automation system (hardware) with the platform. First of all, it is necessary to have BoB, its automation system and a computer with Arduino installed on it.

Once we have this two things ready, open the arduino code called “auto.ino” - you can get the code from this repository Github Link - and set up your local wifi network as shown in Figure 2.:

configuration activity-log
Figure 2. Code configuration.

Then, we need to connect our NodeMCU board to the computer, load the program and open the serial monitor. In this monitor a token will be displayed, we need to copy and paste it in the Project Code input as shown in Figure 3

Adding Project activity-log
Figure 3. Adding a new project.

Once we have an account and a project set, we can visualize the data sensed from Bob. The data can be filtered depending on the date selected. The default setup shows all the data obtained throughout the projects time.

Default data activity-log
Figure 4. All data of default project.
Default data with filter activity-log 2
Figure 5. All data of default project filtered by month.

The advantages of this application are the following; firstly it keeps track and displays it in form of a plot with the most relevant data of the experiments done inside BoB. For example, it could be possible to watch how is it that the color of the medium is changing and after some time relate this plots to the cell proliferation or the time it takes for some cell colonies to grow.

It also displays the CO2 and temperature which are extremely important variables of an incubator, the improvement we are seeking for our hardware.

Cell Count

The cell count software is a beta version image processing program that takes an input image and outputs a close estimate of the number of cells in the picture. The main reasons of it to still be a beta is because we would like to perform more tests on it, and once it’s done, that will return the proliferation percentage.

This software works for two kinds of cell colonies. To use it, it is necessary to access the web application and go to the section of Cell Count found on the top left hand. Upload your picture and wait for the results.

cell selection cellcount
Figure 6. Cell Selection Cell Count
result 1 cellcount
Figure 7. Result Test 1 Cell Count
result 2 cellcount
Figure 8. Result Test 2 Cell Count

This software is planned to be a relief for a lot of researchers that make this process the hard way. This will optimize time, effort and resources letting the scientists do more science and less counting.