Difference between revisions of "Team:TecCEM/Software"
| Line 30: | Line 30: | ||
<div class="row" id="introduction"> | <div class="row" id="introduction"> | ||
<div class="col"> | <div class="col"> | ||
| − | <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> | + | <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> | ||
| + | <p>You can download our suite of software from the following link <a href="https://static.igem.org/mediawiki/2018/e/eb/T--TecCEM--Software.zip" download>Download</a></p> | ||
| + | <p>Alternatively you could following our latest improvements in the github page <a class="text-project" href="https://github.com/iGEM-TEC-CEM/Software-iGEM">Github</a></p> | ||
</div> | </div> | ||
</div> | </div> | ||
| Line 36: | Line 40: | ||
<div class="col"> | <div class="col"> | ||
<h1>Activity Log</h1> | <h1>Activity Log</h1> | ||
| − | <p>The activity log is a really simple piece of software, 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.</p> | + | <p>The activity log is a really simple piece of software, nevertheless very important. This part of |
| − | <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> | + | 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"> | <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" | <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/b/ba/T--TecCEM---sof1.png" | ||
| Line 72: | Line 81: | ||
<img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/c/c9/T--TecCEM--Activity-Log1.png" | <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/c/c9/T--TecCEM--Activity-Log1.png" | ||
alt="Default data activity-log"> | alt="Default data activity-log"> | ||
| − | <figcaption class="figure-caption text-xs-right">Figure 4. Default data config. vs. Data filtered by month | + | <figcaption class="figure-caption text-xs-right">Figure 4. Default data config. vs. |
| + | Data filtered by month | ||
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
</div> | </div> | ||
| − | + | ||
</div> | </div> | ||
<p>The advantages of this application are the following: | <p>The advantages of this application are the following: | ||
</p> | </p> | ||
<ul> | <ul> | ||
| − | + | <li>It keeps track and displays the most relevant data from the experiments in form of a plot. | |
| − | + | 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</li> | ||
| + | <li>It can be accessed from anywhere in the world</li> | ||
</ul> | </ul> | ||
| − | <br> | + | <br> |
<p> | <p> | ||
| − | + | ||
</p> | </p> | ||
</div> | </div> | ||
| Line 94: | Line 107: | ||
<div class="col"> | <div class="col"> | ||
<h1>Cell Count</h1> | <h1>Cell Count</h1> | ||
| − | <p>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 return the confluence percentage, as well as perform more tests on the software. | + | <p>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 return the confluence percentage, as well as perform more | ||
| + | tests on the software. | ||
</p> | </p> | ||
<p> | <p> | ||
| − | This software works for two kinds of cell colonies. | + | 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. | ||
</p> | </p> | ||
<figure class="figure text-center"> | <figure class="figure text-center"> | ||
| Line 123: | Line 141: | ||
</div> | </div> | ||
</div> | </div> | ||
| − | <br> | + | <br> |
<p>The cell counting algorithm works as follows:</p> | <p>The cell counting algorithm works as follows:</p> | ||
| − | <br> | + | <br> |
<figure class="figure text-center"> | <figure class="figure text-center"> | ||
<img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/b/bb/T--TecCEM---sof9.jpg" | <img class="figure-img img-fluid rounded" src="https://static.igem.org/mediawiki/2018/b/bb/T--TecCEM---sof9.jpg" | ||
| Line 157: | Line 175: | ||
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| − | <p>This software is planned to be a relief for a lot of researchers that make this process the hard | + | <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 | way. This will optimize time, effort and resources letting the scientists do more science and | ||
less counting.</p> | less counting.</p> | ||
Revision as of 18:14, 17 October 2018
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!
You can download our suite of software from the following link Download
Alternatively you could following our latest improvements in the github page Github
Activity Log
The activity log is a really simple piece of software, 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.
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.:
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
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.
The advantages of this application are the following:
- It keeps track and displays the most relevant data from the experiments in form of a plot. 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 can be accessed from anywhere in the world
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 return the confluence percentage, as well as perform more tests on the software.
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.
The cell counting algorithm works as follows:
In this example, we got an approximation of 990 cells counted.
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.