Difference between revisions of "Team:Valencia UPV/Software"

Line 98: Line 98:
 
                           opacity: 1;
 
                           opacity: 1;
 
                           ">Models &amp; Experiments</a>
 
                           ">Models &amp; Experiments</a>
−
                           <!--<ul style="list-style-type: circle;">
+
                            
−
                          <li><p>
+
−
                          <a href="#design_process" class="lateral inner-link" style="
+
−
                          color: #353535;
+
−
                          opacity: 1;
+
−
                          ">Modeling process</a>
+
−
                          </p></li>
+
−
                          <li><p>
+
−
                          <a href="#const_models" class="lateral inner-link" style="
+
−
                          color: #353535;
+
−
                          opacity: 1;
+
−
                          ">Constitutive expression models</a>
+
−
                          </p></li>
+
−
                          <li><p>
+
−
                          <a href="#ind_models" class="lateral inner-link" style="
+
−
                          color: #353535;
+
−
                          opacity: 1;
+
−
                          ">Inducible expression models</a>                 
+
−
                          </p></li>
+
−
                          <li><p>
+
−
                          <a href="#optimization" class="lateral inner-link" style="
+
−
                          color: #353535;
+
−
                          opacity: 1;
+
−
                          ">Multi-objective parameter optimization</a>
+
−
                          </p></li>
+
−
                          </ul>-->
+
 
                     </div>
 
                     </div>
 
                   </li>
 
                   </li>
Line 154: Line 129:
 
             <div>
 
             <div>
 
               <a class="anchorOffset" id="Software"></a>
 
               <a class="anchorOffset" id="Software"></a>
−
               <h3>Software</h3>
+
               <h3>Introduction</h3>
 
               <p>
 
               <p>
 
               <b>Do you think it is possible to mathematically describe a cell? Would you like to know the possibilities that modeling offers you?</b>
 
               <b>Do you think it is possible to mathematically describe a cell? Would you like to know the possibilities that modeling offers you?</b>
 
               </p>
 
               </p>
 
               <p>
 
               <p>
−
One of the fundamental bases of the Printeria project has undoubtedly been <b>mathematical modeling</b>. Thanks to the development and application of new mathematical models, it is possible to <b>quantify the expression of proteins</b> in cells, and therefore <b>characterize</b> through different experiments the parts designed by Printeria. From the Printeria Modeling team, we intend to reach different goals:
+
When it comes to automating the process of designing and printing genetic circuits in the lab, there is no denying that Printeria facilitates those tasks for both the average and the experienced user. But, without an interface to define all the necessary parameters, keep track of the device’s inventory, and monitor all of the steps of the process, that would not be possible.
 +
 
 
</p>
 
</p>
−
<ul>
 
−
<li><p>
 
−
<b>Design simple mathematical models</b> based on differential equations that describe the biochemical processes of a cell. With them, we can simulate the different genetic circuits that Printeria allows us to build.
 
−
</p></li>
 
−
<li><p>
 
−
Develop a <b>Simulation Tool</b> that allows the user to visualize a prediction of the results of their experiment before running it in Printeria.
 
−
</p></li>
 
−
<li><p>
 
−
<b>Optimize model parameters</b> to match simulation results to experimental data obtained from Printeria constructions.
 
−
</p></li>
 
−
<li><p>
 
−
<b><a href="https://2018.igem.org/Team:Valencia_UPV/Experiments#imCharact" target="_blank">Characterize the parts</a>of our <a href="https://2018.igem.org/Team:Valencia_UPV/Part_Collection" target="_blank">Part Collection</a></b> from the optimization results and provide the user with all the information about the Printeria kit.
 
−
</p></li>
 
−
</ul>
 
 
<p>
 
<p>
−
Although in the development of the project we have dealt with all these aspects, all of them have a single purpose: demonstrate the importance and many applications of <b>describing in a mathematical way the biological processes</b> that take place inside the cell.
+
We aim to solve that with Printeria Controller, an intuitive software that provides a user-friendly interface meant for all kinds of users, so that everyone can have access to the capabilities of Printeria. This controller help us to achieve the goal of our project: Make synthetic biology easier.
 +
 
 +
</p>
 +
<h3>Design Considerations and working flow</h3>
 +
<h4> A web application </h4>
 +
<p>
 +
Scientists nowadays use computers in the lab to take notes of their experiments, do research, make measurements from the laboratory devices… So we thought, why don’t they also use Printeria from the lab computer? That way, extra devices won’t be necessary. Once that decision was made, we found a setback: Most of laboratory computers are administered by technicians, so lab members cannot install new software in them. To fix this issue, we came up with the idea of making a web application so that no software installation is needed. This allowed everyone to access Printeria’s Controller from their personal computers, tablets or even smartphones. Thereby we allocated the application in a server inside a Raspberry Pi in Printeria.
 +
 
 
                 </p>
 
                 </p>
 
               <!--BOTONES PARA MOVERSE POR LA PÁGINA -->
 
               <!--BOTONES PARA MOVERSE POR LA PÁGINA -->

Revision as of 18:19, 8 October 2018

Stack Multipurpose HTML Template

Index

Introduction

Do you think it is possible to mathematically describe a cell? Would you like to know the possibilities that modeling offers you?

When it comes to automating the process of designing and printing genetic circuits in the lab, there is no denying that Printeria facilitates those tasks for both the average and the experienced user. But, without an interface to define all the necessary parameters, keep track of the device’s inventory, and monitor all of the steps of the process, that would not be possible.

We aim to solve that with Printeria Controller, an intuitive software that provides a user-friendly interface meant for all kinds of users, so that everyone can have access to the capabilities of Printeria. This controller help us to achieve the goal of our project: Make synthetic biology easier.

Design Considerations and working flow

A web application

Scientists nowadays use computers in the lab to take notes of their experiments, do research, make measurements from the laboratory devices… So we thought, why don’t they also use Printeria from the lab computer? That way, extra devices won’t be necessary. Once that decision was made, we found a setback: Most of laboratory computers are administered by technicians, so lab members cannot install new software in them. To fix this issue, we came up with the idea of making a web application so that no software installation is needed. This allowed everyone to access Printeria’s Controller from their personal computers, tablets or even smartphones. Thereby we allocated the application in a server inside a Raspberry Pi in Printeria.

Models & Experiments

Simulation Tool

CONTACT US igem.upv.2018@gmail.com