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project.html
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---
layout: page
title: Our Project
permalink: /project/
---
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<h1>Abstract</h1>
<b><p><big>We do things.</big></p></b>
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<h2>Overview of our project</h2>
<h4> <a href="#target">Psst! -> Click here to jump to our Github Guide!</a></h4>
<p class="animated fadeInUp"> We are very interested in interdisciplinarity. So we are mixing biology, computer science and mathematics in our project. </p>
<p>We want to create a platform that serves as a social network to connect scientists from all over the world. In this platform, they can upload their experiments (for example, of bacteria growth as we propose).
Not only it will serve as a place to upload experiments. They will have a wide range of utilities they can use to extract information, conclusions or improve their studies.</p>
<p class="animated fadeInUp">This app will count with mathematical models that can be use to predict or estimate the possible results of an experiment. We can tune the parameters of
the model in order to see the posterior behaviour of the population of bacterias, for example (all of this can be extrapolated to other kind of experiments).</p>
<p class="animated fadeInUp"> As in an usual social network they can share, comment and rate the experiments so we are favorating the transference of knowledge. We can use other things
like gamification to motivate studies that can be result tedious at first.</p>
<p class="animated fadeInUp">Our work does not end here, Impaciencia has been only the beginning. After that We want to continue developing our software to can facilitate the work of many scientists adding all the capabilities we think it should have to be completed. We also want develop a hardware tool related to our bacteria visual identification compatible with our app.
We can obtain more information and facilitate the work if we had a camera which can continuously take pictures of a petri dish while the experiment is being carried out and then process them and upload them to the platform extracting information from them. This could lead us to live experiments that can be followed all over the world and a true functional social network that could help in the discover of antibiotics
Our whole project has the philosophy of open science so we will use free software (python) and free hardware (arduino).</p>
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<h2>Biology experiments and tutorials</h2>
<p class="animated fadeInUp"> Do you want to learn about how bacterias are cultivated? What can we learn about them? How can you replicate our experiments and do yours? Take a look at our biological repository! Wherever science you came fro, you can learn about this!</a></p>
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<h2>Mathematical simulations</h2>
<p class="animated fadeInUp">How can we predict bacteria behaviour? Can maths help us with this? Absolutely yes! In our mathematical repository you can learn how math models can be applied in bacteria growth. We have develop our main algorithm from a classical numircal scheme in a wellknown (but not to simulated) 2d-equation. Here you can learn about why this equation it's used, discretization an much more. But, what is more important, you can learn basic principles in mathematical modelization to try them in the future with your research or simulation</p>
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<h2>Science Divulgation</h2>
<p class="animated fadeInUp">Interdisciplinary research is fun! And interesting! But let's face it, if you can't communicate ideas, your research may dont reach too far. We know this, that's why we have been promoting our project during the whole competition. We hav develop a solid follower base, cool educational videos and great repositories. Our main goal it is not only to reach people we known or that maybe interested in this, but also everyday people that find science interesting! In our divulgation file you can have a look about our popular science productions an our impact in social media.</p>
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<h2>Bacteria visual recognition </h2>
<p class="animated fadeInUp">XXI Century is here! So are we! We have develop some function that allows you to make machines look at your experiments, locate bacteria colonies via their border and use this information to whatever you want to! (Somebody said machine learning?)</p>
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<h2>Web-App</h2>
<p class="animated fadeInUp">Our final goal! This Web-App let you use all the tools we have develop, and can be used to play, research, learn, EVERYTHING! Interdisciplinary science connects scientist, collaborative science connects people. </p>
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<h2><a id="target">How to guide yourself on our GitHub</a></h2>
<h3>Biological part</h3>
<p>So okay, let’s start with this trip explaining how to go through our GitHub without losing any detail. First we recommend you to check our justification project page. After you read that go to our Biological Documentation repository, there’s a <a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/README.md">README</a> with an index but to help you to guide inside we present you here the links of the files to read in order:</p>
<ul type="circle">
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/An%C3%A1lisis%20de%20la%20Morfolog%C3%ADa%20de%20una%20Colonia%20de%20Microorganismos.md">Análisis de la Morfología de una colonia de Microorganismos</a></li>
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/Biolog%C3%ADa%20de%20Lactobacillus%20casei%20y%20Saccharomyces%20cerevisiae.md">Biología de Lactobacillus casei y Saccharomyces cerevisiae</a></li>
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/L%C3%ADmites%20de%20Tolerancia%20y%20el%20Crecimiento%20Bacteriano.md">Límites de Tolerancia y el Crecimiento Bacteriano</a></li>
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/Manual%20para%20el%20Cultivo%20en%20Placa.md">Manual para el Cultivo en Placa</a></li>
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/Materiales%20y%20equipamiento%20necesarios.md">Materiales y equipamiento necesarios</a></li>
<li><a href="https://github.com/TheOpenBacteriaProject/Biological-Documentation/blob/master/T%C3%A9cnicas%20de%20recuento%20de%20microorganismos.md">Técnicas de recuento de microorganismos</a></li>
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<h3>Image processing</h3>
Once we have the experiment done, we have to take, upload and process the images. Take a look at our <a href="https://github.com/TheOpenBacteriaProject/Image-Processing">Repository</a> of
Image processing to see AI techniques to do this task. We will be able to recognize the Petri dish and calculate the bacteria population area.
<h3>Mathematical part</h3>
We want to compare the experiments obtained to our theorical mathematical models. In this repository we propose a simulation of FKPP equation.
This model is used to model our experiments with bacterias.
We are walking through an unexplored site. since there is little done in simulation of this equation, you can observe in public our position in google when looking for this equation.
Find out our code and documentation in the <a href="https://github.com/TheOpenBacteriaProject/FKPP">Repository</a>
<h3>Webapp</h3>
<p>This time we've decided is better that Paula show you how works our webapp. Enjoy! Remember to visit our repository for more information, files and tutorials: <a href="https://github.com/TheOpenBacteriaProject/webapp">Web App Repository</a></p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/Vh8hHrsI8_E" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
<h3>Divulgation and comunicative part</h3>
<p>This final part is composed by two repositories:</p>
<p>The first one is <a href="https://github.com/TheOpenBacteriaProject/Branding">Branding</a> where you can find all our standarized schemes to make a good brand marketing like logos, pics to help standarized all documentation, our own beamer template, color codes etc.</p>
<p>The second one is <a href="https://github.com/TheOpenBacteriaProject/Divulgation">Divulgation</a> where you can find all our materials we used in ours presentations,<a href="https://github.com/TheOpenBacteriaProject/Divulgation/tree/master/Twitter%20analytics">Twitter campaings</a> , Youtube videos list, impact on Google and digital newspapers, etc.</p>
<p>As you see, we have been very active on social media uploading vlogs and curiosity videos on YouTube, setting up campaigns on Twitter, participating on another launches like Facultad Cero at UGR... And as curiosity we appears on the third result on Google when you find codes of FKPP equation in Python. That's great!</p>
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