Difference between revisions of "Team:MADRID UCM/Software"

Revision as of 20:59, 21 October 2019

Software – iGem Madrid

SOFTWARE

1 Software contributions

One of the main strengths of this team was the interdisciplinarity involved, as we had engineers to deal with the Software-related aspects. That is why this project had a strong software component, being one of our main contributions the Artifical Intelligence algorithms developed to improve the SELEX process. We trained a GAN network with a library that we obtained modifying a previous year iGem team (Lyon 2016) improving it, for instance by making possible multithreading execution. We tested the quality of our algorithm with the Rosetta software for molecules modelling and we are extremely satisfied with both the obtained results and the efficiency in doing so.

GITHUB

You can check all the documentation in our GitHub repository.

Go!

We did not stop there and also developed a Search Engine for iGem words -from every year and team- as well as programmed several protocols for the Opentrons robot, where we also had to deal with other software modifications for the Ninja-PCR thermocycler and other Hardware modules.

Hence, the software of our team can be divided into three rather wide parts:

The GAN network with CNN neuronal nets and its Data Base here.

Several Python protocols for the OT2 robot and related software for custom Hardware explained here.

A nice extra tool: a Search Engine for words in other teams websites, since 2009.

2 Search Engine for iGem

You can use our Search Engine for words in previous or this year's team's websites. This is a python search engine with GUI for searching words in each competition year and team's website.

You can run it from your terminal using:

$ python search.py

You might have some dependencies not installed, you just need to do:

$ sudo pip install

3 Python Protocols

You can use our Search Engine for words in previous or this year's team's websites. This is a python search engine with GUI for searching words in each competition year and team's website.

You can run it from your terminal using:

$ python search.py

You might have some dependencies not installed, you just need to do:

$ sudo pip install

Folder OT_Robot in our GitHub contains biotechnological protocols for obtaining trained libraries of DNA aptamer molecules automated with the Opentrons OT-2 robot. This protocol is part of our contribution to the 2019 iGEM international biotechnology competition. For the thermocycler we built the Ninja-PCR.

To use them, you just need to drap and drop or upload the python protocols into the Opentrons App.

You can clone this repo or download the zip. Make sure all the dependencies are covered. First line is for installation of pip at most Linux distributions.

$ sudo apt install python-pip || pacman -S python-pip

$ sudo pip install opentrons subprocess time os

The robot can use the audio robot.mp3 and gets it from Robot Raspberry's /mnt/usbdrive/ (put it there or edit the location). You can load the protocol in the Opentrons application, available here. We also recommend the usage of an external Raspberry Pi to uninterruptedly provide the robot with Wi-Fi. Once you have stablished the Wi-Fi network at the Raspberry, you can connect the Robot too:

# nmcli dev wifi connect password

After the last update of the Robot -by the time this is written- the SSH connection has changed and now you need to exchange with it a public key for a more secure connection. Then when connected via SSH the robot will request the passphrase, at least the first time. Here is how you create the public key (you probably already have one):

$ ssh-key
Generating public/private rsa key pair.
Enter file in which to save the key (/home/.ssh/id_rsa):
/home/pepe/.ssh/id_rsa already exists.
Overwrite (y/n)?
Enter passphrase (empty for no passphrase):
Your identification has been saved in /home/.ssh/id_rsa.
Your public key has been saved in /home/.ssh/id_rsa.pub.
The key fingerprint is:
a9:49:2e:2a:5e:33:3e:a9:de:4e:77:11:58:b6:90:26 pepe@remote_host
The key's randomart image is:
+--[ RSA 2048]----+
| ..o             |
| E o= .          |
| o. o            |
| ..              |
| ..S             |
| o o.            |
| =o.+.           |
|. =++..          |
|o=++.            |
+-----------------+

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-{{MADRID_UCM}}
+{{MADRID_UCM/html/main}}
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+<html lang="en-US">
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+  <meta charset="utf-8"/>
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-<h3>Best Software Tool Special Prize</h3>
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-<li><a href="http://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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0.5)!important;}.header-09 .mini-cart .mini-cart-icon:after{background-color:#fff;color:#222;}.desktop-menu .header-09 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-09 .menu--primary .menu__container > li > a{padding-top:57px;padding-bottom:57px;padding-left:18px;padding-right:18px;}.desktop-menu .header-09 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-09 .menu--primary a{line-height:1.18;font-size:16px;color:#fff;}.header-09 .menu--primary li:hover > a, .header-09 .menu--primary > ul > li > a:hover, .header-09 .menu--primary > ul > li > a:focus, .header-09 .menu--primary .current-menu-ancestor > a, .header-09 .menu--primary .current-menu-item > a{color:#fff;}.header-09.headroom--not-top .page-header-inner{background:rgba(0, 0, 0, 0.9);background-color:rgba(0, 0, 0, 0.9);background-repeat:no-repeat;background-position:center 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a:hover, .header-10 .popup-search-wrap:hover i, .header-10 .mini-cart .mini-cart-icon:hover, .header-10 .page-open-main-menu:hover, .header-10 .page-open-mobile-menu:hover i{color:#111;}.header-10 .mini-cart .mini-cart-icon:after{background-color:#111;color:#fff;}.desktop-menu .header-10 .header-center{margin-top:80px;margin-bottom:0px;margin-left:-60px;margin-right:-60px;}.desktop-menu .header-10 .menu--primary .menu__container > li > a{padding-top:21px;padding-bottom:21px;padding-left:60px;padding-right:60px;}.desktop-menu .header-10 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-10 .menu--primary a{font-weight:600;line-height:1.18;font-size:16px;color:#222222;}.header-10 .menu--primary li:hover > a, .header-10 .menu--primary > ul > li > a:hover, .header-10 .menu--primary > ul > li > a:focus, .header-10 .menu--primary .current-menu-ancestor > a, .header-10 .menu--primary .current-menu-item > a{color:#222222;}.header-10.headroom--not-top .page-header-inner{background:#ffffff;background-color:#ffffff;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-11 .page-header-inner{border-bottom-width:0px;border-color:rgba(255, 255, 255, 0.3);background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-11 .wpml-ls-item-toggle, .header-11 .header-social-networks a, .header-11 .page-open-mobile-menu i, .header-11 .popup-search-wrap i, .header-11 .mini-cart .mini-cart-icon{color:#222;}.header-11 .header-social-networks a:hover, .header-11 .page-open-mobile-menu:hover i, .header-11 .popup-search-wrap:hover i, .header-11 .mini-cart .mini-cart-icon:hover{color:#222;}.header-11 .wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#222!important;}.header-11 .mini-cart .mini-cart-icon:after{background-color:#222222;color:#fff;}.desktop-menu .header-11 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-11 .menu--primary .menu__container > li > a{padding-top:57px;padding-bottom:57px;padding-left:18px;padding-right:18px;}.desktop-menu .header-11 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-11 .menu--primary a{line-height:1.18;font-size:16px;color:#222;}.header-11 .menu--primary li:hover > a, .header-11 .menu--primary > ul > li > a:hover, .header-11 .menu--primary > ul > li > a:focus, .header-11 .menu--primary .current-menu-ancestor > a, .header-11 .menu--primary .current-menu-item > a{color:#222;}.header-11.headroom--not-top .page-header-inner{background:#ffffff;background-color:#ffffff;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-12 .page-header-inner{border-bottom-width:0px;border-color:#222;background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;padding-top:24px;padding-bottom:24px;padding-left:0px;padding-right:0px;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-12 .wpml-ls-item-toggle, .header-12 .page-open-mobile-menu, .header-12 .page-open-main-menu, .header-12 .popup-search-wrap i, .header-12 .mini-cart .mini-cart-icon{color:#222;}.header-12 .page-open-main-menu:hover, .header-12 .page-open-mobile-menu:hover i, .header-12 .popup-search-wrap:hover i, .header-12 .mini-cart .mini-cart-icon:hover{color:#0038E3;}.header-12 .wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#0038E3!important;}.header-12 .mini-cart .mini-cart-icon:after{background-color:#222;color:#fff;}.desktop-menu .header-12 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-12 .menu--primary .menu__container > li > a{padding-top:57px;padding-bottom:57px;padding-left:18px;padding-right:18px;}.header-12.headroom--not-top .page-header-inner{background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-13 .page-header-inner{border-bottom-width:0px;border-color:#222;}.header-13 .page-header-inner .header-left-wrap{background:#222;background-color:#222;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-13 .page-header-inner .header-right-wrap{background:#19d2a8;background-color:#19d2a8;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-13 .page-open-mobile-menu, .header-13 .page-open-main-menu, .header-13 .popup-search-wrap i, .header-13 .mini-cart .mini-cart-icon{color:#fff;}.header-13 .page-open-main-menu:hover, .header-13 .page-open-mobile-menu:hover i, .header-13 .popup-search-wrap:hover i, .header-13 .mini-cart .mini-cart-icon:hover{color:#fff;}.header-13 .mini-cart .mini-cart-icon:after{background-color:#fff;color:#222;}.header-13.headroom--not-top .page-header-inner{background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-14 .page-header-inner{border-bottom-width:0px;border-color:rgba(255, 255, 255, 0.3);background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-14 .wpml-ls-item-toggle, .header-14 .page-open-mobile-menu, .header-14 .header-social-networks a, .header-14 .popup-search-wrap i, .header-14 .mini-cart .mini-cart-icon{color:#fff;}.header-14 .header-social-networks a:hover, .header-14 .page-open-mobile-menu:hover i, .header-14 .popup-search-wrap:hover i, .header-14 .mini-cart .mini-cart-icon:hover{color:#fff;}.header-14 .wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#fff!important;}.header-14 .mini-cart .mini-cart-icon:after{background-color:#fff;color:#222;}.desktop-menu .header-14 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-14 .menu--primary .menu__container > li > a{padding-top:51px;padding-bottom:51px;padding-left:18px;padding-right:18px;}.header-14 .menu--primary a{font-weight:500;line-height:1.18;font-size:16px;color:#fff;}.header-14 .menu--primary li:hover > a, .header-14 .menu--primary > ul > li > a:hover, .header-14 .menu--primary > ul > li > a:focus, .header-14 .menu--primary .current-menu-ancestor > a, .header-14 .menu--primary .current-menu-item > a{color:#fff;}.header-14.headroom--not-top .page-header-inner{background:#001029;background-color:#001029;background-repeat:no-repeat;background-position:center 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.wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#fff!important;}.header-15 .mini-cart .mini-cart-icon:after{background-color:#fff;color:#222;}.header-15.headroom--not-top .page-header-inner{background:#000;background-color:#000;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-16 .page-header-inner{border-bottom-width:0px;border-color:rgba(255, 255, 255, 0.3);background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-16 .wpml-ls-item-toggle, .header-16 .page-open-mobile-menu i, .header-16 .popup-search-wrap i, .header-16 .mini-cart .mini-cart-icon{color:#fff;}.header-16 .page-open-mobile-menu:hover i, .header-16 .popup-search-wrap:hover i, .header-16 .mini-cart .mini-cart-icon:hover{color:#fff;}.header-16 .wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#fff!important;}.header-16 .mini-cart .mini-cart-icon:after{background-color:#fff;color:#222;}.desktop-menu .header-16 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-16 .menu--primary .menu__container > li > a{padding-top:41px;padding-bottom:41px;padding-left:15px;padding-right:15px;}.desktop-menu .header-16 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-16 .menu--primary a{font-weight:600;line-height:1.18;font-size:16px;color:#fff;}.header-16 .menu--primary li:hover > a, .header-16 .menu--primary > ul > li > a:hover, .header-16 .menu--primary > ul > li > a:focus, .header-16 .menu--primary .current-menu-ancestor > a, .header-16 .menu--primary .current-menu-item > a{color:#fff;}.header-16 .tm-button{color:#222;border-color:#fff;background-color:#fff;}.header-16 .tm-button:hover{color:#222;border-color:#fff;background-color:#fff;}.header-16.headroom--not-top .page-header-inner{background:rgba(0, 0, 0, 0.9);background-color:rgba(0, 0, 0, 0.9);background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-17.headroom--top .header-wrap{padding-top:32px;padding-bottom:32px;padding-left:0px;padding-right:0px;}.header-17 .page-header-inner{border-bottom-width:0px;border-color:#222;background-repeat:no-repeat;background-position:center center;background-attachment:scroll;-webkit-background-size:cover;-moz-background-size:cover;-ms-background-size:cover;-o-background-size:cover;background-size:cover;}.header-17 .wpml-ls-item-toggle, .header-17 .header-social-networks a, .header-17 .page-open-mobile-menu, .header-17 .page-open-main-menu, .header-17 .popup-search-wrap i, .header-17 .mini-cart .mini-cart-icon{color:#222;}.header-17 .page-open-main-menu:hover, .header-17 .page-open-mobile-menu:hover i, .header-17 .popup-search-wrap:hover i, .header-17 .mini-cart .mini-cart-icon:hover{color:#222;}.header-17 .wpml-ls-slot-shortcode_actions:hover > .js-wpml-ls-item-toggle{color:#222!important;}.header-17 .header-social-networks a:hover{background-color:#222;border-color:#222;}.header-17 .mini-cart .mini-cart-icon:after{background-color:#222;color:#fff;}.header-17 .tm-button{color:#222;border-color:#eee;background-color:#fff;}.header-17 .tm-button:hover{color:#fff;border-color:#222;background-color:#222;}.header-17.headroom--not-top .page-header-inner{background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center 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a:hover{background-color:#222;border-color:#222;}.header-18 .mini-cart .mini-cart-icon:after{background-color:#222;color:#fff;}.desktop-menu .header-18 .menu__container{margin-top:0px;margin-bottom:0px;margin-left:-15px;margin-right:0px;}.desktop-menu .header-18 .menu--primary .menu__container > li > a{padding-top:58px;padding-bottom:58px;padding-left:15px;padding-right:15px;}.desktop-menu .header-18 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-18 .menu--primary a{font-weight:700;line-height:1.18;font-size:18px;color:#222222;}.header-18 .menu--primary li:hover > a, .header-18 .menu--primary > ul > li > a:hover, .header-18 .menu--primary > ul > li > a:focus, .header-18 .menu--primary .current-menu-ancestor > a, .header-18 .menu--primary .current-menu-item > a{color:#0038E3;}.header-18.headroom--not-top .page-header-inner{background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center 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.menu__container{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.desktop-menu .header-19 .menu--primary .menu__container > li > a{padding-top:41px;padding-bottom:41px;padding-left:15px;padding-right:15px;}.desktop-menu .header-19 .menu--primary .menu__container > li{margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;}.header-19 .menu--primary a{font-weight:600;line-height:1.18;font-size:16px;color:#111;}.header-19 .menu--primary li:hover > a, .header-19 .menu--primary > ul > li > a:hover, .header-19 .menu--primary > ul > li > a:focus, .header-19 .menu--primary .current-menu-ancestor > a, .header-19 .menu--primary .current-menu-item > a{color:#111;}.header-19 .tm-button{color:#222;border-color:#fff;background-color:#fff;}.header-19 .tm-button:hover{color:#222;border-color:#fff;background-color:#fff;}.header-19.headroom--not-top .page-header-inner{background:#fff;background-color:#fff;background-repeat:no-repeat;background-position:center 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+  </style>
+  <noscript>
+   <style>
+    .wpb_animate_when_almost_visible { opacity: 1; }
+   </style>
+  </noscript>
+ </head>
+ <body class="page-template-default page page-id-5086 desktop desktop-menu page-has-animation scroll-nav-style-01 header-sticky-both wide page-has-no-sidebar wpb-js-composer js-comp-ver-6.0.5 vc_responsive" data-content-width="1200" data-font="Open Sans Helvetica, Arial, sans-serif" data-header-sticky-height="80" data-site-width="1200px">
+<div class="header-sticky-both wpb-js-composer">
+  <div class="page-loading clearfix" id="page-preloader">
+   <div class="page-load-inner">
+    <div class="preloader-wrap">
+     <div class="wrap-2">
+      <div class="">
+       <img alt="Brook Preloader" src="/wiki/images/8/8b/T--MADRID_UCM--wp-content~uploads~2019~10~BUENO.gif"/>
+      </div>
+     </div>
+    </div>
+   </div>
+  </div>
+  <div class="site" id="page">
+   <div class="content-wrapper">
+    <header class="page-header header-09 header-layout-fixed light-logo-version" id="page-header">
+     <div class="page-header-place-holder">
+     </div>
+     <div class="page-header-inner" data-sticky="1" id="page-header-inner">
+      <div class="container">
+       <div class="row">
+        <div class="col-xs-12">
+         <div class="header-wrap">
+          <div class="branding">
+           <div class="branding__logo">
+            <a href="index.html" rel="home">
+             <img alt="iGem Madrid" class="light-logo" src="/wiki/images/e/e1/T--MADRID_UCM--wp-content~uploads~2019~10~aegis_logo_color-y-blanco_reduc-18.png"/>
+             <img alt="iGem Madrid" class="dark-logo" src="/wiki/images/1/1f/T--MADRID_UCM--wp-content~uploads~2019~09~aegis_logo_color_reduc.png"/>
+            </a>
+           </div>
+          </div>
+          <div class="header-right">
+           <div class="navigation page-navigation" id="page-navigation">
+            <nav class="menu menu--primary" id="menu">
+             <ul class="menu__container sm sm-simple" id="menu-our-menu">
+              <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-3567 level-1" id="menu-item-3567">
+               <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM">
+                <div class="menu-item-wrap">
+                 <span class="menu-item-title">
+                  Home
+                 </span>
+                </div>
+               </a>
+              </li>
+              <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-3571 level-1" id="menu-item-3571">
+               <a data-ps2id-api="true">
+                <div class="menu-item-wrap">
+                 <span class="menu-item-title">
+                  Our Project
+                 </span>
+                 <span class="toggle-sub-menu">
+                 </span>
+                </div>
+               </a>
+               <ul class="sub-menu">
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5034" id="menu-item-5034">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Description">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Description
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5006" id="menu-item-5006">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Design">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Our Design
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5007" id="menu-item-5007">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Collaborations">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Collaborations
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5008" id="menu-item-5008">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Attributions">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Attributions
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5009" id="menu-item-5009">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Team">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Team
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5010" id="menu-item-5010">
+                 <a data-ps2id-api="true" href="http://2019.igem.org/Team:MADRID_UCM/Sponsors">
+                  <div class="menu-item-wrap">
+                   <span class="menu-item-title">
+                    Sponsors
+                   </span>
+                  </div>
+                 </a>
+                </li>
+                <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-5011" id="menu-item-5011">
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+                  <div class="menu-item-wrap">
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+          </div>
+         </div>
+        </div>
+       </div>
+      </div>
+     </div>
+    </header>
+    <div class="page-content" id="page-content">
+     <div class="container">
+      <div class="row">
+       <div class="page-main-content" id="page-main-content">
+        <article class="post-5086 page type-page status-publish hentry post-no-thumbnail" id="post-5086">
+         <div class="vc_row vc_row-outer vc_row-fluid vc_container-has-overlay" data-vc-full-width="true" data-vc-full-width-init="false" data-vc-stretch-content="true" id="tm-row-5dae03405b78f">
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+            <title>
+             Wave
+            </title>
+            <defs>
+            </defs>
+            <path d="">
+            </path>
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+           <svg class="wavify-item" data-wavify-amplitude="50" data-wavify-background="#ffffff" data-wavify-bones="5" data-wavify-height="0" height="100%" version="1.1" width="100%" xmlns="http://www.w3.org/2000/svg">
+            <title>
+             Wave
+            </title>
+            <defs>
+            </defs>
+            <path d="">
+            </path>
+           </svg>
+          </div>
+          <div class="wpb_column vc_column_container vc_col-sm-12" id="tm-column-5dae03405c3be">
+           <div class="vc_column-inner">
+            <div class="wpb_wrapper">
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+             </div>
+             <div class="tm-heading center tm-animation move-left" id="tm-heading-5dae03405c60d">
+              <h3 class="heading" style="">
+               SOFTWARE
+              </h3>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae03405c8c5">
+             </div>
+            </div>
+           </div>
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+         </div>
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+         </div>
+         <div class="vc_row vc_row-outer vc_row-fluid collapse" data-vc-full-width="true" data-vc-full-width-init="false" data-vc-stretch-content="true" id="tm-row-5dae03405ccfd">
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+           </div>
+          </div>
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+              <div class="wpb_wrapper">
+               <p style="font-size: 20px; color: #15d3ff;">
+                <strong>
+                 INDEX
+                </strong>
+               </p>
+              </div>
+             </div>
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+               <p>
+                <a href="#nav1">
+. Our Code
+                </a>
+               </p>
+              </div>
+             </div>
+             <div class="wpb_text_column wpb_content_element sidenav-menu-entry tm-animation move-up">
+              <div class="wpb_wrapper">
+               <p>
+                <a class="_ps2id" data-ps2id-offset="" href="#nav2">
+. Search Engine
+                </a>
+               </p>
+              </div>
+             </div>
+             <div class="wpb_text_column wpb_content_element sidenav-menu-entry tm-animation move-up">
+              <div class="wpb_wrapper">
+               <p>
+                <a class="_ps2id" data-ps2id-offset="" href="#nav3">
+. Python protocols
+                </a>
+               </p>
+              </div>
+             </div>
+            </div>
+           </div>
+          </div>
+         </div>
+         <div class="vc_row-full-width vc_clearfix">
+         </div>
+         <div class="vc_row vc_row-outer vc_row-fluid" id="tm-row-5dae03405d462">
+          <div class="wpb_column vc_column_container vc_col-sm-1/5" id="tm-column-5dae03405d696">
+           <div class="vc_column-inner">
+            <div class="wpb_wrapper">
+            </div>
+           </div>
+          </div>
+          <div class="wpb_column vc_column_container vc_col-sm-4/5" id="tm-column-5dae03405d7ec">
+           <div class="vc_column-inner">
+            <div class="wpb_wrapper">
+             <div class="wpb_text_column wpb_content_element tm-animation move-up">
+              <div class="wpb_wrapper">
+              </div>
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae03405da9e">
+              <h3 class="heading" style="">
+               <mark>
+               </mark>
+               Software contributions
+              </h3>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae03405dda8">
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae03405de57">
+              <div class="heading" style="">
+               One of the main strengths of this team was the interdisciplinarity involved, as we had engineers to deal with the Software-related aspects. That is why this project had a strong software component, being one of our main contributions the Artifical Intelligence algorithms developed to improve the SELEX process. We trained a GAN network with a library that we obtained modifying a previous year iGem team (Lyon 2016) improving it, for instance by making possible multithreading execution. We tested the quality of our algorithm with the Rosetta software for molecules modelling and we are extremely satisfied with both the obtained results and the efficiency in doing so.
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae03405e12f">
+             </div>
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+               <div class="vc_column-inner">
+                <div class="wpb_wrapper">
+                </div>
+               </div>
+              </div>
+              <div class="wpb_column vc_column_container vc_col-sm-4" id="tm-column-inner-5dae03405f022">
+               <div class="vc_column-inner">
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+                 <div class="tm-box-icon image_boxed style-01 tm-animation move-up" id="tm-box-icon-5dae03405f204">
+                  <div class="content-wrap">
+                   <div class="image">
+                    <img alt="github-image-796x418" src="/wiki/images/0/00/T--MADRID_UCM--wp-content~uploads~2019~10~github-image-796x418.png"/>
+                   </div>
+                   <div class="content">
+                    <h4 class="heading">
+                     GITHUB
+                    </h4>
+                    <div class="text">
+                     You can check all the documentation in our GitHub repository.
+                    </div>
+                   </div>
+                   <a class="tm-box-icon__btn tm-button style-text" href="https://github.com/igemsoftware2019/MADRID_UCM" target=" _blank">
+                    <span class="button-text">
+                     Go!
+                    </span>
+                    <span class="button-icon fa fa-arrow-right">
+                    </span>
+                   </a>
+                  </div>
+                 </div>
+                </div>
+               </div>
+              </div>
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+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae03406025d">
+              <div class="heading" style="">
+               We did not stop there and also developed a Search Engine for iGem words -from every year and team- as well as programmed several protocols for the Opentrons robot, where we also had to deal with other software modifications for the Ninja-PCR thermocycler and other Hardware modules.
+               <p>
+               </p>
+               <p>
+                Hence, the software of our team can be divided into three rather wide parts:
+               </p>
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae034060527">
+             </div>
+             <div class="tm-list style-modern-icon tm-animation move-up" id="tm-list-5dae0340605ab">
+              <div class="list-item">
+               <div class="list-header">
+                <div class="marker">
+                 <i class="tm-list__icon far fa-grip-lines">
+                 </i>
+                </div>
+                <div class="title-wrap">
+                 <div class="desc">
+                  The GAN network with CNN neuronal nets and its Data Base here.
+                 </div>
+                </div>
+               </div>
+              </div>
+              <div class="list-item">
+               <div class="list-header">
+                <div class="marker">
+                 <i class="tm-list__icon far fa-grip-lines">
+                 </i>
+                </div>
+                <div class="title-wrap">
+                 <div class="desc">
+                  Several Python protocols for the OT2 robot and related software for custom Hardware explained here.
+                 </div>
+                </div>
+               </div>
+              </div>
+              <div class="list-item">
+               <div class="list-header">
+                <div class="marker">
+                 <i class="tm-list__icon far fa-grip-lines">
+                 </i>
+                </div>
+                <div class="title-wrap">
+                 <div class="desc">
+                  A nice extra tool: a Search Engine for words in other teams websites, since 2009.
+                 </div>
+                </div>
+               </div>
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae03406086c">
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae034060920">
+              <h3 class="heading" style="">
+               <mark>
+               </mark>
+               Search Engine for iGem
+              </h3>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae034061bb8">
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae034061c75">
+              <div class="heading" style="">
+               You can use our Search Engine for words in previous or this year's team's websites. This is a python search engine with GUI for searching words in each competition year and team's website.
+               <p>
+               </p>
+               <p>
+                You can run it from your terminal using:
+               </p>
+               <p>
+                <mark>
+                 $ python search.py
+                </mark>
+               </p>
+               <p>
+                You might have some dependencies not installed, you just need to do:
+               </p>
+               <p>
+                <mark>
+                 $ sudo pip install
+                </mark>
+               </p>
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae034061f27">
+             </div>
+             <div class="tm-image tm-animation move-up" id="tm-image-5dae034061f83">
+              <div class="image">
+               <img alt="1" src=""/>
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae0340629fe">
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae034062aa9">
+              <h3 class="heading" style="">
+               <mark>
+               </mark>
+               Python Protocols
+              </h3>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae034062da0">
+             </div>
+             <div class="tm-heading left tm-animation move-up" id="tm-heading-5dae034062e51">
+              <div class="heading" style="">
+               You can use our Search Engine for words in previous or this year's team's websites. This is a python search engine with GUI for searching words in each competition year and team's website.
+               <p>
+               </p>
+               <p>
+                You can run it from your terminal using:
+               </p>
+               <p>
+                <mark>
+                 $ python search.py
+                </mark>
+               </p>
+               <p>
+                You might have some dependencies not installed, you just need to do:
+               </p>
+               <p>
+                <mark>
+                 $ sudo pip install
+                </mark>
+               </p>
+               <p>
+                Folder OT_Robot in our GitHub contains biotechnological protocols for obtaining trained libraries of DNA aptamer molecules automated with the Opentrons OT-2 robot. This protocol is part of our contribution to the 2019 iGEM international biotechnology competition. For the thermocycler we built the Ninja-PCR.
+               </p>
+               <p>
+                To use them, you just need to drap and drop or upload the python protocols into the Opentrons App.
+               </p>
+               <p>
+                You can clone this repo or download the zip. Make sure all the dependencies are covered. First line is for installation of pip at most Linux distributions.
+               </p>
+               <p>
+                <mark>
+                 $ sudo apt install python-pip || pacman -S python-pip
+                </mark>
+               </p>
+               <p>
+                <mark>
+                 $ sudo pip install opentrons subprocess time os
+                </mark>
+               </p>
+               <p>
+                The robot can use the audio robot.mp3 and gets it from Robot Raspberry's /mnt/usbdrive/ (put it there or edit the location). You can load the protocol in the Opentrons application, available here. We also recommend the usage of an external Raspberry Pi to uninterruptedly provide the robot with Wi-Fi. Once you have stablished the Wi-Fi network at the Raspberry, you can connect the Robot too:
+               </p>
+               <p>
+                <mark>
+                 # nmcli dev wifi connect password
+                </mark>
+               </p>
+               <p>
+                After the last update of the Robot -by the time this is written- the SSH connection has changed and now you need to exchange with it a public key for a more secure connection. Then when connected via SSH the robot will request the passphrase, at least the first time. Here is how you create the public key (you probably already have one):
+               </p>
+              </div>
+             </div>
+             <div class="tm-spacer" id="tm-spacer-5dae034063123">
+             </div>
+             <div class="vc_row vc_inner vc_row-fluid vc_row-o-content-middle vc_row-flex" id="tm-row-inner-5dae034063195">
+              <div class="wpb_column vc_column_container vc_col-sm-6" id="tm-column-inner-5dae03406336f">
+               <div class="vc_column-inner">
+                <div class="wpb_wrapper">
+                 <div class="tm-image tm-animation move-up" id="tm-image-5dae034063535">
+                  <div class="image">
+                   <img alt="robot" src=""/>
+                  </div>
+                 </div>
+                </div>
+               </div>
+              </div>
+              <div class="wpb_column vc_column_container vc_col-sm-6" id="tm-column-inner-5dae034064afb">
+               <div class="vc_column-inner">
+                <div class="wpb_wrapper">
+                 <div class="wpb_text_column wpb_content_element tm-animation move-up">
+                  <div class="wpb_wrapper">
+                   <p class="has-medium-font-size">
+                   </p>
+                   <p class="has-medium-font-size">
+                   </p>
+                   <p class="has-medium-font-size">
+                   </p>
+                   <pre class="wp-block-code"><code>$ ssh-key
+Generating public/private rsa key pair.
+Enter file in which to save the key (/home/.ssh/id_rsa):
+/home/pepe/.ssh/id_rsa already exists.
+Overwrite (y/n)?
+Enter passphrase (empty for no passphrase):
+Your identification has been saved in /home/.ssh/id_rsa.
+Your public key has been saved in /home/.ssh/id_rsa.pub.
+The key fingerprint is:
+a9:49:2e:2a:5e:33:3e:a9:de:4e:77:11:58:b6:90:26 pepe@remote_host
+The key's randomart image is:
++--[ RSA 2048]----+
+| ..o             |
+| E o= .          |
+| o. o            |
+| ..              |
+| ..S             |
+| o o.            |
+| =o.+.           |
+|. =++..          |
+|o=++.            |
++-----------------+
+</code></pre>
+                  </div>
+                 </div>
+                </div>
+               </div>
+              </div>
+             </div>
+            </div>
+           </div>
+          </div>
+         </div>
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