Difference between revisions of "Team:Stuttgart/Notebook"

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{{Stuttgart}}
 
 
<html>
 
<html>
  
 +
<script>
 +
 +
    // This is the jquery part of your template. 
 +
    // Try not modify any of this code too much since it makes your menu work.
 +
 +
    $(document).ready(function() {
 +
 +
        $("#HQ_page").attr('id','');
 +
 +
        // call the functions that control the menu
 +
        menu_functionality();
 +
        hide_show_menu();
 +
 +
 +
 +
        //this function controls the expand and collapse buttons of the menu and changes the +/- symbols
 +
        function menu_functionality() {
 +
 +
            //when clicking on a "menu_button", it will change the "+/-" accordingly and it will show/hide the corresponding submenu
 +
            $(".menu_button").click(function(){
 +
 +
                // add or remove the class "open" , this class holds the "-"
 +
                $(this).children().toggleClass("open");
 +
                // show or hide the submenu
 +
                $(this).next('.submenu_wrapper').fadeToggle(400);
 +
            });
 +
 +
            // when the screen size is smaller than 800px, the display_menu_control button appears and will show/hide the whole menu
 +
            $("#display_menu_control").click(function(){
 +
                $('#menu_content').fadeToggle(400);
 +
            });
 +
 +
            // call the current page highlight function
 +
            highlight_current_page();
 +
        }
 +
 +
 +
        // call the highlight current page function to show it on the menu with a different background color
 +
        function highlight_current_page() {
 +
 +
            // select a page from the menu based on the id assigned to it and the current page name and add the class "current page" to make it change background color
 +
            $("#"+  wgPageName.substring(wgPageName.lastIndexOf("/")+1, wgPageName.length ) + "_page").addClass("current_page");
 +
 +
            // now that the current_page class has been added to a menu item, make the submenu fade in
 +
            $(".current_page").parents(".submenu_wrapper").fadeIn(400);
 +
            // change the +/- symbol of the corresponding menu button
 +
            $(".current_page").parents(".submenu_wrapper").prev().children().toggleClass("open");
 +
 +
        }
 +
 +
 +
 +
        // allow button on the black menu bar to show/hide the side menu
 +
        function hide_show_menu() {
 +
 +
            // in case you preview mode is selected, the menu is hidden for better visibility
 +
            if (window.location.href.indexOf("submit") >= 0) {
 +
                $(".igem_2017_menu_wrapper").hide();
 +
            }
 +
 +
            // if the black menu bar has been loaded
 +
            if (document.getElementById('bars_item')) {
 +
 +
                // when the "bars_item" has been clicked
 +
                $("#bars_item").click(function() {
 +
                    $("#sideMenu").hide();
 +
 +
                    // show/hide the menu wrapper
 +
                    $(".igem_2017_menu_wrapper").fadeToggle("100");
 +
                });
 +
            }
 +
 +
            // because the black menu bars loads at a different time than the rest of the page, this function is set on a time out so it can run again in case it has not been loaded yet
 +
            else {
 +
                setTimeout(hide_show_menu, 15);
 +
            }
 +
        }
 +
 +
 +
    });
 +
 +
 +
</script>
 +
 +
<style>
 +
 +
 +
 +
    /***************************************************** DEFAULT WIKI SETTINGS  ****************************************************/
 +
 +
    /* Clear the default wiki settings */
 +
 +
    #home_logo, #sideMenu { display:none; }
 +
    #sideMenu, #top_title, .patrollink  {display:none;}
 +
    #content { width:100%; padding:0px;  margin-top:-7px; margin-left:0px;}
 +
    body {background-color:white; }
 +
    #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
 +
 +
 +
 +
 +
    /**************************************************************** MENU ***************************************************************/
 +
    /* Wrapper for the menu */
 +
    .igem_2017_menu_wrapper {
 +
        width: 15%;
 +
        height:100vh;
 +
        position:fixed;
 +
        right:0;
 +
        padding:0;
 +
        float:right;
 +
        border-left: 1px solid #d3d3d3;
 +
        background-color:#dddddd;
 +
        text-align:left;
 +
        font-family:Tahoma, Geneva, sans-serif;
 +
        overflow-y: auto;
 +
        overflow-x: hidden;
 +
    }
 +
 +
    /* this hides the scrollbar to keep view consistency */
 +
    .igem_2017_menu_wrappe::-webkit-scrollbar {
 +
        display: none;
 +
    }
 +
 +
 +
    /* styling for links in the menu, removes the line under text */
 +
    .igem_2017_menu_wrapper a {
 +
        text-decoration: none;
 +
    }
 +
 +
 +
    /* styling for the images in the menu */
 +
    .igem_2017_menu_wrapper img {
 +
        width: 100%;
 +
    }
 +
 +
    /* styling for the menu buttons */
 +
    .igem_2017_menu_wrapper .menu_button {
 +
        width: 100%;
 +
        padding: 10px 0px 10px 15px;
 +
        float:left;
 +
        border-bottom: 1px solid #d3d3d3;
 +
        font-size: 12px;
 +
        font-weight: bold;
 +
        color: #5e5f5f;
 +
        cursor: pointer;
 +
    }
 +
 +
 +
    .igem_2017_menu_wrapper .menu_bottom_padding {
 +
        width: 100%;
 +
        height: 30px;
 +
        float:left;
 +
    }
 +
 +
    .menu_button.direct_to_page {
 +
        padding-left: 36px;
 +
    }
 +
 +
 +
    .igem_2017_menu_wrapper .menu_button .expand_collapse_icon {
 +
        width:10%;
 +
        float:left;
 +
    }
 +
 +
    .igem_2017_menu_wrapper .menu_button .expand_collapse_icon::before {
 +
        content: "+";
 +
    }
 +
 +
    .open::before {
 +
        content: "-" !important;
 +
    }
 +
 +
 +
 +
    /* styling for the menu buttons on hover */
 +
    .igem_2017_menu_wrapper .menu_button:hover, .igem_2017_menu_wrapper .submenu_button:hover ,  .submenu_button.current_page:hover {
 +
        background-color: #3399ff;
 +
        text-decoration: none;
 +
        color:#ffffff;
 +
    }
 +
 +
    /* styling for the menu button when it is the current page */
 +
    .current_page {
 +
        background-color:#7fc1f7  !important;
 +
        color:#5e5f5f !important;
 +
    }
 +
 +
 +
    /* styling for the submenu buttons */
 +
    .igem_2017_menu_wrapper .submenu_button {
 +
        width: 100%;
 +
        padding: 10px 0px 10px 34px;
 +
        float:left;
 +
        background-color:#f2f2f2;
 +
        border-bottom: 1px solid #d3d3d3;
 +
        font-size: 12px;
 +
        color: #5e5f5f;
 +
        cursor: pointer;
 +
    }
 +
 +
    /* wrapper for the submenu items, they are hidden by default*/
 +
    .igem_2017_menu_wrapper .submenu_wrapper {
 +
        display:none;
 +
    }
 +
 +
    /* when the page size is bigger than 800px, this show/hide control is hidden by default */
 +
    .igem_2017_menu_wrapper #display_menu_control {
 +
        display:none;
 +
        text-align:center;
 +
    }
 +
 +
 +
    /***************************************************** CONTENT OF THE PAGE ****************************************************/
 +
 +
    /* Wrapper for the content */
 +
    .igem_2017_content_wrapper {
 +
        width: 81%;
 +
        margin: 2%;
 +
        display:block;
 +
        float:left;
 +
        background-color: white;
 +
        font-family:Tahoma, Geneva, sans-serif;
 +
    }
 +
 +
 +
    /********************************* HTML STYLING  *********************************/
 +
 +
    /* styling for the titles h1 h2 */
 +
    .igem_2017_content_wrapper h1, .igem_2017_content_wrapper h2 {
 +
        color:#FFBF00;
 +
        padding:15px 0 25px 0;
 +
        border-bottom: 0;
 +
    }
 +
 +
    /* styling for the titles  h3 h4 h5 h6*/
 +
    .igem_2017_content_wrapper h3, .igem_2017_content_wrapper h4, .igem_2017_content_wrapper h5, .igem_2017_content_wrapper h6 {
 +
        padding:5px 15px;
 +
        border-bottom:0;
 +
    }
 +
 +
    /* font and text */
 +
    .igem_2017_content_wrapper p {
 +
        padding: 15px 0;
 +
        font-size: 13px;
 +
    }
 +
    .igem_2017_content_wrapper img {
 +
        padding: 15px 0;
 +
    }
 +
 +
    /* Links */
 +
    .igem_2017_content_wrapper a {
 +
        font-weight: bold;
 +
        text-decoration: underline;
 +
        text-decoration-color: #3399ff;
 +
        color:  #3399ff;
 +
        -webkit-transition: all 0.4s ease;
 +
        -moz-transition: all 0.4s ease;
 +
        -ms-transition: all 0.4s ease;
 +
        -o-transition: all 0.4s ease;
 +
        transition: all 0.4s ease;
 +
    }
 +
 +
    /* hover for the links */
 +
    .igem_2017_content_wrapper a:hover {
 +
        text-decoration:none;
 +
        color:#000000;
 +
    }
 +
 +
    /* non numbered lists */
 +
    .igem_2017_content_wrapper ul {
 +
        padding:0px 20px;
 +
        font-size: 13px;
 +
        font-family:Tahoma, Geneva, sans-serif;
 +
    }
 +
 +
    /* numbered lists */
 +
    .igem_2017_content_wrapper ol {
 +
        padding:0px;
 +
        font-size: 13px;
 +
        font-family:Tahoma, Geneva, sans-serif;
 +
    }
 +
 +
    /* Table */
 +
    .igem_2017_content_wrapper table {
 +
        width: 97%;
 +
        margin:15px 10px;
 +
        border: 1px solid #d3d3d3;
 +
        border-collapse: collapse;
 +
    }
 +
 +
    /* table cells */
 +
    .igem_2017_content_wrapper  td {
 +
        padding: 10px;
 +
        vertical-align: text-top;
 +
        border: 1px solid #d3d3d3;
 +
        border-collapse: collapse;
 +
    }
 +
 +
    /* table headers */
 +
    .igem_2017_content_wrapper th {
 +
        padding: 10px;
 +
        vertical-align: text-top;
 +
        border: 1px solid #d3d3d3;
 +
        border-collapse: collapse;
 +
        background-color:#f2f2f2;
 +
    }
 +
 +
 +
    /**********************************LAYOUT CLASSES **********************************/
 +
 +
    /* general class for column divs */
 +
    .igem_2017_content_wrapper .column  {
 +
        padding: 10px 0px;
 +
        float:left;
 +
    }
 +
 +
    /* class for a full width column */
 +
    .column .full_size {
 +
        width:100%;
 +
    }
 +
 +
    /* styling for images in a full width column*/
 +
    .column.full_size img {
 +
        width:97%;
 +
        padding: 10px 15px;
 +
    }
 +
 +
    /* class for a half width column */
 +
    .column.half_size {
 +
        width: 50%;
 +
    }
 +
    /* styling for images in a half width column*/
 +
    .column.half_size img {
 +
        width: 94.5%;
 +
        padding: 10px 15px;
 +
    }
 +
 +
 +
 +
 +
    /********************************* SUPPORT CLASSES ********************************/
 +
 +
    /* class that clears content below*/
 +
    .igem_2017_content_wrapper .clear {
 +
        clear:both;
 +
    }
 +
 +
 +
    /* adds extra spacing when clearing content */
 +
    .igem_2017_content_wrapper  .clear.extra_space {
 +
        height: 30px;
 +
    }
 +
 +
 +
    /* highlight class, makes content slightly smaller */
 +
    .igem_2017_content_wrapper .highlight {
 +
        margin: 0px 15px;
 +
        padding: 15px 0px;
 +
    }
 +
 +
 +
    /* highlight class, adds a gray background */
 +
    .igem_2017_content_wrapper .highlight.gray {
 +
        background-color: #f2f2f2;
 +
    }
 +
 +
    /* highlight with decoration blue line on top */
 +
    .igem_2017_content_wrapper .highlight.blue_top {
 +
        border-top: 4px solid #3399ff;
 +
    }
 +
 +
    /* highlight with a full blue border decoration */
 +
    .igem_2017_content_wrapper .highlight.blue_border {
 +
        border: 4px solid  #3399ff;
 +
    }
 +
 +
 +
    /* button class */
 +
    .igem_2017_content_wrapper .button{
 +
        max-width: 35%;
 +
        margin: 30px auto;
 +
        padding: 12px 10px;
 +
        background-color: #3399ff;
 +
        text-align: center;
 +
        color: #ffffff;
 +
        -webkit-transition: all 0.4s ease;
 +
        -moz-transition: all 0.4s ease;
 +
        -ms-transition: all 0.4s ease;
 +
        -o-transition: all 0.4s ease; transition: all 0.4s ease;
 +
    }
 +
 +
    /* styling for button on hover */
 +
    .igem_2017_content_wrapper .button:hover{
 +
        background-color: #3399ff;
 +
        color: #000000;
 +
    }
 +
 +
 +
 +
 +
    /***************************************************** RESPONSIVE STYLING ****************************************************/
 +
 +
    /* IF THE SCREEN IS LESS THAN 1200PX */
 +
    @media only screen and (max-width: 1200px) {
 +
 +
        #content {width:100%; }
 +
        .igem_2017_menu_wrapper {width:15%; right:0;}
 +
        .highlight {padding:10px 0px;}
 +
        .igem_2017_menu_wrapper #display_menu_control { display:none; }
 +
        #menu_content { display:block;}
 +
        .menu_button.direct_to_page {padding-left: 17px;}
 +
 +
    }
 +
 +
    /* IF THE SCREEN IS LESS THAN 800PX */
 +
    @media only screen and (max-width: 800px) {
 +
 +
        .igem_2017_menu_wrapper { width:100%; height: 15%; position:relative; left:0%;}
 +
        .igem_2017_content_wrapper {width:100%; margin-left:0px;}
 +
        .column.half_size  {width:100%; }
 +
        .column.full_size img, .column.half_size img {  width: 100%; padding: 10px 0px;}
 +
        .highlight {padding:15px 5px;}
 +
        .igem_2017_menu_wrapper #display_menu_control { display:block; }
 +
        #menu_content { display:none;}
 +
        .igem_2017_menu_wrapper .menu_button .expand_collapse_icon { width: 5%; }
 +
        .menu_bottom_padding {display:none;}
 +
        .menu_button.direct_to_page { padding-left: 36px; }
 +
    }
 +
 +
 +
 +
 +
    /* special class that the system uses to make sure the team wants a page to be evaluated */
 +
    .judges-will-not-evaluate {
 +
        width: 96.6%;
 +
        margin: 5px 15px;
 +
        display: block;
 +
        border: 4px solid #3399ff;
 +
        font-weight: bold;
 +
    }
 +
 +
</style>
 +
 +
 +
<!--- THIS IS WHERE THE HTML BEGINS --->
 +
 +
<head>
 +
 +
    <!-- This tells the browser that your page is responsive -->
 +
    <meta name="viewport" content="width=device-width, initial-scale=1">
 +
 +
</head>
 +
 +
 +
<!--MENU-->
 +
<div class="igem_2017_menu_wrapper" >
 +
 +
 +
 +
    <a href="https://2017.igem.org/Team:Stuttgart">
 +
        <img src="http://placehold.it/350x150">
 +
    </a>
 +
 +
 +
    <!-- this div is hidden by default and will only be displayed if the screen size is too small -->
 +
    <div class="menu_button" id="display_menu_control">
 +
        MENU
 +
    </div>
 +
 +
    <div id="menu_content">
 +
 +
 +
 +
 +
        <a href="https://2017.igem.org/Team:Stuttgart">
 +
            <div class="menu_button direct_to_page">
 +
                HOME
 +
            </div>
 +
        </a>
 +
 +
 +
 +
        <div class="menu_button">
 +
            <div class="expand_collapse_icon">  </div> TEAM
 +
        </div>
 +
 +
        <div class="submenu_wrapper" id="team_submenu">
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Team">
 +
                <div class="submenu_button" id="Team_page">
 +
                    Team
 +
                </div>
 +
            </a>
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Collaborations">
 +
                <div class="submenu_button"  id="Collaborations_page">
 +
                    Collaborations
 +
                </div>
 +
            </a>
 +
 +
 +
        </div>
 +
 +
 +
 +
 +
 +
        <div class="menu_button">
 +
            <div class="expand_collapse_icon">  </div> PROJECT
 +
        </div>
 +
 +
        <!-- project submenu -->
 +
        <div class="submenu_wrapper">
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Description">
 +
                <div class="submenu_button"  id="Description_page">
 +
                    Description
 +
                </div>
 +
            </a>
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Design">
 +
                <div class="submenu_button"  id="Design_page">
 +
                    Design
 +
                </div>
 +
            </a>
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Experiments">
 +
                <div class="submenu_button"  id="Experiments_page">
 +
                    Experiments
 +
                </div>
 +
            </a>
 +
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Notebook">
 +
                <div class="submenu_button"  id="Notebook_page">
 +
                    Notebook
 +
                </div>
 +
            </a>
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/InterLab">
 +
                <div class="submenu_button"  id="InterLab_page">
 +
                    InterLab
 +
                </div>
 +
            </a>
 +
 +
            <a href="https://2017.igem.org/Team:Stuttgart/Contribution">
 +
                <div class="submenu_button"  id="Contribution_page">
 +
                    Contribution
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<h3><span style="color:#2E9AFE">Überschrift </span style="color:#2E9AFE"></h3><br>
 
  
 
<p><h3>Preparation of chemically competent DH5alpha E. coli cells</h3>
 
<p><h3>Preparation of chemically competent DH5alpha E. coli cells</h3>

Revision as of 12:15, 14 October 2017

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Protocols/Notebook

Preparation of chemically competent DH5alpha E. coli cells


Material:
  • LB media
  • TSS buffer
  • DH5alpha E. coli cells (o/n colonies on agar plates)

Method:
  1. Pick one colony of the plate and transfer into 5 mL of LB media. Grow the culture over night for 16-18 hours at 37 deg. celsius.
  2. Transfer 1 mL of the overnight culture into a shaking flask with 99 mL of LB media. Measure optical density (OD) at 600 nm and incubate culture at 37 deg. celsius (shaking) to an OD of 0,5.
  3. Divide the 100 mL into two 50 mL tubes and incubate 10 min on ice.
  4. Spin the tubes at 3000 rpm for 10 minutes at 4 deg. celsius.
  5. Resuspend the pellet of competent cells with 10 % TSS buffer (5 mL).
  6. Aliquot 100 µL of the cell solution into 1.5 mL microtubes (all steps on ice!).
  7. Store the competent cells at -80 deg. celsius.

Heat-shock Transformation of E. coli cells


Material:
  • SOC media
  • Agar plates with appropriate antibiotic

Method:
  1. Thaw chemically competent cells on ice.
  2. Transfer 50 µL of the cells into a 1.5 mL microtube, add 1 µL of the desired DNA and incubate on ice for 30 minutes.
  3. Place the tube in a 42 deg. celsius water bath for 60 seconds.
  4. After heat shock leave cells on ice for 5 minutes.
  5. Add 950 µL of SOC media and shake cells for 2 hours at 37 deg. celsius.
  6. Pipet 100 µL of the cells onto an appropriate plate and spread them using sterile glass beads. Incubate overnight at 37 deg. Celsius and hope for colonies in the morning to prove a successful transformation.

 

Preparation of LB media


Material:
  • Tryptone
  • NaCl
  • Yeast extract

Method:
  1. Fill a container (bottle) to about 60/70 % its volume with destilled water.
  2. Add 10 g/L Tryptone, 10 g/L NaCl and 5 g/L of yeast extract.
  3. Stir properly and fill up the remaining volume with distilled water.
  4. Treat LB media by autoclave.

Preparation of LB agar


Material:
  • Tryptone
  • NaCl
  • Yeast extract
  • Agar

Method:
  1. Fill a container (bottle) to about 60/70 % its volume with destilled water.
  2. Add 10 g/L Tryptone, 10 g/L NaCl, 5 g/L of yeast extract and 20 g/L agar.
  3. Stir properly and fill up the remaining volume with distilled water.
  4. Treat by autoclave.

Glycerol stocks – storage of bacterial strains


Material:
  • Glycerol

Method:
  1. Mix 700 µL of overnight culture with 300 µL glycerol.
  2. Store at -80 deg. Celsius.