update sanger links to https

about.html

@@ -75,12 +75,12 @@ <h2>About Us</h2>
             <div class="schoolInfo">
               <h2 class="color-1">Wellcome Sanger Institute</h2>
               <h3>Researching Neglected Tropical Diseases</h3>
-              <p>We are scientists at the <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a>, based at Hinxton, near Cambridge, in the UK.  We are researching the biology of a number of the organisms that cause Neglected Tropical Diseases (NTDs).</p>
+              <p>We are scientists at the <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a>, based at Hinxton, near Cambridge, in the UK.  We are researching the biology of a number of the organisms that cause Neglected Tropical Diseases (NTDs).</p>
               <p>We hope that the findings from our research will further understanding of these organisms so that ultimately vaccines, drugs and intervention strategies can be used to reduce, or even eliminate, the diseases.</p>
               <p>These organisms are also fascinating in their own right, often possessing unique and interesting biology, which we hope to learn more about.</p>
               <p class="color-3">Follow the link below to find out more about who we are and the scientific research we do at the Wellcome Sanger Institute.</p>
 
-              <a href="http://www.sanger.ac.uk/science/programmes/infection-genomics" target="_blank" class="btn btn-primary">read more</a>
+              <a href="https://www.sanger.ac.uk/science/programmes/infection-genomics" target="_blank" class="btn btn-primary">read more</a>
             </div>
           </div>
         </div>

blogs/pandemic-on-a-plate.html

@@ -72,7 +72,7 @@ <h2>NTD Researcher Stories</h2>
           <div class="col-sm-12 col-xs-12 block">
               <div>
                 <h1 class="text-center">Pandemic on a Plate</h1>
-                <h2 class="text-center">By <a href="http://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank">Daryl Domman</a></h2>
+                <h2 class="text-center">By <a href="https://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank">Daryl Domman</a></h2>
               </div>
             </div>
         </div>
@@ -98,7 +98,7 @@ <h2 class="text-center">By <a href="http://www.sanger.ac.uk/people/directory/dom
           <div class="col-sm-4 col-xs-12 block">
               <div class="blogImage"> 
                 <img src="../../img/blogs/daryl-domman.jpg" alt="Daryl Domman, Wellcome Sanger Institute" title="Daryl Domman, Wellcome Sanger Institute" class="img-rounded img-responsive">
-                <p class="blogCaption"><a href="http://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank"><em>Daryl Domman, Sanger</em></a></p>
+                <p class="blogCaption"><a href="https://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank"><em>Daryl Domman, Sanger</em></a></p>
               </div>
           </div>
 

blogs/seeing-through-blindness.html

@@ -72,7 +72,7 @@ <h2>NTD Researcher Stories</h2>
           <div class="col-sm-12 col-xs-12 block">
               <div>
                 <h1 class="text-center">Seeing through blindness</h1>
-                <h2 class="text-center">By <a href="http://www.sanger.ac.uk/people/directory/benard-angele" target="_blank">Ang&egrave;le B&eacute;nard</a></h2>
+                <h2 class="text-center">By <a href="https://www.sanger.ac.uk/people/directory/benard-angele" target="_blank">Ang&egrave;le B&eacute;nard</a></h2>
               </div>
             </div>
         </div>
@@ -97,7 +97,7 @@ <h2 class="text-center">By <a href="http://www.sanger.ac.uk/people/directory/ben
           <div class="col-sm-4 col-xs-12 block">
               <div class="blogImage"> 
                 <img src="../../img/blogs/angele-benard.jpg" alt="Ang&egrave;le B&eacute;nard, Wellcome Sanger Institute" title="Ang&egrave;le B&eacute;nard, Wellcome Sanger Institute" class="img-rounded img-responsive">
-                <p class="blogCaption"><a href="http://www.sanger.ac.uk/people/directory/benard-angele" target="_blank"><em>Ang&egrave;le B&eacute;nard, Sanger</em></a></p>
+                <p class="blogCaption"><a href="https://www.sanger.ac.uk/people/directory/benard-angele" target="_blank"><em>Ang&egrave;le B&eacute;nard, Sanger</em></a></p>
               </div>
           </div>
         </div>   

includes/footer-subdir.html

@@ -21,7 +21,7 @@
       <div class="row">
         <div class="col-sm-6 col-xs-12">
           <div class="footerTitle">
-            <a href="http://www.sanger.ac.uk"><img src="../../img/footer/logo-wsi-footer.png"></a>
+            <a href="https://www.sanger.ac.uk"><img src="../../img/footer/logo-wsi-footer.png"></a>
           </div>
           <div class="footerInfo">
             <p><strong>Wellcome Genome Campus</strong> <br /> Hinxton <br />Cambridgeshire <br />CB10 1SA <br /> United Kingdom</p>
@@ -37,7 +37,7 @@ <h4>Useful Links</h4>
           <div class="footerInfo">
             <ul class="list-unstyled footerList">
               <li>
-                <a href="http://www.sanger.ac.uk/science/programmes/infection-genomics">
+                <a href="https://www.sanger.ac.uk/science/programmes/infection-genomics">
                 <i class="fa fa-angle-double-right" aria-hidden="true"></i>Sanger Infection Genomics
                 </a>
               </li>
@@ -81,7 +81,7 @@ <h4>Useful Links</h4>
         </div>
         <div class="col-sm-7 col-sm-pull-5 col-xs-12">
           <div class="copyRightText">
-            <p>&copy; <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> under the <a href="http://www.sanger.ac.uk/legal/" target="_blank">Sanger terms & conditions</a></p>
+            <p>&copy; <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> under the <a href="https://www.sanger.ac.uk/legal/" target="_blank">Sanger terms & conditions</a></p>
           </div>
         </div>
       </div>

includes/footer.html

@@ -21,7 +21,7 @@
       <div class="row">
         <div class="col-sm-6 col-xs-12">
           <div class="footerTitle">
-            <a href="http://www.sanger.ac.uk"><img src="img/footer/logo-wsi-footer.png"></a>
+            <a href="https://www.sanger.ac.uk"><img src="img/footer/logo-wsi-footer.png"></a>
           </div>
           <div class="footerInfo">
             <p><strong>Wellcome Genome Campus</strong> <br /> Hinxton <br />Cambridgeshire <br />CB10 1SA <br /> United Kingdom</p>
@@ -37,7 +37,7 @@ <h4>Useful Links</h4>
           <div class="footerInfo">
             <ul class="list-unstyled footerList">
               <li>
-                <a href="http://www.sanger.ac.uk/science/programmes/infection-genomics">
+                <a href="https://www.sanger.ac.uk/science/programmes/infection-genomics">
                 <i class="fa fa-angle-double-right" aria-hidden="true"></i>Sanger Infection Genomics
                 </a>
               </li>
@@ -81,7 +81,7 @@ <h4>Useful Links</h4>
         </div>
         <div class="col-sm-7 col-sm-pull-5 col-xs-12">
           <div class="copyRightText">
-              <p>&copy; <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> under the <a href="http://www.sanger.ac.uk/legal/" target="_blank">Sanger terms & conditions</a></p>
+              <p>&copy; <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> under the <a href="https://www.sanger.ac.uk/legal/" target="_blank">Sanger terms & conditions</a></p>
             </ul>
           </div>
         </div>

includes/navbar-subdir.html

@@ -7,7 +7,7 @@
       <span class="icon-bar"></span>
       <span class="icon-bar"></span>
     </button>
-    <a class="navbar-brand" href="http://www.sanger.ac.uk"><img src="../../img/logo-ntd.jpg" alt="Neglected tropical disease"></a>
+    <a class="navbar-brand" href="https://www.sanger.ac.uk"><img src="../../img/logo-ntd.jpg" alt="Neglected tropical disease"></a>
   </div>
 	<!-- LOGO END -->
 

includes/navbar.html

@@ -7,7 +7,7 @@
       <span class="icon-bar"></span>
       <span class="icon-bar"></span>
     </button>
-    <a class="navbar-brand" href="http://www.sanger.ac.uk"><img src="img/logo-ntd.jpg" alt="Neglected tropical disease"></a>
+    <a class="navbar-brand" href="https://www.sanger.ac.uk"><img src="img/logo-ntd.jpg" alt="Neglected tropical disease"></a>
   </div>
 	<!-- LOGO END -->
 

ntds/cholera.html

@@ -106,12 +106,12 @@ <h3>Cholera</h3>
               </div>
               <div class="diseaseHeader bg-color-3">Using pathogen material to do research</div>
               <div class="diseaseDetails">
-                <p class="text-justify">At the <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a>, we are using the genome sequences of <em>V. cholerae</em> genomes to understand how different outbreaks of cholera are related to one another. This has allowed us to move toward explaining how this disease is moving across the planet. We are also beginning experimental work with <em>V. cholerae</em> to understand what it is that makes specific lineages of <em>V. cholerae</em> capable of causing global epidemics of disease, and what prevents other populations of this bacterium from doing so.</p>
+                <p class="text-justify">At the <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a>, we are using the genome sequences of <em>V. cholerae</em> genomes to understand how different outbreaks of cholera are related to one another. This has allowed us to move toward explaining how this disease is moving across the planet. We are also beginning experimental work with <em>V. cholerae</em> to understand what it is that makes specific lineages of <em>V. cholerae</em> capable of causing global epidemics of disease, and what prevents other populations of this bacterium from doing so.</p>
               </div>
               <div class="diseaseHeader bg-color-6">Useful links</div>
               <div class="diseaseDetails">
                 <ul class="list-unstyled para-list">
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="http://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank">Daryl Domman</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="https://www.sanger.ac.uk/people/directory/domman-daryl" target="_blank">Daryl Domman</a>.</li>
                   <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Read more about cholera from the <a href="http://www.who.int/cholera/en/" target="_blank">WHO</a>.</li>
                 </ul>
               </div>

ntds/etec-infections.html

@@ -117,7 +117,7 @@ <h3>ETEC infections</h3>
               <div class="diseaseHeader bg-color-6">Useful links</div>
               <div class="diseaseDetails">
                 <ul class="list-unstyled para-list">
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about research groups at the Wellcome Sanger Institute working on ETEC and other bacteria <a href="http://www.sanger.ac.uk/science/groups/dougan-group" target="_blank">here</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about research groups at the Wellcome Sanger Institute working on ETEC and other bacteria <a href="https://www.sanger.ac.uk/science/groups/dougan-group" target="_blank">here</a>.</li>
                   <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Read more about ETEC from the <a href="https://www.cdc.gov/ecoli/etec.html" target="_blank">CDC</a>.</li>
                 </ul>
               </div>

ntds/guinea-worm-disease.html

@@ -116,8 +116,8 @@ <h3>Guinea worm disease</h3>
               <div class="diseaseHeader bg-color-6">Useful links</div>
               <div class="diseaseDetails">
                 <ul class="list-unstyled para-list">
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="http://www.sanger.ac.uk/people/directory/cotton-james" target="_blank">James Cotton</a>.</li>
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at <a href="http://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Sanger</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="https://www.sanger.ac.uk/people/directory/cotton-james" target="_blank">James Cotton</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at <a href="https://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Sanger</a>.</li>
                   <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Read more about the <a href="http://www.who.int/dracunculiasis/eradication/en/" target="_blank">GWD erradication programme</a>.</li>
                 </ul>
               </div>

ntds/leishmania.html

@@ -112,7 +112,7 @@ <h3>Leishmaniasis</h3>
               </div>
               <div class="diseaseHeader bg-color-3">Using pathogen material to do research</div>
               <div class="diseaseDetails">
-                <p class="text-justify">The <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> has a long history of involvement in understanding the genomes of Leishmania parasites, having been involved in producing the first reference genome major, made public in 2005.</p>
+                <p class="text-justify">The <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> has a long history of involvement in understanding the genomes of Leishmania parasites, having been involved in producing the first reference genome major, made public in 2005.</p>
                 <p  class="text-justify">Two major research projects on <em>Leishmania</em> are being done at the Wellcome Sanger Institute:</p>
                 <ol class="text-justify">
                   <li>understanding the evolution and diversity of <em>Leishmania</em> by generating whole-genome sequence data from large-scale collections of parasites (including both human cases of disease and animal reservoirs)</li>
@@ -122,8 +122,8 @@ <h3>Leishmaniasis</h3>
               <div class="diseaseHeader bg-color-6">Useful links</div>
               <div class="diseaseDetails">
                 <ul class="list-unstyled para-list">
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="http://www.sanger.ac.uk/people/directory/cotton-james" target="_blank">James Cotton</a>.</li>
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at the <a href="http://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Wellcome Sanger Institute</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about the author of this page, <a href="https://www.sanger.ac.uk/people/directory/cotton-james" target="_blank">James Cotton</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at the <a href="https://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Wellcome Sanger Institute</a>.</li>
                 </ul>
               </div>
             </div>

ntds/schistosomiasis.html

@@ -118,12 +118,12 @@ <h3>Schistosomiasis</h3>
               <div class="diseaseDetails">
                 <p class="text-justify">Even though the parasite life cycle and the disease were described over one hundred years ago, there is still a huge gap in the knowledge of the basic biology and interactions between the parasite and the host. In 2009, the complete genomes of <em>Schistosoma mansoni</em> and <em>S. japonicum</em> were published, followed by <em>S. haematobium</em> 3 years later. High throughput gene expression studies from developmental stages are also available on <a href="http://www.genedb.org/Homepage/Smansoni" target="_blank">GeneDB</a> and <a href="https://parasite.wormbase.org/index.html" target="_blank">WormBase ParaSite</a>.</p>
 
-                <p class="text-justify">In our Parasite Genomics laboratory at the <a href="http://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> we have set up the complete life cycle of <em>S. mansoni</em>, breeding a colony of susceptible freshwater snails to access all developmental stages. We can isolate parasite biomolecules, e.g. nucleic acids and proteins, and functional approaches are being developed to understand the role of genes relevant for parasite development or important in the interaction with the host. The role of host genes during the infection is also analyzed by employing a murine model of the disease.</p>
+                <p class="text-justify">In our Parasite Genomics laboratory at the <a href="https://www.sanger.ac.uk" target="_blank">Wellcome Sanger Institute</a> we have set up the complete life cycle of <em>S. mansoni</em>, breeding a colony of susceptible freshwater snails to access all developmental stages. We can isolate parasite biomolecules, e.g. nucleic acids and proteins, and functional approaches are being developed to understand the role of genes relevant for parasite development or important in the interaction with the host. The role of host genes during the infection is also analyzed by employing a murine model of the disease.</p>
             </div>
             <div class="diseaseHeader bg-color-6">Useful links</div>
               <div class="diseaseDetails">
                 <ul class="list-unstyled para-list">
-                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at the <a href="http://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Wellcome Sanger Institute</a>.</li>
+                  <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Find out more about parasite genomics at the <a href="https://www.sanger.ac.uk/science/groups/berriman-group" target="_blank">Wellcome Sanger Institute</a>.</li>
                   <li><i class="fa fa-external-link-square " aria-hidden="true"></i> Read more about schistosomiasis from the <a href="http://www.who.int/schistosomiasis/en/" target="_blank">WHO</a>.</li>
                 </ul>
               </div>