edits3

docs/ensembl-help/using-ensembl/ensembl-apps/species-selector/species-selector-intro.md

@@ -79,7 +79,7 @@ Your list of species genomes can be used in all other apps, ie the Genome browse
 
 The lozenges representing the species genomes are displayed in a row at the top of each app.
 
-<img src="/media/multiple-species-selected.png" width="320" alt="Selected species genome lozenges">
+<img src="/media/multiple-species-selected.png" width="450" alt="Selected species genome lozenges">
 
 ### How to find specific genomes in a large table of assemblies
 
@@ -126,11 +126,11 @@ A warning message will be displayed. Select the green 'Remove' button to delete
 
 ## Deactivating a species genome in your list 
 
-<img src="media/use-ss.png" width="320" alt="A Use or do not use slider">
+<img src="media/use-ss.png" width="450" alt="A Use or do not use slider">
 
 You can deactivate a species genome by toogling to 'Don't use' at the top of the Species homepage.
 
-<img src="media/do-not-use-ss.png" width="320" alt="Do not use selected">
+<img src="media/do-not-use-ss.png" width="450" alt="Do not use selected">
 
 The deactivated species genome lozenge will remain in your list and turn grey. Active species genome lozenges remain blue.
 

docs/ensembl-help/using-ensembl/ensembl-apps/vep/vep.md

@@ -9,7 +9,7 @@ description: How to run the Variant Effect Predictor(VEP)
 The Ensembl Variant Effect Predictor (VEP) tool can be found on the toolbar at the top of the Beta site.
 
 <figure>
-  <img src="media/toolbar-vep.png" width="450" alt="toolbar showing the VEP icon" />
+  <img src="media/toolbar-vep.png" width="450" alt="toolbar showing VEP icon"/>
   <figcaption>
     A view of the tool bar showing the Ensembl Variant Effect Predictor (VEP) icon.
   </figcaption>
@@ -21,7 +21,7 @@ To use the  VEP tool, you need to
 * run your job.
 
 <figure>
-  <img src="media/vep-landing-page.png" />
+  <img src="media/vep-landing-page.png"/>
   <figcaption>
     A view of the VEP input interface.
   </figcaption>
@@ -38,33 +38,70 @@ You can search for a species genome or assembly, using the:
 * assembly accession number.
 
 <figure>
-  <img src="media/search-common-name-vep.png" width="450" alt="Search term human in the search box" />
+  <img src="media/search-common-name-vep.png" width="450" alt="search term human in search box"/>
   <figcaption>
     A search for human genomes using the common name.
   </figcaption>
 </figure>
 
 A  table of the genome assemblies for that species will be displayed
 
-Choose the genome assembly of interest  by selecting the box to the left of the assembly followed by the green Add button.
+<figure>
+  <img src="media/human-genome-list-vep.png" alt="A table of all the genome assemblies"/>
+  <figcaption>
+    A table of the genome assemblies produced from a search for human.
+  </figcaption>
+</figure>
+
+Choose the genome assembly of interest by selecting the box to the left of the assembly followed by the green Add button.
+
 The chosen species genome assembly will be displayed in the Species section of the VEP input page.
 
+<figure>
+  <img src="media/search-common-name-vep.png" width="450" alt="The VEP input interface showing the selected genome"/>
+  <figcaption>
+    The selected human genome shown on the VEP input interface.
+  </figcaption>
+</figure>
 
 ## How to upload your variant data
 All variant information must be in Variant Call Format(VCF) to be uploaded into VEP.
 There are two ways to upload your variant data:
 
-Paste: simply copy and paste your variant information (in VCF) into the large text box displaying ‘Paste data’. 
+- Paste: simply copy and paste your variant information (in VCF) into the large text box displaying ‘Paste data’. 
+
+<figure>
+  <img src="media/paste-data-vep.png" width="450" alt="Pasting data into VEP"/>
+  <figcaption>
+    Pasting VCF data into the VEP input.
+  </figcaption>
+</figure>
 
 Then select the Add button and your input data will be displayed in the Variants section
 
-File upload: to upload your file of variants (in VCF) you can either:  
-* drag and drop the file directly onto the cloud icon inside the box  
+- File upload: to upload your file of variants (in VCF) you can either:  
+- drag and drop the file directly onto the cloud icon inside the box  
 or
-* click inside the box and locate the file on your system. 
+- click inside the box and locate the file on your system. 
+
+<figure>
+  <img src="media/uploading-data-vep.png" width="450" alt="Uploading a file of VCF data into VEP"/>
+  <figcaption>
+    Uploading a file of your VCF data into the VEP input form.
+  </figcaption>
+</figure>
 
 Then select the blue Open button and your input data will be displayed in the Variants section.
+
 The variants you are running against the chosen genome assembly  will be displayed in the variant section on the VEP input page.
+
+<figure>
+  <img src="media/" width="450" alt="VEP input interace showing uploaded variant data"/>
+  <figcaption>
+    VEP input interace showing uploaded variant data.
+  </figcaption>
+</figure>
+
 To update or edit your choice of variants select Change to the right-hand side of the Variant section. 
 
 ## Additional information associated with test variants 
@@ -79,8 +116,15 @@ VEP can provide additional information about
 * __Regulatory annotation__ 
 * __Conservation and constraints__ of the location of variants
 
-### Options in the current  versions of VEPs
-In the current version of VEP the Gene symbol and Transcript biotype associated with a variant are  selected by default and will be displayed in the results.
+### Options in the current versions of VEPs
+In the current version of VEP the Gene symbol and Transcript biotype associated with a variant are selected by default and will be displayed in the results.
+
+<figure>
+  <img src="media/current-options-vep.png" width="450" alt="More information options currently available on the VEP interface"/>
+  <figcaption>
+    More information options currently available on the VEP data input interface.
+  </figcaption>
+</figure>
 
 ### Options in future versions of VEPs
 In future versions of VEP you will be able to select additional types of information (listed above) associated with your variants of interest.   
@@ -89,14 +133,32 @@ In future versions of VEP you will be able to select additional types of informa
 You can add a name for the data you upload by typing it into  the box alongside the Submission name. 
 This can make it easier for you to identify jobs and files that you have uploaded to the VEP at a later point.
 
+<figure>
+  <img src="media/job-name-vep.png" width="450" alt=" A VEP input interface showing a filled in job name."/>
+  <figcaption>
+    A VEP input interface showing a filled in job name.
+  </figcaption>
+</figure>
+
 ## Running your VEP job
 To run your job select the green Run button on the top  grey bar to the right-hand side of the Transcript set and you will be taken to the submission page. 
+
 The submissions page will show the jobs that are currently ‘running’ or recently completed. 
+
+<figure>
+  <img src="media/running-job-vep" width="450" alt=" A VEP input interface showing a filled in job name."/>
+  <figcaption>
+    A VEP input interface showing a filled in job name.
+  </figcaption>
+</figure>
+
 A submission ID is assigned to each submission and additional information is provided, including the date and time of submission. 
 
 If you navigate away from the VEP interface, while the job is still running  the status of the query is indicated by the VEP icon in the top panel changing from red to green to prompt you that it has successfully completed.
 Jobs are divided into two lists: ‘Unviewed Jobs’ and ‘Jobs list’.
+
 A submission in the ‘Unviewed jobs’ list, when viewed, is transferred to the ‘Jobs list’ for future reference. Results are available for 7 days and queries can be rerun for 28 days.
+
 Select the blue New job button in the top grey bar (to the left-hand side of ENSEMBL VEP logo) to run another job.
 
 ## How to view your VEP results 
@@ -105,6 +167,13 @@ To view the results of your VEP job  select the Results button to the right-hand
 
 You will be taken to the  results page which will display the table of results for the variant(s) submitted against the genome assembly chosen.
 
+<figure>
+  <img src="media/results-table-vep.png" width="450" alt="A table of VEP results."/>
+  <figcaption>
+    A table of VEP results.
+  </figcaption>
+</figure>
+
 The table currently shows the following information about the variant(s) found on the chosen genome assembly.
 * __Variant type__ eg SNP
 * __Reference allele__ for the variant eg A