Merge pull request #29 from sanger-pathogens/Mar22_updates

Mar22 updates

src/components/Gallery.js

@@ -0,0 +1,16 @@
+import React from 'react';
+import { Box } from '@material-ui/core';
+
+const Gallery = () => (
+  <Box>
+    <img src="/gallery/Get together at Jesus Green.jpg" alt="Get together at Jesus Green" width="50%" />
+    <img src="/gallery/IMG_4013.png" alt="Lunch on the Wellcome Genome Campus grounds" width="50%" />
+    <img src="/gallery/Narender_s first lunch at Sulston building with Steph since lockdown.jpg" alt="Narender's first lunch at Sulston building with Steph since lockdown" width="50%" />
+    <img src="/gallery/Steph_Nida_Meeting during pandemics on Genome campus.jpg" alt="Steph and Nida meeting during pandemics on Genome campus" width="50%" />
+    <img src="/gallery/IMG_4012.png" alt="First group lab meeting after the pandemic" width="50%" />
+    <img src="/gallery/IMG_4014.png" alt="Steph and Uzma talking from a social distance" width="50%" />
+    <img src="/gallery/Get together in front of King_s college.JPG" alt="Get together in front of King's college" width="100%" />
+  </Box>
+);
+
+export default Gallery;

src/components/JoinUs.js

@@ -0,0 +1,14 @@
+import React from 'react';
+import raw from 'raw.macro';
+
+import Markdown from './Markdown';
+
+const mdJoin = raw('../content/joinus.md');
+
+const JoinUs = () => (
+  <React.Fragment>
+    <Markdown md={mdJoin} />
+  </React.Fragment>
+);
+
+export default JoinUs;

src/components/Outreach.js

@@ -0,0 +1,30 @@
+import React from 'react';
+import raw from 'raw.macro';
+import { Grid, Box, Typography, Link } from '@material-ui/core';
+
+import outreach from '../content/outreach';
+import Markdown from './Markdown';
+import TeamDescriptionRenderer from './TeamDescriptionRenderer';
+
+const Item = ({ title, url, description, image }) => (
+  <Box>
+    <img src={image} alt ={`${title}`} width="100%" />
+    <Link variant="h6" href={url}>{title}</Link>
+    <TeamDescriptionRenderer md={description} />
+  </Box>
+);
+
+const Outreach = () => (
+  <Box pt={4} pb={4}>
+    <Grid container spacing={2}>
+      {outreach.map(item => (
+        <Grid key={item.title} item xs={12} sm={6} md={4} lg={4}>
+          <Item {...item} />
+        </Grid>
+      ))}
+    </Grid>
+  </Box>
+);
+
+
+export default Outreach;

src/components/Software.js

@@ -4,8 +4,22 @@ import { Grid, Box, Typography, Link } from '@material-ui/core';
 import softwares from '../content/software';
 import TeamDescriptionRenderer from './TeamDescriptionRenderer';
 
-const Software = ({ name, links, description }) => (
+const Publications = () => (
+  <>
+      <Link
+        variant="h6"
+        href="https://www.sanger.ac.uk/person/bentley-stephen-d/"
+        target="_blank"
+        rel="noopener noreferrer"
+      >
+        Click here to see publications.
+      </Link>
+  </>
+);
+
+const Software = ({ name, links, description, image }) => (
   <Box>
+    <img src={image} alt={`${name}`} width="100%" />
     <Typography variant="h6">{name}</Typography>
     {links.map((link, i) => (
       <Typography key={i} variant="body2">
@@ -30,4 +44,17 @@ const Softwares = () => (
   </Box>
 );
 
-export default Softwares;
+const PubSoft = () => (
+  <React.Fragment>
+  <Typography variant="h4" style={{ paddingTop: '1rem' }}>
+    Publications
+  </Typography>
+  <Publications />
+    <Typography variant="h4" style={{ paddingTop: '1rem' }}>
+      Software
+    </Typography>
+    <Softwares />
+  </React.Fragment>
+);
+
+export default PubSoft;

src/components/Team.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import raw from 'raw.macro';
-import { Grid, Box, Typography } from '@material-ui/core';
+import { Grid, Box, Typography, Link } from '@material-ui/core';
 
 import currentTeam from '../content/team';
 import honoraryTeam from '../content/honorary-team';
@@ -10,10 +10,10 @@ import TeamDescriptionRenderer from './TeamDescriptionRenderer';
 const mdVisitors = raw('../content/visitors.md');
 const mdAlumni = raw('../content/alumni.md');
 
-const Person = ({ name, role, imageUrl, description }) => (
+const Person = ({ name, role, imageUrl, sangerProfile, description }) => (
   <Box>
     <img src={imageUrl} alt={`${name} - ${role}`} width="100%" />
-    <Typography variant="h6">{name}</Typography>
+    <Link variant="h6" href={sangerProfile}>{name}</Link>
     <Typography variant="subtitle1">
       <i>{role}</i>
     </Typography>

src/content/alumni.md

@@ -1,11 +1,17 @@
 - Alison Maguire
 
+- [Chrispin Chaguza](https://medicine.yale.edu/profile/chrispin_chaguza/)
+
+- Christine J. Boinett
+
 - [Claire Chewapreecha](https://www.tropicalmedicine.ox.ac.uk/team/claire-chewapreecha)
 
 - Ebrima Bojang
 
 - Feyruz Yalcin
 
+- Gareth Peat
+
 - [John Lees](https://www.imperial.ac.uk/people/j.lees)
 
 - [Jyothish Bhai](https://www.ebi.ac.uk/about/people/jyothish-bhai)

src/content/honorary-team.json

@@ -10,5 +10,17 @@
         "role": "Visiting Researcher",
         "imageUrl": "/people/Felix_BW_square.png",
         "description": "My interest is in analysing microbial populations (with a focus on *Streptococcus pneumoniae*) to understand the epidemiology and spread of antimicrobial resistance."
+    },
+    {
+        "name": "Dr. Neil MacAlasdair",
+        "role": "Postdoctoral fellow",
+        "imageUrl": "/people/Neil_1_BW.jpg",
+        "description": "I study recombination and its effects on evolution in *Neisseria meningitidis* and how this affects various populations."
+    },
+    {
+        "name": "Dr. Gerry Tonkin-Hill",
+        "role": "Postdoctoral fellow",
+        "imageUrl": "/people/Gerry_1_BW.jpg",
+        "description": "I study within-host evolution and transmission in *Streptococcus pneumoniae* as well as  developing statistical and bioinformatics methods for microbial genomics."
     }
-]
+]

src/content/joinus.md

@@ -0,0 +1,9 @@
+- [Sanger's 4-Year PhD Programme](https://www.sanger.ac.uk/about/study/phd-programmes/4-year-phd-programme/)
+
+- [Sanger's Clinical PhD Programme](https://www.sanger.ac.uk/about/study/phd-programmes/clinical-phd-programme/)
+
+- [Sanger's MPhil Programme](https://www.sanger.ac.uk/about/study/masters-programmes/)
+
+- [SEED Postdoctoral Fellowships](https://www.sanger.ac.uk/about/careers/seed-fellowship-sanger-evolutionary-and-epidemiological-dynamics/)
+
+- [Gates Cambridge Scholarship Programme](https://www.cam.ac.uk/gatesalumni)

src/content/navigationAnchored.json

@@ -1,7 +1,9 @@
 [
     { "label": "About Us", "url": "about"},
     { "label": "Research", "url": "research"},
-    { "label": "Software", "url": "software"},
+    { "label": "Publications & Software", "url": "software"},
     { "label": "Team", "url": "team"},
-    { "label": "Publications", "url": "publications"}
+    { "label": "Outreach", "url": "outreach"},
+    { "label": "Gallery", "url": "gallery"},
+    { "label": "Join Us", "url": "joinus"}
 ]

src/content/outreach.json

@@ -0,0 +1,14 @@
+[
+    {
+        "title": "Decoding Life Podcast",
+        "url": "https://anchor.fm/decoding-life-pod",
+        "description": "This podcast tells stories of the science at the Wellcome Genome Campus and the people behind it. From PhD students to group leaders, software developers to diversity champions -- we speak with these individuals and discover the paths they have taken throughout their careers, what it’s really like to do some of these jobs, and learn about some of the science along the way. This podcast is co-hosted by Kathryn Murie and Sophie Belman and is funded by [Wellcome Genome Campus Public Engagement](https://publicengagement.wellcomeconnectingscience.org/).  It is available to listen on [Spotify](https://open.spotify.com/show/2J2W9Ob3GHdTzRUh8GrUmq?si=wrNwAoVJRd21YGHZiJ1C0g&dl_branch=1&nd=1), [Apple Podcasts](https://podcasts.apple.com/us/podcast/decoding-life/id1556132006), or anywhere else you get your podcasts.",
+        "image": "/decodinglife.png"
+    },
+    {
+        "title": "Your Digital Mentor Podcast",
+        "url": "https://coursesandconferences.wellcomeconnectingscience.org/our-events/your-digital-mentor-podcast/",
+        "description": "The podcast is a series that aims to provide access to conversations around mentoring and other aspects of research and career development. This is delivered as part of a collaborative project between the [Wellcome Sanger Institute](https://www.sanger.ac.uk/), [Wellcome Connecting Science](https://www.wellcomeconnectingscience.org/), and the [Social Entrepreneurship to Spur Health](https://www.seshglobal.org/).",
+        "image": "/digitalmentor.png"
+    }
+]

src/content/sections.js

@@ -1,9 +1,11 @@
 import AboutUs from '../components/AboutUs';
 import ResearchThemes from '../components/ResearchThemes';
-import Publications from '../components/Publications';
 import Software from '../components/Software';
 import Team from '../components/Team';
 import Collaborators from '../components/Collaborators';
+import Outreach from '../components/Outreach';
+import Gallery from '../components/Gallery';
+import JoinUs from '../components/JoinUs';
 
 export default [
   {
@@ -19,8 +21,8 @@ export default [
     ContentComponent: ResearchThemes,
   },
   {
-    label: 'Software',
-    title: 'Software',
+    label: 'Publications & Software',
+    title: 'Publications & Software',
     url: 'software',
     ContentComponent: Software,
   },
@@ -37,9 +39,21 @@ export default [
     ContentComponent: Collaborators,
   },
   {
-    label: 'Papers',
-    title: 'Selected papers',
-    url: 'papers',
-    ContentComponent: Publications,
+    label: 'Outreach',
+    title: 'Outreach',
+    url: 'outreach',
+    ContentComponent: Outreach,
+  },
+  {
+    label: 'Gallery',
+    title: 'Gallery',
+    url: 'gallery',
+    ContentComponent: Gallery,
+  },
+  {
+    label: 'Join Us',
+    title: 'Join Us',
+    url: 'joinus',
+    ContentComponent: JoinUs,
   },
 ];

src/content/software.json

@@ -7,7 +7,8 @@
                 "url": "https://github.com/gtonkinhill/fastbaps"
             }
         ],
-        "description": "Fastbaps is a fast solution to the genetic clustering problem. It rapidly identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10–100 times larger including over 110,000 sequences of HIV-1 pol genes."
+        "description": "Fastbaps is a fast solution to the genetic clustering problem. It rapidly identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10–100 times larger including over 110,000 sequences of HIV-1 pol genes.",
+        "image": "/software/FastBAPS.png"
     },
     {
         "name": "Gubbins",
@@ -17,7 +18,8 @@
                 "url": "http://sanger-pathogens.github.io/gubbins/"
             }
         ],
-        "description": "Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) identifies recombination regions in the bacterial genome using an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions."
+        "description": "Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) identifies recombination regions in the bacterial genome using an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.",
+        "image": "/software/Gubbins.jpg"
     },
     {
         "name": "Pairsnp",
@@ -27,7 +29,8 @@
                 "url": "https://github.com/gtonkinhill/pairsnp"
             }
         ],
-        "description": "Pairsnp is used to quickly obtain pairwise SNP distance matrices from multiple sequence alignments. For larger alignments, pairsnp is an order of magnitude faster than approaches based on pairwise comparison of every site."
+        "description": "Pairsnp is used to quickly obtain pairwise SNP distance matrices from multiple sequence alignments. For larger alignments, pairsnp is an order of magnitude faster than approaches based on pairwise comparison of every site.",
+        "image": "/software/pairsnp.png"
     },
     {
         "name": "Panaroo",
@@ -37,7 +40,8 @@
                 "url": "https://github.com/gtonkinhill/panaroo"
             }
         ],
-        "description": "Panaroo is a graph based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies."
+        "description": "Panaroo is a graph based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies.",
+        "image": "/software/panaroo.png"
     },
     {
         "name": "PopPUNK",
@@ -47,7 +51,8 @@
                 "url": "https://poppunk.readthedocs.io/en/latest/"
             }
         ],
-        "description": "PopPUNK (Population Partitioning Using Nucleotide K-mers) uses scalable and expandable annotation- and alignment-free methods for population analysis and clustering."
+        "description": "PopPUNK (Population Partitioning Using Nucleotide K-mers) uses scalable and expandable annotation- and alignment-free methods for population analysis and clustering.",
+        "image": "/software/poppunk_v2.png"
     },
     {
         "name": "SEER and PYSEER",
@@ -61,6 +66,7 @@
                 "url": "https://pyseer.readthedocs.io/en/master/"
             }
         ],
-        "description": "SEER (sequence element enrichment analysis) is a statistical method that identifies sequence elements that are significantly enriched in a phenotype of interest. PYSEER is a further implementation of seer written in python with additional features. Both pyseer and its predecessor, seer, allow for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses."
+        "description": "SEER (sequence element enrichment analysis) is a statistical method that identifies sequence elements that are significantly enriched in a phenotype of interest. PYSEER is a further implementation of seer written in python with additional features. Both pyseer and its predecessor, seer, allow for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses.",
+        "image": "/software/pyseer_logo.png"
     }
-]
+]