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Merge branch 'main' of https://github.com/harvardinformatics/informat…
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…ics-website
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@microlei
microlei committed Dec 18, 2023
2 parents f17e89d + add5b07 commit b7bf1b6
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41 changes: 18 additions & 23 deletions .github/workflows/gh-pages.yml
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Expand Up @@ -28,36 +28,31 @@ jobs:
runs-on: ubuntu-latest
needs: build
steps:
- uses: ruby/setup-ruby@v1
with:
ruby-version: '3.2' # Not needed with a .ruby-version file
bundler-cache: true # runs 'bundle install' and caches installed gems automatically
cache-version: 0 # https://github.com/ruby/setup-ruby#dealing-with-a-corrupted-cache
- name: install htmlproofer
run: gem install html-proofer -v 5.0.8
# Cache HTMLProofer external URL results for 30 days
# https://github.com/gjtorikian/html-proofer/#caching-with-continuous-integration
- uses: actions/cache/restore@v3
id: restore-cache-htmlproofer
with:
path: tmp/.htmlproofer
key: ${{ runner.os }}-html-proofer
# Cache lychee external URL results for 30 days
- name: Download site
uses: actions/download-artifact@v3
with:
name: github-pages
- run: tar -xf artifact.tar && rm artifact.tar
- name: run htmlproofer
# keep --swap-urls in sync with mkdocs.yml site_url
run: |
htmlproofer --ignore-missing-alt --cache '{"timeframe": {"external": "30d"}}' --swap-urls /informatics-website/:/
# https://github.com/actions/cache/blob/main/save/README.md#always-save-cache
- uses: actions/cache/save@v3
id: save-cache-htmlproofer
# https://github.com/lycheeverse/lychee-action#utilising-the-cache-feature
- name: Restore lychee cache
id: restore-cache
uses: actions/cache/restore@v3
with:
path: .lycheecache
key: cache-lychee-${{ github.sha }}
restore-keys: cache-lychee-
- name: Run lychee
uses: lycheeverse/lychee-action@v1.8.0
with:
args: "--base . --cache --max-cache-age 30d --require-https --timeout 5 --exclude 'fonts.gstatic.com' --exclude 'www.microsoft.com/en-us/microsoft-365/onedrive/online-cloud-storage' --exclude-path 404.html -- './**/*.html' './**/*.css'"
fail: true
- name: Save lychee cache
uses: actions/cache/save@v3
if: always()
with:
path: tmp/.htmlproofer
key: ${{ runner.os }}-html-proofer
path: .lycheecache
key: ${{ steps.restore-cache.outputs.cache-primary-key }}

deploy:
if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
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344 changes: 344 additions & 0 deletions data/people/people.json
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@@ -0,0 +1,344 @@
{
"Bioinformatics": {
"Director": {
"Tim Sackton": {
"id": "1",
"name": "Tim Sackton",
"title" : "Director of Bioinformatics",
"email" : "tsackton@g.harvard.edu",
"office" : "B227.10",
"img": "img/people/timsackton.jpg",
"date-added": "12-05-2023",
"date-joined": "07-01-2017",
"date-left": "",
"status" : "active",
"link": "people/timsackton/",
"pubs": "https://scholar.google.com/citations?hl=en&user=u8RfnXoAAAAJ&view_op=list_works&sortby=pubdate",
"github": "https://github.com/tsackton",
"profile": "Tim runs the Bioinformatics group. While his background is population and comparative genomics, these days he does a little bit of everything."
}
},
"Senior Bioinformatics Scientists": {
"Adam Freedman": {
"id": "10",
"name": "Adam Freedman",
"title" : "Senior Bioinformatics Scientist",
"email" : "afreedman@fas.harvard.edu",
"office" : "B227.30",
"img": "img/people/adamfreedman.png",
"date-added": "12-05-2023",
"date-joined": "06-01-2015",
"date-left": "",
"status" : "active",
"link": "https://ahfgenomics.com/",
"pubs": "https://scholar.google.com/citations?hl=en&user=6Bt9l1wAAAAJ&view_op=list_works&sortby=pubdate",
"github": "https://github.com/adamfreedman",
"profile": "Adam is our resident expert in genome annotation and RNA-seq analysis, and also has a background in population and conservation genetics."
},
"Danielle Khost": {
"id": "11",
"name": "Danielle Khost",
"title" : "Senior Bioinformatics Scientist",
"email" : "danielle_khost@fas.harvard.edu",
"office" : "B227.65",
"img": "img/people/daniellekhost.jpg",
"date-added": "12-05-2023",
"date-joined": "06-27-2019",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "",
"github": "https://github.com/danielle-khost",
"profile": "Danielle is our resident expert in long read sequencing, and works on a variety of challenging genome assembly problems."
},
"Gregg Thomas": {
"id": "12",
"name": "Gregg Thomas",
"title" : "Senior Bioinformatics Scientist",
"email" : "gthomas@fas.harvard.edu",
"office" : "B227.65",
"img": "img/people/greggthomas.jpg",
"date-added": "12-05-2023",
"date-joined": "07-06-2021",
"date-left": "",
"status" : "active",
"link": "https://gwct.github.io/",
"pubs": "https://scholar.google.com/citations?hl=en&user=4pydfEUAAAAJ&view_op=list_works&sortby=pubdate",
"github": "https://github.com/gwct",
"profile": "Gregg develops phylogenetic methods and has studied convergent evolution, molecular evolution of rodents and insects, and mutation rates in primates."
},
"Lei Ma": {
"id": "13",
"name": "Lei Ma",
"title" : "Senior Bioinformatics Scientist",
"email" : "lei_ma@g.harvard.edu",
"office" : "B227.20",
"img": "img/people/leima.jpg",
"date-added": "12-05-2023",
"date-joined": "09-11-2023",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "",
"github": "https://github.com/microlei",
"profile": "Lei is primarily responsible for developing training and outreach material; she also has a background in metagenomics and microbial ecology."
},
"Rawan Olayan": {
"id": "14",
"name": "Rawan Olayan",
"title" : "Senior Bioinformatics Scientist",
"email" : "",
"office" : "B227.40",
"img": "img/people/rawanolayan.jpg",
"date-added": "12-05-2023",
"date-joined": "05-17-2021",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "https://scholar.google.com/citations?hl=en&user=qxUMqP4AAAAJ&view_op=list_works&sortby=pubdate",
"github": "",
"profile": "Rawan is funded by a collaboration with Boehringer Ingelheim, and works on single cell RNA-seq methods."
},
"Allison Shultz": {
"id": "15",
"name": "Allison Shultz",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "09-11-2017",
"date-left": "09-07-2018",
"status" : "moved",
"link": "https://www.allisonshultz.com/",
"profile": "Allison is now the Associate Curator of Ornithology at the Natural History Museum of Los Angeles County."
},
"Brian Arnold": {
"id": "16",
"name": "Brian Arnold",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "09-24-2018",
"date-left": "09-23-2020",
"status" : "moved",
"link": "https://brian-arnold.github.io/about/",
"profile": "Brian is now a departmental data scientist with the Ecology and Evolutionary Biology department at Princeton."
},
"Ming Tang": {
"id": "17",
"name": "Ming \"Tommy\" Tang",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "10-01-2018",
"date-left": "03-27-2020",
"status" : "moved",
"link": "https://tommytang.bio.link/",
"profile": "Tommy is now the Director of Computational Biology at Immunitas Therapeutics."
},
"Scott Van Buren": {
"id": "18",
"name": "Scott Van Buren",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "09-01-2020",
"date-left": "06-16-2022",
"status" : "moved",
"link": "",
"profile": "Scott is now a Scientific Investigator in Computational Biology at GSK."
},
"Juerg Straubhaar": {
"id": "19",
"name": "Juerg Straubhaar",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "01-08-2017",
"date-left": "01-08-2021",
"status" : "moved",
"link": "",
"profile": "Juerg worked primarily on proteomics data with the Mass Spec Core and the Melton Lab while he was in the group."
},
"John Gaspar": {
"id": "20",
"name": "John Gaspar",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "03-01-2017",
"date-left": "01-18-2019",
"status" : "moved",
"link": "",
"profile": "John is now a Data Science and Bioinformatics Team Lead at Merck."
},
"Yasin Kaymaz": {
"id": "21",
"name": "Yasin Kaymaz",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "08-01-2017",
"date-left": "09-01-2020",
"status" : "moved",
"link": "",
"profile": "Yasin is now an Assistant Professor at Ege University in Izmir, Turkey."
},
"Alexandria D'Souza": {
"id": "22",
"name": "Alexandria D'Souza",
"title": "Senior Bioinformatics Scientist",
"date-added": "12-05-2023",
"date-joined": "09-30-2019",
"date-left": "09-19-2022",
"status" : "moved",
"link": "",
"profile": "Alexandria primarily worked with the mass spec core and the Woo lab while she was in the group."
}
},
"Postdoctoral Researchers": {
"Subir Shakya": {
"id": "30",
"name": "Subir Shakya",
"title" : "Postdoctoral Fellow",
"email" : "subirshakya@fas.harvard.edu",
"office" : "B227.65",
"img": "img/people/subirshakya.jpg",
"date-added": "12-05-2023",
"date-joined": "03-01-2021",
"date-left": "",
"status" : "active",
"link": "https://www.subir.com.np/",
"pubs": "https://scholar.google.com/citations?hl=en&user=ETGvbj0AAAAJ&view_op=list_works&sortby=pubdate",
"github": "",
"profile": "Subir works on population and comparative genomics of birds, funded by an NIH grant to study enhancer evolution in birds."
},
"Ekaterina Osipova": {
"id": "31",
"name": "Katya Osipova",
"title" : "Postdoctoral Fellow",
"email" : "",
"office" : "B227.65",
"img": "img/people/katyaosipova.jpg",
"date-added": "12-05-2023",
"date-joined": "11-01-2022",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "https://scholar.google.com/citations?hl=en&user=OhvZN8cAAAAJ&view_op=list_works&sortby=pubdate",
"github": "https://github.com/osipovarev",
"profile": "Katya works on convergent evolution of brood parasitic birds, funded by an NSF grant to study the genomics of these species."
},
"Sara Smith Wuitchik": {
"id": "32",
"name": "Sara Smith Wuitchik",
"title" : "Postdoctoral Fellow",
"date-added": "12-05-2023",
"date-joined": "05-06-2019",
"date-left": "08-31-2021",
"status" : "moved",
"link": "https://www.mtroyal.ca/ProgramsCourses/FacultiesSchoolsCentres/ScienceTechnology/Departments/Biology/Faculty/Sara-Smith-Wuitchik.htm",
"profile": "Sara is now an Assistant Professor at Mount Royal University in Calgary, Canada."
},
"Alex Llanos Garrido": {
"id": "33",
"name": "Alex Llanos Garrido",
"title" : "Postdoctoral Fellow",
"date-added": "12-05-2023",
"date-joined": "09-01-2019",
"date-left": "08-31-2021",
"status" : "moved",
"link": "",
"profile": "Alex is now at the Universidad Complutense Madrid."
},
"Veronika Laine": {
"id": "34",
"name": "Veronika Laine",
"title" : "Postdoctoral Fellow",
"date-added": "12-05-2023",
"date-joined": "01-01-2019",
"date-left": "06-16-2019",
"status" : "moved",
"link": "https://veronikalaine.netlify.app/",
"profile": "Veronika is now at the Finnish Museum of Natural History working on bats."
}
}
},
"Software Operations": {
"Director": {
"Aaron Kitzmiller": {
"id": "50",
"name": "Aaron Kitzmiller",
"title" : "Director of Software Operations",
"email" : "",
"office" : "B227.70",
"img": "img/people/aaronkitzmiller.jpg",
"date-added": "12-05-2023",
"date-joined": "",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "",
"github": "",
"profile": ""
}
},
"Staff": {
"David D'Antonio": {
"id": "60",
"name": "David D'Antonio",
"title" : "",
"office" : "",
"email" : "",
"img": "img/people/ddantonio.jpg",
"date-added": "12-05-2023",
"date-joined": "",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "",
"github": "",
"profile": ""
},
"Nathan Weeks": {
"id": "61",
"name": "Nathan Weeks",
"title" : "",
"office" : "B227.30",
"email" : "",
"img": "img/people/nathanweeks.jpg",
"date-added": "12-05-2023",
"date-joined": "",
"date-left": "",
"status" : "active",
"link": "",
"pubs": "",
"github": "",
"profile": ""
},
"Meghan Correa": {
"id": "62",
"name": "Meghan Correa",
"title" : "",
"office" : "",
"email" : "",
"date-added": "12-05-2023",
"date-joined": "",
"date-left": "",
"status" : "moved",
"link": "",
"pubs": "",
"github": "",
"profile": ""
},
"Andy Bryant": {
"id": "63",
"name": "Andy Bryant",
"title" : "",
"office" : "",
"email" : "",
"date-added": "12-05-2023",
"date-joined": "",
"date-left": "",
"status" : "moved",
"link": "",
"pubs": "",
"github": "",
"profile": ""
}
}
}
}

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