mpa139 · roychoudhuri · Jan 8, 2020 · Jan 8, 2020 · Jan 13, 2020 · Jan 13, 2020
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -0,0 +1,16 @@
+name: Jekyll site CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Build the site in the jekyll/builder container
+      run: |
+        docker run \
+        -v ${{ github.workspace }}:/srv/jekyll -v ${{ github.workspace }}/_site:/srv/jekyll/_site \
+        jekyll/builder:latest /bin/bash -c "chmod 777 /srv/jekyll && jekyll build --future"
diff --git a/CNAME b/CNAME
diff --git a/README.md b/README.md
@@ -1,11 +1,5 @@
-# Allan Lab Website
+# Roychoudhuri Lab Website
 
-This is the website of our academic research group at Leiden University.
-
-This website is powered by Jekyll and some Bootstrap, Bootwatch. We tried to make it simple yet adaptable, so that it is easy for you to use it as a template. Plese feel free to copy and modify for your own purposes.  You don't have to link to us or mention us (but of course we appreciate it).
-
-Go to *aboutwebsite.md*  to learn how to copy and modidy this page for your purpose. 
-
-
-Copyright Allan Lab. Code released under the MIT License.
+This is the website of our academic research group at the Department of Pathology at Cambridge University.
 
+Go to *about.md*  to learn how to copy and modidy this page for your purpose. 
diff --git a/_config.yml → _config.yml_inactivated b/_config.yml → _config.yml_inactivated
@@ -6,14 +6,12 @@
 # 'jekyll serve'. If you change this file, please restart the server process.
 
 # Site settings
-title: The Allan Lab
-email: [email protected]
+title: Roychoudhuri Lab - Immune regulation in inflammation and cancer
+email: [email protected]  
 description: > # this means to ignore newlines until "baseurl:"
-  Write an awesome description for your new site here. You can edit this
-  line in _config.yml. It will appear in your document head meta (for
-  Google search results) and in your feed.xml site description.
+  Immune regulation in inflammation and cancer. We are located at the Department of Pathology at the University of Cambridge, Cambridge, UK. We study the immunoregulatory mechanisms that suppress immune activation under homeostasis and cancer immunosuppression. We are interested in the differentiation and function of CD4+ T cells, including Foxp3+ regulatory T cells, and CD8+ T cells with cytotoxic function. We are interested in the mechanisms that restrict T cell activation and CD8+ T cell memory in the context of adoptive immunotherapy and immune checkpoint blockade therapy. 
 baseurl: ""
-url: ""
+url: "http://roychoudhurilab.org"
 
 include:
   - .htaccess
@@ -29,8 +27,14 @@ lsi: false
 excerpt_separator: "\n\n"
 incremental: false
 
-
-
+#Collections
+collections:
+  members:
+    output: true
+    permalink: member/:name
+    sort_by: tier    
+
+
 # Markdown Processing
 kramdown:
   input: GFM
@@ -43,3 +47,5 @@ kramdown:
   enable_coderay: false
   parse_block_html: true # default for kramdown is false. This will enable using Markdown links
 
+
+theme: jekyll-theme-slate
diff --git a/_data/.DS_Store b/_data/.DS_Store
diff --git a/_data/affiliations.yml b/_data/affiliations.yml
@@ -0,0 +1,8 @@
+- title: Department of Pathology (Cambridge)
+  link: https://www.path.cam.ac.uk/
+
+- title: CRUK Cambridge Centre (Cambridge)
+  link: https://crukcambridgecentre.org.uk/
+
+- title: Babraham Institute (Cambridge)
+  link: https://www.babraham.ac.uk
diff --git a/_data/alumni_bsc.yml b/_data/alumni_bsc.yml
diff --git a/_data/alumni_members.yml b/_data/alumni_members.yml
diff --git a/_data/alumni_msc.yml b/_data/alumni_msc.yml
diff --git a/_data/alumni_visitors.yml b/_data/alumni_visitors.yml
diff --git a/_data/collaborations.yml b/_data/collaborations.yml
@@ -0,0 +1,16 @@
+- title: Klaus Okkenhaug (Pathology)
+  link: https://www.path.cam.ac.uk/directory/klaus-okkenhaug
+
+- title: David Adams (Sanger)
+  link: https://www.sanger.ac.uk/person/adams-david/
+
+- title: Nicholas Restifo (NIH, US)
+
+- title: Gosia Trynka (Sanger)
+
+- title: Enrico Lugli (Humanitas, Milan)
+  link: https://www.humanitas-research.org/researcher/dr-enrico-lugli/
+
+- title: Tim Halim (CRUK CI)
+
+- title: Luca Gattinoni (NIH, US)
diff --git a/_data/facilities.yml b/_data/facilities.yml
@@ -0,0 +1,19 @@
+- title: University Biomedical Services (Cambridge)
+  link: https://www.ubs.admin.cam.ac.uk/
+
+- title: High-throughput sequencing (Pathology)
+  link: https://www.cgs.path.cam.ac.uk/
+
+- title: Genomics core facility (CRUK CI)
+  link: https://www.cruk.cam.ac.uk/core-facilities/genomics-core
+
+- title: Flow cytometry (Pathology)
+  link: https://www.bio.cam.ac.uk/facilities/flow
+
+- title: NIHR cell phenotyping hub (Cambridge)
+  link: https://www.med.cam.ac.uk/nihr-cambridge-brc-cell-phenotyping-hub/
+
+- title: High-throughput sequencing (Pathology)
+  link: https://www.cgs.path.cam.ac.uk/
+
+
diff --git a/_data/news.yml b/_data/news.yml
@@ -1,129 +1,9 @@
 
-- date: 10. December 2019
-  headline: "<b>Koen defends his PhD with a cum laude (top 5%)!</b>"
-
-- date: 5. September 2019
-  headline: "The noise doubling paper is published in <a href='https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.104506'>Phys. Rev. B</a>!"
-
-- date: 25. August 2019
-  headline: "<b>Doohee got an assistant professor job at Yonsei University!</b>"
-
-- date: 25. July 2019
-  headline: "<b>The inhomogeneous superfluid paper is published in <a href='https://www.nature.com/articles/s41586-019-1408-8'>Nature</a>!</b><img src='/images/newspic/SFnews.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 15. July 2019
-  headline: "We imaged the doubling of shot noise due to Andreev reflections in a STM, posted <a href='https://arxiv.org/abs/1907.05808'> on arXiv</a>."
-
-- date: 24. May 2019
-  headline: "The smart tip paper <a href='https://iopscience.iop.org/article/10.1088/1361-6528/ab1c7f/pdf'> is finally published !</a> A collaboration with the <a href='http://groeblacherlab.tudelft.nl/'>Gröblacher Lab</a> at TU Delft.<img src='/images/newspic/SmartTip.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 08. May 2019
-  headline: "<b>Irene defends her PhD!</b>"
-
-- date: 08. May 2019
-  headline: "Dome makes it on the <a href='https://www.universiteitleiden.nl/nieuws/2019/05/de-meest-stabiele-microscoop-ter-wereld'>University website</a>. <img src='/images/newspic/Saphireheadline.jpeg' class='img-responsive' style='max-width: 192px' />"
-
-- date: 13. December 2018
-  headline: "Our paper about how to construct an STM is in <a href='https://aip.scitation.org/doi/10.1063/1.5064442'>Review of Scientific Instruments</a>. <img src='/images/newspic/DomeNews.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 08. October 2018
-  headline: "We discovered charge trapping in a high-Tc superconductor! Publication in <a href='https://www.nature.com/articles/s41567-018-0300-z'>Nature Physics</a>. <img src='/images/pubpic/Pub_BCl.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 27. September 2018
-  headline: "Our MHz amplifier for STM is published in <a href='https://aip.scitation.org/doi/10.1063/1.5043267'>Review of Scientific Instruments</a>. <img src='/images/newspic/amp.PNG' class='img-responsive' style='max-width: 192px' />"
-
-- date: 16. May 2018
-  headline: "Milan, Koen and Irene talk about superconductivity in <a href='https://youtu.be/hxz22AYUGhM'>Made in Leiden</a>."
-
-- date: 4. May 2018
-  headline: "Welcome Ram!"
-
-- date: 5.-9. March 2018
-  headline: "Irene and Milan are at the March Meeting (Talk <a href='http://meetings.aps.org/Meeting/MAR18/Session/E45.11'>Tue 10am, session E45</a>)"
-
-- date: 13. November 2017
-  headline: "<a href='http://www.beilstein-journals.org/bjnano/content/pdf/2190-4286-8-238.pdf'> New paper</a> published in collaboration with the group of Jan van Ruitenbeek"
-
-- date: 10. November 2017
-  headline: "Doohee makes the third place at the <a href='https://www.universiteitleiden.nl/en/news/2017/11/sander-blok-wins-lion-image-award-2017'>LION Image Award</a>. <img src='/images/newspic/doohee_prize.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 9. October 2017
-  headline: "We contributed to Miguel and Jan's  <a href='https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.134507'>new paper</a>.  "
-
-- date: 12. August 2017
-  headline: "<a href='https://www.universiteitleiden.nl/en/news/2017/08/two-erc-grants-for-leiden-physics'>We got an ERC starting grant</a>."
-
-- date: 10. August 2017
-  headline: "Our paper is published in <a href='https://scipost.org/SciPostPhys.3.2.010/pdf'>SciPost Physics</a>."
-
-- date: 17. - 21. July 2017
-  headline: "<a href='https://www.universiteitleiden.nl/en/news/2017/07/milan-allan-wins-bryan-r.-coles-prize'>Milan wins the Bryan R. Coles prize</a> at SCES 2017, Prague. Koen received the best poster presentation award.  <img src='/images/newspic/scesprizes.jpg' class='img-responsive' style='max-width: 192px' />"
-
-- date: 17. - 21. July 2017
-  headline: "Koen, Maarten and Milan will be at SCES 2017, Prague. Come check out our posters on Tuesday&Thursday and talk on Thursday!"
-
-- date: 18. June 2017
-  headline: "<b>Paper on poor electronic screening published in  <a href='https://journals.aps.org/prb/abstract/10.1103/PhysRevB.95.235141'>  PRB</a> as Editors' selection! </b>"
-
-- date: 15. May 2017
-  headline: Welcome Doohee!
-
-- date: 13. - 17. March 2017
-  headline: Koen & Irene give talks at the APS March Meeting in New Orleans.
-
-- date: 27. January - 3. March 2017
-  headline: "We are looking forward to co-hosting <a href='http://www.lorentzcenter.nl/lc/web/2017/877/info.php3?wsid=877&venue=Oort'>the workshop on unconventional superconductivity</a> at the Lorentz center. <img src='/images/newspic/LCposter.jpg' class='img-responsive' style='max-width: 192px' />"
-
-- date: 17-18. January 2017
-  headline: Irene, Koen, Maarten and Milan will be at Physics@Veldhoven 2017. (Talk at PT6.1 and poster at P9.022).
-
-- date: 25. November 2016
-  headline: "We are part of a newly granted <a href='https://www.fom.nl/en/research/research-programmes/general-information//'>Vrije Programma</a> on strange metals, together with the groups of <b> Hussey, Golden, vHeumen, Zaanen, Schalm, Stoof and Vandoren</b>, see <a href='https://www.fom.nl/en/news/press-releases/2016/11/21/fom-awards-15-1-million-euros-to-highly-promising-research/'>press release</a>. We also got a <a href='https://www.fom.nl/en/news/press-releases/2016/11/18/28634/'>Projectruimte</a>."
-
-- date: 19. September 2016
-  headline: "<b> Our first paper from Leiden is <a href='http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys3894.html'>online at Nature Physics</a>! </b><img src='/images/newspic/NewsNP.png' class='img-responsive' style='max-width: 192px' /> "
-
-- date: 12. September 2016
-  headline: Koen is at Correl16, Julich.
-
-- date: 01. July 2016
-  headline: Milan is at the strongly correlated electron GRC 2016.
-
-- date: 24. June 2016
-  headline: Felix Baumberger is visiting.
-
-- date: 17. June 2016
-  headline: Irene is at SNS2016.
-
-- date: 28. April 2016
-  headline: <b> Our results on the Mott & pseudo gap physics posted on <a href='http://arxiv.org/abs/1604.08343'>arXiv</a> ! </b>
-
-- date: 14. May 2016
-  headline: Ivan Bozovic is visiting.
-
-- date: 17. March 2016
-  headline: Koen, Irene & Vitaly present a poster at Sun Sailing Science.
-
-- date: 17. Jan 2016
-  headline: "We discover electronic order and pseudogap in a non-cuprate materal! <img src='/images/newspic/order.png' class='img-responsive' style='max-width: 192px' />"
-
-- date: 01. Jan 2016
-  headline: Welcome Vitaly!
-
-- date: 17. June 2015
-  headline: Welcome Kees!
-
-- date: 17. June 2015
-  headline: "Maarten wins the LION image award! Check out his <a href='https://www.physics.leidenuniv.nl/index.php?id=11573&news=757&type=lion&ln=EN'>submission</a>.<img src='/images/newspic/Contest.jpg' class='img-responsive' style='max-width:192px' />"
-
-- date: 17. June 2015
-  headline: "<b> We win a Vidi grant: 800kEUR to invest in science! (<a href='http://www.news.leiden.edu/news-2015/5-vidis-for-leiden-reserachers.html'>Leiden news</a>, <a href='http://www.fom.nl/live/english/news/archives/pressreleases2015/artikel.pag?objectnumber=297954'>FOM news item</a>) </b>"
-
-- date: 01. Sept 2015
-  headline: "Welcome Koen and Maarten: from Master- to PhD-students"
-
-- date: 17. June 2015
-  headline: "We got our commercial STM from <a href='http://www.unisoku.com/'>Unisoku</a>, and we are already busy modifying."
-
-- date: 01. Jan 2015
-  headline: Welcome Irene, Gijsbert & Milan — <b> our lab is officially starting</b>!
+- date: 9th September 2019
+  headline: "<b>Francis Grant defends his doctrate</b>"
+
+- date: 5th September 2019
+  headline: "<b>Firas publishes in <a href = 'https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpim.84'>Current Protocols in Immunology</a></b>"
+
+- date: 1st April 2019
+  headline: "<b>Dr Paula Kuo joins the lab!</b>"
diff --git a/_data/pictures_Leiden.yml b/_data/pictures_Leiden.yml