diff --git a/src/LandingPage/landingPage.jsx b/src/LandingPage/landingPage.jsx index 698846a0..1c608187 100644 --- a/src/LandingPage/landingPage.jsx +++ b/src/LandingPage/landingPage.jsx @@ -15,6 +15,7 @@ import BackgroundVideoImage from '../assets/LandingPageGraphics/background_video import LayerRunner from '../assets/LandingPageGraphics/Data_Layer_Runner.png'; import RatFigurePaass1b from '../assets/LandingPageGraphics/rat-figure-pass1b.svg'; import LandscapeAbstract from '../assets/LandingPageGraphics/landscape_abstract.gif'; +import NatureIssueCover from '../assets/LandingPageGraphics/nature_issue_cover.jpg'; import BackgroundVideo from './components/backgroundVideo'; import Figure1C from './components/figure1c'; @@ -163,7 +164,7 @@ export function LandingPage({ isAuthenticated, profile }) { }, [networkNodes]); const goToExternalLink = useCallback(() => { - window.open('https://www.nature.com/articles/s41586-023-06877-w', '_blank'); + window.open('https://www.nature.com/nature/volumes/629/issues/8010', '_blank'); }, []); // Redirect authenticated users to protected route @@ -261,7 +262,7 @@ export function LandingPage({ isAuthenticated, profile }) {
-
+

MoTrPAC animal endurance training exercise study paper now published in @@ -278,15 +279,15 @@ export function LandingPage({ isAuthenticated, profile }) { LEARN MORE

-
- Landscape Paper Abstract +
+
+ Landscape Paper Abstract +
+
Cover image by Nik Spencer/Nature
diff --git a/src/MultiOmicsWorkingGroups/preCAWG.jsx b/src/MultiOmicsWorkingGroups/preCAWG.jsx index 7a050090..69279a41 100644 --- a/src/MultiOmicsWorkingGroups/preCAWG.jsx +++ b/src/MultiOmicsWorkingGroups/preCAWG.jsx @@ -557,15 +557,17 @@ function PreCAWG() { below).
  • - Download and install the{' '} + Download and install the + {' '} Google Command Line Tools {' '} - on your preferred work computer. + on your preferred work computer and connect them to the institutional + Google account you created (See Google CLI instructions).
  • Set up a{' '} @@ -666,7 +668,8 @@ function PreCAWG() { rel="noreferrer" > jzhen@stanford.edu - {' '} + + {' '} and your local site PI with a written request for the following access permissions:
      @@ -713,6 +716,19 @@ function PreCAWG() {
    • +
  • + Once this is done, you should be able to open a PowerShell (Windows) or + Terminal (Mac) and run the command + {' '} + gsutil ls gs://motrpac-data-hub + . If you can, that means your Google Cloud CLI is set up and your GCP + access is working correctly. If this fails, but you think you have access, + check that + {' '} + gsutil + {' '} + is in your PATH. +
  • Clone the following two GitHub repositories once you are granted access: @@ -738,45 +754,88 @@ function PreCAWG() {
  • - Install the{' '} + Install the + {' '} MoTrPAC/MotrpacHumanPreSuspension - {' '} + + {' '} package - this package gives you programmatic access to the PreCAWG - data. Also review the README.md + data. Also review the + {' '} + README.md + {' '} + which explains how to install from the local clone of the repo. This + package cannot be installed directly from GitHub.com.
  • - Read the{' '} + Read the + {' '} MoTrPAC/precovid-analyses - {' '} - README.md - this repo is where novel analysis code must + + {' '} + README.md + {' '} + - this repo is where novel analysis code must be stored
  • - Set up your motrpac_config.json configuration file + Set up your + {' '} + motrpac_config.json + {' '} + configuration file as described in the + {' '} + + MoTrPAC/precovid-analyses + + {' '} + README.md
  • - Open Rstudio and attempt to run{' '} + Open Rstudio and attempt to run + {' '} human-precovid-sed-adu_t07-adipose_prot-ph_metadata_qc-report_v1.Rmd - {' '} - (after pointing to your motrpac_config.json file. + + {' '} + (after pointing to your + {' '} + motrpac_config.json + {' '} + file). This R markdown file is in the + {' '} + + MoTrPAC/precovid-analyses + + {' '} + repo in the QC folder.
  • - Then ensure that{' '} - MotrpacHumanPreSuspension::load_differential_analysis{' '} + Then ensure that + {' '} + MotrpacHumanPreSuspension::load_differential_analysis + {' '} runs for you.
    • -
  • If #13 and #15 are running, you are ready to go!
    • +
  • If #13 and #14 are running, you are ready to go!
    • diff --git a/src/Publications/publications.jsx b/src/Publications/publications.jsx index c75d2b28..20b8f683 100644 --- a/src/Publications/publications.jsx +++ b/src/Publications/publications.jsx @@ -2,16 +2,15 @@ import React from 'react'; import { Helmet } from 'react-helmet'; import PageTitle from '../lib/ui/pageTitle'; import ExternalLink from '../lib/ui/externalLink'; +import MitoPaper from '../assets/publications/mito_paper.gif'; +import LandscapePaper from '../assets/publications/landscape_paper.gif'; +import GinaPaper from '../assets/publications/gina_paper.gif'; +import SimonPaper from '../assets/publications/simon_paper.gif'; +import VenuPaper from '../assets/publications/venu_paper.gif'; +import NikPaper from '../assets/publications/nik_paper.gif'; +import MarkerPaper from '../assets/publications/marker_paper.gif'; -const publications = [ - { - url: 'https://doi.org/10.1016/j.cmet.2023.12.021', - title: - 'The mitochondrial multi-omic response to exercise training across tissues', - authors: - 'Amar D, Gay NR, Jimenez-Morales D, Jean Beltran PM, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul DA, Hershman SG, Ferrasse A, Xia A, Lanza I, Fernández FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector SR, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME and The MoTrPAC Study Group.', - cite: 'Cell Metabolism 36, 1-19, June 4, 2024.', - }, +const landscapePublications = [ { url: 'https://www.nature.com/articles/s41586-023-06877-w', title: @@ -19,6 +18,19 @@ const publications = [ authors: 'MoTrPAC Study Group, David Amar, Nicole R. Gay, Pierre M. Jean Beltran, Joshua N. Adkins, Jose J. Almagro Armenteros, Euan Ashley, Julian Avila-Pacheco, Dam Bae, Nasim Bararpour, Charles Burant, Clary Clish, Gary Cutter, Surendra Dasari, Courtney Dennis, Charles R. Evans, Facundo M. Fernández, David Gaul, Yongchao Ge, Robert Gerszten, Laurie J. Goodyear, Zhenxin Hou, Olga Ilkayeva, Anna A. Ivanova, David Jimenez-Morales, Maureen T. Kachman, Hasmik Keshishian, William E. Kraus, Ian R. Lanza, Jun Li, Malene E. Lindholm, Ana C. Lira, Gina M. Many, Shruti Marwaha, Michael E. Miller, Michael J. Muehlbauer, K. Sreekumaran Nair, Venugopalan D. Nair, Archana Natarajan Raja, Christopher Newgard, Eric A. Ortlund, Paul D. Piehowski, David M. Presby, Wei-Jun Qian, Jessica L. Rooney, James A. Sanford, Evan Savage, Stuart C. Sealfon, Gregory R. Smith, Kevin S. Smith, Alec Steep, Cynthia L. Stowe, Yifei Sun, Russell Tracy, Nikolai G. Vetr, Martin J. Walsh, Si Wu, Tiantian Zhang, Bingqing Zhao, Jimmy Zhen, Brent G. Albertson, Mary Anne S. Amper, Ali Tugrul Balci, Marcas Bamman, Elisabeth R. Barton, Bryan Bergman, Daniel Bessesen, Frank Booth, Brian Bouverat, Thomas W. Buford, Tiziana Caputo, Toby L. Chambers, Clarisa Chavez, Maria Chikina, Roxanne Chiu, Michael Cicha, Paul M. Coen, Dan Cooper, Elaine Cornell, Karen P. Dalton, Luis Oliveria De Sousa, Roger Farrar, Kishore Gadde, Nicole Gagne, Bret H. Goodpaster, Marina A. Gritsenko, Kristy Guevara, Fadia Haddad, Joshua R. Hansen, Melissa Harris, Trevor Hastie, Krista M. Hennig, Steven G. Hershman, Andrea Hevener, Michael F. Hirshman, Fang-Chi Hsu, Kim M. Huffman, Chia-Jui Hung, Chelsea Hutchinson-Bunch, Bailey E. Jackson, Catherine Jankowski, Christopher A. Jin, Neil M. Johannsen, Benjamin G. Ke, Wendy M. Kohrt, Kyle S. Kramer, Christiaan Leeuwenburgh, Sarah J. Lessard, Bridget Lester, Xueyun Liu, Ching-ju Lu, Nathan S. Makarewicz, Kristal M. Maner-Smith, DR Mani, Nada Marjanovic, Andrea Marshall, Sandy May, Edward Melanson, Matthew E. Monroe, Ronald J. Moore, Samuel Moore, Kerrie L. Moreau, Charles C. Mundorff, Nicolas Musi, Daniel Nachun, Michael D. Nestor, Robert L. Newton Jr., Barbara Nicklas, Pasquale Nigro, German Nudelman, Marco Pahor, Cadence Pearce, Vladislav A. Petyuk, Hanna Pincas, Scott Powers, Shlomit Radom-Aizik, Krithika Ramachandran, Megan E. Ramaker, Irene Ramos, Tuomo Rankinen, Alexander (Sasha) Raskind, Blake B. Rasmussen, Eric Ravussin, R. Scott Rector, W. Jack Rejeski, Collyn Richards, Stas Rirak, Jeremy M. Robbins, Aliza B. Rubenstein, Frederique Ruf-Zamojski, Scott Rushing, Tyler J. Sagendorf, Mihir Samdarshi, Irene E. Schauer, Robert Schwartz, Nitish Seenarine, Tanu Soni, Lauren M. Sparks, Christopher Teng, Anna Thalacker-Mercer, John Thyfault, Rob Tibshirani, Scott Trappe, Todd A. Trappe, Karan Uppal, Sindhu Vangeti, Mital Vasoya, Elena Volpi, Alexandria Vornholt, Michael P. Walkup, John Williams, Ashley Xia, Zhen Yan, Xuechen Yu, Chongzhi Zang, Elena Zaslavsky, Navid Zebarjadi, Sue C. Bodine, Steven Carr, Karyn Esser, Stephen B. Montgomery, Simon Schenk, Michael P. Snyder, Matthew T. Wheeler.', cite: 'Nature 629, May 1, 2024.', + image: LandscapePaper, + }, +]; + +const companionPublications = [ + { + url: 'https://www.cell.com/cell-metabolism/fulltext/S1550-4131(23)00472-2', + title: + 'The mitochondrial multi-omic response to exercise training across tissues', + authors: + 'Amar D, Gay NR, Jimenez-Morales D, Jean Beltran PM, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul DA, Hershman SG, Ferrasse A, Xia A, Lanza I, Fernández FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector SR, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME and The MoTrPAC Study Group.', + cite: 'Cell Metabolism 36, 1-19, June 4, 2024.', + image: MitoPaper, }, { url: 'https://doi.org/10.1038/s42255-023-00959-9', @@ -27,6 +39,7 @@ const publications = [ authors: 'Gina M Many, James A Sanford, Tyler J Sagendorf, Zhenxin Hou, Pasquale Nigro, Katie L Whytock, David Amar, Tiziana Caputo, Nicole R Gay, David A Gaul, Michael F Hirshman, David Jimenez-Morales, Malene E Lindholm, Michael J Muehlbauer, Maria Vamvini, Bryan C Bergman, Facundo M Fernández, Laurie J Goodyear, Andrea L Hevener, Eric A Ortlund, Lauren M Sparks, Ashley Xia, Joshua N Adkins, Sue C Bodine, Christopher B Newgard, Simon Schenk and The MoTrPAC Study Group.', cite: 'Nat. Metab., 2024.', + image: GinaPaper, }, { url: 'https://doi.org/10.1093/function/zqae014', @@ -35,6 +48,7 @@ const publications = [ authors: 'Simon Schenk S, Sagendorf TJ, Many GM, Lira AK, DeSousa LGO, Bae D, Cicha M, Kyle Kramer KS, Muehlbauer M, Hevener AL, Rector RS, Thyfault JP, Williams JP, Goodyear LJ, Esser KA, Newgard CB, Bodine SC, and The MoTrPAC Study Group.', cite: 'Function, zqae014, 2024.', + image: SimonPaper, }, { url: 'https://doi.org/10.1016/j.xgen.2023.100421', @@ -43,6 +57,7 @@ const publications = [ authors: 'Nair VD, Pincas H, Smith GR, Zaslavsky E, Ge Y, Amper MAS, Vasoya M, Chikina M, Sun Y, Raja AN, Mao W, Gay NR, Esser KA, Smith KS, Zhao B, Wiel L, Singh A, Lindholm ME, Amar D, Montgomery S, Snyder MP, Walsh MJ, Sealfon CS, and The MoTrPAC Study Group.', cite: 'Cell Genomics, 4: 100421, 2024.', + image: VenuPaper, }, { url: 'https://doi.org/10.1038/s41467-024-45966-w', @@ -51,6 +66,7 @@ const publications = [ authors: 'Nikolai G Vetr, Nicole R Gay, Stephen B Montgomery, and The MoTrPAC Study Group.', cite: 'Nature Communications 15, no. 1, May 1, 2024.', + image: NikPaper, }, { url: 'https://www.cell.com/cell/fulltext/S0092-8674(20)30691-7', @@ -59,6 +75,7 @@ const publications = [ authors: 'James A. Sanford, Christopher D. Nogiec, Malene E. Lindholm, Joshua N. Adkins, David Amar, Surendra Dasari, Jonelle K. Drugan, Facundo M. Fernández, Shlomit Radom-Aizik, Simon Schenk, Michael P. Snyder, Russell P. Tracy, Patrick Vanderboom, Scott Trappe, Martin J. Walsh, and the Molecular Transducers of Physical Activity Consortium.', cite: 'Cell 181/7, 1464-1474, June 25, 2020.', + image: MarkerPaper, }, ]; @@ -69,11 +86,20 @@ const publications = [ */ function Publications() { // Render list of publications - function renderPublications() { + function renderPublications(category) { + if (category === 'landscape') { + return ( +
    + {landscapePublications.map((pub) => ( + + ))} +
    + ); + } return (
    - {publications.map((pub) => ( - + {companionPublications.map((pub) => ( + ))}
    ); @@ -86,39 +112,128 @@ function Publications() { Publications - MoTrPAC Data Hub -
    -
    {renderPublications()}
    -
    -
    -
    + +
    +
    {renderPublications('landscape')}
    +
    +
    +
    {renderPublications('companion')}
    +
    +
    + ); +} + +// Landscape publication component +function LandscapePublication({ pub }) { + const [showAllAuthors, setShowAllAuthors] = React.useState(false); + const truncateLength = 623; + const truncatedAuthors = !showAllAuthors + ? `${pub.authors.substring(0, truncateLength)}...` + : pub.authors; + + return ( +
    +
    +

    Highlights

    +
    +
    ); } -function Publication({ pub }) { +// Companion publication component +function CompanionPublication({ pub }) { return ( -
    -

    - {pub.title} -

    -

    - {pub.authors} - {pub.cite} - - - -

    +
    +
    +
    + + Publication + +
    +
    +

    + {pub.title} +

    +

    + {pub.authors} + {pub.cite} + + + +

    +
    +
    ); } diff --git a/src/assets/LandingPageGraphics/nature_issue_cover.jpg b/src/assets/LandingPageGraphics/nature_issue_cover.jpg new file mode 100644 index 00000000..aa2270d4 Binary files /dev/null and b/src/assets/LandingPageGraphics/nature_issue_cover.jpg differ diff --git a/src/assets/publications/gina_paper.gif b/src/assets/publications/gina_paper.gif new file mode 100644 index 00000000..5d3be8e5 Binary files /dev/null and b/src/assets/publications/gina_paper.gif differ diff --git a/src/assets/publications/landscape_paper.gif b/src/assets/publications/landscape_paper.gif new file mode 100644 index 00000000..43cda099 Binary files /dev/null and b/src/assets/publications/landscape_paper.gif differ diff --git a/src/assets/publications/marker_paper.gif b/src/assets/publications/marker_paper.gif new file mode 100644 index 00000000..8b28ce5c Binary files /dev/null and b/src/assets/publications/marker_paper.gif differ diff --git a/src/assets/publications/mito_paper.gif b/src/assets/publications/mito_paper.gif new file mode 100644 index 00000000..8220555d Binary files /dev/null and b/src/assets/publications/mito_paper.gif differ diff --git a/src/assets/publications/nik_paper.gif b/src/assets/publications/nik_paper.gif new file mode 100644 index 00000000..7cf44e97 Binary files /dev/null and b/src/assets/publications/nik_paper.gif differ diff --git a/src/assets/publications/simon_paper.gif b/src/assets/publications/simon_paper.gif new file mode 100644 index 00000000..5bc7823e Binary files /dev/null and b/src/assets/publications/simon_paper.gif differ diff --git a/src/assets/publications/venu_paper.gif b/src/assets/publications/venu_paper.gif new file mode 100644 index 00000000..a44d397e Binary files /dev/null and b/src/assets/publications/venu_paper.gif differ diff --git a/src/sass/_landingPage.scss b/src/sass/_landingPage.scss index 7d439a35..0cb5996f 100644 --- a/src/sass/_landingPage.scss +++ b/src/sass/_landingPage.scss @@ -191,19 +191,18 @@ padding-top: 15px; padding-bottom: 15px; - .content-landscape-preprint { - + .content-landscape-paper { .feature-image { background-color: #fff; border-radius: 0.75rem; box-shadow: 0 2em 3em rgba(0, 0, 0, 0.5); cursor: pointer; - padding: 2.5rem 2.65rem; + padding: 1.45rem 1.6rem; text-align: center; transition: all 0.25s ease-out; &:hover { - padding: 2.25rem 2.4rem; + padding: 1.25rem 1.4rem; } img { @@ -211,6 +210,13 @@ height: 100%; } } + + .feature-image-attribution { + color: #fff; + font-size: 0.9rem; + font-weight: 400; + opacity: 0.4; + } } .content { diff --git a/src/sass/_publications.scss b/src/sass/_publications.scss index eac7530c..2a2c4c93 100644 --- a/src/sass/_publications.scss +++ b/src/sass/_publications.scss @@ -10,10 +10,28 @@ .publicationsPage { .pub-item-content { + .pub-image { + background-color: #fff; + border: 1px solid #ccc; + height: fit-content; + margin: 5px 0 25px 0; + padding: 12px; + + img { + + width: 100%; + } + } + .pub-title { font-weight: 600; } + .show-authors-control { + font-weight: 400; + text-decoration: underline; + } + .fulltext-link { font-weight: 500; @@ -29,5 +47,27 @@ } } } + + &.landscape-paper { + background-color: lighten($primary-blue, 43%);; + border-radius: 8px; + } + } + + .external-links-content-container { + .link-item { + a { + text-decoration: none; + } + } + } +} + +/* Medium devices (tablets, less than 992px) */ +@include media-breakpoint-down(md) { + .publicationsPage { + .external-links-content-container { + display: block !important; + } } } \ No newline at end of file