20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 wisulliv Fri Feb 9 09:38:15 2024 -0800 Will SSPsyGene V1 Updates. diff --git src/hg/cirm/gateway/htdocs/cirmIndex.html src/hg/cirm/gateway/htdocs/cirmIndex.html index 6b562dc..5f4519c 100755 --- src/hg/cirm/gateway/htdocs/cirmIndex.html +++ src/hg/cirm/gateway/htdocs/cirmIndex.html @@ -1,142 +1,84 @@ <!DOCTYPE html> <!--#set var="TITLE" value="CIRM Stem Cell Hub at UCSC Homepage" --> <!--#include virtual="setRoot.html" --> <!--#include virtual="${ROOT}inc/header.html" --> <div class="cirm-page-body"> <div class="cirm-page-title back-gray"> - <h5 class="cirm-page-title-text">Welcome to the CESCG Stem Cell Hub!</h5> + <h5 class="cirm-page-title-text">Welcome to the SSPsyGene Staging Portal!</h5> </div> <div class="container-fluid"> <div class="row" style="margin-bottom: 15px"> <div class="card col-12"> <div class="row" style="padding: 10px 0px"> <div class="col-md-1 text-right"> <a href="<!--#echo var='ROOT'-->cgi-bin/cdwWebBrowse?cdwCommand=browseFiles" style="text-decoration:none"> <span> <br> <i class="fas fa-search fa-4x text-dark-pink"></i> </div> <div class="col-md-2"> <h3 class="text-dark-pink">Browse Files</h3> <p> Filter, view, and download files </p> More > </span> </a> </div> <div class="col-md-1 text-right"> - <a href="<!--#echo var='ROOT'-->projects" style="text-decoration:none"> + <a href="<!--#echo var='ROOT'-->cgi-bin/cdwWebBrowse?hgsid=404732858_euZmAKjIhaPrZe0sWnFvKJdj2TYu&cdwCommand=browseDataSets" style="text-decoration:none"> <span> <br> <i class="fas fa-project-diagram fa-4x text-light-blue"></i> </div> <div class="col-md-2"> <h3 class="text-light-blue">View Datasets</h3> <p> Explore the datasets and assays available </p> More > </span> </a> </div> - <div class="col-md-1 text-right"> - <a href="<!--#echo var='ROOT'-->cescg/cescgPubs" style="text-decoration:none"> - <span> - <br> - <i class="fas fa-file-alt fa-4x text-dark-pink"></i> - </div> - <div class="col-md-2"> - <h3 class="text-dark-pink">Read Articles</h3> - <p> - Read publications about CESCG research - </p> - More > - </span> - </a> - </div> - <div class="col-md-1 text-right"> - <a href="<!--#echo var='ROOT'-->tools" style="text-decoration:none"> - <span> - <br> - <i class="fas fa-toolbox fa-4x text-light-green"></i> - </div> - <div class="col-md-2"> - <h3 class="text-light-green">Use Tools</h3> - <p> - Take advantage of CESCG analysis tools - </p> - More > - </span> - </a> - </div> </div> </div> </div> <div class="row" style="margin-bottom: 15px"> <div class="card col-md-12"> <div class="row no-gutters"> <div class="card-body col-md-3"> <img src="images/cirmInsulinCells.jpg" class="img-fluid" alt=""> </div> <div class="col" style="padding: 0px 15px"> <div class="card-body"> <div class="row"> <!-- <div class="col-md-6"> --> <div class="col-md-12"> - <h6>Welcome to the Stem Cell Hub web site!</h6> - <p class="card-text"> - The CIRM Center of Excellence in Stem Cell Genomics (CESCG) - was established with the goal to apply genomics and - bioinformatics approaches to stem cell research to accelerate - fundamental understanding of human biology and disease - mechanisms, enhance cell and tissue production and advance - personalized cellular therapies. The Stem Cell Hub was built - with funding from CIRM to host high-quality genomic data - collected under the CESCG Collaborative Research Programs - (CRP).</p> - <p class="card-text"> - The Stem Cell Hub contains many terabytes of data that cover - a large variety of sequencing assays, including a vast amount - of single-cell data. It houses primary data files such as DNA - reads in fastq format, as well as many types of files derived - from mapping and other analysis of the primary data, and PDF - and other document files describing protocols. Sequenced - samples in the Stem Cell Hub include naturally developing - human tissues as well as cells engineered from healthy skin - and blood cells to become replacements for diseased cells and - tissues, including data from ethically and scientifically - careful human clinical trials.</p> - - <p class="card-text"> - We hope that the Stem Cell Hub will be useful to a wide range - of scientists from clinicians to cell biologists to - bioinformaticians doing custom analysis and combining data - from multiple projects. Please see the help link for - additional information on how to use the site.</p> - + Welcome to the DRACCs Data Portal, the central hub for accessing and exploring the data generated by the laboratories participating in the “Scalable and Systematic + Neurobiology of Psychiatric and Neurodevelopmental Disorder Risk Genes (SSPsyGene)” Consortium. This consortium, funded by the National Institute of Mental Health + (NIMH), is dedicated to systematically characterizing the genotypes and phenotypes of neurodevelopmental and psychiatric disorder risk gene deletion models. + To learn more about the labs are projects visit: <a href = "https://sspsygene.ucsc.edu/" target="_blank" rel="noopener noreferrer">https://sspsygene.ucsc.edu/<a/> <p class="card-text"> - If you have any questions, or if you'd like to contribute - data to the Stem Cell Hub, please contact our support team - at <a href = "mailto:cirm-wrangler-group@ucsc.edu">cirm-wrangler-group@ucsc.edu</a></p> + If you have any questions, or if you'd like to contribute data to the SSPsyGene Data Portal, + please contact our support team at <a href = "mailto:wranglers@ucsc.edu" target="_blank" rel="noopener noreferrer">wranglers@ucsc.edu</a></p> <!-- </div> <div class="col-md-6"> <h6>What is the Stem Cell Hub?</h6> <p class="card-text"> The Stem Cell Hub combines state of the art software with careful human curation. The software runs quality checks that ensure the data is in the proper format, contains no contamination, that the DNA aligns in expected places, that the level of mitochondrial and ribosomal data are within expected range, and gathers statistics on how well replicates agree using a number of statistical measures. The system supports tagging the data using a flexible metadata system that allows experiments to be described in a concise but rich manner that reflects any natural hierarchies or control/experiment groups that are