9112364a57f18875a89a3047f0fc44d60ac3fc0e bnguy Mon Jan 27 14:43:54 2020 -0800 Remove search box in header.html. Add Northstar and NDEx card, Add Scimtar logo in tools.html, Updated MISCE pdf, Updated Home page Description in index.html, Rearrange (Alphabetize) dataset in project.html diff --git src/hg/cirm/gateway/htdocs/tools.html src/hg/cirm/gateway/htdocs/tools.html index 0fcf41c..4967832 100755 --- src/hg/cirm/gateway/htdocs/tools.html +++ src/hg/cirm/gateway/htdocs/tools.html @@ -104,32 +104,35 @@ </li> <li class="list-group-item"><a href="https://github.com/billgreenwald/pgltools" target="_blank">Pgltools GitHub</a> <i class="fab fa-github" aria-hidden="true"></i></li> </ul> </div> <div class="card-footer"> <small class="text-muted"> The Pgltools package was created by Bill Greenwald. </small> </div> </div> <a name="SCIMITAR"></a> <div class="card"> <div class="card-body text-center"> <span class="padded-top-img"> - <img src=""> + <br> + <img class="card-img-top"Style="max-width: 300px" + src="https://raw.githubusercontent.com/dimenwarper/scimitar/master/logo.png"> </span> + <br> <p class="lead"><span style="color: #1E90FF">SCIMITAR:</span> Single Cell Inference of MorphIng Trajectories and their Associated Regulation</p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item">The SCIMITAR package contains a number of tools to help scientists analyze cell trajectory maps based on single cell sequencing data.</li> <li class="list-group-item"> Cordero P, Stuart JM. <a href="http://dx.doi.org/10.1142/9789813207813_0053" target="_blank"> Tracing co-regulatory network dynamics in noisy, single-cell transcriptome trajectories</a> <i class="far fa-file-pdf" aria-hidden="true"></i>. <em>Pac Symp Biocomput</em>. 2016;22:576-587. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27897008" target="_blank">27897008</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203771/" target="_blank">PMC5203771</a> </li> <li class="list-group-item"> @@ -221,32 +224,31 @@ src="https://cellatlas.ucsc.edu/static/media/logo.3369643f.svg"> <p class="lead"><span style="color: #1E90FF">UCSC Cell Atlas</span></p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item"> <p> The UCSC Cell Atlas is a growing compendium of single-cell mRNA seq data coupled with visualizations and query abilities designed to expedite the process of biological discovery from single-cell mRNA seq experiments. We aim to augment research by providing an intuitive web interface for browsing single-cell mRNA seq experiments and a seamless connection from browsing to analysis through a RESTful API. Also under development is a cell type labeling app geared to ease the burden of manual annotation and creation of publication quality figures for newly generated data.</p> </li> <li class="list-group-item"><a href="https://cellatlas.ucsc.edu/" - target="_blank">UCSC Cell Atlas Website</a> <i class="fas fa-external-link-alt" - aria-hidden="true"></i></p></li> + target="_blank">UCSC Cell Atlas Website</a> <i class="fas fa-external-link-alt" aria-hidden="true"></i></p></li> </ul> </div> <div class="card-footer"> <small class="text-muted"> The UCSC Cell Atlas was created by the Josh Stuart Lab at UCSC. </small> </div> </div> <a name="MISCE"></a> <div class="card"> <div class="card-body text-center"> <img class="card-img-top" style="max-width: 300px" src="<!--#echo var='ROOT'-->images/misce1.png"> <p class="lead"><span style="color: #1E90FF">MISCE:</span> A Minimum Information About a Stem Cell Experiment</p> @@ -256,32 +258,98 @@ MISCE, or Minimum Information about a Stem Cell Expriment, is a spreadsheet that attempts to collect a rich set of useful information (metadata) about any experiment involving stem cells. The hope is that in using MISCE, the detailed metadata will make the experimental data useful to others attempting to use it in the future.</p> <p> MISCE consists of a number of different modules with each module describing a different experimental process, e.g. celluar reprogramming or RNA sequencing, and all of the important information related to this process, e.g. "Biosample disease stage" or "Assay platform". Each module can be included or excluded based on the type of experiment being performed. For example, you might not include the "Assay_DNAMethyl" module if you are not performing DNA methylation assays as part of your experiment.</p> </li> <li class="list-group-item"> - <a href="<!--#echo var='ROOT'-->MISCEv1.1.pdf">PDF of MISCE modules</a> + <a href="<!--#echo var='ROOT'-->MISCE2.0.pdf">PDF of MISCE modules</a> <i class="far fa-file-pdf" aria-hidden="true"></i> </li> </ul> </div> <div class="card-footer"> <small class="text-muted"> MISCE was created by Sagar Jain and Richard Scheuermann; it is currently maintained by UCSC. </small> </div> </div> </div> </div> + <br> + <div class="row no-gutters"> + <div class="card-deck"> + <div class="card"> + <div class="card-body text-center"> + <br> + <img class="card-img-top"Style="max-width: 300px" + src="https://northstaratlas.github.io/atlas_landmarks/static/logo.png"> + <p class="lead"><span style="color: #1E90FF">Northstar:</span> + Leveraging Previous Annotations to Label New Datasets</p> + <ul class="list-group list-group-flush text-left"> + <li class="list-group-item"> + <p> + Northstar is a computational package that can be used to apply cell + type labels to a dataset by leveraging previously annotated + datasets. Cells can be assigned new cell type labels or added to + previously annotated cell types. Northstar also provides a number + of pre-labeled cell atlases covering organs such as pancreas, liver, + and more.</p> + </li> + <li class="list-group-item"><a href="https://github.com/northstaratlas/northstar" + target="_blank">Northstar GitHub</a> <i class="fab fa-github" aria-hidden="true"></i></li> + <li class="list-group-item"><a href="https://northstaratlas.github.io/atlas_landmarks/" + target="_blank">Northstar Atlas Landmarks</a> <i class="fas fa-external-link-alt" + aria-hidden="true"></i></li> + </ul> + </div> + <div class="card-footer"> + <small class="text-muted"> + Northstar was created by the Quake lab at Stanford University. + </small> + </div> + </div> + <div class="card"> + <div class="card-body text-center"> + <br> + <img class="card-img-top"Style="max-width: 300px" + src="https://pbs.twimg.com/profile_images/931231956360032256/g5K2SQQz_400x400.jpg"> + <p class="lead"><span style="color: #1E90FF">NDEx:</span> + The Network Data Exchange</p> + <ul class="list-group list-group-flush text-left"> + <li class="list-group-item"> + <p> + NDEx, the Network Data Exchange, is an online commons where scientists can + upload, share, and publicly distribute networks. Networks in NDEx + receive globally unique accession IDs and can be stored for private + use, shared in pre-publication collaboration, or released for + public access.</p> + </li> + <li class="list-group-item"><a + href="https://www.ndexbio.org/#/" + target="_blank">NDEx Website</a> <i class="fas fa-external-link-alt" aria-hidden="true"></i></li> + <li class="list-group-item"> PMID: <a + href="https://www.ncbi.nlm.nih.gov/pubmed/26594663" target="_blank">26594663</a>; PMC: <a + href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649937/" target="_blank">PMC4649937</a></li> + </ul> + </div> + <div class="card-footer"> + <small class="text-muted"> + NDEx Project was created by the NDEx Team at UC San Diego. + </small> + </div> + </div> + + </div> + </div> </div> <!--#include virtual="${ROOT}inc/footer.html" -->