fcf6915a32e7ef9843f3435e69a62e4c3c5c5675 mspeir Tue Apr 21 13:36:07 2020 -0700 Changing image links for those we serve from our images directory to be relative links, no redmine. diff --git src/hg/cirm/gateway/htdocs/tools.html src/hg/cirm/gateway/htdocs/tools.html index ded488d..1e35265 100755 --- src/hg/cirm/gateway/htdocs/tools.html +++ src/hg/cirm/gateway/htdocs/tools.html @@ -29,31 +29,31 @@ Browser Website</a> <i class="fas fa-external-link-alt" aria-hidden="true"></i></li> <li class="list-group-item"><a href="https://github.com/maximilianh/cellBrowser" target="_blank">Cell Browser GitHub</a> <i class="fab fa-github" aria-hidden="true"></i> </li> </ul> </div> <div class="card-footer"> <small class="text-muted"> The Cell Browser was created by Max Haeussler. </small> </div> </div> <a name="PluriTest"></a> <div class="card"> <div class="card-body text-center"> - <a href="https://cirm.ucsc.edu/images/pluritestWelcome.png" target="_blank"> + <a href="<!--#echo var='ROOT'-->images/pluritestWelcome.png" target="_blank"> <img class="card-top-img" style="max-width: 300px" src="<!--#echo var='ROOT'-->images/pluritestWelcome.png"> </a> <p class="lead"><span style="color: #1E90FF">PluriTest:</span> Check for Pluripotency</p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item"> Pluritest allows you check your samples for pluripotentcy through uploading RNA-seq fastq files or Affymetrix and Illumina arrays. Note: Use of Pluritest requires you to register an account. </li> <li class="list-group-item"> Müller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, Danner S, Goldmann JE, Herbst A, Schmidt NO <em>et al</em>. <a href="http://dx.doi.org/10.1038/nmeth.1580" target="_blank"> A bioinformatic assay for pluripotency in human cells</a>. @@ -151,31 +151,31 @@ </div> <div class="card-footer"> <small class="text-muted"> SCIMITAR was created Pablo Cordero. </small> </div> </div> </div> </div> <br> <div class="row no-gutters"> <div class="card-deck"> <a name="tagStorm"></a> <div class="card"> <div class="card-body text-center"> - <a href="https://cirm.ucsc.edu/images/tagStormImage.png" target="_blank"> + <a href="<!--#echo var='ROOT'-->images/tagStormImage.png" target="_blank"> <img class="card-top-img" style="max-width: 300px" src="<!--#echo var='ROOT'-->images/tagStormImage.png"> </a> <p class="lead"><span style="color: #1E90FF">Tag Storm:</span> Metadata made simple</p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item"> <p> The tag storm format offers an easy way to describe a hierarchical set of metadata for your data. The tag storm format is made up of a number of key/value pairs spread across stanzas at various indentation levels. Lower indentation levels inherit information from higher levels, so the most general metadata, e.g. lab or dataset names, are generally found at the highest level and more specifc metadata, e.g. sex or file name, are found at the lower level.</p> <p> The Tag Storm GitHub page contains more information about the format as well as a @@ -184,31 +184,31 @@ <li class="list-group-item"> <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/tagStorm" target="_blank">Tag Storm GitHub</a> <i class="fab fa-github" aria-hidden="true"></i></p> </li> </ul> </div> <div class="card-footer"> <small class="text-muted"> TagStorm format and utilities were developed by Jim Kent. </small> </div> </div> <a name="RIGGLE"></a> <div class="card"> <div class="card-body text-center"> - <a href="https://cirm.ucsc.edu/images/RIGGLE_demo.png" target="_blank"> + <a href="<!--#echo var='ROOT'-->images/RIGGLE_demo.png" target="_blank"> <img class="card-top-img" style="max-width: 300px" src="<!--#echo var='ROOT'-->images/RIGGLE_demo.png"> </a> <p class="lead"><span style="color: #1E90FF">RIGGLE:</span> Regulator Inference by Graph-Guided LASSO Estimation</p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item"> <p> RIGGLE (Regulatory Inference by Graph-Guided LASSO Estimation) is a machine learning framework designed to discover the transcription factor regulators of a cell development trajectory by taking in expression data, known transcription factor targets, and a cell development graph.</p> <p> This process produces predictions for the transcription factor's activities in each of the cell types represented in the graph based on the @@ -249,31 +249,31 @@ 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> </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"> - <a href="https://cirm.ucsc.edu/images/misce1.png" target="_blank"> + <a href="<!--#echo var='ROOT'-->images/misce1.png" target="_blank"> <img class="card-img-top" style="max-width: 300px" src="<!--#echo var='ROOT'-->images/misce1.png"> </a> <p class="lead"><span style="color: #1E90FF">MISCE:</span> A Minimum Information About a Stem Cell Experiment</p> <ul class="list-group list-group-flush text-left"> <li class="list-group-item"> <p> 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