This is an automated email from the ASF dual-hosted git repository. machristie pushed a commit to branch dreg-gateway in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 7c4ac016feaf359d0b08343da128e22f4e94d85e Author: root <[email protected]> AuthorDate: Mon Dec 3 22:12:09 2018 +0000 dTOX 1st version --- app/libraries/CommonUtilities.php | 4 +- app/libraries/ExperimentUtilities.php | 1 + app/libraries/FileTransfer.php | 117 ++++++++-------- app/routes.php | 7 +- app/views/account/dashboard.blade.php | 2 +- app/views/experiment/create-complete.blade.php | 2 +- app/views/experiment/create.blade.php | 2 +- app/views/partials/experiment-info.blade.php | 36 ++++- public/themes/dreg/assets/img/dTOX-model.png | Bin 0 -> 99342 bytes .../themes/dreg/assets/img/dreg-dtox-gateway.png | Bin 0 -> 132589 bytes public/themes/dreg/assets/img/dtox.create.exp.png | Bin 0 -> 17154 bytes public/themes/dreg/assets/img/dtox.create.exp2.png | Bin 0 -> 42088 bytes public/themes/dreg/partials/about.blade.php | 23 +++- public/themes/dreg/partials/doc.blade.php | 95 +++++++++---- .../partials/{doc.blade.php => dtox-doc.blade.php} | 153 ++++++++++++--------- public/themes/dreg/partials/header.blade.php | 7 +- public/themes/dreg/partials/software.blade.php | 58 ++++++++ public/themes/dreg/partials/template.blade.php | 130 +++++++++++------ 18 files changed, 427 insertions(+), 210 deletions(-) diff --git a/app/libraries/CommonUtilities.php b/app/libraries/CommonUtilities.php index c2df0df..e8dba9d 100644 --- a/app/libraries/CommonUtilities.php +++ b/app/libraries/CommonUtilities.php @@ -199,7 +199,7 @@ class CommonUtilities || Session::has('admin-read-only'))){ if( Session::get("nav-active") == "experiment" && $_SERVER['REQUEST_URI']== "/xperiment/create") $active = "active"; - $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/create"><span class="glyphicon glyphicon-plus-sign"></span> Start dREG</a></li>'; + $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/create"><span class="glyphicon glyphicon-plus-sign"></span> Start dREG/dTOX</a></li>'; } $active = ""; @@ -207,7 +207,7 @@ class CommonUtilities || Session::has('admin-read-only'))){ if( Session::get("nav-active") == "experiment" && $_SERVER['REQUEST_URI']== "/experiment/browse") $active = "active"; - $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/browse"><span class="glyphicon glyphicon-list"></span> Saved dREG runs</a></li>'; + $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/browse"><span class="glyphicon glyphicon-list"></span> Saved runs</a></li>'; } // <<- dREG diff --git a/app/libraries/ExperimentUtilities.php b/app/libraries/ExperimentUtilities.php index ade7873..89f5809 100755 --- a/app/libraries/ExperimentUtilities.php +++ b/app/libraries/ExperimentUtilities.php @@ -829,6 +829,7 @@ class ExperimentUtilities echo '<option value="'.$vals[$i].'">'.$vals[$i] .'</option>'; } echo '</select>'; + echo '</div>'; }else{ echo '<input '.$disabled . ' value="' . $input->value . '" type="text" class="form-control" name="' . $input->sanitizedFormName . '" id="' . $input->sanitizedFormName . diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php index 73882a6..470139c 100644 --- a/app/libraries/FileTransfer.php +++ b/app/libraries/FileTransfer.php @@ -13,7 +13,7 @@ use \TusServer\TusServer; class FileTransfer { - public static function gbrowser($filelist ){ + public static function gbrowser_dREG($filelist ){ $protocol = 'http'; if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https') $protocol = 'https'; @@ -42,7 +42,7 @@ class FileTransfer { $content = $content . ' { type:"bigwig", url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '", - name: "'. $filelist[3] .'", + name: "'. $filelist[2] .'", #fixedscale:{min:0,max:20}, summarymethod:"min", colorpositive:"#C5000B", @@ -76,64 +76,61 @@ class FileTransfer { },'. "\n"; - #$content = $content . '{ - # type:"bedgraph", - # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'", - # name: "dREG Info. Sites:", - # mode: "show", - # colorpositive:"#B30086", - # colornegative:"#0000e5", - # backgroundcolor:"#ffffe5", - # height:40, - # fixedscale:{min:0, max:1}, - #},'. "\n"; - - #$content = $content . '{ - # type:"bedgraph", - # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'", - # name: "dREG Peak Calling:", - # mode: "show", - # colorpositive:"#B30086", - # colornegative:"#0000e5", - # backgroundcolor:"#ffffe5", - # height:40, - # fixedscale:{min:0.2, max:1.0}, - #},'. "\n"; - - - #$content = $content . '{ - # type:"bigwig", - # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'", - # name: "imputed DNase-I signal:", - # #fixedscale:{min:0,max:20}, - # summarymethod:"max", - # colorpositive:"#00B306", - # backgroundcolor:"#ffffe5", - # height:100, - # mode: "show", - #},'. "\n"; - - #$content = $content . '{ - # type:"bedgraph", - # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.relaxed.bed.gz').'", - # name: "dREG.HD relaxed peaks:", - # mode: "show", - # colorpositive:"#0000e5/#B30086", - # backgroundcolor:"#ffffe5", - # height:40, - # fixedscale:{min:0, max:1}, - #},'. "\n"; - - #$content = $content . '{ - # type:"bedgraph", - # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.stringent.bed.gz').'", - # name: "dREG.HD stringent peaks:", - # mode: "show", - # colorpositive:"#0000e5/#B30086", - # backgroundcolor:"#ffffe5", - # height:40, - # fixedscale:{min:0, max:1}, - #},'. "\n"; + $content = $content . ']'; + return Response::make($content, 200) + ->header('Content-Type', 'text/plain'); + } + + public static function gbrowser_dTOX($filelist ){ + $protocol = 'http'; + if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https') + $protocol = 'https'; + + include("basecode.php"); + + $dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"]; + $filelist = explode("\n", RBase64::decode( $filelist ) ); + $folder_path=$filelist[0]. "ARCHIVE" ; + $content = "[ \n"; + $out_prefix = $filelist[3]; + + $content = $content . ' { + type:"bigwig", + url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[1]). '", + name: "'. $filelist[1] .'", + #fixedscale:{min:0,max:20}, + summarymethod:"max", + colorpositive:"#C5000B", + colornegative:"#0084D1", + height:100, + mode: "show", + },'. "\n" ; + + + $content = $content . ' { + type:"bigwig", + url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '", + name: "'. $filelist[2] .'", + #fixedscale:{min:0,max:20}, + summarymethod:"min", + colorpositive:"#C5000B", + colornegative:"#0084D1", + height:100, + mode: "show", + },'. "\n" ; + + $content = $content . '{ + type:"bigwig", + url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dTOX.bound.bed.gz').'", + name: "dTOX bound status:", + mode: "show", + colorpositive:"#B30086", + colornegative:"#0000e5", + backgroundcolor:"#ffffe5", + height:40, + fixedscale:{min:0, max:1}, + },'. "\n"; + $content = $content . ']'; return Response::make($content, 200) diff --git a/app/routes.php b/app/routes.php index 1ab5acd..e201de3 100755 --- a/app/routes.php +++ b/app/routes.php @@ -178,7 +178,12 @@ Route::get("files/get","FilemanagerController@get"); // Added by dREG Route::get("gbrowser/{filelist}", function($filelist){ - return FileTransfer::gbrowser($filelist); + return FileTransfer::gbrowser_dREG($filelist); +}); + +//Added by dTOX +Route::get("gbrowser1/{filelist}", function($filelist){ + return FileTransfer::gbrowser_dTOX($filelist); }); Route::get("gbfile/{file}", function($file){ diff --git a/app/views/account/dashboard.blade.php b/app/views/account/dashboard.blade.php index 8cc8501..d6c7eae3 100644 --- a/app/views/account/dashboard.blade.php +++ b/app/views/account/dashboard.blade.php @@ -250,7 +250,7 @@ <span class="glyphicon glyphicon-plus-sign console-icon"></span> </div> <div class="col-md-12"> - <h4>Start dREG</h4> + <h4>Start dREG/dTOX</h4> </div> </div> </a> diff --git a/app/views/experiment/create-complete.blade.php b/app/views/experiment/create-complete.blade.php index 7b1ab36..7dafa54 100755 --- a/app/views/experiment/create-complete.blade.php +++ b/app/views/experiment/create-complete.blade.php @@ -11,7 +11,7 @@ {{-- Commented by dREG <h1>Create a new experiment</h1> --}} - <h1>Create a new dREG experiment</h1> + <h1>Create a new dREG or dTOX experiment</h1> <!-- <form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" enctype="multipart/form-data"> --> <form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" > diff --git a/app/views/experiment/create.blade.php b/app/views/experiment/create.blade.php index 0a1ce01..cc4e215 100755 --- a/app/views/experiment/create.blade.php +++ b/app/views/experiment/create.blade.php @@ -18,7 +18,7 @@ {{-- Added by dREG <h1>Create a new experiment</h1> --}} - <h1>Create a new dREG experiment</h1> + <h1>Create a new dREG or dTOX experiment</h1> <form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" enctype="multipart/form-data"> diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php old mode 100755 new mode 100644 index 55c4c3f..4715e6d --- a/app/views/partials/experiment-info.blade.php +++ b/app/views/partials/experiment-info.blade.php @@ -220,6 +220,8 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d } ?> <td> + +@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" ) <select id="download"> <option value=''>Select results</option> @if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') ) @@ -235,20 +237,46 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d <option value=<?php echo $param_prefix.".dREG.peak.score.bed.gz"?>>dREG peak(only with scores)</option> @endif </select> +@else + <select id="download"> + <option value=''>Select results</option> +@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') ) + <option value=<?php echo $param_prefix.".tar.gz" ?>>Full results</option> +@endif +@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTOX.full.bed.gz') ) + <option value=<?php echo $param_prefix.".dTOX.full.bed.gz"?>>all dTOX regions</option> +@endif +@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTox.bound.bed.gz') ) + <option value=<?php echo $param_prefix.".dTOX.bound.bed.gz"?>>dTOX bound regions </option> +@endif + </select> + + +@endif + -<!-- <a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a> --> <button id="retLinks" style="color: #fff; background-color: #3e5a43; border-color: #46b8da; border: 1px solid transparent;" >Download <span class="glyphicon glyphicon-save" style="width:20px"></span></button> </td> </tr> <tr> <td><strong>Genome Browser</strong></td> <td> + +@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" ) <select id="genomebuilder"> <option value="">Select genome </option> <option value="hg19">hg19</option> <option value="hg38">hg38</option> <option value="mm10">mm10</option> - </select> + </select> +@else + <select id="genomebuilder"> + <option value="">Select genome </option> + <option value="hg19">hg19</option> + <option value="mm10">mm10</option> + </select> +@endif + or input <input type="text" id="customeGB" style="width:40px"/> <!-- <a href="#1" target="_blank" id="gbLinks">Switch to genome browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></a> --> @@ -547,7 +575,11 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d if (gb == '') return false; +@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" ) var gbUrl = "http://epigenomegateway.wustl.edu/browser/?datahub={{ $protocol .'://'. $_SERVER['HTTP_HOST']. '/gbrowser/'. RBase64::encode( $filelist ) }}&genome="; +@else + var gbUrl = "http://epigenomegateway.wustl.edu/browser/?datahub={{ $protocol .'://'. $_SERVER['HTTP_HOST']. '/gbrowser1/'. RBase64::encode( $filelist ) }}&genome="; +@endif window.open(gbUrl + gb); return false; }); diff --git a/public/themes/dreg/assets/img/dTOX-model.png b/public/themes/dreg/assets/img/dTOX-model.png new file mode 100644 index 0000000..906fa45 Binary files /dev/null and b/public/themes/dreg/assets/img/dTOX-model.png differ diff --git a/public/themes/dreg/assets/img/dreg-dtox-gateway.png b/public/themes/dreg/assets/img/dreg-dtox-gateway.png new file mode 100644 index 0000000..798a04e Binary files /dev/null and b/public/themes/dreg/assets/img/dreg-dtox-gateway.png differ diff --git a/public/themes/dreg/assets/img/dtox.create.exp.png b/public/themes/dreg/assets/img/dtox.create.exp.png new file mode 100644 index 0000000..3601c78 Binary files /dev/null and b/public/themes/dreg/assets/img/dtox.create.exp.png differ diff --git a/public/themes/dreg/assets/img/dtox.create.exp2.png b/public/themes/dreg/assets/img/dtox.create.exp2.png new file mode 100644 index 0000000..c4d0843 Binary files /dev/null and b/public/themes/dreg/assets/img/dtox.create.exp2.png differ diff --git a/public/themes/dreg/partials/about.blade.php b/public/themes/dreg/partials/about.blade.php index 53b8c4e..d485a2d 100755 --- a/public/themes/dreg/partials/about.blade.php +++ b/public/themes/dreg/partials/about.blade.php @@ -3,14 +3,27 @@ <h1 class="text-center top-space">About dREG gateway</h1> <p dir="ltr"> The <A title="dREG gateway" href="http://dreg.dnasequence.org";>dREG gateway</A> -is a cloud service that predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The hosted service is developed by the Danko lab at the Baker Institute and Cornell University and supported by the <A title="SciGaP" href="http://www.scigap.org";>SciGap</A> (Science Gateway Platform as a Service) and <A title="XSEDE" href="http://www.xsede.org";>XSEDE</A> (Extreme Science and Engineering Discovery Environment). +is a cloud platform that hosts two bioinformatics online services for functional analysis of sequencing data, dREG transcriptional regulatory element peak calling and dTOX transcription factor binding prediction. These online services are developed by the Danko lab at the Baker Institute and Cornell University and supported by the <A title="SciGaP" target=_blank href="http://www.scigap.org";>SciGap</A> (Science Gateway Platform as a Service) and <A title="XSEDE" target=_blank href="http: [...] </p> - <p dir="ltr"><A title="SciGaP" href="http://www.scigap.org";>SciGaP</A> supports access to core infrastructure services required by Science Gateways, including: user identity, accounts, authorization, and access to multiple computational resources from XSEDE. </p> - <p dir="ltr"><A title="XSEDE" href="http://www.xsede.org";>XSEDE</A> provides GPU resources under the project (TG-BIO160048: dREG Science Gateway).</p> + <p dir="ltr">The gateway is built on the infrastructure services of SciGaP and the computional resources of XSEDE as the following architecture, the details can be found in this paper: <A target=_blank href="https://dl.acm.org/citation.cfm?id=3219141";>"Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata"</A>. In PEARC 2018: Practice and Experience in Advanced Research Computing, July 22-26, 2018, Pittsburgh, PA, USA. + + <p dir="ltr"><A title="SciGaP" target=_blank href="http://www.scigap.org";>SciGaP</A> supports access to core infrastructure services required by Science Gateways, including: user identity, accounts, authorization, and access to multiple computational resources from XSEDE. </p> + <p dir="ltr"><A title="XSEDE" target=_blank href="http://www.xsede.org";>XSEDE</A> provides GPU resources under the project (TG-BIO160048 and TG-BIO180027: dREG Science Gateway).</p> + + <div> + <img id="myImg" alt="dREG Gateway" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg-dtox-gateway.png" style="display: block;margin-left: auto; margin-right: auto; width:80%"></img> + <p class="text-center"><small> Gateway Architecture</small></p> + + <div id="myModal" class="modal" onkeypress="document.getElementById('myModal').style.display='none'" > + <span class="close" onclick="document.getElementById('myModal').style.display='none'">×</span> + <img class="modal-content" id="img01"> + <div id="caption"></div> + </div> <h1 class="text-center top-space">About Danko Lab</h1> - <p dir="ltr"><A title="Danko Lab" href="http://www.dankolab.org";>Danko Lab</A> at the Cornell University studies how gene expression programs are encoded in mammalian DNA sequences, and how these ‘regulatory codes’ contribute to evolution, development, and disease. Our specialty is developing statistics and machine-learning approaches to analyze genomic sequencing data, prepared using DNase-I-seq, ATAC-seq, PRO-seq, RNA-seq, and related assays. Our tools borrow a wide variety of ideas [...] - + <p dir="ltr"><A title="Danko Lab" href="http://www.dankolab.org";>Danko Lab</A> +at Cornell University studies how gene expression programs are encoded in mammalian DNA sequences, and how these 'regulatory codes' contribute to evolution, development, and disease. Our specialty is developing statistics and machine-learning approaches to analyze genomic sequencing data, prepared using DNase-I-seq, ATAC-seq, PRO-seq, RNA-seq, and related assays. Our tools borrow a wide variety of ideas from the fields of statistics and machine-learning, including recent uses of hidden M [...] + <h1 class="text-center top-space">About Apache Airavata</h1> <p dir="ltr"><A title="Apache Airavata" href="http://airavata.apache.org/";>Apache Airavata</A> is a software framework that enables you to compose, manage, execute, and monitor large scale applications and workflows on distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds. </p> diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php index edb984b..dd70744 100755 --- a/public/themes/dreg/partials/doc.blade.php +++ b/public/themes/dreg/partials/doc.blade.php @@ -1,15 +1,15 @@ <div class="container"> <div class="content"> <div class="text-center"> - <h2 class="title top-space">Documentation</h2> + <h2 class="title top-space">dREG Documentation</h2> </div> <ul class="nav nav-tabs nav-justified" role="tablist"> <li role="presentation" class="active"><a href="#instructure" role="tab" data-toggle="tab">Instructions</a></li> - <li role="presentation"><a href="#sp" role="tab" data-toggle="tab">Software/Package</a></li> <li role="presentation"><a href="#input" role="tab" data-toggle="tab">Input</a></li> <li role="presentation"><a href="#output" role="tab" data-toggle="tab">Output</a></li> - </ul> + <li role="presentation"><a href="#faq" role="tab" data-toggle="tab">FAQ</a></li> +</ul> <div class="tab-content"> <div role="tabpanel" class="tab-pane active" id="instructure"> @@ -49,7 +49,7 @@ Click the 'save and launch' button. BigWig file are transferred to the XSEDE se <p class="description" style="padding:16px"> 6) <b>Check the status</b><br> -The user can check the status of their 'experiment' by clicking the menu 'Saved dREG runs' below the dREG logo. +The user can check the status of their 'experiment' by clicking the menu 'Saved runs' below the dREG logo. </p> <div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment browse" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.list.png"></img></div> @@ -119,28 +119,6 @@ After the experiment is complete, no results can be downloaded and job status sh </div> -<!---- SOFTWARE PANEL --> - <div role="tabpanel" class="tab-pane" id="sp"> - <div class="row"> - <div class="col-sm-offset-1 col-sm-10 col-xs-12"> - <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p> - - <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG";>https://github.com/Danko-Lab/dREG</A>.</p> - <p class="description"> -The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p> - <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD";>https://github.com/Danko-Lab/dREG.HD</A>.</p> - <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p> - <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm";>https://github.com/Danko-Lab/Rgtsvm</A>.</p> - <p class="description"> -Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p> - - <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git";>https://github.com/apache/airavata-php-gateway.git</A>.</p> <p class="description"> -Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE. -</p> - - </div> - </div> - </div> <!---- INPUT PANEL --> @@ -308,6 +286,71 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi </div> </div> +<!---- FAQ PANEL --> + + + <div role="tabpanel" class="tab-pane" id="faq"> + <div class="row"> + <div class="col-sm-offset-1 col-sm-10 col-xs-12"> + +<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p> + +<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p> +<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0";> here </A>.</p> + +<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p> +<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure";> here</A>.</p> + +<p><b>Q: Which browser works well with the dREG gateway?</b></p> +<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p> + + +<p><b>Q: What should the Safari users be aware of?</b></p> +<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/";> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br> +Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab". +</p> + +<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p> +<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p> + +<p><b>Q: Will the dREG gateway work with my data type?</b></p> +<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p> + +<p><b>Q: Will the pre-trained models work using data from my species?</b></p> +<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p> + +<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p> +<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html";>supplementary figure 3 in dREG paper</A>.</p> + +<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p> +<p>A: One month.</p> + +<p><b>Q: How to I cite the dREG gateway?</b></p> +<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/> +<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html";> +(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p> +<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract";> +(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P> + + +<p><b>Q: Do I have to create account before using this service?</b></p> +<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org";>XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p> + +<p><b>Q: How do I know the status of the computational nodes? </b></p> +<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md";>here</A> on the dREG page based on the notifications of the XSEDE community. </p> + +<p><b>Q: Who do I thank for the computing power? </b></p> +<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org";>SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/";>Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org";>XSEDE</A>.</p> + +<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p> +<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p> + + + </div> + </div> +</div> + +<!---- OUTPUT PANEL --> </div><!-- /.content --> diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/dtox-doc.blade.php similarity index 72% copy from public/themes/dreg/partials/doc.blade.php copy to public/themes/dreg/partials/dtox-doc.blade.php index edb984b..d54bdea 100755 --- a/public/themes/dreg/partials/doc.blade.php +++ b/public/themes/dreg/partials/dtox-doc.blade.php @@ -1,46 +1,46 @@ <div class="container"> <div class="content"> <div class="text-center"> - <h2 class="title top-space">Documentation</h2> + <h2 class="title top-space">dTOX Documentation</h2> </div> <ul class="nav nav-tabs nav-justified" role="tablist"> <li role="presentation" class="active"><a href="#instructure" role="tab" data-toggle="tab">Instructions</a></li> - <li role="presentation"><a href="#sp" role="tab" data-toggle="tab">Software/Package</a></li> <li role="presentation"><a href="#input" role="tab" data-toggle="tab">Input</a></li> <li role="presentation"><a href="#output" role="tab" data-toggle="tab">Output</a></li> - </ul> + <li role="presentation"><a href="#faq" role="tab" data-toggle="tab">FAQ</a></li> +</ul> <div class="tab-content"> <div role="tabpanel" class="tab-pane active" id="instructure"> <div class="row"> <div class="col-sm-offset-1 col-sm-10 col-xs-12"> <p class="description" style="padding:16px"> - 1) <b>Login</b>:<br> + 1) <b>Login</b>:(same as dREG)<br> The user needs to log in by clicking 'login' link at the top-right corner of the page. Having an account provides a number of benefits, and is free and easy. </p> <div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG login" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.login.png" ></img></div> <p class="description" style="padding:16px"> - 2) <b>Create a new project (optional)</b><br> -Optionally, users can choose to make a new 'project' in the dREG gateway to archive a collection of dREG data from related experiments. This will allow a collection of experiments to be stored in close proximity to each other.</p> + 2) <b>Create a new project (optional, same as dREG)</b><br> +Optionally, users can choose to make a new 'project' in the dREG/dTOX gateway to archive a collection of sequencing data from related experiments. This will allow a collection of experiments to be stored in close proximity to each other.</p> <div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG project" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.project.png" ></img></div> <p class="description" style="padding:16px"> - 3) <b>Start new dREG</b><br> -Select the menu 'Start dREG' below the dREG logo to create an data analysis for your data, as the following screenshot. + 3) <b>Start new dTOX</b><br> +Select the menu 'Start dREG/dTOX' below the dREG logo to create an data analysis for your data, as the following screenshot. Please notice to select the "dTOX prediction" Application. </p> -<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.exp.png" ></img></div> +<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dtox.create.exp.png" ></img></div> <p class="description" style="padding:16px"> - 4) <b>Select bigWig files</b><br> -Select bigWig files representing PRO-seq, GRO-seq, or ChRO-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/";>Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges";>Bridges.psc.edu</A>. + 4) <b>Fill experiment form</b><br> +Select bigWig files representing PRO-seq, ATAC-seq, or dNase-I-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/";>Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges";>Bridges.psc.edu</A>. </p> -<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.exp2.png" ></img></div> +<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dtox.create.exp2.png" ></img></div> <p class="description" style="padding:16px"> 5) <b>Submit the job</b><br> @@ -49,7 +49,7 @@ Click the 'save and launch' button. BigWig file are transferred to the XSEDE se <p class="description" style="padding:16px"> 6) <b>Check the status</b><br> -The user can check the status of their 'experiment' by clicking the menu 'Saved dREG runs' below the dREG logo. +The user can check the status of their 'experiment' by clicking the menu 'Saved runs' below the dREG logo. </p> <div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment browse" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.list.png"></img></div> @@ -119,29 +119,6 @@ After the experiment is complete, no results can be downloaded and job status sh </div> -<!---- SOFTWARE PANEL --> - <div role="tabpanel" class="tab-pane" id="sp"> - <div class="row"> - <div class="col-sm-offset-1 col-sm-10 col-xs-12"> - <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p> - - <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG";>https://github.com/Danko-Lab/dREG</A>.</p> - <p class="description"> -The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p> - <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD";>https://github.com/Danko-Lab/dREG.HD</A>.</p> - <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p> - <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm";>https://github.com/Danko-Lab/Rgtsvm</A>.</p> - <p class="description"> -Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p> - - <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git";>https://github.com/apache/airavata-php-gateway.git</A>.</p> <p class="description"> -Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE. -</p> - - </div> - </div> - </div> - <!---- INPUT PANEL --> <div role="tabpanel" class="tab-pane" id="input"> @@ -209,26 +186,17 @@ Airavata PHP Gateway provides an API to build web sites which interact with high <th>Description</th> </tr> <tr> - <td>$PREFIX.dREG.infp.bed.gz</td> - <td>Informative positions with dREG scores predicted by the dREG model. Decompress it with 'gunzip' in Linux.</td> + <td>$PREFIX.dTOX.full.bed.gz</td> + <td>TFBS regions with full information including chromosome, start, ending, MOTIF ID, RTFBSDB score, strand, Transcription factor, dTOX score, bound status. Decompress it with 'gunzip' in Linux.</td> </tr> <tr> - <td>$PREFIX.dREG.peak.full.bed.gz</td> - <td>Significant peaks (FDR < 0.05) with dREG scores, p-values and center positions where the maximum dREG scores are located. Decompress it with 'gunzip' in Linux.</td> - </tr> - <tr> - <td>$PREFIX.dREG.peak.score.bed.gz</td> - <td>Significant peaks (FDR < 0.05) only with dREG scores. Decompress it with 'gunzip' in Linux.</td> - </tr> - - <tr> - <td>$PREFIX.dREG.peak.prob.bed.gz</td> - <td>Significant peaks (FDR < 0.05) only with p-values. Decompress it with 'gunzip' in Linux.</td> + <td>$PREFIX.dTOX.bound.bed.gz</td> + <td>TFBS regions only with bound status. Decompress it with 'gunzip' in Linux.</td> </tr> <tr> - <td>$PREFIX.dREG.raw.peak.bed.gz</td> - <td>All raw peaks generated by dREG peak calling, including dREG scores, uncorrected p-values, center positions where the maximum are located in smoothed curves, center positions where the maximim are lcoated in original curve, centroid. Only available in the Web storage.</td> + <td>$PREFIX.dTOX.rtfbsdb.bed.gz</td> + <td>>TFBS regions only with RTFBSDB score. Decompress it with 'gunzip' in Linux.</td> </tr> <tr> @@ -249,11 +217,11 @@ border-color: #dadada;" data-expandable-box-container="true"> <p><b>Informative position:</b> Loci denoted as "informative positions" meet the following criteria: contain more than 3 reads in 100 bp interval on either strand, or more than 1 read in 1Kbp interval on both strands. Informative positions are used to predict the dREG scores for TRE (Transcription Regulatory Element) identification. </p> -<p><b>dREG score:</b> +<p><b>dTOX score:</b> Training and prediction is done using a Support Vector Regression model where a label of 1 indicates RNA polymerase II initialization or transciption through the informative position. The predicted values from the pre-trained model are called dREG scores. A dREG score close to 1 indicates that a position likely a TRE. </p> -<p><b>Peak p-value:</b> +<p><b>RTFBSDB score:</b> We test 5 dREG scores around each candidate peak center using the NULL hypothesis that each point within this peak is drawn from the non-TRE distribution. This test estimates the statistical confidence of each candidate dREG peak. In the final result, FDR is applied to do multiple correction and only the peaks with adjusted p-value < 0.05 are reported. </p> @@ -270,19 +238,11 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi <tr> <th>File name</th> <th>Description</th> </tr> <tr> - <td>$PREFIX.dREG.infp.bw</td> - <td>The bigWig file converted from the bed file of informative positions ($PREFIX.dREG.infp.bed.gz).</td> - </tr> <tr> - <td>$PREFIX.dREG.peak.score.bw</td> + <td>$PREFIX.dTOX.bound.bw</td> <td>The bigWig file converted from the significant peaks (FDR < 0.05) with dREG scores ($PREFIX.dREG.peak.score.bed.gz).</td> </tr> - <tr> - <td>$PREFIX.dREG.peak.prob.bw</td> - <td>The bigWig file converted from the significant peaks (FDR < 0.05) with p-values ($PREFIX.dREG.peak.prob.bed.gz). </td> - </tr> - - <tr> + <tr> <td>*.bed.gz.tbi</td> <td> The index files generated from the corresponding bed files. Please ignore them if you download the results.</td> </tr> @@ -295,7 +255,7 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi <tr> <th>File name</th> <th>Description</th> </tr> <tr> - <td>$PREFIX.dREG.log</td> + <td>$PREFIX.dTOX.log</td> <td>Print the summary information after peak calling. If the bigWigs don't meet the requirements of dREG, the warning information will be outputted in this file. </td> </tr> @@ -308,6 +268,71 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi </div> </div> +<!---- FAQ PANEL --> + + + <div role="tabpanel" class="tab-pane" id="faq"> + <div class="row"> + <div class="col-sm-offset-1 col-sm-10 col-xs-12"> + +<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p> + +<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p> +<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0";> here </A>.</p> + +<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p> +<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure";> here</A>.</p> + +<p><b>Q: Which browser works well with the dREG gateway?</b></p> +<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p> + + +<p><b>Q: What should the Safari users be aware of?</b></p> +<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/";> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br> +Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab". +</p> + +<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p> +<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p> + +<p><b>Q: Will the dREG gateway work with my data type?</b></p> +<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p> + +<p><b>Q: Will the pre-trained models work using data from my species?</b></p> +<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p> + +<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p> +<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html";>supplementary figure 3 in dREG paper</A>.</p> + +<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p> +<p>A: One month.</p> + +<p><b>Q: How to I cite the dREG gateway?</b></p> +<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/> +<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html";> +(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p> +<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract";> +(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P> + + +<p><b>Q: Do I have to create account before using this service?</b></p> +<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org";>XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p> + +<p><b>Q: How do I know the status of the computational nodes? </b></p> +<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md";>here</A> on the dREG page based on the notifications of the XSEDE community. </p> + +<p><b>Q: Who do I thank for the computing power? </b></p> +<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org";>SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/";>Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org";>XSEDE</A>.</p> + +<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p> +<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p> + + + </div> + </div> +</div> + +<!---- OUTPUT PANEL --> </div><!-- /.content --> diff --git a/public/themes/dreg/partials/header.blade.php b/public/themes/dreg/partials/header.blade.php index 043860d..a470341 100755 --- a/public/themes/dreg/partials/header.blade.php +++ b/public/themes/dreg/partials/header.blade.php @@ -19,11 +19,12 @@ color:blue; <div class="collapse navbar-collapse" > <ul class="nav navbar-nav navbar-right"> <li><a class="scroll hidden" href="#home"></a></li> - <li><a class="scroll" @if( $_SERVER['REQUEST_URI'] === "/" ) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/">Home</a></li> + <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">dREG Documentation</a></li> + <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/dtox-doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/dtox-doc">dTOX dcumentation</a></li> + <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/software") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/software">Software/Package</a></li> <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/about") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/about">About</a></li> - <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">Documentation</a></li> - <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/faq") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/faq">FAQ</a></li> + <!-- @if(! Session::has('loggedin')) <li><a class="scroll" href="{{ URL::to('/') }}/create">Create Account</a></li> diff --git a/public/themes/dreg/partials/software.blade.php b/public/themes/dreg/partials/software.blade.php new file mode 100755 index 0000000..686983c --- /dev/null +++ b/public/themes/dreg/partials/software.blade.php @@ -0,0 +1,58 @@ +<div class="container"> + + +<h1 class="text-center top-space">Software/Package</h1> +<div class="post-entry"> + + <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p> + + <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG";>https://github.com/Danko-Lab/dREG</A>.</p> + <p class="description"> +The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p> + + <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD";>https://github.com/Danko-Lab/dREG.HD</A>.</p> + <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p> + + <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm";>https://github.com/Danko-Lab/Rgtsvm</A>.</p> + <p class="description"> +Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p> + + <p class="description">[4] <B>rtfbsdb package</B>: <A href="https://github.com/Danko-Lab/rtfbs_db";>https://github.com/Danko-Lab/rtfbs_db</A>.</p> + <p class="description"> +Rtfbsdb implements TFBS scaning acorss whole genome and TF enrichment test with the aid of CIS-BP, Jolma and other TF databases. + </p> + + <p class="description">[5] <B>tfTarget package</B>: <A href="https://github.com/Danko-Lab/tfTarget";>https://github.com/Danko-Lab/tfTarget</A>.</p> + <p class="description"> +Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data. + </p> + + <p class="description">[6] <B>Proseq 2.0</B>: <A href="https://github.com/Danko-Lab/proseq2.0";>https://github.com/Danko-Lab/proseq2.0</A>.</p> + <p class="description"> +Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing. + </p> + + <p class="description">[7] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git";>https://github.com/apache/airavata-php-gateway.git</A>.</p> + <p class="description"> +Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE. + </p> + +</div> +<!-- end of .post-entry --> + +<br style="clear:both"/> +<hr style="color:green"/> + +</div> + +<div class="col-md-12 text-center" style=" padding: 20px 0 20px 0; background-color:#FFFFFF"> + <a href="http://airavata.apache.org/"; target="_blank"> + <img width="200px" src="{{URL::to('/')}}/themes/{{Session::get('theme')}}/assets/img/poweredby-airavata-logo.png"> + </a> + <a href="http://www.nsf.gov/"; target="_blank" class="logo-seperation"> + <img width="200px" src="{{URL::to('/')}}/themes/{{Session::get('theme')}}/assets/img/nsf-logo.png"> + </a> + <a href="https://www.xsede.org/"; target="_blank" class="logo-seperation"> + <img width="200px" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/powered-by-xsede.gif"> + </a> +</div> diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php index 8dff7b8..0110898 100755 --- a/public/themes/dreg/partials/template.blade.php +++ b/public/themes/dreg/partials/template.blade.php @@ -1,28 +1,64 @@ <link media="all" type="text/css" rel="stylesheet" href="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/css/zoom.css"/> <div class="col-md-offset-2 col-md-8 breathing-space scigap-info" > - <h1 class="text-center">Welcome to dREG gateway!</h1> - <p class="text-center" style="color:#cccccc;"> - Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/> - </p> - <p class="text-center" style="color:#444444;"> -The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md";><B>here!</b></A> -</p> - <hr/> - - <div class="col-md-5" style="margin-left: 5%"> - <H2> How does it work?</H2> - <p style="font-size:14px; margin-top:20px; text-align:justify"> -The dREG gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG and dREG-HD models to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The dREG gateway uses pre-trained models that work in any mammalian organism (other or [...] -<img id="myImg" alt="dREG Gateway" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-works.png" style="width:100%"></img> -<p class="text-center"><small>Click the figure to enlarge it</small></p> - -<div id="myModal" class="modal" onkeypress="document.getElementById('myModal').style.display='none'" > - <span class="close" onclick="document.getElementById('myModal').style.display='none'">×</span> - <img class="modal-content" id="img01"> - <div id="caption"></div> + <h1 class="text-center">Welcome to dREG and dTOX gateway!</h1> + <p class="text-center" style="color:#cccccc;"> + Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/> + </p> + <p class="text-center" style="color:#444444;"> + The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md";><B>here!</b></A> + </p> + <hr/> + +<div class="col-md-offset-1 col-md-5" style="margin-left: 5%" > + <H2> How is dREG used?</H2> + <p style="font-size:14px; margin-top:10px; text-align:justify"> + The dREG model in the gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG model to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The current dREG model works in any mammalian organism.</p> + <p style="font-size:14px; margin-top:10px;text-align:justify"> +Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p> + + <p style="font-size:14px; margin-top:5px;text-align:justify"> + <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img> + Use the Danko lab's <b>mapping pipeline</b> (<A target=_blank href="https://github.com/Danko-Lab/proseq2.0";>here</A>) to prepare bigWig files from fastq files or <b>convert BAM files</b> of mapped reads to bigWig (<A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig";>here</A>). + </p> + + <p style="font-size:14px; margin-top:5px;text-align:justify"> + <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img> + See our <A href="{{ URL::to('/') }}/pages/doc#faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/doc">documentation</a> or <A target=_blank href="https://www.dropbox.com/s/jzlamnd0mej0z76/Chu.dREG_protocol.pdf?dl=0";>dREG protocol manuscript</A> for additional questions.</p> + + <img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img> + <p class="text-center"><small>Click the figure to enlarge it</small></p> + <div id="myModal2" class="modal" onkeypress="document.getElementById('myModal2').style.display='none'" > + <span class="close" onclick="document.getElementById('myModal2').style.display='none'">×</span> + <img class="modal-content" id="img02"> + <div id="caption"></div> + </div> +</div> + + +<div class="col-md-offset-1 col-md-5" style="margin-left: 5%"> + <H2> How is dTOX used? </H2> + <p color="red">Under construction, please ignore this section! </p> + <p style="font-size:14px; margin-top:10px;text-align:justify"> +The dTOX models in the gateway predict the binding status of transcription factor binding sites using PRO-seq, ATAC-seq, or DNase-1-seq data. The server takes as input bigWig files provided by the user, which represent the PRO-seq, ATAC-seq, or DNase-1-seq signal on the plus and minus strand. Once the user selects the transcription factors to predict on, the gateway uses a pre-trained dTOX model to identify transcription factor binding patterns. The current dTOX models work in any mammal [...] + <p style="font-size:14px; margin-top:10px;text-align:justify"> +The web operations are same as the dREG model. Users need to login -> upload data -> run data. Results can be downloaded or viewed in the WashU Genome browser.</p> + + <p style="font-size:14px; margin-top:5px;text-align:justify"> + <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img> + See our <A href="{{ URL::to('/') }}/pages/dtox-doc#faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/dtox-doc">documentation</a> for additional questions. + </p> + + <img id="myImg3" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dTOX-model.png" style="width:100%"></img> + <p class="text-center"><small>Click the figure to enlarge it</small></p> + <div id="myModal3" class="modal" onkeypress="document.getElementById('myModal3').style.display='none'" > + <span class="close" onclick="document.getElementById('myModal3').style.display='none'">×</span> + <img class="modal-content" id="img03"> + <div id="caption"></div> + </div> </div> + <script> // Get the modal var modal = document.getElementById('myModal'); @@ -43,29 +79,6 @@ span.onclick = function() { } </script> - </div> - - <div class="col-md-offset-1 col-md-5" style="margin-left: 5%"> - <H2> How is it used?</H2> - <p style="font-size:14px; margin-top:20px;text-align:justify"> -Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p> - -<p style="font-size:14px; margin-top:5px;text-align:justify"> -<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img> -Use the Danko lab's <b>mapping pipeline</b> (<A target=_blank href="https://github.com/Danko-Lab/proseq2.0";>here</A>) to prepare bigWig files from fastq files or <b>convert BAM files</b> of mapped reads to bigWig (<A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig";>here</A>). -</p> - -<p style="font-size:14px; margin-top:5px;text-align:justify"> -<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img> -See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/doc">documentation</a> or <A target=_blank href="https://www.dropbox.com/s/jzlamnd0mej0z76/Chu.dREG_protocol.pdf?dl=0";>dREG protocol manuscript</A> for additional questions. -</p> -<img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img> -<p class="text-center"><small>Click the figure to enlarge it</small></p> -<div id="myModal2" class="modal" onkeypress="document.getElementById('myModal2').style.display='none'" > - <span class="close" onclick="document.getElementById('myModal2').style.display='none'">×</span> - <img class="modal-content" id="img02"> - <div id="caption"></div> -</div> <script> // Get the modal @@ -87,11 +100,40 @@ span.onclick = function() { } </script> - </div> +<script> +// Get the modal +var modal = document.getElementById('myModal3'); +// Get the image and insert it inside the modal - use its "alt" text as a caption +var img = document.getElementById('myImg3'); +var modalImg = document.getElementById("img03"); +var captionText = document.getElementById("caption"); +img.onclick = function(){ + modal.style.display = "block"; + modalImg.src = this.src; + captionText.innerHTML = this.alt; +} +// Get the <span> element that closes the modal +var span = document.getElementsByClassName("close")[0]; +// When the user clicks on <span> (x), close the modal +span.onclick = function() { + modal.style.display = "none"; +} +</script> + <br style="clear:both"/> <hr style="color:green"/> +<h1 class="text-center">Gateway Introduction</h1> + +<div style="width: 92%; margin-left: 5%; padding-left:15px"> +<p> +The dREG gateway is a cloud platform developed by the <A target=_blank href="http://www.dankolab.org/";>Danko lab</a> at the <A target=_blank href="https://www2.vet.cornell.edu/departments-centers-and-institutes/baker-institute";>Baker Institute</A>, <A target=_blank href="http://www.cornell.edu";>Cornell University</A> and supported by the <A target=_blank href="https://www.scigap.org/";>SciGap</A> (Science Gateway Platform as a Service) and <A target=_blank href="https://www.xsede.org/";>XS [...] +Currently, this gateway hosts two bioinformatics services for functional analysis of sequencing data, dREG transcriptional regulatory element peak calling and dTOX transcription factor binding prediction. Both services take as input files (either PRO-seq, GRO-seq, ATAC-seq or DNase-1-seq) provided by the user, and then uses pre-trained models to conduct prediction and post-processing on GPU computing nodes. The architecture and details are <A href="{{ URL::to('/') }}/pages/about">here</a>. +</div> + +<hr style="color:green"/> + <h1 class="text-center">Publications</h1> <div style="width: 92%; margin-left: 5%; padding-left:15px"> <table>
