Repository: airavata-php-gateway Updated Branches: refs/heads/dreg-gateway dae6cd756 -> e11970022
dreg theme Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/25339377 Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/25339377 Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/25339377 Branch: refs/heads/dreg-gateway Commit: 253393770494ddef4444e5a84d0fd1861854939f Parents: dae6cd7 Author: root <root@osboxes> Authored: Wed Feb 1 18:25:59 2017 +0000 Committer: root <root@osboxes> Committed: Wed Feb 1 18:25:59 2017 +0000 ---------------------------------------------------------------------- public/themes/dreg/LICENSE | 201 ++++++++++++ public/themes/dreg/README.md | 2 + public/themes/dreg/assets/css/style.css | 304 +++++++++++++++++++ public/themes/dreg/assets/css/zoom.css | 87 ++++++ public/themes/dreg/assets/img/Twitter26x21.png | Bin 0 -> 3227 bytes public/themes/dreg/assets/img/airavata-logo.png | Bin 0 -> 19733 bytes public/themes/dreg/assets/img/baker-logo.png | Bin 0 -> 33980 bytes public/themes/dreg/assets/img/cornell-logo.png | Bin 0 -> 23327 bytes .../themes/dreg/assets/img/dREG-logo-muted.png | Bin 0 -> 42728 bytes public/themes/dreg/assets/img/dREG-model.png | Bin 0 -> 39864 bytes public/themes/dreg/assets/img/dREG-works.png | Bin 0 -> 139455 bytes public/themes/dreg/assets/img/dREG.Preprint.png | Bin 0 -> 3027 bytes public/themes/dreg/assets/img/dankolab-logo.png | Bin 0 -> 228884 bytes public/themes/dreg/assets/img/distributed.png | Bin 0 -> 11690 bytes .../themes/dreg/assets/img/dreg.create.exp.png | Bin 0 -> 27066 bytes .../themes/dreg/assets/img/dreg.create.exp2.png | Bin 0 -> 53061 bytes .../dreg/assets/img/dreg.create.project.png | Bin 0 -> 14208 bytes .../themes/dreg/assets/img/dreg.exp.folder.png | Bin 0 -> 25789 bytes public/themes/dreg/assets/img/dreg.exp.list.png | Bin 0 -> 33567 bytes .../themes/dreg/assets/img/dreg.exp.summary.png | Bin 0 -> 48376 bytes public/themes/dreg/assets/img/dreg.login.png | Bin 0 -> 6381 bytes public/themes/dreg/assets/img/dreg.project.png | Bin 0 -> 24380 bytes public/themes/dreg/assets/img/nsf-logo.gif | Bin 0 -> 12384 bytes public/themes/dreg/assets/img/nsf-logo.png | Bin 0 -> 48920 bytes .../themes/dreg/assets/img/powered-by-xsede.gif | Bin 0 -> 2973 bytes .../dreg/assets/img/poweredby-airavata-logo.png | Bin 0 -> 20008 bytes public/themes/dreg/assets/img/scigap-logo.png | Bin 0 -> 40135 bytes .../dreg/assets/img/webdev-bullet-icon.png | Bin 0 -> 17598 bytes .../themes/dreg/assets/img/xsede-full-color.png | Bin 0 -> 57042 bytes public/themes/dreg/layouts/default.blade.php | 1 + public/themes/dreg/partials/about.blade.php | 51 ++++ public/themes/dreg/partials/doc.blade.php | 156 ++++++++++ public/themes/dreg/partials/faq.blade.php | 50 +++ public/themes/dreg/partials/footer.blade.php | 45 +++ public/themes/dreg/partials/header.blade.php | 54 ++++ public/themes/dreg/partials/template.blade.php | 118 +++++++ public/themes/dreg/views/index.blade.php | 0 37 files changed, 1069 insertions(+) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/LICENSE ---------------------------------------------------------------------- diff --git a/public/themes/dreg/LICENSE b/public/themes/dreg/LICENSE new file mode 100755 index 0000000..8dada3e --- /dev/null +++ b/public/themes/dreg/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/README.md ---------------------------------------------------------------------- diff --git a/public/themes/dreg/README.md b/public/themes/dreg/README.md new file mode 100755 index 0000000..3d840d0 --- /dev/null +++ b/public/themes/dreg/README.md @@ -0,0 +1,2 @@ +# scigap-portal-theme +PGA theme for SciGaP Website and Portal - https://scigap.org/ http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/assets/css/style.css ---------------------------------------------------------------------- diff --git a/public/themes/dreg/assets/css/style.css b/public/themes/dreg/assets/css/style.css new file mode 100755 index 0000000..8a37a94 --- /dev/null +++ b/public/themes/dreg/assets/css/style.css @@ -0,0 +1,304 @@ +body{ + background: #fff !important; +} + +.navbar{ + border-radius: 0; +} + +.navbar-inverse{ + background-color:; +} + +.navbar-inverse .navbar-nav>li>a{ + color: #c1e2e9; +} + +.navbar-brand{ + height:100px; +} + +.brand-logo{ + width:135px; + height:35px; + margin-top:7px; + background-size: cover; +} + +.scigap-logo img{ + margin-top: -10px; + height:100px; +} + +.top-space{ + margin-top: 100px; +} + +.scigap-top .breadcrumb li{ + font-size: 1.5em; +} + +.hero-unit { + width: 100%; + background:url('../img/banner.png') no-repeat center center; + background-size:cover; + } + +.hero-unit h1 { + color: #FFFFFF; + font-size: 60px; + letter-spacing: -1px; + line-height: 1; + margin-bottom: 0; +} +.hero-unit h2 { + font-size: 25px; + color: #FFFFFF; + +} +.fill{width:100%;height:350px;background-position:center;background-size:cover; +} + +/* Large desktop */ +@media (min-width: 1200px) { ... } + +/* Portrait tablet to landscape and desktop */ +@media (min-width: 768px) and (max-width: 979px) { ... } + +/* Landscape phone to portrait tablet */ +@media (max-width: 767px) { ... } + +/* Landscape phones and down */ +@media (max-width: 480px) { ... } + + +.blue-bg{ + background: #20b2aa; +} + +.darker-blue-bg{ + background: #2c3e50; +} + +.video-space{ + text-align: center; + color: #fff; + width:90%; + margin-left: 5%; + margin-bottom: 5%; +} + +.video-space img{ + width: 100%; +} +.breathing-space{ + margin-top:3%; + margin-bottom:0%; +} + +.news{ + background: #666666; + color: #ffffff; + text-align: center; + padding: 1%; + margin-bottom:7%; + min-height: 300px; +} + +.read-more{ + padding:18.3%; + background: #fff; +} + +.read-more a{ + font-size:3.5em; +} + +.team{ + margin-top: 2.5%; + margin-bottom: 2.5%; +} + +.new-collaborators, .old-collaborators{ + margin-bottom: 10px; +} + +.new-collaborators img, .old-collaborators img{ +} + +.new-collaborators{ + /*margin-bottom: 2.5%;*/ +} + +.old-collaborators{ + margin-top: 2.5%; +} + +.download-click{ + color: #fff; + text-align: center; + min-height: 250px; + font-size: 2em; + padding-top: 100px; + +} + +.separation-line{ + width: 100%; + height: 4px; + margin-left: auto; + margin-right: auto; + color:#FF0066; + border: 0 none; +} + +.font-1-5{ + font-size:1.5em; +} + + +/*------------------------ floating-scaling arrow -----------------------------*/ + +.floating{ + margin-left:-6%; + margin-top:-2%; + -webkit-animation-name: Floatingx; + -webkit-animation-duration: 3s; + -webkit-animation-iteration-count: infinite; + -webkit-animation-timing-function: ease-in-out; + -moz-animation-name: Floating; + -moz-animation-duration: 3s; + -moz-animation-iteration-count: infinite; + -moz-animation-timing-function: ease-in-out; + /*margin-left: 30px; + margin-top: 5px;*/ + +} + +@-webkit-keyframes Floatingx{ + from {-webkit-transform:translate(0, 0px);} + 65% {-webkit-transform:translate(0, 15px);} + to {-webkit-transform: translate(0, -0px); } +} + +@-moz-keyframes Floating{ + from {-moz-transform:translate(0, 0px);} + 65% {-moz-transform:translate(0, 15px);} + to {-moz-transform: translate(0, -0px);} +} + + +.scaling{ + margin-left:-6%; + margin-top:-6%; + -webkit-animation-name: scalex; + -webkit-animation-duration:3s; + -webkit-animation-iteration-count:infinite; + -webkit-animation-timing-function:ease-in-out; + -moz-animation-name: scale; + -moz-animation-duration:3s; + -moz-animation-iteration-count:infinite; + -moz-animation-timing-function:ease-in-out; +} + +@-webkit-keyframes scalex{ + from {-webkit-transform: scale(0.9);} + 65% {-webkit-transform: scale(1.0);} + to {-webkit-transform: scale(0.9);} +} + +@-moz-keyframes scale{ + from {-moz-transform: scale(0.9);} + 65% {-moz-transform: scale(1.0);} + to {-moz-transform: scale(0.9);} +} + +.cite-area{ + font-size: 0.85em; +} + + + .portrait { + top: 0; + width: 100%; + margin-bottom: 20px; + overflow: hidden; + + -webkit-transition: .5s; + transition: .5s; + } + + + + a.portrait-wrapper { + display: block; + position: relative; + margin: 0 auto; + margin-bottom: 30px; + height: 200px; + width: 200px; + overflow: hidden; + background-color: #ddd; + border: 3px solid #ddd; + + -webkit-border-radius: 50%; + -moz-border-radius: 50%; + border-radius: 50%; + + -webkit-transition: .25s; + transition: .25s; + } + a.portrait-wrapper .overlay { + -webkit-border-radius: 50%; + -moz-border-radius: 50%; + border-radius: 50%; + } + + + + .overlay { + position: absolute; + z-index: 8; + left: 0; + top: 0; + bottom: 0; + right: 0; + text-align: center; + border: 0px solid rgba(0,0,0,0); + background-color: rgba(0,0,0,.2); + + -webkit-transition: .3s; + transition: .3s; + + /* Cross Browser Opacity */ + -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=0)"; + filter: alpha(opacity=0); + -moz-opacity: 0; + -khtml-opacity: 0; + opacity: 0; + } + .overlay:hover { + /* Cross Browser Opacity */ + -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=100)"; + filter: alpha(opacity=100); + -moz-opacity: 1; + -khtml-opacity: 1; + opacity: 1; + } + .overlay i, .overlay span.title { + color: #fff; + font-size: 40px; + position: relative; + top: -40px; + + -webkit-transition: .3s; + transition: .3s; + } + .overlay span.title { font-size: 30px; } + .overlay:hover i, .overlay:hover span.title, .overlay:hover p.stats { + top: 5px; + } + + + + http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/assets/css/zoom.css ---------------------------------------------------------------------- diff --git a/public/themes/dreg/assets/css/zoom.css b/public/themes/dreg/assets/css/zoom.css new file mode 100755 index 0000000..17d4810 --- /dev/null +++ b/public/themes/dreg/assets/css/zoom.css @@ -0,0 +1,87 @@ + /* Style the Image Used to Trigger the Modal */ +#myImg, #myImg2 { + border-radius: 5px; + cursor: pointer; + transition: 0.3s; +} + +#myImg:hover, #myImg2:hover {opacity: 0.7;} + +/* The Modal (background) */ +.modal, .modal2 { + display: none; /* Hidden by default */ + position: fixed; /* Stay in place */ + z-index: 1000; /* Sit on top */ + padding-top: 200px; /* Location of the box */ + left: 0; + top: 0; + width: 100%; /* Full width */ + height: 100%; /* Full height */ + overflow: auto; /* Enable scroll if needed */ + background-color: rgb(0,0,0); /* Fallback color */ + background-color: rgba(0,0,0,0.9); /* Black w/ opacity */ +} + +/* Modal Content (Image) */ +.modal-content { + margin: auto; + display: block; + width: 80%; + max-width: 1024px; +} + +/* Caption of Modal Image (Image Text) - Same Width as the Image */ +#caption { + margin: auto; + display: block; + width: 80%; + max-width: 1024px; + text-align: center; + color: #ccc; + padding: 10px 0; + height: 150px; +} + +/* Add Animation - Zoom in the Modal */ +.modal-content, #caption { + -webkit-animation-name: zoom; + -webkit-animation-duration: 0.6s; + animation-name: zoom; + animation-duration: 0.6s; +} + +@-webkit-keyframes zoom { + from {-webkit-transform:scale(0)} + to {-webkit-transform:scale(1)} +} + +@keyframes zoom { + from {transform:scale(0)} + to {transform:scale(1)} +} + +/* The Close Button */ +.close { + position: absolute; + top: 15px; + right: 35px; + color: #f1f1f1; + font-size: 40px; + font-weight: bold; + transition: 0.3s; +} + +.close:hover, +.close:focus { + color: #bbb; + text-decoration: none; + cursor: pointer; +} + +/* 100% Image Width on Smaller Screens */ +@media only screen and (max-width: 700px){ + .modal-content { + width: 100%; + } +} + http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/assets/img/Twitter26x21.png ---------------------------------------------------------------------- diff --git a/public/themes/dreg/assets/img/Twitter26x21.png b/public/themes/dreg/assets/img/Twitter26x21.png new file mode 100755 index 0000000..564db19 Binary files /dev/null and b/public/themes/dreg/assets/img/Twitter26x21.png differ http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/assets/img/airavata-logo.png ---------------------------------------------------------------------- diff --git a/public/themes/dreg/assets/img/airavata-logo.png b/public/themes/dreg/assets/img/airavata-logo.png new file mode 100755 index 0000000..165f8a2 Binary files /dev/null and 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a/public/themes/dreg/partials/about.blade.php b/public/themes/dreg/partials/about.blade.php new file mode 100755 index 0000000..53b8c4e --- /dev/null +++ b/public/themes/dreg/partials/about.blade.php @@ -0,0 +1,51 @@ +<div class="container"> +<div> + <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). + </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> + + <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 âregulatory codesâ 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 Markov models, support vector machines, and artificial neural networks.</p> + + <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> + <p dir="ltr"><A title="PHP Gateway with Airavata" href="https://testdrive.airavata.org/";>PGA</A>(PHP Gateway with Airavata) +is a framework to build science gateway with the Airavata API. <A title="dREG gateway" href="http://dreg.dnasequence.org";>dREG gateway</A> is built on top of PGA by modifying it. </p> + +</div> + +<div class="post-edit"></div> + <h1 class="text-center top-space">Contact</h1> + <div class="col-md-10 col-md-offset-1 text-center breathing-spaces"> + <div class="col-md-6"> + <span class="glyphicon glyphicon-envelope" style="font-size:6em;"></span><br> + You can contact Gateway Admin by sending a mail to <a href="mailto:zw...@cornell.edu";>Contact E-mail</a> + </div> + <div class="col-md-6"> + <span class="glyphicon glyphicon-edit" style="font-size:6em;"></span><br> + You can also create a <span id="serviceDeskHelp">JIRA ticket</span> by signing in <a href="https://scigap.atlassian.net/servicedesk/customer/portal/8"; target="_blank">here</a>. + </div> + </div> + +<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> + http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/partials/doc.blade.php ---------------------------------------------------------------------- diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php new file mode 100755 index 0000000..97fc169 --- /dev/null +++ b/public/themes/dreg/partials/doc.blade.php @@ -0,0 +1,156 @@ +<div class="container"> + <div class="content"> + <div class="text-center"> + <h2 class="title top-space">Documents</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="#output" role="tab" data-toggle="tab">Output</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> +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> +<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. +</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> + + <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. + </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> + + <p class="description" style="padding:16px"> + 5) <b>Submit the job</b><br> +Click the 'save and launch' button. BigWig file are transferred to the XSEDE server and a GPU queue is scheduled to run dREG. After submitting, the user can check the status in the next web page, as shown below. Depend on the queue status, the job maybe wait for a long time to start prediction. Once started, it will only take 1-4 hours to complete.</p> + + + <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. + </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> + + <p class="description" style="padding:16px"> + 7) <b>Check the results</b><br> +Once a job is completed, the user can click <B>'Download Results'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page. Or the user can check the results in the Genome Browser by clicking <b>'Switch to Genome Browser'</B> link. + +</p> +<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div> + + <p class="description" style="padding:16px"> + 8) <b>Check the storage</b><br> +the user can click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments). The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p> + +<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div> + + + </div> + </div> + + </div> + + <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 package 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> + + <div role="tabpanel" class="tab-pane" id="output"> + <div class="row"> + <div class="col-sm-offset-1 col-sm-10 col-xs-12"> + + <p class="description"> +dREG run generates a compressed file including the dREG and dREG.HD results as follows: + </p> +<p class="description"> </p> + + <table class="table"> + <tr> + <th>File name</th> + <th>Description</th> + </tr> + <tr> + <td>out.dREG.pred.gz</td> + <td>Informative positions with the scores predicted by the dREG model</td> + </tr> + <tr> + <td>out.dREG.peak.gz</td> + <td>dREG peaks called using the threshold 0.8 </td> + </tr> + <tr> + <td>out.dREG.HD.imputedDnase.bw</td> + <td>The imputed DNase-I signal called by dREG.HD.</td> + </tr> + <tr> + <td>out.dREG.HD.relaxed.bed</td> + <td>dREG.HD peaks called under relaxed condition (FDR=16%)</td> + </tr> + <tr> + <td>out.dREG.HD.stringent.bed</td> + <td>dREG.HD peaks called under stringent condition (FDR=10%)</td> + </tr> + </table> + + </div> + </div> + </div> + + + </div><!-- /.content --> + +<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> http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/partials/faq.blade.php ---------------------------------------------------------------------- diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php new file mode 100755 index 0000000..09e508a --- /dev/null +++ b/public/themes/dreg/partials/faq.blade.php @@ -0,0 +1,50 @@ +<div class="container"> + + +<h1 class="text-center top-space">FAQ</h1> +<div class="post-entry"> +<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/tutorials/blob/master/PRO-seq.md#read-mapping";> here </A>.</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 âactiveâ 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 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 href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html";> +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> +<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: 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> +<!-- 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> http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/partials/footer.blade.php ---------------------------------------------------------------------- diff --git a/public/themes/dreg/partials/footer.blade.php b/public/themes/dreg/partials/footer.blade.php new file mode 100755 index 0000000..6d6203a --- /dev/null +++ b/public/themes/dreg/partials/footer.blade.php @@ -0,0 +1,45 @@ +<style> +@media (min-width: 768px) { +.logo-seperation{ + margin-left:100px; 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+} +</style> + <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/about") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/about">About</a></li> + <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">Documents</a></li> + <li><a class="scroll" @if(strpos($_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> + <li><a class="scroll" href="{{ URL::to('/') }}/login">Login</a></li> + @endif + --> + </ul> + </div><!--/.nav-collapse --> + </div> + </div> + + <link href='https://fonts.googleapis.com/css?family=Lato:100,300,400,700,900,100italic,300italic,400italic,700italic,900italic' rel='stylesheet' type='text/css'> + <link href='https://fonts.googleapis.com/css?family=Arvo:400,700' rel='stylesheet' type='text/css'> + + + <!--[if IE 9]> + <script src="js/PIE_IE9.js"></script> + <![endif]--> + <!--[if lt IE 9]> + <script src="js/PIE_IE678.js"></script> + <![endif]--> + + <!--[if lt IE 9]> + <script src="js/html5shiv.js"></script> + <![endif]--> + +<link media="all" type="text/css" rel="stylesheet" href="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/css/style.css"/> + http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/partials/template.blade.php ---------------------------------------------------------------------- diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php new file mode 100755 index 0000000..d1c5099 --- /dev/null +++ b/public/themes/dreg/partials/template.blade.php @@ -0,0 +1,118 @@ +<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> + <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 organisms coming soon).</p> +<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> +</div> + +<script> +// Get the modal +var modal = document.getElementById('myModal'); +// Get the image and insert it inside the modal - use its "alt" text as a caption +var img = document.getElementById('myImg'); +var modalImg = document.getElementById("img01"); +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> + + </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 userâs 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>Click <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping";> this link </A> to check <B>how to prepare your PRO-seq, GRO-seq, or ChRO-seq data in bigWig format</B>. + +</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="https://osboxes/pages/faq";>FAQ</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 +var modal = document.getElementById('myModal2'); +// Get the image and insert it inside the modal - use its "alt" text as a caption +var img = document.getElementById('myImg2'); +var modalImg = document.getElementById("img02"); +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> + + </div> + +<br style="clear:both"/> +<hr style="color:green"/> + +<h1 class="text-center">Publications</h1> +<div style="width: 92%; margin-left: 5%; padding-left:15px"> +<table> +<tr> +<td width="100px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG.Preprint.png" style="width:100%"></img></td> +<td> +<p class="text-left" style="margin-left: 25px"><A href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html";> +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> +</td> +</tr> +</table> +</div> + +<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> + http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/25339377/public/themes/dreg/views/index.blade.php ---------------------------------------------------------------------- diff --git a/public/themes/dreg/views/index.blade.php b/public/themes/dreg/views/index.blade.php new file mode 100755 index 0000000..e69de29
