grnsight 3.0.0 → 5.1.0

package/web-client/views/upload.pug

@@ -0,0 +1,587 @@
+doctype html
+html
+  head
+    title GRNsight
+    link(href="//netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css", rel="stylesheet")
+    link(href="stylesheets/grnsight.css", rel="stylesheet")
+    link(href="stylesheets/print.css", rel="stylesheet", media="print")
+    link(href="//code.jquery.com/ui/1.10.1/themes/base/jquery-ui.css", rel="stylesheet")
+    script(src="//code.jquery.com/jquery-1.9.1.js")
+    script(src="//code.jquery.com/ui/1.10.1/jquery-ui.js")
+    script.
+      (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
+          (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+          m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+      })(window,document,"script","//www.google-analytics.com/analytics.js","ga");
+      ga("create", "UA-54882218-1", "auto");
+
+  body
+    nav(class='navbar navbar-default' role='navigation')
+      div(class='container-fluid')
+        div(class='navbar-header')
+          button(type='button' class='navbar-toggle' data-toggle='collapse' data-target='#header-nav')
+            span(class='sr-only') Toggle Navigation
+            span(class='icon-bar')
+            span(class='icon-bar')
+            span(class='icon-bar')
+        div(class='collapse navbar-collapse' id='header-nav')
+          ul(class='nav navbar-nav')
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') File
+              ul(class='dropdown-menu' role='menu')
+                li
+                  a(class='upload' href='#' id='open-item')
+                    label(for='upload' id='open')
+                      span(class='glyphicon glyphicon-folder-open')
+                      |   Open File
+                      i  (.xlsx, .sif, .graphml)
+                    input(type='file' name='upload' id='upload' accept='application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, .sif, .graphml')
+                    input(type='hidden' id='service-root' value=`${serviceRoot}`)
+                li(class='startDisabled disabled')
+                  a(href='#' id='reload')
+                    span(class='glyphicon glyphicon-repeat')
+                    |   Reload
+                li(class='divider')
+                li(class='dropdown-submenu')
+                  a(href='#')
+                    span(class='glyphicon glyphicon-export')
+                    |   Export Data
+                  ul(class='dropdown-menu')
+                    //- Temporary hardcoded display: none pending further testing of the Excel export feature.
+                    li(class='startDisabled disabled unweighted export' style='display: none')
+                      a(href='#' id='exportAsExcelWkbk') To Excel Workbook
+                    //- Need to omit the divider too.
+                    li(class='divider' style='display: none')
+                    li(class='startDisabled disabled unweighted export')
+                      a(href='#' id='exportAsUnweightedSif') To Unweighted SIF
+                    li(class='startDisabled disabled weighted export')
+                      a(href='#' id='exportAsWeightedSif') To Weighted SIF
+                    li(class='divider')
+                    li(class='startDisabled disabled unweighted export')
+                      a(href='#' id='exportAsUnweightedGraphMl') To Unweighted GraphML
+                    li(class='startDisabled disabled weighted export')
+                      a(href='#' id='exportAsWeightedGraphMl') To Weighted GraphML
+                    li(class='divider')
+                    //- li(class='startDisabled disabled unweighted export')
+                      a(href='#' id='exportAsUnweightedExcel') To Unweighted Excel
+                    //- li(class='startDisabled disabled weighted export')
+                    //-   a(href='#' id='exportAsWeightedExcel') To Weighted Excel
+                    li(class='startDisabled disabled export')
+                      a(href='#' id='exportAsExcel') To Excel
+
+                li(class='dropdown-submenu')
+                  a(href='#')
+                    span(class='glyphicon glyphicon-picture')
+                    |   Export Image
+                  ul(class='dropdown-menu')
+                    li(class='startDisabled disabled')
+                      a(href='#' id='exportAsPng') To PNG
+                    li(class='startDisabled disabled')
+                      a(href='#' id='exportAsSvg') To SVG
+                    li(class='startDisabled disabled')
+                      a(href='#' id='exportAsPdf') To PDF
+                li(class='divider')
+                li(class='startDisabled disabled')
+                  a(href='#' id='printGraph')
+                    span(class='glyphicon glyphicon-print')
+                    |   Print
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle', data-toggle='dropdown') Layout
+              ul(class='dropdown-menu' role='menu')
+                span(class='menu-subheader') Graph Options
+                li
+                  a(href='#' id='forceGraph' class='layout' checked)
+                    span(class='glyphicon glyphicon-ok')
+                    |   Force Graph
+                  a(href='#' id='gridLayout' class='layout')
+                    span(class='glyphicon')
+                    |   Grid Layout
+                li(class='divider')
+                li
+                  a(href='#' id='lockSlidersMenu' class="lockSliders")
+                    span(class='glyphicon invisible')
+                    |   Lock Force Graph Parameters
+                li
+                  a(href='#' id='resetSlidersMenu' class="resetSliders")
+                    span(class='glyphicon invisible')
+                    |   Reset Force Graph Parameters
+                li(class='disabled')
+                  a(href='#' id='undoResetMenu' class="undoSliderReset")
+                    span(class='glyphicon invisible')
+                    |   Undo Reset
+                li(class='divider')
+                li
+                  a(href='#' id='link-distance' class='with-input')
+                    span(class='glyphicon invisible')
+                    |   Link Distance (1 - 1000)  
+                    input(type='number' id='link-distance-menu' class='keepopen' value='500' aria-describedby='basic-addon1')
+                li
+                  a(href='#' id='charge' class='with-input')
+                    span(class='glyphicon invisible')
+                    |   Charge (-2000 - 0)  
+                    input(type='number' id='charge-menu' class='keepopen' value='-50' aria-describedby='basic-addon1')
+
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Node
+              ul(class='dropdown-menu' role='menu')
+                li(class='node-coloring-menu disabled')
+                  a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle')
+                    span(class='glyphicon')
+                    |   Enable Node Coloring
+                li(class='divider')
+                li(class='node-coloring-menu dropdown-submenu disabled')
+                  a(href='#')
+                    span(class='glyphicon invisible')
+                    |   Select Top Dataset
+                  ul(class='dropdown-menu' id='topDatasetDropdownMenu')
+                li(class='node-coloring-menu disabled')
+                  a(href='#' id='averageDataTopMenu' class='nodeColoring')
+                    span(class='glyphicon')
+                    |   Average Replicate Values for Top Dataset
+                li(class='divider')
+                li(class='node-coloring-menu dropdown-submenu disabled')
+                  a(href='#')
+                    span(class='glyphicon invisible')
+                    |   Select Bottom Dataset
+                  ul(class='dropdown-menu' id='bottomDatasetDropdownMenu')
+                li(class='node-coloring-menu disabled')
+                  a(href='#' id='averageDataBottomMenu' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Average Replicate Values for Bottom Dataset
+                li(class='divider')
+                li(class='node-coloring-menu disabled')
+                  a(href='#' class='nodeOptions with-input')
+                    span(class='glyphicon invisible')
+                    |   Log Fold Change Max Value (0.01 - 100):  
+                    input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1')                  
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Edge
+              ul(class='dropdown-menu')
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='colorEdges' class='colorEdges active')
+                    span(class='glyphicon glyphicon-ok')
+                    |   Enable Edge Coloring Based on Weight Values
+                li(class='divider')
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='weightsMouseOverMenu' class='weightsMouseOver' class='selected')
+                    span(class='glyphicon glyphicon-ok')
+                    |   Only Show Edge Weights With Mouse Over
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='weightsAlwaysMenu' class='weightsAlways')
+                    span(class='glyphicon')
+                    |   Always Show Edge Weights
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='weightsNeverMenu' class='weightsNever')
+                    span(class='glyphicon')
+                    |   Never Show Edge Weights
+                li(class='divider')
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' class='with-input')
+                    span(class='glyphicon invisible')
+                    |   Edge Weight Normalization Factor (0.0001 - 1000)  
+                    input(type='number' id='edge-weight-normalization-factor-menu' class='keepopen' placeholder='' step='0.0001' aria-describedby='basic-addon1')
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='reset-normalization-factor-menu')
+                    span(class='glyphicon invisible')
+                    |   Reset Edge Weight Normalization Factor
+                li(class='divider')
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' class='with-input')
+                    span(class='glyphicon invisible')
+                    |   Gray Edge Threshold (0 - 100%)  
+                    input(type='number' id='gray-edge-threshold-menu' class='keepopen' value='5' aria-describedby='basic-addon1')
+                    | %
+                li(class='weightedGraphOptionsMenu disabled')
+                  a(href='#' id='grey-edges-dashed-menu')
+                    span(class='glyphicon')
+                    |   Show Gray Edges as Dashed
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') View
+              ul(class='dropdown-menu' role='menu')
+                span(class='menu-subheader') Viewport Size
+                li
+                  a(href='#' id='viewport-size-s' class='viewportOption active' value='containerS')
+                    span(class='glyphicon')
+                    |   Small (1104 x 648 pixels)
+                li
+                  a(href='#' id='viewport-size-m' class='viewportOption' value='containerM')
+                    span(class='glyphicon glyphicon-ok')
+                    |   Medium (1414 x 840 pixels)
+                li
+                  a(href='#' id='viewport-size-l' class='viewportOption' value='containerL')
+                    span(class='glyphicon')
+                    |   Large (1920 x 1080 pixels)
+                li
+                  a(href='#' id='viewport-size-fit' class='viewportOption' value='containerFit')
+                    span(class='glyphicon')
+                    |   Fit To Window
+                li(class='divider')
+                li
+                  a(href='#' id='restrict-graph-to-viewport' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Restrict Graph to Viewport
+                li(class='divider')
+                li(class='startDisabled disabled')
+                  a(href='#' id='zoom' class='with-input')
+                    span(class='glyphicon invisible')
+                    |   Zoom (
+                    span(class='minimum-zoom-display')
+                    | –
+                    span(class='maximum-zoom-display')
+                    | %)  
+                    input(type='number' id='zoomInput' min='1' max='200' value='100' class='zoom keepopen' aria-describedby='basic-addon1' disabled="true")
+                    span
+                    |   %
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Species
+              ul(class='dropdown-menu' role='menu')
+                span(class='menu-subheader') Current Species
+                li
+                  a(href='#' id='Arabidopsis_thaliana' class='viewportOption active')
+                    span(class='glyphicon')
+                    |   Arabidopsis thaliana
+                li
+                  a(href='#' id='Caenorhabditis_elegans' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Caenorhabditis elegans
+                li
+                  a(href='#' id='Drosophila_melanogaster' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Drosophilia melanogaster
+                li
+                  a(href='#' id='Homo_sapiens' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Homo sapiens
+                li
+                  a(href='#' id='Mus_musculus' class='viewportOption')
+                    span(class='glyphicon')
+                    |   Mus musculus
+                li
+                  a(href='#' id='Saccharomyces_cerevisiae' class='viewportOption')
+                    span(class='glyphicon glyphicon-ok')
+                    |   Saccharomyces cerevisiae
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Help
+              ul(class='dropdown-menu' role='menu')
+                li
+                  a(href='//dondi.github.io/GRNsight/documentation.html#gettingStarted', target='_blank') Getting Started
+                li
+                  a(href='https://github.com/dondi/GRNsight/wiki', target='_blank') GRNsight Wiki
+                li
+                  a(href='//dondi.github.io/GRNsight/about.html', target='_blank') About GRNsight
+
+            li(class='dropdown')
+              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Demo
+              ul(class='dropdown-menu' role='menu')
+                li
+                  a(href='#' id='unweighted') Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
+                li
+                  a(href='#' id='weighted') Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
+                li
+                  a(href='#' id='schadeInput') Demo #3: Unweighted GRN (21 genes, 31 edges)
+                li
+                  a(href='#' id='schadeOutput') Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)
+            li
+              a(href='#' id='fileName')
+          ul(class='nav navbar-nav navbar-right graph-metadata-container')
+            li(class='navbar-text text-right')
+              small(id='graph-metadata')
+
+    div(class='container')
+      div(class='grnsight-container' data-iframe-width data-iframe-height)
+        div(class='scale-and-scroll')
+          table(class='scrollTable')
+            tr
+              td
+              td(class='scrollBtn scrollUp')
+                  p(class='movementArrow') ↑
+              td
+            tr
+              td(class='scrollBtn scrollLeft')
+                p(class='movementArrow') ←
+              td(class='scrollBtn center')
+                p(class='movementArrow') ☼
+              td(class='scrollBtn scrollRight')
+                p(class='movementArrow') →
+            tr
+              td
+              td(class='scrollBtn scrollDown')
+                p(class='movementArrow') ↓
+              td
+
+          span(class="pull-left zoomLabel")
+            b
+              | Zoom (
+              span(class='minimum-zoom-display')
+              | –
+              span(class='maximum-zoom-display')
+              | %): 
+          span(class="pull-right zoomLabel" id="zoomPercent") 100%
+          br
+          table(class='zoomTable')
+            tr
+              td
+                div(class="zoomCenter")
+                input(id="zoomSlider" class="zoom" type="range" min="0" max="8" value="4" step="0.25" disabled="true")
+
+    div(class='sidebar' data-iframe-height)
+      div(class='panel-group')
+        //- Sliders should have the ID convention of -Name-Val and -Name-Input in order to work properly in the javascript
+        div(class="force-graph panel panel-default")
+            p(class='panel-title sidebarPanelHeader')
+              a(data-toggle='collapse' data-target='#layoutSidebarPanel') Layout
+            div(id="layoutSidebarPanel" class="panel-collapse collapse")
+              div(class="panel-body")
+                  form(class='buttonPairContainer')
+                    //- Value is set to empty to ensure that the MVC cycle takes care of the button’s label.
+                    input(id='forceGraphButton' type='button' class='btn btn-default' value='Force Graph')
+                    input(id='gridLayoutButton' type='button' class='btn btn-default' value='Grid Layout')
+                  form(class='forceParameterContainer')
+                    div(class='labelWithValueContainer')
+                      label(for='linkDistInput', class='info', data-toggle='tooltip', title='Increases/decreases the length of the edges that connect the nodes.') Link Distance (1-1000):
+                      span(id='linkDistVal' class='forceVal') 500
+                    input(class='sidebarSlider', type='range', min='1', max='1000', value='500', step='1', id='linkDistInput', name='linkDistInput')
+                    div(class='labelWithValueContainer')
+                      label(for='chargeInput', class='info', data-toggle='tooltip', title='Increases/decreases the strength of the force that causes the nodes to repel each other.') Charge (–2000-0):
+                      span(id='chargeVal' class='forceVal') -50
+                    input(class='sidebarSlider', type='range', min='-2000', max='0', value='-50', step='1', id='chargeInput', name='chargeInput')
+                  form
+                    input(id='lockSlidersButton', type='checkbox', value='lockSliders' class="lockSliders")
+                    label(for='lockSlidersButton' class='sideLabel') Lock Force Parameters
+                  form
+                    input(id='resetSlidersButton' type='button' class='btn btn-default btnSidebar resetSliders' value='Reset Force Parameters')
+                    input(id='undoResetButton' type='button' class='btn btn-default btnSidebar undoSliderReset' value='Undo Reset' disabled)
+                  p(id='warningMessage' data-toggle='modal' data-target='#warningsModal')
+
+        div(class="node-coloring disabled panel panel-default disabled")
+          p(class='panel-title sidebarPanelHeader disabledOnLaunch')
+            a(id='nodeColoringHeaderLink' data-toggle='collapse' data-target='#nodeColoringSidebarPanel') Node
+          div(id="nodeColoringSidebarPanel" class="panel-collapse collapse")
+            div(class="panel-body")
+              div(class='edgeControl')
+                input(id='nodeColoringToggleSidebar' class='nodeColoringToggle' type='checkbox' checked)
+                label(for='nodeColoringToggleSidebar' class='sideLabel') Enable Node Coloring
+              div(class="nodeColoringSidebarBody")
+                p(class='sideHeader info' data-toggle='tooltip') Select from user-uploaded expression data, or use data from our Expression Database
+                p(class='sideHeader info' data-toggle='tooltip') Top Dataset
+                select(id="dataset-top")
+                form
+                  input(id='averageDataTop', type='checkbox' checked)
+                  label(for='averageDataTop' class='sideLabel') Average Replicate Values
+                p(class='sideHeader info' data-toggle='tooltip') Bottom Dataset
+                select(id="dataset-bottom")
+                form
+                  input(id='averageDataBottom', type='checkbox' checked)
+                  label(for='averageDataBottom' class='sideLabel') Average Replicate Values
+                p(class='sideHeader' id="logFoldChangeMaxValue") Log Fold Change Max Value (0.01-100):
+                div(class='logFoldChangeControlContainer')
+                  input(type='number' min='1' max='100' step='1' id='log-fold-change-max-value-sidebar' class='logFoldChangeMaxValue' aria-describedby='basic-addon1')
+                  button(type="button" class='btn btn-default s' id="log-fold-change-button") Set
+                div(class="node-coloring-legend")
+                div(class="expression-db-loader-text") Expression Database is Loading
+                div(class="expression-db-loader")
+
+        div(class='edge-weight-sidebar disabled panel panel-default disabled')
+          p(class='panel-title sidebarPanelHeader disabledOnLaunch')
+            a(id="edgeWeightHeaderLink" data-toggle='collapse' data-target='#edgeSidebarPanel') Edge
+          div(id="edgeSidebarPanel" class="panel-collapse collapse")
+            div(class="panel-body")
+              form(class='weightedGraphOptions hidden')
+                div(class='edgeControl')
+                  input(id='colorEdgesSidebar' class='colorEdges' type='checkbox' checked)
+                  label(for='colorEdgesSidebar' class='sideLabel') Enable Edge Coloring
+                p(class='sideHeader') Hide/Show Edge Weights
+                div(class='edgeControl')
+                  input(type='radio' id='weightsMouseOverSide' class='weightsMouseOver' name='size' class='selected' checked)
+                  label(for='weightsMouseOverSide' class='sideLabel') Show With Mouse Over
+                div(class='edgeControl')
+                  input(type='radio' id='weightsAlwaysSide' class='weightsAlways' name='size')
+                  label(for='weightsAlwaysSide' class='sideLabel') Always Show Edge Weights
+                div(class='edgeControl')
+                  input(type='radio' id='weightsNeverSide' class='weightsNever' name='size')
+                  label(for='weightsNeverSide' class='sideLabel') Never Show Edge Weights
+              div(class='weightedGraphOptions hidden')
+                p(class='sideHeader' id="normLabel") Edge Weight Normalization Factor (0.0001-1000):
+                input(type='number' class='normalization-form' id='normalization-max' placeholder='maximum' step='0.0001' aria-describedby='basic-addon1')
+                div(class='buttonPairContainer')
+                  button(type="button" class='btn btn-default s' id="normalization-button") Set Factor
+                  button(type='button' class='btn btn-default btn-norm' id='resetNormalizationButton') Reset Factor
+              div(class='weightedGraphOptions hidden')
+                div(class='labelWithValueContainer')
+                  label(id='grayLabel' for='grayThresholdInput', class='info', data-toggle='tooltip', title='Increases/decreases the threshold at which edges appear gray. Edges with normalized weight values below this percentage are shown as gray.') Gray Threshold (0-100%):    
+                  span(class='forceVal', id='grayThresholdValue') 5%
+                input(id='grayThresholdInput', class='sidebarSlider', type='range', min='0', max='1', value='0.05', step='0.01')
+                div(class='edgeControl')
+                  input(id='dashedGrayLineButton', type='checkbox', value='dashedGrayLine')
+                  label(for='dashedGrayLineButton' class='sideLabel') Show Gray Edges as Dashed
+
+        div(class='view-sidebar panel panel-default')
+          p(class='panel-title sidebarPanelHeader')
+            a(data-toggle='collapse' data-target='#viewportSidebarPanel') View
+          div(id="viewportSidebarPanel" class="panel-collapse collapse")
+            div(class="panel-body")
+              label(class='sideHeader') Size
+              form
+                input(type='radio' id='boundBoxS' class='boundBoxSize' name='size' value='containerS')
+                label(for='boundBoxS' class='sideLabel')
+                  | Small #[small (1104 X 648 pixels)]
+                br
+                input(type='radio' id='boundBoxM' class='boundBoxSize' name='size' value='containerM')
+                label(for='boundBoxM' class='sideLabel')
+                  | Medium #[small (1414 X 840 pixels)]
+                br
+                input(type='radio' id='boundBoxL' class='boundBoxSize' name='size' value='containerL')
+                label(for='boundBoxL' class='sideLabel')
+                  | Large #[small (1920 X 1080 pixels)]
+                br
+                input(type='radio' id='boundBoxFit' class='boundBoxSize' name='size' value='containerFit')
+                label(for='boundBoxFit' class='sideLabel') Fit to window
+                br
+                input(type='checkbox' id='viewport' class='viewport' name='viewport' value='viewport')
+                label(for='viewport' class='sideLabel') Restrict graph to viewport
+        
+        div(class="species-display panel panel-default")
+          p(class='panel-title sidebarPanelHeader')
+            a(id='speciesHeaderLink' data-toggle='collapse' data-target='#speciesSidebarPanel') Species
+          div(id="speciesSidebarPanel" class="panel-collapse collapse")
+            div(class="panel-body")
+              div(class="sideHeader currentSpecies") Current Species
+                select(class="speciesIdentifiedDropdown" id='speciesDropdown' href='#')
+                  option(href='#' id='cressOption' value='Arabidopsis_thaliana') Arabidopsis thaliana
+                  option(href='#' id='nematodeOption' value='Caenorhabditis_elegans') Caenorhabditis elegans
+                  option(href='#' id='fruitflyOption' value='Drosophila_melanogaster') Drosophila melanogaster
+                  option(href='#' id='humanOption' value='Homo_sapiens') Homo sapiens
+                  option(href='#' id='mouseOption' value='Mus_musculus') Mus musculus
+                  option(href='#' id='yeastOption' value='Saccharomyces_cerevisiae') Saccharomyces cerevisiae
+
+
+    div(class='graph-statistics-container hidden')
+      div(class='panel panel-default')
+        div(class='panel-heading' role='tab' id='graph-statistics-heading')
+          h4(class='panel-title')
+            a(role='button' data-toggle='collapse' href='#graph-statistics' aria-expanded='true') Graph Statistics
+        div(id='graph-statistics' class='panel-collapse collapse' role='tabpanel' aria-labelledby='graph-statistics-heading')
+          div(class='panel-body')
+            table(class='table table-condensed')
+              thead
+                tr
+                  th(rowspan='2')
+                  th(rowspan='2') Betweenness Centrality
+                  th(class='shortest-path-header') Shortest Path
+                tr(class='shortest-path-column-headers')
+              tbody
+
+    div(id='errorModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+      div(class='modal-dialog')
+        div(class='modal-content')
+          div(class='modal-header')
+            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
+              span(aria-hidden='true') ×
+            h4(class='modal-title') Error
+          div(class='modal-body')
+            p(id='error')
+          div(class='modal-footer')
+            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
+            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload').click()")
+
+    div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+      div(class='modal-dialog')
+        div(class='modal-content')
+          div(class='modal-header')
+            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
+              span(aria-hidden='true') ×
+            h4(class='modal-title') Warning
+          div(class='modal-body' overflow='scroll')
+            p(id='warningIntro')
+            div(class='panel-group' id='accordion' role='tablist' aria-multiselectable='true')
+              div(class='panel panel-default')
+                div(class='panel-heading' role='tab' id='warningsHeader')
+                  h4(class='panel-title')
+                    a(data-toggle='collapse' data-parent='accordian' href='#warningsInfo' aria-expanded='true' aria-controls='warningsInfo') Warnings List
+                div(id='warningsInfo' class='panel-collapse collapse' role='tabpanel' aria-labelledby='warningsHeader')
+                  div(class='panel-body' id='list-frame')
+                    p(id='warningsList')
+
+          div(class='modal-footer')
+            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
+            //- input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload').click()")
+    div(id='exportExcelModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+      div(class='modal-dialog')
+        div(class='modal-content')
+          div(class='modal-header')
+            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
+              span(aria-hidden='true') ×
+            h4(class='modal-title') Export to Excel
+          div(class='modal-body')
+            div(id='exportExcelQuestions-containter')
+              //- form(id='exportExcelForm1')
+              //-   div(class='form-group')
+              //-     p(id='exportExcelNetwork')
+              //-     ul(class='export-radio-group' id='export-excel-weights-list' style="list-style-type:none;")
+              //-   div(class='form-group')
+              //-     p(id='exportExcelExpressionSources')
+              //-     ul(class='export-radio-group' id='export-excel-expression-source-list' style="list-style-type:none;")
+              //-       li
+              //-         input(type='radio' name='expressionSource' checked="true" value="userInput" id='exportExcelExpressionSource-userInputRadio' class='export-radio')
+              //-         label(for='exportExcelExpressionSource-userInputCheckbox' id='exportExcelExpressionSource-userInput' class='export-radio-label')
+              //-       li
+              //-         input(type='radio' name='expressionSource' value="Dahlquist_2018" id='exportExcelExpressionSource-DahlquistRadio' class='export-radio')
+              //-         label(for='exportExcelExpressionSource-DahlquistCheckbox' id='exportExcelExpressionSource-Dahlquist' class='export-radio-label')
+              //-       li
+              //-         input(type='radio' name='expressionSource' value="Kitagawa_2002" id='exportExcelExpressionSource-KitagawaRadio' class='export-radio')
+              //-         label(for='exportExcelExpressionSource-KitagawaCheckbox' id='exportExcelExpressionSource-Kitagawa' class='export-radio-label')
+              //-       li
+              //-         input(type='radio' name='expressionSource' value="Thorsen_2007" id='exportExcelExpressionSource-ThorsenRadio' class='export-radio')
+              //-         label(for='exportExcelExpressionSource-ThorsenCheckbox' id='exportExcelExpressionSource-Thorsen' class='export-radio-label')
+              //-       li
+              //-         input(type='radio' name='expressionSource' value="Barreto_2012" id='exportExcelExpressionSource-BarretoRadio' class='export-radio')
+              //-         label(for='exportExcelExpressionSource-BarretoCheckbox' id='exportExcelExpressionSource-Barreto' class='export-radio-label')   
+              //-   button(type='submit' class='btn btn-default' id='exportExcelContinueButton') Continue
+              //- form(id='exportExcelForm2')
+              //-   div(class='form-group')
+              //-     p(id='exportExcelExpressionSheets')
+              //-     ul(class='exportExcelExpressionSheets' id='export-excel-expression-sheet-list' style="list-style-type:none;")
+              //-       //- input(type='checkbox' value='expression_sheet_name_expressionSuffix')
+              //-   button(type='submit' class='btn btn-default' id='exportExcelButton') Export Workbook
+          div(class='modal-footer')
+            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
+            //- input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload').click()")
+
+    div(id='warningsModalSpecies' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+      div(class='modal-dialog')
+        div(class='modal-content')
+          div(class='modal-header')
+            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
+              span(aria-hidden='true') ×
+            h4(class='modal-title') Warning
+          div(class='modal-body' overflow='scroll')
+            p(id='warningIntroSpecies')
+          div(class='modal-footer')
+            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
+            //- input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload').click()")
+
+    div(id='importErrorModal' class='modal fade' tab-index='-1' role='dialog' aria-hidden='true')
+      div(class='modal-dialog')
+        div(class='modal-content')
+          div(class='modal-header')
+            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
+              span(aria-hidden='true') ×
+            h4(class='modal-title') Import Error
+          div(class='modal-body')
+            p The following error was encountered during the import attempt:
+            blockquote(id='importErrorMessage')
+            div Please verify that the file being imported is in the right format then try the import again.
+          div(class='modal-footer')
+            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
+  script(src='//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js')
+  script(src='lib/bootstrap.file-input/bootstrap.file-input.js')
+  script(src='lib/iframeSizer.contentWindow.min.js')
+  script(src='//cdnjs.cloudflare.com/ajax/libs/d3/4.10.2/d3.min.js')
+  script(src='//d3js.org/d3-scale-chromatic.v1.min.js')
+  script(src='js/grnsight.min.js')

package/_gh_pages/Gemfile

@@ -1,7 +0,0 @@
-source 'https://rubygems.org'
-
-require 'json'
-require 'open-uri'
-versions = JSON.parse(open('https://pages.github.com/versions.json').read)
-
-gem 'github-pages', versions['github-pages']