What is bioinformatics?
Adapting the VU template to
Drupal: the CCSB@V.
Jerome Jourquin, PhD MS
Quaranta Lab
Center for Cancer Systems Biology at Vanderbilt
Department of Cancer Biology
jerome.jourquin@vanderbilt.edu
What is bioinformatics?Why Drupal?
2
10/28/2010
2006
2007
2008
2009
2010
http://vicbc.vanderbilt.edu/ccsb
“Collaborative
website”
Center for Cancer
Systems Biology at
Vanderbilt (CCSB@V)
Vanderbilt Integrative Cancer
Biology Center (VICBC)
Quaranta Lab
iTumor
Protein
Expression
User’s Club
What is bioinformatics?The task at hands
3
10/28/2010
http://www.vanderbilt.edu/publicaffairs/webcomm/2010/05/vanderbilt-brand-bar/
http://www.vanderbilt.edu/publicaffairs/webcomm/2010/05/simple-template-files-released/
What is bioinformatics?Drupal theme engine
4
10/28/2010
http://drupal.org/node/171194
What is bioinformatics?
5
10/28/2010
What is bioinformatics?
6
10/28/2010
What is bioinformatics?
name = CCSB Theme
description = Based on 960.gs, this theme was developed for the Center for Cancer Systems Biology at Vanderbilt
University.
screenshot = screenshot.png
core = 6.x
base theme = ninesixty
stylesheets[all][] = ccsb_theme.css
stylesheets[all][] = featuredcontentglider.css
regions[firstlinks] = First Links
regions[secondlinks] = Second Links
regions[footer] = Footer
regions[left] = Left
regions[right] = Right
regions[content] = Content
regions[account] = Account
regions[links] = Links
regions[pictures] = Pictures
regions[over_text] = Over-Text
regions[develp] = Development
regions[calendar] = Mini Calendar
regions[frontpagelinks] = Frontpage Links
regions[frontcontact] = Frontpage Contact
ccsb_theme.info
7
10/28/2010
What is bioinformatics?
8
10/28/2010
What is bioinformatics?
9
10/28/2010
menu
calendar
views
menu
site title, slogan, account
page
cck
What is bioinformatics?Rendering the front page slideshow
10
10/28/2010
CCK
ImageField
ImageCache
ImageAPI
What is bioinformatics?Rendering the front page slideshow
11
10/28/2010
• CCK
• ImageField
• ImageCache
• ImageAPI
<div id="secslides" style="margin-top: -40px;"><div class="vslides"></
<script type="text/javascript" language="javascript">
/* <![CDATA[ */
$('.vslides').wwfvslides([
<?php
$slides = '';
foreach ($images as $key=>$value) { $slides .= "{
'backgroundImage': '".$images[$key]."',
'headline': '".$headlines[$key]."',
'thumbnail': '".$thumbnails[$key]."',
'href': '".$links[$key]."' },"; }
print $slides;
?>
])
/* ]]> */
</script>
</div><!-- /secslides -->
// dimension images: main 650*311, thumbnail: 76*57
$nodes = array();
$result = db_query("SELECT nid FROM {node} WHERE type = '%s'", 'frontpage_image');
while($row = db_fetch_object($result)) { $nodes[] = node_load($row->nid); }
$images = array(); $headlines = array(); $thumbnails = array(); $links = array();
foreach ($nodes as $object) {
$imagepath = $object->field_fpi_image[0]['filepath'];
$image = 'files/ccsb/'.$object->field_fpi_image[0]['filename'].'-image.jpg';
$thumbnail = 'files/ccsb/'.$object->field_fpi_image[0]['filename'].'-thumbnail.jpg';
$imageapi = imageapi_image_open($imagepath);
imageapi_image_scale_and_crop($imageapi, '650', '311');
imageapi_image_close($imageapi, $image);
$width = '0'; $height = '0';
$imageapi = imageapi_image_open($imagepath);
$width = $imageapi->info['width'];
$height = $imageapi->info['height'] * 650 / $imageapi->info['width'];
imageapi_image_scale($imageapi, '650');
imageapi_image_crop($imageapi, '250', ($height/2), '76', '57');
imageapi_image_close($imageapi, $thumbnail);
$images[] = $image; $thumbnails[] = $thumbnail;
What is bioinformatics?Drupal theme engine
12
10/28/2010
page-front.tpl.php
page.tpl.php
What is bioinformatics?
13
10/28/2010
http://pratul.in/drupal-makes-me-hapi

Adapting the VU template to drupal

  • 1.
    What is bioinformatics? Adaptingthe VU template to Drupal: the CCSB@V. Jerome Jourquin, PhD MS Quaranta Lab Center for Cancer Systems Biology at Vanderbilt Department of Cancer Biology jerome.jourquin@vanderbilt.edu
  • 2.
    What is bioinformatics?WhyDrupal? 2 10/28/2010 2006 2007 2008 2009 2010 http://vicbc.vanderbilt.edu/ccsb “Collaborative website” Center for Cancer Systems Biology at Vanderbilt (CCSB@V) Vanderbilt Integrative Cancer Biology Center (VICBC) Quaranta Lab iTumor Protein Expression User’s Club
  • 3.
    What is bioinformatics?Thetask at hands 3 10/28/2010 http://www.vanderbilt.edu/publicaffairs/webcomm/2010/05/vanderbilt-brand-bar/ http://www.vanderbilt.edu/publicaffairs/webcomm/2010/05/simple-template-files-released/
  • 4.
    What is bioinformatics?Drupaltheme engine 4 10/28/2010 http://drupal.org/node/171194
  • 5.
  • 6.
  • 7.
    What is bioinformatics? name= CCSB Theme description = Based on 960.gs, this theme was developed for the Center for Cancer Systems Biology at Vanderbilt University. screenshot = screenshot.png core = 6.x base theme = ninesixty stylesheets[all][] = ccsb_theme.css stylesheets[all][] = featuredcontentglider.css regions[firstlinks] = First Links regions[secondlinks] = Second Links regions[footer] = Footer regions[left] = Left regions[right] = Right regions[content] = Content regions[account] = Account regions[links] = Links regions[pictures] = Pictures regions[over_text] = Over-Text regions[develp] = Development regions[calendar] = Mini Calendar regions[frontpagelinks] = Frontpage Links regions[frontcontact] = Frontpage Contact ccsb_theme.info 7 10/28/2010
  • 8.
  • 9.
  • 10.
    What is bioinformatics?Renderingthe front page slideshow 10 10/28/2010 CCK ImageField ImageCache ImageAPI
  • 11.
    What is bioinformatics?Renderingthe front page slideshow 11 10/28/2010 • CCK • ImageField • ImageCache • ImageAPI <div id="secslides" style="margin-top: -40px;"><div class="vslides"></ <script type="text/javascript" language="javascript"> /* <![CDATA[ */ $('.vslides').wwfvslides([ <?php $slides = ''; foreach ($images as $key=>$value) { $slides .= "{ 'backgroundImage': '".$images[$key]."', 'headline': '".$headlines[$key]."', 'thumbnail': '".$thumbnails[$key]."', 'href': '".$links[$key]."' },"; } print $slides; ?> ]) /* ]]> */ </script> </div><!-- /secslides --> // dimension images: main 650*311, thumbnail: 76*57 $nodes = array(); $result = db_query("SELECT nid FROM {node} WHERE type = '%s'", 'frontpage_image'); while($row = db_fetch_object($result)) { $nodes[] = node_load($row->nid); } $images = array(); $headlines = array(); $thumbnails = array(); $links = array(); foreach ($nodes as $object) { $imagepath = $object->field_fpi_image[0]['filepath']; $image = 'files/ccsb/'.$object->field_fpi_image[0]['filename'].'-image.jpg'; $thumbnail = 'files/ccsb/'.$object->field_fpi_image[0]['filename'].'-thumbnail.jpg'; $imageapi = imageapi_image_open($imagepath); imageapi_image_scale_and_crop($imageapi, '650', '311'); imageapi_image_close($imageapi, $image); $width = '0'; $height = '0'; $imageapi = imageapi_image_open($imagepath); $width = $imageapi->info['width']; $height = $imageapi->info['height'] * 650 / $imageapi->info['width']; imageapi_image_scale($imageapi, '650'); imageapi_image_crop($imageapi, '250', ($height/2), '76', '57'); imageapi_image_close($imageapi, $thumbnail); $images[] = $image; $thumbnails[] = $thumbnail;
  • 12.
    What is bioinformatics?Drupaltheme engine 12 10/28/2010 page-front.tpl.php page.tpl.php
  • 13.