[Swift-commit] r5350 - in wwwdev: case_studies case_studies/images inc main
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Wed Dec 7 11:53:27 CST 2011
Author: davidk
Date: 2011-12-07 11:53:27 -0600 (Wed, 07 Dec 2011)
New Revision: 5350
Added:
wwwdev/case_studies/Glass-Structure.php
wwwdev/case_studies/Hydrology.php
wwwdev/case_studies/Protein-RNA.php
wwwdev/case_studies/Protein-Structure.php
wwwdev/case_studies/images/climate.png
wwwdev/case_studies/images/glass.png
wwwdev/case_studies/images/protein1.png
wwwdev/case_studies/images/protein2.png
wwwdev/case_studies/images/protein3.png
wwwdev/case_studies/images/rdcep1.png
wwwdev/case_studies/images/rdcep2.png
wwwdev/case_studies/images/rdcep3.png
wwwdev/case_studies/images/rdcep4.png
wwwdev/case_studies/images/rna.png
Modified:
wwwdev/case_studies/index.php
wwwdev/inc/header2.php
wwwdev/main/index.php
Log:
Updates to case studies
Added: wwwdev/case_studies/Glass-Structure.php
===================================================================
--- wwwdev/case_studies/Glass-Structure.php (rev 0)
+++ wwwdev/case_studies/Glass-Structure.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -0,0 +1,63 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<title>Swift - Case Studies</title>
+<link href="../css/960_12_col.css" rel="stylesheet" type="text/css" />
+<link href="../css/reset.css" rel="stylesheet" type="text/css" />
+<link href="../css/style3.css" rel="stylesheet" type="text/css" />
+<script type="text/javascript" src="http://use.typekit.com/dbf2lqy.js"></script>
+<script type="text/javascript">try{Typekit.load();}catch(e){}</script>
+</head>
+
+<body>
+<div class="container_12">
+ <!-- header -->
+ <?php require('../inc/header2.php') ?>
+ <!-- end header -->
+<div class="grid_12 page-header">
+ <h1>Case Studies</h1>
+</div>
+<div class="clear"></div>
+<!-- end .grid_12 -->
+
+ <div class="grid_9">
+ <h3>Glass Structure Modeling</h3>
+ <p>
+This project models of aspects of glass structure at a theoretical chemistry level, by Glen Hocky and David Reichmann, Columbia University Department of Chemistry.
+</p>
+ <img src="images/glass.png" style="padding:0px 0px 15px 20px;" />
+ <p><b>Approach.</b>
+Recent studies of the glass transition in model systems have focused on calculating from theory or simulation what is known as the “mosaic length”. This project evaluated a new “cavity method” for measuring this length scale. Correlation functions are calculated at the interior of cavities of varying sizes and averaged over many independent simulations to determine a thermodynamic length. Using Swift on the Uchicago Beagle supercomputer and the Open Science Grid, Hocky investigated whether this thermodynamic length causes variations among seemingly identical systems. ~1M Beagle CPU hours were used, and many hundreds of thousand of hours of computing were performed using Swift on the Open Science Grid.
+ <p><b>Results.</b>
+Three simple models of glassy behavior were studied. All appear the same (top, abc) but only two of which have particles relaxing at the same rate for the same temperature (top, d). This would imply that the glass structure does not dictate the dynamics. A new computational technique was used to extract a length scale on which the liquid is ordered in an otherwise undetectable way. Results (bottom) showed that using this length we can distinguish the two systems which have the same dynamics as separate from the third which has faster dynamics than the other two.
+
+A manuscript is in preparation for Physical Review Letters.
+</p>
+ <p> </p>
+ </div>
+ <!-- end .grid_9 -->
+ <div class="grid_3">
+ <?php require('../inc/case_study_sidebar.php') ?>
+ <p> </p>
+ </div>
+ <!-- end .grid_3 -->
+
+ <div class="clear"></div>
+
+ </div>
+<!-- end .container_12 -->
+<!-- footer -->
+<?php require('../inc/footer2.php') ?>
+<!-- end footer -->
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try {
+var pageTracker = _gat._getTracker("UA-106257-5");
+pageTracker._trackPageview();
+} catch(err) {}</script>
+</body>
+</html>
Added: wwwdev/case_studies/Hydrology.php
===================================================================
--- wwwdev/case_studies/Hydrology.php (rev 0)
+++ wwwdev/case_studies/Hydrology.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -0,0 +1,64 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<title>Swift - Case Studies</title>
+<link href="../css/960_12_col.css" rel="stylesheet" type="text/css" />
+<link href="../css/reset.css" rel="stylesheet" type="text/css" />
+<link href="../css/style3.css" rel="stylesheet" type="text/css" />
+<script type="text/javascript" src="http://use.typekit.com/dbf2lqy.js"></script>
+<script type="text/javascript">try{Typekit.load();}catch(e){}</script>
+</head>
+
+<body>
+<div class="container_12">
+ <!-- header -->
+ <?php require('../inc/header2.php') ?>
+ <!-- end header -->
+<div class="grid_12 page-header">
+ <h1>Case Studies</h1>
+</div>
+<div class="clear"></div>
+<!-- end .grid_12 -->
+
+ <div class="grid_9">
+ <h3>Modeling Climate Impact on Hydrology</h3>
+ <p>
+Modeling the hydrology of the Mississippi river basin to assess the impacts of climate change and crop changes driven by energy/economics factors.
+</p>
+ <img src="images/hydrology.png" style="padding:0px 0px 15px 20px;" />
+ <p><b>Approach.</b>
+wift is used to perform large-scale modeling runs using SWAT, the Soil and Water Assesment Tool, to study of the impact of global temperature increase on on water and plant productivity in the Upper Mississippi River Basin.
+
+These studies use Swift to perform calibration, sensitivity studies, and optimzation using SCE optimization methods (structured complex evolution) methods. All of these computational modling procedures involve multiple runs of thousands of invocations of SWAT to model the timing and magnitude of changes in runoff, soil moisture, water quality, water availability, and crop yield in important
+agricultural areas.
+ <p><b>Results.</b>
+Results of this research demonstrate that plausible changes in temperature and precipitation caused by increases in atmospheric greenhouse gas concentrations could have major impacts on both
+</p>
+ <p> </p>
+ </div>
+ <!-- end .grid_9 -->
+ <div class="grid_3">
+ <?php require('../inc/case_study_sidebar.php') ?>
+ <p> </p>
+ </div>
+ <!-- end .grid_3 -->
+
+ <div class="clear"></div>
+
+ </div>
+<!-- end .container_12 -->
+<!-- footer -->
+<?php require('../inc/footer2.php') ?>
+<!-- end footer -->
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try {
+var pageTracker = _gat._getTracker("UA-106257-5");
+pageTracker._trackPageview();
+} catch(err) {}</script>
+</body>
+</html>
Added: wwwdev/case_studies/Protein-RNA.php
===================================================================
--- wwwdev/case_studies/Protein-RNA.php (rev 0)
+++ wwwdev/case_studies/Protein-RNA.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -0,0 +1,62 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<title>Swift - Case Studies</title>
+<link href="../css/960_12_col.css" rel="stylesheet" type="text/css" />
+<link href="../css/reset.css" rel="stylesheet" type="text/css" />
+<link href="../css/style3.css" rel="stylesheet" type="text/css" />
+<script type="text/javascript" src="http://use.typekit.com/dbf2lqy.js"></script>
+<script type="text/javascript">try{Typekit.load();}catch(e){}</script>
+</head>
+
+<body>
+<div class="container_12">
+ <!-- header -->
+ <?php require('../inc/header2.php') ?>
+ <!-- end header -->
+<div class="grid_12 page-header">
+ <h1>Case Studies</h1>
+</div>
+<div class="clear"></div>
+<!-- end .grid_12 -->
+
+ <div class="grid_9">
+ <h3>Protein-RNA Interaction Modeling</h3>
+ <p>
+M. Parisien (with T. Sosnick, T. Pan, and K. Freed) used Beagle to develop a first-generation algorithm for the prediction of the RNA-protein interactome.
+</p>
+ <img src="images/rna.png" style="padding:0px 0px 15px 20px;" />
+ <p><b>Approach.</b>
+Non-coding RNAs often function in cells through specific interactions with their protein partners. Experiments alone cannot provide a complete picture of the RNA-protein interactome. To complement experimental methods, computational approaches are highly desirable. No existing method, however, can provide genome-wide predictions of docked RNA-protein complexes.
+the application of computational predictions, together with experimental methods, will provide a more complete understanding on cellular networks and function of RNPs. The approach makes use of a rigid-body docking algorithm and a scoring function custom- tailored for protein-tRNA interactions. Using Swift, Beagle screened about 300 proteins per day on 80 nodes of 24 cores (11% of the total XE6’s power).
+ <p><b>Results.</b>
+The scoring function can identify the native docking conformation in large sets of decoys (100,000) for many known protein-tRNA complexes (4TRA shown here). (left) Scores for true positive complexes (●)(N=28) are compared to true negative ones of low (▼)(N=40) and high (▲) (N=40) isoelectric points. (right) Because the density curve of the true positives, which have pI < 7, has minimal overlap with the curve of the low pI true negatives (blue area), the scoring function has the specificity to identify tRNA-binding proteins.
+</p>
+ <p> </p>
+ </div>
+ <!-- end .grid_9 -->
+ <div class="grid_3">
+ <?php require('../inc/case_study_sidebar.php') ?>
+ <p> </p>
+ </div>
+ <!-- end .grid_3 -->
+
+ <div class="clear"></div>
+
+ </div>
+<!-- end .container_12 -->
+<!-- footer -->
+<?php require('../inc/footer2.php') ?>
+<!-- end footer -->
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try {
+var pageTracker = _gat._getTracker("UA-106257-5");
+pageTracker._trackPageview();
+} catch(err) {}</script>
+</body>
+</html>
Added: wwwdev/case_studies/Protein-Structure.php
===================================================================
--- wwwdev/case_studies/Protein-Structure.php (rev 0)
+++ wwwdev/case_studies/Protein-Structure.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -0,0 +1,66 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<title>Swift - Case Studies</title>
+<link href="../css/960_12_col.css" rel="stylesheet" type="text/css" />
+<link href="../css/reset.css" rel="stylesheet" type="text/css" />
+<link href="../css/style3.css" rel="stylesheet" type="text/css" />
+<script type="text/javascript" src="http://use.typekit.com/dbf2lqy.js"></script>
+<script type="text/javascript">try{Typekit.load();}catch(e){}</script>
+</head>
+
+<body>
+<div class="container_12">
+ <!-- header -->
+ <?php require('../inc/header2.php') ?>
+ <!-- end header -->
+<div class="grid_12 page-header">
+ <h1>Case Studies</h1>
+</div>
+<div class="clear"></div>
+<!-- end .grid_12 -->
+
+ <div class="grid_9">
+ <h3>Protein Structure Prediction</h3>
+ <p>The laboratories of Karl Freed and Tobin Sosnick use Swift to develop and validate methods to predict protein structure using homology-free approaches.</p>
+ <img src="images/protein1.png" style="padding:0px 0px 15px 20px;" />
+ <p><b>Approach.</b>A. Adhikari (under K. Freed and T. Sosnick) has developed new structure prediction
+ techniques based on Monte Carlo simulated annealing which employ novel, compact molecular
+ representations and innovative “moves” of the protein backbone to achieve accurate prediction
+ with far less computation then previous methods. One of the applications of the method involves
+ rebuilding local regions in protein structures, called “loop modeling”, a problem which the group
+ tackled with considerable success in the CASP protein folding tournament(shown in right). They are
+ now testing further algorithmic innovations using the computational power of Beagle.
+
+ <p><b>Results.</b>
+ The group is now developing a new iterative algorithm for predicting protein structure and folding
+ pathway starting only from the amino acid sequence. In progress, no publications yet from Beagle studies.
+</p>
+ <p> </p>
+ </div>
+ <!-- end .grid_9 -->
+ <div class="grid_3">
+ <?php require('../inc/case_study_sidebar.php') ?>
+ <p> </p>
+ </div>
+ <!-- end .grid_3 -->
+
+ <div class="clear"></div>
+
+ </div>
+<!-- end .container_12 -->
+<!-- footer -->
+<?php require('../inc/footer2.php') ?>
+<!-- end footer -->
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try {
+var pageTracker = _gat._getTracker("UA-106257-5");
+pageTracker._trackPageview();
+} catch(err) {}</script>
+</body>
+</html>
Added: wwwdev/case_studies/images/climate.png
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+ application/octet-stream
Added: wwwdev/case_studies/images/glass.png
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
Added: wwwdev/case_studies/images/rna.png
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(Binary files differ)
Property changes on: wwwdev/case_studies/images/rna.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: wwwdev/case_studies/index.php
===================================================================
--- wwwdev/case_studies/index.php 2011-12-06 21:40:37 UTC (rev 5349)
+++ wwwdev/case_studies/index.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -30,25 +30,25 @@
<h3>Protein Structure Prediction</h3>
<p>The laboratories of Karl Freed and Tobin Sosnick use Beagle to develop and validate methods to predict protein structure using homology-free approaches.</p>
- <a href="#" class="trailingLink">learn more</a>
+ <a href="../case_studies/Protein-Structure.php" class="trailingLink">learn more</a>
<p> </p>
<div class="clear"></div>
<h3>Protein-RNA interaction modeling</h3>
<p>M. Parisien (with T. Sosnick, T. Pan, and K. Freed) used Beagle to develop a first-generation algorithm for the prediction of the RNA-protein interactome.</p>
- <a href="#" class="trailingLink">learn more</a>
+ <a href="Protein-RNA.php" class="trailingLink">learn more</a>
<p> </p>
<div class="clear"></div>
<h3>Glass Structure Modeling</h3>
<p>This project models of aspects of glass structure at a theoretical chemistry level. (Hocky/Reichman)</p>
- <a href="#" class="trailingLink">learn more</a>
+ <a href="Glass-Structure.php" class="trailingLink">learn more</a>
<p> </p>
<div class="clear"></div>
<h3>Modeling climate impact on hydrology</h3>
<p>Projecting biofuel production impact on hydrology (E. Yan)</p>
- <a href="#" class="trailingLink">learn more</a>
+ <a href="Hydrology.php" class="trailingLink">learn more</a>
<p> </p>
<div class="clear"></div>
Modified: wwwdev/inc/header2.php
===================================================================
--- wwwdev/inc/header2.php 2011-12-06 21:40:37 UTC (rev 5349)
+++ wwwdev/inc/header2.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -13,9 +13,7 @@
<ul id="nav">
<li><a href="../downloads/index.php"<?php if (strpos($p, 'downloads')) echo' class="current"'?>>downloads</a></li>
<li><a href="../docs/index.php"<?php if (strpos($p, 'docs')) echo' class="current"'?>>documentation</a></li>
- <!--
<li><a href="../case_studies/index.php"<?php if (strpos($p, 'case_studies')) echo' class="current"'?>>case studies</a></li>
- -->
<li><a href="../papers/index.php"<?php if (strpos($p, 'papers')) echo' class="current"'?>>papers</a></li>
<li class="last"><a href="../support/index.php"<?php if (strpos($p, 'support')) echo' class="current"'?>>support</a></li>
</ul>
Modified: wwwdev/main/index.php
===================================================================
--- wwwdev/main/index.php 2011-12-06 21:40:37 UTC (rev 5349)
+++ wwwdev/main/index.php 2011-12-07 17:53:27 UTC (rev 5350)
@@ -3,7 +3,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<meta name="robots" content="noindex">
-<title>Swift - A system for rapid and reliable specification, execution, and management of large scale workflows</title>
+<title>Swift - The Parallel Scripting Language</title>
<link href="../css/960_12_col.css" rel="stylesheet" type="text/css" />
<link href="../css/reset.css" rel="stylesheet" type="text/css" />
<link href="../css/style3.css" rel="stylesheet" type="text/css" />
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