Warp2D - 2D Time Alignment Workflow
Created: 2010-05-20 18:46:07
Last updated: 2010-11-22 10:32:03
2D Time Alignment
We describe a new time alignment method that takes advantage of both dimensions of LC-MS data to resolve ambiguities in peak matching while remaining computationally efficient. This approach, Warp2D, combines peak extraction with a two-dimensional correlation function to provide a reliable alignment scoring function that is insensitive to spurious peaks and background noise. One-dimensional alignment methods are often based on the total-ion-current elution profile of the spectrum and are unable to distinguish peaks of different masses.
Click Here to try out yourself!
We have an online version of this approach as SaaS(Software as a Service) i.e Web Services to facilitate large number of audience. This service enable you to upload Generic Peak lists and get back your Results. And of course don't worry about processing power, we are Grid enabled.
2D Time Alignment i.e warping web service is powered by Data Analysis Framework (DAF)
Data Analysis Framework (DAF) services are available here and source code here
Discuss with us here
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Workflow Components
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Titles (0)
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Dependencies (0)
Processors (20)
| Name |
Type |
Description |
| warp2D |
wsdl |
Wsdlhttp://129.125.169.67:8080/axis2/services/Warp2D?wsdlWsdl Operationwarp2D |
| warp2D_input |
xmlsplitter |
|
| warp2D_output |
xmlsplitter |
|
| AuthKey_value |
stringconstant |
Valuei.ahmad@rug.nl |
| maxPeaksPerSegment_value |
stringconstant |
Value60 |
| MZwidth_value |
stringconstant |
Value0.1 |
| RTwidth_value |
stringconstant |
Value0.40 |
| winSize_value |
stringconstant |
Value40 |
| slack_value |
stringconstant |
Value8 |
| NTimePoints_value |
stringconstant |
Value3000 |
| sampShift_value |
stringconstant |
Value0 |
| outputWarpedFileName_value |
stringconstant |
Valuetaverna_warped |
| refPeakListFileName_value |
stringconstant |
Value/data_home/2006053.pks |
| alignPeakListFileName_value |
stringconstant |
Value/data_home/17060510.pks |
| JobMonitor |
beanshell |
Scriptout_jobId = "";
if ( in_jobId != void) {
out_jobId = in_jobId
// sleep 60 seconds before calling remove monitor
try {
Thread.sleep(60000);
}catch (InterruptedException e){
}
} |
| getJobState |
wsdl |
Wsdlhttp://129.125.169.67:8080/axis2/services/Warp2D?wsdlWsdl OperationgetJobState |
| getJobState_input |
xmlsplitter |
|
| getJobState_output |
xmlsplitter |
|
| Sleep |
beanshell |
ScriptThread.sleep(60000);
out = in; |
| WaitPlease |
beanshell |
ScriptThread.sleep(60000);
out = in; |
Beanshells (3)
| Name |
Description |
Inputs |
Outputs |
| JobMonitor |
|
in_jobId
jobStatus
|
out_jobId
|
| Sleep |
|
in
|
out
|
| WaitPlease |
|
in
|
out
|
Datalinks (19)
| Source |
Sink |
| warp2D_input:output |
warp2D:parameters |
| AuthKey_value:value |
warp2D_input:AuthKey |
| maxPeaksPerSegment_value:value |
warp2D_input:maxPeaksPerSegment |
| MZwidth_value:value |
warp2D_input:MZwidth |
| RTwidth_value:value |
warp2D_input:RTwidth |
| winSize_value:value |
warp2D_input:winSize |
| slack_value:value |
warp2D_input:slack |
| NTimePoints_value:value |
warp2D_input:NTimePoints |
| sampShift_value:value |
warp2D_input:sampShift |
| outputWarpedFileName_value:value |
warp2D_input:outputWarpedFileName |
| refPeakListFileName_value:value |
warp2D_input:refPeakListFileName |
| alignPeakListFileName_value:value |
warp2D_input:alignPeakListFileName |
| warp2D:parameters |
warp2D_output:input |
| getJobState_input:output |
getJobState:parameters |
| AuthKey_value:value |
getJobState_input:AuthKey |
| Sleep:out |
getJobState_input:jobId |
| getJobState:parameters |
getJobState_output:input |
| warp2D_output:return |
Sleep:in |
| JobMonitor:out_jobId |
WaitPlease:in |
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