Engineering:UCSD - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:15:08Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna at 22:04, 3 June 2014

2014-06-03T22:04:09Z

Marianna at 22:03, 3 June 2014

2014-06-03T22:03:51Z

Mruiz at 17:34, 19 June 2010

2010-06-19T17:34:49Z

Mruiz at 20:39, 28 February 2010

2010-02-28T20:39:52Z

Mruiz at 18:00, 24 February 2010

2010-02-24T18:00:31Z

Mruiz at 22:02, 9 February 2010

2010-02-09T22:02:16Z

Mruiz at 23:29, 8 February 2010

2010-02-08T23:29:41Z

Mruiz: /* Monthly Progress (since July 2007) */

2010-02-08T13:47:06Z

Monthly Progress (since July 2007)

Kikinis at 12:52, 8 February 2010

2010-02-08T12:52:23Z

@@ Line 77: / Line 77: @@
 ''March 2008''
 * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
-* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
+* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [https://www.slicer.org/wiki/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
 * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].
@@ Line 86: / Line 86: @@
 ''May 2008''
 * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
-** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
+** [https://www.slicer.org/wiki/Slicer3:Chain_CLMs Functional Specification].
 ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

← Older revision		Revision as of 22:04, 3 June 2014
Line 1:		Line 1:
−	~~__NOTOC_~~	+	__NOTOC__
	Back to [[Engineering:Main\|NA-MIC Engineering]]		Back to [[Engineering:Main\|NA-MIC Engineering]]

← Older revision		Revision as of 22:03, 3 June 2014
Line 1:		Line 1:
		+	__NOTOC_
	Back to [[Engineering:Main\|NA-MIC Engineering]]		Back to [[Engineering:Main\|NA-MIC Engineering]]

@@ Line 8: / Line 8: @@
 A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise).  This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment.  This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.
-A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology.  It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:
+A basic consideration of the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:
 * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
@@ Line 17: / Line 17: @@
 = Projects =
-== Grid Wizard Enterprise (GWE) ==
+For more information on these projects visit their respective project site; which contains all relevant information, including setup ready bundles, detailed user guides, demo videos, presentations, step by step tutorials, usage samples and complete source code.
 The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers.  GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention.  The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.
@@ Line 34: / Line 39: @@
-== Record Set Explorer (GWE's RSE) ==
+== ''2. Record Set Explorer (GWE's RSE)'' ==
-Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.
 [[image:Rse-xnat.gif|thumb|left|300px|Posting XNAT query and exploring its resulting records]]
@@ Line 44: / Line 52: @@
 = Progress (since July 2007) =
 ''July - September 2007''
@@ Line 180: / Line 158: @@
 ''March 2010''
 * GWE's RSE version 0.6.1.alpha release
 = Miscellaneous =

@@ Line 37: / Line 37: @@
 Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.
-[[image:Rse-5-definition-gwe.png|thumb|left|300px|Record Set Definition (Results of executing a parameter exploration experiment using GWE)]]
+[[image:Rse-xnat.gif|thumb|left|300px|Posting XNAT query and exploring its resulting records]]
-[[image:Rse-7-exploration-gwe-2.png|thumb|left|300px|Exploration (Without filtering by volume image)]]
+[[image:Rse-oasis.gif|thumb|left|300px|Exploring OASIS Cross Sectional Database]]
-[[image:Rse-gwe-3.png|thumb|left|300px|Exploration (Filtering to navigate through records with volume image equal to 'brain')]]
+[[image:Rse-gwe-exp.gif|thumb|left|300px|Exploring the results of a GWE parameter exploration experiment]]

@@ Line 20: / Line 20: @@
 The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers.  GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention.  The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.
-[[image:Wcp-queue-1.png|thumb|left|300px|Queueing Parameter Exploration Experiment]]
+[[image:Wcp-grid-1.png|thumb|left|300px|Configuration (clusters and keystores)]]
-[[image:Wcp-order-3.png|thumb|left|300px|Reviewing Execution Status of Parameter Exploration Experiment]]
+[[image:Wcp-cluster-1.png|thumb|left|300px|Cluster setup (just a single click after configured!)]]

@@ Line 15: / Line 15: @@
 * Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.
-= Systems =
+= Projects =
 == Grid Wizard Enterprise (GWE) ==
 The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers.  GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention.  The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.
-[[File:Wcp-queue-1.png]]
+[[image:Wcp-queue-1.png|thumb|left|300px|Queueing Parameter Exploration Experiment]]
-[[File:Wcp-order-3.png]]
+[[image:Wcp-order-3.png|thumb|left|300px|Reviewing Execution Status of Parameter Exploration Experiment]]
@@ Line 29: / Line 29: @@
 Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.
-[[File:Rse-5-definition-gwe.png]]
+[[image:Rse-5-definition-gwe.png|thumb|left|300px|Record Set Definition (Results of executing a parameter exploration experiment using GWE)]]
-[[File:Rse-7-exploration-gwe-2.png]]
+[[image:Rse-7-exploration-gwe-2.png|thumb|left|300px|Exploration (Without filtering by volume image)]]
-[[File:Rse-gwe-3.png]]
+[[image:Rse-gwe-3.png|thumb|left|300px|Exploration (Filtering to navigate through records with volume image equal to 'brain')]]
 = Information =
 * GWE
@@ Line 54: / Line 58: @@
 ** GSlicer  - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]
-* Tutorials
+* Tutorials - Provided via the [[Slicer3.2:Training| Slicer Training Site]].  Links to the tutorials provided through this site are also provided below.
 ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
 ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

@@ Line 1: / Line 1: @@
 Back to [[Engineering:Main|NA-MIC Engineering]]
-= UCSD (PI: Mark Ellisman) =
+= UCSD (PI: Jeffrey S. Grethe) =
 [[Image:GWE-logo.jpg]]
 = Overview =
-A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise).  This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment.  This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.
+A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise).  This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment.  This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.
 A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology.  It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:
@@ Line 13: / Line 13: @@
 * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
 * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
-= Grid Wizard Enterprise (GWE) Background =
+= Systems =
-= GWE Information =
+== Grid Wizard Enterprise (GWE) ==
 * GWE
@@ Line 40: / Line 60: @@
 ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
 ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]
 = Monthly Progress (since July 2007) =

@@ Line 121: / Line 121: @@
 * [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].
-''February 2009''
+''March 2009''
 * GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
 * [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
 * [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]
 = Miscellaneous =

← Older revision		Revision as of 12:52, 8 February 2010
Line 1:		Line 1:
		+	Back to [[Engineering:Main\|NA-MIC Engineering]]
		+
	= UCSD (PI: Mark Ellisman) =		= UCSD (PI: Mark Ellisman) =