Add Existing Module To add an existing module to the pipeline: 1 Click on the "Library" tab on the bottom right hand corner of the "LONI Pipeline v3.0" window 2 Click ...

To add a new Parameter to a newly created module, complete the following steps 1 After you have created a name and path for you module and clicked "OK" a screen will ...

These are the steps to adding a new resource (a data variable) to the pipeline Select Workflow- Data Click on "New" Enter a name in the label field Enter additional ...

This page documents the steps to adding function definitions to the pipeline ontology 1 step 1... 1 step 2... Main.MichaelJPan 03 May 2005

The following steps should be taken to add a new group or a new user in the UserAndGroupManagement dialog: Adding a new group 1. Click the "New Group" button or right ...

Description: This feature allows developers to add any third-party external jar file as an extension. Instructions: Creating an external jar file (yourExtension ...

A RemoteServerOptionsPanel represents the panel to be displayed in the ServerAdministrationPanelGUI when its corresponding button is selected in the ButtonBar . This ...

This document outlines the steps necessary to add a new ServerCommand for remote server administration 1. Create the ServerCommand class A. Use package edu.ucla.loni ...

ApplicationsManager is a class that manages the relationship between the external viewing applications and the LONI Pipeline. Main.JagadeeswaranRajendiran 22 Feb ...

Overview ApplicationsManager is the class that manages the relationship between external visualization applications (like Slicer, Shiva and LOVE) and the LONI Pipeline ...

An ArgumentCell represents a PipeCell's argument in the PipeGraph . Like PipeCells , ArgumentCells are a persistant object model. An ArgumentCellView represents a ...

ArgumentCellView represents a view of an ArgumentCell . An ArgumentCellRenderer is used to actually render the ArgumentCellView in the PipeGraph . Main.RonNor 01 ...

Pipeline v.3.0 beta client has been releaseed. Please see StableBuild for more information

CCB Meetings This is a list of the minutes of the CCB meetings related to the Pipeline Presentations SigFlowMeetings Miscellaneous MeetingMinutes200510281400

ReleaseNumberConvention provides information as to our numbering scheme. Upcoming changes in the next release Current release 3.0 beta 6.3 released 28 february 2006 ...

Changing Profiles (without using GUI): If the user has multiple profiles, the best way to reflect the changes directly: 1. Each profile has its own directory (with ...

At the top of every pipeline module file is a set of class definitions. These class definitions define the various classes of objects to be manipulated, e.g. File ...

Once the classes have been defined, class instances are defined. In OWL, all objects are resources, and provided an ID, to which it can be referred. To define an Analyze ...

To configure the client, in the Pipeline menubar, click on "Application", then "Options...". A configuration dialog should appear allowing for configuration. ConfigureExtensions ...

InstallingPipelineApplication RunningPipelineApplication SoftwareRequirements PipelineGlossary UpgradingFromV1 LibraryModules PipelineModules ShortUsageTutorial ClientConfiguration ...

client 3.0.beta1.1 (released 6 July 2005) added archiving of files in postprocessing added pause and resume functionality for both local and remote execution corrected ...

client 3.0.beta1.2 (released 12 July 2005) singleton status pane now displays validation errors for singletonmonitors fixed network communications due to various ...

client 3.0.beta1.0 (released 24 June 2005) possible connections highlighted (default off) added popup menu item for connecting parameters (default off) fixed bug ...

client 3.0.beta2.4 (released 12 August 2005) note that this list includes improvements made to beta2.3 Added Reset button to Run Panel Added a new Zoom panel below ...

client 3.0.beta2.2 (released 5 August 2005) note that this list includes improvements made to beta2.1 Fixed bug that would not allow a module to be moved if it was ...

client 3.0.beta2.0 (released 20 July 2005) Fixed bug that allowed connections to be drawn by dragging on a parameter cell that wasn't an input or output parameter ...

client 3.0.beta0.0 (released 11 June 2005) GUI split into its own package included licensing info for external libraries xml files split into xul and config directories ...

The clustering modules functionality allows for a researcher to select a group of connected modules, and abstract them as a single node. This action clusters them ...

Pipelines- Pipelines are modules that nest other modules. All contained modules BranchPipelines IterationPipelines

Application directory This directory is the location that the application uses. Defaults to the tmp directory of the root file system c:\tmp\pipeline (on Windows ...

Enable grid engine Defaults to false. If configured to use the grid engine, then need to also specify a preferred grid engine monitor class. Currently defaults to ...

Please refer to: http://www.loni.ucla.edu/twiki/bin/view/Pipeline/AddingExtensions Main.JagadeeswaranRajendiran 21 Oct 2005

The following is an explanation of the options that are configurable that affect the user interface: Canvas grab and scroll factor How fast the user can pan a Pipeline ...

Network port This is the port on which the server is listening for connections Defaults to 8000 The server can alias a particular hostname. This is particular helpful ...

Pipeline server settings can be configured. ConfigureExtensions ConfigureExecution ConfigureNetworking ConfigureCacheDirectory

Generic Viewer 1. When one clicks on a parameter with type (eg: AnalyzeImageFile, extension 'img'), if a viewer does not already exist, the following screen will ...

The Pipeline need the user to explicitly specify that two different modules are connected. Two modules are automatically connected if one of each of their arguments ...

as a guest (default) you will be able to view all the pages, but cannot edit. to edit the pages, these are the steps to start making modifications on wiki 1 register ...

The core library contains the interfaces and classes that support the modular architecture of the Pipeline application. The interfaces are Component Event The classes ...

You can create a new module using the following steps 1. Select, in the menu, "Workspace- New" 1. You will then be prompted for either a Pipeline (which contains other ...

Once you have created a new pipeline, the main canvas should now show a blank graph. You can now add modules to this pipeline by following the directions in CreateNewModule ...

If you selected "System executable" in CreateNewModule, you will now be prompted for the location of the program. You will then be prompted for either a Pipeline ...

Creating Pipeline Lists Pipeline lists allow you to specify values for multiple iterations of a module. A Pipeline list can either be specified from a file (referred ...

-- Main.JonMorra 09 Jan 2006 PLEASE DO NOT CREATE ANY MORE JDIALOGS IN PIPELINE The !DialogManager is intended to be the only way JDialogs are made. The !DialogManager ...

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We have revamped the Pipeline framework to be extension based. That is, the functionalities of the application will be modularized, and packaged into their own extensions ...

DesignGoal SourceCodeRepository CodingStyle NetworkingAPI UnitTesting AddingExtensions (how to create an extension for the Pipeline) UsingSwiXML (how to use XML to ...

Diffie-Hellman key exchange (alternatively key agreement or key negotiation) is a cryptographic protocol which allows two parties to agree on a secret key over an ...

The LONI Pipeline is released under the LONI License. The LONI Pipeline client v.3.0.beta6.3 has been released as of 28 February 2006. A copy can be downloaded from ...

1 Enter a name in for "label" 1 Add a comment 1 Select Type- either "Command Line Option" or "File" 1 If File is selected then select "Connection Type"- either "Input ...

When adding or editing a group, you have the option to specify GroupPermissions for the particular group that you are adding or editing. A group may have zero or more ...

The following steps should be taken to edit a group or user in the UserAndGroupManagement dialog: Editing a group 1. Double-click the group you would like to edit ...

The Pipeline networking library provides for secure communications using TCP. The encryption protocol uses DiffieHellman algorithm to allow for a client and server ...

Using the Execution Wizard To open the Execution Wizard: 1 Go to "Tasks" menu 1 Click on "Execution Wizard..." 1 Follow the instructions in the window. Functions ...

LONI Pipeline makes extensive use of external libraries. In order to avoid potential licensing issues which may arise with the distribution of these packages, you ...

PipelineCollaborators FundingInstitutions Other workflow systems Kepler SCIRun Taverna

File dependencies are another example of the usefulness of definitions. For example, Analyze image files have two separate parts- an image header file, and an image ...

File permissions in the Pipeline follow the same schema for file permissions in most operating systems. That is, each permission specifies a path, and has a read, ...

This module will run the Firefox browser, with an optional url input to be set as the start page. Some notes: The node describes the executable. It specifies the url ...

To format a pipeline module for use in pipeline ontology: 1. Open up .module in Emacs or other text editor 2. In text editor, save another version of module as .owl ...

Freesurfer tutorial module This is the Pipeline module for the recon-all script in the Freesurfer tutorial. Screenshots Usage Some caveats: This requires Freesurfer ...

A pipeline at its core is a sequence of Functions applied to a data set. Hence function definitions are crucial. Since functions are resources as well, we can define ...

This is an example of the function definitions index file used by the pipeline to load all the function definitions.

This FunctionPipeline refers to 6 different functions, but only 5 distinct ones. Additionally, even though it referes to !CropExecutableFile twice, it remaps the functions ...

Main.MichaelJPan 23 Feb 2005

The following have generously contributed to the funding of the Pipeline development National Center for Research Resources (NCRR) National Centers for Biomedical ...

ModulesPanesHolder Tabs should be created from an actual object with access to modules, variables, functions, classes, etc. PipelineDocument class PipelineOntologyDocument ...

The GlobalViewGraph displays a miniature view of the main graph. The entire graph is scaled to fit into the area of the GlobalViewGraph for a quick overview of all ...

Group permissions in the Pipeline are resolved using logical connectives. These include (possibly nested) conjunctions, disjunctions, and negations of a FilePermission ...

Features Directory: /nethome/users/{user-name}/{pipeline-dir}/pipeline/pipeline/ BR Filename: groups.xml Format ... ... Variable Definitions groupname: : Name ...

These are the hot keys that help navigate through the Pipeline application Shift-mouse: Pan graph (both main and global) Alt-shift-mouse: Zoom (main graph only) Other ...

How To Use the Wiki We encourage you to change the contents of a Wiki web page and to add your own web page topics that is what a Wiki is all about ! Edit a Wiki ...

This package consists of the modules of the 22 ITK exercises that help with familiarizing the user to learning ITK. Some notes: each of the functions in the modules ...

ITK Multi-Modality rigid registration This module is a Pipeline wrapper around MultiModalityRigidRegistration executable. MultiModalityRigidRegistration.module: Pipeline ...

This document describe the steps needed to extend the edu.ucla.loni.pipeline.net.URL class. This has to be different than java.net.URL (though have the same methods ...

ITK Installation This pipeline module has been created for users who intend to automate the download and compilation process of the ITK software. To install ITK ...

ITK Installation This pipeline module has been created for users who intend to automate the download and compilation process of the ITK software. To install ITK ...

ITK Installation (Version 3) This pipeline module can be used with Pipeline Version 3. Unix Platform (most flavours): Download the pipelne module Itkinstall unix ...

ITK Installation This pipeline module has been created for users who intend to automate the download and compilation process of the ITK software. To install ITK ...

VTK Installation This pipeline module has been created for users who intend to automate the download and compilation process of the VTK software. To install VTK ...

The Pipeline application is a self-contained, executable Java jar file. That means, as long as you have Java installed on your system, there is no additional installation ...

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Hibernate has problems when running under !JUnit. Fixes are proposed here. However, this does not seem to work for us yet. Once you have it working, you can automate ...

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The modules distributed with the Pipeline client are modules to programs that exist on the Pipeline server hosted at LONI. To run these modules, you will need a LONI ...

The LogMessagesPane is a user interface that tracks log events. It is composed of two portions. The bottom portion is a panel that displays a table of log messages ...

The main menu manages all the menus and menu items that appear in the menu bar of the Pipeline GUI. It provides access to the RecentModuleManager and the execution ...

The main panel is everything below the main menu bar. It defines many different panels and split panes that represent the main user interface window. The top portion ...

Teleconferences TeleconferenceMinutes200508121000 NAMIC teleconferences External meetings MeetingMinutesOctober2006PipelineSCIRun MeetingMinutes200601111300 MeetingMinutes200508161030 ...

24 september 2004 2pm present: MAINWEB .ScottNeu, Karen Crawford, Rebecca Blanton, Amanda Hammond, Allan Mac Kenzie Graham, Craig Schwartz, MAINWEB .MichaelJPan, ...

12 November 2004 3:30pm present: MAINWEB .ScottNeu, Allan Mac Kenzie Graham, MAINWEB .MichaelJPan, Ivo Dinov, Arthur Toga, Jyl Boline, Daniel Valentino, Rico Magispoc ...

10 January 2005 10am present: MAINWEB .MichaelJPan, Ron Nor, Jags Rajendiran Ron and Jags brought up to date with Pipeline development and assigned various tasks ...

10 february 2004 10am present: MAINWEB .DavidRex, David Shattuck, MAINWEB .ScottNeu, Karen Crawford, MAINWEB .MichaelJPan mapped out components of entire LONI Brain ...

10 february 2004 1pm present: MAINWEB .DavidRex, Jeff Ma, MAINWEB .MichaelJPan mapped out components of Pipeline processing environment. agreed to branch current ...

17 february 2004 10am present: MAINWEB .DavidRex, David Shattuck, MAINWEB .ScottNeu, Karen Crawford, MAINWEB .MichaelJPan worked through a use-case, touched on the ...

7 june 2005 11:30am present: Rico Magispoc, Karen Crawford, MAINWEB .MichaelJPan Pipeline database requirements User authentication Group management Runtime information ...

16 august 2005, 10:30am present: MAINWEB .IvoDinov, MAINWEB .MichaelJPan, David Weinstein, Michael Callahan, !McKay Davis, J. Davison de St. Germain, Jagadeeswaran ...

Agenda Introduction of members Identification of grand challenges Application integration Matlab R !SCIRun Slicer XGrid Shiva Condor SRB IDA Workflow description ...

Agenda The agenda of this meeting is to address the the necessary computational resources necessary to improve labwide productivity. Goals Interoperability Accessibility ...

Agenda Roll call Status update Proposal of new features integration with Pygr integration with databases, eg !GraphDB and BLASTgres Formulate of roadmap (1, 3, and ...

Agenda Roll call Status update Deployment roadmap (2, 4, 6 weeks) Development roadmap (1, 3, and 6 months) Research roadmap (6, 12, 18 months) Minutes In attendance ...

SciRun Meeting @ SCI Institute Present: Martin Cole, Main.MichaelJPan, Jagadeeswaran Rajendiran Minutes ... ... Action items possible new xml format for .net files ...

Pipeline Meetings Pipeline/SCIRun Interaction Meeting (TeleConference CAll, DATE!) Online Pipeline Calendar General Pipeline Meetings LONIR Meetings Pipeline Meetings ...

Pipeline Meetings Pipeline/SCIRun Interaction Meeting (Tele-Conference Call, DATE!) Online Pipeline Calendar CCB Meetings LONIR Meetings Pipeline Meetings Participants ...

Pipeline Meetings Pipeline/SCIRun Interaction Meeting 10/12/06 Minutes Online Pipeline Calendar CCB Meetings LONIR Meetings Pipeline/SCIRun TCon Meeting (10/12 ...

FunctionPipeline AddFunctionAssignment ModifyFunctionAssignment FunctionSingleton AddArgumentAssignment ModifyArgumentAssignment Main.MichaelJPan 25 Mar 2005

ModifyExistingPipelineModule ModifyExistingSingletonModule

AddNewClass ModifyExistingClass AddNewResource ModifyExistingResource AddNewFunction AddExistingFunction ModifyExistingFunction CreateNewModule AddExistingModule ...

To modify a value of an existing resource (Workflow Data) 1 Go to "Workflow" menu 1 Click "Data" 1 Select desired variable 1 Click "Edit" Button ATTACHURL /Picture9 ...

Activating a parameter To activate a parameter 1 Right click on an the module 1 Select "activate"-- Select parameter to be activated Deactivating a parameter To deactivate ...

Module types CompositeModules SingletonModuless- Singletons wrap around a single Function. They refer to this function by its ID. Module argument assignments- The ...

A ModuleErrorPane dispalys a table that contains errors for a given module. Main.RonNor 01 Feb 2006

ModuleInfoPane displays information about a module when it is selected. Main.RonNor 01 Feb 2006

A ModuleProcessPane displays a table that contains the children processes of a module. When the user double-clicks on a row in this table, a ModuleCanvas is added ...

ModuleSyntaxUpdate: To Do List GUI Changes Edge Drawing Current Implementation After modules are drawn on the graph, edges are added with !PipeGraph.addEdges() Iterates ...

The ModulesPanesHolder contains a tabbed pane. Tab panels include one for the "Working List", one for the "Library", and one for the "User List" if the user has provided ...

Many to one value binding The Pipeline will bind multiple values to a single argument on your behalf. To specify multiple values for an argument, edit the variable ...

Namespaces are defined in the document's root element

Communications with a Pipeline server is accomplished with the use of TCP sockets. There are 3 parts of the total packet structure. The first 4 bytes of a packet specify ...

At this stage, the server will authenticate the user information. If authenticated, the server will send back a SuccessfulAuthenticationPacket. If not authenticated ...

Both sides of a connection need to inform the other side once they have established the encryption ciphers, so that encrypted communications can begin. The following ...

This is an example of a DiffieHellman parameters packet 45428 45428 AES 128 161409185729581153775647009132494411332525 879318039955946978758100904429530726656032 187867234343861292704739684762474760744077 ...

Once the Pipeline application (client or server) has received the NetworkingAPIDiffieHellmanParametersPacket, it will use these parameters to establish its private ...

Upon connection, the server (the one who accepted the connection) will send over a NetworkingAPIDiffieHellmanParametersPacket to the client (the one who initiated ...

Once the other end's public key has been received, and one's own asymmetric keys have been established, the DiffieHellman algorithm is used to generate the shared ...

This step simply waits for the other end to send over their public key, in a NetworkingAPIPublicKeyPacket. Main.MichaelJPan 22 Mar 2005

First open a tcp socket. Main.MichaelJPan 22 Mar 2005

This is a packet that requests a file file request ${USER} ${PASSWORD} 17.0.0.1 37308 127.0.0.2 37308 Main.MichaelJPan 23 May 2005

This is a packet that encapsulates a part of a file file send ${USER} ${PASSWORD} 127.0.0.2 1096 127.0.0.1 1096 ${FILEURL} 0 65536 To specify that a packet is the ...

The server, immediately after the NetworkingAPICipherEstablishedPacket from the client, uses the credentials provided by the client in that packet to authenticate ...

Command packets allow a client to specify actions for the server to complete on its behalf. Some of these actions include load execute pause resume reset abort close ...

This packet allows for the server to inform the client of the status of workflows it is running on behalf of the user.

An example of such a public key packet. 45428 45428 308201a63082011a06092a864886f70d0103013082 010b02818100e5dab412c80776a5dd2c2d51ea6b97 2aecc55372a0b25227bae3dd3f6f5f46ca417b1e16 ...

Once the connection has been established, packets queued to be sent to the user while the user is logged out is sent.

Once the user has authenticated with the user, the server will send over information about the permissions the user has on the server in a NetworkingAPIUserPermissionsPacket ...

This packet provides the client with information about the permissions that the user has on the server.

If the client has jobs on the server from a previous session, the server will send over a NetworkingAPIWorkflowsSynchronizationPacket

This packet allows for a client and a server to synchronize on the workflows that the server may be executing on behalf of the user from a previous session.

Nightly builds If you are an internal user, you can grab a copy of the nightly build from /loni/mjpan/pipeline.builds/nightly/ on an internal LONI machine which mounts ...

Class definitions in the ontology distributed with the Pipeline application ClassDefinitions.owl: FunctionDefinitionsIndex

Class: edu.ucla.loni.pipeline.gui.Options The Options object manages user interface options. Upon construction, it loads default option values, and tries to overwrite ...

Bugs Mantis #1306 Mantis #1311 Documentation FunctionFactory.java Difference between cardinality and iteration Client Server communication flow (setup, status updates ...

-- Main.JonMorra 01 Mar 2006 The way that data is passed around in all of the classes that extend !AbstractGUI have now changed Now everything that extends !AbstractGUI ...

The are the classes in the Pipeline that have been defined for persistence so far !UserAccount (not in Hibernate yet) Group !RootGroup !UserGroup !GenericGroup Predicate ...

PipeCanvas extends a CloseableTabbedPane . A PipeCanvas is created with a root Pipeline module. There is a one-to-one match between modules in the "Working List" ...

A PipeCell represents a module in a PipeGraph . PipeCells are a persistant object model. A PipeCellView represents a view of a PipeCell . The PipeCellView is more ...

PipeCellView represents a view of a PipeCell . It has methods to determine its sizing and placement information based on information provided by its PipeCell . A ...

A PipeEdge represents a connection in the PipeGraph . Like PipeCells , PipeEdges are a persistant object model. A PipeEdgeView represents a view of a PipeEdge . PipeEdges ...

PipeEdgeView represents a view of a PipeEdge . A PipeEdgeRenderer is used to actually render the PipeEdgeView in the PipeGraph . Main.RonNor 01 Feb 2006

PipeFrame is a Pipeline extension that is used for GUI management. It extends the AbstractComponent class and runs on its own thread. PipeFrame processes events that ...

PipeGraph is a graph representation of a Pipeline. Child modules are added as PipeCells . Module arguments are represented with ArgumentCells . Connections between ...

The PipeGraphKeyListener listens for key events in a PipeGraph . Key events handled Up/Down/Left/Right "budges" a PipeCell in the corresponding direction Delete Removes ...

The PipeGraphTransferHandler is used to accept a drop in a drag-and-drop operation. The types of objects that can be dropped into a PipeGraph are Module , Function ...

PipeGraphUI handles most user interaction with a PipeGraph. It contains methods that paint the background grid and LONI logo to the PipeGraph . PipeGraphUI is mainly ...

The LONI Pipeline Processing Environment is hosted at UCLA's Laboratory of Neuro Imaging. It has been used quite successfully since its release in the neuroimaging ...

PipelineCanvas is a ModuleCanvas that contains a ModuleProcessPane , ModuleErrorPane , and a scrollpane that holds a PipeGraph . The ModuleProcessPane and ModuleErrorPane ...

The following people and instututions have collaborations with the Pipeline Center for Computational Biology (CCB) Biomedical Informatics Research Network (BIRN) National ...

This is a list of the packets that are used to communicate messages NetworkingAPIDiffieHellmanParametersPacket NetworkingAPIPublicKeyPacket NetworkingAPICipherEstablishedPacket ...

Current contributors Principal investigator Arthur W Toga Technical lead Main.MichaelJPan Programmer Main.JagadeeswaranRajendiran Liaison to NA-MIC Main responsibilities ...

Pipeline Download the latest release of the Pipeline, and view the release notes for more information.

How can I help to improve Pipeline? The best way to help out is by using Pipeline and giving us feedback. You can sends comments/suggestions to us by email at pipeline ...

The LONI Pipeline v3 has the following features Modular architecture Server/client communications via TCP AES encrypted communications Ontology enabled data processing ...

The PipelineGUI holds references to the main menu, main panel, root JFrame component, and PipelineListener . Main menu Main panel PipelineListener Main.RonNor 31 ...

Function something that takes a set of inputs and returns a set of outputs. (technically, programs dont return anything... all the outputs are side effects, but ...

Pipeline Development Group Action Items 2008 December December, 2008, Week 1 December, 2008, Week 2 Back to main Pipeline Wiki

PipelineListener listens for ActionCommands and calls the appropriate action methods for a command. It is also registered as a WindowListener for the root frame. ...

PipelineModules are !XML descriptors of program usage. These descriptors provided information about how a program is run, so that the Pipeline can correctly execute ...

The packet attachment is a binary data, of a length specified in the header. In order to provide for file streaming, the length of this attachment is limited to 65536 ...

The PipelinePacketHeader specifies meta-data about the particular packet. Some of this info includes the size of the attachment the encryption of the attachment source ...

User Links Demos Quick Guide (.pdf) Creating a Basic Pipeline (.mov) Creating a list for Multiple Inputs (.mov) Steps Required for Running a Pipeline on the LONI ...

PipelineModules are stored in XML. There are currently 2 iterations of the XML DTD for PipelineModules. PipelineV1Syntax PipelineV3Syntax Main.MichaelJPan 02 Feb ...

A PipelineTransferHandler is used by the Pipeline application to create Module, Function, or Resource Transferable objects for drag-and-drop operations. It also provides ...

PipelineModules in Pipeline v3 are stored in OWL, which is a recommended specification of the World Wide Web Consortium (W3C). The Web Ontology Language for Services ...

Past presentations The following is a list of presentations of the Pipeline pipeline.20041210.ppt: This was presented to NAMIC collaborators at the NAMIC Toolkit ...

A ProcessCanvas is a ModuleCanvas that holds a table of error values for a ProcessMonitor . Main.RonNor 01 Feb 2006

Overview ProcessScheduler schedules all submitted processes based on its 'acquired' priority. It is responsible for enqueuing processes, dequeuing processes and ...

ModuleSyntaxUpdateToDo RemoteServerAdministrationDevDoc Tutorials AddingNewServerCommandTutorial AddingNewRemoteServerOptionsPanelTutorial GUI Documentation PipeFrame ...

The RecentModuleManager keeps track of the recent module documents that have been opened or saved recently by the user. By default, a file is saved to ~/.pipeline ...

The following is a humorous comparison of the release numbering of the LONI Pipeline v3 against various organizations LONI Pipeline Open source Microsoft Google Apple ...

Current development schedule: Client/standalone pre-alpha release (Released 30 March 2005) Client/standalone alpha release (Released 18 April 2005) Client/standalone ...

Remote Server Administration: Developer Documentation !BetaRelease 20060120 contains a framework for remote server administration. This document outlines the design ...

The following steps should be taken to remove a group or user in the UserAndGroupManagement dialog: 1. Right-click on the user or group node you would like to remove ...

Bugs (as well as feature requests) in the Pipeline software can be reported to our bug-tracking software Mantis, which is located here Please feel free to add comments ...

The following are publications related to the Pipeline. If you use the Pipeline in your research, please cite one of the following publications. Also available is ...

@inproceedings{toga2001pipeline, author {Arthur W Toga and David E Rex and Jeff Ma}, title {A graphical interoperable processing pipeline}, booktitle {7th Annual ...

IDs- Following RDF specifications, everything in a pipeline is a resource. Every resource can be uniquely identified by its ID, specified by its "rdf:ID" attribute ...

Resource values are constructed in a complicated manner, taking into account several factors: host flipping because communications between client and server is facilitated ...

This script will run the Pipeline using Ant, by including all the external libraries for you in the classpath. You will have to modify some properties ${lib.dir} all ...

This script will run the Pipeline under a bash shell, by including all the external libraries for you in the classpath. Modify $LIB DIR to match the directory where ...

Main.JonMorra 09 Jan 2006 Before running any Matlab commands, Matlab must be started contact your administrator for help Running Matlab Commands Create a new Matlab ...

Windows double click on the pipeline.jar file MacOSX double click on the pipeline.jar file Command line (shell) type "java jar pipeline.jar" from the directory ...

Main.JonMorra 09 Jan 2006 Before running any R commands, R must be started contact your administrator for help Running R Commands Create a new R Command module ...

To run your own server on cerebro-sn1, using XML-based Authentication, please follow these steps: 1. Make sure your {user.home}/.pipeline/config/ exists on cerebro ...

These are the client features released along with the beta server consolidate ontology functions into one pane ask user for permission to overwrite existing files ...

These are the steps for setting up a server to run. Ensure SoftwareRequirements Define users, groups, and permissions in UserAndGroupManagement ConfigureServerSettings ...

The following rules apply when setting a user or group's parent: The user or group must not be descended from the new parent The parent must be a group (green or gray ...

Follow these steps 1. CreateNewModule (or CreateNewPipelineModule) 2. AddNewParameter 3. AddNewResource 4. ModifyExistingModule or, try the ExecutionWizard.

SIGFlow meetings MeetingMinutes200510271300 MeetingMinutes200511221300 MeetingMinutes200512201300

This document provides the instructions for enabling Java WebStart delivery of the Pipeline processing environment. Creating the key to create the key to sign the ...

Simple align module This pipeline module aligns images to a standard. Screenshot Files simpleAlign.pm: Pipeline v1 module simpleAlign.module: Pipeline v3 module ...

A SingletonCanvas is a ModuleCanvas that displays information on child processes, module errors, and the execution status of the Singleton module associated with it ...

The LONI Pipeline is available under the LONI software license. This license is an open source license, similar to the Apache software license, with an additional ...

The following are the requirements for running the Pipeline. Pipeline application Java 1.4.2+ Binary executables Please note that the LONI Pipeline is an environment ...

Source code repository Internal access Make sure you are in the following groups: hackers, piplncmt, piplndev server(s): any system that mounts the /loni file system ...

The following is a list of requirements for each class to be persisted by Hibernate Default constructor (i.e. no parameters) get/set methods for every field to be ...

The following are statistics about the source code of the various versions of the Pipeline, calculated by using sclc, on the latest version of the code checked out ...

Sources will be released via anonymous cvs once we have determined that a majority of the source code has reached stable status, and once we have established an infrastructure ...

Pipeline v.3.0.beta4.0 has been released as of 10 November 2005. The current Java jar package includes both the standalone client and the server. A copy can be downloaded ...

Generic start The Pipeline can be started with the following command java classpath pipeline.jar edu.ucla.loni.pipeline.Server Starting on Cerebro These directions ...

P Petrosyan 12.09.08: Implementing pipeline server failover Z Liu 12.10.08: Pipeline test suite BR 12.10.08: Pipeline SGE6.2/DRMAA1.0 integration K Lozev 12.10.08 ...

P Petrosyan Z Liu K Losev J Pierce R Magsipoc C Hojatkashani Main.RicoMagsipoc 10 Dec 2008

P Petrosyan 12.09.08: Implementing Pipeline server failover. 12.15.08: Already have the draft for failover without Aliasing. Working on aliases. 12.17.08: Created ...

12 august 2005, 10:00am present: MAINWEB .IvoDinov, MAINWEB .MichaelJPan, Darby Vanuitert, David Weinstein, Michael Callahan, !McKay Davis, J. Davison de St. Germain ...

3.0beta5.4 (released 18 january 2006) ability to specify default values for a parameter added parameter type "side effect output" automatically binds variables to ...

3.0.beta5.1 (released 22 november 2005) extracted server code to its own package corrected bug with "Save as" option reset of a monitor over a network now works fixed ...

3.0beta5.3 (released 10 january 2006) fixed an !OutOfMemoryException various GUI fixes

3.0beta5.2 (released 20 december 2005) fixed application non loading bug if upgrading from beta5.0 now validates prior to execution to ensure that resources are bound ...

3.0.beta5.0 (release 10 november 2005) Fixed interface delay issues with loading of a pipeline module Status of enclosing pipeline is now displayed Disabled some ...

3.0.beta4.0 (released 18 October 2005) fixes to URL resolution SRB integration Added ability to view/edit a class definition User can now specify an extension for ...

3.0beta6.1 (released 3 february 2006) fixed issue with using ${iteration} variable in values of output arguments fixed remove administration of users and groups ...

3.0beta6.2 (released 15 february 2006) fixed issue with execution configuration where cache directory was being hardcoded fixed ability to specify whether a workflow ...

3.0beta6.2 (released 15 february 2006) fixed issue with dragging a library function onto the canvas

3.0beta6.0 (released 25 january 2006) fixed issue with dragging functions into working document XML based account managers now will create default administrative ...

3.0.beta3.1 (released 13 September 2005) various fixes to issues with global graph synchronization grid engine integration now possible with commandline tools (eg ...

3.0.beta3.2 (released 4 October 2005) fixed bug with phantom parameter attribute fixed bug associated with occasional packet corruption server now supports execution ...

3.0.beta3.0 (released 31 August 2005) Note that this is the first release with a stable server Fixed !EditFunctionPanel so that changes are not applied until the ...

Java virtual machine issues Requires Java 1.4.2 to run (all older versions of Java have reached end-of-life support by Sun) This version cannot run on SGI IRIX machines ...

Shape analysis module This module is developed by Martin Styner at UNC for shape analysis. Screenshots Module UNC SHAPE.module:

The LONI Pipeline makes use of JUnit for unit testing. Existing tests Current we have the following test classes Additional tests needed loading saving a pipeline ...

Updating modules There are 2 ways for upgrading from V1. The first is an ad-hoc method; the 2nd is more structured. In the ad-hoc method, one simply needs to load ...

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Groups in the Pipeline application are managed in a tree. At the top of this tree is the root node. All nodes that do not have any parents specified have this root ...

Features Directory: /nethome/users/{user-name}/{pipeline-dir}/pipeline/pipeline/ BR Filename: users.xml Format Variable Definitions username: : Name of the user ...

UsingHibernate PersistentClasses Hibernate Mapping Hibernate calls SourceCodeRequirementsForHibernate JUnitHibernateInteraction

SwiXML GUIs This document provides the instructions for using SwiXML to split the GUI. The end result should be 3 files. These files are an execution class a GUI ...

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Currently the version string is "20050412".

A VirtualPipelineCanvas contains a top panel that displays the module monitor information and a bottom panel that displays errors for a virtual pipeline. Main.RonNor ...

This page contains screenshots and videos of the Pipeline in action. All the videos and screenshots have been taken off the site because they were way out of date ...

INCLUDE{" TWIKIWEB .WebChanges"}

The LONI Pipeline is a simple graphical environment for constructing complex scientific analyses of data. It provides a visually intuitive interface to data analysis ...

SEARCH{"\. " scope "topic" regex "on" nosearch "on"} See also the faster WebTopicList

VisualGallery PipelineFeatures PipelineModules ReleaseRoadmap DownloadSoftware ClientDocumentation ServerDocumentation DeveloperDocumentation PresentationSlides ResearchPublications ...

This is a subscription service to be automatically notified by e-mail when topics change in this Pipeline web. This is a convenient service, so you do not have to ...

TWiki.Pipeline Web Preferences The following settings are web preferences of the TWiki.Pipeline web. These preferences overwrite the site-level preferences in TWIKIWEB ...

TWiki's Pipeline web SCRIPTURL /view SCRIPTSUFFIX /Pipeline The Pipeline web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE ...

INCLUDE{" TWIKIWEB .WebSearch"}

Statistics for Pipeline Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 6306 0 ...

TOPICLIST{" $name "} See also the verbose WebIndex.

The Workspace holds a hash of PipeCanvas objects. Each PipeCanvas object corresponds to a module in the Working List of the application. The getCanvas() method of ...

The ZoomPanel displays controls for adjusting the zoom level of the graph. It contains a zoom text field and a zoom slider. ZoomTextField A textfield that allows the ...