Session

Time

Topic

 

Session A

 

Working with

Pipeline

Client

8:30-9:00

Registration

 

9:00-9:25

 

Introduction

-        What is the Pipeline and how it relates to other Graphical workflow Environments?

-        The Pipeline Web-Site (navigation, documentation, forum, help, support, handbook)

-        Launching Pipeline client with Web Start

-        Installing Pipeline client ( software requirements, downloading, launching )

-        Online Server Library Navigator

 

9:25-9:45

 

Pipeline Graphical User Interface (GUI) overview

-        Server and Personal libraries

-        Open pipe files from URL

-        Workflow area iconography

-        Connection manager

-        Server usage status

-        Preferences

 

9:45-10:20

 

Running workflows

-        Validation

-        Execution

-        Module Execution Statuses

-        Previewer

-        Disconnect/Reconnect

-        Pause/Resume

-        Module and instance restart

-        Cancel instance

-        Execution logs

-        Viewing outputs

-        Command line execution / batch mode

 

10:20-10:30

Discussion

 

10:30-10:45

Morning Break

 

10:45-11:10

 

Creating your first workflow (Example of Registration Using AIR )

-        Using pre-defined modules

-        Creating data sources

-        Connecting modules

-        Running and checking results

 

11:10-11:45

 

Creating modules and more advanced workflows

-        Grouping the modules

-        Workflow variables

-        Using "Server changer" feature

-        Browsing remote files

-        Examining Workflow provenance

-        Using "Module suggest" feature

-        Defining new execution modules

-        Using "Module creation utility"

-        Creating Annotations and images

-        Defining Data sources and data sinks

-        Getting data from IDA/XNAT databases

-        Working with Study modules

-        Using Data extraction feature

-        Meta-data augmentation

-        Creating Conditional modules

-        Creating Web-services modules

-        Comparing Workflows ( Diff )

 

 

 

11:45-12:00

 

Working with module parameters

-        Setting Parameter types

-        Using Flow controls

-        Defining new File types

-        Defining Parameter Cardinalities

-        Setting Parameter Dependencies

-        Performing Parameter Transformations

12:00-12:15

Discussion

Lunch

12:15-1:15

Lunch Break

Session B

 

Workflow

Examples

1:15-2:15

 

Examples of common neuroimaging data, modules and workflows

-        FreeSurfer, FSL, AFNI, MNC, LONI Tools, etc.

-        fMRI Workflows, DTI Workflows

2:15-2:30

Discussion

2:30-2:45

Afternoon Break

2:45-3:15

 

Shape Analysis Workflows (LSA & GSA)

3:15-3:45

 

Informatics and Genomics Workflow Protocols

3:45-4:00

 

Future /Ongoing Developments

-        Pipeline WebApp, Workflow Suggest feature, Server to Server, Web service enhancements, etc.

4:00

Discussion / Start example workflows

 

9:00-9:30

Review of previous workflow executions ( UC/CCHMC )

Session C

 

Server

Management

9:30-10:00

 

Distributed Pipeline Server

-        Software requirements

-        Downloading

-        GUI Installation

-        Command line Installation

10:00-10:30

 

Server Configuration

-        General configuration

-        Server library

-        Grid configuration

-        User management

-        Packages

-        Executables

-        Authentication

10:30-10:45

Morning break

10:45-11:00

 

Grid Plugin API

11:00-11:15

 

Server monitoring and administration

11:15-11:30

 

Deploying Pipeline Web-Start (PWS)

11:30

Discussions, Conclusions, Evaluations, and Adjourn