SCIRun/BioPSE/map3d Workshop Schedule

Rob MacLeod and Dave Weinstein


Overview

Welcome to the 2003 edition of the SCIRun/BioPSE/map3d Workshop conducted by the SCI Institute and the NCRR Center for Bioelectric Field Modeling, Simulation, and Visualization. Our goal is to provide instruction for using and expanding the capabilities of the software we create and publish and ultimately to make the software work for you.

Venue

The lecture/presentation sessions will all happen in the SCI Conference Room (SCR) in Merrill Engineering Building. The lab sessions will be in the Visual Supercomputing Center (VSC), also in Merrill Engineering Building.

Detailed Outline

The workshop consists of a few joint sessions and then parallel tracks of lectures and lab time. We encourage you to move between the two threads based on your knowledge and ambitions. The workshop starts with background and introductory material directed mostly at what we call ``users'' of the software. We then progress into the details of the software and provide more and more information specific to the ``developer'', i.e., the person who is likely to install/maintain the program or to add new functionality by writing additional modules.

In the lab sessions that run parallel to the lectures, there will always be at least one lab assistant (typically a SCIRun/BioPSE developer) available for help and consulting. The VSC has computers available and we hope many of you will bring laptops onto which we can install the software for your use during the workshop and when you are back in your home lab.

SCI Scientific Computing and Imaging Institute hallway outside conference room
SCR SCI Institute Conference Room
VSC Visual Supercomputing Center

Day #1: Sunday

The goal of Day #1 is to develop basic skills among users based on background knowledge, elements of BioPSE/SCIRun and map3d, demo sessions, and hands on experience with existing networks and data.

Morning (SCR)

  1. 10:00 Introduction
    1. Welcome (Chris)
    2. Overview of the workshop (1.1) (Rob)
    3. Logistics (meals, user accounts, transportation, etc.,) (Allyne)
  2. 10:10 Introduction to the NCRR Center (1.2) (Rob)
  3. 10:20 Background / concepts for BioPSE/SCIRun (1.3) (Dave)
  4. 10:35 Sample problems, nets, tutorials (1.4)
    1. Survey of datasets (Dave),
    2. Tutorials: SCIRun/BioPSE Tutorial and PowerApps (Darby)

  5. 11:00 Coffee break

  6. 11:15 Intro to map3d (1.5) (Rob)
  7. 11:45 Elements of BioPSE/SCIRun (1.6) (Dave)
    1. dataflow
    2. datatypes
    3. module categories
    4. UIs
    5. scheduler
    6. network interactions: creating/editing nets, subnets, annotations, menus
  8. 12:15 Teem, DTI, and BioTensor (1.7) (Gordon)
  9. 1:00 ITK: Insight Toolkit (1.8) (Dave)

1:15 Lunch

Afternoon

  1. 2:00 Lab time in the VSC: play with existing nets, PowerApps, and map3d scripts
  2. 3:30 Joint presentation session in SCR: short presentation of research problems by all participants

5:00 Return to Guest House; free evening (group dinner)

Day #2: Monday

The goal of Day #2 is to deepen the understanding of the software structure of SCIRun/BioPSE and introduce the concepts required for development of networks and modules. Many users will wish to listen to some or all of the lectures, others will prefer more lab time.

Morning

Developers (SCR): Advanced elements of BioPSE/SCIRun (how it all works)

  1. 9:00 Installation and configuration (2.1) (Dav)
  2. 9:30 Source code organization: Modules, Geom, Threads, ... (2.2) (Dave)
  3. 10:00 SCIRun dataflow datatypes, I/O: Fields and Matrices (2.3) (Dave)
  4. 10:20 Dynamic Compilation (2.4) (Marty)
  5. 10:45 Coffee Break

  6. 11:00 Network editing, subnets (2.5) (Dave))
  7. 11:20 Debugging in SCIRun (2.6) (Dav)
  8. 11:40 Future of SCIRun/BioPSE (2.7) (Steve and Dave)
    1. CCA (Steve)
    2. Separate GUI (Dave)
    3. Performance, application driven, (Dave)
    4. Windows (Dave)
    5. fltk, linear algebra (Dave)
  9. 12:00 map3d options and usage, scripting in map3d (2.8). (Rob)

Users Lab (VSC) 9:00-12:20

  1. Hands on network design
  2. Implementation and debugging of user-defined networks
  3. map3d scripts.

12:20 Lunch

Afternoon

1:20 Lab time (VSC)

  1. Users continue using software
  2. Developers start to work on projects
  3. Dave and Rob meet with each participant to discuss project(s)

Evening

  1. 5:00 Back to Guest House
  2. 6:00 Pick up for dinner
  3. 6:30 Meet at Millcreek Innfor dinner

Day #3: Tuesday

The goal of day #3 is to dive into the developer specific information required to design and create SCIRun/BioPSE modules and for the users to continue with hands on activities

Morning

Developers (SCR): Making your own modules, nets, datasets

  1. 9:00 Module design and creation in SCIRun: ModuleMaker (3.1) (Marty) and the associated source code.
  2. 10:00 Programming conventions and standards (3.2) (Dav)
  3. 10:15 GUI design guidelines (3.3) (Dav)
  4. 10:30 Coffee Break
  5. 10:45 Data import/export (converters, Teem, MatlabInterface) (3.4) (Dave)
  6. 11:15 Contributing code to BioPSE/SCIRun project (3.5) (Dave)
  7. 11:30 Lab time (VSC)

12:30 Lunch

Afternoon

  1. 1:30 Lab Time (VSC)
  2. 4:00 Discussion of SCIRun/BioPSE, and the workshop; debrief on workshop
    1. What features are needed in SCIRun/BioPSE/map3d?
    2. What was good/bad about the workshop?
    3. When should we have the next one?
    4. What conferences does everyone attend?

5:00 Return to Guest House

About this document ...

SCIRun/BioPSE/map3d Workshop Schedule

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