Center for Integrative Biomedical Computing

SCIRun/BioPSE/map3d Workshop 2002

August 4-6, 2002 / University of Utah


On August 4-6, 2002, The SCI Institute sponsored the first NCRR SCIRun/BioPSE/map3d Workshop. The workshop introduced the NCRR Center's scientific computing software, encouraging users and developers to explore its extensive capabilities. The workshop consisted of instructional sessions in addition to hands-on practice with using the software. SCI Institute scientists and developers demonstrated a number of example problems, while users experimented with existing networks, and map3d scripts. Developers also learned how to contribute their own code to the SCIRun/BioPSE project. Additionally, users and developers tested the process for designing, implementing and debugging their own networks and scripts. During feedback sessions, participants discussed ideas, exchanged experiences, and described how the software would best meet their specific project goals. Their feedback included suggestions for new SCIRun/BioPSE features, such as developing new modules, and adding functions that would make the software more efficient and dynamic.

Finally, the workshop included a dinner on the patio at Millcreek Inn where participants and faculty enjoyed a relaxed evening with perfect weather in a classical Utah mountain setting. The highlight of the dinner included a scholarship presentation to SCIRun user, Kai Li. Dr. Rob MacLeod presented Kai Li with a plaque that read: "This scholarship recognizes great courage in the face of untested software, sparse documentation, and grumpy user support. Through his contribution, all of this has improved! (We have partially tested software, mediocre documentation and cheery user support, at least after coffee). For this, we recognized Kai Li's enthusiasm and persistence with the First Annual SCIRun/BioPSE Workshop Scholarship."


Day 1: User day #1

Background to BioPSE/SCIRun and map3d concepts; examination of a sample problems; demos of nets; elements of BioPSE/SCIRun; hands-on playing with existing nets and map3d scripts.


1.1. Introduction

1.2. Overview: The SCIRun and BioPSE Problem Solving Environment

1.3. BioPSE Example: Designing and Implementing a Tikhonov Regularization Network

1.4. Overview of the SCIRun/BioPSE Software Systems

Day 2: User day #2 and Developer day #1

Joint session #1: advanced elements of BioPSE/SCIRun: module categories and organization, fields, I/O mechanisms and file conversion, debugging networks; map3d options and usage, scripting in map3d.

Users' session: hands on design, implementation and debugging of user-defined networks and map3d scripts.

Developers' session: installation and configuration; GUI design options and guidelines; source code organization; threads; persistent I/O; namespace, on-the-fly-compile; contributing code to BioPSE/SCIRun project.

Joint session #2: discussion among users and developers to exchanges experiences, describe projects, identify needs and possible new modules.


2.1. Introduction

2.2. Overview: The SCIRun and BioPSE Problem Solving Environments

2.3. Advanced BioPSE/SCIRun

2.4. Using map3d

2.5. SCIRun/BioPSE Installation and Configuration

2.6. SCIRun2

2.7. Advanced SCIRun/BioPSE Elements: GUIs, Core Libs, Contributions & Support

2.8. Documentation for SCIRun/BioPSE and map3d

2.9. Writing Modules

Day 3: Developer day #2

Discuss suggestions and idea from final session of Day #2 and identify possible modules to extend or construct.

Making a module: designing modules; programming conventions and standards; data structure details; module maker, etc.

Design and implementation: teams will follow through design process to implement modules.