Center for Integrative Biomedical Computing

SCIRun/BioPSE/map3d Workshop 2003

December 14-16  /  University of Utah


A major mission of the NCRR Center at Utah is to develop and distribute advanced software for scientific computing of bioelectric fields problems. An essential component of this process is to present our software to the user and developer community and to solicit their feedback, suggestions, and eventually their contributions. To support this evolution of the software and facilitate its use by biomedical scientists, the NIH/NCRR Center for Bioelectric Field Modeling, Simulation, and Visualization is pleased to offer a pair of workshops for users and developers of our software.


The overall plan is to offer ongoing parallel lecture and lab sessions and allow participants to select what they need at any time. We will develop optional tracks that we will direct toward particular audiences and stage a few sessions that we hope all will attend. We assume users will be present on days 1 and 2 and that developers will attend all three days. Developers with substantial previous knowledge can either join on day 2 or use day 1 for one-on-one sessions with developers in the lab.

Day 1: Users and Developers

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.

Joint session #1: short presentation of research problems by all participants


1.1 Introduction

1.2 Introduction to the NCRR Center

1.3 Background/concepts for BioPSE/SCIRun

1.4 Sample problems, nets, tutorials

1.5 Intro to map3d

1.6 Elements of BioPSE/SCIRun

1.7 Teem, DTI, and BioTensor

1.8 ITK: Insight Toolkit

Day 2: Users and Developers

Advanced elements of BioPSE/SCIRun: module categories and organization, macromodules, network editing, 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; power applications based on SCIRun; threads; persistent I/O; namespace, on-the-fly-compile; contributing code to BioPSE/SCIRun project.

Joint session #2: discussion of projects, SCIRun/BioPSE, and the workshop.


2.1 Installation and configuration

2.2 Source code organization: Modules Geom, Threads, ...

2.3 SCIRun dataflow datatypes, I/O: Fields and Matrices

2.4 Dynamic Compilation

2.5 Network editing, subnets

2.6 Debugging in SCIRun

2.7 Future of SCIRun/BioPSE

2.8 map3d options and usage, scripting in map3d

Day 3: Developers

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


3.1 Module design and creation in SCIRun: ModuleMaker
3.2 Programming conventions and standards

3.3 GUI design guidelines

3.4 Data import/export (converters, Teem, MatlabInterface)

3.5 Contributing code to BioPSE/SCIRun project