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 feedback and contributions.
To support this evolution of the software and facilitate its use by
biomedical scientists, we have proposed a series of workshops and the
purpose of this document is to describe the structure of these workshops.
The overall plan is to have three days organized approximately as
follows:
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;
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
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.
The lecture/presentation sessions will all happen in the SCI Conference
Room in Merrill Engineering Building. The
lab sessions will be in the Visual Supercomputing Center, also in
Merrill Engineering Building.
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.
- 9:30 Pick up at University Guest House
- 9:45 Coffee and snacks
- 10:00 Introduction
- Welcome (Chris)
- Overview of the workshop (Rob)
- Logistics (meals, user accounts, transportation, etc.,)
(Allyne)
- 10:10 Background
- PSE history, motivation, and concepts (Chris)
- BioPSE/SCIRun development history (Dave)
- map3d history and concepts (Rob)
- relationship to NCRR Center and SCI/CVRTI (Rob or Dave)
- 10:30 Example problem (Dave)
- select one of demos as sample problem, e.g., Tikhonov
regularization
- dissect problem from the top down, covering
- problem statement
- solution strategies
- pseudo code
- modules required
- network design
- 11:00 Elements of BioPSE/SCIRun
- simplified installation (Dave)
- documentation structure and layout (Rob)
- dataflow concepts (Dave)
- network design and conventions (Dave)
- modules: UI and algorithms (Dave)
- net files and state description (Dave)
- I/O and bridging of data and third party programs (Dave)
- viewer interaction (Dave)
- 11:45 Demos: run through the BioPSE and map3d demos to illustrate the
functionality and dataflow approach (Chris and Rob)
- 12:30-1:30 Lunch
- 1:30-4:00 Lab Session:
Hands-on experience with existing networks and map3d with
guidance from Center personnel; encourage modification of existing
networks and exploration of features. (All instructors and
development team)
- 4:00 Free evening
The second day begins and ends with joint sessions of the user and
developer groups. In between are parallel sessions to expand on elements
relevant to each group. The final session is especially important as is
should provide the material for the development practice that makes up the
final day of the workshop. This way, users and developers can discuss
together their experiences and ideas with what they wish to achieve with
BioPSE.
- 9:00 Pickup of developer participants at University Guest House
- 9:15 Coffee for developers
- 9:30 Background for developers
- PSE history, motivation, and concepts (Chris)
- BioPSE/SCIRun development history (Dave)
- map3d history and concepts (Rob)
- relationship to NCRR Center and SCI/CVRTI (Rob or Dave)
|
- 9:30 Pickup of user participants at University Guest House
- 9:45 Coffee
- 9:55 Harass Greg
|
- 10:00 Joint session #1 on advanced elements of BioPSE/SCIRun (Dave)
- module categories and organization
- source tree organization and underlying program structure
- packages
- fields and their organization
- I/O, file conversion, and bridging mechanisms and approaches
- on-the-fly compile
- error messages
- debugging networks
- net files
- widgets
- scheduling and event management
- advanced viewer control and rendering, exporting mechanisms
- reporting errors and bugs, feedback
- 11:10 Joint session #2 on map3d (Rob)
- goals and task of map3d
- basis of spatiotemporal surface rendering
- command line options
- interactive controls
- I/O, converters, and graphicsio
6. 11:30 Parallel session--Developers: (Dave)
- Installation and configuration of SCIRun:
- system specs and requirements
- environment settings
- third party codes
- maintaining shared version
- creation and management of local source archives
- Overall design goals and future plans for PSE based
systems, Common Component Architectures, SCIRun2
|
- 11:30 Parallel session Users:
Design and implement an original network based on anticipated use
of BioPSE with the help of Center staff (Rob + Developers)
|
- 12:30 Joint Lunch
- 1:30 Developers Session
- GUIs: relationship between UI and algorithms, design of UIs
- Developer elements:
- source tree structure
- threads
- persistent I/O
- namespaces
- STL
- on-the-fly compile
- Contributing to SCIRun/BioPSE project
- patches
- modules
- documentation
|
- 1:30 Parallel session Users:
Continue to develop networks (Rob + Developers)
|
- 3:30 Joint session #3:
Discuss the experiences using BioPSE and the applications to which
participants wish to apply it. Focus on needs and extensions that
would enhance their effectiveness and generate a project list for
the final day of the workshop.
- 6:00 Depart for dinner
- 6:30 Group dinner
Drinks and hors d'oeuvres on the deck at Millcreek Inn, Millcreek
Canyon, then dinner served also on the outdoor deck. Cash bar
available.
The third day is dedicated to instruction of the developers in the details
of extending the capabilities of BioPSE/SCIRun and applying these new
skills to some of the problems generated in the previous day's session.
- 9:30 Pickup at University Guest House
- 9:45 Coffee
- 10:00 Project Discussion
Discuss project list from Day #2 and identify candidate
problems for discussion and implantation.
- 10:30 Making a module
- module design process
- role and contents of XML files
- pseudo code
- module maker: the process of creating and anatomy of a
module
- coding standards and conventions
- UI design and construction
- modifying ports and data types
- 12:30 Lunch
- 1:30-4:00 Design and implement projects: working in groups, carry
out the design process for some of the target modules identified
from Day #2 and earlier discussion with help of Center developers
- 4:00 End of Workshop
SCIRun/BioPSE Workshop
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