NCRR Meeting Notes
Wednesday, September 11, 2000, 1:00 pm
Rob MacLeod
With these meetings we hope to achieve the following goals
- Make sure all members of the NCRR group know each other
and are aware of both the long terms goals and the course of
progress of the projects.
- Report progress, present ideas, and
solicit feedback and ideas in front of the group.
- Constantly review and upgrade priorities of the various
projects and ensure that tangential concerns do not distract from
the progress of the group.
- Maintain momentum on the high priority projects.
- Meeting plan:
- Dave led a good discussion about how to maximize
the utility of the meetings and some comments include the
following:
- during the reporting round of the general meetings, do not
let the one-on-one discussion go on too long; on the other
hand, people should feel free to ask questions, even if
they may not obviously be of interest to everyone present.
The trick is to find the balance so that informal,
discussion is encouraged but that people come prepared and
try and keep the general discussion at a high level.
- identify sub groups who could better deal with specific
topics that come up in the general discussion; charge this
subgroup with developing the idea and reporting back to the
full group,
- when we have the program more fully developed, encourage
the people more involved in the research end to bring ideas
to the group and present then as proposed applications for
BioPSE; it is not required to have the implementation
developed, but rather than there be a research motivation
for some use of BioPSE,
- consider sessions dedicated to reviewing the state of
specific technical aspects that we wish to implement in
BioPSE; for example, someone might present the basic
strategy of a numerical approach and then outline how they
propose to implement that approach in BioPSE
The immediate plan remains to have every second meeting dedicated to
technical topics and alternate with general meetings. Please contact
Dave or Rob if you have any other suggestions for meeting content and
format.
- Greg is working on two different grant applications to NSF, once
for undergraduate fellowships and the other a project in imaging
with Bill Orrison.
- Utility and Image of SCIRun:
- we need to do a better job of
giving local software developers (e.g., SCI group grad students)
access to SCIRun and to make sure potential users are more aware of
the advantages. It is not necessary for everyone in the SCI group
to use SCIRun, but there are clearly others who could and yet do
not because of obstacles to easy use.
- User support with BioPSE:
- we talked about means of getting users
to register or somehow be counted when we release software.
The motivation for this includes:
- license requirements
- we would like to be able to broadcast information to all
BioPSE and map3d users
- we need to document the impact of our codes and hence count
users
- we would like users to communicate to each other and share
knowledge and ideas
- enter and track bugs
To achieve these ends, we envision some combination of a
registration process at download time, with a very clear
description of why we want to know, and a mailing list.
- Sourceforge:
- We are still waiting for final approval of the open
source agreement from the University Technology Transfer Office.
- Fields class:
- Michael will stabilize a version of the fields
class on a branch and anyone wanting to use the new classes should
work from that tree. Michael will send out email with directions
and instructions. We discussed once again the need to handle time
series of field attributes, an unresolved need. Michael will try
and implement a system in which we can store multiple attributes in
as flexible a way as makes sense.
- Directory structure:
- we had a long discussion about the
directory structure of the SCIRun code.
| Current directory structure |
| SCICore |
PSECore |
PSECommon |
SCIRun |
DaveW |
Yarden |
... |
| - low level libraries |
- mid level data flow functions |
- most
functioning
modules |
- a few modules |
- Dave's version of modules |
Yarden's
modules |
etc., |
The plans and problems with this include:
- Both ``cores'' are actually hierarchical; PSECore requires
SCICore.
- PSECommon is a name a number of people do not like; the
plan is to move everything from PSECommon to SCIRun.
- SCIRun is a directory at the same level as the others but
we want to reserve this name to indicate the entire system.
- Changing the structure and the names would require some CVS
juggling and that all users check their codes in and then
check them back our again; in the past, this has been a
fairly painful process. The ideal situation would be to
have the new versions of things appear as additions and
then to remove the old codes piecewise over time.
- Analytic field generator:
- Alexi is working on this.
- Module review:
- No module reviews at this meeting. The
assignment (note: assignment-no more Mister Nice-Guy!) is
to read the list of modules and come prepared with one to present.
The list is at
www.cvrti.utah.edu/~macleod/ncrr/technical/biopsenotes.html.
Please send email to the group once you select the module you would
like to adopt.
- Module ports :
- we again discussed generalizing the port
specification and creating smart ports that can handle different
data types. For more details on this,
see www.cvrti.utah.edu/~macleod/ncrr/technical/biopsenotes.html
- Scene graph:
- Marty had a question about deleting nodes from a
scene graph which sparked a discussion about the need to rework the
scene graph code and functionality. If anyone is willing to take
this project on, please let Dave know.
- Data flow code:
- Dave suggested that we need to rework the data
flow code and he described the following specific features:
- event manager
- module synching
- module interface and port structure
- network structure and management (pick up Nick Benson's
work)
- Upcoming conferences:
- Conferences coming up that are of special
relevance to the group include:
- Biomedical Engineering Society (BMES): October 12-14, 2000
in Seattle (Rob will be chairing a session).
www.engr.washington.edu/~uw-epp/bmes/
- Visualization 2000: Oct. 09, 2000 - Oct. 13, 2000, Salt
Lake City.
- 7th International Conference on
Numerical Grid Generation in Computational Field
Simulations: September 25-28, 2000, Whistler, British
Columbia, Canada. We would like to send Xinlong to this,
but are not sure if he will be here in time. Xinlong will
attend this conference and present a paper from Dave et al..
- NFSI III: September, 2001, Innsbruck, Austria
www-db.tu-graz.ac.at/nfsi2001
- NCRR Seminars
-
- Tom Feree from U of Oregon has postponed his visit
because of an emergency and will reschedule as time
permits.
- Martin Schweiger from Simon Arridge's lab in London,
England is with us again and we will ask him to present an
NCRR seminar. This project involves diffuse optical
tomography. Chris J. will be the contact on this visit.
Documentation
- New SpecML:
- Ted has finished and the doc group approved a new
SpecML document format to make it simpler and easier to use.
Marty is working on a document that describes using the new spec
template.
- Doc Link:
- The new link for all the BioPSE docs is
www.sci.utah.edu/scirun_docs/doc.
- Doc styles:
- Erik has made a document describing how to use his
style sheets to make consistent documentation. To try this out, go
to www.sci.utah.edu/scirun_docs/doc/ReferenceGuide/doc_markup.html
- Map3d progress:
- Rob, Chris, and now Guo are all working on
getting the version 1.0Beta of map3d ready for placement on the
website.
- License:
- Greg will look into the details of the
options that University already has in place (if any) for this type
of license.
- Xinlong Wang:
- came to the meeting today for the first time. He
has met with Dave and Rob about meshing needs and we will have a
meeting later this week to talk more about how he should proceed.
- Dave:
- has the computation of conductivities working on realistic
geometries going, albeit fairly slowly still.
- Laura's project :
- working with her new dataset from Dave.
- Chris Butson's project:
- no update
- Leah's project:
- is working on some code to parse equations and
asked for any pointers.
- Rob v. Uitert:
- has a formulation for new edge elements he is
using.
- Darby:
- is new to the NCRR group and is busy learning about the
code and how to check it out and use it.
- Data archive:
- Erik has put some of this together and needs to
get some data from Rob.
- BioPSE logo:
- Erik showed Rob a new logo and we will review this
and bring it to the group soon.
- Priorities:
- Erik asked about priorities for the next while and
we decided on:
- page for downloading map3d with user registration
- page for the NCRR data archives
- SCI website reconstruction
- no news
Agenda for for future meetings
Specific agenda items for the next meeting include:
- Update on NCRR seminar speakers and scheduling their talks
- Schedule for NCRR meetings
- Ted and Marty's presentation of the XML module template and tools for
editing and viewing them
- Eric's presentation on Field Class
- Event manager for BioPSE
- Installation of BioPSE
Most of the next meetings will be organized around the brief reports from
all present and then discussion of modules. Each person in the group has
volunteered for one more more modules and will lead the discussion, which
will center on the design and capabilities of the module. For details on
the overall layout of modules and a list of BioPSE modules we have
envisioned so far, go to
www.cvrti.utah.edu/~macleod/ncrr/technical/modules.shtml
NCRR Meeting Notes
Wednesday, September 11, 2000, 1:00 pm
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