Interdisciplinary Scientific Visualization

ASSIGNMENTS
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previous years:  2004* 2003 2002* 2000 1999
* VR Design for Science. Brown/RISD class. Now CS137

Brown          Brown CS          Brown CS Visualization

All handins are due by 10AM the same day of class to allow for review before class.

Please get your reviews and readings done in time. The whole point of the class is to get different points of view for interdisciplinary research problems. It'll make classes much more fun if everybody participates and has an opinion. It's not fair to others to make them always carry the weight of leading the discussions. Prepare for a dynamic and open discussion in almost every class.

Handins are to be made online (logged into a machine in the CS department) to a directory on the CS department machines. You must have a CS account to do this, so please make sure that you get an account the first day of classes. Talk to David and sign up for an account the first day of classes, Tuesday 9/6 at 1:20pm. You can also email Daniel Acevedo (daf@cs.brown.edu) or David Laidlaw (dhl@cs.brown.edu), but you will need to pass by David's office to get the temporary password for your account. They cannot be emailed outside CS.

When you are logged in to a CS machine (in the Sun lab, for instance, or over the network), you can deliver assignments to:

     /pro/web/web/courses/cs237/assignments/DATE/LOGIN.EXT

where you replace DATE with the due date (e.g., 9-7), LOGIN with your CS login (e.g., dhl), and EXT with the type of file (e.g., txt). If multiple handins are due the same day, please number them (e.g., dhl1.txt, dhl2.txt). For handins the first week, those without CS account can e-mail their handins to daf@cs.brown.edu and he will put them into the appropriate assignments directory.

IMPORTANT NOTE!!! Some of the readings needed for the class are PASSWORD PROTECTED due to copyright issues. Make sure to contact Daniel Acevedo (daf@cs.brown.edu) or David Laidlaw (dhl@cs.brown.edu) to get the username and password THE FIRST DAY OF CLASS.

Visit the first 2 links in the links page if you are not familiar with UNIX.

Almost all of the readings we will do are online to reduce copying effort and costs, and to keep color imagery intact. Printing them for your own use is fine. Please look at the color images in color, though! Some of the files are huge (40-50 Mb). You will not be able to get them over a phone line.

Please respect the grant proposals you will be reading. They are not published documents and should not be circulated outside of class. Please make sure that you destroy any copies of those documents when you are finished with them for class.

Due on Thu 9/8/05

If you don't already have one, make sure you are signed up to get a CS computer account! Contact daf@cs.brown.edu.
Hand in (by 10AM Thursday!): personal background
Read, with an eye toward your essay (see below):
Hand in by 10AM Thursday: an essay, 250-750 words, describing three visualization research topics of interest to you. Base the topics on the readings. For each topic, explain your motivation and how it fits in (or doesn't) with all of the readings.

Due on Tue 9/13/05

These readings will give you a feel for what goes into a research grant proposal.

The NSF Grant Proposal Guide (2004) describes how to write a grant proposal. While some of the instructions are specific to NSF, much of the document gives good advice on how to write any proposal.

Here's another shorter document from NSF you must read. It gives some guidelines for proposal writing.
Read a Program Announcement. Typically, NSF accepts both unsolicited grant applications (for whatever a proposer thinks is worth doing) and solicited applications. Applications are solicited via a Program Announcement (PA), sometimes called a Request for Proposals (RFP). The NSF Information Technology Research (ITR) Program Announcement gives one example of what they are looking for.
Read proposal Understanding Unsteady Bioflows through Simulation, Modeling, Visualization, Art, and Psychology (Laidlaw, Swartz, Lauder, Karniadakis, Richardson, Breuer, Tarr, Warren, Drury). This is a proposal in response to the ITR solicitation. It was successful and was partially funded September 2004. You don't need to understand all, but try to get the big picture as an example of a multi-disciplinary research project.
Hand in by 10AM Tuesday: your review
Read NSF reviews of the proposal (after you write yours) and add any new discussion questions to your review.
Hand in a list of four possible collaborators from class or from other disciplines for your class project. Read the RFP for class projects to understand more about the criteria for judging a project idea. Possible collaborators can be from the class, the list of project ideas suggested by various researchers around campus, and any personal contacts you have. Describe the discipline of each possible collaborator and how it is distinct from your area. At least two must be contributors to the list of project ideas or established researchers.

You will need to meet with at least three of the four possible collaborators and report on those meetings on 9/20. These meetings will help you develop the interdisciplinary par project. Get started scheduling these meetings and look at what you'll need to hand in as a report.

Due on Thu 9/15/05

Read Shape Capture and Modeling for Wrist Dynamics and Ancient Pottery Analysis using Manifold Surfaces and Signed-Distance Volume Images (Laidlaw). This is a second example of an interdisciplinary visualization proposal. The application areas are quite different and the proposal is more focused on visualization. Skim the whole proposal, then read the Project Summary and Project Description.
Write: your own review. Do the review before reading the NSF reviews, and then answer the subsequent questions after the other readings.
Read NSF reviews of the proposal (after you write yours) and add any new discussion questions to your review.
Read: annual status report to NSF. Once again, this gives a feel for what NSF is interested in.

Continue interviewing possible collaborators.


Due on Tue 9/20/05

Hand in interview reports.
Hand in at least three possible proposal titles. For each, include a brief description, a list of participants, and your evaluation of the proposal you imagine. Use the RFP to guide your project ideas and to self-evaluate them.
Past proposals for the class can be found in the Ideas page. Two good examples are Danah Beard's 1999 Analysis of Depth Cues project (includes presentation) and Mike Kirby's 2000 Optimal Vector Placement User Study project.

Due on Thu 9/22/05

NIH guide to proposals -- read the interesting and relevant parts.
Review and discuss NIH grant DTI+MRI-based Tools for Analyzing White Matter Variation (Laidlaw, Ahrens, Allman, Bastin)
Read NIH reviews of the proposal (after you write yours) and add any new discussion questions to your review.

Due on Tue 9/27/05

Hand in results from literature search. You should this search on the project you are most seriously considering doing out of all the ideas you have. Look here for links to research publications.
Review the table of contents for the upcoming book Visualization Handbook. For the class, try to see if the topics in the book suggest some extra readings related to your project. Are there any new ideas in there for a different project? The authors are in there also, and these are all the big guys in sci-viz, so google for their web pages and see what other stuff they are working on.
THE BOOK IS ON RESERVE AT THE SCIENCES LIBRARY! Read through it for interesting articles!
You will schedule your meeting with the rethoric fellow to go over your proposal presentation. Please bring your calendars to class !!
Continue developing your project proposal, filling in any weaknesses, fleshing out the related work section, etc.
Be prepared to briefly describe the project idea you are most seriously considering and any issues, concerns, problems, etc. that we can discuss in class.
 
Due on Thu 9/29/05

Quantitative inverse electrocardiography. This proposal is more than 15 years old, so the work is not current. It does show an excellent example of a successful non-clinical NIH grant proposal. Non-clinical work is often quite difficult to get funded by NIH. Note the structure of the proposal, with well-formulated hypotheses to test.
Read partial list of resulting papers
Read R.S. MacLeod, C.R. Johnson, and M.A. Matheson. Visualization of bioelectric fields. IEEE Computer Graphics and Applications, pp. 10-12, July 1993.
Read this PowerPoint presentation about the NIH proposal review process.
Daniel will explain how to make your reading lists in VISWEB. Take a look at this document and print it out before class. You don't need  to do anything with it before the class, just read over it and bring it to class.

Due on Tu 10/04/05

Preliminary proposals due in paper. Proposal presentations in class. Present your Visweb reading list with your related publications.

Due on Th 10/06/05

Proposal presentations in class (cont.)
Due on Tu 10/20/05

Submit a list of 6 papers from the "cs237 interesting papers" list. From that list we'll choose two papers for you to present in class in the following weeks. For each paper indicate:
- Title
- Preference value (1-6 among your six papers. Don't repeat values!)
- Reason why you want to present it.