CS237: Interdisciplinary Scientific Visualization

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How to Hand Stuff In

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. A significant aspect of the class is to get different points of view for interdisciplinary research problems. It'll make classes much more fun and valuable if everybody participates and expresses 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. If you don't have one already, please make sure that you get an account the first day of classes. David or Steve may need to provide the password by phone or in person -- emailing passwords isn't allowed.

If you're not familiar with the CS file system or basic Linux commands, like moving files, please talk to Steve after the first class for help getting up to speed. When you are logged in to a CS machine (in the Sun lab, for instance, or over the network), you can deliver assignments to:


where you replace the_date with the due date (e.g., 9-11), your_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 accounts can e-mail their handins to steveg@cs.brown.edu and he will put them into the appropriate assignments directory.

How to Read Papers and Proposals

Some of the readings needed for the class are password protected due to copyright issues. These links will appear styled like this, as opposed to the public links. The user/pwd is specific to the Vis group website (VisWeb); it is not the same as your CS account. Make sure to contact Steve (steveg@cs.brown.edu) or David (dhl@cs.brown.edu) to get the username and password if you forget it (we'll give it out the first day of class).

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 pretty big (40-50 Mb).

Finally, 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.


Week 1 (back to top)

Date & Topic Assignment

First Class: Thu 9/4


  • Goals
  • Organization
  • Schedule
  • Definition of Visualization

To Do
  • Sign up for a CS account
  • Join the cs237 Google Group. Make sure your settings allow you to receive messages by email. This will be the primary mailing list for the class!
  • Email Steve a small photo of yourself to include on the website

Week 2 (back to top)

Date & Topic Assignment

Tue 9/9

  • Open problems in Visualization
  • What makes a good problem?

Read before class, with an eye toward your essay:

Deliverables (10am)
  • Personal background handed in as yourLogin.txt
  • A fictional essay, 250-750 words. The setting is 5-20 years in the future, and the story should describe how cs237 influenced that future you. In particular, it should describe a plausible way that you will have solved or addressed one or more of the visualization research topics from the readings. Hand in as yourLogin2.txt, as described for personal background handin.

Thur 9/11

  • Review and discuss NSF ITR proposal:
    Understanding Unsteady Bioflows through Simulation, Modeling, Visualization, Art, and Psychology (Laidlaw et al.)
  • Evaluating project possibilities

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

Deliverables (10am)

  • Hand in your own review for the ITR grant as yourLogin.txt
  • Hand in a list of four possible collaborators for your class project as yourLogin2.txt. The collaborators can be from class or from other disciplines. The RFP for class projects will help you 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.

Collaborator's list - You will need to meet with at least three of the four possible collaborators and report on those meetings on 9/18. These meetings will help you develop the interdisciplinary part of the project. Get started scheduling these meetings and look at what you'll need to hand in as a report. Coordinate with other class members for interviewing to avoid duplicating collaborator effort.

Week 3 (back to top)

Date & Topic Assignment

Tue 9/16

  • Review of NSF CAREER proposal Shape Capture and Modeling for Wrist Dynamics and Ancient Pottery Analysis using Manifold Surfaces and Signed-Distance Volume Images (Laidlaw)
  • Evaluating project possibilities
Reading Deliverables (10am)
  • Write your own review (using this form) of the CAREER proposal and hand it in as yourLogin.txt. Do the review before reading the NSF reviews.
  • Continue interviewing possible collaborators.

Thur 9/18

  • VR demos in the old Cave
  • Discuss project ideas

Note: Class will meet at the Cave in the Granoff Center, Studio 4

Reading Deliverables (10am)
  • Interview reports as yourLogin.txt
  • Three possible proposal titles as yourLogin2.txt. 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.

Week 4 (back to top)

Date & Topic Assignment

Tue 9/23

  • Review and discuss NIH proposal
    Quantitative Inverse Electrocardiography (Johnson)
  • Read Quantitative inverse electrocardiography (Johnson). 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. Skim the whole thing and read the four sections starting with Specific Aims.
  • Read partial list of resulting papers
  • Read Visualization of bioelectric fields, MacLeod et al.
  • Read NIH guide to proposals, focusing on the specification of a proposal (pg. 1-16), research plan details (pg. 17), review criteria (pg. 34), and other interesting and relevant parts you find
  • Read this PowerPoint presentation about the NIH proposal review process
Deliverables (10am)

Thur 9/25

  • Review and discuss NSF proposal
    Development of a Next-Generation Interactive Virtual-Reality Display Environment for Science (Laidlaw et al.)
  • Visit the YURT at the end of class

Note: Class will meet in CIT 506

Reading Deliverables (10am)

Week 5 (back to top)

Date & Topic Assignment

Tue 9/30

  • Cave (vrg3d) sample code walkthrough
  • Visualizing multi-dimensional data

Slides about the Cave demo app are available here

  • Read Visualization Handbook's table of contents. For the class, see if the topics in the book suggest some readings related to your project. Are there any new ideas in there for a different project? Google for the authors' web pages and see what other stuff they are working on. If you're interested in reading more, the book is available at the Sciences Library (SciLi).
Deliverables (10am)

You should do 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. 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.

Thur 10/02

  • Proposal presentations
Deliverables (10am)
  • Preliminary proposal handed in as yourLogin.pdf
  • A template for your proposal can be downloaded here. See the README inside for more instructions.
  • Presentation slides handed in as yourLogin_slides.pptx or pdf

Make sure your proposal is saved as a pdf. Put the presentation (PowerPoint or pdf) in the submission folder and make sure it is readable to others. We will log into one account and run all the presentions from there.

Week 6 (back to top)

Date & Topic Assignment

Tue 10/07

  • Proposal presentations

Thur 10/09

  • Improving proposals and examples
    • "Walking > Walking-in-Place > Flying"
    • Evaluating visualizations

Links to papers for in-class activity:

Reading Deliverables (10am)
  • Review the first-draft proposals assigned to you. Use a separate form for each review you write, and name the file proposer_by_reviewer.txt when you hand it in. For instance, if Steve reviews David's proposal, he should hand in a file called dhl_by_steveg.txt.

Week 7 (back to top)

Date & Topic Assignment

Tue 10/14

  • Walkthrough of a project budget
  • Insight-based evaluation: what is it, and should you use it?

Link to paper for in-class activity:

Deliverables (10am)
  • Final proposal handed in as yourLogin.pdf

Thur 10/16

  • Study section (evaluate, score, "fund" proposals)

Link for in-class activity:

  • Table of linked reviews and NIH-style proposal scores: here

Reading Deliverables (10am)
  • Review the final proposals assigned to you. For the final proposals, you only need to hand in reviews for the two proposals where you are R1 or R2. You must read the proposals for which you are R3/R4 and be prepared to discuss them in class. Use a separate form for each review you write, and name the file proposer_by_reviewer.txt when you hand it in. For instance, if Steve reviews David's proposal, he should hand in a file called dhl_by_steveg.txt.
  • Respond to the quick questions in this form as yourLogin.txt

Week 8 (back to top)

Date & Topic Assignment

Tue 10/21

  • Week 1 check-in on projects
  • Teams sketch methods and results on whiteboard
Deliverables (10am)
  • Hand in a summary statement on your "Primary" proposal. Try to capture all the discussion points for the proposal. The length should be however long it takes for you to adequately summarize the discussion. Name the file proposer_by_yourLogin.txt.

Thur 10/23

  • Groups finish sketching methods and results on whiteboard
  • Students annotate other project sketches

In class, we'll look at the whiteboard project sketches together and everyone will get a chance to add questions and other feedback for each project.

Week 9 (back to top)

Date & Topic Assignment

Tue 10/28

  • Week 2 check-in on projects
  • Review VIS 2014 program
    • Keywords, topics in VIS papers
  • Finding related work

In class, we will split into groups and find related work for the "funded" projects.

Thur 10/30

  • Guest: Ryan Boller
    • Life after CS237
    • Iterating from class project to publication
  • Finding related work (cont.)
Reading Deliverables (10am)
  • Bring three (3) questions to ask Ryan during class

Week 10 (back to top)

Date & Topic Assignment

Tue 11/04

  • Week 3 check-in on project schedules
    • What is going well?
    • Challenges and questions

In class, we'll look at each group's project schedule.

Thur 11/06

  • Web-based vis and toolkits
  • Brain connectivity demo

In class, we will review visualization methods provided by popular toolkits and systems. We will have an in-class demo by Ph.D student Hua Guo of a web-based visualization built with the d3.js library. These tools might be of use to you for your projects, or for future visualization development.

Week 11 (back to top)

Date & Topic Assignment

Tue 11/11

  • No Class! IEEE Visualization Conferences in Paris
  • Start the CITI online course, which will certify you to perform "human subjects research", like user studies, at Brown.

Thur 11/13

  • No Class! IEEE Visualization Conferences in Paris
Deliverables (10am)
  • Finish the CITI online course and send your passing Completion Report (pdf) to the TA. If you do not pass on your first try, you must retake the quizzes until you receive a passing grade.

Week 12 (back to top)

Date & Topic Assignment

Tue 11/18

  • Week 5 check-in on project schedules
    • What is going well?
    • Challenges and questions
  • Reading VIS 2014 papers

In class, we will quickly read and evaluate recent visualization papers from the 2014 IEEE visualization conferences.

Thur 11/20

  • Reading (and re-writing) papers

In class, we will split into groups and re-write the abstracts of papers to improve them.

Week 13 (back to top)

Date & Topic Assignment

Tue 11/25

  • Week 6 check-in on project schedules
    • Discussion of final plans for projects
    • Remaining challenges and questions
Deliverables (10am)
  • Bring in your schedules for the final 2 weeks. Project groups will have time to update the class about progress.
  • Start your presentations. Next week, we'll have a dress rehearsal for final presentations. Look ahead in the calendar for more info about our expectations.

Thur 11/27

  • No Class. Happy Thanksgiving!

Week 14 (back to top)

Date & Topic Assignment

Tue 12/02

  • Class review forms to be filled out
  • Research abstracts: what to report and how much?

In class, we will look at examples of successful two-page research abstracts.


Thur 12/04

  • Presentation Dress Rehearsal!

In class, each group will deliver a 5-6 minute presentation about its project.

  • The 'audience' will have 2-3 minutes to ask questions after each talk. You should practice your presentation before class at least three times; remember to focus on contributions and results, and don't go over 6 minutes. We will critique presentations as a class in preparation for the public final presentations.
  • Use the feedback you receive in class to revise your final presentation.
Deliverables (10am)
  • Hand in a pdf of your slideshow (one per group). Name the file login1_login2.pdf corresponding to the group members.

Finishing Up (back to top)

Date & Topic Assignment

Tue 12/09

  • Final Project Presentation
  • Lubrano, 1:00-2:30pm
Present your Final Project and Results
  • Before class time (1pm), hand in a pdf of your slideshow (one per group). Name the file login1_login2.pdf corresponding to the group members.
  • Plan for 5-6 minutes of presentation. You will have access to a large display/projector to present your slides. You will have an few minutes after your talk to answer questions from the audience.

Wed 12/17

  • Final Reports Due
Hand in Final Report
  • By the end of the day (11:59pm), hand in a two-page extended abstract (pdf) for your project as yourLogin.pdf. For groups, each student must write his or her own report, in which s/he is listed as the first author and the other group members as co-authors.
  • Your abstract must match the formatting requirements for our class "proceedings". Templates for Word and latex can be downloaded here. See the README inside for more instructions.

If you're wondering, here's what we did last time: (2012 calendar)