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CSCI2370: Interdisciplinary Scientific Visualization (fall 2022)
Calendar

How to Hand Stuff In

How to: We use a shared Google Drive folder to manage homeworks and some other shared resources. If you haven't been added to it, please send David_Laidlaw at brown.edu email with your brown email address.
Inside the folder, you will deliver your assignments to the subfolder the_due_date/yourBrownShortID.ext.
For example, David could upload his first assignment to foler 09-14 as file dhl.txt.

Due: All handins are due by 9AM 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.

How to Read Papers and Proposals

Some of the readings needed for the class are password protected due to copyright and privacy 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 the instructors 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. 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.

Calendar


Week 1 (back to top)

Date & Topic Assignment

Thu 9/8, 2022

Introduction

Logistics

  • Make sure the course is in your Banner shopping cart before Friday!!!

Week 2 (back to top)

Date & Topic Assignment (due before this class)

Tue 9/13, 2022

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

Logistics

  • Send David (David_Laidlaw at brown.edu) a small photo of yourself to include on the website.
  • Make sure you can use the shared google drive. Email David if you need help.

Reading

Read, with an eye toward your essay (below) and also to discuss in class:

Deliverables (9am)

  • Personal background handed in as yourBrownShortID.txt
  • A fictional essay, 250-750 words. The setting is 5-20 years in the future, and the story 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 yourBrownShortID-2.txt, as described for personal background handin. I'm not looking for mentions of the course or tributes, I'm looking for concrete, creative ideas about how these challenges might be solved.

Thu 9/15, 2022

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

Reading

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

Deliverables (9am)

  • Hand in your own review for the ITR grant as yourBrownShortID.txt
  • Hand in a list of three possible collaborators for your class project as yourBrownShortID-2.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 possible collaborators and report on those meetings on 9/27/2022. 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 and David for interviewing to avoid duplicating collaborator effort. David would like to be present at the first meeting with each collaborator as a mostly-silent facilitator, but don't delay.


Week 3 (back to top)

Date & Topic Assignment

Tue 9/20, 2022

  • Visit by collaborator Ryan Cabeen. He will be available to interview regarding his project idea on the "ideas" page.
  • 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 (9am)

  • Write your own review ( using this form) of the CAREER proposal and hand it in as yourBrownShortID.txt. Do the review before reading the NSF reviews.
  • Continue interviewing possible collaborators.

Thu 9/22, 2022

  • Discuss project ideas

Reading

Deliverables (9am)

  • Three possible proposal titles and summaries as yourBrownShortID-2.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. Clearly identify the research contributions.

Week 4 (back to top)

Date & Topic Assignment

Tue 9/27, 2022

  • Review and discuss NIH proposal Quantitative Inverse Electrocardiography (Johnson)
  • Discuss interviews
  • Proposal needs?
  • Scoring second proposal idea

Reading

  • Read Quantitative inverse electrocardiography (Johnson). This proposal is more than 25 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 Visualizing bioelectric fields, MacLeod et al. (sorry about the pictures...)
  • Read NIH guide to proposals, skimming over the structure of a submission (pg. 1-15), then focusing on the research plan details (pg. 15-18), review criteria (pg. 34), and other interesting and relevant parts you find.
  • Read this PowerPoint presentation about the NIH proposal review process

Deliverables (9am)

Thu 9/29, 2022

  • Comparing project ideas
  • Searching literature for related work
  • Review and discuss additional NSF proposals
  • Visualizing multi-dimensional data

Reading

Deliverables (9am)

  • A list of at least five interesting and reaonably rich sharable observations for the class. Hand in as usual. Do not duplicate observations already handed in. I suggest editing your observations in the handin directory to avoid duplication. If you have less rich observations, include more!

Week 5 (back to top)

Date & Topic Assignment

Tue 10/4/2022

  • Visualization tools
  • Paraview volume rendering
  • Proposal challenges

Reading

  • 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 may be available at the Sciences Library (SciLi) -- it was at some point :-). Some chapters are likely available online. Many topics will have Wikipedia pages or other tutorial-level pages that will help you become visualization experts.
  • Read The Value of Visualization, and The Value of Infovis. Look for ways to understand and motivate the contributions of your proposed projects. Can you find papers that cite these that are helpful? This could lead to some things for your literature review and related work sections.

Deliverables (9am)

  • Hand in results from literature search as yourBrownShortID.txt

    • You should do this search on the project you are most seriously considering doing out of all the ideas you have. Google Scholar is the main place to search for research papers, but there is a list of other options here (Question 3 Where do I search for research papers?). 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.

  • The first item in your literature search should be the paper you think would be most valuable for the class to all read and discuss. Clearly label it as such.
  • Install Paraview on your computer from the first step in the tutorial. Also download the tutorial.vtk file. Bring to class.

Thu 10/6/2022

  • more "Visualization Handbook"
  • citing related work

Reading

  • Read the top papers listed in four of your co-students' literature review handins from last class. Choose the papers of the four students following you in this alphabetical list, wrapping back the beginning if appropriate: James (sli64), Josh (jkruzan), Luca (lfonstad), Naomi (nlee16), Patrick (prmaynar), Shashidhar (spai9), Shixuan (sli221), Yuxuan (yzhao153). Make a list of three discussion observations or questions for each paper, just as you did for the three proposals last week. Consider how your observations or questions can help the proposal author. You should be focused on finishing your proposal drafts, so if you need to do these readings quickly that is ok.
  • entire Visualization Handbook for your perusing/skimming pleasure.

Deliverables (9am)

  • Preliminary proposal handed in as yourBrownShortID.pdf. This should be a full draft, ready for comments by peer reviewers.
  • A template for your proposal can be downloaded here. See the README inside for more instructions. The overleaf read-only repos can be found at proposals and final reports.
  • Be sure to follow the instructions in the RFP

    • Make sure your proposal is saved as a pdf.


Week 6 (back to top)

Date & Topic Assignment

Tue 10/11/2022

  • Proposal presentations, 5 minutes each + 5 discussion, alphabetical order by first name

Reading

  • Read proposals from the shared Google Drive folder

Deliverables (9am)

  • Presentation slides handed in as yourBrownShortID_slides.pptx or pdf. David *much* prefers pptx with all videos and images embedded in the file. Google slides is not ok... (you can create in it, but convert and submit as pptx and make sure that everything plays correctly without the presenter being you.
  • Proposal review assignments are
  • Reviews of the first-draft proposals assigned to you. You are assigned the four proposals following you in the alphabetical list that do not have you as a co-pi. 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 David reviews Ugur's proposal, he should hand in a file called ugur_by_dhl.txt. Review assignments and roles are made explicit in "this spreadsheet". Each proposal is listed with the PI and Co-PI under the "Role" column. That column also shows a "1" for the primary reviewer, a "2" for the secondary reviewer, and a "3" for any tertiary reviewers. At the study section the primary reviewer will summarize the proposal and the factors that influence their scores. The other reviewers will add any additional factors that influenced them.

Thu 10/13/2022

  • Improving proposals and examples
    • Insight-based evaluation: what is it, and should you use it?
    • Evaluating visualizations
    • Response to reviewers

Reading and Revising

Deliverables (9am)

  • Your response to reviewers document. It should be the first part of the final proposal that you hand in next week, and the handin today should also include the preliminary proposal. The response should include all the reviews, with each review point responded to following the point. Distinguish the review text from the response text -- indent one or italicize one, etc. Numbering the individual responses or the comments can help in referring back to something that was commented on and addressed in an earlier part of the response. The response should not debate the comment, it should explain how the final proposal has been changed to address the comment. (Or how it will be changed -- the changes don't have to be made yet.) This is the first time for these responses, so please ask if it's not clear what to do.

    Please refer to this example of a response-to-reviewers document. It is for a paper rather than a proposal, but it should give some idea of what to aim for.


Week 7 (back to top)

Date & Topic Assignment

Mon 10/17/2022

    Not a class; stuff due MONDAY!!

Deliverables (9am)

  • Final proposal handed in as yourBrownShortID.pdf
Date & Topic Assignment

Tue 10/18/2022

  • Study section (evaluate, score, “fund” proposals)
  • IEEE Visualization Conference online (David remote in zoom "laidlaw")

Link for in-class activity:

  • Table of linked reviews and NIH-style proposal scores: {TBD}

Reading

  • Read final proposals from the shared Google folder

Deliverables (9am)

  • Review the final proposals . 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 David reviews Ugur's proposal, he should hand in a file called ugur_by_dhl.txt.
  • Respond to the quick questions in this form as yourBrownShortID.txt

Thu 10/20/2022

  • NO CLASS -- IEEE Visualization Conference



    Week 8 (back to top)

    Date & Topic Assignment

    Tue 10/25/2022

    • IEEE Visualization Conference review

    • Work on projects

    Thu 10/27/2022

    • Week 1 project updates

      Deliverables (9am)

    • Be ready to explain and discuss your project progress with others in class. A Gantt chart can be a good way to show/explain progress.

    Week 9 (back to top)

    Date & Topic Assignment

    Tue 11/1/2022

    • Where would your project fit at the conference?
    • Review VIS 2021 program
    • Relate your project to the VIS conference
    • Work on projects.

    Thu 11/3/2022

    • Week 2 project progress reports.
    • Paper contributions.
    • Prepare week 2 project progress reports.

    Week 10 (back to top)

    Date & Topic Assignment

    Tue 11/8, 2022

    Election Day, No Class.
    Vote!

    Thu 11/10, 2022

    • Week 3 project progress reports.
    • Prepare week 3 project progress reports. Be sure to include a list of the research contributions that your final paper will have and the evidence of those contributions. These should be similar to the research contributions from Vis Conference papers that we listed on the board in class. Images of the board and notes from that class on 11/1 are in the shared google doc https://tinyurl.com/mr3y5uby

    Week 11 (back to top)

    Date & Topic Assignment

    Tue 11/15/2022

    • Vis 2022 paper evaluations

    Thu 11/17/2022

    • Week 4 project progress reports.

    • Prepare week 4 project progress reports.

    Week 12 (back to top)

    Date & Topic Assignment

    Tue 11/22/2022

    • No class. Happy Thanksgiving!

    Thu 11/24/2022

    • No class. Happy Thanksgiving!

    Week 13 (back to top)

    Date & Topic Assignment

    Tue 11/29/2022

    • Week 5 project progress reports

  • Prepare week 5 project progress reports.
  • Include a "cartoon" version of your results section. That includes sketches of visuals, graphs, and any other results that will make the contributions clearer. Each of these is a "panel" for your cartoon results. These should all be placeholder visuals or graphs where you make up some plausible results. Label axes, include legends, and make each panel as complete as you can. At the same time, don't fuss about visual perfection. Bonus points for sketchiness, hand-drawn, quickly produced versions. Content over format! Make sure that the captions for those make clear what the audience should be able to see (eventually) in each panel. And make sure that all contributions are represented in the set of panels.

    • Thu 12/1/2022


    Week 14 (back to top)

    Date & Topic Assignment

    Tue 12/6/2022

    • Week 6 project progress reports

  • Prepare week 6 project progress reports.

    • Thu 12/8/2022

    • Ultimate class
    • Presentation Dress Rehearsal!

    In class, each project group will deliver a 6 minute presentation about their project. This is a dress rehearsal for the final presentation on 12/14.

    • The audience will have 5-10 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 time. We will critique presentations as a class in preparation for the public final presentations.
    • Use the feedback you receive in and after class to revise your final presentation.

    Deliverables (9am)

    • Hand in a pptx of your slideshow (one per group). Name the file login1_login2.pptx corresponding to the group members.

    Feedback on other reports (11:59pm)

  • Provide email feedback about the other four projects to the author(s) and David. Aim for suggestions that could be handled in the remaining few days, thoughts on what worked, or lessons that the authors could take with them for future projects.

    • Weeks 15-16 (back to top)

    Date & Topic Assignment

    Wed 12/14/2022, 2pm (or possibly 4pm)

    • Final Project Presentation
    • Final Project Draft Reports

    Present your Final Project and Results (2pm)

    • Before the presentation slot, hand in a pptx of your slideshow (one per group). Name the file login1_login2.pptx corresponding to the group members.
    • Plan for a maximum of 6 minutes of presentation. Each group member should present some part of the work. You will have a few minutes after your talk to answer questions from the audience.
    • By midnight, hand in a draft two-page extended abstract (pdf) for your project as yourBrownShortID.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. Please use the finalReport templates. See the README inside for more instructions. Referense may continue onto a third page.

    Mon 12/19/2022

    • Final Reports Due

    Hand in Final Report (11:59pm EST)

    • By the end of the day, hand in a two-page extended abstract (pdf) for your project as yourBrownShortID.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. Please use the finalReport templates. See the README inside for more instructions. Referense may continue onto a third page. P.S. the link here is the same as the link for your draft submission.
    If you're wondering, here's what we did last time: (2021 calendar)