Plans and Goals/Fall 2008

Andy

1. Run flowviseval and complete IEEE Vis submission before Nov 1.
2. Co-author NIH grant on new biology research tools
3. [probably] Spend some time working with Huffman and Bradley and others planning improvements to $G
4. Brain project
5. Work with David to identify candidates for new research projects

Brad

1. make research group more productive -- products are
   1. knowledge created
   2. knowledge disseminated
   3. publications published
   4. publications downloaded and cited
   5. code created to make publications
   6. code used by close collaborators
   7. code downloaded (perhaps by and used by outsiders)
   8. group overhead reduced
   9. knowledge created, disseminated, made impactful
2. have work be focused on specific funded grants
3. work independently
4. provide sw engineering help and support to individuals in the group
5. A+: get wrist distance-map tools usable by Trey's group, Evan in particular
   1. registration code broken (manifolds issue)
   2. ligament length code broken (probably manifolds again)
   3. get manifolds into the fold; work from Cindy's source control?
6. A: understand why Evan had to copy code rather that using our source within source control
7. A: help direct Sidra and Wudan to improve visweb
   1. define some google analytics goals and track our performance on them (high time on page, low exit rate, visit download pages, visit other target pages)
   2. update site to improve those metrics, e.g., images not getting well indexed by google because of link structure
   3. review Daniel Acevedo's web e-mail feedback for ideas
   4. focus on brain or wrist to preserve allocability, but make globally useful
   5. better availability of talks and videos that we make
      1. many ppt's already around -- could be videos with a narration
      2. a number of full videos already around, some on web, but not easily found
      3. streaming video server?
      4. put things on utube or other distribution sites?
   6. create a plan to make available brain diffusion imaging data (perhaps coupling to an existing NIH-funded site)
      1. be general enough to also support wrist data, gene data, proteomics data, etc.
   7. is there any kind of "push" technology for sending papers to lists or individuals (spam...)
8. A: shift to more principled software development
   1. do so incrementally to preserve existing knowledge of users and existing code
   2. bug tracking system?
   3. determine some principles for sw
      1. main shared $G is read only
      2. explicit writable checkouts by default instead of implicit
      3. all sw components have tests
   4. nagging scripts
      1. code checked out too long
      2. missing tests
      3. failing tests
      4. regular tests of outside infrastructure (net flakiness, disks filling up, etc.)
   5. address missing tests, etc
   6. better solution for linux compiler versions
      1. don't break windows and other platforms
      2. get off g++/gcc 2.95
      3. have some better mechanism for transitioning to future compiler versions
   7. better documentation setup and documentation
      1. for sw development
         1. guidelines for quick prototyping
         2. guidelines for interfaces for distributable algorithms (e.g., segmentation, ITK?)
         3. goals for full applications that will be shared
      2. for paper production
      3. for running computational experiments (tool development, prototyping, testing)
      4. for production-oriented data-driven work (tool production use, e.g., wrist data, brain data)
      5. for hardware resources (wheatstone, cave, etc.)

Cagatay

1. Publish your first paper on topological analysis of dwi invariants.
   1. See if David can help with any connections to speed up.
2. Refine the 10-problems and finalize thesis commitee candidates.
   1. Constraints: important, high impact, fun, brain-diffusion, better use of powerful & core CS ideas, few-but-ripe.
   2. Aim: conferences:: siggraph, vis, ismrm, cvpr, iccv, miccai. journals:: science, nature, tvcg, neuroimage, tmi.
   3. Add dwi template matching using one-forms to the 10-problems.
3. Wrap up the two manifold coloring papers
   1. siggraph, vis.
4. Publish the math notes on-line.
5. Learn brain neuroanatomy.

David

1. cs137 runs smoothly, with good resulting projects and learning [solid, great students, smooth, could have been more inspired, A-]
2. spring topics course syllabus and schedule complete (by 15 Jan) [very little progress]
3. deliver an inspiring Visualization capstone talk [some mixed feedback, but overall B or B+]
4. improve group infrastructure: sw, data, dissemination, tools (with help from sw engineer, Sidra, and Wudan) [slower than I would like, but moving]
5. more brain project deliverables [good ramp up; continue and concretize]
6. Trey stuff happy [distance pipeline ok, modeling needs attn next semester]
7. support group members' goals and growth, particularly impact and products [good, bump to 15-minute meetings]
8. refine 5-year funding/sabbatical plan -- write some proposals [no progress; need better small steps]
9. keep up on dept service
10. keep up on professional service

David G

1. Learn about the field of proteomics and the research being conducted by Prof. Salomon's group
2. Familiarize myself with the pathway exploration tool that has been developed by Radu Jianu
3. Understand the data sets generated by Prof. Salomon's group and how they are incorporated into the pathway exploration tool
4. Fully integrate the pathway exploration tool into the software infrastructure of Prof. Salomon's lab
5. Test the integration of the pathway exploration tool by using it myself and teaching members of Prof. Salomon's lab to use it
6. Work with lab members using the software to determine other improvements that can be made, and detail requirements to be implemented in the future
7. Familiarize myself with the Human Protein Reference Database (HPRD)
8. Choose a protein of interest and use the pathway exploration tool to understand the other proteins that are associated with it to test a specific hypothesis related to proteomics (to be conducted with member from Prof. Salomon's lab)
9. Create an extended abstract by the end of the semester detailing my achievements/contributions and their relevance

Eni

1. i. work on the augmentation of the NeuroImage paper (write / learn LATEX / become comfortable with the experimental techniques / analyze the data / interpret the results / finish)
2. ii. help prepare preliminary results for the collaboration with S. Correia et. al
3. iii. improve computational linear algebra skills
4. iv. learn about visualization techniques
5. v. improve programming skills
6. vi. gain confidence as a researcher, while learning from the other people in the group & working independently
7. vii. get an ISMRM'09 poster accepted as a talk

Jadrian

1. Papers: make progress on all, submit one or two to ISMRM (abstracts / posters due Nov. 12th)
   1. Work on Jack Simon's longitudinal data, motivating
      1. connective coherence maps
      2. planar differential measures
      3. learning statistics for data analysis
   2. Write a numerical analysis paper on orientation-dependent tractwise scalar measures like parallel and perpendicular diffusivity
   3. Develop a WM microstructure model; maybe look for a neuroanatomy collaborator?
   4. Continue to support data processing for Ron Cohen's HIV study
2. Keep CS137 running smoothly
3. Resubmit comparison visualization paper to EuroVis (abstracts due Nov. 28)
4. Continue cleaning up and generalizing the pipeline
   1. put components in $G
   2. master build scripts in a language that has conditionals (can Make do this?)
   3. keep up to date with processing for all different data sources
5. Document everything I come across in the wiki

dhl sez: get some paper drafts done now!

Jian

1. Projects:
   1. bat wing shape analysis.
2. Papers:
   1. (DONE)Finish the ISVC symposium panel presentation by Dec 3 2008
   2. Help with flow study. Hope to get the paper out by Nov 2. (according to Andy F.)
      1. (DID) pilot myself / discussions /
   3. (DONE) Submit the massing study work to VR 3DUI symposium (abstract due on Oct 24, paper due on Oct 31
      1. (DONE) Dr. Bowman needs the draft by Oct 10th.
   4. (DONE) Finish the ISVC panel submission by Sep. 22.
      1. (DONE)Las Vegas Presentation. (follow up)
   5. (DONE) Finish the Display paper by Sep 19 and submit to CHI
   6. (DONE) Finish the Bat paper and submit to SICB by Sep. 9.
   7. (DONE) Finish Devon's paper.
3. Job
   1. Finish faculty search dossier draft by September 22 (keep discussing this with Prof. David Laidlaw)
      1. (on-going)Look for / create the list of job potentials (done the files. keep improving)
      2. (DONE) Ask for recommendation letters (done by Sep 29th)
      3. (DONE) Update my web page (done by Nov 8th)
      4. Start presentation slides
4. Proposal / fellowship
   1. (DONE) Finish the NSF proposal by Dec. 1. first time, awesome experience - learned a lot from Prof. Laidlaw and Jane
      1. Discuss main ideas
   2. (DONE) Submit L'Oreal fellowship by Oct 31
5. Community
   1. (DONE) 10 paper reviews by Nov 1st.
6. Not sure stuff:
   1. (Dropped) Finish the book chapter about the VR for eduction abstract by Nov 15 2008 and chapter by March 15 2009 (if accepted)
   2. Dr. Setareh's work

dhl sez: adjust for reality (eg devon paper), discuss things only when necessary, doing chapter?, CoPI question?

Laura

1. Keep improving my ethic of work
2. Get experience on running experiments with humans
3. Improve my experimental design skills
4. Develop my scientific writing skills
5. Have a project finished that can be my master's thesis
6. Try to get a paper that can hopefully be submitted

Radu

1. resubmit protein paper
2. to Bioinformatics by Sept 30.
3. to TVCG if answer not positive and response comes before Dec 1.
4. develop and implement a paper for Vis2009
5. write 1 page abstracts/proposals for ideas to evaluate them
6. Phd topic
7. write 2 page abstractrs/proposals for ideas and evaluate them (contain lit search)
8. at least one proposal by the end of Oct. and one by the end of Nov.
9. make progress in Benoist lab
10. write the NIH report for Immgen as it should look at the end of the semester (by Sept 30)
11. genome-viewer (deploy for use, display at Broad)
12. have Leo and other people from the Lab use proteinApp; produce a document with their workflows and suggestions
13. port genomic data into proteinApp
14. create a project plan for cell lineage analysis
15. monitor, help and guide David Ginsburg

dhl sez: responsiveness, deliverables

Sidra

1. visweb page per pub for images etc

Trevor

1. Create FluoroCorrect open source package under BSD license.
   1. Distribute on SourceForge.
2. Vis interactive demo.
   1. Finish implementing demo.
   2. Create poster.
   3. Present at Vis.
3. Revise nerve orientation paper, submit to eurovis
   1. Abstract Submission: Nov 28, 2008
   2. Paper Submission: Dec 05, 2008
4. Consider options for i3D submission.
5. Apply for NSF Graduate Research Fellowship.
6. Evaluate plans for the summer (if those plans might need to be acted on sooner rather than later).
   1. Look into NASA opportunities with Ryan.
   2. Apply to Microsoft Research
   3. Apply to IBM, maybe Autodesk?
7. Research comps at the end of the semester? (move to spring semester.)
8. Get through my classes.
   1. AM261, CS295, CS137, Reading and Research
9. Refine long-term project ideas.
10. Improve time management.
11. Finish TMI Paper.

Wenjin

1. pass research comps
2. DONE: vis conference: poster and presentation
3. Caltech macaque data working:
   1. make sure tensor corrected
   2. show tube
   3. DONE: acquisition parameters verified with caltech
   4. microscopic images of histological scans obtained
4. ISMRM paper submission on diffusion model + microstructure parameters (axon radius, etc) measurement paper (11/12)
5. Continue support Steve's and Ron's group (Anna, Win, etc) working with brainapp

Wudan

1. play with google analytics
2. ? successes wiki
3. demo menu