Plans and Goals

• Andy

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

• Brad

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

• Cagatay

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

• David

- cs137 runs smoothly, with good resulting projects and learning 
- spring topics course syllabus and schedule complete 
- deliver an inspiring Visualization capstone talk 
- improve group infrastructure: sw, data, dissemination, tools (with help from sw engineer, Sidra, and Wudan) 
- more brain project deliverables 
- Trey stuff happy 
- support group members' goals and growth, particularly impact and products 
- refine 5-year funding/sabbatical plan -- write some proposals 
- keep up on dept service 
- keep up on professional service

• David G

- Learn about the field of proteomics and the research being conducted by Prof. Salomon's group 
- Familiarize myself with the pathway exploration tool that has been developed by Radu Jianu 
- Understand the data sets generated by Prof. Salomon's group and how they are incorporated into the pathway exploration tool 
- Fully integrate the pathway exploration tool into the software infrastructure of Prof. Salomon's lab
- Test the integration of the pathway exploration tool by using it myself and teaching members of Prof. Salomon's lab to use it
- Work with lab members using the software to determine other improvements that can be made, and detail requirements to be implemented in the future 
- Familiarize myself with the Human Protein Reference Database (HPRD) 
- 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)
- Create an extended abstract by the end of the semester detailing my achievements/contributions and their relevance

• Eni

- 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) 
- ii. help prepare preliminary results for the collaboration with S. Correia et. al 
- iii. improve computational linear algebra skills 
- iv. learn about visualization techniques 
- v. improve programming skills
- vi. gain confidence as a researcher, while learning from the other people in the group & working independently 

• Jadrian

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

• Jian

- Papers:
  * Submit the massing study work to VR 3DUI symposium (abstract due on Oct 24, paper due on Oct 31
  * Dr. Bowman needs the draft by Oct 10th.
  * Finish the ISVC symposium panel presentation by Dec 3 2008
  * Finish the I3D paper (or TVCG) by Oct 24. Extended from SICB work
  * Help with flow study. Hope to get the paper out by Nov 2. (according to Andy F.)
- Job
  * Finish faculty search dossier draft by September 22 (keep discussing this with Prof. David Laidlaw)
  * Look for / create the list of job potentials (done the file. keep improving)
  * Ask for recommendation letters (done by Sep 29)
  * Update my web page
  * Start presentation slides
  * Proposal 
  * Finish the NSF proposal by Nov.1 (or Dec? depending on the size of the proposal).
  * Start early to get the coPI informed! who are they?
  * Discuss main ideas
- Waiting stage:
  * Devon's paper (finish it right away after getting feedback from Prof. Laidlaw, query Prof. Banks)
- Supporting role
  * Continue to support vis group report, bat group, other vis groupers' work (hope to collaborate / guide students on some cog / interaction related work that I know well.)
  * Fulfill community service obligations (VR 2009 program committee, ISVC committee, and numerous review requests.
- Done:
  * Finish the Display paper by Sep 19 and submit to CHI (done)
  * Finish the Bat paper and submit to SICB by Sep 9 (done).  
  * Finish the ISVC panel submission by Sep. 22 (done).
- Not sure stuff:
  * Finish the book chapter about the VR for eduction abstract by Nov 15 2008 and chapter by March 15 2009 (if accepted)
- Dr. Setareh's work
- dhl sez: adjust for reality (eg devon paper), discuss things only when necessary, doing chapter?, CoPI question?

• Laura

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

• Radu

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

• Sidra

- visweb page per pub for images etc

• Trevor

 -  1.  Finish TMI Paper.
 -  2.  Revise nerve orientation paper, submit to eurovis.                  Abstract Submission: Nov 28, 2008 
               Paper Submission: Dec 05, 2008 
 -  3.  Consider options for i3D submission.
 -  4.  Apply for NSF Fellowship.
 -  5.  Evaluate plans for the summer (if those plans might need to be acted on sooner rather than later).
 -  6.  Research comps at the end of the semester?
 -  7.  Get through my classes.
 -  8.  Refine long-term project ideas.
 -  9.  Try to protect my time more effectively.

• Wenjin

- pass research comps 
- vis conference: poster and presentation 
- Caltech macaque data working:
- make sure tensor corrected
- show tube
- acquisition parameters verified with caltech
- microscopic images of histological scans obtained
- ISMRM paper submission on diffusion model + microstructure parameters (axon radius, etc) measurement paper (11/12) 
- Look into building vis posters into a Euro vis submission (11/28)
- Continue support Steve's and Ron's group (Anna, Win, etc) working with brainapp

• Wudan

- play with google analytics
- ? successes wiki
- demo menu