http://vrl.cs.brown.edu/wiki/index.php?action=history&feed=atom&title=Plans_and_Goals%2FFall_2008Plans and Goals/Fall 2008 - Revision history2026-04-21T02:22:29ZRevision history for this page on the wikiMediaWiki 1.43.1http://vrl.cs.brown.edu/wiki/index.php?title=Plans_and_Goals/Fall_2008&diff=1173&oldid=prevJadrian Miles: New page: == 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 Brad...2009-01-01T19:27:47Z<p>New page: == 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 Brad...</p>
<p><b>New page</b></p><div>== Andy ==<br />
# Run flowviseval and complete IEEE Vis submission before Nov 1. <br />
# Co-author NIH grant on new biology research tools <br />
# [probably] Spend some time working with Huffman and Bradley and others planning improvements to $G<br />
# Brain project<br />
# Work with David to identify candidates for new research projects<br />
<br />
== Brad ==<br />
# make research group more productive -- products are<br />
## knowledge created<br />
## knowledge disseminated<br />
## publications published<br />
## publications downloaded and cited<br />
## code created to make publications<br />
## code used by close collaborators<br />
## code downloaded (perhaps by and used by outsiders)<br />
## group overhead reduced<br />
## knowledge created, disseminated, made impactful<br />
# have work be focused on specific funded grants<br />
# work independently<br />
# provide sw engineering help and support to individuals in the group<br />
# A+: get wrist distance-map tools usable by Trey's group, Evan in particular<br />
## registration code broken (manifolds issue)<br />
## ligament length code broken (probably manifolds again)<br />
## get manifolds into the fold; work from Cindy's source control?<br />
# A: understand why Evan had to copy code rather that using our source within source control<br />
# A: help direct Sidra and Wudan to improve visweb <br />
## 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)<br />
## update site to improve those metrics, e.g., images not getting well indexed by google because of link structure<br />
## review Daniel Acevedo's web e-mail feedback for ideas<br />
## focus on brain or wrist to preserve allocability, but make globally useful<br />
## better availability of talks and videos that we make<br />
### many ppt's already around -- could be videos with a narration<br />
### a number of full videos already around, some on web, but not easily found<br />
### streaming video server?<br />
### put things on utube or other distribution sites?<br />
## create a plan to make available brain diffusion imaging data (perhaps coupling to an existing NIH-funded site)<br />
### be general enough to also support wrist data, gene data, proteomics data, etc.<br />
## is there any kind of "push" technology for sending papers to lists or individuals (spam...)<br />
# A: shift to more principled software development<br />
## do so incrementally to preserve existing knowledge of users and existing code<br />
## bug tracking system?<br />
## determine some principles for sw<br />
### main shared $G is read only<br />
### explicit writable checkouts by default instead of implicit<br />
### all sw components have tests<br />
## nagging scripts<br />
### code checked out too long<br />
### missing tests<br />
### failing tests<br />
### regular tests of outside infrastructure (net flakiness, disks filling up, etc.)<br />
## address missing tests, etc<br />
## better solution for linux compiler versions<br />
### don't break windows and other platforms<br />
### get off g++/gcc 2.95<br />
### have some better mechanism for transitioning to future compiler versions<br />
## better documentation setup and documentation<br />
### for sw development<br />
#### guidelines for quick prototyping<br />
#### guidelines for interfaces for distributable algorithms (e.g., segmentation, ITK?)<br />
#### goals for full applications that will be shared<br />
### for paper production<br />
### for running computational experiments (tool development, prototyping, testing)<br />
### for production-oriented data-driven work (tool production use, e.g., wrist data, brain data)<br />
### for hardware resources (wheatstone, cave, etc.)<br />
<br />
== Cagatay ==<br />
# Publish your first paper on topological analysis of dwi invariants. <br />
## See if David can help with any connections to speed up. <br />
# Refine the 10-problems and finalize thesis commitee candidates. <br />
## Constraints: important, high impact, fun, brain-diffusion, better use of powerful & core CS ideas, few-but-ripe. <br />
## Aim: conferences:: siggraph, vis, ismrm, cvpr, iccv, miccai. journals:: science, nature, tvcg, neuroimage, tmi.<br />
## Add dwi template matching using one-forms to the 10-problems.<br />
# Wrap up the two manifold coloring papers <br />
## siggraph, vis.<br />
# Publish the math notes on-line. <br />
# Learn brain neuroanatomy.<br />
<br />
== David ==<br />
# <s> cs137 runs smoothly, with good resulting projects and learning </s> <i> [solid, great students, smooth, could have been more inspired, A-] </i><br />
# spring topics course syllabus and schedule complete (by 15 Jan) <i> [very little progress] </i><br />
# <s> deliver an inspiring Visualization capstone talk </s> <i> [some mixed feedback, but overall B or B+] </i><br />
# <s> improve group infrastructure: sw, data, dissemination, tools (with help from sw engineer, Sidra, and Wudan) </s> <i> [slower than I would like, but moving] </i><br />
# <s> more brain project deliverables </s> <i> [good ramp up; continue and concretize] </i><br />
# <s> Trey stuff happy </s> <i> [distance pipeline ok, modeling needs attn next semester] </i><br />
# <s> support group members' goals and growth, particularly impact and products </s> <i> [good, bump to 15-minute meetings] </i><br />
# refine 5-year funding/sabbatical plan -- write some proposals <i> [no progress; need better small steps] </i><br />
# <s> keep up on dept service </s><br />
# <s> keep up on professional service </s><br />
<br />
== David G ==<br />
# Learn about the field of proteomics and the research being conducted by Prof. Salomon's group <br />
# Familiarize myself with the pathway exploration tool that has been developed by Radu Jianu <br />
# Understand the data sets generated by Prof. Salomon's group and how they are incorporated into the pathway exploration tool <br />
# Fully integrate the pathway exploration tool into the software infrastructure of Prof. Salomon's lab<br />
# Test the integration of the pathway exploration tool by using it myself and teaching members of Prof. Salomon's lab to use it<br />
# Work with lab members using the software to determine other improvements that can be made, and detail requirements to be implemented in the future <br />
# Familiarize myself with the Human Protein Reference Database (HPRD) <br />
# 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)<br />
# Create an extended abstract by the end of the semester detailing my achievements/contributions and their relevance<br />
<br />
== Eni ==<br />
# 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) <br />
# ii. help prepare preliminary results for the collaboration with S. Correia et. al <br />
# iii. improve computational linear algebra skills <br />
# iv. learn about visualization techniques <br />
# v. improve programming skills<br />
# vi. gain confidence as a researcher, while learning from the other people in the group & working independently <br />
# vii. get an ISMRM'09 poster accepted as a talk<br />
<br />
== Jadrian ==<br />
# Papers: make progress on all, submit one or two to ISMRM (abstracts / posters due Nov. 12th)<br />
## Work on Jack Simon's longitudinal data, motivating <br />
### connective coherence maps <br />
### planar differential measures <br />
### learning statistics for data analysis<br />
## Write a numerical analysis paper on orientation-dependent tractwise scalar measures like parallel and perpendicular diffusivity<br />
## Develop a WM microstructure model; maybe look for a neuroanatomy collaborator? <br />
## Continue to support data processing for Ron Cohen's HIV study<br />
# Keep CS137 running smoothly <br />
# Resubmit comparison visualization paper to EuroVis (abstracts due Nov. 28) <br />
# Continue cleaning up and generalizing the pipeline <br />
## put components in $G <br />
## master build scripts in a language that has conditionals (can Make do this?) <br />
## keep up to date with processing for all different data sources<br />
# Document everything I come across in the wiki<br />
<br />
dhl sez: get some paper drafts done now!<br />
<br />
== Jian ==<br />
# Projects:<br />
## bat wing shape analysis.<br />
# Papers:<br />
## <s>(DONE)Finish the ISVC symposium panel presentation by Dec 3 2008</s><br />
## Help with flow study. Hope to get the paper out by Nov 2. (according to Andy F.)<br />
###<s>(DID) pilot myself / discussions / </s><br />
## <s>(DONE) Submit the massing study work to VR 3DUI symposium (abstract due on Oct 24, paper due on Oct 31</s><br />
### <s>(DONE) Dr. Bowman needs the draft by Oct 10th.</s><br />
## <s>(DONE) Finish the ISVC panel submission by Sep. 22.</s><br />
###<s>(DONE)Las Vegas Presentation. (follow up)</s><br />
## <s>(DONE) Finish the Display paper by Sep 19 and submit to CHI</s><br />
## <s>(DONE) Finish the Bat paper and submit to SICB by Sep. 9.</s><br />
## <s>(DONE) Finish Devon's paper.</s><br />
# Job<br />
## Finish faculty search dossier draft by September 22 (keep discussing this with Prof. David Laidlaw)<br />
### <s>(on-going)Look for / create the list of job potentials (done the files. keep improving)</s><br />
### <s>(DONE) Ask for recommendation letters (done by Sep 29th)</s><br />
### <s>(DONE) Update my web page (done by Nov 8th) </s><br />
### Start presentation slides<br />
# Proposal / fellowship<br />
## <s>(DONE) Finish the NSF proposal by Dec. 1. </s> first time, awesome experience - learned a lot from Prof. Laidlaw and Jane<br />
### Discuss main ideas <br />
## <s>(DONE) Submit L'Oreal fellowship by Oct 31</s><br />
# Community<br />
## <s>(DONE) 10 paper reviews by Nov 1st.</s><br />
# Not sure stuff:<br />
## (Dropped) Finish the book chapter about the VR for eduction abstract by Nov 15 2008 and chapter by March 15 2009 (if accepted)<br />
## Dr. Setareh's work<br />
<br />
dhl sez: adjust for reality (eg devon paper), discuss things only when necessary, doing chapter?, CoPI question?<br />
<br />
== Laura ==<br />
# Keep improving my ethic of work<br />
# Get experience on running experiments with humans<br />
# Improve my experimental design skills<br />
# Develop my scientific writing skills<br />
# Have a project finished that can be my master's thesis<br />
# Try to get a paper that can hopefully be submitted<br />
<br />
== Radu ==<br />
# resubmit protein paper<br />
# to Bioinformatics by Sept 30. <br />
# to TVCG if answer not positive and response comes before Dec 1.<br />
# develop and implement a paper for Vis2009<br />
# write 1 page abstracts/proposals for ideas to evaluate them<br />
# Phd topic<br />
# write 2 page abstractrs/proposals for ideas and evaluate them (contain lit search)<br />
# at least one proposal by the end of Oct. and one by the end of Nov.<br />
# make progress in Benoist lab<br />
# write the NIH report for Immgen as it should look at the end of the semester (by Sept 30)<br />
# genome-viewer (deploy for use, display at Broad)<br />
# have Leo and other people from the Lab use proteinApp; produce a document with their workflows and suggestions<br />
# port genomic data into proteinApp<br />
# create a project plan for cell lineage analysis<br />
# monitor, help and guide David Ginsburg<br />
<br />
dhl sez: responsiveness, deliverables<br />
<br />
== Sidra ==<br />
# visweb page per pub for images etc<br />
<br />
== Trevor ==<br />
<br />
# <s> Create FluoroCorrect open source package under BSD license. </s><br />
## <s> Distribute on SourceForge.</s><br />
# <s> Vis interactive demo. </s><br />
## <s> Finish implementing demo. </s><br />
## <s> Create poster. </s><br />
## <s> Present at Vis. </s><br />
# <s> Revise nerve orientation paper, submit to eurovis </s><br />
## <s> Abstract Submission: Nov 28, 2008 </s> <br />
## <s> Paper Submission: Dec 05, 2008 </s><br />
# <s> Consider options for i3D submission. </s><br />
# <s> Apply for NSF Graduate Research Fellowship. </s><br />
# Evaluate plans for the summer (if those plans might need to be acted on sooner rather than later).<br />
## <s> Look into NASA opportunities with Ryan. </s><br />
## <s> Apply to Microsoft Research </s><br />
## Apply to IBM, maybe Autodesk?<br />
# <s> Research comps at the end of the semester? </s> (move to spring semester.)<br />
# Get through my classes.<br />
## AM261, CS295, CS137, Reading and Research<br />
# Refine long-term project ideas.<br />
# Improve time management.<br />
# Finish TMI Paper.<br />
<br />
== Wenjin ==<br />
# pass research comps <br />
# DONE: vis conference: poster and presentation <br />
# Caltech macaque data working:<br />
## make sure tensor corrected<br />
## show tube<br />
## DONE: acquisition parameters verified with caltech<br />
## microscopic images of histological scans obtained<br />
# ISMRM paper submission on diffusion model + microstructure parameters (axon radius, etc) measurement paper (11/12) <br />
# Continue support Steve's and Ron's group (Anna, Win, etc) working with brainapp<br />
<br />
== Wudan ==<br />
# play with google analytics<br />
# ? successes wiki<br />
# demo menu</div>Jadrian Miles