PhD Committee Members:
Dr. Jian Huang - PhD advisor, visualization and interaction for research and publication venues
Dr. Elissa Chesler - Non-CS member, systems genetics ORNL leader for domain-specific guidance
Dr. Michael Langston - data generation and algorithmic direction for graph-based functionality
Dr. Lynne Parker - learning systems for intuitive and enhanced interaction

Schedule of Deliverables

1. November 5 – Forms – This packet provides links to all completed forms necessary for graduation.
2. November 13 – PhD Proposal – This information should provide you with the PhD proposal document containing milestones for deliverables prior to the PhD proposal scheduled for this date. The PhD proposal presentation will also be posted here.
3. January 15 – SeeGraph Overview – This information should provide you with the context of the larger application for which the PhD dissertation deliverables have been developed, a system known as SeeGraph. This deliverable includes research updates from an early '05 ORNL presentation of v0.40 and an '07 ORNL presentation of v0.83.
4. February 1 – SG Research Contributions – This information provides references to support material and articles in: an IEEE TVCG journal publication, research highlights for the Scientific Discovery through Advanced Computing (SCIDAC), and an invited presentation as part of collaborative work with the Institute for Systems Biology (ISB).
5. February 15 – SG Domain-specific Posters – This information should provide you with a high-level overview of application to other domains. This deliverable includes several large posters for the 30'x8' powerwall at ORNL (EVEREST) developed as part of the SciDAC's Institute for Ultra-Scale Visualization (IUSV).
6. March 1 – Parallel Coordinates – This information should provide you with information regarding research contributions for parallel coordinate plots (PCPs) and its application to climate research for the Community Climate System Model (CCSM).
7. March 15 – Source & Multimedia – A large compilation of links to source code, images, and video for SeeGraph.
8. April 1 – Learning System – This information should provide you with information regarding research contributions submitted to TVCG for using a Simplified Fuzzy ARTMAP (SFAM) and converted to an intuitive representation.
9. April 3 – Manuscript – All deliverables, corresponding code, and the final draft of the PhD dissertation will be posted here prior to the oral defense.
10. April 8 – Defense – Oral defence of the PhD dissertation will be from 11:45am-1:45pm on Wednesday, 4/8/09, in 202 Claxton. The PhD defence presentation and final manuscript will be posted here.
11. May 7 – Graduate Hooding Ceremony

Deliverable #1 - 6 items:
1) Doctoral Committee Appointment Form [232k pdf] - PhD committee formation signatures
2) Admission to Candidacy [437k pdf] - PhD committee candidacy signatures
3) Graduation Application [571k pdf] - application to graduate with academic history
4) Dissertation Defense Schedule [123k pdf] - 4/8/09 at 11:45 in C202
5) Dissertation Defense [322k pdf] - signatures of final exam denoting successful oral defense of the doctoral dissertation
6) Dissertation Acceptance [280k pdf] - signatures of the PhD committee for acceptance of the written doctoral dissertation

Deliverable #2 - 3 items:
1) PhD Proposal [pdf] - proposal entitled "Visual Analytics for Relationships in Scientific Data"
2) Proposal Presentation [32mb ppt] - defense currently undergoing scheduling
3) Admission to Candidacy [3mb pdf] - signed by committee after the proposal presentation on 11/13/08

Deliverable #3 - 3 items:
1) SeeGraph Overview '05 [17mb ppt] - early '05 ORNL research status update presentation of SGv0.40
2) SeeGraph Overview '07 [19mb ppt] - '07 ORNL research status update presentation of SGv0.83
3) Version Info [txt] - readme.txt describing functionality for each version number

Deliverable #4 - 5 items:
1) IEEE TVCG'08 [pdf preprint] - New, Joshua R. and Kendall, Wes and Huang, Jian and Chesler, Elissa (2008). "Dynamic Visualization of Co-expression in Systems Genetics Data." In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 5.
  1a) Demo video [11mb wmv] - IEEE TVCG supplemental material
3) SciDAC Research Highlight #1 [html] - Dynamic Visualization in Genomic and Proteomic Research of Yeast for Bioenergy
4) SciDAC Research Highlight #2 [html] - Dynamic Visualization of Coexpression in Systems Genetics Data
5) SciDAC Research Highlight #3 [html] - Pairwise Axis Ranking for Parallel Coordinates of Large Multivariate Data
6) Gaggle Workshop [html] - "Graph Analysis with SeeGraph" with summary of ORNL's approach to system genetics and a demo of the interpretter goose (allows external executables to operate as a goose).
  6a) Interpretter goose [2mb avi] (requires TSCC Codec) - Gaggle Workshop supplemental material
  6b) SeeGraph Query [2mb avi] (requires TSCC Codec) - Gaggle Workshop supplemental material with audio explaining query functionality

Deliverable #5 - 3 items:
1) EVEREST Poster #1 [8mb png] - example of genetics workflow with sample of results including paraclique visualization
2) EVEREST Poster #2 [4mb png] - proteomics pathway analysis
3) EVEREST Poster #3 [8mb png] - genetics and proteomics applications with explanatory system diagram

Deliverable #6 - 2 items:
1) EuroVis'09 [3mb pdf preprint] - New, Joshua R. and Johnson, Chris and Huang, Jian (2009). "Pairwise Axis Ranking for Parallel Coordinates of Large Multivariate Data." Submitted, may appear in IEEE Transactions on Visualization and Computer Graphics.
2) CCSM'08 [2mb pdf] - CCSM conference poster

Deliverable #7 - 4 items:
1) SeeGraph [html] - SeeGraph source code and instructions for building; includes seeKaryo.
   Note: other source code is under atacama:/export/new/WorkingVersions
2) Linkage disequilibrium (LD) analysis for different strains of mice using paracliques extracted from mutual information of gene expression calculated from microarray data; includes karyotypes and graph analysis. [picasa]
  2a) LD36 AXBXA - LD using seeKaryo.
  2b) LD40 AXBXA - LD using seeKaryo.
  2c) LD67 SI - LD using seeKaryo.
  2d) LD89 BXD - LD using seeKaryo.
  2e) LD Graphs - LD using seeGraph.
3) Cerebellum gene expression of mice and associated gender differences. [picasa]
  3a) Negative Edges - Statistically significant difference of the number of negative edges present in paracliques for male versus female mice at glom=1.
  3b) Male-1 - Male mice with paracliques extracted using glom=1.
  3c) Female-1 - Female mice with paracliques extracted using glom=1.
  3d) Male-2 - Male mice with paracliques extracted using glom=2.
  3e) Female-2 - Female mice with paracliques extracted using glom=2.
4) Videos
  4a) Quantitative Queries [5mb avi] (requires TSCC Codec) - demonstration video of interactive quantitative queries.
  4b) LoD graphs [7mb avi] (requires TSCC Codec) - demonstration video on creating level-of-detail graphs from selections on the block-tridiagonalized (BTD) belt

Deliverable #8 - 1 item:
1) SIGGRAPH Asia '09 [2mb pdf preprint] - New, Joshua R. and Huang, Jian (2009). "Exposing the Black Box: Intuitive Representation of ARTMAP Networks." Submitted, may appear in ACM Transactions on Graphics.