Agenda for Annual Meeting:
Notes taken during the meeting are available here
Day One
8:00 Registration & Breakfast
8:25 Welcome (Trey Ideker, UCSD; Juli Klemm, NCI)
8:35 U24 Genomic Projects Perspective: Brief presentations and Panel Discussion. Discussion topics to include engagement with users; considerations for transitioning to early prototype to broadly used software; obstacles to success; sustainability considerations
Moderator: Jerry Li, NCI
- Trinity: Transcriptome assembly for genetic and functional analysis of cancer – Aviv Regev, Brian Haas
- Cancer Genomics:Integrative and Scalable Solutions in R / Bioconductor – Martin Morgan
- NDEx – the Network Data Exchange A Network Commons for Biologists – Trey Ideker, Dexter Pratt
- Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Xena – David Haussler
10:00 Break
10:15 Keynote – Stephen Friend, President, Sage Bionetworks; Medical Technology Advisor, Apple Computer
11:15 Industry Perspective and Discussion
- Presentation by Dr. Jadwiga Bienkowska, Director, Computational Biology Precision Medicine, Pfizer Inc.
- Discussion on open source software, industry-academic collaborations, and translating novel informatics software to industry.
12:00 Lunch (on-site)
1:00 U24 Clinical Research Projects Perspective – Brief presentations and panel discussion. Discussion topics to include engagement with users; considerations for transitioning to early prototype to broadly used software; obstacles to success
Moderator: Yantian Zhang, NCI
- Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research – Rebecca Crowley Jacobsen
- Informatics Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery – Jayashree Kalpathy-Cramer
- Cancer Deep Phenotype Extraction from Electronic Medical Records – Guergana Savova
- Quantitative Image Informatics for Cancer Research (QIICR) – Andrey Fedorov
- Tools to Analyze Morphology and Spatially Mapped Molecular Data – Joel Saltz
2:30 Break
2:45 Flash Talks: New projects promoting posters
- Computational Framework for Single-Cell Genomics of Tumors – Alexander Krasnitz
- Informatics Links between Histological Features and Genetics in Cancer – Kun Huang
- Advanced Development of an Open-source Platform for Web-based Integrative Digital Image Analysis in Cancer – David Gutman
- GenePattern Notebooks for Cancer Research
- Informatics Quantitative Radiomics System Decoding the Tumor Phenotype – John Quackenbush
3:15 Poster Sessions and Demos
- Posters by new projects; U01 and U24 invited but not “required”. Poster dimensions are 48” (w) x 36” (h)
- 10 Demos by U01 and U24 projects (excluding new awardees), two running simultaneously, 20 min each + 5 min transition
| Track 1 Demos | Track 2 Demos | |
|---|---|---|
| 3:15 | Trinity – Transcriptome assembly for genetic and functional analysis of cancer | Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research |
| 3:40 | Cancer Genomics:Integrative and Scalable Solutions in R / Bioconductor | Informatics Tools for Optimized Imaging Biomarkers for Cancer Research&Discovery |
| 4:05 | NDEx – the Network Data Exchange A Network Commons for Biologists | Cancer Deep Phenotype Extraction from Electronic Medical Records |
| 4:30 | Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Quantitative Image Informatics for Cancer Research (QIICR) |
| 4:55 | Software Tools For Regulatory Analysis of Large Cancer Methylome Datasets | Informatics to Enable Routine Personalized Cancer Therapy |
5:15 Break
6:00 Dinner (on-site)
Day Two
8:30 The Future of ITCR – Juli Klemm, NCI
8:45 Panel Discussion: U01/R01 Projects: Brief presentations and panel discussion. Sign up here. Discussion of challenge and success stories for early-stage development:
Moderator: Juli Klemm, NCI
- Interactive Informatics Resource for Research-Driven Cancer Proteomics – Bobbie-Jo Webb-Robertson
- Informatics Tools for High-throughput Analysis of Cancer Mutations – Michael Ryan, Rachel Karchin
- Software Tools for Regulatory Analysis of Large Cancer Methylome Datasets – Ben Berman
- BMEG – Biomedical Evidence Graph – Josh Stuart, Kyle Ellrott
- Developing Informatics Technologies to Model Cancer Gene Regulation – Peng Jiang
- MeV: Software for Next Generation Genomic Data Analysis – Yaoyu Wang, John Quackenbush
10:15 Break
10:45 Poster Sessions and Demos
- Posters by new projects; U01 and U24 invited but not “required”
- 12 Demos by U01 and U24 projects (excluding new awardees), two running simultaneously, 20 min each + 5 min transition
| Track 1 Demos | Track 2 Demos | |
|---|---|---|
| 10:45 | Interactive Informatics Resource for Research-driven Cancer Proteomics | EMR Adverse Drug Event Detection for Pharmacovigilance |
| 11:10 | Informatics Tools for High-throughput Analysis of Cancer Mutations | Tools to Analyze Morphology and Spatially Mapped Molecular Data |
| 11:35 | OmniSearch – A semantic search tool for discovering microRNAs critical roles in human cancer | Advanced Development of an Open-source Platform for Web-based Integrative Digital Image Analysis in Cancer |
| 12:00 | MeV – Software for Next Generation Genomic Data Analysis |
12:30 Lunch (on-site)
1:30 Poster sessions and demos (continued)
| Track 1 Demos | Track 2 Demos | |
|---|---|---|
| 1:30 | ESCE – DISCOVERING MOLECULAR PROCESSES | Developing Informatics Technologies to Model Cancer Gene Regulation |
| 1:55 | Interpreting massive genomic data sets via summarization | caCDE-QA – A Quality Assurance Platform for Cancer Study Common Data Elements |
2:30 Presentations of proposed collaborations, 5 min each
- Huang/Jiang – CBOE: A community-based bio-ontology evaluation framework
- Karchin/Bernstam Karchin-Meric-Bernstam Collaboration
- Karchin/Ideker – NDEx/CRAVAT-MuPIT Collaboration
- Jiang/Jacobsen/Savova
- Bernstam/Jacobsen/Savova
- Saltz/Fedorov/Kalpathy-Cramer – Digital Pathology: 3D Slicer, Ground Truth, Competitions
- Jingchun Zhu, Haussler Aggregating BRCA Data: Lessons and Visions
- Quackenbush/Aerts/Huang/Gutman/Cooper
3:30 Activities of the Training and Outreach Working Group – Rebecca Crowley Jacobsen
4:00 Closing remarks and adjourn