== '''Agenda for Annual Meeting:''' == Notes taken during the meeting are available [https://nciphub.org/resources/993 here] == '''Day One''' == 8:00 '''Registration & Breakfast''' 8:25 '''Welcome''' (Trey Ideker, UCSD; Juli Klemm, NCI) 8:35 '''[ITCRMeetingPanelDiscussions2015 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 * [https://nciphub.org/resources/952 Trinity: Transcriptome assembly for genetic and functional analysis of cancer] - Aviv Regev, Brian Haas * [https://nciphub.org/resources/940 Cancer Genomics:Integrative and Scalable Solutions in R / Bioconductor] - Martin Morgan * [https://nciphub.org/resources/960 NDEx - the Network Data Exchange A Network Commons for Biologists] - Trey Ideker, Dexter Pratt * [https://nciphub.org/resources/946 Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Xena] - David Haussler 10:00 ''Break'' 10:15 ''' [https://nciphub.org/resources/936 Keynote]''' – Stephen Friend, President, Sage Bionetworks; Medical Technology Advisor, Apple Computer 11:15 '''Industry Perspective and Discussion''' * [https://nciphub.org/resources/950 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 '''[ITCRMeetingPanelDiscussions2015 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 * [https://nciphub.org/resources/964 Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research] - Rebecca Crowley Jacobsen * [https://nciphub.org/resources/954 Informatics Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery] - Jayashree Kalpathy-Cramer * [https://nciphub.org/resources/962 Cancer Deep Phenotype Extraction from Electronic Medical Records] - Guergana Savova * [https://nciphub.org/resources/938 Quantitative Image Informatics for Cancer Research (QIICR)] - Andrey Fedorov * [https://nciphub.org/resources/948 Tools to Analyze Morphology and Spatially Mapped Molecular Data] - Joel Saltz 2:30 ''Break'' 2:45 '''Flash Talks:''' New projects promoting posters # [https://nciphub.org/resources/956 Computational Framework for Single-Cell Genomics of Tumors] - Alexander Krasnitz # [https://nciphub.org/resources/942 Informatics Links between Histological Features and Genetics in Cancer] - Kun Huang # [https://nciphub.org/resources/944 Advanced Development of an Open-source Platform for Web-based Integrative Digital Image Analysis in Cancer] - David Gutman # !GenePattern Notebooks for Cancer Research # [https://nciphub.org/resources/958 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 || [https://nciphub.org/resources/923 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: [ITCRMeetingPanelDiscussions2015 U01/R01 Projects]''': Brief presentations and panel discussion. Sign up [https://docs.google.com/spreadsheets/d/1O7XHLWB9TGJZIi8C2USglu0x3iTm2ao8B6n0xZT2dRE/edit#gid=0 here]. Discussion of challenge and success stories for early-stage development: Moderator: Juli Klemm, NCI * [https://nciphub.org/resources/968 Interactive Informatics Resource for Research-Driven Cancer Proteomics] - Bobbie-Jo Webb-Robertson * [https://nciphub.org/resources/972 Informatics Tools for High-throughput Analysis of Cancer Mutations] - Michael Ryan, Rachel Karchin * [https://nciphub.org/resources/976 Software Tools for Regulatory Analysis of Large Cancer Methylome Datasets] - Ben Berman * [https://nciphub.org/resources/974 BMEG - Biomedical Evidence Graph] - Josh Stuart, Kyle Ellrott * [https://nciphub.org/resources/978 Developing Informatics Technologies to Model Cancer Gene Regulation] - Peng Jiang * [https://nciphub.org/resources/980 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 || [https://nciphub.org/resources/930 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 - [https://nciphub.org/resources/966 CBOE: A community-based bio-ontology evaluation framework] * Karchin/Bernstam [https://nciphub.org/resources/988 Karchin-Meric-Bernstam Collaboration] * Karchin/Ideker - [https://nciphub.org/resources/982 NDEx/CRAVAT-MuPIT Collaboration] * Jiang/Jacobsen/Savova * Bernstam/Jacobsen/Savova * Saltz/Fedorov/Kalpathy-Cramer - [https://nciphub.org/resources/984 Digital Pathology: 3D Slicer, Ground Truth, Competitions] * Jingchun Zhu, Haussler [https://nciphub.org/resources/990 Aggregating BRCA Data: Lessons and Visions] * Quackenbush/Aerts/Huang/Gutman/Cooper 3:30 [https://nciphub.org/resources/986 Activities of the Training and Outreach Working Group] - Rebecca Crowley Jacobsen 4:00 Closing remarks and adjourn