Events by this organizer
Artificial Intelligence / Machine Learning
Natural Language Processing
NCI Genomic Data Commons
NIH High Performance Unix Cluster Biowulf
Single Cell RNA SEQ
Single Cell Technologies
CCR Neuro-Oncology Branch
Data Science Learning Exchange
Earl Stadtman Investigator Program
FNL Science and Technology Group
Frederick National Lab for Cancer Research (FNLCR), Advanced Biomedical Computational Science (ABCS)
NCI and the Society for Immunotherapy of Cancer (SITC)
NCI CCR Liver Cancer Program
NCI Containers and Workflows Interest Group
NCI Data Science Learning Exchange
NHLBI Proteomics Core
NIH Common Fund
NIH HPC Biowulf
NIH Metabolomics Scientific Interest Group
NIH Office of Data Science Strategy (ODSS)
NIH STRIDES Initiative
NIH Training Library
Office of Cancer Clinical Proteomics Research
Scientific Library at Frederick
Single Cell Users Group
Systems Biology Interest Group
Past & Future Events
Only Past Events
Only Future Events
Dr. Pjotr Prins and Arun Isaac will present their Concise Common Workflow Language (CCWL). CCWL makes code reusable and adaptable across a variety of software and hardware environment while following
Dr. Pjotr Prins and Arun Isaac will present their Concise Common Workflow Language (CCWL). CCWL makes code reusable and adaptable across a variety of software and hardware environment while following FAIR+ (Findable, Accessible, Interoperable, Reusable, and Computable) principles. They will also discuss their prototype COVID-19 cloud setup, with a hands-on demonstration of the universal software deployment system Guix, part of the open-source operating system GNU.
CWL is of particular interest to cancer researchers because it provides a standardized machine-readable semantics model for running workflows on virtual environments. Attendees will learn how CCWL, as a CWL compiler, works with a package manager like GNU Guix to improve reproducibility and validation of bioinformatics workflows.
This webinar is part of the monthly Containers and Workflow Interest Group (CWIG) webinar series. CWIG brings together data scientists, bioinformaticians, computer scientists, and researchers to learn more about cloud computing and container technologies, workflows, and pipelines that could drive cancer data science.
The webinar series features a variety of presenters from across NIH, industry, and academia. Though cancer research is the focus of the series, unrelated data science and cloud computing topics are still welcome. In the last year, the CWIG webinar speakers have discussed:
- NIH cloud programs like the NCI Cloud Resources and NIH STRIDES.
- commercial cloud platforms for biomedical data storage and computing.
- pipelines and tools for deep learning and various omics analysis.
Pjotr Prins, Ph.D.
Dr. Prins is a bioinformatician at-large and assistant (coding) professor at the Department of Genetics, Genomics, and Informatics at the University of Tennessee Health Science Center. He is also the director of Genenetwork.org and writes critical software for genetics and pangenomics
Mr. Isaac is a doctoral student at the Department of Computational and Data Sciences, Indian Institute of Science. He regularly contributes to GNU Guix and is the author of guile-email, an email parser for Guile.
(Friday) 3:00 pm - 4:00 pm
Speaker: Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This
Speaker: Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute
Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This open-source software platform offers an interactive tool for exploring large-scale cancer genomics data sets through a user-friendly interface. Using cBioPortal, researchers can integrate genomic and clinical data and have access to a suite of visualization and analysis options, including cohort/patient-level visualization, mutation visualization, survival analysis, and alteration enrichment analysis.
The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a user-friendly interface. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including cohort and patient-level visualization, mutation visualization, survival analysis and alteration enrichment analysis. Features of the portal include OncoPrints, a compact graphical representation of alterations in multiple genes across a cohort, mutational diagrams that show locations and frequencies of mutations in a single gene, subgroup definition and comparison, Kaplan-Meier survival curves, plots that allow the visualization of correlation between different data types (e.g. the correlation between DNA copy number and mRNA expression for a gene of interest), among others. To facilitate interpretation, the cBioPortal also integrates data from several leading knowledgebases and computational resources.
This webinar will introduce basic exploratory, analytic and visualization features of the cBioPortal, as well as several advanced features, including:
– Exploring data with study view
– Running and modifying queries
– OncoPrints, mutation diagrams, survival analysis, enrichment analysis
– Resources integrated into the cBioPortal
– Working with different data types, including mutations, copy number, mRNA expression and protein levels
– Onco Query Language
– Resources to get additional help
(Tuesday) 10:00 am - 11:00 am
Register for the 2021 Clinical Proteomics Tumor Analysis Consortium (CPTAC) Virtual Scientific Symposium to hear CPTAC investigators share their latest discoveries in the field of cancer proteogenomics, cancer
Register for the 2021 Clinical Proteomics Tumor Analysis Consortium (CPTAC) Virtual Scientific Symposium to hear CPTAC investigators share their latest discoveries in the field of cancer proteogenomics, cancer research, and data analysis tools.
In addition to scientific talks on tumor biology and translational studies, there will be demonstrations of these CPTAC-developed data analysis tools:
- FragPipe Computational Pipeline (for comprehensive analysis of mass spectrometry-based proteomics data)
- ProTrack-Kinase Activity Portal (for querying/visualizing/downloading kinase activity scores of multiple cancer types)
- BayesDebulk (analysis method for inferring cell-type composition in bulk tissue using proteogenomics data)
The CPTAC program is a national effort coordinated through NCI’s Office of Cancer Clinical Proteomics Research to accelerate the understanding of cancer biology through the marriage of large-scale proteome and genome analysis, or proteogenomics. Proteogenomics allows CPTAC researchers to paint a more detailed picture of tumor carcinogenesis and progression, micro-environments, and immune landscapes. This information can then be leveraged therapeutically to improve patient care.
(Wednesday) 11:00 am - 3:50 pm
Please plan to attend the Physician-Scientist Early Investigator Program (PEIP) seminar by: Nicholas Rydzewski, M.D. University of Wisconsin
Please plan to attend the Physician-Scientist Early Investigator Program (PEIP) seminar by:
Nicholas Rydzewski, M.D.
University of Wisconsin
Dr. Rydzewski is currently Chief Resident in the Radiation Oncology Residency Program at the University of Wisconsin. He is deeply committed to advancing the use of artificial intelligence and liquid biopsies to better inform precision cancer therapy approaches for patients before and following radiation. This is a significant and timely arena for translational research with great promise to advance the discipline of Radiation Oncology over the years to come.
Meeting LinkMeeting Link
(Thursday) 10:00 am - 11:00 am
Wrapping up its final webinar of 2021, the NCI Cancer Research Data Commons (CRDC) Cancer Genomics Cloud (CGC) welcomes Cold Spring Harbor Laboratory fellow Dr. Pascal Belleau. He will share
Wrapping up its final webinar of 2021, the NCI Cancer Research Data Commons (CRDC) Cancer Genomics Cloud (CGC) welcomes Cold Spring Harbor Laboratory fellow Dr. Pascal Belleau. He will share his findings from recent work on the CGC, typing the Human Leukocyte Antigen (HLA) class II complex in 11,000 patient samples from The Cancer Genome Atlas (TCGA) data set.
Through his study, Dr. Belleau investigated the presence and patterns of the HLA class II complex across 33 tumor types. The HLA class II complex is a molecular component linked to the body’s immune response. Understanding how this molecular complex differs across cancer types can give us insight into how it may mediate the immune system’s response to cancer.
As one of the three Cloud Resources within the NCI CRDC, the Seven Bridges’ CGC provides researchers access to a wide variety of data sets, a catalog of tools to analyze and visualize the data directly from the browser, and scalable computational resources to perform large scale-analysis in the cloud.
Pascal Belleau, Ph.D.
Dr. Belleau is a computational biology postdoctoral fellow at the Quantitative Biology Department of Cold Spring Harbor Laboratory.
(Wednesday) 2:00 pm - 3:00 pm