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Welcome to the CBIIT Speaker Series Wiki

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The NCI Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series presents talks from innovators in the research and informatics community. The biweekly presentations allow thought leaders to share their work and discuss trends across a diverse set of domains and interests. The goals of the Speaker Series are: to share leading edge research; to inform the community of new tools, trends, and ideas; to inspire innovation; and to provide a forum from which new collaborations can begin.

Speakers represent many different institutions, and the topics they address are wide-ranging. Click to view a list of all past speakers, and view their presentations on our NCI CBIIT Speaker Series YouTube playlist!

Location: 9609 Medical Center Drive, Rockville, Maryland 20850

Speaker Series Guidelines for Speakers: Download Word document

Questions or suggestions? If you have questions or would like to recommend a speaker, please email Eve Shalley at eve.shalley@nih.gov

Please refer to the Speaker Calendar below for upcoming speakers.

Notices

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An invitation: If you are interested in presenting your work to our diverse audience of informaticists; basic, translational, and clinical researchers; software developers; and others interested in exploring the uses of informatics in cancer research, contact Eve Shalley at eve.shalley@nih.gov or 240-276-5194.

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Upcoming Speakers:

September 14: Aviv Regez, MIT, Broad Institute

September 28: Funda Meric-Bernstam, University of Texas MD Anderson Cancer Center

October 26: Guoqin Yu, NCI

November 9: John Schnase, NASA

December 7: Samir Courdy, University of Utah and Joyce Niland, City of Hope

January 4: Michael Liebman, IQP Analytics, LLC

Aviv Regev SYNOPSIS:

The cancer transcriptome is shaped by genetic changes, variation in gene transcription, mRNA processing, editing and stability, and the cancer microbiome. Deciphering this variation and understanding its implications on tumorigenesis requires sophisticated computational analyses. Most RNA-Seq analyses rely on methods that first map short reads to a reference genome, and then compare them to annotated transcripts or assemble them. However, this strategy can be limited when the cancer genome is substantially different than the reference or for detecting sequences from the cancer microbiome. "Assembly first" (de novo) methods that combine reads into transcripts without any mapping are a compelling alternative. The assembled transcriptome can then be used to identify mutations, splicing patterns, expression levels, tumor-associated microbes, and – if collected from single cells – characterize tumor heterogeneity. There is thus an enormous need for computationally efficient, accurate and user friendly tools for transcriptome reconstruction and analysis in cancer. In this talk, Dr. Regev will describe how the Trinity, a leading software for de novo RNA-Seq assembly, is used to understand exome expression in cancer research.

Session details...

Jayashree Kalpathy SYNOPSIS:

Over the last couple of decades, “challenges” have been successfully employed to spur scientific research, “leverage ingenuity” and foster the translation of scientific advances into more widespread use. The topics for the challenges have covered a large spectrum of critical issues from self-driving cars and robots for “dangerous, degraded, human-engineered environments” to topics in energy, education and human health.  

“Challenges” have also becoming increasingly important in the medical imaging research community. Such challenges have been an integral part of prestigious conferences such as MICCAI (Medical Image Computing and Computer Assisted Intervention) and International Symposium on Biomedical Imaging (ISBI) and are being planned at a number of other venues. The underlying rationale for these challenges is driven by the realization that every year we see the publication of numerous algorithms published in the scientific literature, yet a very small fraction are translated into clinical use. Challenges can be an effective means to comprehensively assess the performance of algorithms by comparing them on common, sufficiently large and diverse datasets using realistic tasks and valid evaluation metrics.

MedICI is an open-source project that is developing infrastructure and support to  host medical imaging challenges across radiology, digital pathology, and genomics. We will describe the architecture of the system including the integration of CodaLab, caMicrosocope, and ePAD. We will walk through the process of hosting and participating in challenges from the perspective of the organizer and participant, describe past and on-going challenges and share successes as well as lessons learned.

Session details...

Ashish Sharma SYNOPSIS:

caMicroscope and DataScope is one of the three Clinical and Translational Informatics Projects that were funded by NCI/NCIP. This project had two distinct, but integrated goals namely: a) caMicroscope — A digital pathology platform that supports visualization, annotation and analysis of digital pathology data; and b) DataScope — an interactive data integration, query and exploration system. In this talk I will be doing a deep dive into the capabilities of both these systems. caMicroscope provides the community with an open source solution that can visualize whole slide pathology images, create and display both human and machine generated annotations, and run analysis algorithms on the images. In this talk I will provide an overview of caMicroscope, summarize some of it’s deployments, and provide a roadmap for upcoming features. DataScope is part of the Integrative Query System and provides an interactive environment to integrate and explore disparate datasets. Providers can use DataScope to create rich exploration systems that end users can use to slice-dice the underlying datasets, in a highly declarative fashion, without any software development. The talk will touch upon some of its recent deployments and upcoming features.

Session details...

Ewa Deelman SYNOPSIS:

This talk will describe the challenges in the area of scientific workflows, including how they are used to advance science in a number of domains, and how state-of-the-art software systems, such as Pegasus, meet the application and computing infrastructure challenges.  Pegasus enables scientists to describe the workflows in an abstract, resource-independent way. That description includes the definition of the workflow steps and the data they take in and generate, but does not include low-level cyber-infrastructure information. Given the abstract workflow description and the information about the execution environment (composed of potentially distributed data sources and systems), a planner can map the computational tasks onto the available resources and plan the movement of data across distributed resources. The planning process also opens up opportunities for performance optimization and fault-tolerance. The talk will describe example applications, including LIGO, the gravitational-wave physics experiment that recently confirmed the existence of gravitational waves. The talk will touch upon the issues the applications face, and how Pegasus can help them execute in a number of different environments: campus clusters, distributed resources, and clouds.

Session details...

Complete List of Update Posts

Speaker Calendar

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