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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 is a bi-weekly knowledge-sharing forum featuring speakers on topics of interest to the biomedical informatics and research communities. General topics to be discussed include but are not limited to novel experimental approaches in basic research that require innovative informatics solutions; general informatics methodologies for specific tasks such as natural language processing and data exchange/integration; novel software applications (proprietary or open source); standards; ontologies; open-source development projects; human/computer interactions; future trends in biomedical informatics research and development; and CBIIT/NCIP partnerships inside and outside NCI/NIH.

Speaker Series Guidelines for Speakers: Download Word document

Please refer to the Speaker Calendar below for upcoming speakers.

Presentations: Please visit the NCI CBIIT Speaker Series YouTube playlist Exit Disclaimer logo to view past speakers' presentations on video.

Location: 9609 Medical Center Drive, Rockville, Maryland 20850

Questions? Please email Eve Shalley at eve.shalley@nih.gov 

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

October 26: Guoqin Yu, NCI

November 9: John Schnase, NASA

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...

Helen BermanSYNOPSIS:

As the crystal structures of biological macromolecules were being determined, a new field of structural biology was born. Inspired by these new structures, the scientific community worked to establish a home to archive and share the data emerging from these experiments. The Protein Data Bank (PDB) was established in 1971 with seven structures. The PDB provides a repository for scientists who generate the data, and an access point for researchers and students to find the information needed to drive additional studies. Today, the PDB contains and supports online access to ~117,000 biomacromolecules that help researchers understand aspects of biology, including medicine, agriculture, and biological energy. The ways in which the interrelationships among science, technology, and community have driven the evolution of the PDB resource for more than 40 years will be discussed. The PDB archive is managed by the Worldwide Protein Data Bank (wwpdb.org), whose members are the RCSB PDB, PDBe, PDBj and BMRB.

Session details...

Complete List of Update Posts

Speaker Calendar

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