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Anniversary Agenda: A Preview of #BioIT17



May 3, 2017 | At the end of this month, Bio-IT World celebrates a milestone: the 15th anniversary of the Bio-IT World Conference & Expo. Fifteen years after we launched the event, it has grown into a community that we are proud of, a community of clever, innovative people working from all sides on the problems affecting life sciences.

But we’re excited about more than just a champagne toast at this year’s celebration. Our 15th anniversary program in Boston, May 23-25, might be the best yet.

In our first plenary session on Tuesday evening, Rommie Amaro from the University of California, San Diego will set the tone. Amaro’s lab at UCSD uses computational methods to address outstanding questions in drug discovery and molecular-level biophysics, focusing on neglected diseases, Chlamydia, influenza, and cancer.

The CIO panel returns on Wednesday this year featuring informatics heads Andrea Norris at NIH; Bill Mayo at the Broad Institute; Rainer Fuchs at Harvard Medical School; and Aarti Shah at Eli Lilly. We’ve had some lively planning discussions already, and I’m looking forward to the panel and audience discussion of the consumerization of IT, diversity in our community, and the convergence of IT and science.

Ed Liu, president and CEO at the Jackson Laboratories kicks off the final day. It’s been a long time since Liu and I sat down together in Singapore, but we did catch up last summer. Since his time in Singapore, Liu has watched a shift away from the functionalization of the genome. “It was very clear to me from the work that we were doing at the GIS that it wasn’t going to be a one-on-one [relationship], one variant to one outcome. It was going to be much more complex, in a systems manner,” he told me. We need a new vocabulary for uncertainty, Liu says, and he intends for JAX—across its three campuses—to “be the masters of complexity.”  His focus today is on complex genetics and complex genomics at scale. I can’t wait to hear his update.  

The Bio-IT World Expo Awards program includes two awards given by Bio-IT World. Best of Show recognizes outstanding new products. A panel of expert judges choose four category winners, and the entire community weighs in on the People’s Choice Award. Best Practices, announced on Thursday morning, represent some of the best collaborations and partnerships in our space. These projects are tackling tough problems in new ways. Finally, the Benjamin Franklin Award, given by Bioinformatics.org, honors the pioneers in open science. This year’s winner, Rafael Irizarry of Harvard University and the Dana Farber Cancer Institute, will accept his award and give his laureate address.

Free passes to all of this—the plenary sessions and the Expo hall—are available, but that’s just the tip of the iceberg. Here’s some of what else we have flagged in our agendas. –Allison Proffitt, editor

 

Brand new this year, Bio-IT World is hosting the Bio-IT FAIR Data Hackathon. Data scientists and coders will work together to solve today's challenges with real-world data using the principles of FAIR: Findable, Accessible, Interoperable and Reusable Data. The Hackathon program includes tutorials on FAIR data; presentations from Amgen, ONTOFORCE, Biogen, and AstraZeneca; and plenty of time for teams to work together. At the end of the event, a jury will judge progress and award prizes. Participation is free; spread the word!

 

Eric Banks and Geraldine Van der Auwera of the Broad Institute along with Mark Bagley and

Paolo Narvaez of Intel will co-host a luncheon session to describe their collaboration to enhance the GATK environment and scale researchers’ ability to analyze massive amounts of genomic data from diverse sources worldwide. Wednesday, May 24, 12:40 pm 

For the past few years Chris Dagdigian has predicted the end of his “Trends from the Trenches” talk. This year he made good on his threat. Sort of. Instead of keeping up with just Dags, we can enjoy a two-hour session of BioTeam members, each reporting from their own experience building life sciences computing environments (and maybe sharing some of their own experiments at their Converged Lab) and answering questions with Dags’ signature candor. Chris Dwan, veteran of the Broad, New York Genome Center, and the BioTeam, moderates. The panel includes Ari E. Berman; Chris Dagdigian; Aaron Gardner; Adam Kraut; and Asya Shklyar, all of BioTeam; and Christopher Sprangel, Regeneron Genetics Center. Thursday, May 25, 2:00pm 

Diagnostics World has spent a bit of time looking into tuberculosis recently. On Wednesday afternoon, Michael Harris, NIAID, NIH, and Darren Schneider, Deloitte Consulting, will report on the Multiple and Extensively Drug-Resistant Tuberculosis Data Exploration Portal (MXDR-TB DEPOT). The analytics portal supports hypothesis generation and testing aimed at improving TB patient diagnostics and outcomes. The publicly available solution enables clinicians and researchers to create and compare cohorts of patients based on clinical, socioeconomic, genomic, and diagnostic image data. Wednesday, May 24, 4:30pm 

The whole session on big data analytics on cancer genomic data is flagged. Eric Neumann, Foundation Medicine, kicks it off. Foundation Medicine is exploring a new method to map mutational variation into a statistically-defined multidimensional space along with functional and response associations. At Dana-Farber Cancer Institute, John Methot, is working to better use EMR data to correlate to genomic data and inform outcomes and clinical quality research.

Jack DiGiovanna will present Seven Bridges’ Graph Genome tools, an approach to constructing a genome graph that captures variations within a population as branches which diverge from the common reference but later rejoin it. The technology offers improved variant calling and better captures distributions of variations in a population, he says. At lunch, Illumina’s Michael Ball will share how the Mayo Clinic is using BaseSpace Suite to expedite the delivery of its genomic expertise. Jim Lund of WuXi NextCODE will demonstrate the company’s approach using its proprietary genomically ordered relational (gor) database architecture to rapidly and simultaneously explore the diverse data types in TCGA. Wednesday, May 24, starting at 11:00am

John Quackenbush, Dana-Farber Cancer Institute, will share data from the Genotype-Tissue Expression project (GTEx) to explore the factors that influence the manifestation of complex traits. Network and systems methods are providing us with a unique opportunity to explore the associations between genotype and phenotype, he says. Wednesday, May 24, 5:00pm 

Liz Worthey (HudsonAlpha Institute for Biotechnology) consistently delivers. She’ll share application of methods for analyzing, storing, and interpreting variant data that allows us to move beyond molecular diagnostics related to a single variant to support a refined understanding of human health and disease. Thursday, May 25, 2:30pm 

What does it really take to maintain and donate to ClinVar? Aditi Chawla will present Illumina’s workflow for variant classification, including an autoscore system that calculates a variant’s potential to have caused the associated disease, search for literature on variants, and manual clinical curation based on ACMG guidelines. She will discuss strategies for maintaining and updating variant classifications over time, laboratory policy for updating clinical reports as variant classification changes, process for donating to ClinVar, and summary of Illumina’s ClinVar donation. Thursday, May 25, 3:00pm

Ingrid Akerblom, Amgen, takes on the challenges and opportunities facing pharma, and how the drive to bring value to stakeholders—patients, payors or healthcare providers—is transforming pharma approaches to data and analytics for insight generation. Wednesday, May 24, 11:00am 

Angelika Fuchs, Roche pRED Informatics, reports a novel data curation application based on the popular Salesforce platform to enable the outsourcing of data curation tasks to CROs with the required expert knowledge. Wednesday, May 24, 4:30pm 

Pfizer's Causal Reasoning Engine uses causal networks assembled from prior knowledge for the prediction of upstream regulators, boosting genetic signals, and robust patient stratification Enoch S. Huang will present the engine that offers ease-of-interpretation as well as robust results. Thursday, May 25, 2:20pm 

Allotrope Foundation has built a framework comprising an open, standards-based, extensible file format; ontologies and semantic models to provide controlled vocabulary for R&D applications; and APIs to facilitate consistent adoption of the standards. Dana Vanderwall, Bristol-Myers Squibb, will share examples of how the Framework is currently used in the pharmaceutical industry, and the roadmap for ongoing development and releases. Wednesday, May 24, 2:25pm 

Eli Dart is a primary advocate for the Science DMZ design pattern, and works to deploy data-intensive science infrastructure based on the Science DMZ model. He also runs the ESnet network requirements program, which collects, synthesizes, and aggregates the networking needs of the science programs ESnet serves. He’ll introduce Science DMZs, and discuss security when moving data between sites. Wednesday, May 24, 11:00am 

Consent is evolving as more data are available that could be used for research. In parallel, regulatory agencies, legal and privacy views across the world are necessarily changing/evolving to ensure laws and regulations protect the privacy of patients. Catherine Marshall reports on Pfizer’s approach to automating the site level collection of specimens to the order process for specimen and data use. Wednesday, May 24, 4:00pm 

Martin Leach is always up to something interesting. Along with ChoongTeik Ng, Leach will share how Alexion Pharmaceuticals challenged itself to move corporate data center, servers, systems, applications and data to a cloud-based architecture. During the move, the global IT team successfully moved >725 physical and virtual servers, >350 business applications and >250 million files. Leach and Ng will detail Alexion’s approach, pitfalls, lessons learned, and how they engaged their colleagues company-wide. Wednesday, May 24, 11:00am

Dianne Pacheco, The Jackson Laboratory, believes the cloud is essential, but not all service providers are equal. She plans to walk the audience through vetting and managing their service providers to minimize risk of exposing legally protected or sensitive research data. Wednesday, May 24, 4:00pm 

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