2014 tranSMART Foundation Annual Meeting schedule

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Tuesday 14th October 2014

  • Continental Breakfast and Registration

    At 8:15am to 9:00am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Welcome to the 2014 Annual Meeting

    by Brian D. Athey

    At 9:00am to 9:15am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

    Coverage video

  • Review of the 2013 Annual Meeting in Paris

    by Sherry Cao, PhD and Keith Elliston

    At 9:15am to 9:30am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • 2014 Annual Meeting Objectives

    by Keith Elliston and Brian D. Athey

    At 9:30am to 9:45am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Overview of the Hackathons

    by Jay Bergeron and Professor Yike Guo

    Yike Guo and Jay Bergeron will provide an overview of the 2 Hackathons that will be held during this 3 day meeting. They will describe the nature of the challenge and the goals for each project.

    At 9:45am to 10:00am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Overview of the tranSMART Platform v1.2

    by Keith Elliston

    Keith will describe the goals for the Platform set forth in Paris last year and the evolutions and community support that led to the release of v1.2

    At 10:00am to 10:30am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Coffee Break

    At 10:30am to 11:00am, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Keynote: Collaborative Translational Research – Importance, Challenges and Opportunities from a renal disease perspective

    by Matthias Kretzler, MD, PhD

    Biomedical researchers in academia engage in multidisciplinary research that include partnerships with other academic medical center, nonprofit, pharmaceutical, and biotech organizations. Collaboration across these segments is essential to translating biomedical discoveries to improved human health outcomes. Connecting disease knowledge domains in distributed research networks requires a platform for open science, managing, sharing and analyzing highly complex heterogeneous data.

    At 11:00am to 12:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Lunch

    At 12:00pm to 1:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • HACKATHON

    At 1:00pm to 2:30pm, Tuesday 14th October

    In Room D, 3rd Floor, Michigan League

  • Science Track: Powering Prediction for Brain Disease through an Open-Science Platform

    by Magali Haas, MD, PhD

    “Big Data” has become a blanket term for any collection of data so large, diverse and complex that it becomes difficult to process using traditional statistical methods. Advancing big data science is important, and several efforts have been launched to identify new methods to derive knowledge from data, and to construct new infrastructure to manage, curate and share data with the scientific community. However, information is only as useful as the thought that went into gathering and extracting it. Modeling and simulation are essential tools for moving from big data to smart data. Orion Bionetworks is spearheading efforts to bridge TranSmart with other Knowledge Engineering platforms to enable robust brain disease model development.

    At 1:00pm to 1:30pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

    Coverage video

  • Technical Track: NDEx : Infrastructure for Collaboration and Application Development using Biological Networks

    by Dexter Pratt

    NDEx is an open-source platform for collaboration, publication, and applications using biological networks of multiple types and in multiple formats, supported both by industry and NCI. The talk will describe the public NDEx site, private NDEx servers, the use of the NDEx REST API in applications, and will conclude with a discussion of synergy of NDEx with tranSMART.

    At 1:00pm to 1:30pm, Tuesday 14th October

    In Vandenberg, 2nd Floor, Michigan League

  • Science Track: Utilizing TranSMART from Bench to Bedside

    by Kristen Sweet, PhD

    Many pharmaceutical companies utilize tranSMART as a translational medicine tool to help bridge the gap from “bench to bedside”. This talk will demonstrate ways in which the immunology team at Janssen Pharmaceuticals of Johnson & Johnson use tranSMART for all stages of research including hypothesis generation, data analysis, efficacy evaluations, and clinical trial design.

    At 1:30pm to 2:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Technical Track: Connecting tranSMART 1.2 with Spotfire through the REST API

    by Dan Weaver

    In collaboration with the Hyve, we have created a “Spotfire - tranSMART connector” that uses the tranSMART 1.2 REST API. We will present the architecture of the connector, demonstrate the user workflow and experience, and show some examples of unique analyses this connection enables.

    At 1:30pm to 2:00pm, Tuesday 14th October

    In Vandenberg, 2nd Floor, Michigan League

  • Science Track: Improving the v.1.1 experience: collaborative environment, novel data models, and integration of custom R script

    by Tatiana Khasanova

    tranSMART offers a unique combination of features, such as the ability to analyze various types of molecular data in the context of clinical or phenotypic data. In addition, this multi-user platform facilitates data sharing between multiple research teams and organizations. One of our recent projects with included a tranSMART installation in Amazon’s cloud that included customized upgrades to tranSMART’s security module to allow simultaneous and secure access to data for multiple clients. Another project, performed at Merck, had a unique focus on pre-clinical data from in vivo oncology studies and required significant modification of the tranSMART data model. This project also required the addition of custom R scripts to tranSMART’s analytic environment. During the talk we will cover challenges and solutions implemented by the Rancho BioSciences team during these two projects

    At 2:00pm to 2:30pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Technical Track: Wiring tranSMART into a large collection of grey matter

    by Dan Housman

    Dan will review progress in the journey at Deloitte to embed tranSMART into the business of multiple groups within the world’s largest consulting organization. This includes knowledge management for heterogeneous global teams, client engagements such as NIAID, porting to IBM HPC platforms and Hadoop pilots, and constructing the ConvergeHEALTH Miner suite.

    At 2:00pm to 2:30pm, Tuesday 14th October

    In Vandenberg, 2nd Floor, Michigan League

  • Coffee Break

    At 2:30pm to 3:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • HACKATHON

    At 3:00pm to 4:00pm, Tuesday 14th October

    In Room D, 3rd Floor, Michigan League

  • Science Track: Data integration as the centerpiece in translational research

    by Gerrit Meijer

    Translational research aims to bring our increasing knowledge of biology as new diagnostic and therapeutic solutions to patients, thus changing clinical practice. This requires solid evidence, coming from high quality studies that integrate disease phenotype and read outs of biology. For this purpose, originally siloed domains like clinical registries, imaging, biobanking and omics need to converge. Within the European Strategy for Research Infrastructure (ESFRI) multiple biomedical science infrastructures like BBMRI, EATRIS, and ELIXIR have taken up this challenge, e.g. in the context of the BioMedBridges program.

    At 3:00pm to 3:30pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Technical Track: A cross platform genotype-phenotype data model for biomarker discovery and validation

    by Jonathan Sheldon

    Learn how you can enhance tranSMART to accelerate discovery by integrating multi-sourced “Omics”, Real-World, EMR and Clinical Trial data securely at scale with the Oracle Translational Research platform

    At 3:00pm to 3:30pm, Tuesday 14th October

    In Vandenberg, 2nd Floor, Michigan League

    Coverage slide deck

  • Science Track: The next generation of psychiatric pharmacogenomics research and tranSMART: Status report and future plans.

    by Brian D. Athey and Gerry Higgins, M.D., Ph.D.

    Psychiatric Pharmacogenomics has been demonstrated to have value to patients suffering with Treatment Resistant Depression (TRD). This method utilizes Single Nucleotide Polymorphisms (SNPs) and Copy Number Variants (CNVs) in a defined base set of pharmacokinetic and pharmacodynamic genes. This ‘combinatoric genotype’ is then related to a patient’s drug metabolizing phenotype, allowing personalization of drug treatment to be offered by the physician to the affected patient, many of whom have failed earlier treatment. Experiments to this pharmacogenomic panel are currently being planned, to be implemented along with available on the tranSMART v. 1.2 data integration and analysis platform. Prototypes of this psychiatric pharmacogenomics workbench will be discussed.

    At 3:30pm to 4:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

    Coverage video

  • Technical Track: The transmart-core-api and -core-db plugins

    by Gustavo André dos Santos Lopes

    The transmart-core-api and transmart-core-db modules are now more than 18 months old, but they are not well known by the community. An overview of these modules and where they fit in the application will be presented. The RESTful API module and the across trials implementation will be shown as examples of the advantages brought by having an API and SPI.

    At 3:30pm to 4:00pm, Tuesday 14th October

    In Vandenberg, 2nd Floor, Michigan League

    Coverage slide deck

  • Accelerating Parkinson’s disease research through tranSMART

    by Ken Kubota

    The Michael J Fox Foundation is planning and preparing to make many of their already publically available datasets viewable and analyzable on a cloud instance of tranSMART for the research community. By offering this additional service through tranSMART researchers will save time with the ability immediately interrogate the data to answer long standing questions on PD rather than organizing the data.

    At 4:00pm to 4:45pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

    Coverage video

  • SPONSOR: Thomson Reuters

    by Andy Hope

    Data sharing, data mining and data analysis in tranSMART in the Genomic Era. New initiatives from Thomson Reuters to accelerate value creation in translational science.

    With new functionality around NGS data introduced into V1.2 of tranSMART learn about new capabilities and initiatives under way at Thomson Reuters to help increase the value of your genomic data for patient stratification.

    At 4:45pm to 5:00pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Day 1 Summary

    by Keith Elliston

    At 5:00pm to 5:15pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

  • Poster Session

    The Posters and their authors will also be on display during the Reception at their option.

    Seek them out during the Reception if you have questions.

    At 5:30pm to 9:00pm, Tuesday 14th October

    In Concourse outside Ballroom 2nd Floor, Michigan League

  • Reception and Awards Ceremony

    by Keith Elliston, Kees van Bochove and Peter Shaw

    A celebration of the release of v1.2 of the tranSMART Platform.

    The Reception is sponsored by the Hyve and BT - thank them for their support!

    The development community brought together the many branches of the Platform that were spawned in part from the Paris Meeting. During a long summer of coding, testing, bug fixing, re-testing, the team from several different organization, working with the tranSMART coordination, brought the v1.2 to stability and ultimately a release!

    We celebrate their accomplishment and recognize key individuals for their efforts!

    The Posters and their authors will also be on display during the Reception.

    At 5:30pm to 9:30pm, Tuesday 14th October

    In Ballroom 2nd Floor, Michigan League

    Coverage slide deck

Wednesday 15th October 2014