Wednesday April 6th, 2016
tranSMART Community Meeting co-hosted with Thomson Reuters and the Pistoia Alliance
with tranSMART 2016 Corporate Sponsors GeneDx and Rancho BioSciences
5:45 - 8:00 PM at the Seaport Hotel Ballroom
Opening - Rudy Potenzone, VP Marketing, tranSMART Foundation
Welcome and Thomson Reuters Update - Chris McKenna
Welcome and Update on the Pistoia Alliance - Carmen Nitsche
Introduction of the tranSMART Foundation Corporate Sponsors:
GeneDx: Lena Zogaj
Rancho BioSciences: Laura Brovold
Welcome and Update on the tranSMART Foundation - Keith Elliston, CEO, tranSMART Foundation
Dr. Elliston reviewed the current accomplishments of the Foundation and described the upcoming release of the tranSMART Platform as well as the Roadmap for the next 18 months.
Integrating Actigraphy Data from the L-DOPA Response Trial with Clinical Observations in tranSMART
Presented by: Stephen Wicks, Senior Data Scientist, Translational Medicine, Thomson Reuters
Parkinson’s disease is one of a class of disorders characterized by a variety of motor-based phenotypes related either to primary disease progression (e.g. bradykinesia, intentional tremor) or to a motor pathology that arises from long-term treatment with levodopa-based medications (e.g. dyskinesia). The strong movement component associated with the pathology of Parkinson’s disease provides clinicians an opportunity to utilize wearable, accelerometer-based sensors to monitor patient behavior outside the clinic in a continuous fashion. While continuous evaluation of motor status can be informative, placing this kind of data into the context of clinical, demographic, and omics data could potentially yield additional insights. We will describe our experiences integrating actigraphy data with clinical observations and endpoints in the translational platform, tranSMART.
OpenClinica and tranSMART: two open source platforms to address clinical trial data collection and management
Presented by Tatiana Khasanova, PhD, Director of Contract Services at Rancho BioSciences
tranSMART is a translational research platform that allows users to explore clinical and molecular data. One of the platform’s advantages is that information can be easily found, explored, and shared between different research groups or clinical sites. We will discuss one of the projects where we implemented Open Clinica as clinical data QC and management module in theend-to-end solution involving tranSMART.
Understanding ETL Procedures and Options: Comparative Analysis of Various ETL Scripts, Their Limitations & Improvements
Presented by Yulia Skovpen, PhD, Scientist at Rancho BioSciences
As an end users of tranSMART our team has experience with three ETL tools: ICE, original Kettle, and TM Loader. We would like to share technical details about each approach advantages and limitations. In addition, our team had to adapt the loading scripts so they can load large quantities of genomic data in vcf format into tranSMART. We will discuss this challenging task and our approach to solving a slow loading speed problem.
Using Smart R Within tranSMART
Presented by Reinhard Schneider, University of Luxembourg
Reinhardt showed the Smart R Plugin for the upcoming release of the tranSMART Platform and described several interesting use cases that highlighted the new tool.
In a surprise demo, Dr. Schneider also showed for the first time in public, a new integration between the tranSMART Platform and the Qiagen IPA (Ingenuity Pathway Analysis) product!