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.
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
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.
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.
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.
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.
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.
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
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.
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.
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
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.
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.
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.
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.
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.
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.
tranSMART is used today at Harvard Medical School as a comprehensive clinical and genomic database for enabling a multidimensional perspective of autism spectrum disorder and Phelan-McDermid Syndrome (n=1100 patients worldwide). Two live demos of tranSMART will be presented presenting the various sources as Registry data, Patient reported outcome, longitudinal EHR, Patient consent, Biobank, all Exome sequencing data and knowledge from Clinical notes.
14th–16th October 2014