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User Conference 2013 Logo

 

Thanks to all who joined us for the 2013 User Conference and Workshop! We were excited to see a great mix of new faces and established users highlighting the global reach of LabKey Server - attendees from Bern to Bethesda shared their experiences with research taking place all over the world, from Seattle to Cape Town to Wardha. In the videos below, our guest presenters share how they utilize the LabKey Server platform to perform collaborative and reproducible research with globally distributed teams. We hope you're as excited to hear their stories as we were!

2013 Conference Presentations:

Topic The Hutch Integrated Data Repository Archive (HIDRA)
Speaker Paul Fearn, MS, MBA; Biomedical Informatics Lead, Fred Hutchinson Cancer Research Center

Bio

Paul will cover the HIDRA project, which is a collaborative effort across the Fred Hutchinson Cancer Research Center (FHCRC) and University of Washington (UW) Cancer Consortium partner institutions. HIDRA aims to provide clinicians, investigators and staff with simplified and ready access to linked data about all subjects, studies, biospecimens and genomic or other assay data. In 2014, HIDRA will incorporate clinical data from approximately 150,000 Consortium patients and subjects, linked to over 60,000 biospecimens for potential research. This resource will support precision oncology efforts across the Center. HIDRA is being implemented on the LabKey Server platform. More...


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Topic ITN TrialShare: Advancing clinical trial transparency through data sharing
Speaker Tanya Antonille, MPH; Director, Data Management, Immune Tolerance Network

Bio

The movement towards improved clinical trial transparency is steadily growing, driven forward by the scientific and ethical concerns raised by the significant underreporting of clinical trial results. The FDA has recently announced that it intends to consider making public de-identified and masked subject level data to improve the efficiency and effectiveness of medical product development recognizing that external experts should become actively engaged in the research. As part of its commitment to being on the forefront of this transparency movement the Immune Tolerance Network (ITN) has developed ITN TrialShare using the LabKey Server platform. More...


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Topic Putting the pieces together: Integrated Research Data Management Using the LabKey Server
Speaker Jeanne Holden-Wiltse, MPH; Data Management Co-Director, Respiratory Pathogens Research Center (RPRC)
and
Andy Straw, MS; BLIS Lead Developer/Administrator, University of Rochester Medical Center

Bios

A dynamic research environment has many moving and changeable parts creating challenges to research study data management. Commonly study protocols are modified, subject data collection forms revised, novel assay designs created and new high throughput technology data become available. We have developed the Bio Lab Informatics Server (BLIS), based upon the LabKey Server, to provide rapid development and deployment of tools for data capture, reporting/visualization and communication, as well as implementing analysis workflows to respond to the data integration needs across multiple studies/networks and for multiple immunology, virology, metagenomics and genomics labs. Our goal is to provide high quality, real-time data integration enabling study team members to actively use BLIS for study monitoring, data quality review, data exploration, and analysis. In this talk, we will describe how we use various features and extension points of LabKey Server to achieve this goal.

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Topic Using LabKey and the R statistical language to facilitate data integration and reproducible research within the Human Immunology Project Consortium
Speaker Raphael Gottardo, PhD; Associate Member, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center

Bio

The Human Immunology Project Consortium is a major collaborative effort that is generating large amounts of cross-center and cross-assay data – including high-dimensional data – to characterize the status of the immune system in diverse populations under both normal conditions and in response to stimuli. This large data problem has highlighted the importance of implementing data management and analysis plans as an integral part of the program. To try to solve this problem, we are currently developing a database and analysis platform based on the LabKey Server and the open-source R project that combines LabKey's data management system with the analysis power of R. Here I will discuss the current state of the project by giving some specific examples of the tools we have built so far and their application within the HIPC project and will briefly discuss some of the ideas we'd like to implement in the future.


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Topic JDRF nPOD DataShare: Accelerating Type 1 Diabetes Basic Science Research
Speaker John Kaddis, PhD; Data Management Core Director, Network for Pancreatic Organ Donors with Diabetes (nPOD); Staff Scientist. City of Hope
and
Les Jebson, MHA; Executive Director, University of Florida Diabetes Center of Excellence

Bios

The Network for Pancreatic Organ Donors with Diabetes (nPOD) program is a unique multi-national resource funded by the Juvenile Diabetes Research Foundation (JDRF) designed to provide scientists with precious and difficult to obtain human tissue samples, in order to understand how and why type 1 diabetes develops. DataShare is a tool being developed to collaboratively store, organize, analyze, and share data around common biospecimens provided by nPOD. This presentation will detail how nPOD is customizing and extending the LabKey Server platform to meet the needs of DataShare users.


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Topic The use of LabKey Server in a globally distributed research project
Speaker Laura Chery, Program Manager, and Jenny Maki, PhD, Research Coordinator, South Asia International Center of Excellence for Malaria Research (ICEMR)

Bios

The MESA-ICEMR team has worked closely with the LabKey team to develop customized web-based assay and real-time visualization functionality for malaria diagnostic testing, PCR, parasite culture adaptation, selection of parasites under experimental antimalarial pressure and drug sensitivity testing. Data generated at MESA-ICEMR labs in India and captured in LabKey related to the traits and in vitro behavior of parasites is combined with demographic and clinical data captured in REDCap. We will describe the unique aspects of our customized LabKey system and discuss how the MESA-ICEMR uses integrated clinical and laboratory study data to identify associations between the adaptability of malaria parasites and drug resistance, virulence and human immunity at diverse sites across India.


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2013 Workshop Lightning Talks:

During the Workshop, attendees worked on self-selected projects with the aid of LabKey Software’s subject matter experts. Developers from the LabKey Software team were on hand to solve tough problems one-on-one and in small groups. In the talks below members of the LabKey User Community share how they customize LabKey Server to meet their institutions’ needs.

Topic Building Rich Electronic Case Report Forms in LabKey
Speaker Anthony Corbett, University of Rochester, Department of Biostatistics and Computational Biology


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Topic Lung Cancer Research Initiative - Department of Defense
Speaker Bront Davis, Senior Web Application Developer, Markey Cancer Center/Kentucky Cancer Registry, University of Kentucky


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Topic TrialShare - Extending the LabKey Framework
Speaker Dennis Wightman, OCA, TrialShare Lead Programmer, Immune Tolerance Network


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Topic A Framework for Java Assay Module Development
Speaker Andy Straw, MS, BLIS Lead Developer/Administrator, University of Rochester Medical Center


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Archive of 2013 Conference Announcement