2018 LabKey User Conference Presentations

Kira Misura, Ph.D.

Vice President R&D, Alder Biopharmaceuticals

Alder Biopharmaceuticals, Inc. is a clinical-stage biopharmaceutical company committed to transforming the treatment paradigm for patients with migraine and other serious neurological or inflammatory conditions. To realize that goal, Alder discovers, develops and manufactures genetically engineered therapeutic antibodies. Alder’s lead pre-commercial stage product candidate, eptinezumab, has been evaluated for migraine prevention in pivotal phase 3 clinical trials. Eptinezumab is a monoclonal antibody that inhibits calcitonin gene-related peptide (CGRP), a protein that is active in mediating the initiation of migraine.

This presentation will touch on how Alder is using LabKey Biologics in combination with LabKey Server to address varying needs associated with early and late stages in our pipeline. Our LabKey-based infrastructure is designed to provide rapid access to data and meta-data, enable new scientific insights, protect data integrity, and increase efficiency throughout the R&D organization.

Speaker Bio: Dr. Misura currently serves as Vice President, R&D at Alder Biopharmaceuticals and leads efforts in scientific data management and analysis. Previously, Dr. Misura held roles of increasing responsibility at Merck and Amgen, and led the Computational Biology and Genome Sciences department at Amgen prior to joining Alder. Dr. Misura holds a Ph.D. in Biophysics from Stanford University and a B.A. in Chemistry from Brandeis University.

Olivia Finney, Ph.D.

Correlative Studies Laboratory Manager, Seattle Children’s Research Institute

The Immunotherapy Integration Hub at Seattle Children’s conducts immunotherapy clinical trials in which a patient’s own immune cells are engineered in order to better fight cancer cells. The Correlative Studies Laboratory (CSL) focuses on understanding how these reprogrammed T cells react in each patient in terms of their persistence, functionality and efficiency at reducing tumor burden. These data, combined with manufacturing and clinical data generated during clinical trials, enable researchers to answer pressing questions with minimal time and resource investment. However, management of the data across different groups and clinical sites of these diverse datasets is complex, and informatics systems are required to integrate datasets from repositories, reference labs and clinical labs. The CSL has been working with LabKey to integrate, analyze and securely share data generated by these various teams in order to create a truly translational research model. Over the past five years, the CSL has uploaded data for six ongoing clinical trials. They have been working with the LabKey team to customize the database without the use of a full-time developer and to make use of the many “out-of-the-box” interfaces that it provides, specifically the application of the flow cytometry, luminex and general assay modules for assay data, the use of surveys to track specimens, and integration with Medidata Rave for integration of the clinical database. This presentation will highlight their work-in-progress of database development and management as the clinical trials at the Immunotherapy Integration Hub continue to expand and grow.

Speaker Bio: Olivia Finney has been leading the Correlative Studies Laboratory at the Immunotherapy Integration Hub at Seattle Childrens since 2013, where she studies the immunological factors influencing the success or failure of CAR T cell therapy in children with both blood cancers and solid tumors. Her long-term research interest is to use clinical trial samples and data to understand how the immune response responds to treatment, in particular immunotherapy. Olivia’s background includes human immunological studies at the Medical Research Council (UK) in The Gambia and Phase I vaccine studies at Seattle BioMed. She received her BSc from Imperial College London, and her PhD from the London School of Hygiene and Tropical Medicine.

Daniel Nicolalde, Ph.D.

Senior Information Processing Consultant, Wisconsin National Primate Research Center

LabKey modules provide exceptional functionality for all their clients and users. Last year, Wayne Borum from Oregon National Primate Research Center presented about the work done at their primate center that expanded the EHR module for managing non-human primate health and research records. The original code was developed for Wisconsin National Primate Research Center, and during the last eight years, five National Primate Research Centers have adopted and expanded the system. This mainly involves LabKey developers that have provided support and outcomes for each of the teams at the different primate centers. The ultimate goal is that any improvement developed for any primate center can be shared across all the centers using the LabKey server. This has been possible not without some drawbacks. During every update of the system we commonly find small and some big problems that need to be addressed either by each center or by the LabKey team.

Building on the open source model, we at Wisconsin are collaborating to use the LabKey platform in several ways. We have developed modules that can be used by other centers, such as the PrimateID and the Billing module, which will be able to be used by other centers with some small modifications. The PrimateID was completely developed in house by developers at Wisconsin.This module allows a center to uniquely identify animals within their system and assures those generated PrimateIDs are unique across centers. The Billing module, due to its complexity and importance for other centers, was contracted to be developed by LabKey. The Billing Module has first developed for Oregon Nation Primate Research Center.Based on the success and some similarities between centers, Wisconsin decided to build on top of the original code and make it more generic so that other centers can easily make use of it. During this talk Doctor Nicolalde will highlight how developers across seven primate centers and LabKey staff work together to make this sharing possible and will demonstrate how the PrimateID is used at Wisconsin and other centers.

Speaker Bio: Doctor F. Daniel Nicolalde, holds a PhD in Industrial and Systems Engineering. He graduated from University of Wisconsin – Madison while working for Wisconsin National Primate Research Center as the Unit Head of the Informatics and Data Services Unit. Since graduating, the unit has grown and expanded collaborations with other primate centers. He manages all aspects of their LabKey implementation with the help of the center’s IT unit and LabKey staff. His dissertation focused on how to design health technologies with healthy young adults, and he uses these design methodologies to involve end-users at the primate centers to improve how people use LabKey by testing and developing new interfaces to enter data into the system. He also holds a Master in Industrial and System engineering and a BS in Computer Engineering.

Brendan MacLean

Senior Software Engineer, MacCoss Lab, University of Washington

Panorama: Building a Branded Mass Spectrometry Service and Software Around LabKey Server

As a founding partner of LabKey, I was involved in crafting how the company would serve its scientific customers, and early on we decided on a model that was open source, with free installation and helped scientists to cultivate their own brands. When I left LabKey in 2008 to start work on Skyline, the now popular software for analysis of targeted mass spectrometry, I hoped to one day build a server-side component for Skyline on LabKey Server. It took over 3 years, but in 2011 the MacCoss lab at UW Genome Sciences started work on the “targetedms” LabKey module, which we branded Panorama.

Nearly 7 years later, Panorama is used by hundreds of labs worldwide via panoramaweb.org, a hosted instance of LabKey Server running Panorama, as well as on-premise at some of the world’s largest pharmaceutical companies. Working in partnership with LabKey on Panorama has both accelerated our own development efforts and also made our team feel more elastic, with LabKey developers stepping in to create new features and areas for us when funding has allowed. This presentation will focus on how the partnership between the MacCoss Lab and LabKey functions and share insights on making the most of a partnership with LabKey building on LabKey Server.

Speaker Bio: Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LabKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Mass Spec Environment and its growing worldwide user community.

Drienna Holman

Senior Project Manager, CAVD DataSpace, Biostatistics, Bioinformatics, and Epidemiology (BBE), Vaccine and Infectious Disease Division (VIDD), Fred Hutch

Jason Taylor

Bioinformatics Analyst, CAVD DataSpace, Biostatistics, Bioinformatics, and Epidemiology (BBE), Vaccine and Infectious Disease Division (VIDD), Fred Hutch

The Collaboration for AIDS Vaccine Discovery (CAVD) is an international network whose primary mission is to accelerate the development of a safe and effective HIV vaccine through a combined effort across research institutions. DataSpace (dataspace.cavd.org) is an integral part of the CAVD’s Global Access policy which requires public access to data and information from CAVD studies.

DataSpace is a data sharing and discovery tool developed to empower HIV vaccine researchers. This LabKey-based software application is designed to facilitate self-guided data exploration across studies and increase awareness of the scientific questions being evaluated in the field of HIV vaccines. Currently, binding antibody, neutralization antibody, and cellular immunoassay results from over 192 vaccine products tested in 64 studies conducted in the CAVD have been harmonized and are available for exploration and download. Data are included from both clinical trials and studies of non-human primates and other animals.

This presentation will provide an introduction to DataSpace and discuss two recent initiatives – membership expansion to the public and the release of a new interface customized to handle monoclonal antibody characterization data.

Speaker Bios: Drienna Holman and Jason Taylor are members of the Collaborative DataSpace team at the Vaccine Immunology Statistical Center (VISC) in the Hutch’s Vaccine and Infectious Disease Division. Drienna is a program manager with over 20 years experience in study and data operations for HIV vaccine trials, serving vaccine networks such as the CAVD, HIV Vaccine Trials Network (HVTN), and the AIDS Vaccine Evaluation Group (AVEG). Jason Taylor is the team’s lead bioinformatics analyst, bringing over 8 years of programming and analysis experience to the role. Jason has considerable expertise in R programming which he has leveraged for in-application reports, quality control, and data processing packages, such as the new monoclonal antibody assay data recently incorporated into DataSpace.