2019 LabKey User Conference & Workshop | Seattle, WA
$550.00 – $1,300.00
October 3-4, 2019
Pan Pacific Hotel, Seattle, WA
Join us for the 2019 LabKey User Conference and Workshop! This two-day event will include a full program of user presentations, technical workshops, and networking opportunities. Attendees of the LabKey User Conference also have the unique opportunity to work side-by-side with LabKey developers during open work sessions and provide feedback on new LabKey development.
Attendees will leave this event with an expanded technical knowledge of LabKey Server and lasting connections with other LabKey users.
Thursday, October 3rd
Day one at the LabKey User Conference is all about connecting with other LabKey users and learning more about LabKey solutions through collaboration.
Friday, October 4th
Day two at the LabKey User Conference is focused on connecting with the LabKey team and expanding your technical knowledge of the LabKey platform. Whether you are a new user attending LabKey Server Training or an experienced LabKey developer working side-by-side with a LabKey dev to solve a current challenge at our open work sessions, you will be sure to end day two with an expanded understanding of LabKey. Tech Talks, open work spaces, and LabKey Fundamentals Training run concurrently throughout the day. Attendees can feel free to move between rooms and sessions.
Day 1 Program
Thursday, October 3
A Wayfarer’s Guide to the Galaxy of LabKey inside the NIHR Oxford Biomedical Research Center
Oliver Freeman, Oxford Biomedical Research Centre Clinical Informatics Group, University of Oxford We will discuss a few of the use cases and key challenges of using LabKey inside the NIHR Oxford BRC starting with one of our first LabKey projects as a data collection tool for our Hepatology Research Project. This is a LabKey study with a custom-built UI on top of the LabKey UI and utilises LabKey ETLs for extracting information to be fed to the CDW for circular population. We will then look at the NIHR HIC Hepatitis Project and the way LabKey is used to allow submission of files into the collation system, followed by the viewing and querying of the collated data through LabKey’s external schemas. From here we will look at the deployment of LabKey inside the NIHR Oxford BRC and how we maintain multiple live copies with relatively little effort. Finally, we will explore the future (grand scheme) of our use of LabKey as a portal for clinical research data products; designed using the Metadata Catalogue, produced from the Clinical Data Warehouse and then rendered into LabKey’s datasets using project and folder level security combined with LDAP authentication to control who has access to the data product, in theory involving little, to no, development time from the Clinical Informatics Group.
Mapping Cell Line Development Workflows with LabKey Biologics
Bo Zhai, Cell & Developability Science, Janssen Research & Development As biopharmaceuticals have been at the center stage of the pipeline of almost every pharmaceutical company, high-yield, stably expressing cell lines are of critical importance for economically viable biopharmaceutical production processes. Tracking CLD process have been proven challenging given the number of clones generated, as well as tests performed to identify producer cell lines suitable for industrial, large-scale manufacturing processes. Using LabKey Biologics, we mapped the whole cell line development process with proper linage tracking. Associate the molecule entity as well as analytical testing information with samples at different CLD stages effectively reduced clone selection timeline.
LabKey for Multicenter R&D on Biofuels and Bio-based Products
James R Collett, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory (PNNL) The Feedstock-Conversion Interface Consortium seeks to understand and mitigate the effects of feedstock variability on system performance in the production of biofuels and bioproducts from biomass. We are using LabKey running on AWS as a common platform for data integration, analysis, and dissemination among task teams distributed across eight Department of Energy national laboratories. Information being handled in LabKey includes bioreactor and other time series process data, process feedstock and intermediate sample tracking and metadata, laboratory assay results, and dataset integration within studies focused within and across unit operations. Opportunities and challenges in adapting LabKey to support industrial biomanufacturing workflows will be discussed.
LabKey and ORIEN Informatics at City of Hope
Vincent La, City of Hope The Oncology Research Information Exchange Network (ORIEN) is a consortium of 18 institutions across the nation that brings together clinical and genomic data to further precision-based therapies. All patients are under a common protocol known as Total Cancer Care. Patients enrolled in this protocol are followed throughout their life allowing respective member sites to collect both clinical and genomic data. Specimens obtained from patients undergo whole exome sequencing and whole transcriptome sequencing at a qualifying vendor. City of Hope, the third institution to join the consortium, has recently moved forward with ORIEN and has begun sending specimens for sequencing with corresponding clinical data. As such, the institution has developed an ORIEN Informatics roadmap to support the data acquisition, governance, access, and downstream analytics. The roadmap supports Laboratory Information Management System (LIMS) data for specimen collection, clinical data stored in City of Hope’s enterprise data warehouse (EDW), and genomic data that will be accessible through the cloud as well as within City of Hope’s HPCC environment. Since the data of interest exists in disparate sources, a software solution was chosen in our roadmap for integration across systems. LabKey Server, an open source platform, is that solution. LabKey provides a graphical user interface, querying capabilities, and report building tools. The platform seamlessly integrates with the EDW, provides analytics of meta-data, supports API development, allows for collaboration, coordinates workflows, maintains an audit trail in a compliant environment, and acts as a user-friendly front door to many systems. LabKey will support the overarching goal of the ORIEN informatics roadmap to provide clinicians and researchers with data and tools to progress precision medicine.
Molding and Maximizing the LabKey Platform for Clinical Translational Research
Anthony Corbett, Research Data Integration and Analytics Group, University of Rochester Medical Center (URMC) This talk will review how the Research Data Integration and Analytic Group uses the LabKey platform to manage the research data life cycle and improve data management workflows and communication among clinical and lab study teams. From data capture, querying and reporting I will briefly discuss and show examples of integrating external operational systems like electronic data capture systems (REDCap) and biospecimen and inventory management systems (BSI), as well as, managing data from laboratory assays and instrument generated output. Finally, I will show examples of reporting and visualization in study dashboards.
Discussion Group: Multi-Attribute Method (MAM) Analysis
with Richard Rogers, co-chair of the MAM Consortium Characterization of complex biotherapeutics using highly resolving mass spectrometry has resulted in a better understanding of the post-translational modifications (critical quality attributes (CQAs)) that are crucial for safety and efficacy. These CQAs are used to guide the manufacturing process and the release strategy for biotherapeutics. A mass spectrometry-based multi-attribute method (MAM) has been developed and implemented at many Biopharma Companies. MAM monitors known CQAs but also can identify new CQAs on the biotherapeutics. This group discussion will explore how Panorama (LabKey Server’s targeted mass spec module) and its companion tool, Skyline, can provide tools to enable MAM analysis. Leveraging Panorama and Skyline, for MAM, has the potential to reduce the cost and increase efficiencies for MAM compared to traditional non-mass spec assays.
Day 2 Tech Talks
Friday, October 4
Day two at the LabKey User Conference is focused on connecting with the LabKey team and expanding your technical knowledge of the LabKey platform. Whether you are a new user attending LabKey Server Training or an experienced LabKey developer working side-by-side with a LabKey expert to solve a current challenge at our open work sessions, you will be sure to end day two with an expanded understanding of LabKey. Technical talks given by LabKey experts offer insight into specific areas of the platform and the opportunity to ask questions. This year’s topics are listed below. Tech talks, open work spaces, and LabKey Fundamentals Training run concurrently throughout the day. Attendees can feel free to move between rooms and sessions.
ReactJS Development: Getting Started
Learn about best practices for building ReactJS based applications with LabKey. Development tips and tricks, practical examples, and advice for developers.
Learn how Sample Derivation works in LabKey Server. Explore underlying data structures and use of APIs. See how to access lineage in LabKey.
Visualizing LabKey Data
An overview of how external integrations expand your options for creating reports and visualizations. See how to present LabKey data using Tableau, Spotfire, Matlab, Shiny and more!
LabKey Development Process
Find out about the internal LabKey development process. Covers feature branch workflow, pull requests, test automation, formal and patch releases, and other things external developers need to know.
Quality Control with LabKey Server
Explore numerous strategies for quality control and reporting within LabKey Server and Biologics. Learn to incorporate QC trend reporting, automatic QC options during import, and setting of QC states into your workflows.
LabKey User Conference & Workshop attendees can book accommodations for a reduced nightly rate at the conference hotel. Limited rooms are available; we recommend you book accommodations as early as possible. (For the reduced rate, reservations must be made before September 9, 2019).
Hotel: Pan Pacific Hotel
Address: 2125 Terry Ave, Seattle, WA 98121
Conference Room Rate: $235/night
Please contact the Pan Pacific Reservations department using the phone or email below to make reservations. When making your reservation, please reference the LabKey 2019 User Conference to receive discounted rates. Discounted rooms are available on a first-come-first-served basis, and all conference reservations must be received by no later than 5:00PM PST on September 9, 2019. To avoid cancellation fees, guests may cancel their reservation before 4 pm PST at least 48 hours prior to arrival.
2125 Terry Ave, Seattle, WA 98121
Seattle-Tacoma International Airport offers a variety of transportation options for travelers.
Major ride sharing services, including Uber and Lyft, offer pick-up and drop-off service to airport travelers.
Upon arrival at Sea-Tac Airport:
- Request your ride after you’ve landed and collected your bags.
- From the main terminal, follow the directions to ground transportation/the parking garage.
- Head towards the sky bridges (they are halfway between the top and baggage floors of the main terminal).
- Once in the parking garage, go down to the third floor and look for Row i.
- There you’ll find the Rideshare/TNC pickup zone.
All rental car companies currently operating at Sea-Tac Airport operate at a separate rental car facility, with dedicated shuttle buses operating on a 24-hour-a-day schedule. Two passenger pick-up areas are located outside baggage claim at the north and south ends of the main terminal.
Upon arrival at Sea-Tac Airport:
- Proceed to the baggage claim level and pick up your checked bags.
- Exit the sliding glass doors near carousel #1 or #15 and walk to one of the two designated shuttle bus pick-up areas.
- Shuttle buses depart frequently for the rental car facility.
If you are returning a vehicle, take SR518 and follow signs for the Rental Car Facility.
Driving Directions from Sea-Tac International Airport
Travel north on I-5, exit left at Seneca Street and turn right on 6th Avenue. Turn right on Westlake Avenue, right again on Denny Avenue and right once more on terry Avenue, where the hotel plaza entrance is located on your right.
James R Collett, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory (PNNL)
Presentation Title: LabKey for Multicenter R&D on Biofuels and Bio-based Products
Jim Collett is a bioprocess scientist who combines computational and experimental approaches in industrial biotechnology R&D for the production of biofuels and bioproducts. His work at the Pacific Northwest National Laboratory (PNNL) ranges from genomes to biorefineries, and has included metabolic network modeling, strain development, bioreactor scale-up, online spectroscopy for process analysis and control, and data integration for techno-economic analysis of biochemical manufacturing.
Anthony Corbett, Research Data Integration and Analytics Group, University of Rochester Medical Center (URMC)
Presentation Title: Molding and Maximizing the LabKey Platform for Clinical Translational Research
Anthony Corbett has a MS in Bioinformatics from Rochester Institute of Technology and has 10 years of experience as both a Software Engineer and Informatics Analyst. He is Technical Lead for the Research Data Integration and Analytics Group within the Clinical Translational Science Institute. The group has been using the LabKey platform to provide basic science and clinical translation informatic solutions since 2010 to a broad variety of departments and projects at the University of Rochester Medical Center.
Oliver Freeman, Oxford Biomedical Research Centre Clinical Informatics Group, University of Oxford
Presentation Title: A Wayfarer’s Guide to the Galaxy of LabKey inside the NIHR Oxford Biomedical Research Center
Oliver Freeman has an MSc w/ Distinction in Computer Science from the University of Birmingham and has worked as a Software Engineer within the Clinical Informatics Group for five years. When Oliver started with the group, he redesigned and built the Genomics England Ltd Data Acquisition and Management System (DAMS), during which time he worked closely with LabKey, to engineer and optimise the interaction of DAMS with the LabKey Clinical Review Portals. Whilst doing this he repurposed the same data collection system to help collate data for the NIHR Health Informatics Collaborative (NIHR HIC) Hepatitis theme. Since then he has rebuilt the CIG’s Metadata Catalogue backend in Grails and augmented it to make future development faster and easier. He recently took over as the Technical Lead and Architect on the OUH NHS Foundation Trust’s Clinical Data Warehouse. This is aimed at collating all the clinical data from across the Trust’s systems into one standardised and modularised location for clinical and research use. The CIG uses LabKey to provide IG approved, research data products in a secure way to each team who needs them.
Vincent La, City of Hope
Presentation Title: LabKey and ORIEN Informatics at City of Hope
Vincent La has been leading the informatics component of ORIEN (Oncological Research Information Exchange Network), a Precision Medicine research initiative at City of Hope Cancer Research Hospital in Duarte, California. He is the team’s project and data lead, bringing his experience in product management and data expertise from health startups and other health enterprises like Kaiser Permanente to the role. With the genomics from the ORIEN study, he works in the space of Radiogenomics where he collaborates with radiologists, data scientists, and the Precision Imaging Lab in discovering biomarkers for brain cancers and success or failures of CAR-T cell immunotherapies. Vincent has considerable experience in R programming and SQL, which he has used for quality control, data processing, and reporting for research at City of Hope. He received his Bachelor’s in Public Health: Infectious Diseases from UC Berkeley. Vincent has a desire to make an impact in Precision Medicine.
Bo Zhai, Cell & Developability Science, Janssen Research & Development
Presentation Title: Mapping Cell Line Development Workflows with LabKey Biologics
Bo Zhai is a Senior Scientist at the Cell & Developability Sciences (CDS) group of Janssen Research & Development. He provides mass spectrometry characterization to support programs in the large molecule value stream in both discovery and early development. He also leads efforts in building automated workflows for high throughput data analysis. Bo was a Mass Spec Analytic Scientist at St Jude Children’s Research Hospital developing multiple mass spectrometry based analytical assays for the characterization of biopharmaceuticals under GMP setting. Bo holds a PhD in Biochemistry and Molecular Biology from the Institute of Biochemistry and Molecular Biology, Chinese Academy of Sciences and had his postdoctoral training at Harvard Medical School.