Director of Industry Consulting, Genomics England
This presentation will explore how Genomics England is constructing clinical, phenotypic and sequence data in LabKey Server to allow researchers to look for ‘signal’ across all subject characteristics. David Brown will also share how the team has overcome complex challenges to filter out important genotypic data from sequence information.
David has over 25 years experience in the pharmaceuticals industry working across IT, clinical research and commercial. Within Genomics England David works with industry partners to ensure they can effectively us the Genomics England research dataset.
Basu Chaudhuri, Ph.D.
Director, Software Engineering, Allen Institute for Cell Science
The mission of the Allen Institute for Cell Science is to integrate diverse technologies and approaches at a large scale in order to study the cell as an integrated system, and to predict cell behaviors. The current project uses live cell imaging of major cellular organelles to establish a platform for developing predictive and mechanistic models. Our approach is based on an integrated workflow with interdisciplinary teams working towards a common goal. Using human induced pluripotent stem (hiPS) cells the Gene Editing team creates new cell lines, tagging certain structures with fluorescent proteins. Working with the Assay Development team they take the cell lines through a rigorous quality control process to ensure the cells behave normally. The Microscopy team images these cells, and working with Assay Development they develop tools to process the images. Using machine learning techniques the Modeling team uses the images and the data to generate predictive models. The Animated Cell Team, working with Modeling visualizes the data and the images. All of this is made public on our website http://allencell.org. The Software Engineering team provides the infrastructure to support the data management and flow integral to the above workflow. LabKey plays a key role in providing much of the LIMS capabilities integral to the first part of the workflow tracking gene editing data and microscopy cell culture data. Additionally we are using LabKey to surface views into our file management system.
Basu Chaudhuri joined the Allen Institute for Cell Science in 2016 as the Director for Software Engineering. His team is tasked with implementing the data management and computation infrastructure to handle the petabyte scale data being produced at the Institute, supporting its mission to combine diverse technologies and approaches in order to study the cell as an integrated system.
Basu received his Ph.D. in Theoretical Physics from Cornell University. He started his career as the first employee at Gene Network Sciences, now GNS Healthcare where he developed the VisualCell/DigitalCell platform for in silico biology to build predictive models while setting up the IT and network infrastructure. He spent 9 years at Blue Origin as a part of a commercial spaceflight endeavor. There he developed software to author and visualize complex systems automation and a framework for distributed computational workflows spanning the local machines and the AWS cloud dynamically provisioning clusters on demand. He also led a small team to develop a scalable geographically distributed micro-services-based time series data management system.
J. Alex Taylor, Ph.D.
Scientist IV, Molecular Design Group, Just Biotherapeutics
Just Biotherapeutics was formed with the goal of inventing and internally applying the technologies required to drastically reduce the cost of biotherapeutic development and manufacturing. To realize this goal we must measure and capture all aspects of our development process from molecular properties through production characteristics. LabKey Biologics enables this registration and data capture across a wide variety of biopharmaceutical steps and also enables high throughput, plate-based automation efforts. Utilizing a combination of structured data and full entity and sample lineages we are able to build predictive models which allow us to refine our processes to expand capacity and shorten development times, resulting in lower cost biotherapeutics for the world.
Alex Taylor is a scientific software developer in the Molecular Design group at Just Biotherapeutics. He is the developer of Abacus, Just’s platform for the analysis and engineering of antibodies and antibody-like molecules, which is used to design therapeutics with improved process and manufacturing characteristics. Alex is also leading Just’s effort to drive development and use of the LabKey Biologics system for end-to-end data capture, process automation, and data mining.
Alex received his Ph.D. in Biochemistry from the University of Washington where he studied protein chemistry and pioneered software for the interpretation of protein mass spectrometry data in the laboratory of Ken Walsh. In 1997, Alex joined the Bioinformatics group at Immunex where he supported the Proteomics & Protein Chemistry groups by developing specialty scientific applications and infrastructure. During more than a decade as part of the Translational Sciences and Research Informatics departments at Amgen, Alex designed and implemented infrastructure and numerous systems for antibody analysis/engineering, genomics, proteomics, clinical immunology, sequence analysis, and bioinformatics.
Nicole Villaverde, MS
Research Program Coordinator, Laboratory of Dr. Judy Cho, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
World renowned for their scientific discovery, the Icahn School of Medicine at Mount Sinai contains many research projects with varying objectives and would greatly benefit from a secure platform to share data across studies. Through combination of multiple independent databases with a similar focus, the LabKey Server-based Inflammatory Bowel Disease (IBD) Integrated Database provides a clear overview of available research resources. IBD-centered studies at Mount Sinai have collected a plethora of data and samples from over 6,000 IBD-affected and non-affected study participants. Study contributions include large genotype datasets, questionnaire responses, clinical data, and a variety of samples, such as DNA, sera and tissue. In addition to providing a valuable resource for the Mount Sinai research community to make major contribution in understanding IBD, the integrated database also guides new research projects through the supply of a framework, including data templates and dictionaries.
Nicole Villaverde is a Research Program Coordinator for the Genetics and Genomic Sciences Department at the Icahn School of Medicine at Mount Sinai. In this position, she guides research projects through the management of their methodologies and analysis. Her primary research focus is Inflammatory Bowel Disease (IBD), with much of her work on IBD-centered studies and the NIDDK IBD Genetics Consortium. One of her major initiatives is the integration of independent study databases to one system to increase resource utilization, collaboration, and research discovery. Previously, Nicole spent most of her time in the laboratory performing functional studies on disease associated variants, which she still enjoys doing when time permits.
Wayne A. Borum
Information Systems Manager, Oregon National Primate Research Center
The maintenance of a large colony of non-human primate research and breeding animals requires a sophisticated computer application to manage a wide range of interrelated health care data and animal husbandry information, as well as administrative and billing records. The LabKey Electronic Healthcare Records (EHR) module provides the foundation for creating a comprehensive records system for managing our animal data on an individual and colony-wide basis. This presentation will provide a brief overview of how we have implemented the LabKey EHR module at the Oregon National Primate Research Center.
Wayne Borum has been part of the IT department at ONPRC through three complete technology changes and now leads a team of 3 developers in maintaining and enhancing the LabKey based electronic health records system that has been branded PRIMe (Primate Records and Information Management) at the Center.
Paul A. Fearn, Ph.D., MBA
Chief, Surveillance Informatics Branch, Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI)
Towards a Scalable Clinical Data Annotation and Processing Pipeline to Support Cancer Surveillance
Central cancer registries that are funded by the NCI’s Surveillance, Epidemiology, and End Results (SEER) program collect cancer diagnosis, treatment, and survival data for about 30% of the US population. This national resource fuels thousands of cancer research projects and national cancer statistics. The SEER program is investing in tools, processes, and pilot projects to advance, standardize, and scale the application of computation (e.g., natural language processing, machine learning) for information extraction, de-identification, and data quality improvement. The LabKey NLP Pipeline is an integral part of this work.
This presentation will cover the background and goals of the SEER program, work in-progress to create and scale processes for clinical annotation and automation, and the role and enhancements of LabKey to support pilot projects.
Principal Scientist, MedImmune, a Member of the AstraZeneca Group
New generation of proteomics technology using high-resolution and fast tandem mass spectrometry, coupled to multiplex-quantitation technique can routinely quantify most of the proteomes (~8000 proteins in cell lysates or >1000 proteins in plasma). After careful evaluation, an open-source platform, LabKey, was introduced to manage the proteomics and other data. In this presentation, we will describe the overall approaches, data architecture, pipeline and various customizations made possible by the power and flexibility of LabKey platform.
One of the first workflow being implemented is TMT-based multiplex quantitation of the total proteome. Following the data acquisition and processing in ProteomeDiscoverer, the experimental design, peptide and protein identification and quantitation are imported into LabKey where a custom-built data ingestion pipeline written in R will transform the data and prepare them for deposition in a Microsoft SQL database. Additional workflows will be implemented to support label-free quantitation by Maxquant. Targeted quantitation via MRM will also be supported via SkyLine/Panorama integration in LabKey.
One of the key strengths of LabKey is the flexibility of custom query, visualization and report with SQL/R or point-n-click interface. For example, boxplot, volcano plot can be readily generated in LabKey and shared with other researchers. Once a study is established in LabKey, its experimental design, LcMsMs runs, protein identification and quantitation can be inspected via the web-interface as data grids or plots. To visualize the raw MS and MS/MS data, another open-source program, OpenSlice, was adopted. It will pre-process the raw files to allow instantaneous review of spectrum and XIC trace. We’ve integrated both OpenSlice and LabKey to enable drill-down of the experimental evidences from summary levels downward.
Wen Yu is a principal scientist in the research bioinformatics group at MedImmune, AstraZeneca, where he is leading the efforts to develop, implement and support novel bioinformatics solutions designed to drive the interrogation of human disease biology using proteomics and other data types. Prior to joining MedImmune, he was a member of computational biology group at Amgen working on the biomarker discovery and development in early clinical trials. Wen started his career with Genetics Institute in the field of biological mass spectrometry and proteomics.
Assistant Director, Systems Programming & Administration, Immune Tolerance Network
Two New Ways of Sharing Data with the LabKey Platform
The Immune Tolerance Network’s TrialShare web application has been sharing clinical, mechanistic, and specimen data for immunological clinical trials for several years now. TrialShare, based on a custom-built version of the LabKey platform, has been looking for new ways to share very large files while keeping them in scientific context. By partnering with LabKey and Globus, TrialShare will now be able to allow users to join study information from datasets with corresponding files on the ITN Globus Endpoint and initiate endpoint downloads from inside TrialShare using Single Sign On. We’d also like to introduce a small open source client side application that allows end users to remotely query any LabKey platform with LabKey SQL and populate a local database with the results of their query. This tool was developed internally by the TrialShare programming team to assist in our internal processes and data validation, but should be of great use in making data sharing from any LabKey platform easier and less error-prone.
LabKey Tech Workshops
Assays, Studies, Lists, Specimens, and more! Data Modeling in LabKey Server
Presenter: Karl Lum, Dave Bradlee
In this workshop, the LabKey team will explore the various data types available in LabKey Server, how their capabilities compare, and how to determine which is right for different usage scenarios.
Developing with the New LabKey Server UI
Presenters: Nick Kerr, Cory Nathe
In this workshop, Nick Kerr will walk through the recent changes to the LabKey Server UI infrastructure and how these changes impact/enhance development of LabKey Server-based applications.
Configuring Your LabKey Server for Security & Compliance
Presenter: Josh Eckels, Angelica Omaiye
In this workshop, Josh Eckels will share best practices for configuring you LabKey Server instance to meet the security and compliance needs of your organization as well as an in depth look at recently added functionality to support HIPAA, FISMA and CFR Part 11 compliance.
Building Biologics: Extending LabKey Server Foundation to Support Large Molecule Research
Presenters: Kevin Krouse, Josh Date
In this workshop, Kevin Krouse will walk through how his team utilized LabKey Server platform as the foundation for the LabKey Biologics application and extended it to support a specific user case; large molecule research and development.