Presenter: Michael Graham, Research Specialist, Laboratory of David O’Connor, AIDS Vaccine Research Laboratory, University of Wisconsin-Madison
Real-Time Open Data Sharing of Zika Virus Research using LabKey
The laboratory of David O’Connor at the University of Wisconsin-Madison has been involved in Zika virus research during the recent outbreak in the Americas. The laboratory is conducting studies with non-human primates to establish the natural history of infection and create a model that can be used to target future vaccine development. A key component of the lab’s work is the usage of the LabKey platform to share data in real-time with researchers worldwide and to be able to aggregate diverse types of data that have been contributed by a large group of researchers to a central place.
Michael Graham is a Research Specialist in the Laboratory of David O’Connor at the University of Wisconsin-Madison. He works as a bioinformatics specialist providing data analysis and software development support to research projects focused on the genetics of immune response related genes in non-human primates. He also serves as a primary user and content administrator of the lab’s internal LabKey system as well as the O’Connor Lab’s LabKey hosted zika virus research web portal.
Presenter: Mi-Youn Brusniak, Ph.D., PMP., Director of Bioinformatics, Optides Program, Fred Hutch
Optide-Hunter: Informatics Solutions for Optimized Peptide Drug Development Through the Integration of Heterogeneous Data and Protein Engineering Hierarchy
Traditional pharmaceutical and biotech therapeutic agents have shown some limitations in certain biological targets. Small molecules cannot hit protein-protein interactions and ion channels with sufficient specificity to gain a reasonable therapeutic index. Large molecules like antibodies have been successful with high specificity and predictable outcomes in clinical trials. However, they have inherent shortcomings such as intracellular targets or for targets behind the blood-brain barrier. We have developed a new platform called Optide [optimized peptide] for drug discovery that has the potential to yield drugs for diseases that are currently considered incurable. Optide-Hunter is built by customizing LabKey software to track Optide library inventories, hierarchical compound relationships and their associated analytical and biological data. It also generates hierarchical and peer views with critical assay data for easy data mining and drug development strategy ideas.
Mi-Youn Brusniak Obtained her Ph.D. from the College of Pharmacy at the University of Texas at Austin in Computational Chemistry for drug development. In the past, she worked in both nonprofit organizations such as the Institute for Systems Biology and for biotech companies such as Integrated Diagnostics, Inc. She has expertise in design and development of discovery and validation analytical software for both drug design and protein biomarkers. She is continuously interested in design of data and analytical workflows that result in the development of new insights into drug and biomarker discoveries. She currently holds a Bioinformatics Director position in the Optides program at the Fred Hutchinson Cancer Research Center.
Presenter: Randal R. Ketchem, Ph.D., VP of Molecular Design, Just Biotherapeutics
Therapeutic Antibody Designs for Efficacy and Manufacturability
Antibodies undergo genomic recombination and somatic hypermutation in order to obtain their high levels of both antigen specificity and affinity. These very mechanisms by which the adaptive immune system is able to generate antibodies against any antigen also lead to molecular issues as therapeutic candidates. Large scale data capture in LabKey Biologics of sequence, cellular expression, purification, efficacy, biophysical characterization, and atomic-level characterization will enable methods development to better predict and repair molecular attributes such as post translational modifications and stability. Pushing this level of molecular design earlier in the therapeutic pathway will help lower the cost of biologics-based therapeutics.
Dr. Randal Ketchem received his Ph.D. in Molecular Biophysics from The Florida State University, focusing on experimental protein structure determination, resulting in the first membrane-bound protein structure solved by Solid State NMR. As part of this effort he developed computational methods for the structure calculation and refinement of membrane-bound proteins. Randy continued his training in structural biology in a postdoctoral fellowship at The Scripps Research Institute where he expanded his experimental and computational efforts into solution-based protein structure. Randy then joined Immunex in 1997 to apply his expertise in protein structure modeling and analysis to efforts in the development of biologic-based therapeutics. During his many years of experience at Immunex, Amgen, and Just Biotherapeutics he has led efforts to engineer protein therapeutics, invented novel therapeutic modalities and computational methods for therapeutic design, and developed computational and experimental approaches to understanding and controlling biophysical properties of biological macromolecules. Randy has made significant contributions in antibody design, epitope mapping, molecular assessment, stability engineering, construct design, protein structure analysis, and protein engineering. At Just Randy leads the Molecular Design team, integrating molecular design strategies into the entire therapeutic pipeline.
Presenter: Kristin Wildsmith, OMNI Biomarker Development, Development Sciences, Genentech, Inc. (a member of the Roche Group)
Skyline and Panorama: Key Tools for Establishing a Targeted LC/MS Workflow
Although identification and development of clinically relevant biomarkers is challenging, they are critical for successful drug development and for ensuring the right drugs are given the right patients. Targeted mass spectrometry is one key technology we employ to evaluate candidate biomarkers. Due to its ability to support a multitude of different LC/MS assay and instrument types, we are partnering with Labkey and the University of Washington through the Panorama Partnership program to implement and refine a Skyline centric LC/MS data workflow. Skyline is an open-source software for targeted LC/MS method development, and Panorama (implemented through Labkey), is a data management platform supporting Skyline. They enable us to create, organize, share, search and analyze our data. This includes the ability to track instrument performance and build libraries required to support discovery proteomics approaches. Our vision is to utilize Skyline and Panorama in partnership with Labkey to streamline our LC/MS workflow in order to impact clinical programs through accelerated biomarker discovery and development.
Kristin Wildsmith is currently a scientist in the Biomarker Development group at Genentech. She develops biomarker strategies to support preclinical and clinical trials with a focus on Alzheimer’s disease (AD). Mass spectrometry approaches are a key part of her strategies. Prior to joining Genentech in late 2010, Kristin completed her postdoctoral training in Randall Bateman’s lab at Washington University in St. Louis. While at WashU, Kristin performed translational AD research, developing LC/MS assays to elucidate the in vivo kinetics of AD biomarkers in the CNS. Kristin received her Ph.D. in Biochemistry and Molecular Biology from St. Louis University where she used mass spectrometry to study the metabolism of lipid biomarkers of cardiovascular disease. Kristin received her B.S. in Chemistry from Furman University.
Presenter: David Smith, PhD Student, Barnes Group, University of Oxford, UK
Integrating Clinical and Laboratory Data from National Health Service Hospitals for Viral Hepatitis Research
Viral Hepatitis has become a leading cause of death across the globe, and has been recently shown to kill more people than TB, Malaria or HIV/AIDS (Stanaway JD,Lancet,2016). The aim of the National Institute for Health Research Health Informatics Collaborative (NIHR HIC) (http://www.nihr.ac.uk/about/
David Smith is a DPhil (PhD) Student in the Barnes group at the University of Oxford, UK. He is studying the effects of viral resistance on the efficacy of direct acting antivirals drugs against Hepatitis C Virus using next generation viral sequencing technologies. He works within the national STOP-HCV Consortium (http://www.stop-hcv.ox.ac.uk/home), integrating viral sequencing, host genetics, biomarkers and immune parameters with clinical data and outcomes. David is developing a system to manage the sample and clinical data of the viral sequencing work strand using the LabKey Platform. David also continues to work on the NIHR HIC project further developing and supporting the use of the LabKey systems in this project.
Presenter: Susan Hert, Senior Software Engineer, LabKey
Business Process Workflows
Join LabKey Senior Software Engineer, Susan Hert, for a workshop highlighting the business process workflow capabilities of LabKey Server. This session will include an overview of the LabKey Server workflow module, steps for integrating workflows into your LabKey Server, and a look at example applications using these workflow capabilities.
Presenter: Josh Eckels, VP of Engineering, LabKey
Quality control (QC) is an essential part of any lab’s workflow and data management needs. In this workshop, LabKey’s Josh Eckels will show examples of current QC analysis tools available in LabKey Server for Luminex and targeted mass spec data, how assay and other data can be tagged with QC metadata, and explore other potential use cases.
Presenter: Cory Nathe, Senior Software Engineer, LabKey
Learn about LabKey Server visualization capabilities, including recent enhancements and upcoming functionality additions, explore unique applications of visualization tools implemented by LabKey users and dive into technical Q& A with LabKey expert, Cory Nathe.
Presenter: Brian Connolly, Senior Systems Engingeer, LabKey
Best Practices for Server Administration
Join LabKey Server operations expert, Brian Connolly, for a presenation of best practices for administration, synchronization, and upgrading LabKey Server.