Segment: Academic Research

06 Apr 2016
CAVD DataSpace

CAVD DataSpace

The CAVD DataSpace (CDS) data portal is one component of an innovative pilot program funded by the Bill & Melinda Gates Foundation that is led bythe Statistical Center for HIV/ AIDS Research and Prevention (SCHARP) at the Fred Hutchinson Cancer Research Center (Fred Hutch). The project aims to help the HIV vaccine research community gain new insights from completed studies by pooling data and expertise. The overall CDS program includes: (1) a study catalog and integrated data; (2) services that facilitate data use; (3) leadership and governance; and (4) the web-based CDS portal and tools.

The CDS portal will lower the bar to exploring hypotheses across multiple studies by providing access to integrated, annotated data under a global data sharing and use agreement. The user-friendly CDS interface will help researchers discover study data contributed by multiple HIV consortia; filter, combine, visualize, and export information of interest; and comply with agreements and regulations on data security. This self-service approach will help scientists get their research questions answered faster while encouraging cross-lab communications.

Related Resources

CAVD DataSpace Video

07 Mar 2016

Panorama

The Dr. Michael MacCoss Lab at the University of Washington partnered with LabKey Software to develop Panorama, a LabKey Server module, which integrates closely with Skyline, the lab’s widely-adopted targeted mass spectrometry desktop application. Together, Panorama and Skyline enable a robust assay workflow, offering sensitive and quantitative analysis. The tools offer an intuitive approach for exploring targeted mass spec and building assays. They are both free, open source software, and have been enthusiastically adopted by the proteomics community.

Panorama serves as a repository for Skyline documents; provides a way to collaborate and iterate within a lab; enables extensive reporting and searching of vast amounts of data; and supports disseminating results securely among collaborators or publicly as supporting data for a publication. Groups such as the Clinical Proteomic Tumor Analysis Consortium (CPTAC) use Panorama to host data that they wish to display through a custom data portal; they integrate the portal with Panorama via LabKey Server’s client APIs.

The MacCoss Lab hosts an installation of Panorama, PanoramaWeb, and offers free accounts to the proteomics community. Dozens of labs and other groups are using the server to house their data. At the same time, certain organizations need to host their data in-house to satisfy strict confidentiality requirements. For this reason, the lab has collaborated with LabKey Software to develop the Panorama Partners Program.

P3 helps organizations host their own in-house deployments of Panorama, gives users direct access to the developers in the MacCoss Lab and LabKey Software, and affords a unique opportunity to shape the ongoing development of the software. A number of major pharmaceutical companies have joined the program.

Related Resources

Panorama: An Introduction
Panorama Partners Program

07 Mar 2016
Primate EHRs

Primate EHRs

LabKey Software partnered with the Wisconsin National Primate Center (WNPRC) and Oregon National Primate Research Center (ONPRC) to develop systems for managing and reporting on electronic health records (EHR) and related research data for primate colonies. These systems help the Centers gain insight into combined lab, clinical and operational information; meet regulatory requirements; and coordinate the activities required to support animal care and research projects. The Centers share a common core EHR implementation, built on LabKey Server, which each Center further customizes to support its own unique workflows and requirements.

Center staff use their LabKey-based systems to enter and track everyday animal information, including weights and behavioral observations; medications and other treatments; scheduling and request approval for activities such as blood draws and surgeries; birth, death, and necropsy information; lab results such as chem panels; and more. Staff members with access to the EHR system can easily query information about specific animals and find matching animals based on search criteria. A flexible permission model ensures that only approved staff members can add, approve, and edit information.

Both Centers rely heavily on the system to help manage regulatory and compliance data as well as to prevent errors. IACUCs, SOPs, trainings and related information are stored and queryable. Data validation catches many problems before they are entered, such as scheduling of blood draws that would exceed species-specific limits. Automated reports send alerts when problems appear, such as animals with conflicting housing records or who are overdue to be weighed.

Additionally, both Centers have integrated lab research data with the clinical and demographic information from the EHR, allowing researchers to access detailed animal records without needing to maintain their own copies. Labs have their own private areas that manage sequencing, immunology, and other assay data. Selected information is pushed back into the EHR on a manual or automated basis depending on the desired workflow.

The technology was first developed specifically for WNPRC, and was later extended to support ONPRC as well. Each center migrated decades of health and research data into their LabKey-based system to provide a single, complete resource for primate information. Both Centers then migrated to doing clinical data entry directly into the LabKey Server-based system.

In Fall of 2014, LabKey Software began collaborating with the Southwest National Primate Research Center (SNPRC) to adapt the EHR to their needs.

07 Mar 2016
MESA-ICEMR Map

MESA-ICEMR LabKey Server

The Malaria Evolution in South Asia (MESA) International Center for Excellence in Malaria Research (ICEMR) is a multinational collaboration that investigates how malaria parasite adaptability affects virulence, immunity, and drug resistance across India. The MESA-ICEMR installation of LabKey Server facilitates collection and analysis of experimental data; integration of clinical and laboratory data from diverse field sites; and real-time data access across continents.

In collaboration with LabKey Software, the group has used LabKey Server’s assay infrastructure to

develop custom, web-based workflows that standardize data collection for parasite experiments. These workflows enable consistent data acquisition, immediate quality control, and real-time data access, visualization and reporting. They help the MESA-ICEMR team execute and interpret complex experiments that involve as many as 5000 data entries per experiment per sample and last as long as 60 days, including malaria diagnostic tests, PCR, drug sensitivity tests, and adaptation and selection experiments.

The MESA-ICEMR LabKey Server also eases data synthesis by enabling the team to combine parasite information captured in LabKey Server with demographic and clinical data captured in REDCap.

Related Resources

2013 User Conference Presentation

07 Mar 2016

Adair/Kiem LabKey Server

The labs of Jennifer Adair and Hans-Peter Kiem at the Fred Hutchinson Cancer Research Center use LabKey Server to speed efforts in development of stem cell gene therapy for wide range of diseases, from HIV/AIDS to cancers.

LabKey Server-based assay tools free lab members to focus on data interpretation instead of manual processing, help them look quickly across results collected from multiple experiments over time, and enable them to scale up analysis as fast as sequencing throughput.

They use LabKey Server’s assay infrastructure to automate manual workflows and provide rich, real-time reporting. Instead of painstakingly stitching together a multiplicity of spreadsheets to answer questions about their data, lab staff can see results right away. Transformation scripts pre-process data during import, so quality control statistics are available immediately through a web-based interface. If results require normalization, adjustments can be made in bulk, with changes tracked. Once data and metadata are in the system, lab members can view real-time reports written in R that summarize and visualize results, or use LabKey Server’s graphical tools to further sort, filter, combine, and chart results.

The team employs an Ion Torrent sequencer, so each run generates tens of thousands of data rows. These results must not only be processed for analysis, but also stored for potential reuse. LabKey Server provides both a back-end repository for archiving results and tools for looking across multiple runs, enabling comparison of results over time or across experiments. LabKey Software hosts the Kiem Lab instance of LabKey Server, so storage capacity and version upgrades are handled transparently.

The Adair/Kiem lab has used LabKey Server to develop ground-breaking approaches to gene therapy and chemotherapy, such as a treatment for glioblastoma that has already extended survival for a small number of cancer patients from months to years. LabKey Server helps the team pursue projects that range from identifying genes that protect stem cells from chemotherapy to investigating safer viral vectors for gene therapy.

Related Resources

‘Breakthrough’ treatment boosts survival in battle with deadly brain tumor
Insertional mutagenesis reveals role of new gene in blood cell development

07 Mar 2016

O’Connor LabKey Server

Professor David O’Connor’s lab at the University of Wisconsin uses LabKey Server as its “operating system,” speeding its efforts to understand how genetics affects immunity to viruses such as HIV/SIV.

The lab uses LabKey Server to manage its extensive list of experiments, Illumina sequencing data, purchases, oligonucleotides, freezer samples, and other lab inventory, as well as to provide basic electronic lab notebook (ELN) functionality. Data, files, protocols, grant information, and experiment descriptions recorded on the server can be searched and queried, allowing lab members to look across experiments performed over more than ten years to find what they need quickly.

Further, the server hosts an informational portal for an NIH-funded contract on major histocompatibility complex (MHC) genetics, allowing different subsets of data to be exposed to the scientific community and the funding agency.

LabKey Server enables the lab to automate genotyping workflows for efficiency and consistency; perform comprehensive review of available genomic and clinical information for primate subjects; and gain analysis, querying, visualization, export, and search capabilities across many different data types. Today, the system helps the lab track data and metadata for tens of thousands of experiments, eliminate manual workflows, and securely share data with collaborators.

In February of 2016, the O’Connor lab became the first group to make real-time Zika data publicly available via their LabKey Server. Results are updated daily and are accessible online through the Zika experimental science team (ZEST) data portal.

Related Resources

Zika researchers release real-time data on viral infection study in monkeys (Nature, 23 Feburary 2016)
Presentation: Managing Next Generation Sequencing and Multiplexed Genotyping Data Using Open Source LabKey Server

07 Mar 2016
Atlas Science Portal

Atlas Science Portal

The Statistical Center for HIV & AIDS Research and Prevention (SCHARP) at the Fred Hutchinson Cancer Research Center (Fred Hutch) created the Atlas Science Portal to serve as a data integration and operational hub for multiple HIV research networks. These include the HIV Vaccine Trials Network (HVTN), the Center for AIDS Vaccine Discovery (CAVD), the HIV Prevention Trials Network (HPTN), and the Microbicide Trials Network (MTN).

Atlas helps these networks gain a wider view of their projects by bringing together disparate sources and types of information, opening the door to novel scientific insights and smoother operations. Teams use Atlas to pre-empt data integration challenges and collect better data from the get-go through data annotation, standardization, QC, and review during data acquisition. The system also facilitates collaboration, helping these networks leverage distributed perspectives and specialized expertise.

The Atlas portal uses LabKey Server’s sophisticated security model to support multiple research networks on a single server. Organizations and individuals can only see the studies and data they are authorized to view. Permissions can be set at the project, study, dataset, or view level, allowing fine-grained control of data security. Heterogeneous data can be integrated at the study level; at the same time, LabKey Server’s security model ensures cohort blinding when appropriate. The Atlas team has used LabKey Server’s built-in reporting and visualization tools to develop summary dashboards and visualizations. Users can quickly build and share their own custom data views, analyses, and visualizations, as well as download data and reports.

As of early 2014, Atlas includes over 1600 active users, contains tens of thousands of assay runs, and records over a million specimen vial transfers.

Related Resources

2012 User Conference Presentation
LabKey Server: An open source platform for scientific data integration, analysis and collaboration (BMC Bioinformatics 2011)
LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays (BMC Immunology 2012)
Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform (BMC Bioinformatics 2013)

07 Mar 2016

ITN Trial Share

The Immune Tolerance Network (ITN) developed ITN TrialShare as a research web portal for both operational data management and post-publication sharing of data from clinical trials. The ITN is a multinational effort that encompasses over 100 investigators, over 40 phase I/II clinical trials, and over 100 sites.

ITN TrialShare is exceptional in how it serves as a public portal for de-identified data, annotations, analyses, and fully interactive figures from published clinical trials. In August 2013, ITN TrialShare broke new ground for clinical trial transparency by directly linking a major clinical trial publication to participant-level data and interactive analyses. Members of the public can use the portal to re-run and validate statistical analyses, interactively explore alternative hypotheses, and export data for external analysis. In July 2014, the National Academies named ITN TrialShare as the winner of the Data and Information Challenge. See: ITN TrialShare: Enabling True Clinical Trial Transparency.

Many of the data exploration tools available in ITN TrialShare are part of the core LabKey Server platform; others involve leveraging the platform’s API, source code customization, and custom coding using the frameworks and languages supported by LabKey Server. ITN TrialShare also utilizes LabKey Server’s de-identification tools to de-identify participant-level data before public release to help ensure patient confidentiality. As of mid-2014, ITN TrialShare contained clinical and mechanistic assay data from 35 clinical trials, including 3,200 patients and 72,000 study visits.

Related Resources

2013 User Conference Presentation
ITN TrialShare Website

07 Mar 2016
Argos

Argos

Argos is a data exploration and visualization portal for the Hutch Integrated Data Repository & Archive (HIDRA), a collaborative effort of the Fred Hutchinson Cancer Research Center/University of Washington Cancer Consortium. HIDRA provides a centralized and standardized way to securely distribute data for every patient and research subject of the Consortium – approximately 335,000 historical individuals as of late 2014, with over 5000 new patients annually. HIDRA aims to help Consortium scientists and physicians learn from every patient who is diagnosed or treated at the Center and translate this information into individually-tailored treatments, new hypotheses, innovative clinical trials, and larger-scale studies.

Researchers and clinicians can use the HIDRA Argos portal to pursue precision oncology by efficiently accessing and analyzing a larger volume and variety of related data than was previously possible. For example, they can compare genetic markers for an individual tumor with rich historical data to explore which treatments were effective for cancers with similar markers.

Argos is an extension to the LabKey Server open-source platform. It has been designed to be adaptable to the needs of other research organizations.

Related Resources

Presentation at the 2014 LabKey User Conference
Fred Hutch Argos Overview on HIDRA Website
Fred Hutch Argos Training Slide Deck

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