News Category: In the News

LabKey collaborators at the O’Connor Lab (University of Wisconsin—Madison) were featured in a recent Washington Post article “Zika infections last much longer during pregnancy, monkey study shows” sharing insights from on-going Zika virus research. O’Connor’s team is investigating a number of hypothesis’ to explain the persistence of the virus in pregnant monkeys:

One possible explanation is that the immune system is weakened by pregnancy and can’t get rid of the virus as fast.

Another hypothesis researchers are testing is that the fetus also becomes infected and produces virus that then goes back into the mother’s bloodstream.

The O’Connor Lab use’s the LabKey Zika Open-Research Portal to manage and publicly share real-time research data. View Real-Time O’Connor Research >

Fast Co. Design has released an article featuring LabKey collaborator Artefact and the recently launched CAVD DataSpace project. The CAVD DataSpace portal is a LabKey Server-based “hypothesis engine” and visualization tool, designed in collaboration with Seattle-based design firm Artefact to facilitate open science and collaborative research. The user-friendly CDS interface  helps researchers explore data across HIV studies and filter, combine, visualize, and export precise datasets of interest.

The DataSpace portal features an intuitive UI designed by Artefact, but the data integration behind the scene is what really makes this platform so invaluable to researchers.

“The secret sauce is that aforementioned data harmonization. Artefact learned which sorts of data points were most helpful in HIV research from scientists, and, working with LabKey and SCHARP, hand-coded that data into the back-end of DataSpace so they could be easily correlated and compared. Basically, the graphs are nice—but the real magic of the platform is thanks to the invisible labor ensuring all study results were presented in the same apples-to-apples figures.”

LabKey collaborators at the O’Connor Lab (University of Wisconsin-Madison) were recently featured on NPR, sharing details about their current work researching the Zika virus and decision to share research data with the public in real-time.

In the article, Dave O’Connor expressed that even with journals committing to make data free to access without pre-empting future publication, the process may still take longer than what is ideal under emergency conditions.

“In the case of a public health emergency like Zika virus, the journals are aware that there is certain urgency to communicating the results,” says O’Connor, “but that process can still take weeks to months.”

He didn’t want to wait. Doing the experiment publicly means that other experts can contact him and suggest changes or offer help. Plus the early results could maybe help other groups better plan their own Zika studies, so they could get results faster and use fewer animals.

They team sees their open-data sharing as an experiment in and of itself.

“You’re seeing a shift, as you are in many other aspects of culture, where information can be shared much more broadly and much more quickly than it ever could before,” says Thomas Friedrich, a researcher at the University of Wisconsin, Madison who is collaborating with O’Connor on the Zika experiments in monkeys. “Part of what we’re testing here is the viability of real-time public data sharing.”

The O’Connor Lab is making their data available real-time through the Zika Open-Research portal, a LabKey hosted instance of LabKey Server.

Learn More or Request a Project > 

JAMA Pediatrics has released an article authored by LabKey collaborator Dave O’Connor highlighting “Real-Time Sharing of Zika Virus Data in an Interconnected World.” In the piece, O’Connor shares about the development of the Zika experimental science team (ZEST) and the evolution of Zika virus open-data sharing.

“As Zika virus reemerged in 2015, an internal HipChat (https://www.hipchat.com/) group chat was started to share ideas and information. What was first a small chat room with a few infectious disease researchers from our laboratories soon grew to include an interdisciplinary team of reproductive biologists, arbovirologists, clinicians, and other specialists from the United States and Brazil. Soon, the diverse collections of voices were unified under a single moniker: the Zika experimental science team (ZEST). Soon we were confronted with a new question: how could we continue to capture the viewpoints of all the ZEST participants as we began studies with Zika virus? We realized the open-source scientific collaboration platform LabKey Server⁹ enabled us to publish data in real-time, not just to our team but also to anyone else who was interested. So that is what we did (https://goo.gl/rmNCqf). ”

“We were surprised to discover that our results portal attracted a broad audience. Users in 98 countries viewed our data (Figure). Even though our experience is anecdotal, it suggests that there is a global interest in real-time data on emerging infectious disease outbreaks that mirrors the general public’s interest in Zika virus. This need not be limited to laboratory data. Clinical information, epidemiologic data, and behavioral studies could also be made available directly and immediately. Indeed, we have worked with LabKey to create a centralized server (http://zika.labkey.com) where other researchers can share any type of Zika virus data in real-time. Already, investigators from Brazil and the United States are preparing data sets for sharing, and we hope that others follow suit.”

Corresponding Author: David H. O’Connor, PhD, Wisconsin National Primate Research Center, University of Wisconsin, Madison, 555 Science Dr, Madison, WI 53711 (doconnor@primate.wisc.edu).

Published Online: March 31, 2016. doi:10.1001/jamapediatrics.2016.0857.

Conflict of Interest Disclosures: None reported.

Additional Contributions: We thank Project ZEST team members for constructive comments and helpful suggestions on this Viewpoint. The Wisconsin National Primate Research Center base grant P51 5P51OD011106-54 supported our initial laboratory studies with Zika virus, and grant 3R01AI116382-01A1S1 from the National Institutes of Health supports our ongoing Zika virus projects. Mark Igra, BA, initially encouraged us to use LabKey Server to manage data, and Josh Eckels, BS, LabKey, San Diego, California, facilitates our sharing of Zika virus data. LabKey is a subcontractor on an unrelated National Institutes of Health contract and receives compensation for managing the server that initially hosted the Zika virus data. LabKey did not receive any compensation for assisting with the setup and configuration of the Zika virus data, nor did LabKey receive any compensation for setting up and configuring the zika.labkey.com server that is offering to host projects for other investigators.

A new article in the Fred Hutch News, Easing cancer’s heavy financial burden, covers both the Hutch Institute for Outcomes Research (HICOR) 2015 Value in Cancer Care (VCC) Summit and the debut of HICOR IQ.

HICOR IQ is an instance of LabKey Server. According to the Hutch News:

The Hutch’s HICOR IQ overview describes the system:

GeekWire article featuring Argos, a tool developed by LabKey in collaboration with the Hutch.

The Fred Hutchinson Cancer Research Center launched a new application today to make it easier for doctors and researchers in its Cancer Consortium to search its database for patterns that will help with cancer treatment.

The tool, called Argos, is built on the Hutch Integrated Data Repository and Archive, which includes thousands of medical records, databases and tissue inventories maintained by Fred Hutch and its partners UW Medicine, Seattle Children’s Hospital and Seattle Cancer Care Alliance. Right now, Argos provides analytics tools for brain, gastrointestinal, head and neck and thoracic cancer tumors, but is slated to expand to all cancers later.

It’s designed to help researchers and clinicians find patterns in cancer development, progression and treatment response in a secure application. Future updates to the application could allow access to up to 300,000 records, and are supposed to include more information like tumor genetic and molecular data.

Only researchers in the Cancer Consortium have access to the data through Argos, and access is controlled based on a user’s responsibilities in order to maximize security of patient data.

The tool was developed in conjunction with LabKey Software, a Seattle-based company that spun out of Fred Hutch in 2005. In addition to building Argos, the company works with a number of other groups at Fred Hutch and researchers around the world.

BY BLAIR HANLEY FRANK, GeekWire’s Bay Area Correspondent, on March 16, 2015 at 1:06 pm

View the original article on GeekWire.com

We congratulate the Immune Tolerance Network (ITN) on ITN TrialShare’s debut in the New England Journal of Medicine (NEJM).  TrialShare has received recognition for how it provides public, interactive access to de-identified data, analyses and figures for published clinical trials, in this case ITN’s RAVE study, published in the NEJM on August 1.

An accompanying NEJM editorial (Participant-Level Data and the New Frontier in Trial Transparency) stresses the unusual openness of TrialShare:

“…the article by investigators from the Immune Tolerance Network (ITN) of the National Institute of Allergy and Infectious Diseases… is accompanied by open public access to participant-level data without the need for a specific research plan or approval of the qualifications of the investigators.”

Separately, a Nature Medicine article (Immunologist effort aims to improve hyperlinking of research papers to raw data) explores how TrialShare opens doors to data reuse and re-analysis:

“According to its authors, the study is the first to contain hyperlinked charts or graphs that redirect users to an information-sharing system called TrialShare, where they can instantly access data amassed during this clinical trial and others.

…The creators of the TrialShare web portal hope that scientists drawn to the site after reading published papers that reference it will experiment with the data available there to test new hypotheses. The site, which has been available to ITN members since last October, also makes it possible to search through related publications or request biopsies that may still be available from a particular study. “By making a wealth of data available, we’re hoping to leverage the expertise of other researchers to learn more,” says Laurence Turka, a transplant immunologist at the Massachusetts General Hospital, in Boston, Massachusetts, and a deputy director at the ITN.

The National Institute of Allergy and Infectious Diseases (NIAID) also comments on how TrialShare can support future discoveries:

“The website provides access to the study’s raw data and statistical analyses, allowing researchers to re-analyze the data and develop new hypotheses.”

In a world where simply providing access to de-identified data is a step forward for clinical trials, TrialShare’s support for live interaction with both data and analyses is exceptional.

For further details, see ITN’s commentary:  ITN Achieves Scientific Manuscript First – Provides Open, Interactive Access to Clinical Trial Data with New Publication: Rituximab Therapy Effective for ANCA-associated Vasculitis

ITN TrialShare is an installation of LabKey Server that was developed by the ITN in partnership with LabKey Software.