Do you have questions about data or software sharing?

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On Friday, November 4, Technology Transfer & Business Development and the Data Jamboree are co-hosting a panel presentation and round-table discussion on sharing and securing data and software through open source and creative commons licensing.  OHSU community members will learn about the importance of securing rights, as well the ways in which data and software can be licensed to meet researcher and community goals.

Panelists include:

  • Tammy Buist, VP and Chief Business Development Officer, Seattle’s Cancer Research & Biostatistics Institute
  • Brad Biddle, Owner, Biddle Law LLP
  • Frank Curci, Partner, Ater Wynne LLP

The presentations will be followed by two round-table discussions led by OHSU researchers Drs. Kemal Sonmez, Melissa Haendel, and Steven Bedrick.  The round tables will explore goals and issues related to intellectual property, research aims, and scientific communication through the lens of project case studies.  Attendees will have an opportunity to ask questions and share their ideas about what it means and how to share data and software openly and responsibly.

All OHSU faculty, students, and staff are welcome!  Food and drink will be served.

Friday, November 4, 2:00 – 5:00 PM

  • Presentations 2:00 – 3:30
  • Food and drink will be served at 3:30
  • Round table discussions 4:00 – 5:00

Doernbecher Children’s Hospital, Vey Auditorium, 11th floor

Questions:  champieu@ohsu.edu

This special event is presented by OHSU Technology Transfer & Business Development, Computational Biology, and the OHSU Library.

OHSU Library Collaborates with DMICE to Make Biomedical Big Data Science Open Educational Resources Available

For the last couple years, faculty from the OHSU Department of Medical Informatics & Clinical Epidemiology (DMICE) and Library have been developing open educational resources (OERs) in the area of Biomedical Big Data Science. Funded by a grant from the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) Program, OERs have been produced that can be downloaded, used, and repurposed for a variety of educational audiences by both learners and educators.

Development of the OERs is an ongoing process, but we have reached the point where a critical mass of the content is being made available for use and to obtain feedback. The OERs are intended to be flexible and customizable and we encourage others to use or repurpose these materials for training, workshops and professional development or for dissemination to instructors in various fields. They can be used as “out of the box” courses for students, or as materials for educators to use in courses, training programs, and other learning activities. We ultimately aim to create 32 modules on the following topics:

  1. Biomedical Big Data Science
  2. Introduction to Big Data in Biology and Medicine
  3. Ethical Issues in Use of Big Data
  4. Clinical Standards Related to Big Data
  5. Basic Research Data Standards
  6. Public Health and Big Data
  7. Team Science
  8. Secondary Use (Reuse) of Clinical Data
  9. Publication and Peer Review
  10. Information Retrieval
  11. Version Control and Identifiers
  12. Data Annotation and Curation
  13. Data Tools and Landscape
  14. Ontologies 101
  15. Data Metadata and Provenance
  16. Semantic Data Interoperability
  17. Choice of Algorithms and Algorithm Dynamics
  18. Visualization and Interpretation
  19. Replication, Validation and the Spectrum of Reproducibility
  20. Regulatory Issues in Big Data for Genomics and Health Semantic Web Data
  21. Hosting Data Dissemination and Data Stewardship Workshops
  22. Guidelines for Reporting, Publications, and Data Sharing
  23. Terminology of Biomedical, Clinical, and Translational Research
  24. Computing Concepts for Big Data
  25. Data Modeling
  26. Semantic Web Data
  27. Context-based Selection of Data
  28. Translating the Question
  29. Implications of Provenance and Pre-processing
  30. Data Tells a Story
  31. Statistical Significance, P-hacking and Multiple-testing
  32. Displaying Confidence and Uncertainty

At the present time, 20 of the above modules are available for download and use. We are encouraging their use and seeking feedback from those who make use of them. The feedback will be used to improve the available modules and guide development of those not yet released.

We have also been developing mappings to research competencies in other areas, such as for the NIH Clinical and Translational Science Award (CTSA) consortium research competency requirements and the Medical Library Association professional competencies for health sciences librarians. To this end, we have been able to link these materials to existing efforts, and provide training opportunities for learners and educators working in these areas. We ultimately aim to complete this mapping across all of the BD2K training offerings, to align with other groups, avoid redundancy and to ensure we are meeting the needs of these various groups.

This project is actually one of several projects that have been funded by grants to develop and provide education in biomedical informatics and data science. The other projects include:

We hope that all of these materials are useful for many audiences and look forward to feedback enabling their improvement.

For more information, please contact Nicole Vasilevsky.

Maija Anderson appointed to Associate Professor in the OHSU Library

maijaWe are pleased to announce that Maija Anderson, MA, MLIS was appointed as Associate Professor at OHSU Library. As Director of Curatorial Services, Maija oversees the library’s special collections, university archives, and digital assets management program. Since November 2010, Maija has developed projects and partnerships that bring OHSU history to new audiences, while expanding and improving core services to the university community. Maija has presented and published scholarship on archives management, digitization, and Pacific Northwest medical history, and is an active leader in the Society of American Archivists.

Steve Duckworth, University Archivist

duckworth_2016-10-18-copySteve Duckworth recently joined OHSU Library’s Historical Collections & Archives as the University Archivist. Steve comes most recently from working as the Processing Archivist for the University of Florida. Previously, he served as a Project Archivist for the National Park Service in Anchorage, AK and as an Archives Processor with the “Hidden Collections” project of the Philadelphia Area Consortium of Special Collections Libraries (PACSCL). He has also conducted archival processing in Philadelphia’s John J. Wilcox, Jr. LGBT Archive and the Sigma Sound Studio Audio Archive (at Drexel University), and even once served as the Assistant Librarian for the Allentown (PA) Symphony Orchestra.

Steve has an MSLIS with a concentration in Archives Management from Drexel University (as well as a couple of other degrees in music performance). He has recently completed the Digital Archives Specialist certification from the Society of American Archivists (SAA). He serves on SAA’s Diversity Committee and as a member of the SAA Issues & Advocacy Roundtable’s On-Call Research Teams. He has recently conducted research into artifact processing within traditionally paper-based archival environments and has previously participated with teams that published or presented on web archiving, reprocessing archival collections, and enhancing finding aids for accessibility and usability.

Steve is excited to bring his experience and inquisitive nature to this position where he hopes to enhance current collections while increasing the diversity and substance of the holdings of HC&A. Additionally, he hopes to contribute to a more diverse work place and profession through various initiatives and outreach efforts. Being new to Portland, Steve is also looking forward to exploring this beautiful area and getting to know the people and places that make the Pacific Northwest so unique.

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Nicole Vasilevsky appointed to Research Assistant Professor in the OHSU Library

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The OHSU Library is pleased to announce that Nicole Vasilevsky, PhD, was appointed to Research Assistant Professor in the OHSU Library. Nicole works as a biocurator and ontologist in the Ontology Development Group. Currently she is focusing on biocuration of the rare disease literature for the Monarch Initiative (monarchinitiative.org), ontology development for the Monarch Disease Ontology, Human Phenotype Ontology and the Cell Ontology, and is developing educational resources for the Big Data to Knowledge projects in DMICE and the Library.

Register for Science Hack Day

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Science Hack Day Portland is just a couple days away. Starting with a kick-off reception this Friday at 6:30 PM, OHSU students, scientists, and staff will team up with developers, designers, librarians, roboticists, and science enthusiasts to tackle projects and build new connections.

Science Hack Day Portland is open to everyone, free, and a great opportunity to solve research issues, build your network, and have fun with science! Over 125 attendees have already formed teams to automate lab procedures, visualize and open up data, explore new techniques, and just have fun code and hardware. Want some inspiration? Read about what the OHSU Laboratory of Brain, Hearing, and Behavior will be working on.

You can register for Science Hack Day Portland now, or just show up! You can come with an idea ready to form a team, or just some curiosity and a desire to tinker. Doors open this Friday, October 7, at 6:30 PM at the XOXO Outpost. Food and drink will be provided. No worries if you can’t make it on Friday, you can still join and form teams on Saturday. View the full schedule here.

If you have questions or ideas about Science Hack Day Portland, please contact Robin Champieux at champieu@ohsu.edu or the event organizers at sciencehackdaypdx@gmail.com.

OHSU Science Hack Day team aims to reduce human errors with robotic upgrade

shd2In the Oregon Hearing Research Center’s Laboratory of Brain, Hearing, and Behavior, led by Dr. Stephen David, we study how the auditory brain interprets sounds in different behavioral conditions.

Listening to a friend talking in a noisy room seems like an effortless task for most people, but it can be challenging for people with even mild hearing impairments. Understanding how the healthy brain solves these problems is important to develop better treatments for the hearing impaired.

We use a number of techniques to study brain activity during auditory behavior. Recently, we have begun using optogenetics to precisely control neural activity in specific brain regions, which requires shining a laser light over the area under study.

One of the key pieces of equipment for our experiments is a stereotactic micromanipulator. This manipulator has three axes that can be moved to precise, targeted positions by the careful adjustment of manipulator knobs by the skilled hands of one of our lab members. This technique is subject to human error due to relatively low accuracy and replicability of human movements.

In an effort to reduce these potentially confounding human errors, our lab will team up at the first Science Hack Day in Portland (October 7-8) to upgrade our existing manual stereotactic micromanipulator to a robotic one.

We will use affordable, commercially available CNC equipment and open source CNC controlling software such that the experimenter will be able to control the position and the speed of each movement digitally, with a precision of about 3 micrometers per turn. This will make our experimental control about 10 times more accurate and reproducible.

OHSU students Saderi and Lawson receive scholarships to attend OpenCon

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For the second year, the OHSU Library is sponsoring two scholarships to OpenCon 2016 in Washington DC.  OpenCon is a conference and platform for the the next generation of scientists, clinicians, and scholars to learn about Open Access, Open Data, and Open Education, develop critical skills, and catalyze action toward a more open system of research and education.

Because of their existing activities related to OpenCon’s mission and their visions for effecting local change, Daniela Saderi, a PhD candidate in the neuroscience graduate program, and Katy Lawson, an OHSU medical student, have been selected to attend the conference and will receive full travel support from the Library.  OpenCon draws participants from around the world.  Daniela and Katy will have the opportunity to build an international network and engage with key leaders in research, government, and publishing.

Daniela works in the laboratory of brain, hearing, and behavior lead by Dr. Stephen David. She was awarded an NIH F31 predoctoral fellowship to study how behavioral state shapes neuronal responses to sound in the auditory midbrain.  An active open science advocate, Daniela co-leads the Open Insight project sponsored by the OHSU Library and funded by NIH. She is excited about joining the OpenCon community to continue her mission toward promoting openness in science and find new routes for collaboration.

Katy Lawson is in her final year of medical school and will pursue a residency in pathology. With a background in basic science research and a master’s degree in clinical research, she is motivated by the creation and dissemination of knowledge to improve medical outcomes. Katy is committed to the principles of collaboration and open access to resources, education, and research that aim to propel knowledge toward the advancement of health.

The OHSU Library and the OpenCon organizers were impressed by the applications we received from across the OHSU student and early career researcher communities.  Thank you to everyone that expressed an interest and we will be working to offer opportunities to engage with the conference locally.

Congratulations to Daniela and Katy!

Monarch Initiative receives $5 million award to help researchers learn more about the genetic causes of disease

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Dr. Melissa Haendel, Associate Professor in the OHSU Library and DMICE, and the  Monarch Initiative team have been awarded a $5 million grant from the National Institutes of Health Office of the Director to increase the utility of animal models and improve our understanding of human diseases.

The Monarch Initiative is a global, translational consortium, which includes OHSU, the Lawrence Berkeley National Laboratory, the Jackson Laboratory, the University of Pittsburgh, Charité Hospital, Queen Mary University of London, and the Garvan Institute of Medical Research.  It provides sophisticated algorithms for phenotype comparison within and across species, leveraging a large corpus of deeply integrated and structured information about genetics, descriptions of resulting malformations, clinical signs, and symptoms.

Without a big-picture view of phenotype data, many questions in genetics are difficult or impossible to answer.  Monarch’s computational tools, bioinformatics analyses, and interactive visualizations provide clinicians and researchers with previously unavailable insight from numerous information sources to shorten the path of information exchange between the bench and clinic, with the ultimate goal of advancing rare disease diagnosis and personalized medicine.  Towards these ends, the project has already achieved success.

The $5 million award over 4 years will support extension of the scope and precision of Monarch disease modeling by including a greater diversity of species and sources that focus on a broader range of common and complex diseases and new categories of clinical data. This work will enhance Monarch’s capabilities to inform diagnostics, mechanism discovery, and improved phenotyping.

“We are deeply excited to continue this work in translational phenomics, and are dedicating to making more basic research data available for clinical applications”, said Dr. Haendel.  “With this funding we will be developing new user-focused tools for maximizing the utility of the data for patients, researchers, and clinicians.”