jdahm – Page 6 – HSLS Update

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Director Spotlight

Renae Barger
Associate Vice Chancellor for the Health Sciences Library System
rbarger@pitt.edu

Barbara Epstein announced her retirement as HSLS Director in last month’s issue of the HSLS Update. It is my privilege to call Barbara my friend, colleague, and mentor. As I begin my appointment as Associate Vice Chancellor for the Health Sciences Library System, I am grateful for the opportunity to have learned from her example. Her leadership has made a lasting impact on our profession, on HSLS as a leading academic health sciences library, and on me, both personally and professionally.

I am a proud Pitt alumnus, earning a BS from the School of Health and Rehabilitation Sciences, MLIS from the School of Information Sciences, and Masters Certificate from the Department of Biomedical Informatics. I began my career at HSLS in 2002, starting as a trainee in the Library and Biomedical Informatics Trainee Program and continuing as Reference Librarian and Coordinator for Document Delivery Services. I then advanced to Head of Access Services and Assistant Director for Access Services. From 2011 to 2021, I served as Executive Director and then Program Lead for the Network of the National Library of Medicine, Middle Atlantic Region, building a highly regarded program that was recognized regionally and nationally for innovative health information outreach. Continue reading →

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Options for Publishing Research Protocols

Typically if a researcher is asked what they think of when they hear the word “publication,” a “traditional” research journal article likely comes to mind. However, if the entire research workflow is considered, there are many research outputs that could be published including articles, preprints, protocols, datasets, and software. (We are defining “published” simply as “disseminated,” although terms such as “shared” or “posted” may be more appropriate depending on the output.)

The number of venues for publishing these outputs is growing and includes data repositories and preprint servers like DRYAD and medRxiv. New journals such as the Journal of Open Source Software (JOSS) and Scientific Data have been founded specifically to allow these research outputs to be recognized within the scholarly system. In addition, expanded publication types are now offered by established journals like PLOS ONE, which introduced Lab and Study Protocol types in early 2021.

This article will provide options for publishing research protocols, however the Where Should I Publish? Guide linked on the left of the Scholarly Communication Guide also compares options for other research outputs. Continue reading →

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Meet Your Match: Finding ‘omics Analysis Resources Using the HSLS Database/Tools Search

Wouldn’t it make your research life much easier if you had “the perfect tool” to help you analyze your ‘omics data? Sure, you could certainly use (or develop) your programming skills to create your own. However, before you go to all that effort, why not check to see if such a resource already exists?

Many different sources continually release new web-based resources for freely available bioinformatics software and biological databases, so it can be a challenge to locate them. The HSLS Molecular Biology Information Service (HSLS MolBio) has provided shortcuts to access such resources for years, and we recently updated our Database/Tools Search engine. Located in the middle of the HSLS MolBio homepage, use the prominent search bar to find molecular databases and software tools with a combined search of the Online Bioinformatics Resource Collection (OBRC), Nucleic Acids Research (NAR) Database/Web Server issues, and an HSLS MolBio-generated filtered PubMed search. Let us explore each of these sources. Continue reading →

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Photoshop and Illustrator Apps for iPad

After Photoshop was created for the iPad in 2019, Adobe also launched Illustrator for the iPad in 2020. Both programs have been a gold standard for desktop image editing, while the new versions for iPad have come to fulfill their own niche. Both apps require an Adobe license for access. Pitt faculty and students can register to license Adobe Software through Pitt IT. This perk is available at no cost for students’ coursework or for personal use by faculty.

Both the Photoshop app and Illustrator app are compatible with iPads that use iPadOS 13.1 and later. You can open PSD or AI files through Adobe cloud storage and continue working on your projects like you would using a computer. Both applications use the same tools (with some limitations) as their desktop counterparts. Continue reading →

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Treasures from the Rare Book Room: Medal of Andreas Vesalius

Profile of person on a medal Have you ever looked at the HSLS collection of medical and scientific medals? Numismatic materials, including medals, coins, and tokens are not typical resources in a medical library. The first medals were produced in Italy in the 15th century. They were based on Roman coins, cast in bronze, and usually had portraits of emperors. The earliest medal in our collection is the Caracalla Medal. It was struck in Venice, Italy in 1466. Over the centuries, the techniques changed and new metals were used in production with later medals being cast or struck in silver or gold. By the 19th century, the medallic art became a recognizable new art form taught as a separate subject in art schools. Books and French transcription on a medal Medals, unlike coins, or at times tokens, are not monetary instruments. They are frequently used to commemorate people, events, or things. As a perfect medium, and due to their permanence, they pass along information about past events and man’s achievements to future generations.

The Andreas Vesalius medal, slightly bigger than an American silver dollar, is a typical commemorative medal. Continue reading →

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HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

Names in bold are HSLS-affiliated

News

Renae Barger was appointed Associate Vice Chancellor for the Health Sciences Library System. Since 2017, Renae served as HSLS Associate Director of Research, Instruction, and Clinical Information Services and was the Program Lead of the Network of the National Library of Medicine, Middle Atlantic Region. Please also see “Director Spotlight” in this issue.

Helenmary Sheridan, Data Services Librarian, was appointed to the RDAP (Research Data Access & Preservation) Education and Resources Committee for a one-year term, starting in July 2021.

Continue reading →

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Transitions

I am retiring as HSLS Library Director, effective July 1, 2021. Except for two years away*, I have been at Pitt in one role or another since 1969: first as an undergraduate, then as a “personal librarian” to the chair of psychiatry, next as Librarian and Library Director at Western Psychiatric Institute & Clinic (now UPMC Western Psychiatric Hospital), and finally as Associate Director, Interim Director, and Director of HSLS. If you prick my finger, I bleed blue and gold. I have had a wonderful career, and have appreciated the opportunities that I have enjoyed at Pitt. I cherish the friendship, collegiality, and expertise of our HSLS staff and the Pitt community, and I am enormously proud of our accomplishments as a leading health sciences library on the national scene. Continue reading →

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HSLS Congratulates Barbara Epstein on Her Prestigious Career

It is with mixed emotions that we would like to congratulate Barbara Epstein, HSLS Director, on her retirement after 17 years as director and a long career at Pitt. During her time with HSLS, Barbara has been an essential part of the library’s success. We have had the pleasure to not only work alongside Barbara but also to thrive under her excellent leadership. While we are saddened to see her leave, we would like to take a moment to reflect on her many noteworthy accomplishments.

Barbara has been an instrumental leader in health sciences librarianship. She became the 2017-18 Medical Library Association (MLA) president, after serving as president-elect the previous year. In addition, she was on the MLA Board of Directors and Executive Committee. During her time with MLA, she had the opportunity to connect with officers of health sciences library associations from Europe, Canada, Australia, Taiwan, Africa, and the U.S. to share ideas and challenges. She was selected to present the Janet Doe Lecture at MLA’s 2015 annual meeting. In 2016, MLA bestowed the honor of Fellow to Barbara based on her accomplishments and contributions to the health sciences information profession. Continue reading →

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Make File Management Simpler with Version Control

Works in progress can become unruly. As a piece of research code grows, it often spawns new files that iterate on the original: this version fixes one bug but introduces another, or that version swaps two similar functions. The same is true for manuscript drafts which pass among co-authors, accumulating new text (and usually new filenames) as they travel. It can be difficult to tell these versions apart from each other, or trace the history of how one version evolved from another. Version control systems make this work easier.

Version control is defined as “a system that records changes to a file or set of files over time so that you can recall specific versions later” in Pro Git (second edition, 2014), an excellent open textbook by Scott Chacon and Ben Straub. Version control allows a user to see all changes made to a file, who made the changes, and when they were made. It can let an author approve or reject edits made to a manuscript, or quickly determine which set of figures are the right ones to submit to a journal. Continue reading →

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EndNote 20: What’s New and What’s Not?

If you’re a regular EndNote X9 user, you may have seen a pop-up notice encouraging you to upgrade to the new EndNote 20. EndNote 20 is the latest version of the software, and looks much different from prior updates. Despite the visual makeover, much of the functionality is the same. Cite While You Write in Word has not changed, and most features remain. So what’s different about the new EndNote?

New Design

While EndNote 20 retains the three-paned structure of EndNote X9, the interface has been simplified. Previously you could search PubMed and other databases by switching to Online Search or Integrated Mode. EndNote 20 has combined that feature into the main library, essentially making Integrated Mode the default. EndNote 20 also has a darker color scheme and larger displays. The toolbar has been removed and replaced with a few large icons above the middle library pane. Continue reading →

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Does My Funder Require Me to Publish Open Access?

If you have ever received grant funding for your research, particularly through a federal agency such as the National Institutes of Health (NIH), you may be aware that there are requirements for making your research available to the public. For example, NIH’s Public Access Policy states that “all investigators funded by the NIH submit…to PubMed Central an electronic version of their final peer-reviewed manuscripts upon acceptance for publication” within 12 months. Many federal agencies in the United States have similar policies, designating a specific repository for submission of final research manuscripts within a certain time frame. These policies can be located on the funder’s website or by browsing a resource such as SPARC’s Browse Article and Data Sharing Requirements by Federal Agency. Continue reading →

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Remembering Nancy Tannery

Colleagues and friends mourn the death of Nancy Hrinya Tannery, MLS, former HSLS Senior Associate Director, who passed away on Friday, May 14, 2021.

Nancy had a long history of service to the University and to the profession of health sciences librarianship. She completed an undergraduate degree from Penn State in medical technology, and enjoyed a 20-year career in research before earning her MLS degree from Pitt. She began her career as a Reference Librarian at HSLS in 1996. Her professional skills as a Faculty Librarian and ability to lead and mentor led to a steady rise through a succession of HSLS management positions. Nancy left HSLS in 2017 to serve as Assistant Provost, and retired from the University in 2020 with emerita status. Continue reading →

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2021 MLA Participation

HSLS librarians were active participants in the Medical Library Association’s Annual Meeting from May 10-27, 2021.

Immersion Sessions

Helena VonVille, Research and Instruction Librarian, presented “Protocol Development Using Health Research Reporting Guidelines and Critical Appraisal Tools.”

Tess Wilson, All of Us Community Engagement Coordinator, NNLM, presented “Leadership and Management Best Practices for Leveraging Community Connections to Improve Access to Health Information.” Continue reading →

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Featured Workshop: Exploring and Cleaning Data with OpenRefine

HSLS offers classes in a wide array of subjects—molecular biology, database searching, bibliographic management, and more! You can quickly view all Upcoming Classes and Events or sign up to receive the weekly Upcoming HSLS Classes and Workshops email.

This month’s featured workshop is Exploring and Cleaning Data with OpenRefine. The workshop will take place on Friday, June 11, 2021, from 10-11:30 a.m.

Exploring and Cleaning Data with OpenRefine is a workshop that introduces participants to the basics of working with OpenRefine to clean, organize, and transform messy datasets.

OpenRefine (formerly Google Refine) is a powerful, free, open-source tool for working with unorganized tabular data. Since OpenRefine works offline in a web browser, your private data is not uploaded to the cloud and will stay on your local computer. Note that you are always working on a copy of your data, your raw data files are kept in their original form. Another benefit of OpenRefine is that while the program has a graphical interface, the system documents steps that have been completed to allow for reproducibility in data cleaning. These steps can be saved as JSON scripts and used to automate steps to clean other similar files. Continue reading →