Molecular Biology Information Service

The HSLS Molecular Biology Information Service has a mission: providing bioinformatics resources via software procurement, implementation, and training to assist biomedical scientists with solving their research questions. Also referred to as “HSLS MolBio,” our service has supported Pitt researchers since 2002.

HSLS MolBio follows a four-facet approach:

  1. Identify, procure, and implement commercially licensed bioinformatics software. Free software access is provided to eligible Pitt affiliates.
  2. Teach hands-on workshops spanning a wide array of topics, notably in contemporary bioinformatics, such as bulk and single-cell RNA-Seq data analysis, pathway enrichment analysis, and gene expression visualization. Use HSLS-licensed software featuring a user-friendly graphical interface, eliminating the need for prior programming experience. Furthermore, introduce participants to the R programming language, emphasizing data wrangling, visualization, and population-based health and genomics data analysis through the All of Us Researcher Workbench.
  3. Provide one-on-one consultations on software/databases.
  4. Maintain a web portal providing overall guidance on accessing and using bioinformatics resources and HSLS MolBio-created web tools.

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Scholarly Publishing Services

Not sure who to ask when you have questions about publishing? Librarians at HSLS are prepared to answer your questions, teach classes in the curriculum or lab journal club, and provide individual and group consultations on a variety of publishing topics.

Where to publish?

Whether you’ve published many times before, or if it’s your first time going through the process, there is much to consider when finding a suitable journal for your work. We can provide ideas for how to put your manuscript into a framework to identify relevant journals, as well as how to evaluate the quality of a journal. From understanding the different ways to make your work open access, negotiating your author rights, complying with public access policies, or publishing research outputs such as preprints, HSLS librarians are ready to help make this process easier.

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HSLS Staff News

HSLS Staff News

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

News

Farewell to Brendan Vaughan, Main Desk Library Associate, who is leaving the HSLS Main Desk team to become a Library Public Service Specialist in the Research and Library Support Organization team at Hillman Library.

Publication

Rebekah Miller, Research and Instruction Librarian, co-authored the article:

Whitfield, D. L., Miller, R. S., Escobar-Viera, C. G., Mammadli, T., Brown, A. L., Gordon, J. D., & Chandler, C. (2023). Effects of internalised racism and internalised homophobia on sexual behaviours among black gay and bisexual men in the USA: a systematic review protocol. BMJ Open, 13(7), e070969. https://doi.org/10.1136/bmjopen-2022-070969

Two New Resources for Writing NIH Data Management & Sharing Plans: Sample Plans and Pitt-Specific Guidance

While investigators have been hard at work preparing grant proposals under the new NIH Data Management & Sharing Policy, the community of librarians and data professionals that support them have been developing tools to simplify the process. Since our last update in April 2023, two new resources have appeared that HSLS Data Services wants to share:

  1. The NIH now provides 13 sample data management and sharing plans for a variety of data types, research domains, and institutes and centers. These samples were produced from real data management and sharing plans and contain details specific to their research projects; they are not meant to be used as templates, only as examples of the types of details and level of specificity that can be included in the plan.
  2. DMPTool, an interactive tool that walks researchers through the process of creating a data management and sharing plan (DMSP), now includes Pitt-specific guidance such as the language for Element 6, “Oversight of Data Management and Sharing,” recommended by the Office of Sponsored Programs and the Office of Research Protections.

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Freedom House Ambulance Service of Pittsburgh – Making Medical History

Freedom House Ambulance Service was established in Pittsburgh in 1967. It was a cooperation between Freedom House Enterprises, a non-profit Black-administered organization focused on the development of Black-owned and operated businesses, and the Presbyterian University Hospital. Freedom House provided training for unemployed members of the Hill District community, teaching them to become Emergency Medical Technicians (EMTs) and deliver paramedic service to the area that lacked access to emergency services. This training equipped future paramedics with skills like intubation and defibrillation, which no one had performed in the out-of-hospital setting before. The Freedom House training would eventually become the model for the national standard of EMT training.

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Featured Class: Protecting Your Privacy Online

Join us for this class:
Wednesday, August 9, 2023, noon-1 p.m.
Online
Register for Protecting Your Privacy Online*

Have you ever clicked “I agree” without reading an app’s terms and conditions? Given a browser extension permission to read and change data on all sites you visit?

The aggregation of data collected by apps and websites can be used by advertisers, law enforcement, and propagators of misinformation to predict and shape human behavior.

In this hour-long class, you will learn who is collecting your data and what they may be doing with it, and you will learn about options to increase your privacy and control over your own data.

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Modernized ClinicalTrials.gov Website

The modernized ClinicalTrials.gov officially launched on June 21, 2023. The world’s largest clinical trial and results registry, ClinicalTrials.gov contains information about nearly 450,000 clinical research studies, including information about study results. Overall improvements to the website include standard features to ease navigation and optimize use of the site on mobile devices.

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HSLS Staff News

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

Publications

Julia Dahm, Assistant Director for Technology Integration and Fulfillment Services, was acknowledged for her assistance in figure preparation in the article:

Guo, X., Liu, S., Sheng, Y., Zenati, M., Billiar, T., Herbert, A., & Wang, Q. (2023). ADAR1 Zα domain P195A mutation activates the MDA5-dependent RNA-sensing signaling pathway in brain without decreasing overall RNA editing. Cell reports, 42(7), 112733. Advance online publication. doi: 10.1016/j.celrep.2023.112733

Michele Klein-Fedyshin, Research and Clinical Instruction Librarian, and Andrea Ketchum, Research and Instruction Librarian Emeritus, co-authored the article:

Klein-Fedyshin M, Ketchum AM. PubMed’s core clinical journals filter: redesigned for contemporary clinical impact and utility . J Med Libr Assoc. 2023 Jul 10;111(3):665-676. doi: 10.5195/jmla.2023.1631.

This article was also featured as the JMLA Spotlight in the Association News blog on July 13, 2023.

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Charting the Future of Scientific Literature Exploration with AI: Introducing Elicit.org

The advent of ChatGPT, an innovative AI tool from OpenAI, has sparked both intrigue and caution within the scientific research community. Its capacity to revolutionize our search for information is profound, particularly evident in the rise of AI tools for scientific literature exploration.

One such tool making waves is Elicit.org. Designed as a research assistant, it employs language models such as GPT-3 to automate elements of researchers’ workflows, refining the literature review process. AI tools such as this are promising for the future of scientific research, but understanding their functions and limitations is crucial when employing them.

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Syllabus Review from HSTalks: High-Quality Multimedia Content for Your Course

The fall semester is quickly approaching, and instructors working on finalizing content for hybrid or online courses can find useful resources and support at HSLS. Before you begin creating additional slides and presentations, check out the high-quality, well-produced material available from Henry Stewart Talks (HSTalks).

The Biomedical and Life Sciences Collection: Lectures by leading world experts, from HSTalks, contains valuable resources for personal or classroom education in basic sciences and medical topics. The database is primarily known for providing animated, online, audio-visual lectures, seminar-style talks, and case studies.

Content is labeled with a level, so it is easy to identify which talks are suitable for undergraduates versus which might be better for advanced researchers. Content from the talks can easily be linked to or embedded within Canvas or other LMS. In addition, complete courses, including lectures, exam questions, and supplemental materials, are available.

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Treasures From the Rare Book Room: Is It Really About the Witchcraft?

Etching-style portrait of the author, with his name: Ioannes Wiervs
Etching portrait of Johann Weyer, author of “De praestigiis Daemonum”

“De praestigiis Daemonum” by Johann Weyer (Basil 1563)

This year is the 460th anniversary of the publishing of “De praestigiis Daemonum” (“On the Tricks of the Devil”), written by Dutch physician Johann Weyer (1515-1588). This book is one of the gems in our collection. Continue reading →

Featured Class: Exploring and Cleaning Data with OpenRefine

Join us for this class:
Tuesday, July 18, 2023, noon-1:30 p.m.
Scaife Hall, Falk Library, Library Classroom
Register for Exploring and Cleaning Data with OpenRefine*

OpenRefine is a free, open source tool for working with messy tabular data. It runs offline in a web browser and allows for reproducibility in data cleaning. Any student, faculty member, or researcher who works with data can benefit from learning to use this powerful tool.

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ClinicalKey’s Spring 2023 Content Updates

ClinicalKey recently released a large batch of “Spring 2023” content updates (for March, April, and May). Content updates typically occur monthly, so this was a larger than usual batch. The full list is currently available via the “Get News and Updates” section on the ClinicalKey home page. Here are some highlights among the newly added e-books:

  • Avery’s Diseases of the Newborn, 11th edition
  • Basic Immunology, 7th edition
  • Berne & Levy Physiology, 8th edition
  • Elsevier’s 2024 Intravenous Medications, 40th edition (Note: past editions were titled “Gahart’s Intravenous Medications”)
  • Harriet Lane Handbook, 23rd edition
  • Little and Falace’s Dental Management of the Medically Compromised Patient, 10th edition
  • Plotkin’s Vaccines, 8th edition

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