Streamline Your Workflow with LabArchives

labarchives Chance Favors the Organized Lab labarchives.comWhat is LabArchives? It is ERN software licensed by Pitt since 2016 for the organization, communication, instruction, sharing, and management of scientific research and data.

What is an ERN? An Electronic Research Notebook is a secure, cloud-based platform to organize and manage your research and lab data safely.

Why use LabArchives? Digital notebooks offer features that are not possible with traditional paper lab notebooks. Continue reading

Open Access COVID Datasets and Software

“Sharing vital information across scientific and medical communities is key to accelerating our ability to respond to the coronavirus pandemic,” said Dr. Cori Bargmann, Head of Science at the Chan Zuckerberg Initiative, regarding a call to action to develop new text and data mining techniques that can help the science community answer high-priority scientific questions related to COVID-19.

Over the past few weeks, two notable resources have been made available, providing open access to COVID datasets and related software:

COVID-19 Open Research Dataset (CORD-19) Continue reading

Filtering by Article Type in PubMed

If you’re a frequent user of PubMed, you may be familiar with the Article Types filter available on the Search Results page. This filter limits search results by attaching an additional search term to your search string. So, for example, if you enter the search terms “therapeutic hypothermia cardiac arrest” in PubMed, applying the Clinical Trial filter adds “AND Clinical Trial[pytyp]” to the end of the PubMed search string. That will limit your search to records tagged with Medical Subject Headings such as Clinical Trial, Controlled Clinical Trial, or Randomized Controlled Trial.

While the Article Types filter is one option for limiting to a particular study type, it can severely reduce the number of records you see and, more importantly, miss the records of very recently published articles. If that is a concern for you, check out another set of PubMed filters available through PubMed Clinical Queries. Also found as link on the PubMed home page, this set of filters is more “sensitive” than the Article Types filter, meaning they are more likely to find relevant records, including records for recently published studies. Continue reading

Tutorials for the New PubMed Now Available

Pubmed.govThe new version of PubMed will soon be live. Now is a good time to familiarize yourself with the new format. The National Library of Medicine has developed a number of short, to-the-point tutorials on how to search the new PubMed by topic, subject, author, and more. To view the list of tutorials, visit “PubMed Essentials: New Quick Tours and On-Demand Class on the New PubMed” in the March-April 2020 issue of the NLM Technical Bulletin.

Going forward, the bi-weekly HSLS Painless PubMed class will focus on the new PubMed.

Treasures from the Rare Book Room: Humphrey Ridley Remembered

Humphrey Ridley (1653-1708) was a little-known English neuroanatomist who studied medicine at Merton College in Oxford, and received his medical degree from Leyden University in 1679. Upon his return to England, he was a physician at Cambridge University and a member of Royal College of Physicians. There is not much known of his personal life, and he left only three published works: first on the topic of venereal diseases (1679), next on anatomy of the brain (1695), and the third on asthma (1703).

His book, Anatomy of the Brain Containing Its Mechanism and Physiology, followed two earlier and more commonly cited works in neurology, one by Thomas Willis and the other by Raymond Vieussens, but Ridley’s was the first neuroanatomy treatise in the English language. He acknowledged the brilliance of his predecessors, but also corrected some of their mistakes and omissions. He was the first to describe the ophthalmic artery and the ganglion of the fifth cranial nerve. According to Thakur, et al., Ridley was also the first to describe arachnoid cisterns and the arachnoid membrane, but because his contributions were not previously mentioned, Bichat and Ruysch held this claim even though their works were published later. Thakur and his colleagues speculated that Ridley’s stationary life and lack of clinical legacy might have contributed to the sad fact that his mastery in cadaveric injections and his novel contributions have gone unnoticed and uncited for so long.

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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


Carrie Iwema, Coordinator of Basic Science Services, has become a Certified Carpentries Instructor. The Carpentries project includes Software Carpentry, Data Carpentry, and Library Carpentry with the shared mission to teach foundational computational and data science skills to researchers.


Holly Hill joined the HSLS staff as the new Program Manager and will be supporting HSLS’s partnership with UPMC for providing digital library resources and services. Holly previously held administrative positions at UPMC and in the business sector. Continue reading

Classes for April 2020

Due to recent University of Pittsburgh restrictions, HSLS will be offering all classes online until further notice.

Painless PubMed, Wednesday, April 1, 8:30–9:30 a.m.

Basic Python through Jupyter, Friday, April 3, 1–4 p.m.

Basic EndNote, Tuesday, April 7, 11 a.m.–12 p.m.

Genetic Variation, Wednesday, April 8, 10 a.m.–3 p.m.

Share Data with the Pitt Data Catalog, Thursday, April 9, 10:30–11 a.m.

Beyond Beginner Workshop: Getting Going with Pandas in Python, Friday, April 10, 1–4 p.m.

Visual Abstracts, Monday, April 13, 10:30 a.m.–12 p.m.

Painless PubMed, Monday, April 13, 12–1 p.m.

Bulk RNA-Seq., Wednesday, April 15, 10 a.m.–3 p.m.

Advanced OpenRefine Functions, Thursday, April 16, 3–4 p.m.

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