2018 – Page 6 – HSLS Update

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Expand Your Data Analysis Universe with Galaxy

The life sciences are erupting with data. Thanks to advancements in DNA sequencing technologies and the speed and capacity of computational algorithms, the generation of vast quantities of genomic and proteomic data is now commonplace and expected. However, analysis of this data is not keeping pace with its acquisition (storage space is yet another issue…). One limiting factor is that many biomedical scientists do not yet know how to access, much less use, the available analytical resources. This article describes a platform for multi-omic data analysis that is accessible, reproducible, and transparent, and recommends resources on how to use it.

Galaxy is a community-supported platform that provides access to over 5,500 tools for a multitude of analytical needs, in categories such as variant analysis, imaging, and statistics. Its components include the Galaxy Software Framework and the Public Galaxy Service. The software framework is an open-source, web-based application that functions as an intermediary between researchers without informatics expertise and the computational infrastructure that runs and stores the analyses. The public service includes the main instance, which is an installation of the Galaxy software combined with many tools and data, as well as over 80 public servers. Some of these servers are even domain-specific (ImmPort Galaxy, focusing on flow cytometry analysis) or tool-publishing (MBAC Metabiome Server, simplifying the control, usage, access, and analysis of microbiome, metabalome, and immunome data). Local institutional instances are also possible; the University of Pittsburgh has a Galaxy server hosted by the Center for Research Computing.

The scale of Galaxy is initially a bit daunting. Fortunately, there are numerous resources to help researchers navigate the analytical possibilities. Everything to get you started is at galaxyproject.org, including Galaxy 101, dataset collections, interactive tours, and a growing collection of tutorials developed and maintained by the worldwide Galaxy community and Galaxy Training Network.

The HSLS Molecular Biology Information Service can also assist you with using Galaxy for your research. During the spring 2018 semester we are introducing two hands-on workshops that will teach the basics of Galaxy including (1) interface navigation and interaction and (2) how to create, modify, and extract workflows.

ChIP-Seq & Galaxy (April 13)
RNA-Seq & Galaxy (April 27)

To learn more, read the bioRxiv article on “Community-Driven Data Analysis Training for Biology” or contact the HSLS Molecular Biology Information Service.

~Carrie Iwema

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Study Spaces at Falk Library

Need a place to study? HSLS provides a variety of study spaces for individuals and groups.

Individual Study

Study desks with privacy walls are available in two locations:

A newly renovated area on the main floor contains 44 study desks. Each station has power outlet access.
The upper floor has seating for 20 individuals across from Classroom 2.

Standing and stools:

Counters and standing desks are available on the main and upper floors, both providing easy access to power outlets.

Group Study

The recently opened study room on the main floor has 11 tables with 3-4 chairs each. Larger groups can use the tables pushed together.
Additional larger tables are interspersed with the computer stations on the main and upper floors.
The upper floor Study Lounge is located on the far end of the upper floor.

Comfortable Seating

Armchairs are available on the main floor near the leisure reading collection and on the upper floor in the Study Lounge.

Study Areas Reserved for the Schools of the Health Sciences

Group Study Rooms can be used for individual or group study for four hours at a time. Rooms must be reserved online. Keys to access the room are checked out at the Technology Help Desk with a valid Pitt ID.

The main floor room with individual study carrels will soon feature access for Health Sciences students via their Pitt ID.

~Julia Dahm

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The Class That Wouldn’t Die

HSLS has a robust portfolio of classes available. We offer classes on core topics such as searching PubMed and using EndNote software, with more specialized classes added based on our expertise, changes in the information environment, and patron needs.

Most class additions are initiated by HSLS research and instruction librarians. But sometimes a new class is born from patron requests. As an example, here is a brief history of one class, “Searching for Dollars: Grant Seeking to Support Research.” Continue reading →

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Thieme E-Book Library Name Change

The Thieme E-Book Library has been renamed, and is now known as MedOne Education. HSLS provides direct access to this collection on the Databases A-Z list, and the access notes for the e-books will continue to show as being available via Thieme. This will have no effect on Thieme e-journals as their name remains unchanged. There is a freely available MedOne app that allows users the opportunity to access subscribed content on both Android and iOS devices.

~Misti Kane

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HSLS Staff News

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

Publication

Author name in bold is HSLS-affiliated

Jonathon Erlen, history of medicine librarian, along with co-author Megan Conway, published “Disability Studies: Disabilities Abstracts” in The Review of Disability Studies: An International Journal, 14(1), 2018.

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Classes for April 2018

FlashClasses

Painless PubMed*, Friday, April 6, 8-9 a.m.

EndNote Basics, Tuesday, April 10, 10 a.m.-12 p.m.

Painless PubMed*, Monday, April 16, 12-1 p.m.

Molecular Biology Information Service

Can Learning Be Fun? (How-To Talks by Postdocs), Thursday April 5, 12-1 p.m.

The Application of Mass Spectrometry in Biomedical Research (How-To Talks by Postdocs), Tuesday, April 10, 1-2 p.m.

ChIP-Seq & CLC Genomics, Wednesday, April 11, 1-4 p.m.

ChIP-Seq & Galaxy, Friday, April 13, 1-4 p.m.

Gene Regulation, Wednesday, April 18, 1-4 p.m.

Gemstones from the Mud: Technical overview of protein purification (How-To Talks by Postdocs), Thursday, April 19, 1-2 p.m.

RNA-Seq & CLC Genomics, Wednesday, April 25, 1-4 p.m.

How to Create a Quality Scientific Poster (How-To Talks by Postdocs), Thursday, April 26, 1-2 p.m.

RNA-Seq & Galaxy, Friday, April 27, 1-4 p.m.

Continue reading →

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ORCID iD and Automated Altmetrics Reports

ORCID ID logo An ORCID iD is your lifetime author identifier that connects all aspects of your research career, no matter how often or where you move, or if your name changes for any reason. Database searchers worldwide will find your complete body of work, connecting you to potential co-authors, new opportunities, award nominations, or speaking invitations. Once your ORCID iD is registered, use Scopus to perform an author search and export all your publications to your ORCID account using these instructions. This will also connect the two systems for automatic updates.

ORCID’s coordination of all your associated works makes it easier to analyze the immediate impact of your ‘science communication’ with society. Altmetrics cover both academic and public or community engagement with publications, books, news stories, blogs, YouTube videos, Twitter, Facebook, slide presentations, workshops, data, software, and other shared work. Recognition of your work can be tracked through Altmetrics reporting, which tracks your scholarly activities throughout online media, and which depends on your ORCID iD. Altmetrics reports can:

be used in grant applications to demonstrate real-world applications and science communication or public engagement skills.

be helpful in annual assessments to display enhanced research dissemination.

encourage new research relationships and global collaborations.

As an example of the value to a funding agency, the National Science Foundation (NSF) evaluates these activities, among other options, as evidence of Broader Impacts, the second half of the merit review process.

Pitt uses altmetrics leader PlumX to analyze publications deposited in Pitt’s repository, D-Scholarship@Pitt. Browse or search the repository without logging in to view examples of a PlumX analysis.

For faculty, another option is to view your record in Pitt’s Faculty Information System (FIS), accessible via my.pitt.edu. On the far right side, scroll down to the FIS link and press enter. In your record, scroll to your “Claimed Publications.” Click on a publication title. In the upper right, under the citation, click on the D-Scholarship link. This will take you to the publication record in D-Scholarship@Pitt, where you can view the PlumX analysis at the bottom of the page.

For more information, see the HSLS guides: Scholarly Communication and Research Impact-Enhance Your Impact. You can also contact Andrea Ketchum at ketchum@pitt.edu or call 412-648-9757.

~Andrea Ketchum

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Get Some OOMF for Your Tech with New Charging Packs

Oomf charger Finding a power outlet can be tough, so why not bring a power source with you? Falk Library now has two Oomf Omnicharge stations in the library. This is a free technology loan program that works with the Oomf app to borrow a charging pack for 24 hours.

If you are new to Oomf, get started by downloading the app, available for iPhone and Android. You will need to set up an account; although borrowing is free, your credit card information is collected for any applicable late fees if the device is not returned after 24 hours. Visit one of the charging stations, either at the library Main Desk or at the upper floor Technology Help Desk. When your phone is near the charging station, it will connect via Bluetooth and unlock one of the available charging packs. Take the pack with you, and use your device’s charging cord. The Technology Help Desk also lends charging cords for phones and laptops that are compatible with the charging packs. Multiple devices can be connected to one Oomf charger, via two USB slots and one AC outlet.

Oomf is available to support any issues at support@theoomf.com.

~Julia Dahm

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National Library of Medicine Team Visits HSLS

Photo of Kate Flewelling — Kate Flewelling
Executive Director, NNLM MAR

On February 1-2, 2018, four visitors from the National Library of Medicine conducted a site visit with staff from the National Network of Libraries of Medicine, Middle Atlantic Region (NNLM MAR), and the NNLM Web Services Office (NWSO). Both NNLM MAR and NWSO are based at HSLS and are funded from 2016-2021 as part of a cooperative agreement with the National Library of Medicine.

The site visit team included Amanda Wilson, head, National Network Coordinating Office; Alan Vanbiervliet, program officer, Extramural Programs; and Franda Liu and Nichelle Midon, project scientists, National Network Coordinating Office. Continue reading →

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Director’s Reflections…THANK YOU to our Generous Donors

Barbara Epstein
HSLS Director
bepstein@pitt.edu

Below is a list of those generous people who have made donations to the library in 2017. With the support of these thoughtful people, HSLS can continue to provide essential resources to enhance the quality of health care in western Pennsylvania and beyond.

Ms. Patricia W. Bookamyer

Dr. Nancy Breslen

Mr. Arnold and Mrs. Barbara Epstein

Dr. Carol E. Roach Mattes

Ms. Maureen K. Perrino

Dr. Elizabeth A. Schlenk

Dr. John B. Schumann and Mrs. Maria Pimentel-Schumann

Dr. Frederick J. and Mrs. Nancy Tannery Continue reading →

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Novel Guidelines Address Fatigue in the Ambulance

Fatigue is a persistent problem for EMS providers. Over half report work-related fatigue, creating potential hazards for their patients as well as drivers who share the road with them. But there have never been any credible recommendations to mitigate risk.

Until now. In January, the Fatigue in EMS Project issued first-ever evidence-based guidelines for EMS professionals and those who manage their schedules:

Use fatigue/sleepiness survey instruments to measure and monitor fatigue.
Limit work shifts to less than 24 hours.
Provide access to caffeine.
Provide the opportunity to nap while on duty.
Provide education and training to mitigate fatigue and fatigue-related risks.

From this librarian’s perspective, what distinguished this project from others were its blitz-like pace and output. Within 21 months of my first meeting with lead investigator Daniel Patterson, assistant professor of emergency medicine, his project team had published the five guidelines and the seven systematic reviews on which they were based. These publications will be the basis for a special supplement of Prehospital Emergency Care.

Full disclosure: Things did not start from scratch at the point when I joined the team. By then, Patterson’s multidisciplinary expert panel had already completed a structured, iterative process to select seven research questions. These were in PICO format (Population, Intervention, Comparison, Outcome) and had been registered in PROSPERO, an international database of systematic reviews.

My search strategies concentrated on the population and intervention concepts. Population was constant, defined as people at least 18 years old working in EMS and other extended shift professions, including firefighters, police, pilots, truckers, nurses, physicians, and military personnel. Interventions evaluated are reflected in the five guidelines above. Evidence for two additional interventions was not strong enough to warrant recommendations.

The seven literature searches covered six databases, included thousands of search terms, and retrieved over 38,000 items, all of which the team reviewed for relevant evidence that was distilled into the guidelines.

The National Association of State EMS Officials (NASEMO) partnered with Patterson’s research team. Funding from the National Highway Safety Administration supported the project.

Patterson, currently a paramedic for Parkview EMS in O’Hara, says that he has a healthy respect and fear of fatigue when on duty. “It is that fear of what could happen when fatigued that drives me to do my best to use the strategies I know to work for me and supported by the evidence.”

~Pat Weiss

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Treasures from the Rare Book Room: Golgi’s Investigations on the Finer Structure of the Central and Peripheral Nervous System

Camillo Golgi (1843-1926) was an Italian pathologist associated with the University of Pavia, where he studied and worked as professor of histology, chair of pathology, and dean and rector of the University. He is known for his work on the central nervous system, for which he was awarded the Nobel Prize in Physiology or Medicine in 1906, and which he shared with Santiago Ramón y Cajal.

While studying at the University of Pavia, under the influence of Cesare Lombroso, Golgi started his scientific career researching mental diseases, but quickly abandoned psychiatry in order to study the structure of the nervous system. Though tissue staining techniques in histological research were introduced in the mid-19th century, they were not sophisticated enough for investigating the nervous system. Golgi started his search for a better technique and ultimately discovered staining using potassium dichromate and silver nitrate (mentioned by him in 1873). This revolutionary technique of “black reaction,” later named after him (Golgi staining or Golgi impregnation), allowed for the first time a clear visualization and description of nerve cells. This discovery was a critical point in the development of modern neurology. Though Golgi himself could not see beyond the “reticular theory” (the belief that the nervous system consists of nervous fibers forming an intricate but continuous network), his work led to the establishment of neurons as a basic cell unit of the nervous system. He will be remembered as a man who pushed neurological research forward. 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.

News

Donna Perkins has been promoted to Web Editor and will continue assisting at the Main Desk. She previously was working nights and weekends, but will now be working Monday through Friday during the day.

Brendan Vaughan has joined the HSLS staff as a library specialist. In his new position, he will be working at the Main Desk and will provide customer service. Continue reading →

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