HSHSL Updates

DABS (Data and Bioinformation Stuff) Volume 1 Issue 6: Phylogenetic Trees

Posted on February 12, 2021 by HS/HSL

The Center for Data and Bioinformation Services (CDABS) is the University of Maryland Health Sciences and Human Services Library hub for data and bioinformation learning, services, resources, and communication.

This week (Feb 8-12) we celebrated Love Data Week and the official launch of CDABS. Check out our center, a virtual center, at our homepage: https://www2.hshsl.umaryland.edu/cdabs/

Our topic in this edition is all about phylogenetic trees! A key concept to understanding the evolution of organisms and molecules. A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two descendants that split from the same node are called sister groups. This weeks links will guide you to repositories of reference molecular data to build trees as well as some software for building trees that is open source. Happy reading!

Berkley’s Understanding Evolution team is a starting point to get an overview of phylogenetic systematics. In the tutorial, they cover how to read an evolutionary tree, how to classify organisms based on evolutionary trees, how to reconstruct an evolutionary tree, and how evolutionary trees are used. (5–minute read) https://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_01
Finding high quality, reliable data is fundamental to building phylogenetic trees that are reliable. GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. The knowledgebase automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information. (5-minute overview & Infinite time exploring) https://www.genecards.org/
To build a molecular phylogenetic tree you will need to run a multiple sequence alignment and use the phylogenetic tree output. One of the fundamental molecular biology tools for doing so is Clustal Omega “The last alignment program you’ll ever need”. Clustal Omega can be downloaded and run on your computer or you can also access a webserver to perform your alignment. (5-minute overview) http://www.clustal.org/omega/
Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree formats, such as Newick/Phylip, Nexus, Nhx and PhyloXML, and provides a range of visualization options, using fifteen types of custom annotation datasets. (5-minute overview) www.evolgenius.info/evolview/
Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. In addition it is a tool for building phylogenetic trees. (5-minute overview) https://cytoscape.org
There is an R package RCy3 that can be leveraged for creating phylogenetic trees in R and visualizing them in Cytoscape. This vignette will show you how to work the popular Newick format for phylogenetic trees in Cytoscape by conversion to igraph and import via RCy3. (5-minute overview) http://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Phylogenetic-trees.nb.html

Questions?

Contact: Amy Yarnell, Data Services Librarian and Jean-Paul Courneya, Bioinformationist — at data@hshsl.umaryland.edu.

Posted in Data/Bioinformation | Tagged bioinformatics, bioinformation, CDABS, data, evolution, phylogenetics | Comments Off

DABS (Data and Bioinformation Stuff) Volume 1 Issue 5: Black History Month

Posted on February 5, 2021 by Amy Yarnell

Next week (Feb 8-12) we will be celebrating Love Data Week and the official launch of CDABS. Check out our full schedule of events and sign up for a workshop or three!

This week, in honor of Black History Month, we would like to highlight a few of the great projects and organizations that are led by Black scholars and data scientists and that focus on issues of data and racial equity and justice.

The Algorithmic Justice League, founded by Poet of Code Joy Buolamwini (@jovialjoy), aims “to raise public awareness about the impacts of AI, equip advocates with empirical research to bolster campaigns, build the voice and choice of most impacted communities, and galvanize researchers, policymakers, and industry practitioners to mitigate AI bias and harms.” Twitter: @AJLUnited

Black Girls Code, founded by Kimberly Bryant (@6Gems), aims “to increase the number of women of color in the digital space by empowering girls of color ages 7 to 17 to become innovators in STEM fields, leaders in their communities, and builders of their own futures through exposure to computer science and technology. To provide African-American youth with the skills to occupy some of the 1.4 million computing job openings expected to be available in the U.S. by 2020, and to train 1 million girls by 2040.” Twitter: @BlackGirlsCode

Black in Data, founded by Dr. Ruth Agbakoba (@RuthAgbakoba) and Simone Webb (@SimSci9), “represents a community of academics, professionals, and students working in various areas of data. We gather to support, learn from, and share opportunities with one another, and ultimately increase representation of Black people in data fields.” Twitter: @BlkInData

COVID Black, founded by Dr. Kim Gallon (@BlackDigitalHum), is “a Black Health data organization that uses data to tell stories about the Black lived experience to advocate for health equity. ” Twitter: @COVIDBLK

The COVID Racial Data Tracker, initiated by Dr. Ibram X. Kendi (@DrIbram), “advocates for, collects, publishes, and analyzes racial data on the pandemic across the United States. It’s a collaboration between the COVID Tracking Project and the Boston University Center for Antiracist Research.” Twitter: @COVID19Tracking and @AntiracismCtr

Data For Black Lives, founded by Yeshimabeit Milner (@YESHICAN), is “a movement of activists, organizers, and mathematicians committed to the mission of using data science to create concrete and measurable change in the lives of Black people.” Twitter: @Data4BlackLives

Questions? Contact: Amy Yarnell, Data Services Librarian and Jean-Paul Courneya, Bioinformationist — at data@hshsl.umaryland.edu.

Posted in Data/Bioinformation | Tagged bioinformation, Black History Month, CDABS, DABS, data, Love Data Week | Comments Off

NIH/NLM Call for Proposals for COVID-19 Infodemic Symposium

Posted on February 4, 2021 by ebrown

The NIH/NLM has put out a call for proposals for paper presentations and panelists for a COVID-19 Infodemic Symposium. The event will take place April 8 – 9, 2021. Deadline for submissions is February 26, 2021. For submissions, go to: https://bit.ly/COVID19Symposium

Posted in Announcement | Tagged Call for Proposals, covid-19, nih, NLM, symposium | Comments Off

Click for a Cheerful Message!

Posted on February 1, 2021 by ebrown

The “Mr. Rogers Jar” is back in virtual form. We missed having our jar of encouraging, funny, and positive messages at the Information Services Desk, and we heard that some of you did too. So, we dreamed up a virtual one. Click the jar for a dose of optimism.

original Mr. Rogers jar — A reminder of a simpler time, the original “Mr. Rogers” jar

Posted in Announcement | Tagged Mr. Rogers Jar, Positive Affirmations | Comments Off

#ColorOurCollections at the HSHSL

Posted on February 1, 2021 by Tara Wink

Every February since 2016, the New York Academy of Medicine hosts the #ColorOurCollections event meant to highlight the diverse images in the form of coloring sheets and books from libraries, archives, and other cultural institutions. This year the HSHSL Historical Collections Department is proud to be part of the event, which occurs February 1-5, 2021. Join in the festivities by downloading the HSHSL’s very own coloring book and sharing your masterpieces using the #ColorOurCollections and by sharing with the HSHSL (@UMBHSHSL) on Facebook, Twitter, or Instagram. We look forward to seeing your artwork!

Posted in Events, Historical Collections | Tagged Botanical, Color Our Collections, Coloring Book, Herbals | Comments Off

DABS (Data and Bioinformation Stuff) Volume 1 Issue 4: Love Data Week and the Launch of CDABS!

Posted on January 29, 2021 by Amy Yarnell

Love Data Week is coming February 8!

Love Data Week (Feb. 8 to 12) is an international celebration of all things data! Each year we hope to engage with our community on issues like data management, sharing, wrangling, and visualization, as well as open and reproducible science. This year we are excited to celebrate with the official launch of the new Center for Data and Bioinformation Services (CDABS) at the Health Sciences and Human Services Library (HSHSL) and a week of activities.

Schedule

Ongoing – All week

Visit the UMB Data Catalog. Explore the great research being done at UMB. Talk to us about cataloging your datasets! For more on the Data Catalog check out this video introduction!
Take part in ICPSR’s Adopt a Dataset program. ICPSR is an extensive repository of social, behavioral, and political data and the official organizer of Love Data Week. Choose a dataset from their list to adopt and share insights about it on social media.
Share why you love data on Twitter. Be sure to use the hashtags #LoveData21 and #UMBLovesData

Monday Feb. 8

Noon
Introduction to the Center for Data and Bioinformation Services
Join us for an information session to learn more about the Center for Data and Bioinformation Services (CDABS) and discover the many ways we can work with you at all stages of your research. CDABS is the new hub for data and bioinformation learning, services, resources, and communication at the Health Sciences & Human Services Library. Register

12:30PM-2:00PM
CDABS Launch Party!
Hang around after our introductory session, bring your own refreshments and celebrate the launch of the new Center. We are available to talk about anything you want and party! Register

Tuesday Feb. 9, Noon

Best Practices for Research Data Management
Get organized and avoid a “data disaster”! This workshop provides basic strategies and best practices for effectively managing research data to ensure its organization and accessibility. Topics covered include: funder and journal requirements for data management and sharing, standards for file naming and structure, resources for data management planning and sharing, and strategies for storing data during research and preserving it for the future. Register

Wednesday Feb. 10

Noon
Writing Data Management Plans with DMPTool
Researchers, do you have an upcoming grant application that requires you to write a data management or data sharing plan? Are you striving to maintain well-organized research projects? In this workshop, we will cover the components of good data management plans with a particular eye toward NIH data sharing requirements. Participants will also be introduced to DMPTool, an online platform which provides plan templates and guidance from most major funders. Additionally, we will be providing participants with time during the workshop to work on plans for their own projects and ask questions and receive guidance from the instructors. Register

1:00PM – 2:00PM
Open Data Office hours
Meet one on one with the CDABS team to talk about any questions or concerns. We can help with data management challenges, R programming, choosing visualizations, finding data, and developing a sharing strategy. Get signed up for All of Us Researcher Workbench, create an ORCID ID, or take a tour of our High-Performance Computer. Register

Thursday Feb 11, Noon

Introduction to GitHub
This online workshop will provide a rich overview of GitHub.com – what it is, why use it, and how. Participants will take a guided tour of GitHub’s main features, including project management, collaboration, and web publishing capabilities, and explore the endless amount of code, data, and other projects shared by millions of others on GitHub. The workshop is well suited for researchers working with data or software scripted tasks, as well as anyone with an interest in GitHub or open source collaboration. Register

Friday Feb 12, 11am

Getting Connected to your Data – A Reproducible Workflow for Data Wrangling
Wrangling. Munging. Data Sanitation. These and other names describe an aspect of the data analysis life cycle typically thought of as boring and unglamorous, but which occupies the majority of time spent during a data analysis project. The time you spend in preparing your data for analysis, while crucial, cuts into the time available for using software to produce a visualization, calculate a statistic, or run a favorite machine learning algorithm. The goal of this seminar is to provide a reproducible workflow for performing your own data wrangling. I will suggest methods to help you to: 1) get to know your data, 2) cultivate habits that will help you to spend less time on wrangling, and 3) optimally prepare your data for the output you’re interested in producing. Register

For questions contact Jean-Paul Courneya, Bioinformationist and Amy Yarnell, Data Services Librarian at data@hshsl.umaryland.edu.

Posted in Announcement, Data/Bioinformation, Workshops | Tagged bioinformation, CDABS, DABS, data, Love Data Week | Comments Off

DABS (Data and Bioinformation Stuff) Volume 1 Issue 3: Webinar Extravaganza!

Posted on January 22, 2021 by HS/HSL

Over the past year, RStudio has made significant enhancements to their products with respect to their support for Python and the ability to interoperate. In this webinar, you will learn how RStudio helps organizations tackle the challenge of working with R and Python, with a focus on some of the recent additions that have helped deepen the happy relationship between R and Python. (3-minute registration): https://pages.rstudio.net/RStudio_R_Python.html
CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Their extensible platforms provide data storage, bioinformatics tools, data visualization, interactive analyses, cloud services, APIs, and more. Every other Friday they provide free, half-hour webinars on science and technology topics to help you do your research and share your discoveries and include Q&A with data science experts. Video-recordings and other materials are made available after each live event. (3-minute registration): https://cyverse.org/webinars
Join Trifacta on April 7-9 for the Wrangle Summit 2021, the first event focused exclusively on data wrangling— the most interesting, messy, and opportunity-rich area of the data lifecycle that comes before analysis. Trifacta’s mission is to create radical productivity for people who analyze data. They’re deeply focused on solving for the biggest bottleneck in the data lifecycle, data wrangling, by making it more intuitive and efficient for anyone who works with data. (5–minute read & 5-minute registration): https://www.trifacta.com/events/wrangle-summit-2021/
Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy Webinar Series features short online talks that have Galaxy as a focus. Anyone can attend these. Videos of most webinars are available. Webinars are hosted all over the world and happen at least once a month. (5-minute read & 5-minute registration): https://galaxyproject.org/events/webinars/
European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organization, EMBL’s European Bioinformatics Institute (EMBL-EBI), webinar series is a freely accessible collection of live seminars focused on EMBL-EBI resources. They provide both brief introductions to a range of databases and more in-depth coverage of new features and tools to assist you in your research. Each webinar is delivered by an EMBL-EBI expert and is followed by a question-and-answer session. (5-minute read & 3-minute registration): https://www.ebi.ac.uk/training/webinars

Questions?

Contact: Amy Yarnell, Data Services Librarian and Jean-Paul Courneya, Bioinformationist — at data@hshsl.umaryland.edu.

Posted in Data/Bioinformation | Tagged bioinformatics, bioinformation, CDABS, DABS, data, data management | Comments Off

A History of the UMB Presidency

Posted on January 20, 2021 by Tara Wink

_{The Health Sciences and Human Services Library Historical Collections’ strives to provide broad access to our diverse collections both in person and digitally. Materials in our collections appear as they originally were published or created and may contain offensive or inappropriate language or images and may be offensive to users. The University of Maryland, Baltimore does not endorse the views expressed in these materials. Materials should be viewed in the context in which they were created.}

The inauguration of the 46^th president of the United States occurs Wednesday, January 20, 2021. The United States and World will watch as Joseph R. Biden Jr. is sworn in as President along with Vice President Kamala Harris. In celebration of the United States Inaugural events, the Historical Collections Department of the Health Sciences and Human Services Library, is taking a moment to look back on our own Presidential history.

In 2020, the University of Maryland, Baltimore welcomed its own new President, Dr. Bruce Jarrell after nearly nine months as interim president following the departure of President, Dr. Jay Perman for the Chancellor’s Office in the University of Maryland System’s. Dr. Jarrell began his tenure as UMB President in a letter to the UMB community on his first official day, September 11, 2020.

In this letter, Dr. Jarrell mentions becoming the seventh president of UMB. While there have only been seven presidents in our more recent history; there have actually been 25 leaders of the University of Maryland, Baltimore. These leaders have had various roles and titles including, President, Provost, and Chancellor from its founding as the College of Medicine of Maryland in 1807 to today’s University. The following is a brief history of UMB and its leaders.

Early Campus History, Presidents and Provosts (1807-1920):

George Brown, President College of Medicine of Maryland (1807-1812)
Charles A. Warfield, President Board of Regents (1812-1813)
Robert Smith, Provost (1813-1815)
James Kemp, Provost (1815-1826)
Roger B. Taney, Provost (1826-1839)
Ashton Alexander, Provost (1837-1850)
John Pendleton Kennedy, Provost (1850 -1870)
Severn Teackle Wallis, Provost (1870-1890)
Bernard Carter, Provost (1890-1912)
Henry Stockbridge, Acting Provost (1912)
Thomas Fell, Provost (1912-1920)

The University of Maryland, Baltimore traces its founding back to 1807 when the state of Maryland approved a law (Session 216, Chapter 53) opening the College of Medicine of Maryland. Soon after its founding Dr. George Brown was elected president of the College of Medicine of Maryland.

The College of Medicine of Maryland operated under that title until 1812, when a new law (Session 224, Chapter 159) created the University of Maryland. The new University was given the authority to organize a Faculty of medicine, arts and sciences, law, and divinity under the leadership of a Board of Regents. The Board of Regents approved a Provost as head of the campus which grew include five departments or schools (Medicine, Dentistry, Pharmacy, Law, and Liberal Arts, which was located at St. John’s College in Annapolis).

One University of Maryland, One President (1920-1965):

Albert F. Woods (1920-1926)
Raymond A. Pearson (1926 -1935)
Harry C. Byrd (1935-1954)
Wilson H. Elkins (1954-1965)

Following creation of the State System Elkins was named Chancellor and lead until 1978

In 1920, the State of Maryland once again passed a law (Session 310, Chapter 480) joining together the University of Maryland and the Maryland State Agricultural College (today’s University of Maryland, College Park). Under this law, the two schools operated as one state school with one president under the University of Maryland name. The college park campus was primarily used for undergraduate education, while the Baltimore campus operated the professional schools of Medicine, Dentistry, Pharmacy, Nursing, Law, and by 1961 Social Work.

Creation of the University of Maryland State System, UMB Chancellors & Presidents (1965-Present):

Albin O. Kuhn, Chancellor UMB & UMBC (1965-1971)
Albin O. Kuhn, Full time Chancellor at UMB (1971-1980)
Albert Farmer, Chancellor (1981-1984)
John M. Dennis, Interim Chancellor (1984)
Edward N. Brandt Jr., President (1984-1988)
William J. Kinnard Jr., Acting President (1989-1990)
Errol L. Reese, President (1990-1993)
John W. Ryan, Interim President (1993-1994)
David Ramsay, President (1994-2010)
Jay Perman, President (2010-2020)
Bruce Jarrell, President (2020 -Present)

In 1963, a state law (Session 358, Chapter 537) established the University of Maryland, Baltimore County (UMBC) branch, which opened in 1966. One chancellor, Dr. Albin O. Kuhn, oversaw both Baltimore campuses beginning in 1965. In 1970 the University of Maryland State System of five campuses was formed. The campuses included: University of Maryland at Baltimore; University of Maryland Baltimore County; University of Maryland, College Park; University of Maryland Eastern Shore; and University of Maryland University College. The five campuses, with the exception of Baltimore and Baltimore County, had their own chancellor. However, in 1971, the two Baltimore campuses (UMB and UMBC) hired their own chancellors, and Dr. Albin O. Kuhn became the first chancellor of UMB.

In 1988, the head of the individual campuses’ title was changed to president; thus, UMB’s first modern day president was Edward N. Brandt Jr. The term Chancellor was used for the individual overseeing the entire state system. Since that time, the University of Maryland, Baltimore, has had seven full-time and interim presidents at the helm. The presidents have faced a variety of challenges but have expanded the physical space of the campus as well as the national and international prestige.

References and further reading:

Cordell, Eugene. (1903) The medical annals of Maryland, 1799-1899; prepared for the centennial of the Medical and Chirurgical Faculty.
Cordell, Eugene. (1907) University of Maryland, 1807-1907, its history, influence, equipment and characteristics, with biographical sketches and portraits of its founders, benefactors, regents, faculty and alumni.
University of Maryland, Baltimore Yearbooks.
University of Maryland, Baltimore Newsletters, Magazines, and Reports.
University of Maryland, School of Medicine Newsletters, Magazines, and Bulletins.
University of Maryland, Office of the President Digital Archives.

Posted in Historical Collections | Tagged Presidents, UMB History, UMB Presidents | Comments Off

DABS (Data and Bioinformation Stuff) Volume 1 Issue 2: Spotlight on DMPTool

Posted on January 15, 2021 by Amy Yarnell

At least once a month, we will use this space to talk about a useful tool or resource. This month’s spotlight is on DMPTool, a free online platform offering templates and guidance from major funders on writing data management plans (DMPs). UMB is now a participating institution in DMPTool. A major benefit of this affiliation for researchers is that it gives you the ability to request personalized feedback on your plans from the CDABS team from within the platform. In the near future, additional features will be available, including single sign-on with your UMB credentials, and templates and guidance geared specifically toward the UMB community.

A data management plan is a key component of all research projects. You may be required to include one as part of a grant, but even when not required, having a DMP is a great way to help everyone in your lab have the same understanding and expectations surrounding your project data. A good DMP will explain what data is being collected or generated, how it is being described, collected, and secured, and how and when the data will be accessed and preserved after the project’s completion.

To get started writing data management plans with DMPTool, go to https://dmptool.org/, select Option 1 under Sign In, and type “Baltimore” in the search bar, then select “University of Maryland, Baltimore (umaryland.edu)“. If you already have an account with DMPTool, you can edit your account profile to list UMB as your organization.

To learn more about writing data management plans with DMPTool, sign up for our upcoming online workshop:
Writing Data Management Plans with DMPTool
Thursday, January 21 @ 12:00PM
Workshop description: Researchers, do you have an upcoming grant application that requires you to write a data management or data sharing plan? Are you striving to maintain well-organized research projects? In this workshop, we will cover the components of good data management plans with a particular eye toward NIH data sharing requirements. Participants will also be introduced to DMPTool, an online platform which provides plan templates and guidance from most major funders. Additionally, we will be providing participants with time during the workshop to work on plans for their own projects and ask questions and receive guidance from the instructors. sign up

Questions?
Contact: Amy Yarnell, Data Services Librarian and Jean-Paul Courneya, Bioinformationist — at data@hshsl.umaryland.edu.

Posted in Data/Bioinformation, Research Data Management, Workshops | Tagged bioinformatics, bioinformation, CDABS, DABS, data, data management | Comments Off

HSHSL Closed 1/18 in Honor of MLK Day

Posted on January 14, 2021 by ebrown