Meet the Makers: Baltimore Makers Unite for COVID-19

“Makers Unite: Baltimore’s Grassroots Response to the Pandemic”

April 6, 2021
Noon-1 p.m. EST
Online Zoom event – RSVP for Zoom link

The Health Sciences and Human Services Library and The Grid are proud to host Will Holman, Open Works‘ Executive Director, and Jay Nwachu, Innovation Works‘ President and CEO, for our next Meet the Makers guest speaker event.

The two leaders will reflect on Makers Unite, Baltimore’s crowdsourced PPE drive at the start of the pandemic, and discuss a new model for mutual aid that uses makerspaces, digital fabrication, and online organizing to address critical social issues.

In late March 2020, hundreds of people around Baltimore with 3D printers at home began making parts for face shields and other personal protective equipment (PPE). Known as Makers Unite, the effort was organized by Open Works, a community maker and studio space that pivoted quickly to PPE manufacturing.

Together with Innovation Works, a social innovation hub and non-profit, a website was set up to facilitate PPE distribution and maker contributions (totaling over 28,000 PPE units). Health care workers at the University of Maryland, Baltimore are among those who received such equipment.

Both Open Works and Innovation Works continue to adapt their programming and services to the community’s needs, including support for students struggling with remote learning, and more.

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DABS (Data and Bioinformation Stuff) Volume 1 Issue 8: Cloud Computing

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.

We are wrapping up another week (Feb 22 -26) of learning and growing at CDABS. Our adventures had us working on HPC (High Performance Computing) at IU (Indiana University) as part of their HPC Onboarding for Biologist workshop. The National Center for Genome Analysis Support (NCGAS) provides this HPC workshop to help new users learn about HPC resources available to them, other course offerings, and NCGAS services. This workshop and a video linked below had me thinking quite a bit about research computing particularly computing on the cloud. Folks let me say that computing on the cloud is becoming more pervasive in research computing. Knowing about this topic is worth your time since as researchers in the modern age we will be faced with having to use the cloud to do our computing more and more. Datasets are moving to the cloud. Software has already moved to the cloud. And some day our workstations may only be terminals to connect to our actual computers which exist on the cloud. 
 
Check out these links for resources and learning about computing for genomics on the cloud.
  1. This article, freely available in PMC (Pubmed Central), by Ben Langmead and Abhinav Nellore describes how cloud computing is used in genomics for research and large-scale collaborations, and argues that its elasticity, reproducibility and privacy features make it ideally suited for the large-scale reanalysis of publicly available archived data, including privacy-protected data. (10 minute read) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452449/ 
  2. Keynote from European Bioconductor Meeting 2020: Sehyun Oh – Bioinformatics On Cloud: How to leverage cloud-based resources for your bioinformatics works. (40 minute watch) https://youtu.be/bFvT4_fqpwE
  3. The Seven Bridges Platform is a cloud-based environment for analyzing genomics data. Use the Platform to securely store, analyze, and share data amongst team members working both locally and globally. The Platform co-locates analysis workflows alongside genomic datasets to optimize processing. Read and learn more at the SevenBridges knowledge center. (10 minute overview) https://docs.sevenbridges.com/
  4. Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. The vision of Terra is to enable the next generation of collaborative biomedical research. There are several projects that exist independently on the platform – AnVIL, BioData Catalyst, and FireCloud, for example. Each project on Terra serves a unique research purpose, while still offering the benefits of the Terra platform to every user. (10 minute read) https://terra.bio/
  5. Galaxy is an open source, web-based platform for data intensive biomedical research. The main Galaxy instance is an installation of the Galaxy software combined with many common tools and data; this site has been available since 2007 for anyone to analyze their data free of charge. The site provides substantial CPU and disk space, making it possible to analyze large datasets. You can even install your own Galaxy and choose from thousands of tools from the Tool Shed. (10 minute overview) https://galaxyproject.org/tutorials/g101/ (Galaxy Main) https://usegalaxy.org/

Questions?  

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

To read more of our content and stay informed please visit our communications page and fill out the form to subscribe. Subscribe here: https://www2.hshsl.umaryland.edu/cdabs/communications

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A Brief History of UMB African American Student Organizations

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.

As Black History Month 2021 draws to a close, the Historical Collections in the HSHSL could not let the month past without looking back on UMB’s African American history. The following highlights a few of the many student organizations throughout UMB’s history in an attempt to acknowledge the work of many to make our campus more inclusive and diverse.

In 1954 the Board of Regents of the University of Maryland (which then included College Park) voted to allow African American Students admittance to both Undergraduate and Graduate schools.  It was the culmination of years of segregation as well as legal battles between the University and African American students who wished to attend the school. The 1954 decision allowed African Americans to enter the University but the early students still faced the well-ingrained roots of segregation and discrimination policies.

As more and more African American students entered the University of Maryland, Baltimore the students founded organizations to support one another academically, encourage more diversity in the professional schools, and reduce the feeling of isolation felt by early minority students.  Additionally, these organizations provided a way to educate the students’ white colleagues and faculty on the needs of minority students, patients, and clients. Each of the professional schools at UMB had an African American Student Organizations; the following is a brief history of some of these groups.

Collage of two images, top image is in color, a group of students from 2020, the bottom image is in black and white, a group of students from 1975Student National Dental Association, School of Dentistry

On July 28, 1869, at a meeting in Atlanta, Georgia, the Southern Dental Association (precursor to the National Dental Association) was formed by minority dentists, who felt their needs were not being addressed by other professional dental associations. In 1972, UMB dental students including first African American SOD graduate, Elton Preston Maddox Jr. ‘72, established a branch of the Student National Dental Association (SNDA). The goal, according to the 1988 Mirror Yearbook, was “to promote and encourage minority enrollment in all dental schools, improve dental health care delivery to disadvantaged people, promote a viable academic and social environment conducive to the mental health and well-being of minority students.” Since its founding, the UMB SNDA has had a tremendous effect on campus, in Baltimore, and nationally.

In the past seven years, the organization has taken home first or second place honors at the National SNDA chapter of the year competition, which scores the competitors based on the success of each chapter in fundraising, performing community service, and launching new initiatives. The group is active in the community through their Generation NeXT Program, which mentors local high school students in training to become dental assistants, as well as visits to local elementary schools, where they teach young children about oral health. In 2020 the group received the Colgate Bright Smiles, Bright Futures Award and in 2021 were the recipient of a Rev. Dr. Martin Luther King Diversity Recognition Award from UMB. (Diversity Advisory Council Website News, 2021)

Black and white newspaper clipping of a student sitting in the front of a classroom reading a book to a group of students sitting on the floor.Black Student Nurses Association, School of Nursing

The Black Student Nurses Association (BSNA) was founded in 1982. The mission of the organization as stated in the School of Nursing’s 2002 Self Study was to “encourage interaction of minority students & … to develop a common mainstay for student support and enrichment.” Through its history the BSNA supported a variety of initiatives including community service projects, hosting events such as speakers during Black History Month, and worked with the School of Nursing’s Office of Admissions to support both black applicants and UMB students. Additionally, the organization performed community service projects, as the clipping from the 1991 Voice shows and worked with community groups to encourage Baltimore youth to consider Nursing as a career.

Black American Law Student Association, School of LawBlack and white newspaper clipping of four people standing and smiling, to the left is a man presenting a check to a woman; to the right is a woman presenting an award to a man

The National Black Law Student Association (BALSA) was established in 1968 and soon after a chapter of the organization was established at UMB. BALSA was responsible for a variety of activities in the School of Law including working to recruit black students to the school, helping black graduates find good job placements, and hosting an annual award banquet every Spring. The banquet honored black lawyers whose “hard work and personal sacrifices…created the opportunities enjoyed by black law students today.” (Happenings, Vol. 10, No. 31, 1981) In 1989, the organization was awarded the Golden Rule Award from J.C. Penny; the award acknowledged outstanding volunteer service in Central Maryland and was awarded to BALSA because of their work with the Booker T. Washington Middle School. (Voice, Vol. 6, No. 19, 1989)

Today, BALSA is known simply as the Black Law Students Association. The organization continues to provide support for UMB African American law students and gives back to the community.  For the past ten years, the organization has taken first place at the Mid-Atlantic Regions Mock Trial Competition. (February 20, 2020, SOL News Website)

Color newspaper clipping of a group of people, two people are standing, three people are sittingOrganization of African-American Students in Social Work, School of Social Work

The Organization of African-American Students in Social Work (OASIS) was founded in 2000.  Other organizations, such as the School of Social Work and Community Planning’s Black Student Union, existed prior to today’s OASIS.  Unfortunately, there was not a lot about these organizations in the Archives.  Like other organizations at UMB, these SSW’s Black Student Union appears to have planned and hosted events about minority issues.

OASIS’ mission today according to their charter is, to “promote unity among African-Americans and to empower students by providing academic, professional, social, and spiritual support.” (OASIS Organization Website, Charter) The organization hosts events including lectures, movie screenings, and workshops, for the School of Social Work during Black History Month as well as throughout the year.   

Student National Medical Association, School of Medicine

Two newspaper clippings, one on left in black and white, photograph of woman looking at camera; image on right in color, group of students standing around a posterThe Student National Medical Association (SNMA) was founded in 1964 by students from Howard University and Meharry Medical Schools. The organization has been on UMB’s campus for over 50 years. Its mission, according to the organization’s website, is “educating, serving and empowering underserved communities through health education, screening, and youth enrichment programs.”

Today the organization provides programs that mentor local high school and undergraduate students through the Minority Association of Premedical Students (MAPS), volunteers at Lexington Market’s CommunityFest to provide free medical tests and services, and hosts on campus talks and events. Additionally, each year a senior medical student is acknowledged with the SNMA’s service award for demonstrating leadership to the organization and making outstanding contributions for the minority community. In 2011, SNMA won the national chapter of the year award.

Student National Pharmaceutical Association, School of Pharmacy

Color clipping with two images, bottom left is a group of people in international attire; top right is a student working with a community memberThe national organization of the Student National Pharmaceutical Association (SNPhA) was founded in 1972 at Florida A&M University by Sharon Roquemore and John J. Scrivens. UMB’s chapter was established by Alex Taylor ’76, who served as its first president, and Clarence Jeffers III ’75. Taylor and Jeffers sought to eliminate the isolation felt on campus by minority students, help these students with academics, and educate the minority groups in the community about the pharmacy profession. (Happenings, Vol. 5, No. 38, 1976)

Today the mission of UMB’s SNPhA states, “The purpose of SNPhA is to plan, organize, coordinate and execute programs geared toward the improvement for the health, educational, and social environment of the community.” (SNPhA Website) The organization continues to be active on campus and hosts academic, professional, and social events for its members and the campus community at large, including their annual International Feast/Fiesta and Diversity Day (shown in the Capsule clipping). In 2019, UMB’s chapter was awarded chapter of the year from the national organization.

Joint UMB African American Organizations and Conclusion

In 1983,  the Black Professional Student Alliance was created in an effort to “promote equitable educational opportunities and experiences for Black people at UMAB; to promote intellectual and socio-cultural activities from the Black perspective for the university community; to assist in the general improvement and enhancement of the quality of life in the Greater Baltimore minority community.” (Student Voice, Vol. 1, No. 2, 1983) This group sought to join the four (BALSA, SNMA, SNPhA, BSN) existing African American Organizations across campus into one campus wide association.  The hope was to have a larger voice with then UMB Chancellor (like today’s President); however, the chancellor refused to acknowledge any student organizations except for the University Student Government Association (USGA).  As a result of this, the BPSA disbanded sometime in 1984. (Student Voice, Vol. 1, No. 4, 1983)

In 1988, another organization, the Coalition of Minority Professional Students (COMPS), was formed by Carolyn Morris, School of Dentistry Class of 1988, and Dr. Louis J. Murdock, then associate vice chancellor for student affairs. COMPS hosted campus events on minority issues and was a sponsor of Black History Month events. (Voice, Vol. 5, No. 13, 1988)

While these organizations were formed as a way to eliminate the isolation felt by African American Students in the 1960s and 70s, the tradition of African American student associations remains strong on UMB’s campus.  A majority of the organizations featured here still remain on campus, supporting the needs of African Americans, while also providing leadership opportunity for students and educating the campus and community about diversity needs and concerns. 

References and Further Reding:

For more information on UMB’s African American History see the February 3, 2020 Post on HS/HSL Updates.

Information on these organizations as well as other campus events and history can be found in the Campus Newsletters known as Happenings and The Voice.

Photographs of the following organizations can be found in the Yearbooks (1970s-1990s):

  • Student National Pharmaceutical Association
  • Black Student Nursing Association
  • Student National Dental Association
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DABS (Data and Bioinformation Stuff) Volume 1 Issue 7: Get to know ICPSR

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, we will get to know ICPSR, the world’s largest collection of digital social science data.

Finding Data

ICPSR data covers a wide range of topics that are of interest to health sciences researchers including demography, education, child care, health care, crime, minority populations, aging, terrorism, substance abuse, mental health, public policy, sociology, political science, economics, international relations and more. If you need some data for secondary research or instruction – this is a great place to go!

All University of Maryland Baltimore staff, students, and faculty have access to the extensive ICPSR data holdings for free! Get started by browsing their themed collections, or comparing variables of interest across datasets. See how others have used ICPSR data through their extensive bibliography.

Sharing Data

ICPSR is also an excellent place for sharing your own research data. There is no cost associated with depositing data, and since ICPSR has an experienced team of curators, you can be sure your data is in good hands. Another major benefit is that ICPSR can even handle sensitive data with options like secure downloads, virtual enclaves, and embargoed publishing.

Summer Program

Registration is now open for ICPSR’s long-running and well-respected Summer Program in Quantitative Methods. This program (entirely virtual this year) offers a mix of intensive four-week sessions, shorter workshops, and lectures series throughout the summer on topics such as research design, statistics, data analysis, and social science methodology. Courses are for beginning or advanced students of quantitative methods. The program attracts university faculty and researchers, graduate students, and nonacademic research scientists. As members of ICPSR, the UMB community receives a significant discount on tuition. There are also a number of scholarships available to help defray costs even further. The application deadline for all ICPSR scholarships is Monday, March 29, 2021. Registration closes 72 hours before the start of workshops and courses.

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

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UMB and the United States Presidency: Faculty and Alumni Ties to the Country’s Highest Office

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.

In celebration of President’s Day, Historical Collections at the HSHSL is looking back on University of Maryland, Baltimore’s connections to the United States Presidency.  With a founding date of 1807, UMB is just thirty-one years shy of sharing a birthyear with the United States and with a home in Baltimore a mere thirty-eight miles from Washington, D.C. it is not surprising to find ties to the U.S. Presidency.  The following outlines three UMB faculty and alumni and their ties to the highest U.S. Office. 

Dr. Robley Dunglison, 1798-1869
School of Medicine Faculty Member, 1833-1836
School of Medicine Dean 1834-1835

 During his lifetime, Dr. Robley Dunglison served as physician to four U.S. Presidents and founding fathers: President Thomas Jefferson, President James Monroe, President Andrew Jackson, and President James Madison. 

Dr. Dunglison was born in England in January 1798.  He studied medicine at the Universities of Edinburg and Paris before receiving his MD from the University of Erlangen in Germany in 1824.  Soon after receiving his MD, he was recruited by Francis Walker Gilmer on behalf of third U.S. President Thomas Jefferson and the University of Virginia to found its School of Medicine.  While at UVA, Dr. Dunglison was Professor of Anatomy and Medicine and served as the personal physician for President Jefferson. President Jefferson was reportedly distrustful of doctors until he met Dr. Dunglison. In 1826, when President Jefferson died, Dr. Dunglison was at his bedside.

Dr. Dunglison also met and formed a friendship with fourth U.S. President James Madison while teaching at UVA.  President Madison, like President Jefferson, respected Dr. Dunglison so much he would not take any medicine without his approval.  Dunglison dedicated his Human Physiology textbook to President Madison in 1832. 

Dr. Dunglison service to U.S. Presidents James Monroe and Andrew Jackson was less intimate. Dunglison treated President Monroe, while he served as U.S. President as well as after his term (1817-1825.  President Andrew Jackson was treated once by Dr. Dunglison for “pain in his side.” 

Dr. Dunglison came to the University of Maryland in 1833 as Professor of Materia Medica and Therapeutics, Hygiene and Medical Jurisprudence and established the first medical school course on preventive medicine in America.  Dr. Dunglison also published the first American textbook on hygiene and preventative medicine.  In 1834 he was named the eleventh dean of the School of Medicine; he held the position until 1835. In 1836, Dr. Dunglison moved to Philadelphia as Professor of Institutes of Medicine at Jefferson Medical College; in 1854 he was named dean, which he held until his retirement in 1868. 

Dr. Dunglison was married in October 1824; he and his wife, Harriette Leadam, had seven children.  His son, Richard James was the editor of the first American edition of Gray’s Anatomy in 1859.  In addition to his professorships and service to U.S. Presidents, Dr. Dunglison served as an officer for the Pennsylvania Institution of the Blind (now Overbrook School for the Blind), as President of the Musical Fund Society of Philadelphia, as a member of the Franklin Institute of the State of Pennsylvania for the Promotion of Mechanic Arts, was an attending physician at the Philadelphia Hospital, and helped establish an asylum for Philadelphia’s impoverished and mentally ill.

Dr. Dunglison died of complications due to heart disease and dropsy in 1869.  He is known as the “Father of American Physiology.”

Dr. Henry Albert Parr, 1843-1932
Baltimore College of Dental Surgery, Class of 1884

Dr. Henry Albert Parr was born in Canada in 1843. He joined the Confederate Army, serving under General John Hung Morgan until he escaped capture at a raid by Union troops in Ohio and Indiana in July 1863.  Following this raid, he became a spy for the Confederates. As a spy he was involved in the takeover of the steamship Cheasapeake, where the engineer, Owen Schaffer, was killed.

Following the Civil War, Parr returned to Canada and established a dental and pharmaceutical practice. He returned to the United States in 1878 and was charged with the death of Schaffer. He was granted amnesty for this crime by a law protecting former Confederate Soldiers from their war crimes passed by President Andrew Johnson. 

After charges were dropped, Parr came to Baltimore to attend the Baltimore College of Dental Surgery (merged with the University of Maryland, School of Dentistry in 1924), graduating in 1884. Dr. Parr became a clinical instructor in Mechanical Corps with the school following graduation remaining until 1888. Dr. Parr set up a practice in New York and became a nationally known expert in crowns and bridgework, inventing and patenting the Universal Separator.

His expertise attracted the attention of former Civil War General and U.S. President Ulysses S. Grant and his wife Julia in 1884 as well as U.S. President Chester A. Arthur. In 1926, the gold and platinum plates belonging to these patients were stolen from Dr. Parr along with what is rumored to be the first removable bridge made. These items were never recovered.

Dr. Parr married his wife, Florence, in 1869 and had four children: Florence Parr Gere, Sarah, Henry A. Parr, and Marion Parr Johnson. His daughter Florence Parr Gere was a well-known pianist and composer. Dr. Parr continued his work as a dentist in New York City until his death on August 4, 1932.

Dr. James Julius Richardson, 1868-1933
School of Medicine, Class of 1889

Dr. James Julius Richardson was born in Sardis, Ohio on January 23, 1868; his family moved to Martinsville, West Virginia in his youth. He graduated from the School of Medicine in 1889 at the age of 18, after which he traveled to Europe to attend additional medical lectures and gain experience in Edinburgh, Vienna, Heidelberg and London hospitals and universities.  Upon returning to the United States, Dr. Richardson set up practice in Washington D.C. and became a leading nose and throat specialist. Due to his expertise and location, he served as personal physician and throat specialist for Presidents William McKinley, Theodore Roosevelt, William Howard Taft, and Warren G. Harding as well as presidential candidate John W. Davis and U.S. Senator Albert J. Beveridge.

As personal physician to Presidents Theodore Roosevelt and William Howard Taft as well as presidential candidate Davis, Dr. Richardson traveled on campaign and speaking tours to help care and maintain the politician’s voices. As physician to President Taft, it is reported that Dr. Richardson tried to keep the president from speaking when not on stage, a tactic that reportedly did not work. In addition to the doctor’s high-profile clients, Dr. Richardson helped to found the American College of Surgeons.

Dr. Richardson married Dorothy Flynn, the daughter of Oklahoma delegate Dennis Flynn, on April 20, 1903.  The couple did not have children. He retired from practice in 1931 because of health concerns and moved to Atlantic City, where he died in 1933 from heart disease. 

References:

  • Baltimore College of Dental Surgery Academic Catalogs: https://archive.hshsl.umaryland.edu/handle/10713/138/browse?type=dateissued.
  •  Centuries of Leadership: Deans of the University of Maryland School of Medicine. (2000). University of Maryland, School of Medicine, Baltimore. Available at: http://hdl.handle.net/10713/4797.
  • “Dr. James J. Richardson Is Dead at Atlantic City.” (29 Jun 1933). New York Herald Tribune (1926-1962); ProQuest Historical Newspapers: New York Tribune / Herald Tribune. Pg. 23
  • “Dr. Parr Dead; Dental Surgeon Here 50 Years.” (6 Aug 1932). New York Herald Tribune (1926-1962); ProQuest Historical Newspapers: New York Tribune / Herald Tribune. Pg. 11.
  •  Hinton Daily News. (3 Jul 1933). Newspapers.com: World Collection. Pg. 4.
  • “Keeping Taft Well.” (1 Oct 1909). The Florida Star. Newspapers.com: World Collection. Pg. 3.
  • Pitrof, Larry. (2006). 1807-2007: University of Maryland School of Medicine: The First Two Centuries. Medical Alumni Association of the University of Maryland, Inc.: Baltimore.

Image Credits:

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

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! 

  1. 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 
  2. 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/ 
  3. 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/  
  4. 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/ 
  5. 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 
  6. 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 — atdata@hshsl.umaryland.edu. 

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

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.

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.

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

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

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Click for a Cheerful Message!

take a cheerful message jar

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
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#ColorOurCollections at the HSHSL

Color Our Collections Heading, Image of two Men in 17th or 18th century attire coloring at a table. Image includes date of event February 1-5, 2021.

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!

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