NCBI Virtual Workshop Series: Getting Started with NCBI Data in Python

DABS: DATA AND BIOINFORMATION STUFF

NCBI Virtual Workshop Series: Getting Started with NCBI Data in Python

The National Center for Biotechnology Information (NCBI) is pleased to announce an upcoming virtual workshop that is now accepting applications. The NCBI Education Team invites you to apply and share this opportunity with any colleagues who may be interested. The NCBI Virtual Workshops series was developed last fall to expand our reach to individuals who use NCBI resources for biological/biomedical research, science education, and clinical application efforts. Please review the workshop description to understand the intended audience. Each workshop will accept a limited number of participants to facilitate the best possible educational experience.

Title: Getting Started with NCBI Data in Python

Date and time: Tuesday, April 19, 2022, 1:00pm – 4:00pm ET

Description: Learn how to tackle bigger biomolecular datasets more reliably with the power of Python programming. This workshop is designed for biologists without programming experience. Our examples will use genomic, transcript, and protein sequence data, but the programming skills will be broadly relevant for all biologists.

In this workshop you will learn how to:

  • Use Python programming to download, analyze, and visualize data.
  • Use Jupyter to create data analysis ‘lab notebooks’ that make it easy to reproduce & share your work.
  • Find data that is relevant to your project using the new NCBI Datasets resource. Explore metadata to learn about which datasets are available.
  • Download sequence data with NCBI Datasets and manipulate it with the BioPython package.

Apply here: https://ncbiinsights.ncbi.nlm.nih.gov/event/getting-started-with-ncbi-data-in-python-04-22/

Application close date: March 29, 2022

Please note, this workshop was designed for people with a good understanding of molecular biology, but who have limited or no programming experience.

Due to curricular and technical limits, the number of spots have been capped to provide the best workshop experience. If you register to apply, you will be notified of your application status 2 weeks before the scheduled event.

They recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

More information can be found on the new Outreach Events page of the NCBI Insights Blog. See also the FAQ page and if you still have questions about the NCBI Outreach Events program or this specific workshop, email NCBI Education Team at workshops@ncbi.nlm.nih.gov.

Questions? Contact: Jean-Paul Courneya, bioinformationist, and Amy Yarnell, data services librarian at data@hshsl.umaryland.edu.


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

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Registration Open for ICPSR Summer Program in Quantitative Methods

DABS: DATA AND BIOINFORMATION STUFF

Registration Open for ICPSR Summer Program in Quantitative Methods

ICPSR Summer Program logo

Improve your statistical analysis skills with ICPSR’S Summer Program!

ICPSR (Inter-university Consortium for Political and Social Research), is home to the world’s largest collection of digital social science data. Register now for ICPSR’s long-running and well-respected Summer Program in Quantitative Methods. This program offers a mix of intensive four-week sessions, shorter workshops, and lectures series throughout the summer This year’s program is hybrid with opportunities for virtual attendance or on-location attendance in Ann Arbor, MI. 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. 

Example workshop topics include:

  • Race, Ethnicity, and Quantitative Methodology
  • Regression Analysis
  • Multivariate Statistical Methods: Advanced Topics
  • Machine Learning: Applications in Social Science Research
  • Data Science and Text Analysis
  • Panel Data and Longitudinal Analysis
  • Bayesian Modeling

Important dates:

  • Scholarship Deadline: March 28, 2022
  • Early Registration Discount Deadline: April 30, 2022
  • Registration closes for Session 1: June 12, 2022
  • Registration closes for Session 2: July 10, 2022
  • Session 1: June 20 – July 15, 2022
  • Session 2: July 18 – August 12, 2022
  • Short Workshops: Multiple dates from May through August 2022.

Questions? Contact: Amy Yarnell, data services librarian, and Jean-Paul Courneya, bioinformationist, at data@hshsl.umaryland.edu.


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

Sign up to get DABS delivered to your email or RSS feed.

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First Women of the University of Maryland, Baltimore: Exhibit Returns

Image has seven women wearing 20th century nurses dresses and caps seated. Above the image is the words "First Women of the University of Maryland, Baltimore" Behind the text is two orange circles.In March 2020, the HSHSL was celebrating Women’s History Month with a gallery exhibit featuring the accomplishments of the First Women of the University of Maryland, Baltimore. Unfortunately, a week after the exhibit opened, the COVID-19 pandemic arrived in Maryland and the university transitioned to mandatory telework. During the shutdown, the exhibit sat for months, unseen in a deserted gallery. Now, two years later, the HSHSL is showing a new, expanded version of the First Women of the University of Maryland, Baltimore in the HSHSL Weise Gallery.

The exhibit honors women who paved the way for progress and change at UMB. When the university was founded in 1807 as the College of Medicine of Maryland, women were not permitted to enroll in coursework. Nor were women present on the faculty or staff until much later in the university’s history. When women were finally admitted – first as students, and later as faculty members to the UMB schools – they faced intense hardship, criticism, and discrimination. They endured, nevertheless, and their remarkable contributions and achievements have paved the way for future UMB women students, faculty, and leaders.

This exhibit highlights nearly 150 years of women’s history at UMB. Its panels feature the stories of Dr. Emilie Foeking, Louisa Parsons, Dr. Lady Mary Johnson, Ruth Lee Briscoe, Dr. B. Olive Cole, Dr. Teresa Ora Snaith, Esther E. McCready, Dr. Ruth H. Young, Dr. Barbara C. Hansen, Alice Cary, and Dr. Natalie D. Eddington. In addition, two supporting exhibit cases feature works by UMB women authors from the HSHSL collection. 

The exhibit will remain on display in the Weise Gallery through April 2022.

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Reference Help at the HSHSL

Have a question? Need guidance on where to find a journal article or which citation manager to use? The HSHSL’s Information Services desk is here to provide you with fast and friendly reference help. Come by in person, email: hshsl@umaryland.edu, call: 410-706-7995, or chat!

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Roof Construction: Noise Alert

If you hear noises throughout the HSHSL it is because essential repairs are being made to the roof.  The noise will be most noticeable on the 5th floor, so we invite you to consider studying and working from the lower floors.

Construction will generally begin at 7:00 am and end at 5:00 pm, Monday – Friday.  Weather delays may cause construction to continue into the weekend days.  It is hoped that the project will be complete by the end of April.

We apologize for the inconvenience.  Please come by the 1st floor Information Services Desk for free ear plugs.

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How Do I Access HSHSL Resources From Off-Campus?

To login to library resources from off-campus click on the blue “Off-Campus Access” button on the upper right-hand side of the library’s website. You will be prompted to enter your UMID and password. If you don’t have a UMID and password, go to: https://directory.umaryland.edu to create one. Choose “New User, Set Up Account.”

2. What if I’m having problems signing in?

If you are unable to sign up for a UMID, please contact the IT Help Desk at 410-706-4357 or help@umaryland.edu.  For other questions, contact the HSHSL Information Services Desk (410-706-7995) or email Everly Brown at ebrown@hshsl.umaryland.edu

3. Who has access?

Generaly, only UMB faculty/staff who are in the UMB payroll system and currently enrolled students (except those in the School of Law*), are allowed off-campus access to e-resources. E-resources include: e-journals, e-books, databases and e-reserves.

*UM faculty, staff and students in the School of Law have access to e-resources through the Thurgood Marshall Law Library.

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Data and Bioinformation Stuff (DABS): 10 Simple Rules for Improving Research Data Discovery

To wrap up another Love Data Week, we are going to talk about a topic that goes hand-in-hand with data sharing, but may often be overlooked – data discoverability. If you’re familiar with the FAIR data principles, you may remember that F stands for Findable, and that’s what we’re talking about here. It’s hard to use data if you can’t find it, after all!

One of our favorite things here at CDABS is getting to collaborate with our data colleagues at other universities, especially members of the Data Discovery Collaboration (DDC).  Recently, members of the DDC (including yours truly), produced this handy guide on making your research data more discoverable.

  1. Decide what level of access you can provide – Data discovery and data access are related but distinct concepts. Data discovery is the ability to find if and where datasets exist, whereas data access refers to the processes for viewing and downloading data. It’s helpful to decide the level of access first, so you can be sure to describe your data accurately, and use appropriate tools to make data discoverable.  For example, even if you cannot openly share your data, you can still share metadata about your data through the UMB Data Catalog.
  2. Comply with ethical standards – Ethics come into play in decisions and discussions throughout the life span of your research project, and will certainly be a part of decisions about data access and storage. Be especially careful about any data you collect regarding vulnerable populations, and keep in mind that advances in data and technology may outpace changes in regulations.
  3. Deposit your data somewhere trusted – In some fields and for some data types there is a clear place to deposit data, but for others there are more options. Look for recommendations from journals, funding agencies, professional associations, and your friendly neighborhood data librarian to find discipline specific or appropriate generalist repositories. Your data may be more findable if stored in the same place as other data from your field.
  4. Use persistent identifiers – Persistent identifiers or PIDs include things like ORCID iDs for people and DOIs for datasets, journal articles, and more. These identifiers provide a stable, unique link to data and the scholars who created it. PIDs are machine readable and thus an important building block of research data computing infrastructure.
  5. Create thoughtful and rich metadata – metadata is information about your data, and includes things like title, creator, subject, description, data types. Good metadata is also structured in a way that makes it both machine and human readable. When you search for something in a repository or catalog, it is the metadata that helps you find it. The UMB Data Catalog uses a robust metadata schema, so listing your data there is a great way to make sure your data is richly and accurately described.
  6. Choose your keywords carefully – not every repository or catalog will allow you to provide keywords, but this is another way you can add descriptive information to your data and potentially link it with other similar datasets that are described with the same terms (like how hashtags help you find tweets).
  7. Create links to related resources – think of your data as part of a larger research ecosystem that includes authors, publications, grants, institutions, software, code, etc. Link all these things together whenever you can. Creating multiple pathways to your data makes it more findable.
  8. Make supporting information discoverable too – It is often possible to submit your data along with an article to a journal. But these systems are not really designed for finding or storing data. A better bet is to submit data to a trusted repository and link to that data in your article.
  9. Include an accurate Data Availability Statement with your publications – a great way to make your data findable is to tell people exactly where to find it. You may have the opportunity in a publication to explain where one can find the associated data. Take the opportunity to provide a PID to your data, which is hopefully located in a trusted repository (see? we’re pulling it all together now). Also, pro tip – PubMed Central has special filters available that facilitate finding articles with data availability statements
  10. Talk to your institutional librarian – we called them “simple” rules, but we know they can actually be quite daunting! But have no fear, we at CDABS are here to help! Have questions about making your data more discoverable? Contact us for a research data consultation!

For more information, be sure to check out the full article!

This blog post has been adapted under a Creative Commons Attribution License, from Ten simple rules for improving research data discovery. PLoS Comput Biol 18(2): e1009768. https://doi.org/10.1371/journal.pcbi.1009768 by Contaxis N, Clark J, Dellureficio A, Gonzales S, Mannheimer S, Oxley PR, Ratajeski MA, Surkis A, Yarnell AM, Yee M, and Holmes K.   

Questions?

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

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.

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

 

 

 

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Get Your Poster Printed at the HSHSL

Poster Printing Service


The HSHSL offers poster printing to all UMB faculty, students, and staff and University of Maryland Medical Center staff. Posters are printed in support of academic, professional, and research purposes. 

Posters are printed up to a maximum of 42″ x 72″.

You have your choice of material:

  • Our paper option is Glossy Photo Paper and costs $55.
    Great for class assignments and single-use displays.
  • Our fabric option is Matte Lightweight Poly Canvas and costs $55.
    Perfect for traveling exhibits and multiple-use displays.

Poster printing may take up to two business days, please plan accordingly.

All posters must be submitted as a PDF file. Please pay close attention to the information on sizing and formatting your poster.

Posters can be picked up at the Information Services Desk.

For questions, please e-mail poster@hshsl.umaryland.edu or call 410-706-7996.



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Love Data Week 2022 Starts Monday, Feb 14!

Love Data Week (Feb. 14 to 18) is an international celebration of all things data! Each year, the Center for Data and Bioinformation Services (CDABS) at the Health Sciences and Human Services Library (HSHSL) looks forward to engaging our community on issues like data management, sharing, wrangling, and visualization, as well as open and reproducible science.

Want to participate in Love Data Week? Here’s how:

  • Join CDABS on Tuesday, Feb. 15, at noon for a virtual, interactive, introductory workshop on the Open Science Framework (OSF), a research project management and collaboration tool from the Center for Open Science. The University of Maryland, Baltimore recently became an OSF member institution. Learn more about what that means for you, and register here.
  • Adopt a Dataset or attend a webinar with ICPSR, the official Love Data Week organizers and an excellent place to find data! Visit their site for more information.
  • Join our friends at the National Library of Medicine throughout the week for their series of workshops on topics including Census Tools to Better Understand Your Community, the National Institutes of Health (NIH) Data Sharing and Management Plan, DMPTool Basics, and Doing No Harm with Data Viz. (Note: You must sign up for a free NLM account to register).
  • Attend the Community Building Convention for NIH’s Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity (AIM-AHEAD). The goal of AIM-AHEAD is to enhance diversity in the field of artificial intelligence and machine learning (AI/ML), with emphasis on reducing health disparities and promoting health equity. Listening sessions will be held for different communities throughout the week. Find your session and register.

Finally, as always, you can join the conversation on social media #LoveData22 and #UMBLovesData.

Questions? Contact Amy Yarnell, data services librarian, at data@hshsl.umaryland.edu.

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.

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

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Woven Stories: Faith and music inspire Anna-Marie

Woven Stories: Out of Many we are One imageThe HSHSL is currently collecting submissions for Woven Stories, a project aiming to highlight the diversity of UMB’s campus by sharing photographs and supporting stories of items of personal cultural significance.  The following is Anna-Marie Epp’s submission.  Anna-Marie is a Program Specialist in the Health Sciences and Human Services Library. Read on for inspiration and please consider submitting your own story!

Collage of two hymnal covers

I grew up in a Baptist church in a predominantly black community in Virginia where generations of my family prayed and worshiped, lived and worked. I Imagine, if there was one thing my family did since my great grandparents joined First Baptist Church in 1904, it was sing! It may be the reason music has always been what drew us closer in love and in faith. It’s why we’ve always known far more hymns than scriptures. It’s in our blood! 

Photograph of the cover of Gospel Pearls HymnalThese hymnals belonged to my Grandmother, Cleo Marie Wynn Bolling, a high school music teacher, church pianist, and choir director. The oldest of these is the Gospel Pearls Hymnal purchased by our church in the 1930’s and was likely her first hymnal. It holds old favorites like Amazing Grace, a hymn which my brother and I can still sing all 5 stanzas and not miss one word. 

Photograph of Peace Like a River Sheet musicMusic was the love of my grandmother’s life and among her favorite things to do was teach the stanzas of the hymns to our Junior Chorus. One of our favorites, Peace Like a River, is a hymn I still hum quietly to myself when I need to feel restored. My brother, cousins and I sang in that choir even after my grandmother’s passing in 1996 – after which my mother, Anna, became director.

Although I’ve changed and I no longer attend church often, I am in awe of each lesson, each value, each sweet line that I carry with me each day. Every time I think of a hymn, I sing it quietly with the joy of my young self, with the love of my grandmother and with the gratefulness to the faith (and the church) that raised me and made me who I am. 

 

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