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Center for Data and Bioinformation Services

Communications and Contributions

Follow our blog for CDABS updates, information about data and bioinformation related opportunities and events at UMB and beyond, and in-depth looks at useful tools and resources. Check out our research contributions (including supporting data and code) and presentations to see how we are enhancing the field of data and bioinformation.

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Learn R this summer with CDABS
Posted on Friday, June 3, 2022

DABS: DATA AND BIOINFORMATION STUFF

Learn R this summer with CDABS

The Center for Data and Bioinformation Services (CDABS) will be holding an R workshop every Thursday in July. All sessions run from 12:00pm to 3:00pm and meet online. Space is limited so register now!

R is an open-source programming language that is ideal for working with statistics and data. Here at CDABS, we love R for many reasons: It's free, flexible, and friendly! It's also a great tool for creating reproducible data analyses and visualizations.

In this series we'll start with the basics of R and the RStudio environment, move to more complex data wrangling and visualization tasks, and finally look at the extended R ecosystem and tools for sharing your work with interactive reports, notebooks, and applications. Sign up for the whole series, or just the sessions that interest you most, but be advised that the later sessions will require at least a little familiarity with R.

See full session descriptions below and register here:

July 7: Introduction to R and RStudio

This session will provide a solid foundation in working with R and RStudio and lay the groundwork to enable participants to explore more advanced topics in R programming. No experience with R or programming is required.

Topics covered will include:

  • Navigating the RStudio interface, installing packages, getting help
  • Naming and working with objects
  • Using functions
  • Identifying R data types and structures
  • Working with scripts

July 14: Data Wrangling with R -- Introduction to the Tidyverse

This session will introduce the concept of “tidy” data, and the versatile collection of packages known as the Tidyverse.  Participants will get hands-on experience wrangling real datasets.

Topics covered include:

  • Loading data from external files
  • Subsetting data
  • Transforming data from wide to long
  • Working with dates
  • Joining multiple datasets

Prerequisites: Session one in this series, or have previous experience with base R.

July 21: Data Visualization in R with ggplot2

Learn how to use the ggplot2, a robust Tidyverse package  used to create high quality graphics for exploring and communicating your data. We will go beyond basic graphs and learn how to customize and annotate our graphs for more effective storytelling. Participants will have the best experience if they attended session two in this series or have some previous experience with R and the Tidyverse.

Topics covered include:

  • Visualization best practices
  • Grammar of graphics - ggplot2 layers, aesthetics, and geoms
  • Choosing an effective graph type for your data
  • Customizing labels, axes, legends, and more
  • Choosing a color palette and themes

Prerequisites: Session two in this series, or have previous experience with R.

July 28: Introduction to Reproducible Research and Interactive Data Applications in R

This session will provide a high-level overview of the vast ecosystem in R for reproducible research and creating interactive data visualizations. Users will learn about version control, packages available in R for creating reports, online books, and even blogs. There will also be an introduction to creating data applications/ dynamic dashboards using the Shiny package in R. Participants will have the best experience if they have some familiarity with R syntax and the RStudio interface.

Topics covered will include:

  • Version control with Git
  • Integrating RStudio and GitHub for project data and code management and version control.
  • Reproducible research reports with code and prose with RMarkdown
  • Sharing your work on the web with Bookdown/Blogdown
  • Interact, analyze, and communicate your data with Shiny

Prerequisites: Session one in this series, or have previous experience with R.

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.


NHGRI Roundtable discussion: "Does genetic and genomic screening keep open the door to eugenics?" - May 25th
Posted on Monday, May 16, 2022

DABS: DATA AND BIOINFORMATION STUFF

Register now! NHGRI Roundtable - May 25

The National Human Genome Research Institute (NHGRI) invites you to join them on Wednesday, May 25, from 1-3 p.m. ET for a conversation on the complexities surrounding historical and present-day eugenics, scientific racism and ableism in the context of genetic and genomic screening and diagnostic technologies.  

  • What are the historical connections between the eugenics movement and genetic counseling, and what are their continuing legacies today? 
  • How are ethical and scientific experts addressing the development of contemporary genetic counseling, reproductive choice and clinically informed decision-making?
  • How can the scientific community discuss health, disease and disability in an empathetic way?  

An internationally recognized group of experts have been assembled to help answer these questions and more. NHGRI will also answer select questions from registered audience members. 

This event is free and open to the public. Sign language interpreting and CART services will be provided.

You can register here: https://nih.zoomgov.com/webinar/register/WN_ERdPQCJcTNqUJmA6WkDRTQ

The agenda for the event is available here: https://www.genome.gov/event-calendar/roundtable-discussion-does-genetic-and-genomic-screening-keep-open-the-door-to-eugenics

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

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


NIH Releases Guidance on Informed Consent Language for Data Sharing
Posted on Friday, May 13, 2022

DABS: DATA AND BIOINFORMATION STUFF

NIH Releases Guidance on Informed Consent Language for Data Sharing

Last month we talked about the new NIH Policy for Data Management and Sharing. Yesterday, the NIH released related documentation which provides suggested language to include in informed consent documents regarding the storage and sharing of research data for future use. As we like to say here at CDABS, it's best to plan for sharing your data from the very start of your research project. This is why it's so important to have a data management and sharing plan.

Some notes about the guidance:

  • The use of the sample language in this document is recommended but voluntary.
  • The language is intended to be incorporated in to the main informed consent document, not to replace or serve as a separate document, and its use does not obviate the need for IRB review.
  • The sample language is generic, and other considerations/language may be necessary in cases where data is being collected from vulnerable populations and communities, from certain cultural groups and from Tribal Nations, and when collecting genomic data.
  • The guidance and sample language generally do not distinguish between the sharing of data and of biospecimens, but participants may feel differently about the storage and sharing of each, and you might consider allowing them to consent separately to each.

The guidance recommends addressing the following topics in consent documents:

  • Time frame for data and biospecimen storage
  • Who will manage control of and access to data and biospecimens, or if data will be made available without restrictions
  • If identifiers will be retained, and the likelihood of re-identification
  • Whether sharing data and biospecimens will be optional and what happens in cases of withdrawal of consent
  • Associated risks and benefits of data and biospecimens being stored and shared
  • Potential commercial uses or applications that may result from stored and shared data and biospecimens

Other resources:

Access the full guidance document here: https://osp.od.nih.gov/2022/05/12/nih-issues-new-resources-for-implementing-the-nih-policy-for-data-management-and-sharing-2/

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

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


NIH Policy for Data Management and Sharing 2023
Posted on Monday, April 11, 2022

DABS: DATA AND BIOINFORMATION STUFF

NIH Policy for Data Management and Sharing 2023

You may have heard something by now about the new NIH Policy for Data Management and Sharing coming into effect January 2023. Concerned about what this policy means for you and your research? Have no fear; CDABS is here to help! We will be releasing resources and workshops over the next several months to help prepare the campus for this change. 

This post will cover some basic information about what this new policy entails:

What: A policy requiring 1) submission of a data management and sharing plan with all NIH grant applications for projects that generate scientific data, and 2) compliance with that plan. Note that the current NIH policy, which has been in effect since 2003, has this requirement only for projects requesting $500,000 or more in funds. So this is a much more expansive policy.

Importantly, this policy does not absolutely require you to share data. The policy recognizes that this may not always be possible given the sensitive nature of much health science research. However, according to the policy, NIH expects that in drafting Plans, researchers will maximize the appropriate sharing of scientific data, while also being mindful of ethical considerations.

When: Effective January 25, 2023

Who: Researchers seeking any funding from NIH for their research that generates scientific data.

Why: To accelerate discovery, improve rigor and reproducibility, provide access to high-value datasets, promote data reuse, and ultimately, to expedite the translation of research to knowledge. (See the NIH full statement)

Where: Visit the new NIH Data Sharing website for policy breakdown, supplemental information, and news.

For the full policy text visit: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-21-013.html

How:

  1. Familiarize yourself with some of the great resources for working with data available for UMB researchers.
    • DMPTool provides templates for writing plans and allows you to request feedback on your plan from the CDABS team. Use your UMID and password to authenticate.
    • OSF is a collaborative tool for keeping your project documents organized.
    • ICPSR and QDR are excellent repository options for sharing sensitive data.
    • The UMB Data Catalog can hold a record of your shared data, with metadata and access instructions.
  2. Schedule a consult with us to talk more in-depth about your personalized data management needs, finding an appropriate repository, and anything else data-related!
  3. Stay informed by subscribing to CDABS updates!

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

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


Citation List

  • A Model for Centralizing Data and Bioinformation Services at the Health Sciences and Human Services Library. Courneya JP, Yarnell A. Project Briefing presented at: Coalition for Networked Information (CNI) Fall Membership Meeting; 2020 Nov 10 - Dec 15; Virtual.

    (CDABS primary work)

  • Creating campuswide engagement opportunities with library professionals through promotion of Love Data Week 2020. Yarnell A, Courneya JP. Posted presented at: Medical Library Association, Mid-Atlantic Chapter (MAC/MLA) Annual Meeting; 2020 Oct 19-21; Virtual.

    (CDABS primary work)

  • Delayed microglial depletion after spinal cord injury reduces chronic inflammation and neurodegeneration in the brain and improves neurological recovery in male mice. Li Y, Ritzel RM, Khan N, Cao T, He J, Lei Z, Matyas JJ, Sabirzhanov B, Liu S, Li H, Stoica BA, Loane DJ, Faden AI, Wu J. Theranostics. 2020 Sep 14;10(25):11376-11403. doi: 10.7150/thno.49199.

      Read It

    (CDABS contribution: Functional gene enrichment analysis)

  • Full-length IL-33 regulates Smad3 phosphorylation and gene transcription in a distinctive AP2-dependent manner. Luzina IG, Fishelevich R, Hampton BS, Courneya JP, Parisella FR, Lugkey KN, Baleno FX, Choi D, Kopach P, Lockatell V, Todd NW, Atamas SP. Cell Immunol. 2020 Nov;357:104203. doi: 10.1016/j.cellimm.2020.104203. Epub 2020 Sep 2.

      Read It

    (CDABS contribution: Bioinformatics, Visualization)

  • High-performance computing service for bioinformatics and data science. Courneya JP, Mayo A. J Med Libr Assoc. 2018 Oct;106(4):494-495. doi: 10.5195/jmla.2018.512. Epub 2018 Oct 1.

      Read It

    (CDABS primary work)

  • High-performance computing service in the Health Science and Human Services Library at University of Maryland Baltimore. Mayo A and Courneya JP. [version 1; not peer reviewed]. F1000Research 2018, 7(ISCB Comm J):1089 (https://doi.org/10.7490/f1000research.1115828.1)

      Read It

    (CDABS primary work)

  • PubRunner: A light-weight framework for updating text mining results. Anekalla KR, Courneya JP, Fiorini N, Lever J, Muchow M, Busby B. F1000Res. 2017 May 2;6:612. doi: 10.12688/f1000research.11389.2.

      Read It

    (CDABS contribution: Informatics, programming)