Health Sciences: Open Data Week

This guide provides resources, services, and tools of interest to VT researchers investigating health topics and initiatives, including across disciplines and VT Beyond Boundaries' areas: 'Integrated Health and Wellness,' and 'The Adaptive Brain.'

Banner image: Open Data Week - featuring ContentMine

Workshop Materials, Contacts, and Event Recordings from VT Open Data Week, April 10-13, 2017

Event Twitter hashtag: #VTODW

Contentmine Workshop Materials: http://bit.ly/cm-vtodw

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Contacts

  • Event Overall - Contact: Ginny Pannabecker, vpannabe@vt.edu; Anne Brown, ambrown7@vt.edu; Philip Young, pyoung1@vt.edu
  • Get in touch with event speakers about Fellowships, Projects, or to Collaborate
  • Materials: are linked below when available
  • icon representing video cameraRecordings: 3 programs were recorded (Open Research/Open Data Forum; An Intro to ContentMine session; and the Text and Data Mining Forum). Links to recordings are posted below and on each program page on this guide.
  • Looking for assistance, or to collaborate on TDM data source access or tools? Contact Anne Brown, Data and Informatics Consultant, Sciences: ambrown7@vt.edu, Ginny Pannabecker, Health Sciences Research Support Coordinator, vpannabe@vt.edu, or VT Libraries Data Services at dataservices@vt.edu - we'll work with you, or connect you with others.

 

Open Research/Open Data Forum: Transparency, Sharing, and Reproducibility in Scholarship
Held: Monday, April 10th, 6:30-8:00pm, in Torgersen Hall 1100
Description: Discussion on challenges and opportunities related to sharing and using open data in research, including meeting funder and journal guidelines.

icon representing video cameraRecording: http://vtechworks.lib.vt.edu/handle/10919/77859

Panelists:

Daniel Chen (Ph.D. candidate in Genetics, Bioinformatics, and Computational Biology)

Karen DePauw (Vice President and Dean for Graduate Education)

Sally Morton (Dean, College of Science)

Jon Petters (Data Management Consultant, University Libraries)

David Radcliffe (English)

Laura Sands (Center for Gerontology)

Peter Potter (Panel moderator, Director, Digital Publishing Strategies, University Libraries)

Philip Young (Panel organizer, Scholarly Communication Librarian, University Libraries)


Introduction to ContentMine Tools for Mining Scholarly & Research Literature 
Held: Tuesday, 4/11, 9:30-10:45am, Newman Multipurpose Room
Description: ContentMine instructors, Thomas Arrow and Stefan Kasberger presented an overview of text and data mining, and an introduction to ContentMine open source tools for mining scholarly and research literature.

Presenters and Materials: 
Thomas Arrow and Stefan Kasberger: contact@contentmine.org
Presentation and workshop materials

 

Data visualization with Tableau
Held: Tuesday, 4/11, 10:30 am -12:00 pm, Torgersen Hall 1100
Description: With the Tableau data visualization software, you or your students can easily turn research data into detailed, interactive visualizations that tell the story that numbers alone struggle to express. The software can link directly to your data sources so you always have the most up-to-date data on hand without exporting manually, and easily generate hundreds of types of visualizations that include interactive elements.

Presenter: 
Jonathan Bradley, bradley1@vt.edu

 

Introduction to ContentMine Tools for Mining Scholarly & Research Literature
Held: Wednesday, 4/12, 9:00-9:55am, Newman Multipurpose Room
Description: ContentMine instructors, Thomas Arrow and Stefan Kasberger presented an overview of text and data mining, and an introduction to ContentMine open source tools for mining scholarly and research literature

icon representing video cameraRecording: https://vtechworks.lib.vt.edu/handle/10919/77525

Presenters and Materials: 
Thomas Arrow and Stefan Kasberger: contact@contentmine.org
Presentation and workshop materials

 

Making Visible the Invisible: Data Visualization and Poster Design
Held: Wednesday, 4/12, 9:30-11:00am, Newman 207A
Visually representing data helps users and readers engage with the content, understand key findings, and retain information. Exploring, creating, and presenting these visual representations is becoming critical for teaching, academic research, and professional engagement. In this session we will explore the basics of data visualization and poster design, and look at a few tools to create different kinds of visualizations. We will also discuss the academic and professional value in visualizing data.

Presenters and Materials: 
Chreston Miller, chmille3@vt.edu | Michael Stamper, mstamper@vt.edu
 

Introduction to ContentMine Tools for Life Sciences Research 
Held: Wednesday, 4/12, 11:15-12:05pm, Newman MultiPurpose Room
Participants joined students in a computational biochemistry informatics class session for an introduction to ContentMine open source tools for text and data mining to explore research literature sources, with a focus on tools related to mining and exploring content for Life Sciences research (phylogeny and and visualization).

Presenters and Materials: 
Thomas Arrow and Stefan Kasberger: contact@contentmine.org
Presentation and workshop materials


Text and Data Mining Forum 
Held: Wednesday, 4/12, 2:30-3:45pm, Newman MultiPurpose Room
A discussion with researchers and ContentMine guests about opportunities and challenges related to text and data mining, with a focus on information access.

icon representing video cameraRecording: https://vtechworks.lib.vt.edu/handle/10919/77526

Panelists:

Tom Arrow (ContentMine)

Tom Ewing (College of Liberal Arts and Human Sciences, Virginia Tech)

Weiguo (Patrick) Fan (Pamplin College of Business, Virginia Tech)

Ed Fox (Computer Science, Virginia Tech)

Leanna House (Statistics, Virginia Tech)

Bert Huang (Computer Science, Virginia Tech)

Virginia Pannabecker (Panel moderator, Health Sciences Research Support Coordinator, University Libraries)

Julie Speer (Welcome message, Associate Dean for Research and Informatics, University Libraries)

 

Introduction to ContentMine Tools for Mining Scholarly & Research Literature: 
Held Wednesday, 4/12, 4:00-5:15pm, Newman ScaleUp Classroom 
Participants joined ContentMine instructors and an undergraduate class in computational methods for an overview of text and data mining, and an introduction to ContentMine open source tools for mining scholarly and research literature.

Presenters and Materials: 
Thomas Arrow and Stefan Kasberger: contact@contentmine.org
Presentation and workshop materials

 

ContentMine Tools to Explore Scholarly & Research Literature - Full Day, Hands-On Workshop
Held: Thursday, 4/13, 9:00am - 4:00pm, Newman 207A 
Description: During this workshop objectives for participants were to: (1) ensure the software is functioning on their laptop computer, (2) participate in individual and group hands-on exercises to become more familiar with ContentMine tools, and (3) have the opportunity to experiment with using ContentMine tools with ContentMine instructors’ support - to mine scholarly literature and explore results specific to their own research project goals. Prior to the workshop, attendees will receive instructions to download software and make any other preparations to get the most of of the workshop.

Presenters and Materials: 
Thomas Arrow and Stefan Kasberger: contact@contentmine.org
Presentation and workshop materials