Want to Learn or Teach a Bioinformatics or Genomics Resource? Use OpenHelix

openhelixWhat’s new in 2014?  The Taubman Health Sciences Library now has a subscription to OpenHelix, an excellent web-based resource that provides over 100 tutorial suites on the most powerful and popular bioinformatics and genomics databases and tools.  Each suite contains a video tutorial, downloadable slides and handouts, and exercises to help you learn how to effectively and efficiently use the resource.  Training materials and resources are searchable by keyword.   This resource can be used for teaching oneself how to use specific resources and/or to get ideas and materials for teaching others.

To use OpenHelix, simply go to http://www.openhelix.com/.

What are some of the resources that have tutorial suites in OpenHelix? A few examples are:

  • Allen Mouse Brain Atlas
  • Cytoscape
  • dbSNP
  • FlyBase
  • Galaxy
  • KEGG
  • UCSC Genome Browser

Please note that the above list is just a small sampling of the resources that have tutorials available in OpenHelix.

Training on RNA-Seq Data Analysis & Resources


Are you interested in learning about bioinformatics? The Bioinformatics Core is hosting an RNA-Seq overview class. Come learn about different types of bioinformatics analyses and the prominent tools used to perform these analyses.

What: Bioinformatics Core Training #1: Overview of RNA-Seq data analysis and available resources

When: Thursday, February 14 from 10:00am-12:00pm

Where: Palmer Commons, Great Lakes Central

Register here!

Tools and Technology Seminar Series

The 2013 National Center for Integrative Biomedical Informatics (NCIBI) Tools & Technology Seminar Series will begin on January 17, 2013. The presentation will be every Thursday from 12:00 -1:00 PM in 2036 Palmer Commons.

January NCIBI Tools & Technology Presentations:

Date: January 17
Speaker: Mark Reppell
Title: “Incorporating faster than exponential population growth into the coalescent using FTEC”

Date: January 24
Speaker: Ashwini Bhasi and Zach Wright
Title: “A tool to filter and prioritize NGS datasets to extract user-specific results.”

Date: January 31
Speaker: Alex Ade and Terry Weymouth
Title: “Tools for software development: Git, the GitHub archive, and Jenkins”

MCubed and THL Librarians


Taubman Health Sciences Library librarians, Mark MacEachern and Jean Song, were selected in the last round of MCubed funding.  “MCubed is a two-year seed-funding program designed to empower interdisciplinary teams of University of Michigan faculty to pursue new initiatives with major societal impact. The program minimizes the time between idea conception and successful research results by providing immediate startup funds for novel, high-risk and transformative research projects. The funds are intended to generate data for groundbreaking, high-impact publications, or preliminary results for new, innovative research proposals. The program also includes high-visibility, campus-wide research symposia to showcase the resulting groundbreaking research.”

  • Mark’s project, with partners, Joel Gagnier and Hal Morgenstern, is called:
    Core outcome measures for rotator cuff disorders

    The selection of appropriate outcomes or domains is crucial when designing clinical trials in order to compare directly the effects of different interventions in ways that minimize bias. If the findings are to influence policy and practice then the chosen outcomes need to be relevant and important to key stakeholders including patients and the public, health care professionals and others making decisions about health care. There is a growing recognition that insufficient attention has been paid to the outcomes measured in clinical trials. A recent review of the measurement properties of patient reported outcome measures for rotator cuff disorders revealed a large selection of diverse measures, many with questionable validity, reliability and responsiveness. These issues could be addressed through the development and use of an agreed standardized collection of outcomes, known as a core outcome set (COS), which should be measured and reported in all trials for a specific clinical area. These sets do not imply that outcomes in a particular trial should be restricted to those in the COS. Rather, there is an expectation that the core outcomes will always be collected and reported, and that researchers will continue to explore other outcomes. The purpose of the present project is to develop a COS for rotator cuff disorders. The methods will include a comprehensive systematic literature review and assessment of the properties of outcome measures, identifying and involving relevant stakeholders, and using consensus based methods.

  • Jean’s project, with partners Chuck Burant and Ryan Mills, is called:
    Scientific Needs Assessment and Analysis of Bioinformatics Tools to Support Clinical & Translational Research

    tranSMART is a global open source community using and evolving a data sharing and analysis platform to accelerate clinical and translational research. The tranSMART community includes pharmaceutical and for-profit companies, nonprofit, academic, patient advocacy, and government stakeholders. The tranSMART value proposition relies on its members, who are the best source of innovation. This project will work with early adopters (researchers and their teams) at the University of Michigan to understand scientific workflows, analysis needs and data sharing requirements to support their ongoing research. Results of this project will be used to guide continued development of tranSMART to support research at the University of Michigan and the global community more generally.

To learn more about MCubed, go to: http://mcubed.umich.edu/

Tools & Technology Seminar

The National Center for Integrative Biomedical Informatics (NCIBI) holds a weekly seminar each Thursday, at 12 noon EST, highlighting a tool or technology that is under development or currently being used by NCIBI researchers. These seminars are streamed live using Adobe Connect and are also are archived and made available on the list below for future viewing via Flash video streaming.

The aim of the NCIBI Tools & Technology Seminar Series is to have open and interactive discussions about the software tools and technologies being used in NCIBI led by the people doing the work. Participation is strictly voluntary and based on interest. Collaborators and other interested parties are welcome to attend.

Upcoming seminar details:

Presenter: Bjoern Peters
“The Immune Epitope Database and Analysis Resource.”

Thursday, April 12, 2012
12 noon – 1:00p.m. EST
Room 2036 Palmer Commons
Ann Arbor, MI
Watch via Adobe Connect

The Bioinformatics Core can Help With Your Bioinformatics Needs

Are you a researcher needing bioinformatics support? If so, you should contact the Bioinformatics Core, which is supported by both the Department of Computational Medicine and Bioinformatics (DCM&B, http://www.ccmb.med.umich.edu/home) and the Biomedical Research Core Facilities (BRCF,  http://www.brcf.med.umich.edu/).  The Bioinformatics Core works “…with research scientists (faculty, staff, post-docs and graduate students) to provide analysis of their high-throughput sequencing, proteomics, gene expression, metabolomics and other biological data.”  In addition to data analysis, the Bioinformatics Core also provides custom application development.  More information about the Bioinformatics Core can be found at http://www.ccmb.med.umich.edu/bioinf-core.

New Video Tutorial for MetScape Plugin for Cytoscape

Are you interested in learning how to use the MetScape plugin for Cytoscape? Developed by the National Center for Integrative Biomedical Informatics (NCIBI), MetScape is a Cytoscape plugin used to visualize and interpret metabolomic and expression profiling data in the context of human metabolism.  A video tutorial on MetScape is now available at http://treehouse.ccmb.med.umich.edu/mst.html.  Learn about the pathway and concept filters, how to load data, how to view attribute information, and more.  More information about Metscape and a link to download the plugin can be found at http://metscape.ncibi.org.

Bioinformatics workshop on January 12, 2012

The Taubman Health Sciences Library’s bioinformationist, Marci Brandenburg, will be presenting “Visualizing Protein and Metabolite Interaction Networks with Cytoscape/MetScape” at a workshop to be held in the Biomedical Science Research Building Rooms A,B, and C on Thursday, January 12.  This one day workshop will include a variety of interesting and valuable topics. To learn more and register, go to http://www.sph.umich.edu/niehs/bioinformatics/index.html.

Bioinformatics Workshop on January 12, 2012

The Taubman Health Sciences Library’s Bioinformationist, Marci Brandenburg, will be presenting “Visualizing Protein and Metabolite Interaction Networks with Cytoscape/MetScape” at the Bioinformatics Workshop being held in the Biomedical Science Research Building Rooms A,B, and C on Thursday, January 12.  This one day workshop will include a variety of interesting and valuable topics. To learn more and register, go to http://www.sph.umich.edu/niehs/bioinformatics/index.html.