2014 CRI Bioinformatics Workshop

The 2014 Bioinformatics Workshop, the inaugural event in the CRI’s Workshop Learning Series, took place from December 3-6, 2014 at the University of Chicago. This four-day workshop focused on how to make the most of the latest technologies and tools for working with high-throughput genomics data, including both in-depth practical theory and hands-on training.

See photos from the workshop here!


The focus of our 2014 workshop was on training researchers in the use of computational technologies and the latest bioinformatics analysis tools required to deal with big genomics data. This training covered a complete range of technologies and applications, from the basics of computational thinking to large-scale data analysis on Linux and HPC infrastructures. Topics included microarray data analysis using R, the implementation of open-source-based NGS analysis workflows for RNA-seq data, genomics visualization tools (e.g., IGV, UCSC, circos, etc.), and tools that can perform the most common everyday tasks for bioinformaticians of “omics” data.

For more details, download the PDF of the full workshop schedule.


In addition to the CRI’s team of bioinformaticians, speakers included:

  • Robert Grossman, PhD, Chief Research Informatics Officer for the University of Chicago Biological Sciences Division and Director of the Center for Data Intensive Science
  • Ian Foster, PhD, Director of the Computation Institute
  • Samuel Volchenboum, MD, PhD, Associate Chief Research Informatics Officer and director of the Center for Research Informatics
  • Gang Feng, PhD, developer of the Bioconductor package GeneAnswers and co-developer of the Bioconductor package lumi and its annotation packages
  • Natalia Maltsev, MD, PhD, research associate leading the development of Lynx, a web-based database and a knowledge extraction engine
  • Dinanath Sulakhe, Senior Engagement Manager and Solutions Architect at the Computation Institute and lead architect of the Lynx project
  • Masha Kocherginsky, PhD, biostatistician at the Department of Public Health Studies and member of the Biostatistics Core
  • Sohela Shah, PhD, Field Application Scientist for QIAGEN Bioinformatics
  • Ravi Madduri, MS, Fellow at the Computation Institute and Project Manager in the Mathematics and Computer Science Division at Argonne National Laboratory

Participation and Feedback

A total of 33 graduate students, postdoctoral fellows, faculty, and staff completed our 2014 Bioinformatics Workshop. Thanks to our partnership with the Institute for Translational Medicine and Center for Health and the Social Sciences, 12 students received University of Chicago course credit for their participation in the workshop.

Of the participants who completed a feedback survey after the workshop, 91 percent rated the materials covered as extremely or very useful. Asked about the quality of instruction, 91 percent rated it excellent or very good, and 96 percent considered their instructors extremely or very knowledgeable in the subject matter taught. Comments from participants included:

  • “I was pleased with the wide range of information that was covered during the workshop, and the diversity of skills I got to practice during these four days.”
  • “Despite having background in the content covered, I found it a very good refresher on things I haven’t thought about in a while.”
  • “Even after speaking for ~3 hours, the instructor was not boring at all. […] I heard someone say in the lunch line how this tutor spoke with clarity and command.”
  • “This course was appropriately geared towards researchers who use high-throughput sequencing in their work, regardless of their knowledge level, which I was quite impressed by. […] I am grateful that the CRI held this course and I think the speakers and instructors did an excellent job guiding us through the process.”


The success of our first workshop was made possible in part by the generosity of our institutional partner the Institute for Translational Medicine, and of our sponsors:

QIAGEN Bioinformatics
Continental Resources
Meridian IT