DECART: DATA SCIENCE FOR THE HEALTH SCIENCES
July 10-12, 2017 (The python at the end of the galaxy (A play on the restaurant at the end of the universe)
Galaxy is an open source, web-based platform for data intensive biomedical research. Thousands of bioinformatics tools have been imported into this graphical user interface. This tool enables biomedical informatics exploration and the building and sharing of reusable workflows. Ipython notebooks are now an integral part of galaxy.
Dissertation award entry
Recently graduated doctoral students who have published a dissertation may apply for the CGS/ProQuest Distinguished Dissertation Award, which recognizes excellence in dissertation writing. For 2017, dissertations in the Biological Sciences & Humanities/Fine Arts will be considered.
The BMI department submitted Keith Simmon’s thesis.
Upcoming posters at Curating the Clinical Genome
- ClinVar Miner: Enabling deep exploration of the ClinVar archive
Alexander R. Henrie,1 Brandon Cushman,2 Sarah Hemphill,2 Steven Harrison,2 Marina DiStefano,2 Danielle Azzariti,2 Justin Aronson,3 Lisa M. Vincent,4 Scott R. Goehringer,5 Erin Rooney Riggs,5 Christa Lese Martin,5 Heidi L. Rehm,2,6 Karen Eilbeck1
1Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
2Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA.
3Pierce Middle School, Brookline, MA, USA
4GeneDx, Gaithersburg, MD, USA
5Geisinger Health System, Danville, PA, USA
6Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA USA - A community-developed data model for representing sequence variation
Karen Eilbeck1, Shawn Rynearson1, Gil Alterovitz2, Larry J. Babb3, Robert R. Freimuth4, Sarah E. Hunt5, David Kreda6, Jennifer Lee17, Peter N. Robinson8, David Haussler9, Heidi Rehm10,11, Peter Goodhand12, Reece K. Hart13
1University of Utah School of Medicine, Salt Lake City, Utah, USA. 2Harvard Medical School, Boston, MA, USA. 3Sunquest Information Systems, Boston, MA, USA . 4Mayo Clinic, Rochester, MN, USA. 5EBI, Wellcome Campus, Hinxton, UK. 6Independent Consultant, New York, NY, USA. 7NCBI, National Library of Medicine, Bethesda, MD, USA. 8Jackson Laboratory, Jax Genomic Medicine, Farmington, CT USA. 9University of California, Santa Cruz, CA, USA. 10Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA. 11Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA USA. 12Ontario Institute for Cancer Research, Toronto, CA. 13Invitae, San Francisco, CA, USA. - hgvs-eval: automated evaluation suite to assess HGVS-formatting tools
Nicole Ruiz1, Justin Paschall2, Xing Xu3, David Caplan3, Carolyn Ch’ng4, Karen Eilbeck1, Reece Hart5
1Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT 84108
2University of California Berkeley, Berkeley, CA 94720
3SolveBio, 285 West Broadway, Suite 630, New York, NY 10013
4British Columbia Cancer Agency, Canada’s Michael Smith Genome Sciences Centre, Vancouver
5Invitae, Inc. 475 Brannan St., San Francisco, CA 94107
New Student
Michael Watkins joined the lab from the BYU bioinformatics program to work on variant annotation and representation issues. We are really pleased to have Michael hit the ground running and hope to entice more students from that program to BMI.
Upcoming Med School class
A certificate in Precision Medicine will be offered to the Med school students in the fall, and I will be teaching a session on phenotyping and variant interpretation in September. This will be a hands-on practical class with lots of doing rather than sitting.
Promotion
This summer I was promoted to full professor. There are a lot of people who have been part of the process that I need to thank. First, thanks to my department faculty and admin for their support. Thank you to Joyce Mitchell for hiring me. Thanks to everyone I have worked with over the years, to numerous to name, but this is a nice graph of some of my network: https://utah.pure.elsevier.com/en/persons/karen-eilbeck/network/ . The list goes on, CCTS, BMI DAC and SAC, program for personalized medicine, SOM RPT committee…