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Lots of Updates
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 […]
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Academy of health sciences and other things
As part of my continued interest in the educational needs of the health science community for bioinformatics resources, I have joined the Academy of Health Science Educators at the School of Medicine. MissionThe Academy of Health Science Educators (AHSE) is designed to advance state-of-the-art education at the University of Utah through teaching, research, mentorship and […]
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Compute resources for teaching
We (Amy Sheide and myself) were awarded funds to host our Hands-on Bioinformatics Experience teaching material on XSEDE. This is a huge bonus for us and will enable us to develop our Galaxy based teaching material in a friendly environment. Many thanks to the XSEDE Resource Allocations Service. This resource complements our previous funding to update the […]
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biocuration conference 2017
Nicole Ruiz will be presenting a poster: hgvs-eval: automated evaluation suite to assess HGVS-formatting tools at the biocuration conference at the end of the month. This work is part of a GA4GH initiative. We are grateful to have received a travel fellowship from the conference organizers. The ClinGen clinical domain working group for inborn errors of […]
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VMC workshop
I attended a productive 2 day GA4GH Variation Modeling Collaboration workshop in Cambridge, to continue development of the model and preliminary spec for the sharing of variation from simple variants to haplotypes and genotypes. The mission of the Variation Modeling Collaboration is to enable organizations to reliably share information associated with variation in biological sequences. Instead […]
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Teaching grant and galaxy workshop
In late October I was awarded a teaching grant from the University of Utah Teaching Committee, to incorporate the use of Galaxy into the teaching of bioinformatics in the department. Galaxy is an online framework that embeds bioinformatics tools into a user friendly interface. It also enables the sharing of work flows. This will enable […]
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Shale defended thesis
Shale Dames successfully defended his thesis: Development of a Clinical Next generation Sequencing Assay for Mitochondrial Disorders on Wednesday. He described several years of work developing and testing an NGS pipeline for a clinical mitochondrial disorder panel. He touched many pertinent points such as selecting the nuclear genes implicated in mitochondrial disease and issues related to […]
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GA4GH Variant Modeling Collaboration
I have been virtually attending the GA4GH Variant Modeling Collaboration meeting in Boston, bringing together ClinGen, GA4GH, HL7, FHIR, NCBI and others to find agreement on how we model sequence variation. The Sequence Ontology plays a role here given its history and usage in genomic annotation and variant annotation tools. The outcomes of this group will […]
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Taxonomer update
The manuscript describing Taxonomer is finally out in Genome Biology:Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling The paper has been picked up by various media outlets including the Deseret News, and KEUR radio. The tool is available here through the iobio platform and here through IDbyDNA’s public interface.
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Graduation
Two students from the lab walked on Friday at the graduation ceremony. Congrats to Shale Dames and Paris Vail, and the other BMI students. Lots of good memories of these folks: Jason Jacobs – your contribution to the Chlamydia paper was exceptional, David Jones – it was an honor to go to your weddings (note […]