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Bioinformatics Events and Activities

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Parking for Workshops:

Most workshops are held either in the BRC computer lab (SERF736) or in the Mossman building.  Parking on and near the UT campus is challenging, especially when class is in session.  The most certain way to handle this is to park in the UT visitor parking garage ($1 per half-hour).  Metered street parking is sometimes available north of campus.  Parking on campus and in any other garages is generally by permit only.

 

Useful visitor parking information is available here: https://studentunion.utk.edu/visitor-parking/

 

Google map links:

SERF: https://goo.gl/maps/jzkp2gtmGj8WgvSQ7

Mossman Building:  https://goo.gl/maps/cYaa8f4yVTGRxXnJ9

UT Volunteer Hall Visitor Parking Garage: https://goo.gl/maps/pb4BN5F3T7J68tey8


Upcoming Workshops:

 

 

BRC Integrated Microbial Genomes (IMG) Mini-Workshop

Time: Tuesday, October 22nd, 1pm to 4pm
Place: SERF 736

 

attendance is full for this workshop

IMG is a powerful database and analysis platform for exploring, analyzing, and comparing publicly available prokaryotic genomes and metagenomes. IMG has many tools available; this pilot mini-workshop will focus on two main points:

1. Explore the structure of IMG and how to interact with it.
2. Learn rapid and robust ways to gain insights into functional capabilities of a given prokaryotic genome or set of genomes using both non-targeted surveys (“fishing expeditions”) and hypothesis-driven approaches.

This is a great chance to get an introduction to IMG in a very small work-group setting and to meet like-minded fellow researchers. This mini-workshop, serving up to five attendees, will inform development of future mini-workshops or for a scaled-up workshop.

We will use workstations available in the CEB Bioinformatics Resource Center. The workshop will be comprised of ~1.5 hours of guided material with ~1.5 hours of unstructured group work time; bring your own questions, genomes, and hypotheses!

 

 

 

 

We always have more workshops in development.  Contact us and let us know what you’re interested in learning about!


 

Prior BRC Workshops and Events

 

KBase Workshop: Microbial Communities and Ecosystems

 

UT Knoxville
Mossman 212
Friday, October 18th, 10am – 1pm

 

Join us for a workshop to learn about the Department of Energy Systems Biology Knowledgebase (KBase). KBase is a free, open source software and data platform designed for both bench biologists and bioinformaticians. KBase integrates a large variety of public data and tools into an easy-to-use graphical user interface.

KBase has powerful tools for analyzing microbial communities and developing an understanding of functional interactions between species in microbial ecosystems. This workshop guides users through the basics of using KBase tools to assemble metagenome sequence data and prepare high-quality bins that can be used for comparative phylogenomics, metabolic modeling, and more.


 

 

DNASTAR Lasergene Workshop and Consultation Sessions

 

UT Knoxville
Workshop: Mossman 212, Jan 29th @3:30pm – 5:30pm
Consultation sessions: SERF 736, Jan 30th @9:30am – 12:00pm

https://www.dnastar.com/

Workshop 

On Thursday, Jan. 29th, 3:30pm – ~5:00pm in 212 Mossman, Thomas Leary, bioinformaticist from DNASTAR, reviewed the Genomics (next-gen) and Molecular Biology modules of Lasergene.

Consultations 

On January 30th from 9:30 AM-12:00 PM, Thomas Leary participated in small group consultations for researchers.


 

UT BRC Workshop: Microbial Genomes Atlas (MiGA) Web-server and Metagenome-Annotated Genomes (MAGs)

Strong Hall 101
Thursday, Oct. 4th, 1pm – 5pm
Professor Kostas T. Konstantinidis and Dr. Luis M. Rodriguez-R (Georgia Tech) led a workshop in the use of the Microbial Genomes Atlas (MiGA), an exciting new service aimed at providing “a uniform system for genome-based taxonomic classification and diversity studies”.

 

Please see this article for a description of MiGA

 

 


 

KBase RNA-seq Workshop

May 9th, 2018

 

The BRC hosted Priya Ranjan, Ben Allen, and Meghan Drake from the KBase team for an RNA-seq workshop May 9th, 2018.

Prokaryotic data was used for the hands-on tutorials; however, the tools and skills to be covered are also applicable to plant projects.

KBase can be used for a variety of applications such as transcriptome assembly, gene discovery/annotation, and detection of differential transcript abundances between tissues, developmental stages, genetic backgrounds and environmental conditions. The RNA-seq pipeline inKBase allows researchers to create differential expression estimates and use these to perform functional analysis of genes with similar expression patterns and inform metabolic models.


MG-RAST Workshop

March 15-16, 2018

 

The UT Bioinformatics Resource Center was pleased to welcome Dr. Will Trimble from the MG-RAST team at Argonne National Laboratory for a 1-and-a-half day workshop on MG-RAST. The workshop included seminars and extensive hands-on tutorials from Robert W. Murdoch and Will Trimble on how to use the MG-RAST graphical user-interface (GUI) and advanced programing interfaces (API) of MG-RAST and NCBI.

The curriculum, walkthroughs, and links to additional tutorials can be found here: https://github.com/wltrimbl/UTK-MGRAST

 

 


Integrated Microbial Genomes Workshop

January 8-9th, 2018

The UT Bioinformatics Resource Center was pleased to welcome Natalia Ivanova and Rekha Seshadri from The U.S. Department of Energy Joint Genome Institute (DoE JGI) for a 2-day workshop on Microbial Genomics and Metagenomics (IMG). The workshop included seminars and extensive hands-on tutorials on how to use the IMG interface for comparative analysis of isolate genomes and metagenomes. DoE JGI science and technology was also be highlighted.

The Integrated Microbial Genomes (IMG) system is a comprehensive repository of annotated sequence data of archaeal, bacterial and viral genomes and metagenomes from cultured and uncultured organisms. Researchers who wish to learn to explore the data and leverage tools for comparison and gene discovery should attend this workshop.


CLC Genomics Workbench:

Consultation Sessions and Transcriptomics (RNAseq) Workshop

December 13th, 2017

 

The UT Bioinformatics Resource Center was pleased to host Shawn Prince from the Qiagen CLC Genomics Workbench team!  Shawn was be on hand for small group consulting sessions and will led a transcriptomics (RNA-seq) workshop.


KBase Introductory Workshop

December 1, 2017

The BRC was pleased to welcome the Department of Energy Systems Biology Knowledgebase (KBase) team!  KBase is a free, open source software and data platform designed for both bench biologists and bioinformaticians. KBase integrates a large variety of public data and tools into an easy-to-use graphical user interface.

KBase enables users to upload their own data, analyze it alongside collaborator and public data, build increasingly realistic models, and share their workflows and conclusions. Users do not need to access them from numerous sources or learn multiple systems in order to perform sophisticated systems biology analyses.

The workshop covered a variety of analyses for microbes and microbial communities, including a rich collection of bioinformatics tools for quality control and assessment of reads, de novo assembly, prokaryotic genome annotation, and how to analyze structural and functional features of genomes within KBase.


8th Argonne Soil Metegenomics Meeting

November 1-3, 2017

BRC Coordinator Robert Murdoch attended the soil metagenomics meeting at Argonne National Laboratory, the home of MG-RAST.  Among the most important topics discussed were the current state of 16S amplicon library analysis pipelines and recent improvements to MG-RAST.


CLC Genomics Workbench Workshop: 16S library pipelines and office hours

October 24, 2017

An expert from the CLC Genomics Workbench team led a focused workshop on 16S library analysis pipelines.  Also, the expert was hand throughout the day in SERF 736 for smaller consultation sessions.


JGI IMG Workshop in Walnut Creek, CA

September, 2017

BRC Coordinator Robert Murdoch attended the weeklong IMG workshop at JGI headquarters in Walnut Creek, CA.  Dr. Murdoch will be happy to assist you with the IMG platform.


CLC Genomics Workbench workshop

July, 2017

The CEB BRC welcomed CLC team members in the summer of 2017 for a day-long introductory CLC Genomics Workbench workshop.  The workshop demonstrated many aspects of the software package.  With almost 80 attendees, this was the largest workshop that the CLC team had ever been involved in.

In light of attendee feedback, additional specialized workshops will follow in the year to come!