New Mexico INBRE

When

January, February and March 2021

January 19-29 (9 days 10% off pricing), February 16-26 (9 days 10% off pricing), and tentative March 15-26 (10 days)

Where

Online (by the National Center for Genome Resources (NCGR) Santa Fe, NM)

Audience

This program is geared towards training biologists (undergraduates, graduates and researchers) with minimal or no bioinformatics experience. Space is limited.

Objective

DE: In week 1, students will acquire the skill set to independently analyze RNA-Seq data using the command line interface, analytical workflows and current DE tools. UNIX fundamentals, RNA-Seq, data QC, alignments, read count generation, DE and pathway analysis will be covered. 

Metagenomics: In week 2, students will continue to use the command line interface to learn and conduct 16S Community Profiling and whole genome Metagenomics and metatranscriptomics analysis. Relevant tools such as QIIME2 will be used for community analysis and Centrifuge, MEGAN, DIAMOND and other tools for metatranscriptomics analysis.

Visualization: A ½ -1 day session at the end of week 2 will cover generation of simple graphs using R and utilizing genome browsers such as Integrative Genomics Viewer (IGV) to apply visualization to gene expression data. 

Topic overview

DE entails examining the fraction of the genome that is responsible for making products that drive organismal function. Gene expression is influenced by various extrinsic physiological and environmental as well as several intrinsic properties of the organism. Whole transcriptome profiles are becoming increasingly popular, useful and generate large volumes of data. Knowing how to handle, analyze, and make biological inferences on this scale of data is a valuable skill-set for students and researchers.

Microbes are extremely essential for every part of human life.  Microbes are closely associated with plants and animals and participate in the healthy functioning of hosts by making all nutrients, vitamins and metals available to them.  Our gut microbes for instance make energy from food available to us while protecting us from other pathogenic bacteria. Hence it is evident, microbes do not conduct these functions as single entities, instead as complex communities. Through metagenomics workshop, we will use computational methods to maximize our understanding of the collective genetic composition as well as the acitivies of complex microbial communities sampled from diverse environments.

Workshop Rates

Application: Fill out this online application here: Bioinformatics Intensives Application

Prerequisites

Unix, DE, Metagenomics and other study guides will be provided upon acceptance.

What to expect upon acceptance
Email confirming acceptance into the internship program and further details.

Logistics

The workshop will be conducted virtually using primarily Zoom as our conferencing platform.  We will also use a variety of other software and tools, and you will log onto NCGR’s Unix analysis server for the command line tools.  After the workshop, students can use our analysis server for their research or education purposes for up to one year. 

Contact

Please contact Project Assistant, Ethan Price, with any additional questions you may have at eprice@ncgr.org and we look forward to your participation!

Sponsored by New Mexico IDeA Network for Biomedical Research Excellence (NM-INBRE).