[Taxacom] Workshop announcement: Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics
germman82 at gmail.com
Thu Oct 5 13:25:05 CDT 2017
*Second Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics
*January 15-19 2018*
*Texas A&M University-Corpus Christi*
*Harte Research Institute for Gulf of Mexico Studies*
*6300 Ocean Drive, Corpus Christi, Texas 78412 USA*
*Background:* Morphological identification of benthic meiofauna and
macrofauna samples is labor intensive, time consuming, and costly. A more
efficient method, using DNA markers from metagenomic sequencing of sediment
samples to characterize benthic communities, is being developed. For this
purpose, a reference library for whole genomes of widely distributed
infauna species of the Gulf of Mexico is currently being populated. While
still in its infancies, we are anticipating that this new methodology will
become a standard procedure for ecological surveys and environmental
*Purpose:* The BITMaB workshop is designed to train graduate students and
researchers in the full spectrum involved in this new cutting edge
methodology, including sample preparation, taxonomy of common benthic
meiofauna and macrofauna taxa of the Gulf of Mexico, metagenomics, and
There are two objectives of this workshop. First, we intend to produce
meio- and macrofaunal specimens from which we will generate draft genomes
in support of the development of the eukaryotic genomes reference
databases. We strive to include as many unique families/phyla represented
in the GoM as possible. A complication for many groups is that fresh
material will be required to find and identify individual specimens. As
such this workshop will focus on samples collected each morning during the
workshop from relatively shallow sediments. This aspect of the workshop
will be led by taxonomic experts and provide an opportunity for training
students, at all levels. The anticipated outcome for this activity is to
provide valuable experiences for many students and to produce as many
potential reference samples competent for genome sequencing analysis as
possible during the week. The taxonomy experience will take place in the
facilities at the Harte Research Institute.
The second objective of the workshop is to provide training in core
bioinformatics analysis. These skills are critical to the effective use of
genomic data for analyzing community structure and function. The
bioinformatics workshop will take place every morning during the week.
Students attending the workshop will emerge with core skills in UNIX
(BASH), simple scripting tools and analyzing metagenomics data using open
source bioinformatics programs, such as PhyloSift, iPython workflows, and
data visualization software. This aspect of the proposal will be led by the
UNH and UCR Genomics and Bioinformatics groups. The bioinformatics workshop
will take place in the Harte auditorium. The bioinformatics portion will be
led by Holly Bik, University of California-Riverside.
*Outcomes:* Participating students will (1) learn how to properly prepare
benthic samples for morphological identification of invertebrates and DNA
sequencing alike, (2) acquire taxonomic expertise about common invertebrate
taxa of the Gulf of Mexico, (3) gain deeper understanding on the
metagenomic sequencing approach to characterize the taxonomic composition
of benthic samples, and (4) master the use of sophisticated bioinformatics
tools needed for the analyses of genomic and metagenomic datasets.
*Application and travel support:*
We accept a limited number of participants. Please complete the attached
application form (below), and return it to Holly Bik at holly.bik at gmail.com.
Graduate and undergraduate students should also send a letter of support
from their supervisory professor. The deadline for application is Friday,
November 10, 2017. For any further questions, please email Michael Reuscher
at michael.reuscher at tamucc.edu.
Please indicate on the application form, if you will need travel support.
Travel support for the BITMaB workshop will be limited. There is no
Travel support for the taxonomic experts including travel, room and board
during their participation in the workshop will be provided from the Gulf
of Mexico Research Initiative (GOMRI) grant.
Travel support for workshop participants will be supplemented with funds
from the National Science Foundation, Research Coordination Network
(NSF-RCN) grant to Thomas and Bik.
*Application for Travel Support to the Benthic Invertebrate Taxonomy,
Metagenomics, and Bioinformatics (BITMaB) Workshop to be held in January
15-19, 2018 in Corpus Christi, Texas*
This application is for travel support to the BITMaB workshop. Support will
include transportation, hotel, and meals in Corpus Christi. All expenses
will be paid directly, no reimbursements will be made.
Transportation estimate (for air, bus, train, or auto):
Please provide a brief statement as to why you want to attend the workshop,
and how it will benefit you. Students attach a letter of support from their
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