Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop

General information

Second Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop


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 monitoring procedures.

Learning outcome:

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.

Objective:

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 bioinformatics.

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.

Contact Person: Michael Reuscher (michael.reuscher@tamucc.edu)

Content

The highlighted icons, represent the fields of education (in compliance with ISCED Classification) engaged during this course/programme.

0511 - Biology", "0512 - Biotechnology", "0521 - Ecology", "0522 - Conservation and environmental management", "0688 - Bioinformatics

Venue

Venue: Harte Research Institute for Gulf of Mexico Studies
Corpus Christi, Texas 78412 , United States

Application

Open from
11 Oct 2017 to 10 Nov 2017

Application Procedure:

We accept a limited number of participants. Please complete the attached application form (below), and return it to Holly Bik at holly.bik@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@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 registration fee.

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.

Name:

Title:

Address:

Phone:

Email:

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 research supervisor.

Qualification

Academic level: Master, PhD
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