IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

[Annelida] Updated workshop announcement: Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB)

Reuscher, Michael via annelida%40net.bio.net (by Michael.Reuscher from tamucc.edu)
Thu Nov 2 13:34:59 EST 2017

2nd Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB=
-2) Workshop

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

All those interested in attending MUST submit the following workshop regist=
ration form

https://goo.gl/forms/RL5P6EAOzfQG16kq2  (application deadline November 15, =

Background: Morphological identification of benthic meiofauna and macrofaun=
a 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 in=
fancy, we are anticipating that this new methodology will become a standard=
 procedure for ecological surveys and environmental monitoring procedures.

Purpose: The BITMaB-2 workshop is designed to train graduate students and r=
esearchers in the full spectrum involved in this new cutting edge methodolo=
gy, including sample preparation, taxonomy of common benthic meiofauna and =
macrofauna taxa of the Gulf of Mexico, metagenomics, and bioinformatics. Th=
ere is no registration fee for BITMaB-2.

There are two objectives of this workshop. First, we intend to produce meio=
-and macrofaunal specimens from which we will generate draft genomes in sup=
port of the development of the eukaryotic genomes reference databases.  We =
strive to include as many unique families/phyla represented in the GoM as p=
ossible.  A complication for many groups is that fresh material will be req=
uired to find and identify individual specimens.  As such this workshop wil=
l focus on samples collected each morning during the workshop from relative=
ly 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 experience=
s for many students and to produce as many potential reference samples comp=
etent for genome sequencing analysis as possible during the week.  The taxo=
nomy experience will take place in the facilities at the Harte Research Ins=

Confirmed taxonomic participants:

  *   Maickel Armenteros (University of Havana, Cuba) =96 Nematoda

  *   Noe Barrera (Texas A&M University-Corpus Christi) =96 Mollusca

  *   Richard Heard (University of Southern Mississippi) =96 Isopoda, Amphi=
poda, Tanaidacea

  *   Larry Hyde (Texas A&M University-Corpus Christi) =96 Local macrofauna

  *   Rick Kalke (Texas A&M University-Corpus Christi) =96 Local macrofauna

  *   Kevin Kocot (University of Alabama) - Aplacophora

  *   Francesca Leasi (University of New Hampshire) - Meiofauna from enviro=
nmental samples

  *   Wonchoel Lee (Hanyang University, South Korea) =96 Harpacticoida

  *   Fabio Moretzsohn (Texas A&M University-Corpus Christi) =96 Mollusca

  *   Tiago Pereira (University of California Riverside) =96 Nematoda

  *   Alessandro Prantoni (Federal University of Paran=E1) =96 Oligochaeta

  *   Michael Reuscher (Texas A&M University-Corpus Christi) =96 Polychaeta

  *   Adelaide Rhodes (University of Vermont) =96 Copepoda, Tanaidacea

  *   Melissa Rohal (Texas A&M University-Corpus Christi) =96 Harpacticoida

  *   Martin S=F8rensen (Natural History Museum of Denmark) =96 Kinorhyncha=
, Tardigrada, Gnathostomulida, Loricifera

The second objective of the workshop is to provide training in core bioinfo=
rmatics analysis.  These skills are critical to the effective use of genomi=
c 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 pro=
grams, such as PhyloSift, iPython workflows, and data visualization softwar=
e.  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, Un=
iversity of California-Riverside.

Outcomes:  Participating students will (1) learn how to properly prepare be=
nthic samples for morphological identification of invertebrates and DNA seq=
uencing alike, (2) acquire taxonomic expertise about common invertebrate ta=
xa of the Gulf of Mexico, (3) gain deeper understanding on the metagenomic =
sequencing approach to characterize the taxonomic composition of benthic sa=
mples, and (4) master the use of sophisticated bioinformatics tools needed =
for the analyses of genomic and metagenomic datasets.

Application and travel support:  A limited number of BITMaB-2 travel stipen=
ds (covering airfare, accommodation, and subsistence) are available for wor=
kshop applicants - both US and international applicants are eligible to app=
ly. Travel support will be provided through a combination of funding from a=
 Gulf of Mexico Research Initiative (GOMRI) grant and National Science Foun=
dation, Research Coordination Network (NSF-RCN) EukHiTS grant to Kelly Thom=
as and Holly Bik (more information about RCN EukHiTS can be found at: http:=

To apply for a travel stipend, please answer =93yes=94 to the the relevant =
question on the workshop application form (see Google Form Link at top of t=
his document).

Graduate and undergraduate students should also send a letter of support fr=
om their supervisory professor.  The deadline for application is Wednesday,=
 November 15, 2017. For any further questions, please email Michael Reusche=
r at michael.reuscher from tamucc.edu<mailto:michael.reuscher from tamucc.edu>

Michael Reuscher, Ph.D.
Harte Research Institute for Gulf of Mexico Studies
Texas A&M University - Corpus Christi
6300 Ocean Drive, Unit 5869
Corpus Christi, Texas 78412-5869

More information about the Annelida mailing list

Send comments to us at biosci-help [At] net.bio.net