2017 Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop

RCN EukHits kicked off 2017 with a successful workshop focusing on the intersection of morphological taxonomy and high-throughput sequencing. The first annual Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop was held January 9-13, 2017 at the Harte Research Institute for Gulf of Mexico Studies at Texas A&M University in Corpus Christi, Texas. We had ~50 participants in attendance, representing a range of career stages (undergraduates to Tenured Professors) and taxonomic expertise spanning a wide range of microbial eukaryote groups (nematodes, polychaetes, gastrotrichs, flatworms, molluscs, and other “minor” phyla).

 

2017-01-09 16.40.45-1.jpg

Workshop 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 infancy, we are anticipating that this new methodology will become a standard procedure for ecological surveys and environmental monitoring procedures.

Workshop Purpose: The BITMaB workshop is was 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 the ongoing BITMaB workshops. 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 focused on samples collected each morning during the workshop from relatively shallow sediments. This aspect of this first workshop was led by taxonomic experts and provided an opportunity for training students, at all levels.  Workshop participants gained valuable experience in morphological identifications of diverse eukaryotic groups.  

Taxonomic participants included:

  • Alberto De Jesus Naverrete – Nematoda
  • Rick Hochberg (Lowell, MA) — Gastrotricha, Rotifera
  • Julian Smith III (Winthrop, NC) – Platyhelminthes
  • Martin Sørensen (Denmark) – Kinorhyncha, Tardigrada, Gnathostomulida, Loricifera
  • Anja Schulz (TAMU-Galveston) – Polychaeta, Sipuncula
  • Michael Reuscher (TAMUCC) – Polychaeta
  • Jon Norenburg (SI) – Nemertea, soft-bodied mollusks
  • Melissa Rohal (TAMUCC) – Harpacticoida
  • Francesca Leasi (SI, UNH) – Environmental samples, general taxonomy of meiofauna

The second objective of the workshop was 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 took place every morning during the week.  Students emerged 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.  The bioinformatics workshop was be led by the University of New Hampshire (RCN PI Kelley Thomas) and the University of California, Riverside (RCN PI Holly Bik).

We will be running a second BITMaB workshop in January 2018 – stay tuned for further announcements and a call to participate!

2017-01-12 07.39.10 (1).jpg

Advertisements

Applications now open for the summer 2015 “Bioinformatics & Biodiversity” Undergraduate Workshop

Following on from a highly successful event last year, we’re very excited to announce the second annual “Bioinformatics & Biodiversity” Undergraduate Workshop at the University of New Hampshire, scheduled for July 27-30, 2015 in Durham, NH. Click here to download a PDF flyer – we encourage you to post and share this opportunity!

2015_workshop_flyer

Microscopic eukaryotes (meiofauna e.g. nematode worms, copepods, protists, fungi, etc.) are some of the most abundant animals on Earth, but species within these groups are often overlooked by the general public and even many biologists. This NSF-sponsored workshop will explore the field of environmental DNA sequencing, including collection and analysis of data. Students will learn how high-throughput approaches (rRNA gene surveys, metagenomics) are being used to investigate the biodiversity of microbial eukaryotes and deepen our knowledge of ecosystem function. The workshop program will be a combination of lectures and practical exercises, where students will learn about traditional taxonomic approaches and also gain experience using the command line and bioinformatics tools to analyze environmental DNA datasets.

We welcome applications from undergraduates currently enrolled in any higher-educational institution in the USA.  All applicants are expected to have taken, at minimum, an introductory college-level course in Biology. Successful applicants will receive a stipend to cover all costs including travel.

To apply, e-mail the following materials to eukhits@gmail.com by Monday April 13, 2015:

  • Curriculum Vitae (including contact details for references)
  • Statement of interest (indicating biology courses taken and how attending the workshop would benefit your long-term career goals; maximum length 1 page)
  • Reference letters are recommended but not required

Frequently Asked Questions

Q. Can international/overseas students apply for this workshop? 

A.  No, unfortunately workshop application is restricted to students currently enrolled at US-based institutes (which includes international students attending US colleges). For future workshops we may extend the application process to students enrolled at overseas institutes (this will depend on the conditions of our funding). Thanks for your interest, and keep an eye on on the RCN website for future opportunities.

Q. For the CV (including references), exactly how many and what kind of references are preferred? 

A. One letter of recommendation can accompany the application (written by a professor or research supervisor) – this is optional, but may significantly increase the strength of your application. On your CV you can also list contact information for any additional professional references (up to three references); for example, you may want to list references relating to any relevant work experience or research projects.

 

ESA 2014 – Workshop materials posted

Thanks to everyone for coming out to our workshop at the ESA 2014 annual meeting, entitled “Environmental sequencing approaches and computational tools for ecologists”. We had a great group of participants who helped facilitate some very productive discussions!

Our workshop materials have now been posted online:

  • QIIME demonstration and discussion (PDF slides – Dorota Porazinska and Zhenjiang Xu, University of Colorado, Boulder) Topics covered:
    • Demonstration with default vs. modified parameters in software workflows (covering the different options possible, and how to modify them for different datasets and questions)
    • Explanation of how files are generated, what the software outputs look like, and how users can make use of the different files
    • Discussion will include data visualization tools for data analysis and exploration

Applications now open for “Bioinformatics and Biodiversity” Undergraduate Workshop

Our first student training event for RCN EukHiTS will be a  “Bioinformatics & Biodiversity” Undergraduate Workshop, to be held July 28-31, 2014  at the University of New Hampshire in Durham, NH. Click here to download a PDF flyer

This NSF-sponsored workshop will explore the field of environmental DNA sequencing, including the collection and analysis of data. Students will learn how high-throughput sequencing approaches (rRNA gene surveys, metagenomics) are being used to investigate the biodiversity of microbial eukaryotes and the ecosystem processes taking place in an environment. Students will gain experience in traditional taxonomic methods as well as processing and interpreting metagenomic data from environmental sequencing of whole sediment communities.

We welcome applications from undergraduates currently enrolled in any higher-educational institution in the USA.  All applicants are expected to have taken, at minimum, an introductory college-level course in Biology. Successful applicants will receive a stipend to cover all costs including travel.

To apply, e-mail the following materials to eukhits@gmail.com by Tuesday April 15th:

  • Curriculum Vitae (including references – see comment section below for additional information on references)
  • Statement of interest (indicating biology courses taken and how attending the workshop would benefit your long-term career goals; maximum length 1 page)

workshop_flyer