Bioinformatics & Computational Biology Tools
This working group will address the emerging and established tools for taxonomic identification, functional genomics, de novo assembly, biosynthetic gene cluster mapping, novel species identification, and standards development. These efforts will include benchmarking for all the above categories.
The International Microbiome and Multi'Omics Standards Alliance (IMMSA; https://immsa.org/) invites participants to join the IMMSA-Bioinformatics working group.
The IMMSA-Bioinformatics working group is a collection of scientists, engineers and other professionals that are interested in working collaboratively towards improving the computational methods for multi-omics data, especially from measurements of microbial communities. The working group welcomes people from academia, industry, government or other sectors. In order to sign up for the working group email list, please fill out this Google sheet: https://forms.gle/TAA39T1fLxrCMAFw8.
In 2024, the IMMSA-Bioinformatics working group will host “a year of data-reuse”. As part of this endeavor we will be hosting a seminar series consisting of 4, 1-hour sessions, with two invited speakers at each session. We will ask that the speakers share their expertise reanalyzing single-study data as well as many studies at once. Together, we hope to share our experiences and perspectives across microbiome studies to develop solutions that can enhance data reporting and enable data reproducibility.
Virtual Seminar Series Schedule (held at 12 pm ET)
(webinar invites will be sent via the listserv)
Speakers and Talk Titles:
Feb 15th
“Re-Investigating Microbial Classifications in Cancer Sequencing Data”
Abraham Gihawi, Postdoctoral Fellow (Norwich Medical School, University of East Anglia , Norwich, UK)
“From defaults to databases: simulated samples vs the real world”
Robyn Wright, Mitacs Post Doctoral Fellow (Langille Lab, Dalhousie University, Halifax, Nova Scotia, CA)
April 18th
"Reproducibility, interoperability, reusability, and flexibility in the anvi'o software ecosystem"
A. Murat Eren (Meren), Professor (Helmholtz Institute for Functional Marine Biodiversity at Oldenburg, Oldenburg, DE)
May 9th
"Omics data reuse for synthesizing plant gene-networks and pathways for the Plant Reactome Knowledgebase"
Sushma Naithani, Associate Professor Senior Research (Oregon State University, Oregon, US)
August 8th
Speakers: TBD
Past Working Group Efforts
In 2023 the IMMSA-Bioinformatics working group focused on the question: "How do we define how accurate a microbiome profile is?". There are many bioinformatic and wet lab methods that are used to profile the composition of microbial communities. What is the right way to evaluate those different methods? The interests of the IMMSA-Bioinformatics working group are broad, but we will consider our focal working problem to be the evaluation of taxonomic profiles of microbial communities from shotgun metagenomic sequencing data.