Guidelines for 'omics analyses

On this website you will find a growing and evolving collection of guidelines, tutorials, recommended readings, and method evaluations for various 'omics analyses that are commonly used in studies of nonmodel systems (particularly marine species). Instead of providing rigid "best practices", we aim to encourage data exploration and rigorous quality control through "best principles", paying particular attention to topics for which open access guidelines are scarce. The guidelines are written by members of the MarineOmics working group or the community, then shared for peer review. Comments on current website content or suggestions for new content can be made through the Discussion Forum.

Based on the expertise of the MarineOmics working group, the first topics include:

Topics

Functional Genomics

The guidelines portion of the website should be considered a "preprint". If you are interested in contributing to the peer review process, check out the Discussion Forum.

Panel Seminars

To facilitate discussions about practices and pitfalls in applying 'omics to non-model systems, we hosted Q & A panel seminars with experts on topics ranging from RADseq, population genomics with WGS, and transcriptomics. Check them out on YouTube!

What is the MarineOmics working group?

The original MarineOmics working group is part of the RCN for Evolution in Changing Seas, and was formed to promote reproducible and robust genomic research in nonmodel species, but especially marine and aquatic studies. Methods in next generation sequencing and bioinformatics advance at a pace that quickly render any static set of best practices obsolete. MarineOmics aims to support robust genomic research in ecology and evolution by disseminating guidelines through this dynamic, open-sourced website addressing introductory and advanced topics of population- and functional genomics. We are always looking for folks to join and write content for the website, if interested please contact us!

Rigorous: following best principles to identify and mitigate sources of error in data generation and analysis

Reproducible: when others can reproduce the results with accessible data, code, and documentation

Reproducibility in Marine Genomics

MarineOmics is also interested in evaluating and improving reproducibility in studies that use genomics to study adaptation in marine systems. We are conducting a meta-analysis of reproducibility across genomic studies of environmental adaptation in marine populations with the aim of identifying obstacles and opportunities for reproducing and synthesizing population genomic research. In Spring 2021, three undergraduate research interns contributed to this literature survey, with funding from the RCN-ECS.

Original Working Group Members

Katherine Silliman, PhD, South Carolina Dept. of Natural Resources - sillimank[at]dnr.sc.gov

Sam Bogan, UC-Santa Barbara -snbogan[at]ucsb.edu

Alan Downey-Wall, Northeastern University

Chris Mantegna, University of Washington (Intern)

Danielle Davenport, University of Queensland

Hanny Rivera, PhD, Woods Hole Oceanographic Institute

Jecy Klinkam, College of William and Mary (Intern)

Joe McGirr, PhD, UC-Davis

Kaitlin Macaranas, CSU-Bakersfield (Intern)

Megan Guidry, University of Rhode Island

Natalie Ameral, University of Rhode Island & RI Dept. of Environmental Management

Nicolas Lou, Cornell University

Sara Schaal, Northeastern University

Sara Wuitchik, PhD, Harvard University

Faculty Advisors

Jon Puritz, PhD, University of Rhode Island

Steven Roberts, PhD, University of Washington

Internship

In Spring 2021, MarineOmics hosted three virtual undergraduate research interns with funding from the RCN-ECS: Jecy Klinkam, Kaitlin Macaranas, and Chris Mantegna. These interns were paired with graduate student mentors within the MarineOmics group, as well as participated in training activities while contributing to the Reproducibility literature review.

Contact

For questions about the website and its materials, post to the Discussion Forum! For inquiries about the MarineOmics Working Group activities, please contact us at rcnecs.marineomics@gmail.com.