Swabs to Genomes – Author Interview
We recently published “Swabs to genomes: a comprehensive workflow”. In this study, authors Madison I. Dunitz and David A. Coil and their colleagues examined DNA library preparation and sequencing and present a workflow for the collection of environmental samples to a published microbial genome.
Madison and David commented on their research and experience publishing with us.
PJ: Can you tell us a bit about yourself and your team?
MD: We had a great team. Jonathan (Eisen) is really committed to collaboration, citizen science and open science. As a project scientist David is able to focus on the aspects of science he really enjoys such as teaching and mentoring undergraduates. These traits helped determine the tone and focus of the paper as an open source resource that was accessible to researchers with little to no programming experience.
DC: I’m a Project Scientist in the lab of Jonathan Eisen at UC Davis. Aaron Darling was a Project Scientist in the lab, is now a faculty at the University of Sydney, Jenna Lang is a post-doc in our lab, Guillaume Jospin is our bioinformatician, and Madison Dunitz started this project as an undergrad and stayed on as a Junior Specialist to finish the work. It’s very rare to have a project of this scope led by an undergraduate and Madison did a great job taking on that responsibility.
PJ: Can you briefly explain the research you published in PeerJ?
MD: Swabs to genomes is intended as a comprehensive workflow describing in detail (and in language that is accessible to a programming novice) the steps needed to isolate, sequence and assemble a bacterial genome.
DC: This paper describes a workflow to carry the user from starting with a swab, and ending having published a paper describing the genome of a bacteria isolated, sequenced, and assembled with this workflow. This really isn’t a research paper, it’s more like a very extended protocol with detailed background information.
PJ: Do you have any anecdotes about this research?
MD: At one point we were having trouble finding free and easy to use programs for processing Sanger reads, so David sent out a tweet asking for help. We actually received a few helpful suggestions, and a lot of other people tweeting about having the same problem. Everyone in the Eisen lab was encouraged to be active in the scientific twitter community and we talk a lot about the potential that twitter has as an informational resource and tool for connecting with other experts around the world, but it was really cool to see that actually happen.
DC: This workflow grew out of a different project designed to involve undergraduates in doing real-research. Given the ever-decreasing costs of sequencing we thought the time might be ripe for a group of students to each be able to go through the process of isolating a bacteria and sequencing/assembling the genomes. Along the way we discovered a number of challenges and surprises… navigating all that is what led to this paper. The hope is that others could attempt something similar with much less effort.
PJ: What surprised you the most with these results?
MD: For me the biggest surprise was how many people were interested in using the workflow or had been looking for this type of resource
PJ: What kinds of lessons do you hope the public takes away from the research?
1. Microbes are everywhere (and that’s actually a good thing)
2. Basic bioinformatics is not as hard or as scary as it might appear at first
DC: Our hope is that we have made it easier for small labs, undergraduates, and other groups without access to a lot of equipment and/or computing resources to now access this part of microbiology.
PJ: Where do you hope to go from here?
MD: I’m interested in exploring more aspects of bioinformatics. Big data analysis in general has so much potential (even if it is occasionally overhyped) and big data in biology just opens up so many avenues for new and amazing discoveries. In terms of the workflow when I was last in the Eisen lab we were talking to the head of the honors department about developing a small honors biology course based on completing the workflow over the course of a quarter. It was going to incorporate basic microbiology, lab techniques and basic bioinformatics, ideally resulting in a publication (genome announcement).
DC: We hope to someday make an undergrad course using some modification of this workflow.
PJ: How did you first hear about PeerJ, and what persuaded you to submit to us?
DC: Well the senior author (Jonathan Eisen) is not only a rabid fan of open-access journals but is an Editor for PeerJ
PJ: Do you have any anecdotes about your overall experience with us? Anything surprising?
DC: Our lab has published several papers with PeerJ and have loved the experience.
PJ: How would you describe your experience of our submission/review process?
DC: A paper this long, with this many figures, lists, and command-line information was bound to have a number of formatting issues. Fortunately, we used Authorea which is a new collaborative online writing platform which allows exporting in LaTeX or Markdown which greatly facilitated the submission process.
PJ: Did you get any comments from your colleagues about your publication with PeerJ?
DC: We often get asked about our PeerJ experience and we always suggest others try it.
PJ: Would you submit again, and would you recommend that your colleagues submit?
DC: For sure.
PJ: Anything else you would like to talk about?
MD: I am a big fan of PeerJ’s preprint option. I like that it allows scientists to get their work out for other people to read and review before it is necessarily perfect or complete.
DC: I think that the optional open-review system used by PeerJ is a great offering. Publishing the reviews and previous versions along with the final is really useful for anyone who wants to see the evolution of a paper. I hope that more journals move towards open-review.
PJ: In conclusion, how would you describe PeerJ in three words?
DC: Open, cheap, easy.