We’re two days away from wrapping up an interesting, and perhaps a little tumultuous year 2022. And what a year it has been.
Following our original Deinococcus radiophilus genome release in 2021 (you can find it here), 2022 saw us releasing two more genomes, both previously unsequenced novel organisms.
First new genome of 2022 under Binomica Labs name was Halococcus dombrowskii, a haloarchaea isolated from Permian salt layer. Our assembly GCF_022870485.1 is the first available genome for the species, revealing a fascinating mechanism of plasmid-encoded rRNA operons that carry drastically divergent ITS sequence from its chromosomal counterpart.
Second genome of 2022 for Binomica Labs was also from our very first attempt at sequencing – a complete chloroplast genome of plant Oxalis stricta from our initial 2017 experiment with ONT Nanopore platform- representing the first available chloroplast genome for the species as well.
This year marked our organization and its members’ first official publications as well.
Sebastian was one of the authors for the paper “Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies“, graciously using the Binomica Labs name as his official affiliation.
Hunter BT, Flury JD, Cocioba SS, Cope-Arguello ML, Helms JM, García KH, Dominguez G, Taniguchi DA, Becket E. Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies. BioTechniques. 2022 Sep;73(4):183-91.”doi: https://doi.org/10.2144/btn-2022-0080
I was able to write and publish a preprint based on the Halococcus dombrowskii sequencing work, titled “Analysis of the complete genome sequence for Halococcus dombrowskii ATCC BAA-364“, again under the Binomica Labs banner. The preprint is currently under peer review and polishing step, and I hope to have a full research paper first thing in 2023.
Lim SW, Maurais EG, Farwell AC, Barber N, Olsen AJ, Shalygina KF, Omeragic M, Fedorov EA, MacLea KS. Analysis of the complete genome sequence for Halococcus dombrowskii ATCC BAA-364T. bioRxiv. 2022 Aug 16.”doi: https://doi.org/10.1101/2022.08.16.504008
Research papers addressing interesting new discoveries from the Oxalis stricta chloroplast genome structure, as well as new findings from Deinococcus radiophilus are currently in drafting stages, and we expect to have preprints out for both projects in 2023.
The growing body of work under our organization’s name had us presenting at our first academic/industry conference – Nanopore Community Meeting 2022.
Poster and slides used for the talk are available from Zenodo, and are citable using the format below.
Lim, Sung won, & Cocioba, Sebastian S. (2022). MinION outcome in Amateur Reserch: three genomes from 2018 to 2022. Zenodo.”Poster, doi: https://doi.org/10.5281/zenodo.7474057
Lim, Sung won, & Cocioba, Sebastian S. (2022, December 6). MinION usage and outcome in Amateur Reserch: three genomes from 2018 to 2022. Zenodo.”Slides, doi: https://doi.org/10.5281/zenodo.7474085
And now – having gone through small parts of traditional academic research and publication pipeline, we’d like to announce an important next step for Binomica Labs.
Binomica labs started its operation in earnest back in 2015 to promote the idea of small thoughtful science among amateur and independent biologists.
From the very beginning, we felt that a more equitable and sincere path forward for amateur and independent researchers would require fully embracing two concepts – public repository of knowledge open to all, and participation in generating the said knowledge without obfuscating who we are – amateurs and independents.
A researcher isolated in a secret lab cannot be a practicing scientist, regardless of the furnishings of the location or their personal cultural status. Practicing science implies communicating our findings and conjectures to others in a useful manner, participating in the wonderful, generations long and humanity wide conversation toward better understanding of our universe. Simply put, we feel there’s no real way to have a scientist without scientific publication and feedback from others who share their interest and passion – amateur or otherwise.
Thus, our focus quickly coalesced to finding ways for an amateur to obtain a distinct voice to participate in the scientific conversation on their own terms – with the caveat that they cannot be beholden to an arbitrary gatekeeping authority, and must remain largely free to pursue their own interests within ethical means.
After some time spent researching different methods and participating in traditional research publication pipelines, I think we’re finally close to proposing our contribution to this question. I’m writing you today with a call for submission for our new publication: Willowlands
Simply put – Willowlands is a citable, archived letters publication for very early stage research communication, with primary goal of communicating immediate notes and recruiting comments from peers.
Our format is modeled after academic society meeting publications from around 1910’s (think of something like Comptes rendus des séances de la Société de biologie) – which also tended to serve as society journals.
We will only publish currently ongoing research and its in-progress findings reported in short and concise manner, with requirements being data leading to any claims made in the submission, relevant online lab note, and list of references as supplementals.
The submitted article and data will be archived and assigned DOIs, while a snapshot of the section of the lab note relevant to the submission will be archived as well, but without a DOI. We won’t be charging fees of any kind, though donations to Binomica Patreons would be very much appreciated.
Our goal is to facilitate rapid sharing and feedback for in-progress research in order to improve its eventual outcome, while giving a degree of protection for the submitter by creating immutable and citable DOI records for their work. For those familiar, think of it as a middle ground between a lab note and a poster.
Willowlands itself will be an ISSN assigned online publication, but we will be publishing biannual collection of articles in physical format as well, with separate associated ISSN.
Here’s what Willowlands is looking for –
A letter describing key findings and possible conjectures or future research directions of an ongoing research – maximum two pages including figures.
There are no specific requirements on the format, tone of the letter or the figures themselves- they could be hand sketched and scanned in if needed. However, please keep in mind that you want others to read it and send you feedback.
There are three mandatory supplements for a letter submission:
- Supporting data for content for the letter
- Online lab note relevant to content of the letter, such as more detailed and/or informal description of methods and musings
- A separate references section for any works used during the research so far
If you have something you want to archive, assign DOI and communicate to the research community at large, please get in touch with me at Sung AT Binomicalabs DOT Org!
Here’s what Willowlands isn’t –
Willowlands is not a journal. We did consider a peer-reviewed journal for amateur scientists, but quickly realized an amateur-targeting journal could be resigning hard work of our potential contributors to second-class citizen science status. Science is science regardless of the participant – amateur and independent scientists with solid research product should be publishing in established preprint servers and other numerous open-access journals and be judged on their own merits along with other scientists.
Willowlands will not practice pre-publication peer-review. Purpose of a research publication of any kind is to communicate new findings to other researchers in order to start a conversation – ideally leading to feedback that will improve the research for the better. Again, pre-publication peer-review type of screening is especially ill-suited for the amateur and independent researchers, in that it creates arbitrary barriers (however well meaning) imposed by a select group of people specifically against researchers who would benefit most from immediate, early stage communication and feedback.
Willowlands is not a company, or any type of profit making venture. It’s meant to serve the needs of the amateur and independent research community by collecting and indexing immutable, citable records of their early stage research. It’s a simple tool created to serve a function. We will not be charging for any part of Willowlands publication, though donations would be appreciated.
Willowlands will not publish full-length research papers, preprint or otherwise. There are already numerous and well maintained preprint servers that we know are (through first hand experience) willing to host research output from amateur and independent researchers. Piling yet another journal-server to the list does not offer any benefit to the researchers.
We’re accepting submissions starting January 1st of 2023, with www.willowlands.org set to go live soon. We are also eagerly looking for any feedback or wishlists from interested amateur and independent researchers, so please feel free to contact me at sung AT binomicalabs DOT org
Modern amateur research is still in its infancy, and academic publication is currently in turmoil with many calls for reform. This is an interesting time to try new things, and we’d love for you join us and see what the shape of new science might look like in coming years.