Urban fruits, 3D printed frog legs and gapless genomes: 2024 was wild

December 14, 2024

It’s December again, and our teams of editors and curators are busy with the many submissions we receive at this time of year. Scientists are eager to clear their desks before a well-earned break and it’s time for the annual GigaBlog ritual: Looking back at the year that was at GigaScience Press.

Citizen Science 

2024 was wild, and one recurring theme of 2024 was “Citizen Science.” We’ve always been strong supporters of public involvement in science projects, starting with our own community genome project on the Bauhinia Genome. Nowadays, our journal GigaByte provides a perfect home for sharing data from citizen science projects. Often, raw data collected by citizen scientists doesn’t immediately translate into a full research story, but as an “all-sound-science”-journal, GigaByte enables the timely publication of the underlying datasets, making the data citable and giving the volunteer contributors credit for their efforts.

Let’s look at two of them:

Pomar Urbano: This project, led by Filipi Miranda Soares and colleagues, explored urban fruit bearing plants by engaging Brazilian city dwellers to document their sightings on the popular iNaturalist platform. The project also has a cultural dimension, inspiring art and cooking recipes based on the sampled fruit species. For us this was also an opportunity to again showcase GigaByte‘s multilingual articles, which now also allows the local Brazilian citizen scientists to read the original publication in an author-provided Portuguese version.

Hong Kong Jellyfish Project: A new dataset released in GigaByte documented jellyfish sightings collected by citizen scientists from 2021 to 2023. In a GigaBlog post, the authors explained how “people’s curiosity about jellyfish drives the entire project through their photographs and reports,” which has led to the discovery of several new jellyfish species in Hong Kong waters.

 

Cooperation with GBIF and TDR/WHO

Also in the field of biodiversity, our curation team intensified our cooperation with GBIF (Global Biodiversity Information Facility), a platform which now hosts close to 3 billion records of occurrences. We’re proud to contribute to this effort, particularly also through our “Vectors of Human Diseases” series. So far, this series has mobilized over 700,000 occurrence records and 890,000 specimens from more than 70 countries. The “Special Programme for Research and Training in Tropical Diseases” (TDR, hosted at the World Health Organization), GigaScience Press, and GBIF have just announced a third call for authors to submit data release papers for this series. Please consider submitting your work, and watch this space for news on the on-going series.

Recognizing Outstanding Contributions

Also related to our “Vectors for diseases” series, GigaByte author Victoire Nsabatien won the Ben Barres Spotlight Award for Publicly Reviewed Preprints. This prize, created by eLife, supports underrepresented groups in biology and medicine. Victoire’s two preprints  – publicly reviewed and published by GigaByte (here and here) – share data on Anopheles mosquitoes (malaria) and arbovirus-carrying Aedes mosquitoes in Kinshasa. He remarked, “Malaria is a major public health burden in my country, and this grant will greatly enhance my research into new mosquito control tools.”  You can watch Victoire celebrating his award in the YouTube video below:

Congratulations to Victoire again!

Advancing Spatial Omics

Spatial omics – exploring molecular data like transcriptomes and proteomes in their positional context within cells – emerged as an exciting new area over the last couple of years. To highlight this field, we launched a cross-journal series in GigaByte and GigaScience. To be useful for the community, new tools in this area must be open-source, user-friendly, and capable of handling massive data volumes – aligning perfectly with our long-standing emphasis on open data and code availability.  A rapidly growing new area of research, our Editors attended the VIB Spatial Omics and Human Cell Atlas Asia 2024 meetings get a taste of the excitement in this new field. Watch a preview of the series:

Genomics and a new GigaScience series 

Large-scale genomic resources remain central to our mission, and there’s no end in sight  technological and bioinformatic improvements to collect and analyses genomic data – and in step with this development, the quality standards of GigaScience are also going up. This year, GigaScience emphasized (near) complete, virtually gapless genomes (“telomere-to-telomere”) by launching a new article series  dedicated to “T2T” genomes.

DOME-ML

Another challenging, fast-developing area is machine learning and AI research in the life sciences. We are aware of the difficulties to ensure transparency and reproducibility of machine learning work, and we therefore are experimenting with DOME-ML annotations, a community-wide set of guidelines and checklists for supervised machine learning in biology.  These annotations provide details on the analysis procedures and data structures, and can be referenced in published journal articles. You can see more in the ELIXIR webinar on Machine Learning Best Practices & Recommendations that we presented our work in.

Conference Highlights 

As usual, also this last year our editorial and data curation colleagues attended numerous conferences and seminars to stay connected with authors, reviewers, and board members. A regular highlight on the conference calendar is ISMB, the birthplace of GigaScience. As our Editor-in-Chief noted in GigaBlog, “The heart of the scientific program are the many parallel Communities of Special Interest (COSI) meetings, and of these BOSC – The Bioinformatics Open Source Conference, is a particular fave of ours and we again were silver sponsors”.

Another notable conference we attended was the 8th World Congress on Research Integrity (WCRI), where discussions also centered on double-edged sword that is the use of AI in Scientific Publishing and its effect on research integrity. Reflecting this, we’ve also updated our author guidelines for the proper use of AI tools for the preparation of articles. We now ask authors to declare any such use on submission, and to be fully transparent about the exact procedures and prompts that were used.

Celebrating the FAIR Principles

Another concept dear to our hearts and minds are the FAIR principles (Findability, Accessibility, Interoperability, and Reuse). Marking the 10th anniversary of the FAIR principles, we hosted a GigaBlog Q&A with authors from the Netherlands X-omics Initiative. They discussed applying FAIR principles to research software and workflows, highlighting tools like RO-Crate and WorkflowHub.eu, both technologies showcased and promoted in GigaScience.

More highlights from GigaScience and GigaByte

To round things up, here are just a few other research highlights from 2024:

Cannabis Research and Virtual Seminars: Cannabis sativa featured prominently in GigaByte in 2024, with two articles (here and here) reporting new resources for research on this plant. These papers also showcased interactive features like dynamic figures and protocols. Additionally, in partnership with Cassyni, we hosted a webinar with our author Locedi Mansueto. Cassyni simplifies academic seminar organization and makes seminars citable by assigning DOIs.
Re-watch the webinar here.

DNA Day Genome Releases: As part of a “moonshot for biology”,  the Hong Kong Biodiversity Genomics Consortium published genomes of emblematic species from Hong Kong, including the enigmatic golden birdwing butterfly, blackfaced spoonbill, and long-spined sea urchin.

 

Oriental Stork Genome: A high-quality genome of this endangered species and population genomic data revealed surprisingly strong genetic health.

3D Plant Model: Researchers created a 3D model of a sugar beet using laser scanning and 3D printing, available for download on Thingiverse. The model will serve as a reference for advanced plant phenotyping, but it may also look nice under your Christmas tree – the models are open and free to download!

Clawed Frog Atlas: Jakub Harnos used micro-CT imaging to create a detailed developmental atlas of the important model species Xenopus laevis, also available as 3D printing files.

And finally some necessary money-related news looking forward: To continue our mission, we will slightly adjust the article processing charge (APC) for GigaByte, effective January 1, 2025. The good news is that, being self-published by our own GigaScience Press, publishing in GigaByte remains very affordable: The new APC will be $535 USD. Please note:  Submissions received before the end of December will still benefit from the current rate!

We hope this rundown convinces you that 2024 was wild, and with that we wrap up the looking back and start looking forward to another year of the Open Science journey at GigaScience Press.

Thank you to all our authors, reviewers and editorial board members for your continued support and all the best wishes for 2025!

 

 

References:

Filipi Miranda Soares, Luís Ferreira Pires, Maria Carolina Garcia, Lidio Coradin, Natalia Pirani Ghilardi-Lopes, Rubens Rangel Silva et al.: Citizen science data on urban forageable plants: a case study in Brazil, Gigabyte, 2024  https://doi.org/10.46471/gigabyte.107

Yang S; Liu Y; Zhao X; Chen J; Li H; Liang H; Fan J; Zhou M; Wang S; Zhang X; Shi M; Han L; Yu M; Lu Y; Liu B; Xu Y; Lan T; Hou Z Genomic exploration of the endangered oriental stork, Ciconia boyciana, shed lights on migration adaptation and future conservation” GigaScience. 2024 https://doi.org/10.1093/gigascience/giae081

Braich S et al., A new and improved genome sequence of Cannabis sativa, Gigabyte, 2020 https://doi.org/10.46471/gigabyte.10

Mansueto L et al., CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa, GigaByte, 2024 https://doi.org/10.46471/gigabyte.135

Mansueto L et al., Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research,GigaByte,2024 https://doi.org/10.46471/gigabyte.137

Terenzini J et al. Jellyfish in Hong Kong: a citizen science dataset. GigaByte. 2024. https://doi.org/10.46471/gigabyte.125

Južnič-Zonta Ž et al. Mosquito alert: leveraging citizen science to create a GBIF mosquito occurrence dataset. GigaByte. 2022 May 30;2022:gigabyte54. https://doi.org/10.46471/gigabyte.54

Shimabukuro P et al. Bridging Biodiversity and Health: The Global Biodiversity Information Facility’s initiative on open data on vectors of human diseases. GigaByte. 2024 Apr 11;2024:gigabyte117. https://doi.org/10.46471/gigabyte.117

Bömer J; Esser F; Marks EA; Rosu RA; Behnke S; Klingbeil L; Kuhlmann H; Stachniss C; Mahlein AK; Paulus S. A 3D printed plant model for accurate and reliable 3D plant phenotyping. GigaScience 2024.  https://doi.org/10.1093/gigascience/giae035

Laznovsky J; Kavkova M; Reis A; Robovska-Havelkova P; Maia LA; Krivanek J; Zikmund T; Kaiser J; Buchtova M; Harnos J (2024). Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging. GigaScience giae037 https://doi.org/10.1093/gigascience/giae037