And it's goodbye from me

A new era is starting at GigaScience, today being the last day for the Hong Kong team including Nicole Nogoy, Chris Hunter, Peter Li, Mary Ann Tuli, Bastien Molcrette and Ken Cho. Joining them, and as outgoing Editor in Chief, I thought I would give my thoughts and perspectives on the last 15 years at the Open Science publishing coalface.

It wasn't meant to end this way, but I'm still very grateful for the journey. Carrying out my scientific training in the UK and being taught to write scientifically using the passive voice, I have to push myself out of my comfort zone to write in the first person. But as today is my last day at GigaScience, and after giving 14 years and 11 months of my life to this project, excuse me this final indulgence.

The team received notice 30 days ago that due to "strategic planning and operational optimization, the operation of GigaScience will be transferred to the BGI Research  Shenzhen. Regrettably, this adjustment will lead to the disbandment of the GigaScience Hong Kong team". GigaScience and GigaByte will continue, and we have trained the Shenzhen team well and leave them with a strong legacy to build upon. The last two years receiving our highest numbers of submissions and many of the best papers we have ever published, so we leave a fantastic foundation to build from.

Endpoints are good opportunities for reflection, so I thought I would use my last GigaBlog to talk about my personal highlights of the last 15 years. And thank the people who have helped made GigaScience such a success and pleasure to work on.

Firstly I need to thank Laurie Goodman, for giving a wet behind the ears Scottish-Iranian Londoner with 4 years publishing experience under his belt a break in the Wild East. Recruiting me in October 2010 to setup a journal for BGI in Shenzhen as she didn't want to live in China. And also recruiting GigaScience's first Assistant Editor Alexandra Basford so we could keep each other sane in a giant former shoe factory in the industrial badlands of China with only two other foreigners. I'd had PhD and postdoctoral experience in cancer molecular pathology before moving into Open Access publishing with BioMed Central (BMC). Because I'd done a microarray experiment in my PhD and the other BMC Editors were terrified of bioinformatics and genomics I ended up running what was the highest-submission portfolio of journals in the BMC-series, and launching BMC Medical Genomics. Wooed by stories about this mystical utopian genomics company in a weird place called Shenzhen by our Board Member Stephan Beck, I was crazy enough and had exactly the experience needed to launch a journal in the genomics space. Although as two of my ex-BMC colleagues (Rachael Kotarski and Tom Pollard, both now doing amazing things in the US) had started working for this new organisation called DataCite, I suggested we leverage these new fangled things called data DOIs as well as BGI's data expertise to focus on the broader topic of data publishing.

While the launch of DataCite in 2009 had coincided with the first data journals in Earth Sciences nobody had done this in biomedical and biological science, despite these fields becoming massive producers of data (a genomics organisation like BGI being the perfect example of this). Signing up for DataCite membership, and initially working with the BGI database team, our initial focus was on building our own "GigaDB" database to assist with data hosting so there was no excuse for our authors not to be able to share their data. Coming up with a combined journal-and-data-publishing-as-a-service concept and attempting to do something new and different in the staid and conservative world of academic publishing. Adding in open peer review to make the process transparent, we decided to sign up OA pioneers BMC to be our first publishing partner.  

Accidentally inventing the Tweenome
Being in BGI during their highly productive early years in Shenzhen was a blur of having to help entertain visitors like Sydney Brenner, Eric Lander and many Human Genomic Project luminaries that I'd learned about in my undergraduate studies. While getting ready to launch GigaDB in summer 2011 our BGI colleagues came to me to help them draft a press release announcing they had sequenced the genome of the E. coli 0104:H4 pathogen that was ravaging Germany that summer, killing over 50 people and causing mass panic in Europe. While drafting the PR and browsing the twitter feed I'd set up for BGI (as nobody in China knew what it was) I saw that a German group just released a PR claiming they had sequenced the pathogen first, but hadn't shared any data to back that claim up. Immediately letting the BGI group know there was a race on, I asked them if we could use this opportunity to quickly release the data via the new publishing platform we were setting up. Also giving it our first data DOI and explicitly releasing it into the public domain under a CC0 waiver. I warned them that the consequences of data release in this manner were unknown (for example would journals see this as prior publication), but it was the best way to maximise the visibility, utility and reuse potential of their data during a major public health crisis.  BGI very generously consented to this (thank you JJ and Yingrui) and before the data had even finished uploading to NCBI I shared the FTP links to the data via twitter.

Going to bed, the next morning we woke up to find a huge community of microbial genomicists around the world starting to use this data, taking up the challenge to study the organism collaboratively. A github repository was created to provide a home to these analyses and data, and groups around the world started producing their own annotations and assemblies within 24 hours, also sharing them via twitter. A process that was dubbed in blogs and in book chapters to have made E. coli the first "Tweenome". Within a couple of a days from these collaborative efforts a potential ancestral strain was identified, and the many antibiotic resistance genes and pathogenic features were much more clearly understood. Diagnostic PCR primers were designed and shipped for free by BGI, and anti-microbial agents were produced to help bring the outbreak under control. By releasing the data under a CC0 waiver, this allowed truly open-source analysis, and when the paper was eventually published in NEJM the Editors were most interested in this "Open-Source Genomic Analysis" angle (H/T Nick Loman and Mark Pallen for helping kick off the crowdsourcing and refocusing the paper). This example has subsequently been used as an example for future UK and EU science policy, with the Royal Society in the UK using the E. coli crowdsourcing as an example of "the power of intelligently open data", and highlighting the genome on the cover of their influential "Science as an Open Enterprise" report. Which wasn't a bad outcome from playing around on social media, and it set a very high bar for our subsequent datasets.

After our first data DOI BGI generously let us continue to experiment and seed GigaDB with lots of attractive, unpublished genomic datasets. Allowing us to do very early experiments in Data Citation, using these novel data DOIs to see which journals messed this process up (hello 2012 Nature Genetics), which journals said they wouldn't allow data DOIs but contradicted themselves when given a particularly cover-worthy paper (hello 2014 Cell), and which journals could get this to work right at the beginning (hello and well done 2011 Genome Biology). We wrote up these adventures in data citation to educate more widely on best practices, and this lead to getting involved in the development of the Data Citation Principles, the Software Citation Principles and many other guidelines on the topic of Data Citation.

Caught in the Academic Spring
The early 2010's were an extremely exciting time to be in Open Science publishing. Moving to the BGI Hong Kong office in January 2012 we recruited our first Lead Curator Tam Sneddon and our first Database Administrator Jesse (Si Zhe) Xiao, allowing us to add data curation into the service we provided. After a year Tam handed over the role to Chris Hunter from EBI who built and brilliantly developed and ran the GigaDB platform and growing curation team. Alexandra left and Nicole Nogoy joined the team to help with Commissioning and then the managing of the journal, having launched and been Managing Editor of Genome Medicine. Peter Li joined to lead the IT development, bringing a lot of experience in the reproducibility and computational workflow space and leading lots of the reproducibility experiments we worked on. This core team has remained in place to the present day (with the addition of Mary Ann Tulli and Bastien Molcrette in the curation team and Rija Ménagé and Ken Cho in the development team), and we all leave today proud of these accomplishments. Special mention should also go to former team members Hans Zauner (our most productive and proficient Editor who had to leave a few months ago), Rob Davidson and Chris Armit (our two Data Scientists), and Nafisa Qazi who was running the editorial office.

The year 2012 has been labelled as an "academic spring" as it seemed a major turning point shaking up the centuries old, stale and untransparent system of scientific discourse. With boycotts of the closed-access old guard gathering momentum, influential policy papers signalling government moves towards open access, and the launch of a new generation of journals that were moving beyond that first important step of making published research open access to begin embracing the wider principles of Open Science. These included F1000 Research, eLife, and PeerJ, and, on the 12th July 2012, GigaScience, launched at the ISMB meeting in Long Beach. Every subsequent year we have celebrated with increasingly big birthday parties at the conference, and it feels weird we will not catch up with our many friends at next one in 2026. We realised our ideas about data publishing were timely when I was invited into the offices of one of the major publishers to talk about the subject, and the following week they emailed our entire Editorial Board to try to recruit them for a remarkably similar project they suddenly decided to launch. Amusingly they invited our EBM Wang Jun (who was our main backer at BGI) to one of their recruitment calls and he got me to attend in his place. When the call started and I surprised the publishers I'd just talked to the previous week they were unable to speak for several minutes through shock. Imitation being the most sincere form of flattery, we are proud to see how most of the major publishers now have data journals in their portfolio.

Working with the ISA-Tab, Nanopub, and Research Object communities we collaborated and published many reproducibility case studies, and from this experience I ended up getting involved in the reproducibility research space, being one of the authors on the highly influential FAIR Principles paper, helped in the drafting of the COPE-FORCE11 Data Ethics guidelines, collaborating with ELIXIR on AI standards, and ended up teaching the first Data Management and Curation course at Hong Kong University to MLIM students.

The Establishment Years
Once the journal launched we had to fight hard to get submissions in, which is especially challenging before you are established and indexed. Through the support of our incredible Editorial Board we slowly got many fantastic papers in and the journal built momentum and became a success. Indexing is a huge challenge for journals, and whilst we eventually achieved very high metrics in these we stuck to our DORA signatory guns and refused to market or list them anywhere on our website. Being lean and nimble, and wearing our Open Science principles on our sleeves, we experimented and collaborated with many of the new Open Science platforms that were launching. Many of these projects have now fallen by the wayside, but we were one of the first journals to work with Publons, and second journal to work with Protocols.io (the first with deep integration). These collaborations have continued to the present day, such as recent tie-ins with Cassyni and Sciety, and I hope this history of experimentation will continue. Many of our authors, collaborators and Ed Board Members became great friends, allowing us to visit their labs across the world, and also meet many of the species we published papers on. A highpoint visiting the El Yunque forest breeding facility to see the endangered Puerto Rican parrots we published the genome of (thanks Taras!). We also launched our own awards, the most important acknowledging and presenting COVID-19 hero Zhang Yongzhen with a GigaScience prize for sharing the first SARS-CoV2 sequence.

Cyber Centipedes, Emblematic Genomes and More
Despite having a human genetics background, having free reign to get involved in interesting research experiments meant I managed to get involved in a wide range of research areas I never would have expected. From collaborating with Pensoft to publish the most data-rich species description of a blind cave centipede, to launching our own genome project of Hong Kong's floral emblem.  Being based in Hong Kong, and inspired by the first community funded genome project of the Puerto Rican parrot, the historical and cultural interest of the Hong Kong Bauhinia flower led to our involvement in a community-crowdfunded genome project to try to answer some of the questions on the species' origin and unclear parentage. Reaching out directly to the Hong public and launching a crowdfunding campaign in 2015 raised enough money to start the community Bauhinia Genome project. This lead me to leave my comfort zone with school visits, teaching molecular biology to 7 year olds, CNN interviews, and even a TEDx talk.

What was most satisfying was the "mission accomplished" completion of the project this year, with a publication in GigaScience definitively solving the parentage with a complete, gapless sequence of the Bauhinia genome, spanning from one end of a chromosome to the other. This Citizen Science experience also leading me to help co-found and register a Citizen Science NGO in Hong Kong called CitizenScience.Asia.

The Next Phase of Open Science Publishing
In 2017 we moved from publishing with BMC to Oxford University Press and the journal continued to flourish, winning the 2018 PROSE Award for Innovation in Publishing. We were hungry to do more though, feeling our full potential to carry out Open Science was being frustrated with the legacy publishing infrastructure, incorporating print-based production processes and decades old codebases. No longer being fit for purpose in this non-print, online, more data-centric digital age. This lead us to team up with River Valley Technologies in 2020 to launch our sister journal GigaByte: an Open Science journal that allows rapid publication using custom-built, XML-first and end-to-end publishing technology. Also allowing us to become a press, and handle things like indexing and metadata debugging ourselves. This shake-up of our tech platform enabled much cheaper and quicker publishing, with accepted manuscripts converted to online and PDF-ready articles within a day. Being offered the opportunity to publish and proof papers for 1/5 the cost and 1/30^th of the time you'd have to be completely stupid to turn that down. Working with Kaveh and Maryam Bazargan from River Valley Technologies has been a dream, and the last 5 years have been my most productive and enjoyable time at GigaScience. Allowing us to tackle final barriers in accessibility and Open Science we've always dreamed of like interactive papers, multilingual publishing, FAIR peer review, and making papers much more accessible to humans and machines.

eLife have also been fantastically collaborative in this space, and I would like to thank them for the technical support and help they've provided over the years. Helping us to be the second journal to publish Executable Research Articles (H/T also Stencila), and building the Sciety platform that has allowed GigaByte to join the 'Publish, Review, Curate' revolution through linking reviews and highlighted editor's assessments to their mandated linked preprints.

This month we are finalising the final round of papers from a WHO-sponsored collaboration with GBIF and TDR publishing human vector born disease data of extreme importance to public health. This has diversified and democratised the submission base of GigaByte across Africa and Latin America (including submissions from Congo, Cuba, and Cabo Verde), also leveraging our multi-lingual functions to aid local public health field workers only able to read French, Spanish and Portuguese. Ultimately mobilizing new data on over one million vector specimens into the GBIF database. It has been nice to end on such a rewarding and enjoyable collaboration with GBIF and TDR that has taken me to other unexpected destinations, such as carrying out data publishing training in Borneo. It's touching these efforts have also not gone unrecognized by others, with GigaScience Press and the platforms we've used from River Valley winning many prizes such as the 2022 ALPSP Innovation in Publishing Award. This summer winning the 2025 Crossref Excellence in Metadata Award, having been selected from nearly 150,000 journals and 22,000 publishers using Crossref infrastructure for having the highest metadata completeness in the small publishers category.

Good things unfortunately must come to an end, but it's always good to leave on a high. It's been an absolute privilege to setup and run GigaScience for the last 15 years, and I'd like to wish my successors the very best when they carry on the Open Science mission. None of this would have been possible without my amazing GigaScience team mates, and if anybody is looking to employ the greatest team of Editors, Curators and Developers in the business please get in touch. This job has taken me places I never imagined when as a naive thirty-something I headed Eastward in 2010 with all my belongings in a single rucksack. Apologies to the many people I've forgotten to thank here but this piece is already much too long and you'll have to wait for the extended version in my upcoming memoirs. Thank you to everyone who was a part of this journey, and hope to see you on the next one.