Archiving blogs, pt. 2: The GigaBlog Top of the Pops

In our previous post we announced we are now archived in Rogue Scholar, a new service that provides full-text search, long-term archiving, DOIs and metadata for science blogs such as ours. In the process of going back through our more than 300 posts over 12-years of blogging we thought we would highlight our favourites. And also use this opportunity to show off our shiny new Rogue Scholar DOIs.

Greetings, pop pickers
As we are big fans of top-of-the-pops style countdown lists here we provide a chronological top-10 list of GigaBlogs, trying to balance our most fun posts with ones demonstrating the variety of topics we’ve covered over the years. These include updates from the journal and team, meeting reports, important Editorial policy issues, to our long-running series of author Q&A’s, as well as guest posts from authors, reviewers and other interesting experts with something relevant to announce and discuss.

10. Start Me Up (2011)

It makes sense to start this list at the beginning, with our first blog post announcing the birth of GigaBlog in July 2011. This blog pre-empting the launch of GigaScience journal by a year. Posted for us by our then publishing team at BioMed Central our launch post did quite a good job of predicting that ‘future postings will provide updates on the progress of the journal up to its formal launch…, introduce the editors and editorial board, report on conferences, and provide news on the many current issues surrounding the handling and use of large-scale data and high-throughput biology’.

Anderson G. GigaScience, Giga-database and now GigaBlog: new resources for the big-data community. GigaBlog. Published online July 6 2011

9. Shake the disease (2011)

The launch of the blog in the summer of 2011 was timely, with our new GigaDB data sharing platform ending up right in the middle of the public health battle against the deadly 2011 E. coli 0104:H4 outbreak that killed over 50 people in Germany. The immediate and novel means of sharing our first CC0 dataset with a DOI via twitter kick-started a global crowdsourcing effort that was dubbed by some to have made E. coli the first “Tweenome”. These efforts were highlighted in books (see BioCode) and on the cover of the influential Royal Society “Science as an open enterprise” report, and it would have been nice then to have been able to cite these background posts with a DOI. The legacy of this project, and other related approaches in scientific crowdsourcing (see OpenAshDieback in 2013), has remained a major topic of interest for GigaBlog ever since.

Edmunds S. Notes from an E. coli “tweenome” – lessons learned from our first data DOI. GigaBlog. Published online August 3 2011

8. Everything Counts (2011-2014)

After the launch of GigaDB and our first datasets with DOIs in 2011 a lot of effort was expended in getting these launch GigaDB datasets cited in any journals publishing work using them. These early experiments in Data Citation pre-empted the publication of the Data Citation Principles in 2014, and threw some light on how publishers such as Nature Publishing Group would handle data DOIs well in some of their journals (Nature Biotech allowing DOIs to be included in their supporting data sections in 2011, and cited in the references of a paper in 2012), and badly in others (Nature Genetics stripping out the DOIs of Panda genomes). These efforts culminated in our Polar Bear genome DOI cited in a Cell cover story, providing an useful examplar for future reference as Cell Press were until then the only major biology publisher to state in a survey that they would see the publication of data with a DOI as potential prior publication. These experiments were our first blog posts to be cited in the scientific literature, and it would have been useful to have had Rogue Scholar DOIs that could have been cited rather than the unstable blog URLs.

Edmunds S. The Latest Weapon in Publishing Data: the Polar Bear. GigaBlog. Published online May 14 2014

7. Kung Fu Fighting (2013)

Author Q&A’s are a long running feature in GigaBlog, and its hard to pick which ones we should have highlighted here (honourable mentions to the author Q&As of the Aldabra giant tortoise genome and iGenomics tricorder-like sequencing on a smartphone tool), but one paper in particular has probably sparked the most continued interest. Although the subject of discussion in the Q&A was more because of the unusual “real-time” peer review process, rather than the paper itself.  One of our most highly cited papers, Assemblathon2 was initially submitted to a preprint server and as the named reviewers blogged and commented on their reviews of the paper, this (then) novel approach provided a huge amount of subsequent feedback and follow-up blogs. Titus Brown’s blogging and comments that Assemblathon2 is a damning indictment of computational biology was highlighted in Nature News, and even spawned a #titusischucknorris social media meme.

Edmunds S. Extended Q&A with Assemblathon2 Author Keith Bradnam. GigaBlog. Published online August 20 2013

6. Policy of Truth (2013)

While less likely to go viral and spawn hashtags, one solid use for a blog is its ability to provide a housekeeping role. Providing a platform for announcements and discussions of policy that are too long for social media posts, but otherwise too easily lost in the depths of the journal website. We’ve made a number of such postings, and these are easily cited and used to link out and expand upon points in our Instructions for Authors. For really important and detailed policy points then publishing an Editorial makes more sense than a blog, but these type of pre-emptive blogposts can be a sounding board and almost act like a preprint version of the article (see out authorship policy change announcement in blog and Editorial form). Probably the most useful and prescient of these announcements has been the one clarifying and making consistent all of our open data and content (including for this blog) sharing policies by putting them under creative commons open licenses. Again, having a DOI for these announcements makes them a more easily citeable statement.

Edmunds S. GigaScience goes CC4. A handy cut out and keep guide to our licenses. GigaBlog. Published online December 20 2013

5. Legend (2015)

Back to the example of author Q&A’s we can’t miss out the Q&A with Chris Chang, author of our highest cited paper for Second Generation PLINK. Near single-handedly updating with 1,000 fold speed increases one of the most highly used tools in statistical genetics, all while working in coffee shops. And using skills  honed working in such diverse areas as maths olympiads, medical technology start-ups and games design. The man is a legend, with a fanbase lurking in certain corners of the internet eager to get this sort of behind-the-scenes insight.

Edmunds S. GWAS Reloaded: extended Q&A with PLINK1.9 author Chris Chang. GlgaBlog. Published online February 26 2015

4. Build Me Up Buttercup (2015)

One of the goals of GigaScience is to help promote more open ways of carrying out science, and after our experience with crowdsourcing the “tweenome” (see above), we got further involved in the concept of “Community Genomics” through publishing the “the Peoples Parrot”. The first crowdfunded genome, the Puerto Rican Parrot is an iconic symbol of its home, and taking a grassroots approach the authors appealed directly to the parrot lovers on the island, mobilizing support and raising the sequencing costs of its genome through art and fashion shows promoting parrot conservation. With the rise of crowdfunding platforms other genome and microbiome projects followed in these footsteps (including our own Bauhinia Genome Project), and we covered and promoted many of these projects in GigaBlog. This culminated in us organising a session at BGI’s annual International Conference on Genomics (ICG) in Shenzhen bringing together many of the people and successful projects that have pioneered this new area of open science. The talks filmed and hosted on our Giga-TV youtube channel.

Edmunds S. Community Genomes on GigaTV. GigaBlog. Published online 10 December 2015.

3. Everybody’s Got Something to Hide Except Me and My Monkey (2016)

Sometimes blogs can be helpful in providing context on why something isn’t happening, rather than just making announcements on things that are happening. One such example is when GigaScience received its first Journal Impact Factor (jIF), and having signed DORA (the Declaration of Research Assessment) we wanted to make clear that we would not be posting the details of this on our website and marketing materials. Explaining our rationale that using such a one dimensional, non-transparent, readily gameable, two-years past indication as a stand-in for “impact”, more often than not, promotes bad scientific practices.

Edmunds S. The lowest common denominator: marketing science with jIF. GigaBlog. Published online July 8 2016

2. Some Great Reward (2017-2020)

Trying to think of new ways to promote more open ways of carrying out science in 2017 and 2018 we decided to go one step further and organise our own competition and prize track at the ICG conference. With the aim to promote submission of new, cutting edge research to the journal, we received and published some great submissions, and the talks are all available to watch in our Giga-TV channel. First place received a $1000 prize, the 2017 winner was particularly memorable, presenting the genome of venomous Solenodon, a “giant rat with Freddy Krueger claws“ that the last survivor of a branch of mammals that appeared at the time of the dinosaurs. With the pandemic changing conference accessibility, in 2020 we decided to change the GigaScience Prize to focus on “Outstanding Data Sharing during the COVID-19 Pandemic”. There could be only one winner for this, Prof Zhang Yongzhen’s outstanding efforts in sharing the first whole genome sequence of the deadly COVID-19 virus on January 5th, 2020. Prof Zhang being able to receive the prize in person at the ICG conference held that year in Wuhan.

Edmunds S. COVID-19 Data-Sharing Hero Wins GigaScience Prize. GigaBlog. Published online November 11 2020

1.More Than Words (2022)

With the launch of our second journal GigaByte recent posts have covered the many novel features the journal and its papers have showcased, these features culminating in our winning last years the ALPSP Innovation in Publishing Award. In another first for the novel GigaByte publication platform developed by River Valley Technologies, our favourite feature highlighted was first time multilingual articles have been simultaneously published in English, Spanish and Ukrainian. This showcasing the ability to proof multiple languages in parallel, and even display these in the PubMed Central version of the paper. These new features keep flowing thick and fast, so keep following GigaBlog (and Rogue Scholar) for further updates, news, Q&A’s and more.

Edmunds S. The first English-Spanish-Ukrainian Publication. How to publish multilingual articles with GigaByte. GigaBlog. Published online Published November 28 2022