Data driven blogging from the GigaScience editors

Once again the
 
 GigaScience Press
 
 team has gathered at the yearly ISMB (Intelligent Systems for Molecular Biology) meeting to find out about the state of the art of computational biology, as well as celebrate our birthday

. Hosted this year in the beautiful city of Lyon, and this year collocated with ISMB’s European sibling ECCB, it’s now been 11 years since

 GigaScience

journals launch at ISMB 2012 in Long

Going Large (Language Models) at ISMB2023

GigaScience Press is pleased to announce

 GigaByte

journal is now indexed in PubMed and PubMed Central (PMC) databases run by the US National Library of Medicine. PubMed being a searchable database of biomedical citations and abstracts, and PMC being a free digital archive of the full-text of Open Access articles.

GigaByte now indexed in PubMed and PubMed Central (PMC)

Field notes of early-20th century entomologist Johanna Bonne-Wepster have been turned into crucial new public health data through digitization, filling data gaps and continuing her legacy in forming Dutch tropical medicine research.

Natural history collections contain huge amounts of information on diversity, distribution and ecology of a variety of species; however, much of this valuable information is effectively lost

Converting the Field Records of Early-20th Century Public Health Pioneer to Data

Morpho butterflies are emblematic species of the Amazonian rainforest known for their metallic shades of blue and green. Despite their conspicuous looks and fascinating biology, large-scale genome sequencing efforts have somewhat neglected them – until now.

Amazonian Morpho butterflies: three genomes with a twist

*Series Editors: Jue Ruan (Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences) and Fritz J Sedlazeck (Human Genome Sequencing Center, Baylor College of Medicine) *    While the first draft of the Human Genome was announced back in June 2000 and declared complete in April 2003, it took 20 years for the publication of the first complete, gapless sequence of a human genome in March 2022.

Announcing the GigaScience T2T Series: Closing the Gaps from Telomere-to-Telomere

The Center for Antibody Technologies headed by Professor Andreas Laustsen-Kiel (Technical University of Denmark) used high-throughput methods to systematically analyze the venoms of the 26 most deadly snakes in sub-Saharan Africa. The results are now published in
 
 Gigascience
 
 .

Each year, around 500,000 people in sub-Saharan Africa suffer from snake bites, causing an estimated 7,000 to 20,000 deaths.

What’s your poison? Venom composition of 26 deadly snakes

In another first for the novel GigaByte publication platform developed by River Valley Technologies, this week marks the first time multilingual articles have been simultaneously published in English, Spanish and Ukrainian

Open Science has gained momentum over the past decade, and embracing that, GigaScience Press has aimed at pushing scientific publishing beyond just making articles open access toward making the entire process open

The first English-Spanish-Ukrainian Publication. How to publish multilingual articles with GigaByte

Diversity, Ancestry, and the Tenacious Concept of Race

The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a human rights framework.

Diversity, Ancestry, and the Tenacious Concept of Race: GigaScience at GA4GH

Meetings In the Time of Coronavirus: Conferences go Viral

June-July usually marks peak conference season when the

 GigaScience

team is on the road, but with the COVID-19 pandemic shutting down travel and public gatherings it has been a strangely static summer.

Birthdays and Online Conferences go Viral. ISMB2020 &amp; BCC2020 in the time of COVID-19

This is the last blog post of 2019 and it is time again to look back at some of the amazing research published in

 GigaScience

over the past year. Besides handling manuscripts, reviews and data, the editors and curators also attended conferences near and far, they contributed to policy discussions and prepared the launch of a new journal, GigaByte. More about all these activities below.

Big data, big conferences, big plans: 2019 in review

The 21st meeting of the Genomics Standards Consortium (GSC21) took place last week in Vienna at one of the oldest universities in the world – the University of Vienna – from May 20th-23rd.  We’ve been long time supporters and participants of the Genomics Standards Consortium meetings going back to 2012’s GSC13 in Shenzhen, and have also published a special series of GSC “Best Practice in Genomics Research” papers.

Genomics Standards on the Danube. GigaScience at GSC21 in Vienna

Dr Yang Tuo collecting in Ruili, CC-BY

 Our Biggest Dataset Yet. Oh, Ruili?

* A new Data Note*

 provides genome sequencing data that effectively triples the number of plant species with available genome data.

Planetary Genomes. Creating a Digital Botanical Garden.

It’s DNA day, celebrating two historic milestones: The publication of the structure of DNA in 1953, and the completion of the human genome project in 2003.

DNA day 2020: The genomes of Dominette and Esperanza

As mentioned in our Happy New Year blog post, one of the highlights in 2017 was a second

 GigaScience

hackathon workshop which we held in November last year in our Hong Kong BGI office.

CUDDELing up to metabolomics in Hong Kong

*As a journal focussed on open science we are big promoters of research parasites (and research on parasites), and try to feeds them with open data and tools. It is therefore appropriate this is the second year GigaScience has supported and sponsored the Research Parasite awards.

Research Parasites Wanted. Q&amp;A with Casey Greene &amp; Brian Byrd

While the Guardians of the Galaxy film franchise has just released its second film, the GigaScience Galaxy series has just published its 10
 
 th
 
 , 11
 
 th
 
 and 12
 
 th
 
 papers.

Guardians of the Galaxy Workflow

Gigascience this week published a high quality genome of the apple, the “golden delicious” variety, to be precise. Although a version of the

 Malus domestica

genome has already been available, Xuewei Li

 et al

.’s

 de novo

assembly significantly improves on that previous ressource, using a healthy injection of long reads from third generation, “single-molecule” sequencing technology.

Apple 2.0. A delicious genome.

**

 GigaScience

has Tapeworms and Scabies! And Reproducible Research. **While there has been recent controversy (and hashtags in response) from some of the more conservative sections of the medical community calling those who use or build on previous data “research parasites”, as data publishers we strongly disagree with this.

Reproducible Research Resources for Research(ing) Parasites

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.

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

**All Cats (Microbiomes) are Grey? **Regular readers will have seen our interest in “community genome” projects, supported by crowdfunding and alternative means (fashion shows in case of the “peoples parrot”), and we’ve been pleased to see the Azolla fern and Cactus genome projects that we published guest GigaBlog postings from both achieve their funding targets.

Community Microbiomes: Chatting Cat Scat with Kittybiome’s Holly Ganz

Bats are mammals like no other – airborne, mostly nocturnal, often hidden away in caves, capable of using echolocation for in-flight navigation. No two bat species are alike, however. Their diversity of morphology, life styles and feeding habits is staggering. New bat genomics research published today in
 
 GigaScience
 
 explores

Nectar, fruits, and blood. A genomic view on the feeding habits of bats.

GigaScience Press

Birthdays,

 BOSC, Beatles and Bioinformatics with a Merseybeat

Conference season is upon us, and the

 GigaScience

team have just returned from a magical mystery tour to Liverpool. Regular readers will know

 GigaScience

launched at the ISMB (International Conference on Intelligent Systems for Molecular Biology) in 2012, and every year we attend and celebrate our birthday at the meeting.

Help! I need curation. ISMB meets the Beatles.

The worm that turned (epigenetics)

GigaDB,

 GigaScience

’s associated database, has had a number of new datasets just added, many for data types previously not hosted. Today marks the publication of new research in our sister BMC journal

 Genome Biology

shaking up the epigenetics field by shattering the assumption that DNA methylation is absent in nematodes.

First methylated nematode genome and other new datasets in GigaDB

GigaScience Press is pleased to announce GigaByte journal has been shortlisted as a finalist in the 2022 ALPSP Awards for Innovation in Publishing.

GigaByte a finalist for the ALPSP Awards for Innovation in Publishing 2022

In the midst of a busy few weeks of European meetings,

 GigaScience

is currently in Basel, where ECCB 2012 (the European Conference of Computational Biology) has just ended. Usually overshadowed by its bigger sibling: the ISMB (particularly when both meetings are in Europe and co-hosted), this was the first time that I had attended the stand-alone meeting and it more than justified being a stand-alone event.

ECCB 2012: Bioinformatics with a Swiss Flavour

Not only epidemics themselves come in waves, also research into emerging infectious diseases has ups and downs, a

 Gigascience

paper published today reports. The authors at

 Ben-Gurion University of the Negev

analysed more than 35 million papers and explored research (scientometric trends) related to nine different infectious diseases.

Coronavirus research needs to be a marathon, not a sprint

Photograph by Giang-Son Nguyen (SINTEF)  The Norwegian city of Trondheim seemed the place to be this June – with hotels in high demand

FUNC in the Fjords: Functional Metagenomics 2019 in Trondheim

The 12th International

 Biocuration

Conference was held in Cambridge, UK from April 7-10th 2019. As regular participants of the meeting you can read our write-ups of the meeting going back to 2012. This is a forum for biocurators and developers to discuss their work and to promote collaboration.

Curators Capture Cambridge. Biocuration 2019

The diffraction limit of a microscope hinders the ability to see single molecules as the optics do not allow the researcher to distinguish between two fluorescently labelled molecules that are less than 200nm apart. As a means of overcoming this barrier,

 super-resolution microscopy

utilises various tricks to go beyond the diffraction limit and image sub-cellular nanostructure in cells and tissues.

GigaScience at ESRIC Super-Resolution Clinic

New genomic data from five birds-of-paradise reveal genes that are shaped by selection and help explain the origin of their spectacular plumage.

Birds-of-paradise, with their elaborate and colorful feathers and their complex courtship displays, are a school-book example of sexual selection.

Genomes from paradise

A correspondence we have contributed to has just been published in the

 BMC Research Notes

“Data standardization, sharing and publication series” on the adventures in data-citation and data-release practices surrounding the Sorghum genome that is available in our GigaDB database and that was published last year in

 Genome Biology

. We use Sorghum as an example to highlight the issues surrounding data release and use strong words,

Adventures in Data Citation: sorghum as a standard for data release

Monkey Microbiome Business
 


 Research just out in GigaScience introduces the macaque monkey to the microbial gene catalogue club, joining other important model organisms including the (also recently published in GigaScience) Rat, Mouse, Pig and Cow.

Of Mice and Men (and Monkey) Microbiomes.

**Today,

 GigaScience

published a report on the genome of a truly unique species: the giant squid

 Architeuthis dux

. The elusive animal is the main character in ancient stories about sea monsters and it is known as “the kraken” in many legends. For a long time its mere existence was questionable, until, in 1857, the Danish naturalist Japetus Steenstrup made the link between those legends and the enormous cephalopod.

The genome of an elusive giant

Forget Movember – with all the cool open brain science activities happening at

 GigaScience

and the upcoming Society for Neuroscience (SfN) 2016 meeting in San Diego (November 12-16), we are naming it Neuro-November!

Remember Remember, It’s Neuro-November!

**Pregnant Starfish go Big Data. **Brittle stars are a class of organisms that are closely related to starfish. While most members of this group reproduce externally, there are some species that develop their young internally and ‘give birth’ to live young.

Brooding Brittle Star Babies. Q&amp;A with Jannes Landschoff

An anaerobic digester at BGI.

 Biofuels Research Shows the Utility of Container Publishing

One of the most promising areas in biofuel development is biogas, which has huge potential as a renewable and clean source of energy.

Fermenting a Reproducible Research Revolution

Lead by researchers at the University of Oxford, a group of more than 30 scientific organizations around the globe, have worked to produce a common standard that will make possible the consistent description of enormous and radically different databases compiled in fields ranging from genetics to stem cell science, to environmental studies.

GigaScience Journal Part of Global Data-Sharing Effort: New Standards Allow Disparate Data Sets to Integrate

Take a ride down chromosome highways with a novel web-based platform that allows sharing of private genetic data while maintaining privacy through a colourful dynamic visualization tool.

The Human Genome Project offered new hope that discovering the genetic determinants which mediate chronic disease susceptibility would lead to new avenues for drug development and targeted therapy, yet over decade later the is disappointment

Secure Genetic Data Moves into the Fast Lane of Discovery

New research and data published in
 
 GigaScience
 
 and
 
 PLOS ONE
 
 provides complete open access to detailed 3D images of earthworms

To quote the American cartoonist Gary Larson: all things play a role in nature, even the lowly worm—but perhaps never in such a visually stunning way as that presented in two papers published last week in

 GigaScience

and

 PLOS ONE

. The work and data presented here

The Early Earthworm Catches on to Full Data Release

3000 Rice Genome Sequences Made Publicly Available on World Hunger Day

Yesterday marked the publication in

 GigaScience

of the first data from the 3,000 Rice Genomes Project, a collaboration between the Chinese Academy of Agricultural Sciences (CAAS), the International Rice Research Institute (IRRI), and BGI; as well as a commentary from the Directors of these institutes outlining the goals of this ambitious project.

Publish Data: Fight World Hunger

A guest post from our summer data science intern Raniere Silva from Hong Kong City Uiniversity on his work on Frictionless Data and Interactive Visualisation The post From Frictionless Data to Interactive Visualisation appeared first on GigaBlog.

A guest post from our summer data science intern Raniere Silva. Raniere is a PhD Candidate at City University of Hong Kong and interested in reproducible research.

During July and August 2022, I was a summer intern at GigaScience Press investigating how

 GigaScience

and

 GigaByte

journals could use Frictionless Data to help researchers make data driven discovery faster.

From Frictionless Data to Interactive Visualisation

The h-index is a metric that was invented to summarise the publication output and impact of researchers. In a new

 GigaScience

article, authors from the University of New South Wales (Australia) adopt the controversial metric for a completely different purpose: to explore systematic differences in research interest (

 taxonomic bias

), using mammals as an example.

Not all species are equal: Using the h-index to quantify taxonomic bias (author Q&amp;A)

With the summers conference season over,

 GigaScience

are still keeping mobile, and this week Laurie is taking in “Beyond the Genome”, our BioMed Central stablemates

 Genome Biology

and

 Genome Medicine

meeting in Washington

Beyond the Genome: taking GigaScience into the Clouds

After 2 cancellations due to the pandemic, the Plant and Animal Genomes conference returned to its in-person format in January with its 30th edition. A number of the talks focused on the effects of climate change either on biodiversity or crop development. It seems only fitting then, that the weather provided a suitable demonstration with California experiencing one of the longest periods of sustained rainfall in many years.

Plant and Animal Genomes (PAG) Comes Storming Back!

The Washington DC Walter E. Washington Convention Center was the venue for the recent Cell Bio 2022 Meeting that took place on 3-7 December 2022.  Cell Bio 2022, the joint meeting of the American Society for Cell Biology (ASCB) and European Molecular Biology Organization (EMBO), is the largest yearly gathering for the Cell Biology community.

Cell Biology in Washington DC: GigaScience at ASCB/EMBO Cell Bio 2022

Regular readers will have heard the news that TDR, the Special Programme for Research and Training in Tropical Diseases, GBIF and GigaScience Press have announced a third call for authors to submit Data Release papers on vectors of human disease for inclusion in a thematic series published in

 GigaByte

Journal.

Extended call and webinar for GigaByte’s vectors of human disease series

Human Cell Atlas Asia 2024: A Spatial Omics Odyssey
 

The GigaScience Press Cross Journal (

 GigaScience

and

 GigaByte

) series on “Spatial Omics: Methods and Application” continues to receive and publish submissions. Promoting and providing a home for cutting edge research in new field taking large-scale data-rich biological and biomedical research into new dimensions.

Continuing Journeys in Space: Human Cell Atlas Asia and Our Spatial Omics Series

MicroCT imaging is an exceptional tool for 3D visualisation. A new Data Note published in GigaScience reports on a unique, high-quality series of MicroCT images that covers the lifespan of an amphibian from tadpole to froglet to mature adult frog.

MicroCT Imaging of Metamorphosis in the African Clawed Toad

As we enter a new month, we have to announce some personnel changes to

 GigaScience

, as we welcome Nicole Nogoy to the team as a Commissioning Editor from her base in New Zealand. It is with sadness we also have to say goodbye to our Assistant Editor Alexandra Basford, who has just left us to take up new challenges in Japan.

Hello, Goodbye: new changes to the GigaScience team

*A multitude of papers on novel methods for Spatial Omics are published in a cross-journal series launching today in GigaScience and GigaByte Journals. *  Spatial Omics is a new field that is taking large-scale data-rich biological and biomedical research into new dimensions. Which is having a significant impact on the fundamental fields of biology and biomedicine.

Taking Spatial Omics into the Next Dimension

Researchers have completed and released a chromosome-scale genome sequence of the Aldabra giant tortoise providing a much needed genetic resource for rescue efforts

. The Aldabra giant tortoise is one of only two giant tortoise species left in the world, and it is currently on the threatened list. Conservation efforts are underway, but more and better tools to improve the chance of long-term success are greatly needed.

The Genome of a Gentle Giant

After last months website launch, and work progressing on our associated

 GigaScience

database (including the addition of further datasets, such as the recently published Chinese Hamster Ovary cell-line genome) our next priority is the more traditional job of an editor: papers, papers papers.

Papers, papers, papers

I just got back from attending the IBRO World Congress in Florence and the CNS*2011 meeting in Stockholm.  All I can say is: lucky me.  Okay, clearly that’s not all I can say.  They were both wonderful meetings and it was great to see so much good neuroscience going on.  IBRO had quite the turnout with 4,200 people attending this year.

IBRO and CNS*2011, or happy neuroscience days

High-resolution images of the head of the blind salamander Proteus anguinus reveal adaptations for life in the dark.

The proteus, also called the “olm”, is a strange beast – locals in the 1600s actually believed it was a baby dragon. In fact a blind salamander, it is snake-like in appearance, colorless, and can live up to 100 years.

3D imaging of the proteus, a  mysterious cave-dwelling salamander

This year is the “Year of Neuroscience” in Spain. As a part of this educational movement and celebration of the most recent flowering of Spanish neuroscience, Barcelona hosted the FENS Forum of Neuroscience. Drawing what the Chair of the Host Committee, Mara Dierssen, described as the largest number of attendees ever, the 8

 th

FENS meeting fostered cross-disciplinary discussion and showcased some of the field’s best science.

The FENS Forum: A Good Time to Be in Spain

As part of the FAIRsharing Community Network (see previous blog) and joint Force11 and Research Data Alliance (RDA) FAIRsharing Working Group we have been involved in efforts to develop a shared, cross-publisher list of recommended data deposition repositories. The first fruits of these are a preprint from the working group and DataCite (of which we are also members) summarising what we feel should be the key criteria for selection.

FAIRsharing Guestpost: What Criteria Matters with Data Repository Selection?

Last Christmas we gave you our heart; okay forget George Michael – we gave you beautiful imaging data sets, Virtual Machines, BYO data parties, GigaGitHub, more open peer review plus much more.

We Wish You a GigaChristmas: A 2015 Wrap-Up

Genomics is a powerful technology that helps us understand the Tree of Life. Biodiversity Genomics 2021 was a virtual conference that took place on 27

 th

September-1st October 2021 that demonstrated how genomics can inform conservation and food security, and can additionally help us understand evolutionary novelties such as symbiosis.

Sequencing genomes across the planet at Biodiversity Genomics 2021

**The Human Genetics Massive: #ASHG15 in Baltimore **  This week the human genetics “tribe” (as NIH Director Francis Collins referred to “his people” here) have muscled out the Eastside and Westside crews to take over the Baltimore waterfront for the yearly American Society of Human Genetics (#ASHG15) meeting.

Sharing Genomic Data in the Precision Medicine Era

**That Was The Review Week That Was **If you’ve seen the #peerrevwk15 hashtag on social media, you may have noticed this week is the first ever Peer Review Week.

#peerrevwk15 News: Crediting our Amazing Reviewers with DOIs

**In Sultry Switzerland, Bioinformatics is Radiant at ISMBECCB **    Water cooling of our datacenter (&amp;

Bioinformaticians Baking in Blazing Basel: ISMBECCB and BOSC 2019

GigaScience has spawned a new smaller and more agile sibling: GigaByte, and is the first journal to come from our new GigaScience Press.

Giga Gets Bigger: GigaByte kickstarts GigaScience Press

ConGen (Recent Advances in Conservation Genetics), an international course taught by leading experts in the field, is a fantastic opportunity to learn how the latest genomic and genetic methods contribute to conservation science.

Protecting endangered species also means we have to know as much as possible about them.

Apply for GigaScience Scholarships at ConGen 2018

Giardia, a protozoan parasite which people typically pick up through drinking infected water or contaminated food, can cause diarrhoea and stomach pains. New research published today in
 
 GigaScience
 
 , with supporting data in
 
 GigaDB,
 
 provides insights into the mechanisms that cause the symptoms of giardiasis.

Currently more than 200,000 people are ill with giardiasis and there are 500,000 new cases a year.

How Giardia feeds on ready meals from the gut –   Author Q&amp;A with Kevin Tyler

The Leader of the Curation Pack.

At

 GigaScience

we are keen to maximise the use and utility of our published data, narrative and other research objects.

The Annotometer Results Are In…

Regular reader of this blog will be aware of our efforts to promote data citation using digital object identifiers (DOIs), and this week, alongside Rebecca Lawrence from

 F1000 Research

and Kevin Ashley from the Digital Curation Centre, our Editor in Chief Laurie Goodman has a correspondence in

 Nature

strongly making this case.

Promoting Data Citation in Nature (and Pushing Past Panda Problems)

In this era of “big-data” and supposed data-tsunamis, being able to sift through the vast swathes of information and find what you are looking will become more and more important.

First day of the ISMB Bio-Ontologies Meeting: useful tools in the data-deluge.

As big proponents of Open Data, on top of the many diverse datasets associated with

 GigaScience

papers in our integrated GigaDB database, we are continuing to fill it with datasets produced by our BGI hosts.

Release the Bats! New Halloween #opendata treat in GigaDB

As an Open Science journal, one of the main aims of

 GigaScience

is to break down barriers. Both in the access of research and the underlying data and code supporting it, and the barriers holding back the researchers themselves.

Women in Science – Helping Break the Final Barrier in Open Science

Citizen Science at UNEA4

As

 GigaScience

has the aim of opening and democratising science as far as it can go, we even work towards the involvement of non-professional “citizen scientists” in the scientific process.

Citizen Science goes mainstream. Back at the UN with the Citizen Science Global Partnership.

Photo: UNSW Sydney The cane toad

 Rhinella marina

is native to Central and South America. But thanks to humans and the sugar cane trade, the species now thrives also in Australia and other places where it doesn’t belong. The invasive species comes with an unpleasant surprise for native Australian predators, such as snakes or freshwater crocodiles:

 R. marina

kills them with its toxic secretions.

Toads and toxins: The genome of the invasive cane toad

GigaScience are regular attendees of the International Biocuration Conference, and you may have read our write-ups ups going back to 2012 edition. This year Biocuration is back behind the bamboo curtain, with the 11th conference held in the Crowne Plaza Hotel Shanghai from April 8th-11th and hosted by Fudan University.


 Symbolised by the spectacular Bund waterfront, Shanghai is the very symbol of modern China, and there was a

Biocuration on the Bund

Live and in-person in Madison

A big part of the life of a journal editor is to travel to conferences, keeping on top of the state-of-the art of fields of interest, as well as interacting the research community that publishes, edits and peer reviews for your journal.

Open Science Milestones and the return of in-person meetings at ISMB2022

Citizen Scientists collect and share enormous amounts of data on invasive mosquitoes from the Mosquito Alert project as part of our GBIF and WHO-supported series on vector-borne diseases.

Just out in

 GigaByte

is the latest data release from Mosquito Alert, a citizen science system for investigating and managing disease-carrying mosquitoes, and is part of our WHO-sponsored series on vector borne human diseases.

Publishing Citizen Science data to fight against mosquito borne diseases

GigaScience Press would like to congratulate Victoire Nsabatien for winning a 2024 Ben Barres Spotlight Award for his two preprints publicly reviewed and published by

 GigaByte.

Prizes are a good way of positively reinforcing and incentivizing good practice in opening up science, and eLife should be commended creating the Ben Barres Spotlight Award for groups that are underrepresented in biology and medicine.

GigaByte Author Wins A Ben Barres Spotlight Award for Publicly Reviewed Preprints

This week in
 
 GigaScience
 
 , Hasindu Gamaarachchi and colleagues published a paper on their HARU solution for selective sequencing, to be used alongside the handheld (“tricorder” like) Nanopore MinION device

. With the MinION, it is possible to kick out all non-target DNA strands before they are processed through the device’s pores, thus selectively sequencing specific target regions of the genome.

Selective sequencing on a shoestring: the $300 HARU system

With the upcoming 5th International Plant Phenotyping Symposium (IPPS) set to take place Oct 2-5, in Adelaide, Australia, we look at how the plant phenotyping community has progressed over the last decade and how we can potentially address the issues surrounding data sharing, re-use, and reproducible research.

As we live in an increasingly data-driven era, the genomics community has, in particular, a long history of sharing data to

How Green Became the New Black – Plant Phenotyping Developments Down Under

Due to popular demand we are keeping the paper submission deadline of our ICG prize track open until the end of the month. We’ve already received more submissions than our first competition last year, and a number of other submitters have been putting their finish touches to submission.

Meetings, Meetings And Extended Deadlines For The ICG-13 Prize

A team led by scientists from Monash University have completed a major milestone towards achieving the rescue of the critically endangered helmeted honeyeater.

Genomic and genetic tools for the helmeted honeyeater, Victoria’s endangered state bird

The 12th international meeting on Visualizing Biological Data took place on March 16–18, 2022 (AKA VIZBI 2022). This conference is always a visual treat, and with its focus on transforming how Life Scientists view data from Molecular and Cellular Biology and Biomedical Science this year’s event was no exception.

GigaScience at VIZBI 2022

***With ongoing the 2020 COVID-19 pandemic providing us with unprecedented insight into the progression of a disease outbreak, and unprecedented time in the lock down to turn us all into armchair epidemiologists. This includes near real-time sharing and analysis of genomics data through platforms like nextstrain, and of ways to view the infection, mortality and testing statistics via a growing number of online dashboards.

Guest Blog: Data in the time of Coronavirus, Pt. 2

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.

And it’s goodbye from me

GigaBlog is now archived in Rogue Scholar, a new service that provides what it calls “science blogging on steroids” through including full-text search, long-term archiving, DOIs and metadata for science blogs such as ours.

While this July we celebrated the 11

 th

anniversary of the launch of our first articles at ISMB in Lyon, it was actually the 12

 th

anniversary of the launch of GigaBlog, the blog of GigaScience

Archiving blogs: Rogue Scholar and lessons from Biome

The GSC23 international meeting was held in Bangkok, Thailand earlier this month (Aug 7-11th) and here we have an overview of this meeting. The Genomic Standards Consortium (GSC) is a volunteer-run non-profit organization set up nearly 20 years ago. At a time when “genomic” researchers were painstakingly producing near-complete genomes of just a few organisms.

GSC23: Talking standards in Bangkok

A new
 
 GigaScience
 
 article presents
 
 rich multi-dimensional
 
 data for one Alpine dingo named Cooinda

.

 The high-quality genome sequence, other molecular biology data, and magnetic resonance imaging of brain tissue will serve as a point of reference for exploring the evolutionary history of dingoes.

Multi-dimensional data for Cooinda the dingo

At

 GigaScience

we see more and more of our published papers use computational workflows, as they provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, systems are needed to enable the sharing of these workflows in a reusable form.

Addressing the challenges of sharing computational workflows with Yevis. Q&amp;A with Tazro Ohta.

Plants are full of biochemical potential. Today in
 
 GigaScience,
 
 we publish an article that presents a searchable library of spectra and molecules found in a collection of 1,600 plant extracts.

1,600 plant extracts reveal their secrets

UPDATE: The deadline for the call has been extended until the 30th June.

Second call (and webinar) for GigaByte’s vectors of human disease series

A study published in

 GigaScience

provides an enormous amount of behavioural science data, presented in a detailed videographic virtual library, that was used to explore Obsessive-Compulsive Disorder (OCD) in an animal model.

AI Opportunities for Obsessive-Compulsive Disorder. Q&amp;A with Henry Szechtman

The International Neuroinformatics Coordinating Facility (INCF) had its annual Neuroinformatics Assembly from 12

 th

-16

 th

September 2022.

The Importance of Data Sharing in Neuroscience – GigaScience at INCF 2022

GigaByte Journal wins the ALPSP Innovation Award for their interactive articles and tools aimed at fulfilling the UNESCO Recommendation on Open Science

We at GigaScience Press are very pleased to announce that our newest journal

 GigaByte

has won the 2022 ALPSP Award for Innovation in Scholarly Publishing.

GigaByte Wins 2022 ALPSP Innovation Award

The meeting of the Society for the Preservation of Natural History Collections (SPNHC), International Partner – BHL (Biodiversity Heritage Library) and National Partner – NatSCA (Natural Sciences Collections Association) took place in Edinburgh from June 5

 th

-10

 th

2022.

GigaScience at SPNHC 2022

Our WHO-sponsored series of articles describing biodiversity data relevant to vector-borne diseases has now been published in

 GigaByte

. This special issue presents a wide variety of data relating to the presence, spread, and diversity of organisms that are transmitting viruses, bacteria and parasites to humans.

GigaByte helping the fight against Vector-Borne diseases with data

When coffee is sold as single origin or as the more expensive Arabica beans— do you really know whether you are getting what you’re paying for? Different coffee-producing regions need to enforce the standards and reputation of their coffee, and there is a growing industry looking at different technologies to more accurately classify and test coffee beans from different origins.

Waking Up Publishing with Interactive Coffee Data

We have a Q&amp;A with author Tom Edinburgh from the University of Cambridge on his new GigaByte paper presenting Sepsis-3 criteria in AmsterdamUMCdb, which is one of the largest freely accessible Intensive Care database in Europe.

Opening access and exploring sepsis in an  Intensive Care database. Q&amp;A with Tom Edinburgh

We are pleased to see the 2022 Junior Research Parasite Award go to Jack Pilgrim for his work published last year in GigaScience, so here we highlight the ecosystem of awards acknowledging different parts of the research cycle.

Jokingly spurred by a controversial medical editorial calling people carrying out data re-use and meta-analyses “research parasites”, this gave rise to the launch of the “Research Parasite Awards” focused on

Vectors of data awards: acknowledging the entire data sharing food web

UPDATE: GigaByte and GBIF webinar video added below.

GigaByte and GBIF Webinar: Data papers describing datasets on vectors of human diseases

This end-of-the-year festive summary is different from previous ones:  For the first time, we can look back at a full publication year of our new baby,
 
 GigaByte
 
 journal. The older sibling
 
 GigaScience
 
 will also get the attention it deserves, before celebrating its 10th birthday in 2022.

Let’s first have a look at how the new family member is doing.

The (first) GigaScience Press End-of-Year Review

Published today in

 GigaScience

is a Data Note describing the National COVID-19 Chest Imaging Database (NCCID), a centralised database containing chest X-rays, Computed Tomography (CT) and MRI scans from patients across the UK. Utilising the UK National Health Service’s unique position as the world’s single largest integrated healthcare system, the benefits of collecting chest imaging data this large are extensive and already being used

GigaBlog

GigaScience, Giga-database and now GigaBlog: new resources for the big-data community