Data driven blogging from the GigaScience editors

GigaScience Press

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

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

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

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

A new “multi-modal” data set on arm motion control, published recently in
 
 GigaScience
 
 , is an important contribution to develop robotic prosthetic devices and other tools at the interface between human and machine.

Robotic arms and other devices that support limb movements are getting ever more sophisticated.

Data on arm motion control for the human-machine interface

The software application PLINK is one of the most widely used tools in bioinformatics, particularly for genome-wide association studies (GWAS) that look at genetic variants in different individuals to see if any variant is associated with a trait. With the advent of the thousand dollar genome, the computational demands being made on such programs are exploding.

GWAS Reloaded: extended Q&amp;A with PLINK1.9 author Chris Chang

Watch a DOME Webinar on Machine Learning Best Practices &amp;

Machine Learning Standards in the Wild. DOME Webinar on ML Recommendations and Applications

Following our efforts promoting open science and “community genomics” projects that have included the
 
 
 “Peoples Parrot”
 
 
 ,
 
 
 community cactus, and our very own Bauhinia Genome, today we have a guest posting from the Transbiome team.

Guest Posting: Help Crowdfund the Transbiome

GigaScience Press and River Valley Technologies, with the help of Stencila, launch their first interactive

“

 Executable Research Article

”

 from their new scientific journal, GigaByte.

GigaByte and River Valley Technologies push the boundaries of Executable Research Articles using Stencila and Code Ocean

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)

*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

Cell Bio 2020 Virtual – the online ASCB|EMBO Meeting – took place on 2-16 December 2020 and offered many invaluable insights on the structural and evolutionary basis of biological systems.

GigaScience at Cell Bio 2020 Virtual

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

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

Timed for Peer Review Week 2023, we’d like to announce that GigaByte Journal has integrated a novel ‘Publish, Review, Curate’ (PRC) peer-review model, in partnership with eLife.

Peer Review Week 2023: GigaByte joins the ‘Publish, Review, Curate’ Revolution using Sciety

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 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

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

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.

*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

**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

Two almost complete and gapless genomes of the sex-changing central bearded dragon (Pogona vitticeps) are published today in GigaScience to help tackle the mystery of reptile sex determination. Read more here.

Two almost complete and gapless genomes of the sex-changing central bearded dragon (Pogona vitticeps) are published back-to-back to help tackle the mystery of reptile sex determination.

Double Dragon Genomes Helping Explain Sex Determination of Reptiles

This week we published a new, high-quality genome sequence of one of Australia’s most iconic animals, the short beaked echidna. The almost gapless genome sequence of this egg-laying mammal helps researchers to track genomic reshuffling events that gave rise to a perplexing  sex determination system.

At first glance they may be mistaken for a weird-looking hedgehog.

Sex chromosome madness in the iconic echidna

Last month was the 7th consecutive year we’ve attended our co-publisher BGI’s annual ICG (International Conference on Genomics) gathering in Shenzhen.

And the winner is? Our #ICG12 prize track on GigaTV

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

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 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

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.

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

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

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

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

This week we showcased a new way of peer reviewing software, testing code in an independent manner and providing a CODECHECK

 “certificate of reproducible computation”

when the results in the paper can be reproduced.

Reproducible Classification. Q&amp;A on ShinyLearner &amp; the CODECHECK certificate, pt. 2

Stuck indoors and bored of passively reading information on the coronavirus (and more) when you could be doing something more constructive? GigaScience now has hypothes.is integration for collaborative annotation, and we would encourage readers to interact with our content more collaboratively.

Things to do when stuck at home because of the Coronavirus: Get Annotating

In this data-driven era, research is faced with new challenges, from sharing, storing and accessing data, including how to better integrate data to answer big questions in science. With many data repositories available, it is hard to maintain them all – some repositories are forced to close – meaning loss of access to invaluable datasets.

iMicrobe: Fostering Community-Driven Science and Data Discovery. Q&amp;A with Bonnie Hurwitz

The mock metagenome, MAGs and breaking the first rule of Long Read Club

Nick showing us some of his experiments with an early antecedent Short Read Club… Out today in

 GigaScience

is a new “mock metagenome” Data Note from the Nick Loman lab in Birmingham showcasing the latest long-read sequencing technologies from Oxford Nanopore.

Mock the Metagenome. Author Q&amp;A with Nick Loman &amp; Sam Nicholls

This is the Dawning of the Age of Aequatus

Our ICG Prize is over now for another year, and we’ll shortly follow up with an announcement on which of the six winners won the $1000 first prize. To help you see how great all the entries were we will introduce and profile some of the winning papers.

Meet the GigaScience ICG Prize Winners, Pt. 1: Aequatus

Call for Submissions – Win Prizes and Join us in Shenzhen for ICG-13

Being co-published by BGI we are regular participants at their yearly ICG (International Conference on Genomics) conference in Shenzhen. Since the very first meeting in 2006, ICG has grown to become one of the most influential annual meetings in ‘omics’ research, and is now in its 13th edition.

Enter the 2nd GigaScience Prize Track at ICG-13

We at

 GigaScience

are pleased to have won the 2018 the PROSE Award for Innovation in Journal Publishing in the multidisciplinary category, as innovation has been a key element in our goal to change how scientific publishing is done. The Association of American Publishers (AAP) has been giving awards for 42 years to recognize distinguished professional and scholarly books, reference works, journals.

GigaScience Wins 2018 PROSE Award for Innovation in Publishing

Researchers have sequenced the venomous Solenodon, the last survivor of a branch of mammals that appeared at the time of the dinosaurs.

On the trail of the elusive Solenodon genome. Q&amp;A with Taras Oleksyk

Every summer we celebrate our birthday at the ISMB (Intelligent Systems for Molecular Biology) conference, and this was a particularly memorable and important one – being the 5
 
 th
 
 birthday of GigaScience, and 25
 
 th
 
 edition of the ISMB.

Having ISMB in Prague this year, the historic capital of old Bohemia was particularly appreciated by the attendees, both for its beautiful baroque streets, and its reputation as a

Bohemian Bashfully. Baroque birthdays and bingo in Prague.

Today, GigaScience launched a project providing an alternative way to give authors credit for their work, contributing more to collaboration, transparency and better data. Amye Kenall tells us more about what this is and how it works.

There is a clear need for better transparency and credit around authorship. In the current system researchers are evaluated by publications and the Impact Factor of journals in which they appear.

Putting credit back into the hands of researchers

What does Neuroinformatics and The Great Barrier Reef have in Common? Both are faced with challenges and comprise of beautiful colourful entities that should be freely accessible and shared.
 

This year’s International Neuroinformatics Coordinating Facility (INCF) Neuroinformatics 2015 meeting was held in the northern tropical Queensland city of Cairns, Australia.

Neuroinformatics Gets Tropical Down Under

With our focus on large-scale biological data, mass spectrometry has been one area of particular interest and attention. Metabolomics involves the detection and quantification of small molecules (metabolites) in living organisms using mass spectrometers.

GigaScience Pushes Metabolomics Open Data &amp; Training

Despite the precipitous drop in the price of DNA sequencing, global credit crunches have shrunk the science budgets able to properly take advantage of this. At least in the case of non-medical research.

Community Genomes: From the Peoples Parrot, to “Crowdfernding”.

A paper published in

 Nature Biotechnology

today reveals the most comprehensive catalogue of genes in any single microbiome to date. While the roughly 20,000 genes in the human genome have been available for over a decade, the gene catalogue of the microbiome, our much larger “other genome” has to date been much more poorly understood and characterized.

New GigaDB Dataset: Ever wondered whats in your gut?

Editors: Mark Wass (University of Kent, UK), Iddo Friedberg (Miami University, Oxford, Ohio, USA), Predrag Radivojac (Indiana University, Bloomington, Indiana, USA)

A key to understanding life at the molecular level is based on accurate protein annotation at the functional level.

From function “unknown” to “known”: First papers in our Automated Function Prediction series

Biggest ever contest to put genome assemblers through their paces

If you haven’t caught it yet, the largest systematic assessment the process of genome assembly carried out to date has been published this week in

 GigaScience

. The second Assemblathon competition saw 21 teams submit 43 entries based on data from three different unassembled parrot, cichlid fish, and boa constrictor genomes sequenced using three different

Genome assembly in the spotlight

The speed of data

Last week was the Bio-IT World Asia meeting in Singapore, and while we didn’t attend this year (see last years conference report in

 Genome Biology

), our editorial board member Tin-Lap Lee presented on the GigaGalaxy server that we have been collaborating with him on (see slides). Also timed for the meeting, Aspera made a press release on our recent adoption of their suite of software products to

Faster, Dataset! Kill! Kill!

Bye Bye Bluebells

Bluebell woods, the dense carpets of violet–blue flowers found in ancient woodland are a spectacular and famous springtime sight in Britain, but this picture postcard scene is threatened as never before.

Open Science versus Ash Dieback (and the Tweenome revisited)

The BBSRC has just released an excellent video and article on crowdsourcing killer disease outbreaks very relevant to our recent commentary and blog postings on the OpenAshDB (the Ash Dieback disease crowdsourcing) project.

Tweenome on Film: Excellent Video on Crowdsourcing Killer Outbreaks

UPDATE: Thanks to additional support from GBIF the deadline has been extended to 6th June 2025.

TDR, the Special Programme for Research and Training in Tropical Diseases hosted at the World Health Organization (WHO), 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.

Round three for GigaByte’s vectors of human disease series

We are proud to announce Prof Zhang Yongzhen winner the 2020 ICG-15 GigaScience Prize for Outstanding Data Sharing during the COVID-19 Pandemic

.

 Last month was the 10th consecutive year we’ve attended our co-publisher BGI’s annual ICG (International Conference on Genomics) gathering, and the third time we have presented a prize at the meeting.

This years award was for Dr. Zhang’s outstanding efforts in sharing the first

COVID-19 Data-Sharing Hero Wins GigaScience Prize

In a busy summer for meetings, this month we attended and presented at Bio-IT World Asia conference in Singapore. In this era of more globalized biology, to celebrate the 10th anniversary of the usually Boston based conference series, with Bio-IT World substituted their usual New England lobster for Chili Crab and heading east.

The (genomics) view from the 57th floor

Today marks the first day of the Chinese Lunar New Year, and as we enter the supposedly auspicious year of the Dragon now is a good opportunity to look towards developments in the nascent field of data publication over the upcoming year. This week marked important announcements of new and improved data publication platforms.

Data Citation Enters the (year of the) Dragon

GigaScience

was on hand to witness plenty of lively discussion last week at the annual American Society of Human Genetics jamboree: the International Conference of Human Genetics in Montreal. As always, the meeting had a strong medical genetics presence but the rapid growth and uptake of genomics technologies in the field produced much fascinating work on display this year.

ICHG2011: Genetics and Genomics Gets Personal

Galaxy shines in the land of the midnight sun

Immediately after beer, mussels and genomics at ICG-Europe in Ghent (see BGI’s write-up of the event), last week was a blur of eye-wateringly expensive alcohol, brown cheese and reproducible research at the Galaxy Community Conference in Oslo.

#usegalaxy lights up northern skies

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

We at

 GigaScience

always appreciate good press, and on top of the welcome coverage on blogs (e.g. this in Annals of Botany) and twitter, we are pleased with the profile of the journal in this months

 Bio-IT world

(especially coming on top of the coverage of our database in the previous issue). The article is a nice introduction to the editors, editorial policies, and hopes for the journal, and is useful reading for those who’d

GigaScience in the press (and still on the road)…

This week we are pleased to announce and highlight new updated additions to our long-running collaboration with protocols.io, linked to our first paper with a peer-reviewed protocol featuring a “Peer-reviewed method” badge on protocols.io. Alongside the addition of new functionality in protocols.io to submit protocols as method papers to

 GigaByte

. The new

 GigaByte

paper presents a new method expanding the alphabet and

Publish Peer-Reviewed Protocol Papers with Protocols.io and GigaByte

The 8th World Congress on Research Integrity (WCRI) took place in Athens, Greece from 1st-5th June. GigaScience Press are regular attendees of this conference, and this year our organisation was represented by

 GigaScience

Editor-in-Chief Scott Edmunds, Executive Editor Nicole Nogoy, and Data Scientist Chris Armit.

The Utility and Danger of AI in Scientific Publishing: Riddles of the Sphinx – GigaScience at WCRI 2024

Oat is among the top ten cereal crop species in terms of global production. It can adapt to different climates. Farmers grow it successfully even in harsh environments where other crops such as rice and corn fail. However, not all oat plants are the same. Based on their grains, two major oat varieties can easily be distinguished: Grains of “hulled oat” are covered in a non-edible husk.

Genome data shed light on the domestication of naked oat

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.

Pressing Challenges for the Global Research Community

Continuous growth of the world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and South-East Asia.

Democratising Data: The African Orphan Crops Consortium &amp; International Data Week

As we enter Peer Review Week 2025, we would like to propose the use of FAIR (Findable, Accessible, Interoperable and Reusable) principles for scientific peer review

,

 using these to make the process more scalable, efficient and also better equipped for the increasing use of AI in publishing.

Today marks the start of Peer Review Week 2025 (PRW 2025), an annual event celebrating the vital role peer review plays in ensuring the

#PeerReviewWeek: Why we need a FAIR Principles for Peer Review?

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

I recently returned from the InCoB/ISCB-Asia meeting. The meeting officially ended a couple of days ago but I am still digesting the good food, the good  conversations and the good science, all of which I know will be with me a good while.  In the interest of avoiding a copious monograph, I’ll try to stick to a few personal high points.

InCoB/ISCB-Asia: keynotes and curation

As biological data is now produced faster than it can easily be handled and stored, the dissemination of this data has become a major bottleneck.

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

As those of you who have been paying attention well know, I am currently attending this year’s International Conference on Systems Biology (#ICSB) meeting in either Heidelberg or Mannheim (there’s ongoing debate about the meeting locale).  The meeting opened yesterday with a plenary talk by Jean Peccoud talking about DNA “grammar,” making linguistic models of yeast cell cycle regularly network genetics, and the open source application (with a

Systems, synthetics and semantics

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

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

We want you to use our stuff

We get many queries regarding the policies and licenses associated with our content and supporting data, and as our co-publishers BioMed Central have just announced the migration of their licenses (including ours) to the newly released version 4.0 of the creative commons CC-BY attribution license, we thought it would be a good opportunity to clarify our policies in an easier to understand manner than

GigaScience goes CC4. A handy cut out and keep guide to our licenses

The

 International Ukraine Genetic Diversity Project finds a quarter of the genetic variation in Europe, dramatically increasing information on population diversity and medical genetic variation.

Today, the largest study of genetic diversity in Ukraine was published in

 GigaScience

. The project was an international effort, bringing together researchers in Ukraine, the US and China and is the first fruits of this collaboration to

Ukraine Genome Survey Adds Missing Pieces to Human Diversity Puzzle

Taylor Noble  As the ecology community expands, it is now adopting new ways of making sense of the plethora of data produced from diverse approaches, including ocean research, eco-genomics, limnology, and macrosystems ecology, through more integrative means – improving our understanding of biology in a broader sense.

Jack Rabbits, Lizards and Squirrels, Oh My! Q&amp;A with Taylor Noble

**The Giga-Curation Challenge 2016 **Annotation and curation are under appreciated parts of scholarship, because they allow someone to provide additional insight into a work, and are needed for efficient and easy re-use.

Encouraging community curation through competition

While for much of its history since the great famine of the eighteenth century Ireland has been synonymous with mass emigration, the 23

 rd

ISMB (Intelligent Systems for Molecular Biology) meeting sailing into the regenerated “Silicon Docks” of Dublin last week was a homecoming of sorts for the annual gathering of the global Bioinformatics community.

Birthdays and Homecomings at ISMB-ECCB in Dublin

Researchers release a treasure trove of data on the developing retina, pushing the boundaries of neuroscience publishing by presenting it dynamically and reproducibly.

A new paper in

 GigaScience

today demonstrates a major step forward for reproducible research and public data-sharing in the neurosciences with the publication and release of a huge cache of electrophysiology data resources.

CARMEN, reproducible research and push-button papers

As the

 GigaScience

journal moves from strength-to-strength, with that comes the expansion of the editorial and data management teams that are now spanning three continents – and what better way to meet than at the 8th International Conference on Genomics (ICG8) in Shenzhen, China, co-organised by the BGI and

 GigaScience.

Held at the Thunderbirdsesque Vanke International Conference Centre in the popular seaside resort of

A GigaGathering at ICG8 in the era of big data and crowdsourcing

The precipitous drop in the price of next generation sequencing coupled with its increasing sensitivity has opened up whole new areas of research, one of the most interesting in recent years being the advent of single-cell sequencing. Combining advances in flow-sorting of cells, whole genome amplification and the latest sequencing technologies is now allowing researchers to study tumor evolution on a single-cell level.

New paper in GigaScience: sequencing and the single-cell

To tie in with this week’s Genomic Standards Consortium (GSC) meeting in Shenzhen,

 GigaScience

is launching a call for submissions to a thematic series of discussion and research from the conference and wider community highlighting best practice in genomics research. As the 13th meeting of the GSC, the topic this year is “Genomes to Interactions to Communities to Models” – all areas key to the scope of the journal.

Follow us (on everything)

Another busy week for the

 GigaScience

team, with the release of a new-look database, more datasets, and a number of talks and announcements at BGI’s annual International Conference of Genomics in Shenzhen.

GigaScience at #ICG6: announcing the release of GigaDB and new datasets

GigaScience Press’ has been awarded one of the first CrossRef MetaData Awards, highlighting the Press as a leader in providing essential information to facilitate discovery, identification, and details of online research articles.

This week GigaScience Press has been announced as a winner at the inaugural Crossref Metadata Awards, recognising efforts in scholarly publishing metadata completeness and enrichment in their journal,

GigaScience Press Wins Inaugural Crossref Metadata Award

Following our previous DNA Day 2025 post covering where we are in the T2T (telomere-to-telomer) genomes era, we have a second expert Q&amp;A covering the topic, this time from


 Kateryna Makova on the challenges (and opportunities) of

Where we are in the T2T Genomes Era, Pt 2. T2T Sex Chromosomes

PAG (Plant and Animal Genomes conference) returned to the Town and Country resort San Diego for its 31st installment this January (Jan 12-17, 2024), bigger and better than ever before! The GigaScience Press team are regular attendees of the meeting (see last years write-up), and this year members of our Editorial and Curation teams joined nearly 3000 delegates from over 60 countries.

Plant and Animal Genomes (PAG) 31st annual conference

It’s December, the festive season and the end of  year are approaching fast –  and it’s time for our traditional look back on the past 12 months at
 
 GigaScience Press
 
 . Once more, we are pleased with the view in the rear mirror.  In its 11th year, GigaScience again published exceptional “big data” science (read on for examples). And GigaScience’s

2023 in review: Gigabyte journal coming of age, and more

Working at a data center as big as the BGI, and launching a journal focused on maximizing data use, we have followed the many calls over the years for improved incentives and methods to aid and reward scientists in spending the considerable time and effort to share their data.

Datacite summer meeting

ICSB 2011 left me with a greater than ever appreciation for, to borrow from the title of the last plenary session, the complexity of life. I was impressed by the increasingly complex and explanative models that are being built, and faster and more detailed imaging methods under development, not to mention the exciting new applications of systems biology for disease treatment.I am sure I’m not the only one who feels this way.

The complexity of life

With genetics and genomics being complicated enough, epigenomics adds even more layers of control and regulation of gene expression, and high-throughput global analyses of epigenetic changes further add to the reams of biological information many people are already referring to as the “data-deluge”.

Shanghai (Epigenomics) Surprise

Last week marked two important milestones in the deadly 2011 European

 E. coli

0104:H4 outbreak: the Robert Koch institute announcing the end of the outbreak, and the publication of several papers from the many groups sequencing the pathogen.

Notes from an E. coli “tweenome” – lessons learned from our first data DOI.

Gothenburg, Sweden played host to the Research Data Alliance (RDA) RDA20 plenary from March 20th to 24th 2023. A hybrid event with most sessions recorded and made available via the Whova app for registered participants. Recordings will be made available on Monday, 1 May 2023 to the wider community.