Data driven blogging from the GigaScience editors

Chris Armit

The National Academies of Sciences, Engineering, and Medicine (NASEM) hosted the two-day virtual workshop

 “Changing the Culture of Data Management and Sharing”

on 28th-29th April 2021 to discuss the challenges and opportunities for establishing effective data management and sharing practices and exploring the question of universal availability of scientific data.

Changing the Culture of Data Management and Sharing: A Report on the NASEM Workshop

Scott Edmunds

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

Platypus and echidna genomes reveal mammalian biology and evolution

Today is a big day for the genomics of egg-laying animals, with the coordinated publication of three papers on animal sex chromosome evolution and diversity in

 GigaScience

,

 Nature

, and

 Genome Research

by the Qi Zhou lab at Zhejiang University.

Cracking sex chromosome evolution via egg-laying birds and mammals

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?

The view from the Marie Sklodowska Curie Museum, where Marie lived as a child.  This year’s Neuroinformatics 2019 meeting took place in the beautiful and historic city of Warszawa (Warsaw). Warszawa remains a pilgrimage city for scientists, with arguably its most famous resident Marie Sklodowska Curie being the first woman to win a Nobel Prize, and the only person ever to win the Nobel Prize twice in two different scientific fields.

GigaScience at Neuroinformatics 2019

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.

Draft genome of the living fossil Ginkgo biloba

Not many tree species are iconic enough to have inspired Goethe love poems, but the distinctive and beautiful heart shaped leaves of ginkgo have made it a popular symbol in art and design. Coming from East Asia and having a long association with Buddhist temples and parks in China, Korea and Japan, it was thought to be extinct in the wild and only in more recent times were small wild populations identified in mountain groves in South West China.

Ginkgo genome fills an evolutionary hole

**Deep (ocean) sequencing. Big-(fish) data. **The ocean sunfish, must officially be one of the world’s weirdest creatures to enter the “genome club”, and have its genetic code mapped. Laying the most eggs of any other known vertebrate (up to 300,000,000 at a time), and starting out as the size of the head of a pin, sunfish grow to become to largest bony fish in the sea.

Of big fish and small genomes. Ocean sunfish shines.

A molecular map of lung neuroendocrine neoplasms

Supporting data for "A molecular map of lung neuroendocrine neoplasms."

We have a Q&amp;A with author Matthieu Foll from the WHO International Agency for Research on Cancer

(IARC)

 on his new GigaScience paper presenting multi-omic data from rare lung neuroendocrine neoplasms and his experience having the precious


 Controlled Access data peer reviewed by named peer reviewers.

As a journal focused on reproducibility of research

 GigaScience

has a strict open-science policy, meaning

Accessing and reviewing Controlled Access Data of Rare Cancers. Q&amp;A with Matthieu Foll

Amye Kenall

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

*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

Open Science has emerged into the mainstream, primarily due to concerted efforts from various individuals, institutions, and initiatives. This small, focused gathering brought together several of those community leaders.  The purpose of the meeting was to define common goals, discuss common challenges, and coordinate on common efforts.

‘Open Source, Open Science’ meeting report – March 2015

Quantitative proteomics and transcriptomics data from the anaerobic thermophilic eubacterium Thermoanaerobacter tengcongensis

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!

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

Peter Li

Scientific workflow software such as Taverna, Knime and Pipeline Pilot can overcome interoperability issues relating to the access of tools and data format conversions. Such tasks are automatically handled by the data processing pipeline during its enactment by the workflow software. Galaxy is another workflow system, and its annual conference was held last month at the University of Chicago.

Enabling bioinformatics tools to smoke the peace pipe together

Hans Zauner

Plant phenotyping – the science of gathering precise information and measurements on plants – has seen massive improvements recently, and the combination of sensor technology and AI methods will continue to change the way crops are assessed and improved. A new article in
 
 GigaScience
 
 demonstrates where this is going: Jonas Bömer and colleagues at the Institute of Sugar Beet Research (Göttingen) used

An artificial sugar beet for the eyes of Artificial Intelligence

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

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)

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

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

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

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

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

Open imaging data to assist AI in the COVID-19 fight. Q&amp;A with Dominic Cushnan

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

UPDATE: Deadline extended until 30 March 2022 or until maximum of 15 accepted manuscripts is reached—only a few slots remain!


 GigaScience Press partnering with GBIF are supported by TDR, the Special Programme for Research and Training in Tropical Diseases, hosted at the World Health Organization, to release a special issue for publication of new datasets presenting biodiversity data for research on vectors of human diseases.

GigaByte call for data papers describing datasets on vectors of human diseases

A new article published today in
 
 GigaScience
 
 demonstrates that machine learning can yield “proxy measures” for brain-related health issues from large population data, without the need for a specialist’s assessment.

AI for mental health assessment: Author Q&amp;A

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

 GigaScience

has always been 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. See our recent Review centering on inclusivity on the organization of meetings to see how it is important from an Open Science perspective.

The Women in Science Conference 2021: Challenges are simply a problem waiting for a solution

Embracing identity in Peer Review
 

The COVID-19 pandemic has brought into stark focus is the importance of both a speedy dissemination of research (something our participation in the C19 Rapid Review Consortium has tried to tackle), and the need to be able to trust the validity of this information.

Peer Review Week 2021: Preprints Meet Open Peer 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

GigaScience Press

Chris Hunter

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

GigaScience Presses new

 GigaByte Journal

was launched with the goal of speeding up the dissemination of science,

 publishing at the speed of research

. Beyond speeding up the research process by incentivizing the early release of datasets and software/computational workflows by focusing on short descriptions of these two article types (called Data Release and Technical Release), we’ve also tried to greatly speed up the normally

Update on Updates. GigaByte’s new article type to speed up science

Nicole Nogoy

GigaScience

has always had a focus on reproducibility rather than subjective impact, and it can be challenging for our reviewers to judge this, especially now that more and more tools are being created – bringing data science to the masses.  This also means more efficiency and ease is required especially when multiple collaborators and contributors on a specific project are involved.

Gigantum Joins the Giga Reproducibility Toolkit

Montréal was the venue for Medical Imaging with Deep Learning 2020 (MIDL 2020) that took place on 6-9 July 2020. Due to the COVID-19 crisis, like many meetings this year (such as the ISMB conference we attend every year), the new normal has been to make it a virtual conference.

Medical Imaging with Deep Learning in the Time of Coronavirus

This week in GigaScience we published research revealing a previously hidden diversity of symbiotic bacteria from the genus
 
 Rickettsia
 
 , spanning a wide range of arthropod hosts. Using accidentally amplified sequence data from a barcoding database as a starting point, the results will help to better understand the co-evolution of these intimate symbioses.

One group of bacteria to rule them all

Open Data in the Third Dimension

Data are not just ephemeral units of magnetisation sitting on computer hard drives. The linking of the word to storable computer information only goes back to the mid-20

 th

century, but the use of the latin word

 data

in English goes back to at least the 17

 th

Century.

A step-by-step guide to 3D print a scientific publication.

The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies

With the recent launch of our new GigaByte journal you may have noticed some interesting genome datasets being published, including the banjo frog, common dragonet fish, and extremely rare Nyssa yunnanensis tree. Joining these species on the genomics tree of life this month is a small mouse-like marsupial called the brown antechinus.

Q&amp;A with Parice Brandies on the Antechinus Genome

Updates from sequencing the tree of life. Biodiversity Genomics 2020

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

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.

C19RapidReview: cross publisher collaboration against the coronavirus pandemic

The COVID-19 pandemic has created a new urgency to openly and rapidly share and review relevant research, with the world looking to science to solve the problems we currently face. While we’ve written about constructive things you can do while in lockdown, there are many more things you can’t do while locked out of the lab.

GigaScience joins C19RapidReview: the COVID-19 Rapid Review Initiative

***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

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

With much of the GigaScience team spanning the Hong Kong-Shenzhen border and now confined to remote working, the current 2019-novel coronavirus outbreak has been particularly disruptive and close to home.

Guest Blog: Data in the time of Coronavirus

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)

As publishers of a lot of plant and animal genomes, the biggest conference for this research community is the appropriately named Plant and Animal Genome Conference (PAG). We’ve attended a number of these giant meetings in their San Diego base, and in recent years they have been branching out to host satellites in Asia (PAG Asia, which last year included a workshop that we participated in). And we attended the 28

 th

edition of the

Under Construction: Plant and Animal Genomes Get a Refurb

**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

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

Lessons learned in the evolution of large-scale data sharing
 
 New studies out today elucidate


 the framework for 1 billion years of green plant evolution. The work are the results of nearly a decades work from an international consortium of nearly 200 plant researchers


 generating gene sequences from more than 1100 plant species.

Harvesting the final fruits of the plant tree of life

Alexandra Basford

The Human Variome Project (HVP) Beijing Meeting has officially ended (though a number of delegates will be busy tomorrow at the Advisory Council meeting). The energy and commitment towards better understanding and treatment of heritable diseases displayed by both the speakers and participants was great to see. Peter Taschner’s talk on the Leiden Open (source) Variation Database (LOVD) system was very well received, and a number of

HVP Beijing: dealing with variation

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

EMBL Heidelberg was the venue for the EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life that took place on 9-12 October 2019. This was the second EMBL meeting on imaging data we attending this year after VIZBI (see the write-up here),

 GigaScience

Data Scientist Chris Armit was there and was astonished at how recent breakthroughs in imaging technology are enlightening our understanding of the Life Sciences.

Seeing is Believing

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

Bioinformaticians Baking in Blazing Basel: ISMBECCB and BOSC 2019

Regular readers will know

 GigaScience

has published a lot of plant and animal genomes, and the biggest conference for this research community is the appropriately named Plant &amp;

PAG Asia 2019: Plant and Animal Genomes (with Chinese Characteristics)

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

Marking the 10
 
 th
 
 anniversary of the formulation of the FAIR principles, we have one of our GigaBlog Q&amp;A’s with


 Peter-Bram ’t Hoen, Alain van Gool,


 Anna Niehues and Casper de Visser


 from the Netherlands X-omics Initiative and Radboud University Medical Center in


 Nijmegen, authors of a new paper on publishing FAIR workflows.

A Decade of FAIR – and what next? Q&amp;A on FAIR workflows with the Netherlands X-omics Initiative

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

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

Adapted from Ohdera A et al.

 Three jellyfish genomes are better than one

A new article in

 GigaScience

might make you squirm if you plan to hit the beach this summer. The published work presents the draft genomes of three different jellyfish species.

Genomic Warning Flag Just in Time for Beach Season: Jellyfish Toxins

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

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

In the data driven era, not only in research but in our day-to-day lives, people are creating more and more personal digitized data that enables human-participant research in social sciences and personalized medicine. However, with numerous data streams and types this raises concerns such as how to merge and share such data, as well as ethical problems.

Power to the People and Their Data – The Open Humans Way. Q&amp;A with Bastian Greshake Tzovaras and Mad Price Ball

At

 GigaScience

as our focus is on reproducibility rather than subjective impact, it can be challenging at times to judge this in our papers. Targeting the “bleeding edge” of data-driven research, more and more of our papers utilise technologies, such as Jupyter notebooks, Virtual Machines, and Containers such as Docker.

GigaBlog meets Gigantum: Guest Post from Tyler Whitehouse, Dean Kleissas and Dav Clark

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

Just out in

 GigaScience

is a new paper presenting Rice Galaxy, an open resource for plant science using the Galaxy workflow management system we are so fond of. The authors from the International Rice Research Institute in the Phillipines are winners of our 2018 ICG13 Prize, and as this is the final paper to be published we can now present a summary of the  competition.

And the winner is…volume 2. ICG13 prize winners on GigaTV

FAIRer Sharing via FAIRsharing

Image from FAIRsharing.org. Our aim at

 GigaScience

is to provide the means to open up and share research data. On top of just making these available via our (new look) GigaDB database, we’ve been involved with communities that wants to maximize the utility of these research outputs by making them FAIR: Findable, Accessible, Interoperable and Reusable.

Presenting the FAIRsharing community network

Just out in full text is a our first paper showcasing our latest complete integration with the Sketchfab 3D viewer. In this a 3D fossil seabed from the lower Devonian geologic period has been digitally reconstructed using micro X-ray computed tomography (microCT) imaging.

Lost worlds: via Sketchfab a 3D fossil offers a glimpse of prehistoric marine life

The 10th anniversary of the EMBO Workshop: Visualising Biological Data (VIZBI 2019) took place in EMBL in Heidelberg last week. GigaScience Data Scientist Chris Armit was there and was astonished at the cinematic quality of the visualisations that were showcased over this 3-day meeting.

Visualising Biological Data. GigaScience at VIZBI

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

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.

Assuring Appropriate Authorship.

In our day-to-day work at

 GigaScience

many of the most common and reoccurring problems we keep encountering relate to appropriate authorship. In this “publish or perish” world of science, getting authorship right is of course important.

Authorship Down. Tackling Misguided Incentives.

2018 was yet another eventful year at
 
 GigaScience
 
 . Before most of the editors and data curators take a few days of well-earned break from handling Giga-papers and Giga-data, it’s time to look back over this year’s highlights – of which there are many.

Prizes given and received, and other 2018 highlights

Yesterday we published the winning paper of the second

 GigaScience

prize, with additional detail and coverage in GigaBlog describing why we and the judging panel found it so novel. This was an impressively case study in reproducibility, reassembling &amp; reannotating around 700 microbial eukaryotic transcriptomes to demonstrate this approach can aid in revealing new biologically relevant findings and missed genes from old data.

Meet the GigaScience ICG Prize Winner, Pt. 2: Lisa Johnson Q&amp;A

*Out today is the winner of our ICG13 Prize, presenting work that can aid in revealing new biologically relevant findings and missed genes from previously generated transcriptome assemblies. Teaching old data new tricks, and maximising every last nugget of information from previously funded research.

Reprocessing the Microbial Genomic Goldmine: Winner of the ICG13 Prize

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

While they say one swallow doesn’t make a spring, one swallow genome makes a welcome contribution to the avian genome club.


 Taking advantage of the latest genomic and optical mapping technologies, a team of Scientists from the University of Milan, California State Polytechnic University and the University of Pavia, have carried out the high quality sequencing of the barn swallow genome, published today in Gigascience.

Swallows and Optical Maps For Ever!

**Today in

 GigaScience

we present the genome of the tegu lizard. It is the most complete assembly of any reptile genome so far and will also aid scientists to study other lizards and snakes. ** The tegu has mastered a trick that is highly unusual in the reptile world: it can turn on its own heating system.

Tegu: the most complete assembly of any reptile genome

In

 GigaScience

, Benjamin Makepiece and his co-authors from Liverpool present genome assemblies of two trombidid mite species, the itch-inducing chigger mite and its more benign cousin, the velvet mite.  The bite of the chigger mite can transmit a life-threatening bacterial disease, scrub typhus.

Genomes mite surprise you

View towards the National Wine Centre of Australia (conference venue) from the Adelaide Botanic Garden  Having just attended our first plant phenomics conference – it was great to learn how far the field has progressed and how rapidly it continues to progress with the advancement of new technologies for high-throughput phenotyping.

Phenomics: from under the gum trees to the world – the 5th International Plant Phenotyping Symposium down under

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.

Open Science Trek, The Next


 Integration

Fostering and promoting more open and transparent science is one of the goals of

 GigaScience

, and to do this we have been big promoters of open peer review as well as preprints servers. Combining both of these, Academic Karma was the one of the first platforms to focus on open review of preprints, and has helped facilitate this over the past 3 years.

Preprint.Space, The Final Frontier

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

Mary Ann Tuli

**Web tools and FAIR principles at the core of Life Science publishing in GigaDB **

 As we continue to push the envelope for publishing in the life sciences we have been listening to our users about the things that should be incorporated into the publication process.

A new look GigaDB. Data publishing gets more interactive and FAIR.

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

Boston 2014: More than a (Bioinformatics) Feeling

Following from our previous posting on BOSC, our birthday and the BMC Open Data award party in Boston, on top of having to dash between the many great talks and sessions at ISMB, we were kept even busier than usual helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop at the end

Continuing the push beyond static documents. ISMB, and more on our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop

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.

GigaBlog

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

Improvements for Man and Machine in Scientific Publishing

Gigantum Joins the Giga Reproducibility Toolkit

Changing the Culture of Data Management and Sharing: A Report on the NASEM Workshop

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

Certified Reproducibility. Q&A on ShinyLearner & the CODECHECK certificate, pt. 1