Data driven blogging from the GigaScience editors

GigaScience Press

Chris Hunter

The Annual International Biocuration Conference (AIBC) was held for the first in India, at the Indian Biological Data Centre (IBDC), Regional Centre for Biotechnology (RCB), Faridabad and co-hosted by the Department of Plant Molecular Biology, University of Delhi South Campus. As usual, GigaDB had representation at the event (see write-ups of many previous meetings here), Mary Ann Tuli and Chris Hunter. Both of whom were wearing two hats!

AIBC – India. Biocuration, long days, even longer traffic jams.

Hans Zauner

Few countries have a biodiversity that’s comparable to Brazil’s, including plant-based food sources that are little known elsewhere.  Even in big cities you may pick all kinds of fruit directly from the tree, which can be both tasty and also interesting for the botanist. The Citizen Science project “Pomar Urbano” collects data on urban fruit-bearing plant in Brazilian cities.

Citizen Scientists can see the wood for the trees

Scott Edmunds

*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

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

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

We start the new year with news from the deep, published in
 
 GigaScience
 
 : The genome of a sea cucumber, collected at a depth of 2400 m during a submarine trip to a hydrothermal vent, helps scientists to understand how marine animals can survive in extreme conditions.

Hydrothermal vents are an unlikely environment for animals to flourish.

Some sea cucumbers like it hot

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

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

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

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!

*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

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.

RDA20 Plenary: A Decade of Data 2013-2023. Celebrating 10 years of the Research Data Alliance (RDA)

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

Frictionless Data improves not just machine readability of scientific articles, but also enables humans to directly interact with the data within the article itself.

Improvements for Man and Machine in Scientific Publishing

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

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

Chris Armit

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

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

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

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

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

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

Open data is a critical component of the scientific method, but genomes are both identifiable and predictive.

Personal Genomics Enters a New Phase

Endorsing Data Citation

Nicely timed for the Data Citation Principles workshop at the IDCC meeting in San Francisco yesterday, the finalized Joint Declaration of Data Citation Principles has just been posted on the Force11 website.

Having a finger on the pulse of data citation

Kevin Ashley’s (DCC director) closing remark at the IDCC (International Digital Curation Conference) 2024 meeting was “

 Reflect, Enjoy, Do something!

”. Hopefully you will

 enjoy

my

 doing something.

Reflect, Enjoy, Do something! Lessons from the International Digital Curation Conference

In the beginning

 GigaScience

was at the first AsiaEvo conference, which took place in Shenzhen, China in 2019. Back then, the chair of the first AsiaEvo Conference, Guojie Zhang (longtime friend and board member of

 GigaScience

) said of the history of the AsiaEvo meeting series:

Evolutionary Biology goes Asia: the 3rd AsiaEvo Conference

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

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

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

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

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”.

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

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

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

Andy Kilianski and Sam Minot

Sam Minot from Signature Science, LLC and Andy Kilianski from the Edgewood Chemical Biological Center are part of a team that has been trialling a new palm-sized DNA sequencer to test whether it can characterize viruses and bacteria.

A firsthand perspective of trialling mobile DNA sequencing

OPTIMising Genome Assembly

This month brings new additions to our exciting and on-going Optical Mapping series. Outside of a handful of key genomes, due to deficiencies in the short sequencing read lengths that have backed genome assembly, we lack reference genomes that are finished to high standards that can support comprehensive analyses.

Crossing the Genome Finishing Line – News from our Optical Mapping Series

Nicole Nogoy

Passiflora

, commonly known as Passion Vines or Passion Flowers is a genus encompassing around 500 species, all of which exhibit such huge variation in leaf shape.  To further understand the unique diversity of

 Passiflora

leaves, a recent paper published in

 GigaScience

, presents a morphometric analysis and unique open dataset encompassing over 3,300 leaves from 40 different

 Passiflora

species.

A Passion for Morphing Passiflora Leaves: Author Q&amp;A with Daniel Chitwood

Visualizations are becoming increasing important to graphically illustrate, understand, and glean insight from the explosion of larger and larger datasets in this supposed era of “big data”. Microbial ecology and the study of the microbiome is revolutionizing how we look at health, microorganism diversity and ecological interactions, but these studies are proving challenging to deal with the ever-expanding numbers of specimens sampled.

Moving pictures of the Microbiome in GigaScience

It was a year to remember, for more than one reason: 2022 marked the 10th anniversary of
 
 GigaScience
 
 ’s launch. The journal’s younger sibling
 
 GigaByte
 
 got an award and continued to innovate with living documents and its first trilingual article. And we published lots of memorable research, featuring, for example, a giant tortoise and 26 deadly snakes.

Celebrating and innovating: This was 2022 at GigaScience Press

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

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

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

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.

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 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!

UPDATE: GigaByte and GBIF webinar video added below.

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

Imagine you would like to study a plant species of interest, say for its ability to supply food, fiber, fuel or just to gain a deeper scientific understanding. Two approaches immediately come to mind: an understanding of its underlying genetics and an understanding of plant phenomics, which spans how the genes express themselves across huge length scales from the microscopic to the whole plant itself.

The Complexities of Modern Plant Phenomics: A Guest Blog by our Plant Phenomics Series Guest Editors

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

Peter Li

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

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 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

This week in
 
 GigaScience
 
 we published the genome of the mediterranean cone snail,
 
 Lautoconus ventricosus
 
 . Cone snails produce a wide variety of powerful toxins and the new chromosome-scale genome assembly opens the door for detailed investigations of their diversity and evolution.

Cone snails are beloved by collectors for their often beautiful shells, but they are infamous because of their powerful venom.

Cone snail genome sheds light on venom evolution

The International Neuroinformatics Coordinating Facility (INCF) hosted their Neuroinformatics Assembly on 19

 th

-23

 rd

April 2021. This conference aims to highlight open innovation in neuroscience, and additionally to showcase recently developed software tools and data infrastructures.

A neuroinformagical reunion at the virtual INCF Assembly

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.

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

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

The Human Cell Atlas is a consortium that aims to “create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease.” I first met with consortium members of the Human Cell Atlas at the Human BioMolecular Atlas Program Common Coordinates Framework Workshop based at the National Institutes of Health, Bethesda, USA in December 2017.

Predicting the Outcome of COVID-19: GigaScience at the Human Cell Atlas COVID-19 Virtual Symposium

Scientists in Cambodia, who are supported by the Chan Zuckerberg Initiative, the Chan Zuckerberg Biohub, and the Bill &amp;

A New Monitoring Tool Empowering Infectious Disease Detectives

“Extinction is forever – so our action must be immediate.”

– Sir David Attenborough, Sept 30

 th

2020 Biodiversity Genomics 2020 aimed to bring together researchers across the world to celebrate the global achievement in genome sequencing in an effort to “sequence life for the future of life”. This was a virtual conference that took place on 5

 th

-9

 th

September 2020 and the

 GigaScienc

e team

Updates from sequencing the tree of life. Biodiversity Genomics 2020

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

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

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

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?

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

In Sultry Switzerland, Bioinformatics is Radiant at ISMBECCB

Water cooling of our datacenter (&amp; friends) Regular readers will know

 GigaScience

originally launched at the 2012 ISMB (Intelligent Systems of Molecular Biology) meeting in Long Beach, and every subsequent year the conference has held a special place in our hearts as the place where we celebrate our birthday (see all the previous write-ups in GigaBlog).

Bioinformaticians Baking in Blazing Basel: ISMBECCB and BOSC 2019

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

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 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

It’s DNA day, commemorating the publication of the structure of DNA in 1953, as well as the completion of the Human Genome Project in 2003. Genomics has come a long way since then. Today it is possible to sequence whole genomes with a very reasonable investment of time and money. What an amazing time for scientists who are working with non-model organisms.

DNA Day 2019: How to sequence the genomes of the weird and wonderful

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

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.

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

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

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

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!

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

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.

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

Mary Ann Tuli

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

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

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

The year is almost over and it’s time to review the highlights of
 
 GigaScience
 
 ’s 2017.

“Draft genome of the reindeer (Rangifer tarandus)”Foto: Alexandre Buisse CC-BY-SA 3.0 2017 was as special year for

 GigaScience

: a year of many firsts and we celebrated our 5th birthday! An occasion to look back – and forward, as we did in our anniversary editorial.

… and a Happy New Year

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

With the current annual data creation rate estimated to be in the tens of zettabytes, the flood of information currently being generated in every area of human life is crashing up against limited data storage solutions. However, DNA, which serves as a storage system for biological information,


 has been proposed


 as a potential means


 to store an unlimited amount of information.

Guest Blog from Huanming Yang on using the human genome for big-data storage

GigaScience is always trying to push the boundaries of how we disseminate reproducible research, and to adapt to the challenges of dealing with experiments become more data-intensive.

Data Intensive Software Publishing &amp; Sailing The Code Ocean.  Q&amp;A With Ruibang Luo.

Call for Submissions – Win Prizes and Join us in Shenzhen for ICG-12

Being co-published by BGI and based at their Hong Kong office 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 12th edition.

Enter the GigaScience Prize Track at ICG-12

A high coverage, high quality genome sequence of the butterfly
 
 Bicyclus anynana
 
 is published today in
 
 GigaScience
 
 .
 
 B. anynana
 
 , the squinting bush brown, is a fascinating model species that can modify its morphology in response to environmental clues.

The genome of a shape shifting butterfly

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

The decline of global honeybee populations are a major environment concern, because of their vital role in our food systems and pollination of flowering plants. Twenty first century ‘Omics is coming to the rescue, and published in GigaScience this week is an article that presents the genome and proteome of a mahor threat to bee colonies, the parasitic mite, Tropilaelaps mercedesae.

Getting the Buzz on Bee Parasites. Author Q&amp;A with Tatsuhiko Kadowaki

Cheering Ourselves up with CUDDEL(s) and Hackathons

We have been working closely with the Metabolomics community for a few years now, participating in hackathon events including BYO Data parties and Hack-the-Spec – ISA as a FAIR research object – thanks to our collaboration with the ISA Team at the Oxford e-Research Centre and funding from our BBSRC UK-China partnering award.

GigaBlog

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

Guest posting: Conda as a new standard for Galaxy tool dependencies

Fermenting a Reproducible Research Revolution