Data driven blogging from the GigaScience editors

Scott Edmunds

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

 GigaScience

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

Papers, papers, papers

Hans Zauner

Following FAIR principles is good for your colleagues, it’s good for the community, and it’s good for science. But what’s in it for the researcher, in return for committing to open science?

Open Science is FAIRly easy

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

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

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

Selective sequencing on a shoestring: the $300 HARU system

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.

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

Navigating Pangenome’s Labyrinth

In the two decades since the first genomes were sequenced, with the exponential growth of new and closely related genomes it has become increasingly difficult to visualise and compare their structure. Particularly with the large diversity and difference in genes within microbial genomes.

Making sense of pangenome networks

*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

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.

Amye Kenall

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

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

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

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

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

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

**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

GigaScience Press

Nicole Nogoy

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

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

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

*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

I’m a genomicist, get me into here.

Today is DNA Day, commemorating the day in 1953 when Watson, Crick, Wilkins, Franklin et al. published their Nature papers on the structure of DNA, as well as the day in 2003 that the completion of the Human Genome Project was declared.

DNA Day in the Jungle. Aaron Pomerantz on #JungleOmics

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.

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Updates from sequencing the tree of life. Biodiversity Genomics 2020

*The CRISPR/Cas9 system has opened new horizons in what can be done with genome editing. Here we present an author Q&amp;A with Alun Yonglun Luo discussing his new paper in GigaScience moving this technology towards epigenome editing and testing its efficacy and accuracy.

CRISPR-based Epigenome Editing: Author Q&amp;A with Alun Luo

**A genome scale model of

 Pseudomonas aeruginosa
 
 published recently in
 
 GigaScience
 
 will help scientists to fight multi-drug-resistant superbugs.
 


 Pseudomonas aeruginosa

is one of the world’s most dangerous pathogens, causing life-threatening infections. It is increasingly resistant to all antibiotics.

Genome scale model of a superbug

**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

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

**Over 200 participants spent three eventful days in Berlin last week to discuss ideas, ongoing projects and future developments around Open Science. As an appropriate location to demonstrate the benefits of breaking down barriers, the motto of FORCE2017 was “Changing the culture”. While most of the

 GigaScience

team was in Shenzhen for ICG, Hans Zauner was on hand in what is one of our favourite meetings.

#FORCE2017 in Berlin: “Changing the Culture”

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

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

Authors can now submit their bioRxiv preprints directly to GigaScience via the biorXiv platform, at the push of a button. This handy technical integration is another hallmark of biology preprints becoming a normal, accepted, and speedy way of communicating research results.
 

Pre-prints, versions of a scholarly paper that precede formal publication in a peer-reviewed journal are  becoming increasingly mainstream.

ShoRtcut from bioRxiv to GigaScience

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.

2016: An Eventful Year for GigaScience

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

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.

At Disney World infancy ends at 3, or at least that is the age children have to start purchasing tickets. It seemed appropriate to celebrate our 4th birthday there. Or at least at the #ISMB16 Computational Biology meeting that was held this week at the Walt Disney World Resort.

#ISMB16: A Disney Coming of Age Tale.

Join the Open Data club.

Every year we catch up with fellow enthusiasts of open data, open source and open science at BOSC, the Bioinformatics Open Source Conference that is a Special Interest Group of the ISCB’s annual ISMB conference. This year there is an interesting juxtaposition with the location, being held at the Disney World resort in Orlando.

Open bioinformatics in the house of the mouse.

**Shallow Impact. Tis the season. **In case people didn’t know— the world of scientific publishing has seasons: There is the Inundation season, which starts in November as authors rush to submit their papers before the end of year. Then there is the Recovery season beginning in January as editors come back from holidays to tackle the glut.

The lowest common denominator: marketing science with jIF

Following our announcement this month of a new collaboration and integration with protocols.io, we’ve gone into more detail on the first two papers that have utilised this open access repository of scientific methods and collaborative protocol-centered platform.

Of Parasites &amp; Protocols, Part 3. Author Q&amp;A with Tony Papenfuss

Teams of scientists from Spain have published the first complete genome of the olive tree. The specimen sequenced is of the Spanish Farga variety, and is over 1,200 years old.

Decoding The Tree of Life: Olive joins the Genome Club

Guilhem Sempere

Gigwa—Genotype investigator for genome-wide analyses

GigaScience recently published an article all about a Genotype Investigator for Genome-Wide Analyses, alternatively known as Gigwa. But what is this and how can it help? Guilhem Sempere explains more in a guest post.

Exploring the structure of genomes and analyzing their evolution is essential to understanding the adaptation of organisms to biotic and abiotic environments.

Introducing Gigwa: Genotype Investigator for Genome-Wide Analyses

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

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

The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity

Supporting data for "The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity"

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

**

 GigaScience

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

Reproducible Research Resources for Research(ing) Parasites

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

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

Chris Hunter

The Leader of the Curation Pack.

At

 GigaScience

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

The Annotometer Results Are In…

The great responsibility  Every discipline of science is unique.  Ecology is no exception.  We work in diverse, complex, context-dependent systems. Global change and anthropogenic influences are very real issues for the health of the planet that ecologists often examine.  As a discipline, we have moved from context-dependent, local studies to much larger, integrated studies.

Big Data Challenges and Solutions in Contemporary Ecology: A Guest Blog by Chris Lortie

A new portrait of Obama shows a spineless, slimy, gutter dweller, and in

 GigaScience

today we give you unprecedented insight into what makes them tick. Don’t worry, we haven’t encroached upon Fox News to provide partisan political commentary for the US elections, we are talking about the Obama genus of leaf-shaped Planerians from South America.

See inside Obama in 3D? Yes We Can!

In support of Brain Awareness Week, we have asked Cameron Craddock, Director of the Computational NeuroImaging Lab, Nathan S. Kline Institute for Psychiatric Research and Director of Imaging, Child Mind Institute, to write a blog highlighting open science in neuroimaging, and to announce our upcoming publication of the 2015 Brainhack Proceedings and the Brainhack Thematic Series.

Open Science Resources for Contributing to Brain Imaging Research: A Guest Blog by Cameron Craddock

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

The genomics community has been held up as an exemplar in data sharing practices since the human genome project, but the metabolomics community is catching up fast, with the Metabolights database being the fast growing repository at the EBI.

GigaMetabolomics Strikes Again: More BYO Data Parties and a Thematic Series

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

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

“

 To enable a conversation over the world’s knowledge

” is the slogan for Hypothes.is, a open annotation layer that allows anyone to annotate anything.

The Importance of Annotation: A Q&amp;A with Hypothes.is Director of Biosciences, Maryann Martone

Seek and Deploy.

If you’re a user of GigaDB (and why wouldn’t you be!) you’ll perhaps have been wondering why the search function is so slow and often missing obvious results! Well even if you’re not wondering, I can tell you that this has now been fixed.

GigaScience Gets a Service. What’s new in GigaDB?

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 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

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

#peerrevwk15 News: Crediting our Amazing Reviewers with DOIs

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

**Open is the New Black **While the internet might still be raging over Tim Hunt’s comments about #

 distractlingsexy

gender issues in the lab, and to a lesser extent Lior Pachtor’s recent provocative blog on the “myths” of bioinformatics code availability and licensing, here in Dublin this years BOSC conference was clear as ever about where they stand on both issues.

Open Bioinformatics in The Irish Free Software State

**Bird Genomes Rule the Roost **Yesterday marked the announcement by Guojie Zhang (pictured) in

 Nature

of the launch of the Bird 10,000 genomes (B10K) project (see: http://b10k.genomics.cn/), an initiative to generate representative draft genome sequences from all bird species within the next five years. This ambitious project is the first attempt to sequence the genomes of all living species of a vertebrate class.

Sequencing Order: B10K Reaching for the Skies to Decode All Bird Genomes

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

Ecology data in the 21st Century: multiscaled, and with “big” potential

At

 GigaScience

we are always promoting and finding new ways to foster open data, open science and reproducibility.

Great Lakes of Data: More with Pat Soranno on the challenges of data-integration in ecology

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

When it comes to technology,

 GigaScience

has always been open and willing to embrace new ways of integrating technology in its publishing processes, with the ultimate goal of working towards more reproducible, interactive and executable papers.

Getting Techy With It: GigaScience Technology Update 2014

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

Following our efforts promoting open science and “community genomics” projects such as the


 “Peoples Parrot”

** and

 
 Azolla
 
 
 “crowdfernded” genome
 

, today we have a guest posting from Peng Jiang and Hui Guo at the University of Georgia covering their crowdfunding efforts to**

 sequence the first Cactus genome


 .  While

Guest Posting: Help Crowdfund the “Community Cactus”

Tītitipounamu, Rifleman, female (left) and male (right)

 Our New Zealand based Commissioning Editor, Nicole Nogoy, was asked by Creative Commons Aotearoa (New Zealand) to write a guest blog on open licensing from a Kiwi perspective. Being big users and fans of their licenses we were happy to oblige.

Open Data Publishing Goes New Zealand: A Cross  Posting For Creative Commons Aotearoa

*The field of synthetic biology, designing and building engineered biological systems through DNA synthesis and genetic engineering, is rapidly moving to a genome scale. In a similar trajectory to genomic sequencing and genome projects two decades ago, it has moved from engineering single genes, entire synthetic bacterial genomes (J Craig Venter’s notorious “Synthia”), to the eukaryotic organism stage.

GigaBlog

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

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