Data driven blogging from the GigaScience editors

Scott Edmunds

GigaScience’s T2T Series has now launched, with our first papers showcasing new Telomere-to-Telomere methods and genomic data sets.

While the first draft of the Human Genome was declared complete in April 2003, it took a further two decades for the publication of the first complete, gapless sequence of a human genome in March 2022.

Launch of the T2T Series: Closing the Gaps from Telomere-to-Telomere

Chris Armit

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

MicroCT Imaging of Metamorphosis in the African Clawed Toad

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

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

 GigaByte.

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

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

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

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

 GigaScience

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

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

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

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

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. There are many issues that underlie the appropriateness of authorship, but fortunately there are internationally recognised [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/appropriate-authorship/">Authorship Down. Tackling Misguided Incentives.</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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.

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

GigaScience Press

Nicole Nogoy

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.

Follow us (on everything)

*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

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

**

 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

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 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

“

 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?

**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.

Synthetic Genomics:  Redesign and synthesis of the first multicellular eukaryotic genome

**The Ebola pandemic presents one of the most terrifying world health crises in modern times, with devastating consequences in Western Africa [as this goes to press there are now over 10,000 infections and almost 5,000 deaths]. There is a vast amount of data on this crisis available in rapidly published articles and on the internet (check out PLOS Currents: Outbreaks in particular), including past and current numbers of infected;

Guest Blog: The 2014 Ebola Epidemic: Approaches and resources to slow the spread of infection

Here we present a guest blog by our Editorial Board Member Russell Poldrack, Professor of Psychology at Stanford University, who highlights the challenges and opportunities surrounding imaging data to enable the neuroscience community to “stand on the shoulders of giants”, and an announcement on our new fMRI series.

The sharing of neuroimaging data is an idea whose time has finally come, but many challenges remain.

Guest Blog: Challenges and opportunities with sharing neuroimaging data

Sheer Heart Attack

Diagnosis is key to beginning treatment for preventing coronary heart disease, the most common cause of heart attacks. One useful tool in the fight against this leading killer is magnetic resonance imaging, which allows the direct examination of blood flow to the myocardium of the heart.

Publishing our first virtual box of delights to aid the fight against heart disease

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

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

Secure Genetic Data Moves into the Fast Lane of Discovery

The 2014 International Conference on Systems Biology (ICSB) was hosted in Australia’s most livable city and event, sport, culture and food capital – that is Melbourne, with

 GigaScience

being proud to be one of the media partners.

All systems go at ICSB 2014 and the  Great GigaScience and Galaxy (G3) workshop

Schistocephalus solidus is as an emblematic study system in parasitology, first discovered by Peter Christian Abildgaard as far back as 1790, as having an extremely complicated life-cycle with multiple developmental states and host species (parasitizing crustaceans, fish and birds). Its fitting that such a classical model system has been used to showcase novel mechanisms of crediting and sharing research protocols in a reproducible

Parasite Protocols Part 2. Author Q&amp;A with François Olivier Hébert

Shedding light on what the Optical Mapping System can provide for genome analysis, here we present a guest posting from optical mapping pioneer and developer (and
 
 GigaScience
 
 Editorial Board Member), David C. Schwartz, who is a Professor of Chemistry and Genetics at the University of Wisconsin-Madison.

** Taking the Google Maps approach: providing comprehensive, scalable worldviews** We use maps in our daily lives to

Guest posting: Optical Mapping allows comprehensiveness and scalability that modern sequencing cannot provide

Birthdays are always emotional. The

 GigaScience

team are on their way back from the always jam packed ISMB meeting and its satellite SIGs. This year was a particularly event filled one, with our second birthday, the BMC open data award and drinks reception, and our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop all falling during the meeting.

Bioinformatics, Birthdays, and Booze at Boston BOSC.

3000 Rice Genome Sequences Made Publicly Available on World Hunger Day

Yesterday marked the publication in

 GigaScience

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

Publish Data: Fight World Hunger

The use of “big data” genomics technologies may gather most attention and funding in “big money” settings such as healthcare and agriculture, but due to a precipitous drop in cost its use has become increasingly ubiquitous in all corners of biological research, including biodiversity research and conservation.

Data Driven Conservation. Q&amp;A with Taras Oleksyk on ConGen2016

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

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

 GigaScience

and

 PLOS ONE

. The work and data presented here

The Early Earthworm Catches on to Full Data Release

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

We Wish You a GigaChristmas: A 2015 Wrap-Up

As the

 GigaScience

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

 GigaScience.

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

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

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

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

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

Today we have a guest posting from F1000’s Iain Hrynaszkiewicz covering the topic of medical data sharing

One of the world’s most influential medical journals recently highlighted data sharing as an important issue to be addressed if we are to improve the quality of reporting of biomedical research.

Guest posting: Many journals have determined that they can assist in data sharing

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

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

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

The rate of species extinction has lent increasing urgency to the description of new species, but in this supposedly networked “big data” era the process of cataloging the rich tapestry of life has changed little since the time of Linnaeus.

The cyber-centipede: giving online species descriptions a leg up

Following from his guest blog in October on “Approaches and resources to slow the spread of infection”, Michael Dean from the Center of Cancer Research at the NIH uses his data oriented approach to give an update of where the Ebola epidemic is. While there may be less media coverage (apart from in the UK), this doesn’t relate to the situation on the ground.

Guest Blog: The Ebola Epidemic revisited – where are we in 2015?

Data Club is Gonna Show You How

As science is supposed to be about “standing on the shoulders of giants”, we all know sharing scientific data should be a good thing, but there are obviously large technical and cultural challenges holding things back.

Ain’t No Party like a Bring Your Own Data Party!

Computer game added to armoury in ash dieback fight

Gamers to join ash dieback fight-back

Next time you sit next to someone on the train playing a game on their smartphone don’t be too dismissive. They may be harnessing the most state of the art genomics technology in the fight to save Northern Europe’s woodlands from destruction.

Save the trees. Play facebook games.

Big Data Publishing

(credit Jenny Cham, CC-BY) As mentioned in our previous posting, on top of the many great talks and sessions we attended at ISMB in Berlin last month, we were kept even busy helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop.

More on our ISMB workshop: What Bioinformaticians need to know about digital publishing beyond the PDF

Galaxy shines in the land of the midnight sun

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

#usegalaxy lights up northern skies

**Editors: Mark Wass (University of Kent, UK), Iddo Friedberg (Miami University, Oxford, Ohio, USA), Predrag Radivojac (Indiana University, Bloomington, Indiana, USA)**To tie in with the upcoming Automated Function Prediction Special Interest Group (AFP-SIG) at the ISMB/ECCB 2013 meeting in Berlin,

 GigaScience

and the organisers are launching a call for submissions to a thematic series of research from the meeting and beyond

Automated function prediction – call for papers for a special series

The upcoming 2014 Galaxy Community Conference (GCC2014) has just opened early registration, and following from our series announced at the last meeting we are renewing our call for papers for our special thematic focused series on studies utilizing large-scale datasets and workflows.

Continuing our #usegalaxy series at the 2014 Galaxy Community Conference

The 2013 Galaxy Community Conference (GCC2013) and

 GigaScience

are today announcing a call for papers for a special thematic focused series on studies utilizing large-scale datasets and workflows. Galaxy is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses.

Call for papers for a special GCC2013 Galaxy series

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

Software and supporting material for: “Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification”

Insect goo aids biodiversity research

Apologies to Jonathan Eisen (see Badomics in the journal), but today in

 GigaScience

we publish a new “squishomics” approach for assessing and understanding biodiversity, using the slightly wacky sounding method of combining DNA-soup made from crushed-up insects and the latest sequencing technology.

GigaBlog

Crossing the Open Science Streams: Cassyni X Sciety (and GigaByte) FTW