Data driven blogging from the GigaScience editors

Scott Edmunds

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

A guest posting with the Transbiome team on their community driven research program using crowdfunding and co-creation to discover the diversity of the neo-vaginal microbiome. 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/transbiome-guest-post/">Guest Posting: Help Crowdfund the Transbiome</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

Guest Posting: Help Crowdfund the Transbiome

Chris Armit attended Cell Bio 2020 Virtual (the online ASCB&#124;EMBO Meeting) and here provides a write-up of the excited Cell Biology on display in this conference.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/cell-biology-2020/">GigaScience at Cell Bio 2020 Virtual</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Chris Armit

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

GigaScience at Cell Bio 2020 Virtual

Parice Brandies presents a Q&#038;A and video on her GigaByte paper on the brown antechinus genome (Antechinus stuartii), a fascinating marsupial with many biological surprises to explore.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/qa-parice-brandies-antechinus-genome/">Q&#038;A with Parice Brandies on the Antechinus Genome</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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

This year ISMB2025 and BOSC was in Liverpool, and we embraced the location with our biggest birthday ever (alongside some Beatles themed adventures). Read more in the conference write-up.

GigaScience Press

Birthdays,

 BOSC, Beatles and Bioinformatics with a Merseybeat

Conference season is upon us, and the

 GigaScience

team have just returned from a magical mystery tour to Liverpool. Regular readers will know

 GigaScience

launched at the ISMB (International Conference on Intelligent Systems for Molecular Biology) in 2012, and every year we attend and celebrate our birthday at the meeting.

Help! I need curation. ISMB meets the Beatles.

Chris Armit attended the Global Genome Biodiversity Network (GGBN) Conference 2023 in Mexico and reports on the Biobanking heavy agenda.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/biobanking-at-ggbn-2023/">BioBanking at GGBN 2023: Highlights from GigaScience Press</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

The fourth international Global Genome Biodiversity Network (GGBN) Conference took place in Aguascalientes, Mexico from October 17th to October 20th 2023 where it was hosted by the Universidad Autónoma de Aguascalientes.

BioBanking at GGBN 2023: Highlights from GigaScience Press

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

GigaScience Press team attended the yearly ISMB (Intelligent Systems for Molecular Biology) meeting and learned about Large Language Models.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/">Going Large (Language Models) at ISMB2023</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

We have an author Q&#038;A and video abstract with Tazro Ohta where he gives some insight into archiving workflows and his new Yevis platform.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/yevis-qa-with-tazro-ohta/">Addressing the challenges of sharing computational workflows with Yevis. Q&#038;A with Tazro Ohta.</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

At

 GigaScience

we see more and more of our published papers use computational workflows, as they provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, systems are needed to enable the sharing of these workflows in a reusable form.

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

First full-length genome sequences for three species of Morpho butterflies show inversions on the Z chromosome.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/amazonian-morpho-butterflies-three-genomes-with-a-twist/">Amazonian Morpho butterflies: three genomes with a twist</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Hans Zauner

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

An announcement on the GigaScience T2T (Telomere to Telomere) Series: Closing the Gaps from Telomere-to-Telomere 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/t2t-series/">Announcing the GigaScience T2T Series: Closing the Gaps from Telomere-to-Telomere</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

*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

Chris Hunter

After 2 cancellations due to the pandemic, the Plant and Animal Genomes conference returned to its in-person format in January with its 30th edition. A number of the talks focused on the effects of climate change either on biodiversity or crop development. It seems only fitting then, that the weather provided a suitable demonstration with California experiencing one of the longest periods of sustained rainfall in many years.

Plant and Animal Genomes (PAG) Comes Storming Back!

The Center for Antibody Technologies headed by Professor Andreas Laustsen-Kiel (Technical University of Denmark) used high-throughput methods to systematically analyze the venoms of the 26 most deadly snakes in sub-Saharan Africa. The results are now published in
 
 Gigascience
 
 .

Each year, around 500,000 people in sub-Saharan Africa suffer from snake bites, causing an estimated 7,000 to 20,000 deaths.

What’s your poison? Venom composition of 26 deadly snakes

GigaByte this week marks the first time multilingual articles have been simultaneously published in English, Spanish and Ukrainian. Showcasing a novel and award winning feature from our publishing platform.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/how-to-publish-multilingual-articles/">The first English-Spanish-Ukrainian Publication. How to publish multilingual articles with GigaByte</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

TDR, GBIF and GigaScience Press have announced a second call (and webinar) for the GigaByte series publishing new datasets for research on vectors of human diseases.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/second-call-vector-papers/">Second call (and webinar) for GigaByte’s vectors of human disease series</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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

A guest post from our summer data science intern Raniere Silva from Hong Kong City Uiniversity on his work on Frictionless Data and Interactive Visualisation
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/from-frictionless-data-to-interactive-visualisation/">From Frictionless Data to Interactive Visualisation</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</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

The h-index is a metric that was invented to summarise the publication output and impact of researchers. In a new

 GigaScience

article, authors from the University of New South Wales (Australia) adopt the controversial metric for a completely different purpose: to explore systematic differences in research interest (

 taxonomic bias

), using mammals as an example.

Not all species are equal: Using the h-index to quantify taxonomic bias (author Q&amp;A)

GigaScience Press is pleased to announce GigaByte journal has been shortlisted as a finalist in the 2022 ALPSP Awards for Innovation in Publishing.

GigaByte a finalist for the ALPSP Awards for Innovation in Publishing 2022

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

Citizen Scientists share and publish Mosquito Alert data as part of our GigaByte (&#038; GBIF &#038; TDR supported) series on vector-borne diseases.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/publishing-mosquito-alert-data/">Publishing Citizen Science data to fight against mosquito borne diseases</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Citizen Scientists collect and share enormous amounts of data on invasive mosquitoes from the Mosquito Alert project as part of our GBIF and WHO-supported series on vector-borne diseases.

Just out in

 GigaByte

is the latest data release from Mosquito Alert, a citizen science system for investigating and managing disease-carrying mosquitoes, and is part of our WHO-sponsored series on vector borne human diseases.

Publishing Citizen Science data to fight against mosquito borne diseases

Author Q&#038;A with Julien Wist talking about his interactive coffee dataset just published in GigaByte that features a NMRium browser.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/interactive-coffee-dataset/">Waking Up Publishing with Interactive Coffee Data</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

When coffee is sold as single origin or as the more expensive Arabica beans— do you really know whether you are getting what you’re paying for? Different coffee-producing regions need to enforce the standards and reputation of their coffee, and there is a growing industry looking at different technologies to more accurately classify and test coffee beans from different origins.

Waking Up Publishing with Interactive Coffee Data

A team led by scientists from Monash University have completed a major milestone towards achieving the rescue of the critically endangered helmeted honeyeater.

Genomic and genetic tools for the helmeted honeyeater, Victoria’s endangered state bird

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

Author Q&#038;A with Tom Edinburgh on his new GigaByte paper presenting Sepsis-3 criteria in AmsterdamUMCdb, an Intensive Care database. 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/opening-access-and-exploring-sepsis-in-an-intensive-care-database-qa-with-tom-edinburgh/">Opening access and exploring sepsis in an Intensive Care database. Q&amp;A with Tom Edinburgh</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

We have a Q&amp;A with author Tom Edinburgh from the University of Cambridge on his new GigaByte paper presenting Sepsis-3 criteria in AmsterdamUMCdb, which is one of the largest freely accessible Intensive Care database in Europe.

Opening access and exploring sepsis in an  Intensive Care database. Q&amp;A with Tom Edinburgh

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

Tune in to the GigaByte and GBIF webinar that uncovers the details of the TDR sponsored call for data papers describing datasets on vectors of human diseases. 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/gbif-webinar/">GigaByte and GBIF Webinar: Data papers describing datasets on vectors of human diseases</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

UPDATE: GigaByte and GBIF webinar video added below.

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

We have an author Q&#038;A with Dominic Cushnan, Head of Artificial Intelligence (Imaging) for NHSX, on his Data Note on the National COVID-19 Chest Imaging Database.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/national-covid-19-chest-imaging-database-qa/">Open imaging data to assist AI in the COVID-19 fight. Q&#038;A with Dominic Cushnan</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Published today in

 GigaScience

is a Data Note describing the National COVID-19 Chest Imaging Database (NCCID), a centralised database containing chest X-rays, Computed Tomography (CT) and MRI scans from patients across the UK. Utilising the UK National Health Service’s unique position as the world’s single largest integrated healthcare system, the benefits of collecting chest imaging data this large are extensive and already being used

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

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

We have a Q&#038;A with author Matthieu Foll from the WHO/(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.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/controlled-access-data/">Accessing and reviewing Controlled Access Data of Rare Cancers. Q&#038;A with Matthieu Foll</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

For Open Access Week 2021 we look back over 10 of our favourite GigaScience papers providing examples of barriers we’ve tried to break for more open science.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/gigascience-open-access-week-2021/">Open Access Week 2021: GigaScience&#8217;s 10 Examples of Open</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

This week is International Open Access Week, and with the theme “It Matters How We Open Knowledge: Building Structural Equity”. This aims at highlighting the individual and collective action required alongside the decisions, actions, and investments in knowledge sharing to ensure that equity is foundational.

Open Access Week 2021: GigaScience’s 10 Examples of Open

Identity in Peer Review is the theme of Peer Review Week 2021, and GigaScience Press have a number of new collaborations and integrations embracing this.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/identity-in-peer-review/">Peer Review Week 2021: Preprints Meet Open Peer Review</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Embracing identity in Peer Review
 

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

Peer Review Week 2021: Preprints Meet Open Peer Review

Following the publication of a new software citation guide we explain more the practicalities and importance of citing research software.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/software-citation-guide/">Software Citation Comes of Age</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Since the very start of GigaScience we’ve been strong proponents of Data Citation, helping promote and practice the procedure of affording data the same importance in the scholarly record as citations of other research objects such as publications (see examples of this in GigaBlog and

 BMC Res Notes

). These efforts by the wider community culminated

Software Citation Comes of Age

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

Joining our Giga reproducibility toolkit is Gigantum, with a new paper being our first example using this platform for better collaboration, sharing and making reproducible research easier. 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/gigantum-joins-giga-reproducibility-machine-learning-toolkit/">Gigantum Joins the Giga Reproducibility Toolkit</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

Nicole Nogoy

GigaScience

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

Gigantum Joins the Giga Reproducibility Toolkit

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

New research in GigaScience reveals a previously hidden diversity of symbiotic Rickettsia bacteria. The new data are also relevant for studying human and animal diseases that are caused by some types of Rickettsia.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/rickettsia-bacteria-to-rule-them-all/">One group of bacteria to rule them all</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

GigaScience are huge fans of the VIZBI - Visualising Biological Data - conference and our Data Scientist Chris Armit details the major highlights of VIZBI 2021.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/vizbi-2021/">GigaScience at VIZBI 2021</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

The dizzying complexity of biological systems necessitates an abundance of tools that allow researchers to understand the deluge of sequence, structural, and systems-level data that is being generated in cell, molecular, and developmental biology.

GigaScience at VIZBI 2021

To promote re-use of microCT data and 3D models we have produced a video guide on how to 3D print a scorpion from GigaDB in 10 simple steps. 
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/a-step-by-step-guide-to-3d-print-a-scientific-publication/">A step-by-step guide to 3D print a scientific publication.</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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.

Today we publish the first update in 12 years describing what's new in SAMtools, and for the first time the associated BCFtools and HTSlib software library. Here is a Q&#038;A with the authors.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/play-it-again-samtools/">Play it again, SAMtools. Q&#038;A with the SAMtools team on 12 years of providing bioinformatics &#8220;glue&#8221;</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

The SAMtools suite of tools for manipulating sequencing data one of the most ubiquitous tools in bioinformatics, as the “glue” holding together much of bioinformatics we see it used in pretty much every genomics pipeline we are submitted.

Play it again, SAMtools. Q&amp;A with the SAMtools team on  12 years of providing bioinformatics “glue”

The Ukraine Genome Project finds quarter of the genetic variation in Europe, dramatically increasing information on population diversity and medical genetics.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/ukraine-genome-survey/">Ukraine Genome Survey Adds Missing Pieces to Human Diversity Puzzle</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

The

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

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

 GigaScience

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

Ukraine Genome Survey Adds Missing Pieces to Human Diversity Puzzle

Ducks, Emu's, Platypus and Echidna's, oh my! New work on the duck and other egg-laying animal genomes helps crack sex chromosomes evolution and diversity in a number of bird and monotreme species.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/sex-chromosome-evolution/">Cracking sex chromosome evolution via egg-laying birds and mammals</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

Prof Zhang Yongzhen is winner the 2020 ICG-15 GigaScience Prize for Outstanding Data Sharing during the COVID-19 Pandemic. Last month was the 10th year we’ve attended our co-publisher BGI’s annual ICG (International Conference on Genomics) gathering, and the 3rd time we have presented a prize at the meeting.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/covid-19-hero-wins-gigascience-prize/">COVID-19 Data-Sharing Hero Wins GigaScience Prize</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

.

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

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

COVID-19 Data-Sharing Hero Wins GigaScience Prize

Out this week in GigaScience is a new monitoring tool empowering infectious disease detectives. Scientists in Cambodia, who are supported by the Chan Zuckerberg Initiative, the Chan Zuckerberg Biohub, and the Bill &#038; Melinda Gates Foundation, used the new IDseq tool to help confirm and sequence the whole genome of the country’s first case of COVID-19. Read more here.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/idseq-infectious-disease-detectives/">A New Monitoring Tool Empowering Infectious Disease Detectives</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

Q&#038;A with Michael Fire talking about scientometric trends for coronaviruses and other infectious diseases, looking at why this research can "go viral"
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/scientometric-trends-for-coronaviruses/">Coronavirus research needs to be a marathon, not a sprint</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

It’s DNA day, celebrating two historic milestones: The publication of the structure of DNA in 1953, and the completion of the human genome project in 2003.

DNA day 2020: The genomes of Dominette and Esperanza

Q&#038;A with Stephen Piccolo talking about ShinyLearner, a benchmarking tool for machine-learning classification algorithms, &#038; how it was tested with CODECHECK
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/shinylearner-codecheck/">Reproducible Classification. Q&#038;A on ShinyLearner &#038; the CODECHECK certificate, pt. 2</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

 “certificate of reproducible computation”

when the results in the paper can be reproduced.

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

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

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

Hear more on how an international team led by researchers at the University of Copenhagen has sequenced the elusive giant squid genome.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/the-genome-of-an-elusive-giant/">The genome of an elusive giant</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

**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

Out today in

 GigaScience

is ShinyLearner, a new tool to make it easier to perform benchmark comparisons of classification algorithms. This tool stands out by making this process super systematic and reproducible, and despite needing to interface with many different libraries and languages it uses software containers (and a CodeOcean demo) so end users don’t need to worry about this complexity.

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

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

This is the last blog post of 2019 and it is time again to look back at some of the amazing research published in

 GigaScience

over the past year. Besides handling manuscripts, reviews and data, the editors and curators also attended conferences near and far, they contributed to policy discussions and prepared the launch of a new journal, GigaByte. More about all these activities below.

Big data, big conferences, big plans: 2019 in review

Lessons learned in the evolution of large-scale data sharing New studies out today elucidate the framework for 1 billion years of green plant evolution. The work are the results of nearly a decades work from an international consortium of nearly 200 plant researchers generating gene sequences from more than 1100 plant species. Here and in [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/1kp-capstone-data/">Harvesting the final fruits of the plant tree of life</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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


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


 generating gene sequences from more than 1100 plant species.

Harvesting the final fruits of the plant tree of life

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 [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/neuroinformatics-2019/">GigaScience at Neuroinformatics 2019</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

The Walter E. Washington Convention Center in Washington DC was the venue for this year’s ASCB|EMBO 2019 Meeting that took place on 7-11 December 2019. The American Society of Cell Biology conference, now merged with the EMBO meeting, is the largest yearly gathering for the cell imaging community, and

 GigaScience

has attended in the past.

GigaScience at ASCB|EMBO 2019 Meeting, Washington DC

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 Norwegian city of Trondheim seemed the place to be this June &#8211; with hotels in high demand  due to the BarCode Of Life conference, The Big Challenge Science Festival (including a concert by that famous science communicator Sting), and the Functional Metagenomics 2019 conference (#FMG2019) all taking place over the same period (June 16-19th). [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/func-in-the-fjords-functional-metagenomics-2019/">FUNC in the Fjords: Functional Metagenomics 2019 in Trondheim</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

In Sultry Switzerland, Bioinformatics is Radiant at ISMBECCB 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 [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/basel-ismbeccb-and-bosc-2019/">Bioinformaticians Baking in Blazing Basel: ISMBECCB and BOSC 2019</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

Bioinformaticians Baking in Blazing Basel: ISMBECCB and BOSC 2019

Author Q&#038;A with Bonnie Hurwitz on the iMicrobe platform for open science and metagenomics, relevant to our FAIR principles and reproducible research.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/imicrobe-qa-bonnie-hurwitz/">iMicrobe: Fostering Community-Driven Science and Data Discovery. Q&#038;A with Bonnie Hurwitz</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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

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. The international group of researchers, lead by Joseph Ryan (University of Florida), chose to examine jellyfish that present a [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/jellyfish-genomes/">Genomic Warning Flag Just in Time for Beach Season: Jellyfish Toxins</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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

Read more about Open Humans from Bastian Greshake Tzovaras &#038; Mad Price Ball, a community-based data sharing platform for ethical participant led research.
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/open-humans-qa/">Power to the People and Their Data &#8211; The Open Humans Way. Q&#038;A with Bastian Greshake Tzovaras and Mad Price Ball</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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

The 12th International

 Biocuration

Conference was held in Cambridge, UK from April 7-10th 2019. As regular participants of the meeting you can read our write-ups of the meeting going back to 2012. This is a forum for biocurators and developers to discuss their work and to promote collaboration.

Curators Capture Cambridge. Biocuration 2019

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

The 21st meeting of the Genomics Standards Consortium (GSC21) took place last week in Vienna at one of the oldest universities in the world – the University of Vienna – from May 20th-23rd.  We’ve been long time supporters and participants of the Genomics Standards Consortium meetings going back to 2012’s GSC13 in Shenzhen, and have also published a special series of GSC “Best Practice in Genomics Research” papers.

Genomics Standards on the Danube. GigaScience at GSC21 in Vienna

FAIRer Sharing via FAIRsharing 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 [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/presenting-the-fairsharing-community-network/">Presenting the FAIRsharing community network</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

**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

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

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. Regular readers of this blog and journal will have seen the many crowdfunded and educational community genome projects we have promoted [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/citizen-science-at-unea4/">Citizen Science goes mainstream. Back at the UN with the Citizen Science Global Partnership.</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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.

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

Visualising Biological Data. GigaScience at VIZBI

The diffraction limit of a microscope hinders the ability to see single molecules as the optics do not allow the researcher to distinguish between two fluorescently labelled molecules that are less than 200nm apart. As a means of overcoming this barrier,

 super-resolution microscopy

utilises various tricks to go beyond the diffraction limit and image sub-cellular nanostructure in cells and tissues.

GigaScience at ESRIC Super-Resolution Clinic

New genomic data from five birds-of-paradise reveal genes that are shaped by selection and help explain the origin of their spectacular plumage.

Birds-of-paradise, with their elaborate and colorful feathers and their complex courtship displays, are a school-book example of sexual selection.

Genomes from paradise

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 &#8211; of which there are many. Prizes were handed out and received, we travelled to conferences all over [&#8230;]
The post <a rel="nofollow" href="http://gigasciencejournal.com/blog/prizes-given-and-received-and-other-2018-highlights/">Prizes given and received, and other 2018 highlights</a> appeared first on <a rel="nofollow" href="http://gigasciencejournal.com/blog">GigaBlog</a>.

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

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!

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.