- Sep 2023
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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skin is used for making the membranes of a traditional musical instrument, the erhu
For a video on how snakeskin erhu are made see https://youtu.be/YhDsmXj0TZ8
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- Jan 2020
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academic.oup.com academic.oup.com
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This article argues that it is high time not only to acknowledge Wikipedia's quality but also to start actively promoting its use and development in academia.
This argment is carried on in the Wikipedia Weekly facebook forum https://www.facebook.com/groups/wikipediaweekly/permalink/2538506099530539/
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Linus's Law: “given enough eyeballs, all bugs are shallow,”
See The Cathedral and the Bazaar by Eric Steven Raymond which first named this in honour of Linux creator Linus Torvalds http://www.catb.org/~esr/writings/cathedral-bazaar/cathedral-bazaar/
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initiatives in computational biology
See also the ISCB wikipedia competition that incentivizes (via a cash award) wikipedia entries on computational biology topics. See https://www.iscb.org/iscb-wikipedia-wikidata-competition and https://www.iscb.org/iscb-wikipedia-wikidata-competition
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academic.oup.com academic.oup.com
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The Research Parasite Awards
For more perspectives from one of the founders of the award see this related commentary https://doi.org/10.1093/gigascience/giy129
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academic.oup.com academic.oup.com
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2019 Research Parasite Awards
See the commentary from 2019 Junior Parasite Award winner Claire Duvallet giving her perspective of winning the award https://doi.org/10.1093/gigascience/giz148
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- Dec 2019
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academic.oup.com academic.oup.com
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Abstract
You can see a video abstract and more information on the project in GigaBlog here: http://gigasciencejournal.com/blog/jack-rabbits-lizards-and-squirrels-oh-my-camera-trap/
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- Nov 2019
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academic.oup.com academic.oup.com
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Alzheimer’s Disease Neuroimaging Initiative (ADNI)
The ADNI data is accessible via here http://adni.loni.usc.edu/data-samples/access-data/
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academic.oup.com academic.oup.com
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Common Workflow Language (CWL)
See CWL Website https://www.commonwl.org/
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academic.oup.com academic.oup.com
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nly 37 butterfly species in 6 families including 5 swallowtails (Papilionidae) have had their reference genomes dissected
In July 2019 whole genome data for more than 160 representatives of skipper butterflies was published, although these were not de novo genome assemblies https://doi.org/10.3897/zookeys.861.34686
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academic.oup.com academic.oup.com
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Megadyptes antipodes antipodes Yellow-eyed Wild Otago Peninsula, New Zealand South Island OT 2 9/2/18 August 2018
Data in GigaDB here: http://dx.doi.org/10.5524/102172
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hoiho (yellow-eyed penguin
The rarest penguin species, and in 2019 voted "New Zealand Bird of the Year" https://www.nzherald.co.nz/nz/news/article.cfm?c_id=1&objectid=12284052
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- Oct 2019
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academic.oup.com academic.oup.com
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pallium
AKA the mantle https://en.wikipedia.org/wiki/Mantle_(mollusc)
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[4–6]
Also a growing problem in Cuba and the Caribbean
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- Aug 2019
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europepmc.org europepmc.org
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von Waldeyer-Hartz HWG. Über Karyokinese und ihre Beziehungen zu den Befruchtungsvorgängen. Arch Mikroskop Anat Entwicklungsmechanik 1888;32:1–122.
As this is out of copyright you can read the original work in wikimedia commons https://upload.wikimedia.org/wikipedia/commons/6/60/Ueber_Karyokinese_und_ihre_Beziehungen_zu_den_Befruchtungsvorg%C3%A4ngen.pdf
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forum
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- May 2019
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rvhost-alpha.rivervalleytechnologies.com rvhost-alpha.rivervalleytechnologies.com
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We obtained
I don't believe it!
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- Nov 2018
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diyhpl.us diyhpl.us
- Jul 2018
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rijam.gitlab.io rijam.gitlab.io
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Enable HTTPS
HTTPS is very important, but would this cause problems in China?
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- Jul 2017
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gigadb.org gigadb.org
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RNAs
Ribonucleic Acid
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- Mar 2017
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med.stanford.edu med.stanford.edu
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FAIR (Findable, Accessible, Interoperable, Reusable) principles
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Genome Sequence Archive (GSA)
Database URL is here: http://gsa.big.ac.cn/
Note: metadata is INSDC format, but this database isn't part of the INSDC, so you'll still need to submit your data to one of those databases to meet internationally recognised mandates
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gigadb.org gigadb.org
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notorious
National Geographic and others have dubbed it "Fishzilla" http://natgeotv.com/asia/fishzilla/about
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gigadb.org gigadb.org
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wisent, also known as European bison
According to BMC Biology, 2016 was "the year of the Wisent"dx.doi.org/10.1186/s12915-016-0329-3
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- Jun 2016
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viennaprinciples.org viennaprinciples.org
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copyright
even if not copyrighted, un-interoperable licensing would be an issue too.
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digital form
Following the open definition, worth stressing machine readable too?
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gigadb.org gigadb.org
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Additional information:
More information also in this blog interview with the first author: http://blogs.biomedcentral.com/gigablog/2016/06/08/introducing-gigwa-genotype-investigator-genome-wide-analyses/
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- May 2016
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datascience.codata.org datascience.codata.org
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What is missing and trends.
Cough GigaScience Cough. See integrated GigaDB repo http://database.oxfordjournals.org/content/2014/bau018.full
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- Apr 2016
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gigadb.org gigadb.org
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http://galaxy.cbiit.cuhk.edu.hk/
This has now migrated to: http://gigagalaxy.net/
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IsPreviousVersionOf doi:10.5524/100148
This paper was studied in a case study that lead to some corrections. See the paper here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612
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gigadb.org gigadb.org
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Micro-computed tomography scans and virtual histological slides of a recently described land planarian species of Obama otavioi (Platyhelminthes).
More information on the study (and a video) in this blog posting here: http://blogs.biomedcentral.com/gigablog/2016/03/17/see-inside-obama-3d-yes-can/
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biosharing.org biosharing.org
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Published in 2015
These policies have been built on the Fort Lauderdale principles, see the original policies from 2003 https://www.genome.gov/10506537/
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gigadb.org gigadb.org
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crab-eating macaque
This was sequenced at the same time and is available from http://dx.doi.org/10.5524/100003
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gigadb.org gigadb.org
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Chinese rhesus
This was sequenced at the same time and is available as dataset http://dx.doi.org/10.5524/100002
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gigadb.org gigadb.org
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To maximize its utility
The unusual data released strategy involving crowdsourcing on twitter, is discussed in more detail in this blog http://blogs.biomedcentral.com/gigablog/2011/08/03/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/
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gigadb.org gigadb.org
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ISA Commons communities
The ISA Commons website is here http://www.isa-tools.org/
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gigadb.org gigadb.org
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Workflow, Virtual-Machine
The dockerised workflows are discussed in more detail in this blog posting here: http://blogs.biomedcentral.com/gigablog/2015/07/30/fermenting-reproducible-research-revolution/
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gigadb.org gigadb.org
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Related manuscripts:
See also this population genomics study in Nature Genetics that uses this data: http://www.nature.com/ng/journal/v45/n1/full/ng.2494.html See also this blog posting on data citation of this data (and related problems): http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/
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www.nature.com www.nature.com
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Accession codes
The panda and polar bear datasets should have been included in the data section rather than hidden in the URLs section. Production removed the DOIs and used (now dead) URLs instead, but for the working links and insight see the following blog: http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/
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gigadb.org gigadb.org
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doi:10.1016/j.cell.2014.03.054
More on the backstory and other papers using and citing this data before the Cell publication in ths blog posting: http://blogs.biomedcentral.com/gigablog/2014/05/14/the-latest-weapon-in-publishing-data-the-polar-bear/
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gigadb.org gigadb.org
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genomically poorly explored
Poorly studied in some part to its very high degree of heterozygosity. You can get some more insight here, where it was nominated as a "top ten genome" http://www.homolog.us/blogs/blog/2015/05/08/top-ten-genomes-ix-pacific-oyster/
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gigadb.org gigadb.org
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To date 5'-cytosine methylation (5mC) has not been reported in Caenorhabditis elegans, and using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) the existence of DNA methylation in T. spiralis was detected, making it the first 5mC reported in any species of nematode.
As a novel and potentially controversial finding, the huge amounts of supporting data are depositedhere to assist others to follow on and reproduce the results. This won the BMC Open Data Prize, as the judges were impressed by the numerous extra steps taken by the authors in optimizing the openness and easy accessibility of this data, and were keen to emphasize that the value of open data for such breakthrough science lies not only in providing a resource, but also in conferring transparency to unexpected conclusions that others will naturally wish to challenge. You can see more in the blog posting and interview with the authors here: http://blogs.biomedcentral.com/gigablog/2013/10/02/open-data-for-the-win/
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biosharing.org biosharing.org
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Giga Science Database
For more about GigaDB, see the paper in Database Journal: http://database.oxfordjournals.org/content/2014/bau018.full
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gigadb.org gigadb.org
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Long Fragment Read technology
See Nature doi:10.1038/nature11236 for more on how LFR works: http://www.nature.com/nature/journal/v487/n7406/full/nature11236.html
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