scott edmunds: gigascience datacite meeting rapid fire talk
TRANSCRIPT
Scott Edmunds
:: a new resource for the big-data community.
www.gigasciencejournal.com
1 Illumina HiSeq 2000 (+Truseq upgrade)
= 600Gb/run (12 days)
X 128 Hiseq = 6Tb/day = >2Pb/year
= ~ 2000 Human Genomes/day
Potential sequencing capacity
Incentives/creditCredit where credit is overdue:“One option would be to provide researchers who release data to public repositories with a means of accreditation.”“An ability to search the literature for all online papers that used a particular data set would enable appropriate attribution for those who share. “Nature Biotechnology 27, 579 (2009)
Prepublication data sharing (Toronto International Data Release Workshop)“Data producers benefit from creating a citable reference, as it can later be used to reflect impact of the data sets.”Nature 461, 168-170 (2009)
www.gigasciencejournal.com
Large-Scale Data
Journal/Database
Editor-in-Chief: Laurie Goodman, PhD
Editor: Scott Edmunds, PhD
Assistant Editor: Alexandra Basford, PhD
In conjunction with:
Now taking submissions…
www.gigasciencejournal.com
Criteria and Focus of Journal/Database
Reproducibility/Reuse
Utility/Usability
Standards/Searchability/Scale/Sharing
Hosting/Tools
www.gigasciencejournal.com
Data publishing/DOINew journal format combines standard manuscript publication with an extensive database to host all associated data. Data hosting will follow standard funding agencyand community guidelines.DOI assignment available for submitted data to allow ease of finding and citing datasets, as well as for citation tracking.
To maximize its utility to the research community and aid those fighting the current epidemic, genomic data is released here into the public domain under a CC0 license. Until the publication of research papers on the assembly and whole-genome analysis of this isolate we would ask you to cite this dataset as:
Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X; Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. doi:10.5524/100001 http://dx.doi.org/10.5524/100001
Our first DOI:
To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to Genomic Data from the 2011 E. coli outbreak. This work is published from: China.
“The way that the genetic data of the 2011 E. coli strain were disseminated globally suggests a more effective approach for tackling public health problems. Both groups put their sequencing data on the Internet, so scientists the world over could immediately begin their own analysis of the bug's makeup. BGI scientists also are using Twitter to communicate their latest findings.”
“German scientists and their colleagues at the Beijing Genomics Institute in China have been working on uncovering secrets of the outbreak. BGI scientists revised their draft genetic sequence of the E. coli strain and have been sharing their data with dozens of scientists around the world as a way to "crowdsource" this data. By publishing their data publicy and freely, these other scientists can have a look at the genetic structure, and try to sort it out for themselves.”
G10K Genomes Get DOI®s
doi:10.5524/100004
www.gigasciencejournal.com
We want your
data!
@gigascience