Scott Edmunds talk at BGI's Bio-IT APAC meeting in Shenzhen introducing BGI/BMC's new big-data journal - GigaScience. 7th July 2011

1. Scott Edmunds :: a new resource for the big-data community. www.gigasciencejournal.com

2. Data Tsunami? Flickr cc: opensourceway

3. Sequencing cost($ per Mbp) Moore’s Law ~100,000X Sequencing Source: E Lander/Broad

4. Sequencing Output Data Storage Moore’s/Kryders Law

5. Sequencing Output Data Publication Dissemination?

6. Potential sequencing capacity 1 IlluminaHiSeq 2000 (+Truseq upgrade) = 600Gb/run (12 days) X 128 Hiseq= 6Tb/day = >2Pb/year = ~ 2000 Human Genomes/day

7. Can we keep up? Flickr cc: opensourceway

8. Now taking submissions… Large-Scale Data Journal/Database In conjunction with: Editor-in-Chief: Laurie Goodman, PhD Editor: Scott Edmunds, PhD Assistant Editor: Alexandra Basford, PhD www.gigasciencejournal.com

9. Editorial Board: International Stephen O'Brien, USA HanchuanPeng, USA Ming Qi, China/USA Susanna-AssuntaSansone, UK Michael Schatz, USA David Schwartz, USA SumioSugano, Japan Thomas Wachtler, Germany Jun Wang, China Marie Zins, France Stephan Beck, UK Ann-Shyn Chiang, Taiwan Richard Durbin, UK Paul Flicek, UK Robert Hanner, Canada YoshihideHayashizaki, Japan Henning Hermjakob, UK Gary King, USA Donald Moerman, Canada Karen Nelson, USA www.gigasciencejournal.com

10. Editorial Board: Broad Span (all “big-data”) Stephen O'Brien, Genomics HanchuanPeng, Imaging/Neuro Ming Qi, Genetics/Variome Susanna-AssuntaSansone, Standards Michael Schatz, Genomics/Cloud David Schwartz, Optical Mapping SumioSugano, Genomics Thomas Wachtler, Neuroscience Jun Wang, Genomics Marie Zins, Medicine Stephan Beck, Epigenomics Ann-Shyn Chiang, Neuroscience Richard Durbin, Genetics/Genomics Paul Flicek, Genomics/Databases Robert Hanner, Barcoding/Ecology YoshihideHayashizaki, Genomics Henning Hermjakob, Proteomics Gary King, Medicine/methods Donald Moerman, Functional Genomics Karen Nelson, Metagenomics www.gigasciencejournal.com

12. Utility/Usability

13. Standards/Searchability/Scale/Sharing

14. Data publishing/DOIwww.gigasciencejournal.com

15. Use of Data = Importance + Usability easier to assess subjective? www.gigasciencejournal.com

17. DOI assignment available for submitted data to allow ease of findingand citing datasets, as well as for citation tracking.

18. Datasets tracked by WOS/ISI allowing additional metrics/credit for use.www.gigasciencejournal.com

20. Integrated tools to promote more widespread access, viewing, and analysis of data.

21. Encourage and aid use of workflow systems for methods (e.g. submission of Galaxy XML files).www.gigasciencejournal.com

23. Tools + Test Data (BGI or user) in one place.

24. Aids reproducibility.

25. Aids reviewers (free)

26. Aids authors: visibility (pubmed, etc.) hosting (included/free offers) –contact us: editorial@gigasciencejournal.com Oledoeflickr cc www.gigasciencejournal.com

28. Allsupporting data must be publically available.

29. Ask for MIBBI compliance and use of reporting checklists.

30. Part of the Biosharing network.www.gigasciencejournal.com

31. Benefits of Data-sharing Sharing Detailed Research Data Is Associated with Increased Citation Rate. Piwowar HA, Day RS, Fridsma DB (2007) PLoSONE 2(3): e308. doi:10.1371/journal.pone.0000308 Every 10 datasets collected contributes to at least 4papers in the following 3-years. Piwowar, HA, Vision, TJ, & Whitlock, MC (2011). Data archiving is a good investment Nature, 473 (7347), 285-285 DOI: 10.1038/473285a

32. Our first DOI: 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 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.

35. “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.”

36. G10K Genomes Get DOI®s doi:10.5524/100004

37. We want your data! scott.edmunds@genomics.org.cn editorial@gigasciencejournal.com @gigascience www.gigasciencejournal.com