eLife and innovations for open sharing

Talk presented at APE 2013 in Berlin on 2013-01-30.

Transcript

1. Innovations for Open Sharing at eLife Ian Mulvany Head of Technology
2. World-class backing • Supported by three of the world’s leading research funders • Effective research communication is a critical part of research • Editorially, eLife is entirely independent of the funders Ground-breaking science, selected by experts, published without delay, open for greater influence.
3. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
4. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement
5. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC
6. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC Editorial Board
7. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC Editorial Board 1st Submission
8. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC Editorial Board 1st Submission 1st Publication
9. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC Editorial Board 1st Submission 1st Publication Journal Platform
10. v1 3 Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013 Announcement EIC Editorial Board 1st Submission 1st Publication Journal Platform 60 Publications
11. v1 4 elife.elifesciences.org
12. v1 4 elife.elifesciences.org We launched in December 2012, this made us very happy :)
13. v1 5 Build an Architecture of Attention image: flickr abustaca
14. v1 5 Build an Architecture of Attention image: flickr abustaca In a world of OA abundance, this is what we think publishers should be doing for their authors.
15. v1 6 Make content Promiscuous image: flickr tonicastillo
16. v1 6 Make content Promiscuous image: flickr tonicastillo Do this, and give the work a chance to meet a reader that can use it.
17. v1 Social 7 Robots Humans and
18. v1 Social 7 Robots Humans and We do things to promote sharing that are aimed at both humans and robots.
19. v1 8 CC-BY Being CC-BY works for both humans and robots - WIN!
20. v1 9 Humans image: flickr matthewfield
21. v1 Media policy 2 10 Open Reviews By opening up the review letters, and author response, we hope that we can share the experience of peer review and help readers understand the decision criteria for the journal.
22. v1 11
23. v1 11
24. v1 12
25. v1 12
26. v1 13 94 % Making the decision letter open is at the discretion of the author, 94% of our authors want to make this information open.
27. v1 14 Digests Every paper gets a digest, the digest is a short summary written for a lay audience, with the aim of making the research more accessible to the wider public.
28. Media Policy v1 15 - Authors: openly discuss and share your work whenever you have the chance - eLife: share openly, promote, foster understanding
29. v1 16 No Inglefinger Our media policy is designed to get of of the way of the authors, and increase their ability to talk about their work.
30. v1 17 By the end of October, we will have covered 122 studies from journals for our consumer service. Of those, 45 were embargoed — but we didn’t hit the embargo on 12 of them, because we had better things to do, like cover more interesting studies that weren’t embargoed. - Ivan Oransky 73%
31. v1 17 By the end of October, we will have covered 122 studies from journals for our consumer service. Of those, 45 were embargoed — but we didn’t hit the embargo on 12 of them, because we had better things to do, like cover more interesting studies that weren’t embargoed. - Ivan Oransky 73% There is evidence to suggest that most reported science is not under an embargo in any case
32. v1 18 Robots image: http://damhorst.de/hawkins/wp-content/uploads/2010/06/RobotArmy_Stehickdruff_schwarz.jpg
33. v1 19 Strategy Peer review Traditional Venues This is how publishing usually works
34. v1 20 Peer review Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
35. v1 20 Peer review Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
36. v1 20 Peer review Traditional Venues API Non-Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
37. v1 20 Peer review Traditional Venues API Non-Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
38. v1 20 Peer review Traditional Venues API Non-Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
39. v1 20 All Curated Peer review Traditional Venues API Non-Traditional Venues This is the system that we are building, API driven to increase the surface area of the content, and to deliver usage information to the authors
40. v1 21 We wanted a robust API, that we could create quickly, we chose fluidinfo as a hosted service
41. v1 22 fluidinfo allows the creation of openly writable objects with a fluid data model, we mapped our article XML into key - value pairs in fluidinfo
42. v1 23 Every article has an API endpoint.
43. v1 23 Every article has an API endpoint.
44. v1 24 "2013-01-23T17:35:03.582705", "value": "research-article"}, "elifesciences.org/api_v1/article/pub_date_day": {"username": "elifesciences.org", "2013-01-23T17:35:03.582705", "value": 22}, "elifesciences.org/api_v1/article/correspondence": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "*For correspondence: darnelr@rockefeller.edu"}, "elifesciences.org/api_v1/article/award_group_funding_ {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "Howard Hughes Medical Institute"}, "elifesciences.org/ article/research_organism": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "Mouse"}, "elifesciences.or article/license_url": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "http://creativecommons.org/licen "elifesciences.org/api_v1/article/doi_url": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "http://dx. 10.7554/eLife.00178"}, "elifesciences.org/api_v1/article/pub_date_timestamp": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:3 "value": 1358812800}, "elifesciences.org/api_v1/article/components": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.5827 ["http://dx.doi.org/10.7554/eLife.00178.001", "http://dx.doi.org/10.7554/eLife.00178.002", "http://dx.doi.org/10.7554/eLife.00178.003", "http: 10.7554/eLife.00178.004", "http://dx.doi.org/10.7554/eLife.00178.005", "http://dx.doi.org/10.7554/eLife.00178.006", "http://dx.doi.org/10.7554 00178.007", "http://dx.doi.org/10.7554/eLife.00178.008", "http://dx.doi.org/10.7554/eLife.00178.009", "http://dx.doi.org/10.7554/eLife.00178.0 dx.doi.org/10.7554/eLife.00178.012", "http://dx.doi.org/10.7554/eLife.00178.013", "http://dx.doi.org/10.7554/eLife.00178.014", "http://dx.doi. eLife.00178.015", "http://dx.doi.org/10.7554/eLife.00178.016", "http://dx.doi.org/10.7554/eLife.00178.017", "http://dx.doi.org/10.7554/eLife.0 "http://dx.doi.org/10.7554/eLife.00178.019", "http://dx.doi.org/10.7554/eLife.00178.020", "http://dx.doi.org/10.7554/eLife.00178.021", "http:/ 10.7554/eLife.00178.022", "http://dx.doi.org/10.7554/eLife.00178.023", "http://dx.doi.org/10.7554/eLife.00178.024", "http://dx.doi.org/10.7554 00178.025", "http://dx.doi.org/10.7554/eLife.00178.026", "http://dx.doi.org/10.7554/eLife.00178.027", "http://dx.doi.org/10.7554/eLife.00178.0 dx.doi.org/10.7554/eLife.00178.031"]}, "elifesciences.org/api_v1/article/journal_title": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "eLife"}, "elifesciences.org/api_v1/article/keywords": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": ["HITS-CLIP", "Nonsense mediated decay", "alternative splicing", "RNA regulation", "epilepsy", "neurona "elifesciences.org/api_v1/article/authors": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": ["Taesun Eo Zhang", "Huidong Wang", "Kenneth Lay", "John Fak", "Jeffrey L Noebels", "Robert B Darnell"]}, "elifesciences.org/api_v1/article/award_group_aw {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "NS34389"}, "elifesciences.org/api_v1/article/accepted_ {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": 29}, "elifesciences.org/api_v1/article/accepted_date_da {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "November 29, 2012"}, "elifesciences.org/api_v1/article article_institution": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "University of Toronto"}, "elifes api_v1/article/award_group_principle_award_recipient": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": Darnell"}, "elifesciences.org/api_v1/article/accepted_date_timestamp": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.58 "value": 1354147200}, "elifesciences.org/api_v1/article/refs": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", " ["Blainey PC van Oijen AM Banerjee A Verdine GL Xie XS. 2006. A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr 2009. RNA and disease. Cell 136: 777 \u2013 93.", "Crittenden SL Bernstein DS Bachorik JL Thompson BE Gallegos M Petcherski AG. 2002. A conser binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417: 660 \u2013 3.", "Darnell RB. 2004. Paraneoplastic neurolog windows into neuronal function and tumor immunity. Arch Neurol 61: 30 \u2013 2.", "Darnell RB. 2006. Developing global insight into RNA regula Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco \u2013 98.", "Darnell RB. 1996. Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and Proc Natl Acad Sci USA 93: 4529 \u2013 36.", "Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley In RNA 1: 266 \u2013 86.", "Darnell RB Posner JB. 2011. Paraneoplastic syndromes (contemporary neurology series). USA: Oxford University Press.", Sherman BT Hosack DA Yang J Gao W Lane HC. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.", Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo 23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11 10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass This is what the response looks like
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A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr 2009. RNA and disease. Cell 136: 777 \u2013 93.", "Crittenden SL Bernstein DS Bachorik JL Thompson BE Gallegos M Petcherski AG. 2002. A conser binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417: 660 \u2013 3.", "Darnell RB. 2004. Paraneoplastic neurolog windows into neuronal function and tumor immunity. Arch Neurol 61: 30 \u2013 2.", "Darnell RB. 2006. Developing global insight into RNA regula Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco \u2013 98.", "Darnell RB. 1996. Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and Proc Natl Acad Sci USA 93: 4529 \u2013 36.", "Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley In RNA 1: 266 \u2013 86.", "Darnell RB Posner JB. 2011. Paraneoplastic syndromes (contemporary neurology series). USA: Oxford University Press.", Sherman BT Hosack DA Yang J Gao W Lane HC. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.", Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo 23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11 10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass v1 25 It has key value pairs, lots of them.
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A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr 2009. RNA and disease. 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USA: Oxford University Press.", Sherman BT Hosack DA Yang J Gao W Lane HC. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.", Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo 23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11 10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass v1 25 authors: Taesun Eom", "Chaolin Zhang", "Huidong Wang", "Kenneth Lay", "John Fak", "Jeffrey L Noebels", "Robert B Darnell It has key value pairs, lots of them.
47. v1 26 Some of our services are hooked up already, some are being done manually and some are under development.
48. v1 26 Some of our services are hooked up already, some are being done manually and some are under development.
49. v1 26 Some of our services are hooked up already, some are being done manually and some are under development.
50. v1 26 Some of our services are hooked up already, some are being done manually and some are under development.
51. v1 27 We will pull usage data back to our journal for the authors to see, via our writable API
52. v1 28 https://github.com/ elifesciences Our code is open, have a look, help us make it better. http://dev.elifesciences.org/
53. If you have done any of these, let us know how it went. If you want to try any of these things, ask us about our experiences v1 Conclusion
54. v1 30 Follow us @eLife_sciences @IanMulvany
55. Thank you! v1 31 APE 2013