I need to publish            more and read less                       Cameron Neylon - Munin Conference                   ...
technologies...p://www.flickr.com/photos/cappellmeister/39508741 CC-BY Wednesday, 14 December 11
conceptual                                                         changes...http://www.flickr.com/photos/ivanwalsh/4509575...
...central                                                     principle.http://www.flickr.com/photos/mkumm/2709555496 CC-B...
But first.Wednesday, 14 December 11
@communicating Plausible   Accuracy PIERRE LINDENBAUM Mummi Thorissson     John  Fabiana Kubke Richard Grant              ...
Wednesday, 14 December 11
Wednesday, 14 December 11
Who am I?Wednesday, 14 December 11
I live in Bathhttp://www.flickr.com/photos/andypowe11/3915450391Wednesday, 14 December 11
I work at RALWednesday, 14 December 11
I work on...Wikimedia Commons                               Wikimedia CommonsSuccinate_Dehydrogenase_1YQ3_and_Membrane.png...
I work on...Wednesday, 14 December 11
I work on...Wednesday, 14 December 11
I write grants...http://www.flickr.com/photos/59937401@N07/5929622407 CC-BYWednesday, 14 December 11
...and papers...http://flickr.com/photos/nicmcphee/2756494307/ CC-BYWednesday, 14 December 11
Wednesday, 14 December 11
39 Presentations                            ~100,000 views                            Slideshare - http://slideshare.net/C...
http://cameronneylon.netWednesday, 14 December 11
Papers are not enough...Wednesday, 14 December 11
...software...Wednesday, 14 December 11
...data...Wednesday, 14 December 11
Need to communicate...Wednesday, 14 December 11
all the pieces...http://www.flickr.com/photos/jurvetson/3184362622 CC-BYWednesday, 14 December 11
Need to maximise “impact”...http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11
But that’s ok...Wednesday, 14 December 11
We have new tools...http://www.flickr.com/photos/kylemay/1430449350 CC-BYWednesday, 14 December 11
Many new ways and                            places to publish...Wednesday, 14 December 11
So...Wednesday, 14 December 11
Sortase-Mediated Ligation        group, and finally attachment to the solid support. In addition the        use of intein ...
...publish the data...Wednesday, 14 December 11
...in the right places...Wednesday, 14 December 11
...the software...Wednesday, 14 December 11
...and all the rest?Wednesday, 14 December 11
Wednesday, 14 December 11
http://usefulchem.wikispaces.com/Exp207                                          Flickr tag: UC207Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
http://www.flickr.com/photos/stuartpilbrow/3345896050 CC-BY-SAWednesday, 14 December 11
This is not sustainable...Wednesday, 14 December 11
“I need to publish more”Wednesday, 14 December 11
...not work more...Wednesday, 14 December 11
We have...http://www.flickr.com/photos/schnurrbart/43568532 CC-BY-SAWednesday, 14 December 11
A resource problem...http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SAWednesday, 14 December 11
Whether it’s money...Wednesday, 14 December 11
...or time...http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11
Technical capacity is not enoughWednesday, 14 December 11
...either need to resource itWednesday, 14 December 11
...or make it cheaper.Wednesday, 14 December 11
Wednesday, 14 December 11
Publication as a side  effect of recording....Wednesday, 14 December 11
“Publish@Source”                                    Jeremy Frey,                                    SouthamptonWednesday, ...
Wednesday, 14 December 11
Wednesday, 14 December 11
http://usefulchem.wikispaces.com/Exp258Wednesday, 14 December 11
http://www.carlboettiger.info/Wednesday, 14 December 11
http://www.myexperiment.org/workflows/204.htmlWednesday, 14 December 11
Wednesday, 14 December 11
http://www.flickr.com/photos/psychemedia/Wednesday, 14 December 11
Easy to publish pieces...http://www.flickr.com/photos/horiavarlan/4514164700 CC-BYWednesday, 14 December 11
...and then collectWednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
So we capture and collect...http://www.flickr.com/photos/furtwangl/3851841424Wednesday, 14 December 11
Dionaea muscipula                    Musca domestica                             chomped on                            ......
...aggregate existing pieceshttp://www.flickr.com/photos/lizadaly/2944376209 CC-BYWednesday, 14 December 11
...we can open the floodgates...http://www.flickr.com/photos/bladeflyer/442496389 CC-BYWednesday, 14 December 11
...all the way...http://www.flickr.com/photos/fraz5356/4754482759 CC-BYWednesday, 14 December 11
It’ll be great...right?http://www.flickr.com/photos/62337512@N00/3958637561 CC-BYWednesday, 14 December 11
group, and finally attachment to the solid support. In addition the          use of intein based methods as well as the pr...
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
http://usefulchem.wikispaces.com/Exp207          All of this information...data....                                       ...
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
All of this information...data....Wednesday, 14 December 11
Wednesday, 14 December 11
http://www.flickr.com/photos/waltstoneburner/3372746317 CC-BYWednesday, 14 December 11
Retractions per 100k papers                                                     30                 Retractions per 100k pu...
http://www.flickr.com/photos/oakleyoriginals/2879794262 CC-BYWednesday, 14 December 11
watercannon?http://www.flickr.com/photos/7827294@N04/4621721577 CC-BYWednesday, 14 December 11
Information overload...http://www.flickr.com/photos/dylanroscover/3450505729 CC-BY-SAWednesday, 14 December 11
“I need to read less”Wednesday, 14 December 11
Filter failure?http://www.flickr.com/photos/daveyll/332723930Wednesday, 14 December 11
http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BYWednesday, 14 December 11
Filters block.http://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
You think this is   a good thing...http://www.flickr.com/photos/robmcm/1671702203 CC-BY-SAWednesday, 14 December 11
...we’re “protecting ourcommunity from a deluge”http://www.flickr.com/photos/mrehan00/3700858676 CC-BY-SAWednesday, 14 Dece...
...staying on the                                     straight and narrow...http://www.flickr.com/photos/quinnanya/48139741...
Or are we just limitingour ability to explore...?http://www.flickr.com/photos/jurvetson/2174000357 CC-BYWednesday, 14 Decem...
...and discover...?http://www.flickr.com/photos/joiseyshowaa/2374526016 CC-BYWednesday, 14 December 11
Filters block.http://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
The right filter for me? Right filter for now?http://www.flickr.com/photos/lotzman/3595748169 CC-BYWednesday, 14 December 11
Wednesday, 14 December 11
Remember this graph?                                                     30                 Retractions per 100k publicati...
Remember this graph?                                                     30                 Retractions per 100k publicati...
Remember this graph?                                                     30                 Retractions per 100k publicati...
Remember this graph?                                                     30                 Retractions per 100k publicati...
But how did I discover it?Wednesday, 14 December 11
http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
Wednesday, 14 December 11
http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
Remember these people?Wednesday, 14 December 11
@communicating Plausible   Accuracy PIERRE LINDENBAUM Mummi Thorissson     John  Fabiana Kubke Richard Grant              ...
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Wednesday, 14 December 11
Social aggregation...Wednesday, 14 December 11
...but also...Wednesday, 14 December 11
Wednesday, 14 December 11
Social annotationWednesday, 14 December 11
...and quality                                                           assessmenthttp://www.flickr.com/photos/pinksherbet...
...but also...Wednesday, 14 December 11
http://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/Wednesday, 14 December 11
http://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/Wednesday, 14 December 11
A network of linked objects...Wednesday, 14 December 11
...primed for discovery...Wednesday, 14 December 11
Wednesday, 14 December 11
It’s not filter failurehttp://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
...it’s a discovery deficit...http://www.flickr.com/photos/nationallibrarynz_commons/4078337883 Public DomainWednesday, 14 ...
In the last year...?http://flickr.com/photos/stewart/461099066/Wednesday, 14 December 11
...in the past 24 hours?Wednesday, 14 December 11
Is search the answer?http://www.flickr.com/photos/ezioman/2096469724 CC-BYWednesday, 14 December 11
...or something more...?http://www.flickr.com/photos/mangostrawberry/5490992826 CC-BYWednesday, 14 December 11
Need the right instrument...http://www.flickr.com/photos/conskeptical/269403030 CC-BY-SAWednesday, 14 December 11
...not every problem is a nailhttp://www.flickr.com/photos/bb_matt/207102083 CC-BYWednesday, 14 December 11
Wednesday, 14 December 11
Uploadig objects!                                                                             RSS/Atom Feeds!             ...
Some way away yet...http://www.flickr.com/photos/striatic/125614 CC-BYWednesday, 14 December 11
Wednesday, 14 December 11
technologies...p://www.flickr.com/photos/cappellmeister/39508741 CC-BY Wednesday, 14 December 11
Publication                            Aggregation                             DiscoveryWednesday, 14 December 11
Publication                            Aggregation                             DiscoveryWednesday, 14 December 11
Publication                            Aggregation                             DiscoveryWednesday, 14 December 11
Publication                            Aggregation                             DiscoveryWednesday, 14 December 11
conceptual                                                         changes...http://www.flickr.com/photos/ivanwalsh/4509575...
Publish pieces...then aggregateWednesday, 14 December 11
Don’t filter...enable discoveryWednesday, 14 December 11
...central                                                     principle.http://www.flickr.com/photos/mkumm/2709555496 CC-B...
Networks scaleWednesday, 14 December 11
Average Capacity of Human Researcher                    1.00                    0.75                    0.50              ...
Average Capacity of Norwegian Researcher                    3.00                    2.25                    1.50          ...
People don’t scale...Wednesday, 14 December 11
Neither do computers...http://www.flickr.com/photos/argonne/3323018571 CC-BY-SAWednesday, 14 December 11
...at least not on their ownWednesday, 14 December 11
Open networks scaleWednesday, 14 December 11
...closed networks do not.http://www.flickr.com/photos/andypowe11/3759152528Wednesday, 14 December 11
We need...Wednesday, 14 December 11
http://flickr.com/photos/virtualsugar/316200555/ CC-BYWednesday, 14 December 11
Wednesday, 14 December 11
Open data...http://www.flickr.com/photos/jwyg/4528443760/ CC-BY-SAWednesday, 14 December 11
...but also...Wednesday, 14 December 11
...open platforms for innovationhttp://www.flickr.com/photos/37984062@N03/3495256118 CC-BY-SAWednesday, 14 December 11
Optimise for....http://www.flickr.com/photos/tomarthur/3593729997Wednesday, 14 December 11
....not thishttp://www.flickr.com/photos/vrogy/514733529Wednesday, 14 December 11
Wednesday, 14 December 11
http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BY-SAWednesday, 14 December 11
http://www.flickr.com/photos/tammra/283690669/Wednesday, 14 December 11
Because every time a         permanent job is advertised...Wednesday, 14 December 11
http://www.flickr.com/photos/t3rmin4t0r/3947963283 CC-BYWednesday, 14 December 11
The one with the                                       most Nature papers                                         gets to ...
We optimise for...http://www.flickr.com/photos/klausnahr/4437823757 CC-BY-SAWednesday, 14 December 11
Rather than foruse and re-use...http://www.flickr.com/photos/frozenchipmunk/197591546 CC-BYWednesday, 14 December 11
...because of the incentives...http://www.flickr.com/photos/daquellamanera/3238300837 CC-BYWednesday, 14 December 11
http://www.flickr.com/photos/lifeontheedge/247473398 CC-BY-SAWednesday, 14 December 11
http://www.flickr.com/photos/turtlemom_nancy CC-BY-SAWednesday, 14 December 11
We are stuck with “impact”...http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11
...but we can mould it.http://www.flickr.com/photos/waltstoneburner/5745387762 CC-BYWednesday, 14 December 11
An assertion.Wednesday, 14 December 11
We want to see                            research used.Wednesday, 14 December 11
In the right places...http://www.flickr.com/photos/ol1/6048544977 CC-BY-SAWednesday, 14 December 11
In the right places...http://www.flickr.com/photos/velkr0/3472576304 CC-BYWednesday, 14 December 11
In the right places...http://www.flickr.com/photos/argonne/3465398655 CC-BYWednesday, 14 December 11
...at the right time.http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11
We want research to be                      re-used and re-usableWednesday, 14 December 11
Wednesday, 14 December 11
Impact = Re-useWednesday, 14 December 11
Application = Re-useWednesday, 14 December 11
Commercialised = Re-useWednesday, 14 December 11
Education = Re-useWednesday, 14 December 11
Engagement = Re-useWednesday, 14 December 11
...but also...Wednesday, 14 December 11
Citation = Re-useWednesday, 14 December 11
Can we measure re-use?http://www.flickr.com/photos/sterlic/4299631538 CC-BY-SAWednesday, 14 December 11
Bollen et al., PLoS ONE 4(6): e6022 doi:10.1371/journal.pone.0006022.g002Wednesday, 14 December 11
The web changes everything...http://www.flickr.com/photos/jurvetson/916142 CC-BYWednesday, 14 December 11
New tracks to followhttp://www.flickr.com/photos/mikebaird/2985066755 CC-BYWednesday, 14 December 11
ScienceCard by Martin Fenner - http://sciencecard.org/CameronNeylonWednesday, 14 December 11
Altmetric.com by Euan Adie - http://altmetric.com/interface/explorer.htmlWednesday, 14 December 11
Bookmarks = Re-useWednesday, 14 December 11
Discussion = Re-useWednesday, 14 December 11
...and we can   track them allhttp://www.flickr.com/photos/paul_white/5831407787 CC-BYWednesday, 14 December 11
...on an open network.Wednesday, 14 December 11
But what about...?http://www.flickr.com/photos/11247304@N06/1340979055 CC-BYWednesday, 14 December 11
Maximise potential...http://www.flickr.com/photos/pinksherbet/3370498053 CC-BYWednesday, 14 December 11
...for discovery   and re-use...http://www.flickr.com/photos/pagedooley/3797236989 CC-BYWednesday, 14 December 11
Measure re-use                            and re-usability...http://www.flickr.com/photos/18670024@N06/2164790747 CC-BYWedn...
Optimise for impacthttp://www.flickr.com/photos/gsfc/6147894106 CC-BYWednesday, 14 December 11
...and the easiest way...Wednesday, 14 December 11
http://www.flickr.com/photos/virtualsugar/316200555 CC-BYWednesday, 14 December 11
Not the only way.Wednesday, 14 December 11
...but the easiest                                           and most commonhttp://www.flickr.com/photos/ehamiter/460772879...
The solutions won’t come                  from where we expect...Wednesday, 14 December 11
Open networks scaleWednesday, 14 December 11
...enable solutions to                            discover problems...Wednesday, 14 December 11
...at all levelshttp://www.flickr.com/photos/37850028@N05/5111113034 CC-BYWednesday, 14 December 11
..from the researchhttp://www.flickr.com/photos/30369883@N03/5097547405 CC-BYWednesday, 14 December 11
...to the technology...Wednesday, 14 December 11
...to the architecturehttp://www.flickr.com/photos/yakobusan/2436481628 CC-BYWednesday, 14 December 11
Build open networks...http://www.flickr.com/photos/22746515@N02/4468871811 CC-BYWednesday, 14 December 11
Enable discovery...http://www.flickr.com/photos/pagedooley/2836337974 CC-BYWednesday, 14 December 11
The rest will follow...Wednesday, 14 December 11
Wednesday, 14 December 11
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I want to publish more and read less

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Keynote given at the Munin conference in Tromsø, Norway in November 2011. Describes an overview of the technology and social challenges of scholarly communication in a networked world and discusses social filtering and discovery technologies that might help with scholarly communication information overload.

Published in: Technology, Business

I want to publish more and read less

  1. 1. I need to publish more and read less Cameron Neylon - Munin Conference Tromsø - 22 November 2011Wednesday, 14 December 11
  2. 2. technologies...p://www.flickr.com/photos/cappellmeister/39508741 CC-BY Wednesday, 14 December 11
  3. 3. conceptual changes...http://www.flickr.com/photos/ivanwalsh/4509575889 CC-BYWednesday, 14 December 11
  4. 4. ...central principle.http://www.flickr.com/photos/mkumm/2709555496 CC-BYWednesday, 14 December 11
  5. 5. But first.Wednesday, 14 December 11
  6. 6. @communicating Plausible Accuracy PIERRE LINDENBAUM Mummi Thorissson John Fabiana Kubke Richard Grant Pedro Beltrao Neil Saunders Steve Wilson @gnat Branwen Hide Simon Coles Dupuis Simon Philips Pawel Szcsesny Paul Miller Tony Hey Jeremy Frey Nico Adams Richard Akerman Cavalli Gabriel JonMat Todd Stephen BrennerTim O’Reilly Noel Gorelick Dave de Roure Rich ApodacaUdell ISIS LSS Group Jeremiah Faith Jean-Claude Bradley Nicholas Cole Michael Barton JOHN WILLINSKY Phil Lord Victoria  Stodden Martyn Bull Stephen Friend David CrottyClay Shirky @t John Cumbers Bora Chris Leonard Grace BaynesEva Amsen Egon  Willighagen Mark Borkum Brian Kelly Tony Williams Dan Hagon Maxine Clarke Andrew Milsted Zivkovic Mitch Koch Lab Michael Nielsen Martin Fenner Steph Hannon WaldropGreg Wilson Brian Matthews Leigh Dodds Bill Hooker Glyn Moody Yaroslav Nikolaev Jenny Rohn Rafael Sidi Lee Smolin Frank NormanRicardo Vidal Iain Emsley Paulo Nuin Ariel Waldmann Timo HannayKen Shankland Lorie LeJeune Jonathan Gray PT Sefton Microsoft STFC Deepak Singh Shirley Wu ISIS Computing Group Helen Berman Andrew Peter Binfield Benjamin Good Dorothea Salo Liz Lyons PLoSKasarskis Jen Dodd Lee Dirks Peter Murray-Rust Richard Akerman Carole Goble Jon Eisen Jenny Hale Lakshmi Shastry Steve Koch NPG Ben Goldacre Chad OrzelBill Flanagan Jon Tansley Michael Eisen Matt Wood SciFoo 2008/9 Friendfeed Hope Leman Rufus Pollock Victor HenningGoogle Björn Brembs Jo BadgeAllyson Lister Lisa Green TIM HUBBARD Rebecca Goulding campers Euan Adie John Andy Powell Harry Collins Gavin Bell Jim Downing Matt Johnson Wilbanks Mike Ellis DUNCAN HULL Garret Lisi Jamie McQuay ALAN CANN Catherine Jones Andrew Farke Gavin Baker Peter Suber Sabine HossenfelderFlickr The BioGangKevin KellyPaul Walk Arfon Smith Kaitlin Thaney Richard Curry Atilla Csordas Ian MulvanyWednesday, 14 December 11
  7. 7. Wednesday, 14 December 11
  8. 8. Wednesday, 14 December 11
  9. 9. Who am I?Wednesday, 14 December 11
  10. 10. I live in Bathhttp://www.flickr.com/photos/andypowe11/3915450391Wednesday, 14 December 11
  11. 11. I work at RALWednesday, 14 December 11
  12. 12. I work on...Wikimedia Commons Wikimedia CommonsSuccinate_Dehydrogenase_1YQ3_and_Membrane.png MGMT BDNA_1T38.pngWednesday, 14 December 11
  13. 13. I work on...Wednesday, 14 December 11
  14. 14. I work on...Wednesday, 14 December 11
  15. 15. I write grants...http://www.flickr.com/photos/59937401@N07/5929622407 CC-BYWednesday, 14 December 11
  16. 16. ...and papers...http://flickr.com/photos/nicmcphee/2756494307/ CC-BYWednesday, 14 December 11
  17. 17. Wednesday, 14 December 11
  18. 18. 39 Presentations ~100,000 views Slideshare - http://slideshare.net/CameronNeylon/presentationsWednesday, 14 December 11
  19. 19. http://cameronneylon.netWednesday, 14 December 11
  20. 20. Papers are not enough...Wednesday, 14 December 11
  21. 21. ...software...Wednesday, 14 December 11
  22. 22. ...data...Wednesday, 14 December 11
  23. 23. Need to communicate...Wednesday, 14 December 11
  24. 24. all the pieces...http://www.flickr.com/photos/jurvetson/3184362622 CC-BYWednesday, 14 December 11
  25. 25. Need to maximise “impact”...http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11
  26. 26. But that’s ok...Wednesday, 14 December 11
  27. 27. We have new tools...http://www.flickr.com/photos/kylemay/1430449350 CC-BYWednesday, 14 December 11
  28. 28. Many new ways and places to publish...Wednesday, 14 December 11
  29. 29. So...Wednesday, 14 December 11
  30. 30. Sortase-Mediated Ligation group, and finally attachment to the solid support. In addition the use of intein based methods as well as the preparation of the solid support for Staudinger ligation often require reagents such as phosphines or thiophenols that are toxic and difficult to handle. Therefore there remains a significant need for robust and simple methodologies for protein immobilization that can be applied to wide range of proteins and solid supports. The identification of the Sortase transpeptidase [19] provided an alternative approach to protein ligation. Sortases recognise a specific peptide sequence (LPETG for SrtA of S. aureus used in this work) in proteins targeted for covalent attachment to the cell wall peptidoglycan. The peptide tag sequence is cleaved and then ligated to the pentaglycine moiety on the peptidoglycan precursor Lipid II. Proteins expressed with the C-terminal recognition sequence can be covalently attached to a wide range of constructs with an N-terminal glycine amide motif including peptides [20], PNA [21], full length proteins [22] and small molecule substrates [23]. Another group has independently described an Figure 1. Ligation of fluorescent proteins to polymer beads. (a) GMA example of Sortase mediated ligation to a beaded solid support [22]. beads modified with one, two, or four glycine residues were incubated These reactions proceed under aqueous conditions without the with EGFP-LPETGG-His6 and Sortase. Samples were taken at specific addition of any further reagents beyond the protein, ligation time points and analyzed on a BD FACSAria. Controls contained beads substrate, and Sortase. Thus Sortase has the potential to provide with no glycine or diglycine beads without Sortase. Error bars showing a means of linking expressed proteins to a wide range of solid the standard error in the mean fluorescence are omitted as they are supports which is mild, selective, and can be carried out in a single generally smaller than the data symbols. Errors are given in Supplementary Data S2. step. Here we investigate the ability of S. aureus SrtA to ligate proteins doi:10.1371/journal.pone.0001164.g001 to a range of solid supports. sequence unrelated to TerB in binding buffer (50 mM Tris-HCl, RESULTS 250 mM KCl, 0.1 mM EDTA, 0.1 mM DTT, pH 9). The total Plasmid vectors were constructed for the expression of Blue DNA concentration (Ter plus nonspecific DNA) was 100 nM for fluorescent protein (BFP, Q-Biogene), Enhanced Green Fluores- all samples. The fluorescein and Cy5 fluorescence of the beads was ...when we publish... cent Protein (EGFP), a red fluorescent protein (DsRed), and the determined by FACS analysis. Non-specific DNA binding was sequence specific DNA binding protein Tus [24] with a C- very low in all cases, consistent with the low affinity of Tus for non- terminal LPETGG sequence followed by a hexahistidine tag. The specific DNA in 250 mM KCl [25]. Ter binding showed proteins were expressed in BL21(DE3) and purified before a concentration dependence that was consistent with an attachment to solid supports. equilibrium dissociation constant of 2968 nM (Figure 3), which Our first target was the immobilization of proteins onto cross- compares well with values of KD measured by fluorescence linked polymer beads. Glycidyl methacrylate (GMA) beads were anisotropy (,15 nM at 37uC) or Biacore (,1 nM at 25uC) [25]. modified with a spacer followed by one, two, or four glycine To demonstrate attachment to other solid supports a beaded residues. Mono-glycine, di-glycine, and tetra-glycine beads were agarose affinity support (Affi-Gel 102 resin, Bio-Rad) was modified incubated with EGFP-LPETGG-His6 (85 mM) and His6-Sortase AWednesday, 14 December 11
  31. 31. ...publish the data...Wednesday, 14 December 11
  32. 32. ...in the right places...Wednesday, 14 December 11
  33. 33. ...the software...Wednesday, 14 December 11
  34. 34. ...and all the rest?Wednesday, 14 December 11
  35. 35. Wednesday, 14 December 11
  36. 36. http://usefulchem.wikispaces.com/Exp207 Flickr tag: UC207Wednesday, 14 December 11
  37. 37. Wednesday, 14 December 11
  38. 38. Wednesday, 14 December 11
  39. 39. Wednesday, 14 December 11
  40. 40. Wednesday, 14 December 11
  41. 41. Wednesday, 14 December 11
  42. 42. http://www.flickr.com/photos/stuartpilbrow/3345896050 CC-BY-SAWednesday, 14 December 11
  43. 43. This is not sustainable...Wednesday, 14 December 11
  44. 44. “I need to publish more”Wednesday, 14 December 11
  45. 45. ...not work more...Wednesday, 14 December 11
  46. 46. We have...http://www.flickr.com/photos/schnurrbart/43568532 CC-BY-SAWednesday, 14 December 11
  47. 47. A resource problem...http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SAWednesday, 14 December 11
  48. 48. Whether it’s money...Wednesday, 14 December 11
  49. 49. ...or time...http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11
  50. 50. Technical capacity is not enoughWednesday, 14 December 11
  51. 51. ...either need to resource itWednesday, 14 December 11
  52. 52. ...or make it cheaper.Wednesday, 14 December 11
  53. 53. Wednesday, 14 December 11
  54. 54. Publication as a side effect of recording....Wednesday, 14 December 11
  55. 55. “Publish@Source” Jeremy Frey, SouthamptonWednesday, 14 December 11
  56. 56. Wednesday, 14 December 11
  57. 57. Wednesday, 14 December 11
  58. 58. http://usefulchem.wikispaces.com/Exp258Wednesday, 14 December 11
  59. 59. http://www.carlboettiger.info/Wednesday, 14 December 11
  60. 60. http://www.myexperiment.org/workflows/204.htmlWednesday, 14 December 11
  61. 61. Wednesday, 14 December 11
  62. 62. http://www.flickr.com/photos/psychemedia/Wednesday, 14 December 11
  63. 63. Easy to publish pieces...http://www.flickr.com/photos/horiavarlan/4514164700 CC-BYWednesday, 14 December 11
  64. 64. ...and then collectWednesday, 14 December 11
  65. 65. Wednesday, 14 December 11
  66. 66. Wednesday, 14 December 11
  67. 67. Wednesday, 14 December 11
  68. 68. Wednesday, 14 December 11
  69. 69. Wednesday, 14 December 11
  70. 70. Wednesday, 14 December 11
  71. 71. So we capture and collect...http://www.flickr.com/photos/furtwangl/3851841424Wednesday, 14 December 11
  72. 72. Dionaea muscipula Musca domestica chomped on ...then tell the storyWednesday, 14 December 11
  73. 73. ...aggregate existing pieceshttp://www.flickr.com/photos/lizadaly/2944376209 CC-BYWednesday, 14 December 11
  74. 74. ...we can open the floodgates...http://www.flickr.com/photos/bladeflyer/442496389 CC-BYWednesday, 14 December 11
  75. 75. ...all the way...http://www.flickr.com/photos/fraz5356/4754482759 CC-BYWednesday, 14 December 11
  76. 76. It’ll be great...right?http://www.flickr.com/photos/62337512@N00/3958637561 CC-BYWednesday, 14 December 11
  77. 77. group, and finally attachment to the solid support. In addition the use of intein based methods as well as the preparation of the solid support for Staudinger ligation often require reagents such as phosphines or thiophenols that are toxic and difficult to handle. Therefore there remains a significant need for robust and simple methodologies for protein immobilization that can be applied to wide range of proteins and solid supports. The identification of the Sortase transpeptidase [19] provided an alternative approach to protein ligation. Sortases recognise a specific peptide sequence (LPETG for SrtA of S. aureus used in this work) in proteins targeted for covalent attachment to the cell wall peptidoglycan. The peptide tag sequence is cleaved and then ligated to the pentaglycine moiety on the peptidoglycan precursor Lipid II. Proteins expressed with the C-terminal recognition sequence can be covalently attached to a wide range of constructs with an N-terminal glycine amide motif including peptides [20], PNA [21], full length proteins [22] and small molecule substrates [23]. Another group has independently described an Figure 1. Ligation of fluorescent proteins to polymer beads. (a) GMA example of Sortase mediated ligation to a beaded solid support [22]. All of this information...data.... beads modified with one, two, or four glycine residues were incubated These reactions proceed under aqueous conditions without the with EGFP-LPETGG-His6 and Sortase. Samples were taken at specific addition of any further reagents beyond the protein, ligation time points and analyzed on a BD FACSAria. Controls contained beads substrate, and Sortase. Thus Sortase has the potential to provide with no glycine or diglycine beads without Sortase. Error bars showing a means of linking expressed proteins to a wide range of solid the standard error in the mean fluorescence are omitted as they are supports which is mild, selective, and can be carried out in a single generally smaller than the data symbols. Errors are given in Supplementary Data S2. step. Here we investigate the ability of S. aureus SrtA to ligate proteins doi:10.1371/journal.pone.0001164.g001 to a range of solid supports.Wednesday, 14 December 11
  78. 78. All of this information...data....Wednesday, 14 December 11
  79. 79. All of this information...data....Wednesday, 14 December 11
  80. 80. All of this information...data....Wednesday, 14 December 11
  81. 81. All of this information...data....Wednesday, 14 December 11
  82. 82. All of this information...data....Wednesday, 14 December 11
  83. 83. http://usefulchem.wikispaces.com/Exp207 All of this information...data.... Flickr tag: UC207Wednesday, 14 December 11
  84. 84. All of this information...data....Wednesday, 14 December 11
  85. 85. All of this information...data....Wednesday, 14 December 11
  86. 86. All of this information...data....Wednesday, 14 December 11
  87. 87. All of this information...data....Wednesday, 14 December 11
  88. 88. Wednesday, 14 December 11
  89. 89. http://www.flickr.com/photos/waltstoneburner/3372746317 CC-BYWednesday, 14 December 11
  90. 90. Retractions per 100k papers 30 Retractions per 100k publications 25 20 15 10 5 0 1960 1970 1980 1990 2000 2010 YearWednesday, 14 December 11
  91. 91. http://www.flickr.com/photos/oakleyoriginals/2879794262 CC-BYWednesday, 14 December 11
  92. 92. watercannon?http://www.flickr.com/photos/7827294@N04/4621721577 CC-BYWednesday, 14 December 11
  93. 93. Information overload...http://www.flickr.com/photos/dylanroscover/3450505729 CC-BY-SAWednesday, 14 December 11
  94. 94. “I need to read less”Wednesday, 14 December 11
  95. 95. Filter failure?http://www.flickr.com/photos/daveyll/332723930Wednesday, 14 December 11
  96. 96. http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BYWednesday, 14 December 11
  97. 97. Filters block.http://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
  98. 98. You think this is a good thing...http://www.flickr.com/photos/robmcm/1671702203 CC-BY-SAWednesday, 14 December 11
  99. 99. ...we’re “protecting ourcommunity from a deluge”http://www.flickr.com/photos/mrehan00/3700858676 CC-BY-SAWednesday, 14 December 11
  100. 100. ...staying on the straight and narrow...http://www.flickr.com/photos/quinnanya/4813974125 CC-BYWednesday, 14 December 11
  101. 101. Or are we just limitingour ability to explore...?http://www.flickr.com/photos/jurvetson/2174000357 CC-BYWednesday, 14 December 11
  102. 102. ...and discover...?http://www.flickr.com/photos/joiseyshowaa/2374526016 CC-BYWednesday, 14 December 11
  103. 103. Filters block.http://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
  104. 104. The right filter for me? Right filter for now?http://www.flickr.com/photos/lotzman/3595748169 CC-BYWednesday, 14 December 11
  105. 105. Wednesday, 14 December 11
  106. 106. Remember this graph? 30 Retractions per 100k publications 25 20 15 10 5 0 1960 1970 1980 1990 2000 2010 YearWednesday, 14 December 11
  107. 107. Remember this graph? 30 Retractions per 100k publications 25 20 15 10 5 0 1960 1970 1980 1990 2000 2010 Year Where is the data from?Wednesday, 14 December 11
  108. 108. Remember this graph? 30 Retractions per 100k publications 25 20 15 10 5 0 1960 1970 1980 1990 2000 2010 Year https://github.com/neilfws/PubMed/blob/master/data/retractions.txt Where is the data from?Wednesday, 14 December 11
  109. 109. Remember this graph? 30 Retractions per 100k publications 25 20 15 10 5 0 1960 1970 1980 1990 2000 2010 Year https://github.com/neilfws/PubMed/blob/master/data/retractions.txt Where is the data from?Wednesday, 14 December 11
  110. 110. But how did I discover it?Wednesday, 14 December 11
  111. 111. http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
  112. 112. Wednesday, 14 December 11
  113. 113. http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
  114. 114. http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-yearWednesday, 14 December 11
  115. 115. Remember these people?Wednesday, 14 December 11
  116. 116. @communicating Plausible Accuracy PIERRE LINDENBAUM Mummi Thorissson John Fabiana Kubke Richard Grant Pedro Beltrao Neil Saunders Steve Wilson @gnat Branwen Hide Simon Coles Dupuis Simon Philips Pawel Szcsesny Paul Miller Tony Hey Jeremy Frey Nico Adams Richard Akerman Cavalli Gabriel JonMat Todd Stephen BrennerTim O’Reilly Noel Gorelick Dave de Roure Rich ApodacaUdell ISIS LSS Group Jeremiah Faith Jean-Claude Bradley Nicholas Cole Michael Barton JOHN WILLINSKY Phil Lord Victoria  Stodden Martyn Bull Stephen Friend David CrottyClay Shirky @t John Cumbers Bora Chris Leonard Grace BaynesEva Amsen Egon  Willighagen Mark Borkum Brian Kelly Tony Williams Dan Hagon Maxine Clarke Andrew Milsted Zivkovic Mitch Koch Lab Michael Nielsen Martin Fenner Steph Hannon WaldropGreg Wilson Brian Matthews Leigh Dodds Bill Hooker Glyn Moody Yaroslav Nikolaev Jenny Rohn Rafael Sidi Lee Smolin Frank NormanRicardo Vidal Iain Emsley Paulo Nuin Ariel Waldmann Timo HannayKen Shankland Lorie LeJeune Jonathan Gray PT Sefton Microsoft STFC Deepak Singh Shirley Wu ISIS Computing Group Helen Berman Andrew Peter Binfield Benjamin Good Dorothea Salo Liz Lyons PLoSKasarskis Jen Dodd Lee Dirks Peter Murray-Rust Richard Akerman Carole Goble Jon Eisen Jenny Hale Lakshmi Shastry Steve Koch NPG Ben Goldacre Chad OrzelBill Flanagan Jon Tansley Michael Eisen Matt Wood SciFoo 2008/9 Friendfeed Hope Leman Rufus Pollock Victor HenningGoogle Björn Brembs Jo BadgeAllyson Lister Lisa Green TIM HUBBARD Rebecca Goulding campers Euan Adie John Andy Powell Harry Collins Gavin Bell Jim Downing Matt Johnson Wilbanks Mike Ellis DUNCAN HULL Garret Lisi Jamie McQuay ALAN CANN Catherine Jones Andrew Farke Gavin Baker Peter Suber Sabine HossenfelderFlickr The BioGangKevin KellyPaul Walk Arfon Smith Kaitlin Thaney Richard Curry Atilla Csordas Ian MulvanyWednesday, 14 December 11
  117. 117. Wednesday, 14 December 11
  118. 118. Wednesday, 14 December 11
  119. 119. Wednesday, 14 December 11
  120. 120. Wednesday, 14 December 11
  121. 121. Wednesday, 14 December 11
  122. 122. Social aggregation...Wednesday, 14 December 11
  123. 123. ...but also...Wednesday, 14 December 11
  124. 124. Wednesday, 14 December 11
  125. 125. Social annotationWednesday, 14 December 11
  126. 126. ...and quality assessmenthttp://www.flickr.com/photos/pinksherbet/3209939998 CC-BYWednesday, 14 December 11
  127. 127. ...but also...Wednesday, 14 December 11
  128. 128. http://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/Wednesday, 14 December 11
  129. 129. http://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/Wednesday, 14 December 11
  130. 130. A network of linked objects...Wednesday, 14 December 11
  131. 131. ...primed for discovery...Wednesday, 14 December 11
  132. 132. Wednesday, 14 December 11
  133. 133. It’s not filter failurehttp://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11
  134. 134. ...it’s a discovery deficit...http://www.flickr.com/photos/nationallibrarynz_commons/4078337883 Public DomainWednesday, 14 December 11
  135. 135. In the last year...?http://flickr.com/photos/stewart/461099066/Wednesday, 14 December 11
  136. 136. ...in the past 24 hours?Wednesday, 14 December 11
  137. 137. Is search the answer?http://www.flickr.com/photos/ezioman/2096469724 CC-BYWednesday, 14 December 11
  138. 138. ...or something more...?http://www.flickr.com/photos/mangostrawberry/5490992826 CC-BYWednesday, 14 December 11
  139. 139. Need the right instrument...http://www.flickr.com/photos/conskeptical/269403030 CC-BY-SAWednesday, 14 December 11
  140. 140. ...not every problem is a nailhttp://www.flickr.com/photos/bb_matt/207102083 CC-BYWednesday, 14 December 11
  141. 141. Wednesday, 14 December 11
  142. 142. Uploadig objects! RSS/Atom Feeds! Workflows! Online file stores! LIMS! Blog/Wiki! Map Reduce/! Hadoop! Local file stores! Data repository!Wednesday, 14 December 11
  143. 143. Some way away yet...http://www.flickr.com/photos/striatic/125614 CC-BYWednesday, 14 December 11
  144. 144. Wednesday, 14 December 11
  145. 145. technologies...p://www.flickr.com/photos/cappellmeister/39508741 CC-BY Wednesday, 14 December 11
  146. 146. Publication Aggregation DiscoveryWednesday, 14 December 11
  147. 147. Publication Aggregation DiscoveryWednesday, 14 December 11
  148. 148. Publication Aggregation DiscoveryWednesday, 14 December 11
  149. 149. Publication Aggregation DiscoveryWednesday, 14 December 11
  150. 150. conceptual changes...http://www.flickr.com/photos/ivanwalsh/4509575889 CC-BYWednesday, 14 December 11
  151. 151. Publish pieces...then aggregateWednesday, 14 December 11
  152. 152. Don’t filter...enable discoveryWednesday, 14 December 11
  153. 153. ...central principle.http://www.flickr.com/photos/mkumm/2709555496 CC-BYWednesday, 14 December 11
  154. 154. Networks scaleWednesday, 14 December 11
  155. 155. Average Capacity of Human Researcher 1.00 0.75 0.50 0.25 0 1982 1986 1990 1994 1998 2002 2006Wednesday, 14 December 11
  156. 156. Average Capacity of Norwegian Researcher 3.00 2.25 1.50 0.75 0 1982 1986 1990 1994 1998 2002 2006Wednesday, 14 December 11
  157. 157. People don’t scale...Wednesday, 14 December 11
  158. 158. Neither do computers...http://www.flickr.com/photos/argonne/3323018571 CC-BY-SAWednesday, 14 December 11
  159. 159. ...at least not on their ownWednesday, 14 December 11
  160. 160. Open networks scaleWednesday, 14 December 11
  161. 161. ...closed networks do not.http://www.flickr.com/photos/andypowe11/3759152528Wednesday, 14 December 11
  162. 162. We need...Wednesday, 14 December 11
  163. 163. http://flickr.com/photos/virtualsugar/316200555/ CC-BYWednesday, 14 December 11
  164. 164. Wednesday, 14 December 11
  165. 165. Open data...http://www.flickr.com/photos/jwyg/4528443760/ CC-BY-SAWednesday, 14 December 11
  166. 166. ...but also...Wednesday, 14 December 11
  167. 167. ...open platforms for innovationhttp://www.flickr.com/photos/37984062@N03/3495256118 CC-BY-SAWednesday, 14 December 11
  168. 168. Optimise for....http://www.flickr.com/photos/tomarthur/3593729997Wednesday, 14 December 11
  169. 169. ....not thishttp://www.flickr.com/photos/vrogy/514733529Wednesday, 14 December 11
  170. 170. Wednesday, 14 December 11
  171. 171. http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BY-SAWednesday, 14 December 11
  172. 172. http://www.flickr.com/photos/tammra/283690669/Wednesday, 14 December 11
  173. 173. Because every time a permanent job is advertised...Wednesday, 14 December 11
  174. 174. http://www.flickr.com/photos/t3rmin4t0r/3947963283 CC-BYWednesday, 14 December 11
  175. 175. The one with the most Nature papers gets to mate...http://www.flickr.com/photos/t3rmin4t0r/3947963283 CC-BYWednesday, 14 December 11
  176. 176. We optimise for...http://www.flickr.com/photos/klausnahr/4437823757 CC-BY-SAWednesday, 14 December 11
  177. 177. Rather than foruse and re-use...http://www.flickr.com/photos/frozenchipmunk/197591546 CC-BYWednesday, 14 December 11
  178. 178. ...because of the incentives...http://www.flickr.com/photos/daquellamanera/3238300837 CC-BYWednesday, 14 December 11
  179. 179. http://www.flickr.com/photos/lifeontheedge/247473398 CC-BY-SAWednesday, 14 December 11
  180. 180. http://www.flickr.com/photos/turtlemom_nancy CC-BY-SAWednesday, 14 December 11
  181. 181. We are stuck with “impact”...http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11
  182. 182. ...but we can mould it.http://www.flickr.com/photos/waltstoneburner/5745387762 CC-BYWednesday, 14 December 11
  183. 183. An assertion.Wednesday, 14 December 11
  184. 184. We want to see research used.Wednesday, 14 December 11
  185. 185. In the right places...http://www.flickr.com/photos/ol1/6048544977 CC-BY-SAWednesday, 14 December 11
  186. 186. In the right places...http://www.flickr.com/photos/velkr0/3472576304 CC-BYWednesday, 14 December 11
  187. 187. In the right places...http://www.flickr.com/photos/argonne/3465398655 CC-BYWednesday, 14 December 11
  188. 188. ...at the right time.http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11
  189. 189. We want research to be re-used and re-usableWednesday, 14 December 11
  190. 190. Wednesday, 14 December 11
  191. 191. Impact = Re-useWednesday, 14 December 11
  192. 192. Application = Re-useWednesday, 14 December 11
  193. 193. Commercialised = Re-useWednesday, 14 December 11
  194. 194. Education = Re-useWednesday, 14 December 11
  195. 195. Engagement = Re-useWednesday, 14 December 11
  196. 196. ...but also...Wednesday, 14 December 11
  197. 197. Citation = Re-useWednesday, 14 December 11
  198. 198. Can we measure re-use?http://www.flickr.com/photos/sterlic/4299631538 CC-BY-SAWednesday, 14 December 11
  199. 199. Bollen et al., PLoS ONE 4(6): e6022 doi:10.1371/journal.pone.0006022.g002Wednesday, 14 December 11
  200. 200. The web changes everything...http://www.flickr.com/photos/jurvetson/916142 CC-BYWednesday, 14 December 11
  201. 201. New tracks to followhttp://www.flickr.com/photos/mikebaird/2985066755 CC-BYWednesday, 14 December 11
  202. 202. ScienceCard by Martin Fenner - http://sciencecard.org/CameronNeylonWednesday, 14 December 11
  203. 203. Altmetric.com by Euan Adie - http://altmetric.com/interface/explorer.htmlWednesday, 14 December 11
  204. 204. Bookmarks = Re-useWednesday, 14 December 11
  205. 205. Discussion = Re-useWednesday, 14 December 11
  206. 206. ...and we can track them allhttp://www.flickr.com/photos/paul_white/5831407787 CC-BYWednesday, 14 December 11
  207. 207. ...on an open network.Wednesday, 14 December 11
  208. 208. But what about...?http://www.flickr.com/photos/11247304@N06/1340979055 CC-BYWednesday, 14 December 11
  209. 209. Maximise potential...http://www.flickr.com/photos/pinksherbet/3370498053 CC-BYWednesday, 14 December 11
  210. 210. ...for discovery and re-use...http://www.flickr.com/photos/pagedooley/3797236989 CC-BYWednesday, 14 December 11
  211. 211. Measure re-use and re-usability...http://www.flickr.com/photos/18670024@N06/2164790747 CC-BYWednesday, 14 December 11
  212. 212. Optimise for impacthttp://www.flickr.com/photos/gsfc/6147894106 CC-BYWednesday, 14 December 11
  213. 213. ...and the easiest way...Wednesday, 14 December 11
  214. 214. http://www.flickr.com/photos/virtualsugar/316200555 CC-BYWednesday, 14 December 11
  215. 215. Not the only way.Wednesday, 14 December 11
  216. 216. ...but the easiest and most commonhttp://www.flickr.com/photos/ehamiter/4607728796 CC-BY-SAWednesday, 14 December 11
  217. 217. The solutions won’t come from where we expect...Wednesday, 14 December 11
  218. 218. Open networks scaleWednesday, 14 December 11
  219. 219. ...enable solutions to discover problems...Wednesday, 14 December 11
  220. 220. ...at all levelshttp://www.flickr.com/photos/37850028@N05/5111113034 CC-BYWednesday, 14 December 11
  221. 221. ..from the researchhttp://www.flickr.com/photos/30369883@N03/5097547405 CC-BYWednesday, 14 December 11
  222. 222. ...to the technology...Wednesday, 14 December 11
  223. 223. ...to the architecturehttp://www.flickr.com/photos/yakobusan/2436481628 CC-BYWednesday, 14 December 11
  224. 224. Build open networks...http://www.flickr.com/photos/22746515@N02/4468871811 CC-BYWednesday, 14 December 11
  225. 225. Enable discovery...http://www.flickr.com/photos/pagedooley/2836337974 CC-BYWednesday, 14 December 11
  226. 226. The rest will follow...Wednesday, 14 December 11
  227. 227. Wednesday, 14 December 11
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