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Enro
Science Online: Enro
Breakout 6: Communicating Primary Research Publicly
August 30 - Comment - Share
openscience - Jo Badge
looks like everyone is in here. - Ian Mulvany
mirror in the room makes me feel that I am part of a Dutch Master - Ian Mulvany
yep, our local power block is full! people sitting on the floor - Jo Badge
one idea, blog anything that constitutes the least publishable unit, this then becomes part of the grey literature, and can become cited, if people know how to cite blogs, one can think of persistence, and then tying the conversation back ala postgenomic or such - Ian Mulvany
Introduction around the fine Feynman-quote in the comments. http://network.nature.com/blogs... by Bob O'Hara - Roland Krause
raising the issue of being scooped - Cameron Neylon
how permament are blogs - how does this relate to autobiography - Brian Derby commented that Feynman did write a lot of this up - although after the fact - Cameron Neylon
"the impermanence of blogs" - and there being no formalised connection between the anarchic literature (blogs etc) and the ordered one. - Andrew Walkingshaw
The various forms of scientific communication (peer review, general audience, etc.) - Roland Krause
@Ian: that mirror's kind of cool and kind of creepy in a slightly filmic way, isn't it? - Andrew Walkingshaw
the question of homesteading - sticking down an idea and claiming the area for yourself - Cameron Neylon
Comment: The importance of the idea in molecular biology research. Proposition of embargoed blogs. - Roland Krause
Comment: Use of an internal wiki instead - Roland Krause
Comment: Comparison of blogging to posters and presentations at conferences. - Roland Krause
Just because something is in a journal doesn't mean that it is permanent, in the sense that there are many venues for publication that will never get read. - Ian Mulvany
isues of embargoes and etc being raised - Jenny makes the point that people have already dealt with these issues in conferences - Cameron Neylon
Comment (Maxine Clark): http://www.webcitation.org/ to obtain time stamps - Roland Krause
Question: Why read about the fruitless efforts of scientific research. - Roland Krause
literature as filter - do people want the rest? - Cameron Neylon
Heather Etchevers talking now - Cameron Neylon
Heather Etchevers: Lab notebooks - Roland Krause
what do ou need in a lab notebook at the bench - Cameron Neylon
moving on to discuss lab noteboks, many verrrrry interesting topics are bubbling up, perhaps we need another conference! - Ian Mulvany
What should be in a notebook - motivation, diary, results, figures, transmision of knowledge, analysis, periodic summary - Cameron Neylon
Requirements of a lab note book: Motivation, diary, results, transmission of knowledge - Roland Krause
Periodic summaries - Roland Krause
we've ben talking about running a conference on 'open science' sometime in around 12-18 months - Cameron Neylon
Outsource memory, proof for intellectual process (internal, external) - Roland Krause
desired function - outsourcing memory, preparation, archive for proof of intellectual process - internal and external - Cameron Neylon
example of a paper notebook - Cameron Neylon
so lab books are the comment lines in computer code for wetware! - Ian Mulvany
Data type rich note books... this is where ELN outscore the old book: you can insert imagery, screenshots, and,....really importnatly, the raw data! - Egon Willighagen
Problem of different notebooks for excursions, conferences, lab meetings, real work. Chronological vs subject organization. - Roland Krause
actually need multiple 'notebooks' - multiple projects, field notes, collaborators, large machines, chronological order vs narrative, protocols/cookbooks - Cameron Neylon
how much really goes in? how much do we edit in advance - Cameron Neylon
the need to scribble in the margins - Cameron Neylon
examples of online notebooks - openwetware, evernote, e-CAT, Addgene, blogs - Cameron Neylon
chronilogical versus accuracy/narrative: version control solves this, as JC will discuss in the next presentation, I'm sure :) - Egon Willighagen
need online notebooks to accept graffiti, the writing in the margins, but with an infinite margin. - Ian Mulvany
(which we have a truly marvellous proof of, Cameron, but...) - Andrew Walkingshaw
Advantages: Sharing with collaborators, searching, linking out, remote access. - Roland Krause
I think Egon is getting his FFs mixed up... - Richard P Grant
Ian is the one who keeps wanting a bigger margin isn't it? :-) - Cameron Neylon
Richard, yes, indeed, sorry about that... commenting throughput so fast, that BO5 and BO6 are switching ranking all the time :) - Egon Willighagen
is anyone monitoring the mogulus chat room - for some reason I can't access http://www.mogulus.com/cameron... - Cameron Neylon
i was wondering whether they were going to mention http://www.livescribe.com/ and they did. - Ian Mulvany
I can't access it either... - Egon Willighagen
Voice recording is mentioned, in reply to pen-top computer... I was thinking about getting a mp3 recorder myself, for notes, when on my bike going to work... - Egon Willighagen
have a robot powered by an avatar in SL, and record all of the actions that happen, never have to get out of bed! - Ian Mulvany
The music nerds I know tend to just record memos on their phone rather than phoning home - or more and more carry around a field recorder - think the audio equivalent of a Flip. (I didn't bring mine with me, maybe I should have...) - Andrew Walkingshaw
suggestion of voice recognition - Cameron Neylon
Clearly none of these people are microbiologists - laptop on the bench? The horror! - AJCann
Comment: Idea of recording notes for integration with ELN - Roland Krause
Jean-Claude talking now on Open Notebook Science - Cameron Neylon
Jean-Claude Bradley on open notebook science with 100% transparency. - Roland Krause
and what do you microbiologists do with your mucky paper notebooks? - Jo Badge
That'ts why we use cheap PC's (actually the ones already attached to instruments mostly - avoiding PC's and tablets for the reason AJCann mentions - Cameron Neylon
Blogs don't handle versioning, which is bad for a lab book - you need to track the changes with a timestamp. - Andrew Walkingshaw
JC refers to versioning in LNs, which is why the moved away from blog to wiki for ELN - Egon Willighagen
Safety officers OK with notebooks, not OK with computers on the bench ;) - AJCann
(so they use a wiki, which is "very flexible" - but I'd wonder what you lose in the way of machine-readable semantics... not that anything else on hte market is any better, really) - Andrew Walkingshaw
so what do you do with e.g. a UV spec in the lab? Or something else that has a ocmputer control it anyway? - Cameron Neylon
Andrew, not sure if they do, but they could use a semantic wiki... see what Henry Rzepa has done - Egon Willighagen
"not trying to subvert the traditional publication process, just to communicate what they're doing on a daily basis." - Andrew Walkingshaw
There is no specifc semantics in the wiki at the moment - its human readable, but the aim is to try and translate that to a machine readable form in the future - Cameron Neylon
(@Egon: I'm seriously not sold on any system which requires users to go out of their way to input semantics, and from what I've seen Semantic MediaWiki has a fair bit of that.) - Andrew Walkingshaw
(Andrew, agreed... GUIs is what chemists neeed) - Egon Willighagen
I feel what we need is systems that _encourage_ people to input semantic information as part of the natural work flow - Cameron Neylon
example of people finding a failed experiment - Cameron Neylon
The power explained by showing negative results (here with suggestions on how to improve) - Roland Krause
Cameron: using something like OSCAR (http://oscar3-chem.sourceforge.net/), I guess (at least in part). I've got to believe that the future has to involve the machines automatically capturing and posting the data and metadata; if you've got someone in the loop there's gonna be a day when they've not had enough coffee - or too much!- and... - Andrew Walkingshaw
value of using third party services - Cameron Neylon
JC mentions people being able to contact them about run experiments... this does require good search tools, which require semantics in one way or another... a PNG of the reaction is no longer sufficient - Egon Willighagen
andrew - absolutely - ideally the machines capture the metadata and the human user just connects the threads together - the less human intervention the better really - Cameron Neylon
oh yeah - here comes the bit about taking human mistakes out as far as possible - Cameron Neylon
citing lab notebook pages and raw data: that's very cool - Andrew Walkingshaw
question from Karen James - how hard is to set up the software - Cameron Neylon
advantage of third party services - Cameron Neylon
I can't hide the feeling that the presented approaches are suboptimal... - Egon Willighagen
absolutely but I very much subscribe to jean-Claude's point - communicate first, standardise second - Cameron Neylon
I agree with that. We are communicating now, let's start paying attention the standardization... this is happening, but to a good extend a social problem, which makes this conference so nice... we have room to talk on what we like to achieve... - Egon Willighagen
JCB doesn't care about scooping: It is out under a CC license, so it can be cited. Some people in the audience are concerned that this is limited to this particular field. - Roland Krause
Independent of that - very important work. Nice session, the best so far. - Roland Krause
Based on my exhausting tester experience with Google Research Datasets, I would say that their system, even in it embryonic form is theoretically able to solve all of the problems of handling enormous amount of raw data, open notebook science and publishing primary research too. The problem is cultural: not everything that is functional and nice in open software can be applied to open science. - Attila Csordas
Just got to this - but agree with Attila - the advent of Google Research Datasets changes the ballgame completely. The technical infrastructure is falling into place - Cameron Neylon