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'Mummi' Thorisson › Likes

peter murray-rust
"Disruptive action in scholarly publishing [...] hopefully legal" love it! I'm along for the ride! - Björn Brembs
@BB thanks. We will work this out and I think Open Bibliography is the starting point - peter murray-rust
some Canadian universities - led by UPEI, I think - are creating an open citation index.... not sure how far along they are with it - Christina Pikas
If it's k4all I am afraid there is very little current progress. A vision, but not an implementation or content - peter murray-rust
Nice one: "IFs are per journal. This about as meaningful a measure of worth as deciding that a person is well-dressed because they shop at a given store. You can be badly dressed with expensive cloths and vice versa. ". Might just borrow this analogy for a future presentation..... - 'Mummi' Thorisson
Heather Piwowar
I'm looking forward to the JISC Managing Research Data Programme Workshop in Birmingham UK in March. Will I see you there? http://www.jisc.ac.uk/whatwed...
Just booked my flight. w00t! - Heather Piwowar
Yuu'll definitely be seeing me there! - Cameron Neylon
Please say hello to Torsten Reimer from me when you're there! - Björn Brembs
I did not know about this. Birmingham is definitely do-able. - science3point0
Cool! Mark, hope you can make it. - Heather Piwowar
Will be there too. Looking forward to it! Only ~45min drive from my house in Leicester. - 'Mummi' Thorisson
Truly devastated that I cannot come to this. Who is going to fly the FigShare flag? :) and the website says nothing about documenting sessions/streaming. If anyone wants me, I will be drowning my sorrows at #sameAs.us - science3point0
I can mention figshare. Supposed to be saying something intelligent for ten minutes which is always tough when following Heather so going a bit off piste is probably a good plan. - Cameron Neylon
Cameron, you're listed ahead of me on the schedule. I'm the one who is in trouble :) I'll try to tweet the sessions. - Heather Piwowar
Oh well in that case you better go first because you've got something sensible to say! - Cameron Neylon
I'm getting into Birmingham UK this Sat night. Anyone up for walking/talking/eating Sun or on Mon am? - Heather Piwowar
Any plans to head into London whilst you're here? - Dan Hagon from Android
Alas not this trip, it is too short. But I'll be in London May 6-14th. Are you around then? - Heather Piwowar
I wish... but it's a bit beyond my budget. I'm looking forward to hearing about it! - Brian Westra
@ Heather, yes I shall be around for most of that time. Let me know if you have a free time slot as it would be great to meet up. - Dan Hagon
@Cameron. That would be fantastic, FigShare is a perfect 5 minute filler and great follow up to Dryad!... and any questions people have following your talk just point them in my direction. No prep needed whatsoever! :) But honestly, any shout outs would be greatly appreciated. @Heather, I'll be tweet stalking you on Monday then :) - science3point0
Martin Fenner
How to use Citation Typing Ontology (CiTO) in your blog posts - http://blogs.plos.org/mfenner...
Updated my Link to Link Wordpress plugin to now use a simplified version of CiTO. - Martin Fenner
You guys are doing cool things in WP... makes it tempting to change... - Egon Willighagen
Thanks Egon. I think that Wordpress is an excellent platform for scholarly tools. But we are just at the beginning. - Martin Fenner
Martin, this is fantastic, and thanks for the how-to post. Can't wait to see what is coming next. Looks like my days at hosted wordpress.com are coming to an end... - Heather Piwowar
@Egon @Heather - Come to S3.0 ;) - science3point0
Heather, what Mark said. I can also give you a blog at my testing site blogs.xartrials.org. - Martin Fenner
Also a good option, I have my own wordpress dev playground there :) - science3point0
I'm sold on this stuff already! I set up a free hosted site on wordpress.com to play around, but switchet to my own installation hosted elsewhere so I could play with plugins (which wordpress.com won't allow). I'll certainly give Martin's plugins a go shortly. - 'Mummi' Thorisson
PS I'm historically a Drupal (http://drupal.org) man through-and-through when it comes to building websites. But WP is such a nice, super-user-friendly toolkit for this sort of thing. - 'Mummi' Thorisson
Mmm... has anyone spoken with the people from ResearchBlogging? I guess it should be part of the HTML snippet the create too.... - Egon Willighagen
Egon, I thought about this too. It makes a lot of sense to create the code ResearchBlogging needs with a Wordpress plugin. I will look into this when I start working on a plugin that creates a bibliography in March. - Martin Fenner
Patricia F. Anderson
Kaitlin Thaney
Article on the effects of impact factor emphasis on budding scientists: http://www.pnas.org/content... (via @ReaderMeter) #altmetrics
Cameron Neylon
Apprntly people do care a bit about improving schol comms! Paul Jump's piece in THE got most views ever for section http://www.timeshighereducation.co.uk/story...
great read! Will be adding it to the first day's reading for the thesis students:-). - Mickey Schafer
Asking people whether they care about improving schol comm is like asking whether they approve of truth, justice and ice cream for everyone. Getting them to do more about it than reading a THE article, though -- aye, there's the rub. :-) - Bill Hooker
I should add, lest my previous comment sound overly snarky, that I'm an offender myself: I don't know how many of my pubs are OA, but it's nowhere near 100%. I found a repository that will take my UQ pubs but I left the lab at the end of last century (!) and no longer have preprints... I suck at this just as much as anyone else. (I am resolved never to publish TA again, but that's a different matter.) - Bill Hooker
Actually not sure that caring about improving scholarly comms is motherhood and apple pie. You usually get the "well its got problems but basically its ok....mumble mumble....Churchill...mumble mumble...oh where's the free coffee?". That is even got a response (apparently 10,000 page views in a few days) is much more positive than I expected. Of course who read it, and what their response was is another question entirely... - Cameron Neylon
Anyway, building sympathy has some value even if it doesn't yield immediate action, it lays the ground for later action... - Cameron Neylon
Yes, and that is why I am starting to add peer review and access discussions to my classes, framing it as a "movement" that is gaining speed, and inviting students to consider how their choices vis-a-vis scholarly communication will impact their careers, their patients, as well as their own disciplines. They haven't yet been indoctrinated, and some of them get quite passionate about the topic. - Mickey Schafer
@Cameron, thanks for applying a silver lining of common sense to the dark cloud of my knee-jerk negativity. Absolutely true that getting attention and building sympathy are useful steps and worth celebrating! I didn't actually *intend* any parade-raining there, it was just reflex. - Bill Hooker
It's alright Bill, I always stand well clear of your reflexes... - Cameron Neylon
* is sheepish* - Bill Hooker
Björn Brembs
Reputation management in the age of the world-wide web - http://www.citeulike.org/user...
Trends in Cognitive Sciences, Vol. 14, No. 11. (03 November 2010), pp. 482-488. The reciprocal interactions with others that play such a significant part in our lives depend upon trust; individuals need to be confident that their partners are cooperative, and that they will return favours. Reputation permits the choice of better partners and provides incentives to be more cooperative. These uses of reputation are not unique to humans. However, in complex human societies, with large numbers of potential partners, keeping track of each other's reputation is a vital part of everyday life, and, in an inevitable arms race, ever more powerful strategies of reputation management are being developed. In this article, we bring together insights from different disciplines to throw new light onto the importance and scope of reputation management. Claudio Tennie, Uta Frith, Chris Frith - Björn Brembs
Interesting. Today I submitted a paper that talks about reputation and trust in the context of author identifiers. - Martin Fenner
Maybe it's worth citing this one in the revision... - Björn Brembs
No access ... - Martin Fenner
A couple more interesting articles on this topic (also relevant to Martin's paper, see http://ff.im/wcBBZ): i) reputation on eBay and Wikipedia - Ubois, J. Online reputation systems. Release 1.0. 2003;21:1-33. http://cdn.oreilly.com/radar... ii) reputation & identity in peer review - Frishauf P. Reputation systems: a new vision for publishing and peer review. J Participat Med.... more... - 'Mummi' Thorisson
Should I send it to you, Martin? - Björn Brembs
Yes please. And thank you for the links Mummi. - Martin Fenner
Cameron Neylon
Author Identifier Overview - http://blogs.plos.org/mfenner...
Martin Fenner talking about research reputation in the context of author identifiers. - Cameron Neylon
Interesting technical point with respect to peer review. I had a few minor comments on the pre-print but they didn't seem worthy of a comment and I really wanted to annotate inline. On the other hand, once I've digested I think I'll have some general comments that should be separated out for threaded discussion. Just wanted to note the thought, not sure what it actually means in terms of appropriate plugins/workflows... - Cameron Neylon
Paragraph-level comments in Wordpress is something I'm working on. There are a few plugins, e.g. Anotator http://adfi.usq.edu.au/dev_blo..., but most of them require a customization of the Wordpress theme. - Martin Fenner
Yes, CommentPress is an entire theme isn't it? In a sense does it have to be because otherwise you don't get the layout options you need? - Cameron Neylon
The Django book comment system looks very nice, but not that different from the Wordpress paragraph-level comment systems. Digress.it is another one http://digress.it/ - Martin Fenner
Rich Apodaca
Trouble In the House of Google - http://www.codinghorror.com/blog...
"I can't help noticing that we're not the only site to have serious problems with Google search results in the last few months. In fact, the drum beat of deteriorating Google search quality has been practically deafening of late..." - Rich Apodaca
Jason Priem
Great meeting with @ResearchRemix on our #PLoS #altmetrics study; hoping to release figs, datasets before #scio10
Pierre Lindenbaum
citations-gadget - Project Hosting on Google Code - http://code.google.com/p...
A Google Scholar Universal Gadget which enables users to search for the total number of citations of author(s). It provides a total citation count, total number of cited publications and Jorge E. Hirsch's H-Index. - Pierre Lindenbaum
Not bad. If you put in a couple of keywords, it gets me about right (11 pubs, h=10). I can squeak out n=13, h=11 manually I think, but at that low level it doesn't matter much about +/- one or two pubs/units. [Insert usual disclaimers about reliance on single metrics, lack of meaningful difference between citation count and H-index, quality vs quantity issues in publication count metrics.] - Bill Hooker
Impressive! Very fast, and find about the right numbers for me... - Egon Willighagen
So, does that mean that there is an API for google scholar ?? - Pierre Lindenbaum
(later) no: http://citations-gadget.googlecode.com/svn... : "This gadget calls Google Scholar in the same fashion as a web-browser would Suitable Scholar API needs to be first released in order to get a more useful and accurate code" - Pierre Lindenbaum
ISI should be more than just a little bit worried, I'd say. - Lars Juhl Jensen
Woohoo, I got an H-Index of 53, with only two of my publications found. More interestingly, it also found my self-archived dissertation on my personal site. - Mr. Gunn
I get misassigned a couple of times, it picks simply any "Wegner", which is not accurate enough. Any ideas how to make it more correct? - joergkurtwegner
@joergkurt, using "Wegner JK" does not help? How about keywords in the second field? (NB boolean expressions seem to be required for multiple keywords, "HIV schistosoma" does not work for me but "HIV OR schistosoma" works well.) - Bill Hooker
kinda of works for me but I have reasonably unique name - Pedro Beltrao
Björn Brembs
Impacting your young. Eve Marder, Helmut Kettenmann and Sten Grillner http://www.pnas.org/content...
pq: "Today, too many of our postdocs believe that getting a paper into a prestigious journal is more important to their career than doing the science itself." - Björn Brembs
Telling it like it is... - Björn Brembs
And isn't that belief reinforced by hiring committees who look for Science/Nature/Cell studded CV's? - Rajarshi Guha
Yes, I'm a postdoc searching for a position and I do believe getting a paper into a high-impact-factor journal is the most important factor in getting a job in many institutes. But I believe that because I've been told exactly that numerous times over the past 2 years from people in the relevant hiring committees... - Mickey Kosloff
What Mickey said. They believe it because it's true. There's something rotten in the state of Den---I mean, Science. - Bill Hooker
Quote: "We'll be very interested to hear from you when you publish this research in a journal with an impact factor >10" (heard this exact number from a couple of people, and IF >12 from another person). - Mickey Kosloff
Mickey Kosloff
The Unsuccessful self-treatment of a case of "writer's block". - http://delong.typepad.com/sdj...
The Unsuccessful self-treatment of a case of "writer's block".
All work and no play makes Jack a dull boy... - Eric Jain
Neil Swainston
Straw poll: how long can one PostDoc for before jeopardising one's future prospects?
Does one actually have an option? You need 20 years of experience to get tenure, because there is always one who does... this system sucks big time... effectively we tenure people who haven't given up, instead of the best candidates... - Egon Willighagen
Ideally, you'd want your own lab after 1 maybe 2 postdocs - if you eventually want to get a tenured position that is. The reason: they'll ask for senior author papers and you usually don't get them as a regular postdoc. - Björn Brembs
Sure you do... (well, perhaps I'm an exception...) - Egon Willighagen
Sometimes you do - my thesis advisor let me have a senior authorship during my PhD thesis - but that's pretty rare, I guess... - Björn Brembs
I have an undergrad (HHMI research scholarship recipient) who is getting first authorship on a publication, or so he claims on this resume. I haven't looked up the citation, but was impressed nonetheless. - Mickey Schafer
~3 years into my 1st postdoc and this question is also on my mind these days. My plan is to start looking after this postdoc. I also wonder how many years one should do before moving again. Any tips ? - Pedro Beltrao from Android
I don't think there's any one correct answer. It so very much depends on the field, the CV, what kind of position one is looking for (e.g. "highly ranked" research U. vs. a position with more emphasis on teaching), the particular year. etc. etc. - Mickey Kosloff
The Nobel Prize winner in economics, Joseph Stiglitz, says that his advisor in graduate student told him once, "You can't remain a promising young man forever." - Hope Leman
I'm with Neil and Bjoern: no more than 2, preferably one. Beyond that you are being treated as a fungible data-collection unit in someone's factory, a small stone at the bottom of a large pyramid. (I did 4, though one was so abortive I try to pretend it didn't happen, over 11 years.) - Bill Hooker
@pedro: I don't think it matters much if you spent 3 or 5 years on your first postdoc, as long as you've been productive. I'd definitely start looking for independent positions (in the widest sense) after five years, especially with your track record. They don't have to be tenure-track, but ideally they would. - Björn Brembs
Hmm... I'm currently in an odd position in so far as that I'm coming to the end of my first PostDoc, which I got before I had done a PhD. I'm now (hopefully) going to get a PhD via the work that I've published over the last five years. I've also got ~10 years industrial experience. So does this make me a newly awarded PhD, a one-PostDoc or a washed-up drifter?!? - Neil Swainston from iPhone
Why, the last option, of course :-) - Björn Brembs
It makes you uniquely qualified and uncategorizable. Bottom line no-one's going to care much beyond your publication list and any evidence of being able to bring in funding (industrial experience always looks good in the UK). To be honest in the current climate in the UK I would say all bets are off. There will be opportunities and there will be a lot of pain both institutional and personal so take a look at Deepak's post on serendipity. - Cameron Neylon
Two is too many , unless they are very short. I general not knowing what to do and using multiple postdocs to figure things out can be regarded as a weakness. That said you can do more than two if you want to pick up a new technique or find a mentor who is worth the one additional postdoc label - Hari
Björn Brembs
Mr. Gunn
[Big News!] NIH to use ORCID as Author Identifier. (via @orcid_org) - http://www.weopenid.org/press-r...
has anything happened since this article in September? - Jennifer Melinn
Not AFAIK, but I just saw it tweeted today, so perhaps ask Martin? - Mr. Gunn
The follow-up meeting mentioned in the press release hasn't happened yet. - Martin Fenner
Good news all the same - at least given that before NIH was not playing ball at all (if I remember correctly). - 'Mummi' Thorisson
I hope that there is more to report at the next ORCID Participant meeting November 18 in London. - Martin Fenner
Geoffrey Bilder
How many users have JavaScript disabled? · YDN Blog - http://developer.yahoo.com/blogs...
Heather Piwowar
RT @wilbanks: @creativecommons responds to the CBC's ban on using CC music in podcasts. Please RT. http://creativecommons.org/weblog...
Björn Brembs
Dear colleagues: how do you organize your journal club? With or without PIs? Who choses the papers? Journal Blitz or alphabetical list? What works for you?
Every student is assigned several journals he is 'responsible' for. Once a week each student sends an email to the group with relevant abstracts. Every other week there is a JC meeting in which a student chooses an interesting paper (on his own) presents it and lead a discussion about it. In the week between a student gives a 'research progress' meeting instead. PI is present in all of... more... - Nir London
Students/postdocs propose three or four papers, PI has input into final choice. PI present at every JC and presents at least once. Papers chosen for intrinsic interest ("holy shit that's cool") or applicability to current projects in the lab. Honestly, I've always found JC to be a great idea in theory but a dismal failure in practice. Even with well chosen papers, if the presenter... more... - Bill Hooker
We had three themes, and alternated the themes. PI picks; once every few weeks, in-depth discussion. Students write up review in blog post. - Egon Willighagen
We're currently revamping our journal club due to much of the same problems mentioned here, so please keep the descriptions of your particular method coming! - Björn Brembs
@Bill It is not only the JC that would benefit if the research environment would change it's pace - or at least would acknowledge that there are other important things but mere papers. - Oliver Schuster
Here, the JC is attended by several research groups and the number of people attending varies between 5 to 30 people. Clearly, the presented paper and the presenter determined the number of people in the audience. Sometimes, the paper does not seem relevant to most of the researcher so almost nobody shows up, sometimes the paper is appealing or the presenter is known to present well so... more... - JJ
We had similar issues, mostly due to people either not picking good papers, not preparing for JC, just not being good presenters, or all three. In grad school we had an assessed JC class which had all the same problems, except people prepared a little more. People did come out of the class a little better at public speaking but not better at picking good papers. I still think they're good practice. Previous JCs where papers were assigned were much worse that when people pick their own. - Mr. Gunn from YouFeed
every Friday ,we have JC meeting. We discuss two paper in an hour and we have to send the paper at least 2-3 days before. Every one is supposed to read the paper beforehand.The person talking about the paper give the gist and others are supposed to ask question if there is any doubt about any part of the paper. At the end Paper is critiqued. The paper is chosen by Grad student and the... more... - sushant
No formal journal club for our lab, and I like not having to block of a chunk of time to discuss paper(s) that may or may not be interesting. Instead, PI and lab members are usually around and informal discussion of relevant papers happens randomly, as needed. That said, I was recently visiting another lab and their journal club brought together several labs from different disciplines... more... - Jason Snyder
Once a week one person chooses a paper and each student/postdoc gets a figure. PI is present, but just interjects when things are not being explained properly. I decided on this course after sitting through several miserable journal clubs where the presenter struggled mightily to explain the whole paper. When we started everyone involved was a 1st year masters student. It was made more... more... - Walton Jones
There is a journal club rota, and that person emails round a PDF. They give 10 min intro to the paper at the start, then it's a free for all. Much better for scientific development than someone presenting a paper formally, and much more fun. - Dave Lunt
Our JC is organised centrally and informally. Papers are either picked by the three organisers (all non-PI) or suggested by any of the participants. Articles are then circulated via a closed mailing list and (should be) read by all. Discussion is moderated by the organisers who also give an informal summary in the beginning. Afterwards, conclusions are published on the JC's website.... more... - Arnulf Koehncke
Ramy Karam Aziz
#GoogleScholar is out of control. Trying to be too smart in a well-established area of literature indexing is turning #GoogleScholar into a mess. It's now mixing authors with editors, adding another problem to the duplicate records
Julien Sicot
Another researcher index? ReaderMeter looks to answer with Mendeley - http://www.mendeley.com/blog...
Interesting. But as they themselves note the tool is limited by, obviously, duplicate publication entries in the Mendeley collection + ambiguous author names. The engine "queries the data provider's API for articles matching a given author string". I am not going to bother paying much attention to any of these tools unless there at least *some* basic attempt at resolving author names. - 'Mummi' Thorisson
Martin Fenner
Do you read the papers you cite? "No: I only cite my own work" one possible answer in survey by The Scientist http://blog.the-scientist.com/2010...
The conversation between Martin and Christian Specht is a gem. This is what the internets are *for*. - Bill Hooker
Hey you gotta be honest... - Benjamin Tseng
Also a nice anecdote from Jan Velterop. I think there is material for many more blog posts. My latest post (about Citation Style Language) of course also cites the Laemmli paper... - Martin Fenner
There's another problem here. I often cite a paper for a number or a piece of data. I'll check that number or comment in the paper but will often not read the whole paper. Does that count? - Cameron Neylon
how do you know that paper has the number or comment you want? surely you have to at least scan it? - Christina Pikas
Google...so yes, I skim but I wouldn't call it reading...not in the sense I think is meant in the survey - Cameron Neylon
I actually read every article I cite. Even go through the trouble of having articles translated for me when I don't know the original language when the article has precedence over a specific finding. - Kubke
I fall between Cameron and Fabiana; I will cite papers for a number or single observation or whatever, but I do read enough of the paper to be sure it says what I think it says about that particular datum. (Actually I suspect this is what Cam does as well -- "skimming".) I definitely don't give a close reading to every paper, checking references and scrutinizing controls and statistical... more... - Bill Hooker
I don't think I could cite something I didn't read, how would you know if that paper actually shows what you are claiming in your statement ? Citations serve as foundation for the research problem, methods or discussion. Assuming that you are not constantly changing topics those citations are not going to keep changing dramatically either so getting up to ~100 well understood papers is not that hard .. even at 1 day per article. - Pedro Beltrao
"Assuming that you are not constantly changing topics": schistosomiasis --> HIV replication --> iron homeostasis --> Ebox signaling networks --> HIV diagnostics. In the first two (phd and first postdoc) and in the Ebox work (last postdoc), I probably did have e.g. 100 well understood papers that I had read carefully and cited regularly. But that was the foundational stuff; there are... more... - Bill Hooker
Cameron Neylon
Ok crowd-sourced proposal time. Topic: Research Metrics. Aim: Develop and deploy credible metrics frameworks that encourage "open" behaviours. Value: $30k. Go.
More precisely: I have an agenda, some ideas, and a possible line on about this amount of money. Am interested in any ideas on how most effectively to create change with about this resource and anyone who is interested in taking part (with the caveat that this is not a whole lot of money if it gets split a lot of ways). - Cameron Neylon
Particularly interested in bringing existing projects/initiatives together to maximise effect. I'm aware of a range of things going at the moment but would appreciate pointers to any others. - Cameron Neylon
Quite. More downstream funding might be possible if there was demonstrated value out of the "pilot" or whatever it might be. There are a bunch of JISC funded projects that are sort of, but not really, in this area at the moment (they are focussed on citation) so that's another place to start. - Cameron Neylon
Do we have any existing examples of metrics that encourage open behaviors? - Mr. Gunn
Well I would argue that re-use metrics (downloads, data citation) push in the right direction. I couldn't point to hard evidence to support that tho. - Cameron Neylon
Perhaps the pilot could be to gather such evidence? - Mr. Gunn
Thomson-Reuters shares went down hard in the last 26 minutes. - pn
@D Peter Binfield has talked about Google Analytics style tools provided by a third party to do cross publisher ALMs. Something I always thought was an interesting idea. It could at least provide a consistent way of dealing with that kind of gaming? - Cameron Neylon
@Mr Gunn: It would be difficult to do that prospectively in the time frame of a small grant. Can you think of clean examples which could be looked retrospectively? Key issue is actually persuading funders to adopt something of course. - Cameron Neylon
@Paulo: Don't worry, my next idea will take out Pepsi... - Cameron Neylon
No idea how you'd do it but what I'd really like is to understand _why_ someone downloaded something. Was it for the figures, a specific piece of data, or for the beauty of the whole work... - Cameron Neylon
It's that or some sort of single use citation token as Claudia (I think) suggested at one point. Either would likely lead to bias anyway... - Cameron Neylon
Dorothea - Have you looked at the PIRUS2 and MESUR projects? They are looking measuring usage statistics from mulitple locations (PIRUS) and assesing quality of content (MESUR). They already have done a lot of preliminary work. I would suggest usage metrics as they both argue usage happens earlier in the research cycle than citations. Is there a way to look at any open behavior at the grant application stage, like this thread? That's even earlier in the research process. - Elizabeth Brown
Cameron, if I could think of a way to do something like that retrospectively, I'd already be doing it ;-) Agreed that usage metrics are the way to go, though, to move upstream from citations. - Mr. Gunn
Interested that no-one yet has explicitly brought up the issue of data that metrics are based on... - Cameron Neylon
@Mr Gunn, yes but how far upstream do you think it is possible/sensible to go? - Cameron Neylon
Hate to say it, but I think your funding is short a few zeroes. If this were something you could do for $30K, PLoS or BMC or even Thomson Reuters would already have done it. But so as not to be all negative all the time: how about expanding Heather Piwowar's work on data re-use? The aim would be to compare the rewards (citations, collaborations, etc) reaped by open, re-usable datasets... more... - Bill Hooker
It's alright. I'm not proposing to tie up all the loose ends for this kind of sum. Although I would say that in many cases PLoS/BMC don't have that kind of spare cash just sitting about to do something different. Question to my mind is how to make the most difference with that kind of amount...not necessarily to solve the problem. - Cameron Neylon from twhirl
The question with this kind of thing is always how best to take a small amount and multiply it with existing funds that other people already have... - Cameron Neylon
In that light, I think my dataset idea looks a little better: you might be able to tie in to what Heather is doing now. The real trick would be to get a few *more* related efforts coming together under the same roof. - Bill Hooker
Certainly I'd be pretty happy with building a reference dataset of data citations and/or uses. - Cameron Neylon
I agree that a) this is a very important issue, and b) $30k is not a lot of money. I would use the money to talk to the stakeholders (researchers, institutions, funders, publishers, vendors) - and that would include Thomson Reuters - and write a report that summarizes the key issues and comes up with a set of recommendations. On a very small scale I have started to do just that (Cameron knows about this). - Martin Fenner
Agree with the talk to stakeholders. Less sure about the writing of reports...but that's maybe a personal bias...as a focus for discussion yes, but as an end in itself? But definitely agree that engaging the relevant people is critical. There is no point building/writing about anything that doesn't serve the needs of those whose metrics will be taken seriously by researchers... - Cameron Neylon
Reports indeed have a bad track record. Maybe principles and action points? - Martin Fenner
A set of agreed principles would be a very interesting outcome if it were feasible. Action points seems easier but then actually turning them into action becomes the challenge... - Cameron Neylon
About citations of data and other open science outcomes like code, can current citation metrics make a separate count for numbers of citations of data and code as opposed to articles? Is there some agreed meta-data field that indicates something is data rather than an article? If someone wants to reward open science, then we need to be able to count and aggregate open-sciency citations. - Alex Holcombe
Yes, progress being made on citing data but citing data within a publication rather than the publication itself is some way off. And citing code is still pretty rare (partly because "publishing" code is still pretty rare). Martin and Mummi did a nice double act at Science Online London looking at the use of ORCID to mix and match data and paper citations. - Cameron Neylon
I would suggest to talk the David Shotton (Oxford) on CiTO, and get citation types into the equation... and develop a simply H-index-like thing that is weighted for citation types... type: usesMethodIn -> large positive for H'-index... if type: refutes -> negative (or really small positive) on H'-index... - Egon Willighagen
To my mind the best thing would be a pilot where you pay for (part of) a person or student to piggyback on an established database with appropriate data sets (at EBI, for example, this would be something like PRIDE or ArrayExpress) and track downloads then provide example chunks of end-of-grant-style reports of impact and write a paper or three on it (one on mechanics, one with submitters, one forward-look), etc. - Chris from twhirl
This could then make for a nice proof-of-concept thing to drag in some real money. - Chris from twhirl
I think it's reasonable to go up to the level of the individual experiment, but not sure how possible it is. I really do like the idea of looking at the qualities of a citation, rather than just the A cites B model. - Mr. Gunn from YouFeed
interesting. thinking. fwiw, I have a research proposal drafted and submitted, proposing to lay groundwork on patterns of data citation and reuse tracking. Might could be synergistic? Submitted for what is supposed to be a double-blind review process, so in an attempt to make it ungoogleable I'll just put a link here: https://docs.google.com/documen... - Heather Piwowar
I also have a large set (11k) of "data creation" papers whose citations we could follow, examining for data reuse patterns and citation benefit of sharing. Totally agree on CiTO. Ideally would supplement with data creation papers in other fields/datatypes too, to illustrate differences across fields and datatypes. Not easy, but have some methods. Also, could work with GEO and... more... - Heather Piwowar
That is a great proposal. Wish I were reviewing it... - Chris from Android
Made me think of something that might be complementary: to interview a set of data producers who have submitted somewhere about their attempts to make their data traceable, to claim credit in subsequent funding proposals, and how they think that played out. And ideally, to then revisit those applications with the funders to whom they were submitted. - Chris from Android
I think anyone submitting a proposal like those above should look at the MESUR project in particular- they've already looked at usage stats and compared this to article citations to estimate the quality of work. Some of the questions above have already been answered. My question is, can a list of open behaviors be clearly identified? I think that might be more challenging than the metrics, since most of the tools are evolving so quickly. - Elizabeth Brown
MESUR definitely high on my list (as is PIRUS now) and will also talk to Carl Bergstrom as well. Also liking Chris and Heather's comments. - Cameron Neylon from twhirl
I would like to extend something like http://wikidashboard.appspot.com/ (plus http://orcid.org/ - once workable) to contexts like http://www.science3point0.com/coasped... . Might solve the on-wiki part of the problem. - Daniel Mietchen
Are you crowd-sourcing tips/pointers/suggestions for your own proposal or are you asking people to contribute directly to a 'community' proposal (via google docs for example), with the intention that people who contribute to the grant get a slice of the funding ? - Greg Tyrelle
Greg, A bit of both. I have my own ideas and want to make sure I haven't missed anything obvious but also am looking to try and form a network of people to take this forward in some form. I'll move onto an online document in the next few days to which people are welcome to contribute with the idea of taking part. Bottom line is that at this level there won't be money for much beyond maybe travel/meetings and one FTE for a couple of months. - Cameron Neylon
My basic idea is meeting with stakeholders followed by hacksession "sandpit" out of which the group decides to fund someone already in post to be extended to take most promising aspects a bit further. Open minded as to whether that aspect might be liberated data, some sort of mashup, or a protocol/framework, or a document. - Cameron Neylon
Would love to participate. Sounds interesting. - 'Mummi' Thorisson
Throwing my $0.02 worth into the pool: how about considering also attribution and metrics for less granular contributions than papers/datasets: e.g. output of curator activities, or 'nano-publications' mined from the literature? (http://www.nbic.nl/uploads... http://laikaspoetnik.wordpress.com/2010... ) - 'Mummi' Thorisson
Would certainly very much like to do that in the longer term. Keep it as a longer term target that any thing that gets built needs to be open to? - Cameron Neylon
Agreed. Try and keep the concept of 'contribution' that one gets credit for (and can ideally be formally cited) quite open-ended. - 'Mummi' Thorisson
First GDoc version: https://docs.google.com/documen... It's light on actual substance at the moment but that is kind of deliberate. - Cameron Neylon
Can't edit. :) - Andrew Lang
Ok, fixed the editing problem I think. I ticked the wrong box! :-/ - Cameron Neylon
What D said; I can't think of any substantive changes to suggest. Success will, of course, depend on picking the right people to be at the initial workshop... - Bill Hooker
Absolutely - so phase II - who wants to be involved, who should be involved? Already some good suggestions above. This will necessarily be UK centric but hopefully not entirely so. - Cameron Neylon
Just made some edits. I find two points missing: (1) If funders were to allow for public peer review of (at least some) proposals, the re-use of such proposals and reviews would provide a good use case, and probably be of interest to the funders. (2) As already mentioned above, wikis have solved much of the problem already (... more... - Daniel Mietchen
Agreed. But I would say this proposal is positioned to ask funders what they want first. Not for us to tell them what they should do. On the timeframe of this grant persuading any UK funder to do public peer review is a non-starter. In terms of Wikis, yes as a framework there is a lot there, but as you say the problem is you'd have to bring that content in because getting people to use them is difficult. But as you say the COASPED project would be a good example of the kind of thing that could be done. - Cameron Neylon
So tldr: yes they're good points but they're kind of deliberately not the focus because the intention is to be open ended as to what will come out the other end. - Cameron Neylon
Fair enough. I would like to be involved, but if it has to be via the UK, perhaps @science3point0 would be the best way to do that - would this counts as a "Infrastructure Organization"? - Daniel Mietchen
Sorry for arriving late to the conversation, I've been dipping out, but I'd like to reaffirm Daniels sentiments and would happily offer S3.0 be It as a hosting service to the proof of principle or to act as an infrastructure organisation, either in it's current format or in a tailor made format for those involved, closed group etc - science3point0 from iPhone
Björn Brembs
Battling the Paper Glut -- Siegel and Baveye 329 (5998): 1466 -- Science - http://www.sciencemag.org/cgi...
"One way to accomplish this would be a new generation of review impact indexes, based on information provided by publishers (3, 5). Effectiveness in peer-reviewing should be viewed as an essential skill to acquire for Ph.D. students, worldwide. Journals should demand that for every paper submitted, an author provide three reviews of other manuscripts. Perhaps if authors knew that their reviewing workload would increase dramatically with the number of papers they submit, they would craft fewer and better papers, ultimately benefiting all involved." - Björn Brembs from Bookmarklet
The academic community continues to believe that the formal scholarly publishing process separates sound research from shoddy or biased counterparts. Unfortunately, scholarly publishing may not be able to effectively fulfill its role as a gatekeeper much longer. As soon as the "publish or perish" concept (the imperative to publish work constantly to further or sustain an academic... more... - Bill Hooker
Researchers in countries such as China and India are subjected to a numbers game similar to that in the West, sometimes with the added incentive of monetary rewards for articles published in "top" journals. In 2008, China passed the United States to become the second scholarly producer (in total number of articles) after Europe. Researchers have reacted to this publication glut by... more... - Bill Hooker
Researchers need to fight to contain the current paper glut. The number of articles published per year should never be used, under any circumstance, as a criterion in tenure or promotion decisions, or to rank academic institutions. As the medical community proposed 25 years ago (4), researchers should never be allowed to include more than three publications per year in activity reports;... more... - Bill Hooker
There. Now we can read what we're discussing. - Bill Hooker
lol @Bill :-) Good job, I should've done that... - Björn Brembs
Anyone read "The Republic of Science" by Michael Polanyi? http://bit.ly/b8hfoI - Bala
I think that if you limit the number of papers people are allowed to cite on reports/proposals/CVs, you just increase the pressure to publish in a glamor journal. - Michael Kuhn
@Michael. Possibly. It may also be that reviewers actually start reading papers again. But that may be a tad naive, though... - Björn Brembs
I've reviewed more than three times as many papers as I've submitted, but not at any one journal. For the "review 3 to submit 1" rule to work, publishers would have to cooperate and recognize reciprocal review credits. I don't see that happening somehow. - Bill Hooker
Björn Brembs
"Our work in building large-scale reputation systems suggests that it may be possible to build such a system on two pillars: a system of incentives for authors of papers and reviews alike, and a content-driven way of measuring merit and attributing rewards. The reputation of people as authors would depend, as usual, on their publishing works of high measured value. And crucially, the reputation of people as reviewers would depend on their ability to be early reliable predictors of the future value of a work. Thus, two skills would be required of a successful reviewer: the ability to produce reviews that are later deemed by the community to be accurate, and the ability to do so early, anticipating the consensus. This is the main factor that would drive well-respected people to act as talent scouts, and to review freshly published papers, rather than piling up on works by famous authors. Reviews would be ranked by reputation, thus diminishing irrelevant comments, as Amazon has shown it is possible to do." - Björn Brembs from Bookmarklet
I'd like to comment there with a link to the old threads about reputation systems here, for instance the one with the Yahoo patterns a few years back. Does anyone still have a link for these threads? - Björn Brembs
Anyone interested in trying out an "online collaboration" project? I made a fly nervous system targeted transgene that could be interesting once a transgenic stock is made. Anyhow, will be cool to set up a project development site.. may be using a fly-wiki of sorts. - Bala
@Bala: I'm definitely interested! - Björn Brembs
@Brembs: Cool. How do we do this? It's a calbindin-Gal4/VP16 construct, just gave it for sequencing this morn'. - Bala
@Brembs: I'm a big fan of the github model. http://en.wikipedia.org/wiki... - Bala
You'd have to get extra points for making a prediction (a.k.a. bet) that goes against what most other reviewers predict (or else no one would want to review a controversial paper). Regarding "[...] as Amazon has shown it is possible to do": Amazon has also shown how difficult it is to prevent people from gaming such reputation systems... - Eric Jain
@Bala: either post the info somewhere or send me an email: bjoern@brembs.net We can work on the biology but are not developers, so GitHub is not the way to go, at least not on our side. - Björn Brembs
Looking for points systems - read (or listen to) Eric Weinstein talking about this. Much more sophisticated analysis based on real experience of financial systems. If you go long on something that looks unlikely (or go short on something that everyone agrees with) you get to buy low and sell high. I never quite got my head around whether Eric really meant that this should involve real money. But anyway an interesting thought experiment. - Cameron Neylon
@Cameron: Have a link to a paper or a talk by Eric Weinstein were he talks about this? - Eric Jain
There should be plenty of experience in other reputation systems to come up with a version for scientists that should be a very good starting point, from which optimization could begin. Some of the properties of the system could even be easily crowdsourced. - Björn Brembs
Eric, do a search for PIRSA and Eric Weinstein (and possibly "owes me a dollar") and you'll find the video of a talk he gave a few years back. I haven't tracked down any papers (he really is a hedge fund manager) but you can find some stuff on his personal website (sorry for lack of links don't have proper connection at moment to search) - Cameron Neylon from twhirl
Cameron Neylon
Scribd now requires login and are charging for downloads. Should we move e.g. Beautiful Data Chapter to Nature Precedings? http://pbackwriter.blogspot.com/2010...
absolutely - Graham Steel
I have no problem with people making money off a service but the whole point of putting things there for us was to make them freely available. I've no time to do this this week tho so will try to do it over weekend... - Cameron Neylon
Bummer. Wonder if this would be bad news for us too - the document content-type in the Drupal CMS uploads/retrieves info from scribd.com. Example: http://bit.ly/9r76Y8 - 'Mummi' Thorisson
@Neil The embedded PDF/ Word/etc. functionality we've found quite useful, and the Drupal ipaper module makes this pretty easy to set up. The scribd.com site itself is of little relevance. - 'Mummi' Thorisson
I don't use scribd much, but unlike Neil, like the way it sets things out. One work around is to use posterous - see http://jobadge.posterous.com/can-you... - Jo Badge
I stopped using Scribd about a year ago after my account got suspended for copyright infringement ;-) I use Posterous now instead. - Graham Steel
Apparently this is yet another one of those "we're going to just do this and let people opt out if they want to" things. The mistake they made here was not getting the word out enough in advance for people. - Mr. Gunn
From the link: "Evidently all the money they've been raking in from the Google ads they've posted on my e-book pages hasn't been enough for them." I think this is key -- you don't actually rake in money from online advertising unless you're FaceBook or Kos. It seems as though a lot of people who started with blithe assumptions about paying for everything with advertising are finding they have to make some hard decisions. - Bill Hooker
you can add documents to Slideshare too. - Elizabeth Brown
SlideShare requires a login to download the documents too :-/ - Noel O'Boyle
Damn - hadn't noticed that. Might be a weekend of submitting things to Nature Pre... - Cameron Neylon
wow that is pretty annoying - I put a copy on slideshare http://www.slideshare.net/jcbradl... - Jean-Claude Bradley
Also just submitted to Nature Precedings - all authors should get email alert - let me know if you don't as this has failed in the past - Jean-Claude Bradley
Thanks D - it found Drexel's 2 repositories - Jean-Claude Bradley
kewl :) - Graham Steel
Andrew Lang
"NPG is considering launching a new system for describing and archiving datasets."
npgdata.png
Where is this from? - Cameron Neylon
@Cameron. It is from a survey they sent out. - Andrew Lang
in that EOS article I blogged, they mentioned a journal that just describes datasets like that... Earth System Science Data. Interesting - Christina Pikas
In the words of Manuel et al, 'I know nothing' http://www.youtube.com/watch... - Graham Steel
related: http://www.biomedcentral.com/1756-05... "By publishing Data Notes (often called “data papers” by other publishers), authors in BMC Research Notes can publish peer-reviewed articles that briefly describe a biomedical data set or database, withthe data being readily accessible and attributed to a source." (ObDisclosure: I'm a BMCRN assoc editor, it's a volunteer position) - Bill Hooker
Christina, Earth System Science Data is the journal for the Pangaea project we talked about earlier today. I could provide contact information... - Martin Fenner
+1 Neil Why create yet another journal for this? Why not use the existing repositories? - Mr. Gunn
@Neil, MrG: a cynic would say that Prestige Journals want the Prestige model to carry over to everything, so here they are re-inventing a wheel so that they can slap their brand on it... - Bill Hooker
+1 Neil - Heather Piwowar
Bunch of spreadsheets described by free text and a Nature logo? Not entirely convinced that this would enhance our lives greatly. - Neil Swainston from iPhone
I disagree, as I think that where to deposit primary research datasets is an unsolved problem. Supplementary information is obviously not a good solution. And there just aren't repositories (institutional or domain-specific) for all datasets, let alone standard formats. - Martin Fenner
2 things: (a) how searchable are existing 'general' data repositories (eg datadryad, CRData), what kind of metadata is included in these datasets and how will this compare to the NPG system? (b) what is the best system for long-term stability: a funding-based model or a branding-driven business model? - Thomas Lemberger
Bear in mind that this is a user survey, not a press release. ;) Also, letting people *upload* documents in any format doesn't mean that a system couldn't process them into a format more suited to discovery. - Euan
Ah, yes, branding. I forget how much those within an institution care about it (relative to how little those outside care.) - Mr. Gunn
Cameron Neylon
Free…as in the British Museum - http://cameronneylon.net/blog...
Richard Stallman and Richard Grant, two people who I wouldn’t ever have expected to group together except based on their first name, have recently published articles that have made me think about what we mean when we talk about “Open” stuff. Stallman's piece argues that the word "open" is limiting and misleading. But I feel the same way in many ways about "free". Richard Grant's piece probes the problems of making services open-access, making precisely the point that they are not free. Clearly they are not, and pretending they are is a dangerous way to justify access and accessibility. For me, it is a question of how best to invest to maximise your return. - Cameron Neylon
Free like public libraries: http://politicalhumor.about.com/b... - Björn Brembs
Libraries often market their services as "free" and this has always been problematic, in my opinion. When someone asked me at the publib - I would always tack on - your tax dollars at work! - Christina Pikas
Interesting post and points, and I'd agree that "free" is at least as ambiguous as "open." Re being surprised that British national museums are free: I suspect some are surprised that 18 of the 19 Smithsonian museums and galleries are also free, which is to say, "don't have a ticket fee." - Walt Crawford
I knew I had a better example in mind than the Lincoln Memorial...! You'd think I'd remember that having spent three days doing the various Smithsonian museums (musea?) earlier this year... - Cameron Neylon
Before reading Stallman's article, I never thought of "freedom" when I heard free software, I always thought no-fee, and thus interpreted Open as more useful than Free. It all depends on our background I guess. - Heather Piwowar
The name of my university: Free University of Berlin - founded after WWII as opposed to the university in the not-so-free part of Berlin... - Björn Brembs from iPhone
@Heather - I find it very easy to build up these abstractions in my head built around definitions and then forget other people don't have the same constructs. Free/Open is a classic example but I keep having to remind myself of how differently other people think (half the reason for the post really - partly directed at myself) - Cameron Neylon
Martin Fenner
We're officially a non-profit! Announced today, ORCID initiative is now ORCID, Inc http://www.orcid.org/node/166 (via http://friendfeed.com/orcid...)
I hope that ORCID becomes more visible by becoming a non-profit organization. And with a board of directors you now have people you can contact with questions or suggestions. Please do. - Martin Fenner
Splendid. And congratulations on the appointment on the board, Martin! http://www.orcid.org/board-d... - 'Mummi' Thorisson
Finally some movement on that front! - Björn Brembs
Congratulations, Martin! So sorry I will be in Milan at ESMO when you are next over here :( - Sally Church
Richard Badge
Wondering why the university I work for requires me to tell them about "IT hardware and software" that I own personally?
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