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Thomas Brox Røst › Likes

Shirley Wu
A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...
It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry - Shirley Wu from twhirl
But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented) - Shirley Wu from twhirl
It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant> - Shirley Wu from twhirl
Thanks for doing that. - Mr. Gunn
AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. http://ff.im/airoV ). - Daniel Mietchen
Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! http://acawiki.org/ ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: http://gradturkey.fastcoder.net/ - Jodi Schneider
can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it - Alexey
my comments on the topic in 08/07 http://pimm.wordpress.com/2007... - Attila Csordas
Knol has many journal features built-in. Here is an example of a successful research journal on H1N1: http://knol.google.com/k... - no name
John Wilbanks mentioned doing journal clubs online in his talk here recently: http://bit.ly/3jxnxr - Walter Jessen
this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was... more... - Shirley Wu from twhirl
can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better? - Alexey
@Neil Saunders Were you thinking of JournalFire? We recently updated the site and are looking for feedback. I posted about it yesterday: http://friendfeed.com/the-lif... - John Delacruz
Mike Chelen
"The Open Citations Project is global in scope, designed to change the face of scientific publishing. It aims to make bibliographic citation links as easy to use as Web links. Its goals are three-fold: To establish OpenCitations.net, a public RDF triplestore for biomedical literature citations. (Note: In this context, a bibliographic citation is a reference within a particular citing work to another publication termed the cited work. This use of the word ‘citation’ should be clearly distinguished from the common related use of this word to indicate the cited work itself. Within this application, ‘cite’ and ‘citation’ denote the performative act of citation itself, not the target document of that citation.) To harvest the reference lists from many current and recent open access journal articles, and to convert these datasets into RDF, starting with those in UK Pubmed Central, those published by the Public Library of Science and Biomed Central, those from other publishers willing for... more... - Mike Chelen from Bookmarklet
Lucy Power
I'm looking for some references which show evidence that some basic research is unnecessarily repeated due to a lack of openness or access to data - or is this not true? There are plenty of papers which say secrecy in science makes it difficult to accurately repeat research when necessary, but is there also unnecessary repetition?
@Neil, thanks, interesting idea, I guess that could be one place to start! - Lucy Power
I'm not sure it's that easy to distinguish between lack of openness and literature search failure - Pawel Szczesny from iPhone
In the argument around peer review this came up. I think it might be very difficult to quantify. I can give you a couple of anecdotes but given I've spent the last several days whining about anecdotal evidence... :-) - Cameron Neylon
Back in the late 80s there was some research in the engineering technological gatekeepers literature showing that researchers would not walk 400 feet to the library to find an answer to a question, but would instead repeat the study. This was part of a body of literature examining preferred information sources for different specialties, with similar findings for all professions studied. I used the cite in a paper I wrote, but I no longer have electronic access to the original. If I can find it ... ? - Patricia F. Anderson
delagoya
This book on bioinformatics looks quite good (based on TOC) http://www.amazon.com/Bioinfo...
And available electronically. Nice - Deepak Singh
Bill Hooker
Limitless or limited resources. | Indexed - http://thisisindexed.com/2010...
Limitless or limited resources. | Indexed
Thought experiment: Replace "ideas" by some other noun. I just tried "XML", "money", "weapon-grade Plutonium", "jokes" and "problems", and they all still fit into this general depiction. - Daniel Mietchen
Carl Boettiger
How do you manage citations when writing on the web (blogs, etc?) Would be nice to have a reference manger that works in browser editors like #Mendeley does in office docs
It would be really nice if the Google Docs API supported the right hooks for use to do this. - Mr. Gunn
When you say manage, do you mean insert during the writing process? - AJCann
Yup, that would probably be the most valuable. For instance, even a Wordpress plugin that let me cite using the bibtex reference would be quite nice, if such a thing exists? - Carl Boettiger
Good news: bibtex wordpress plugin exists. bad news: formatting fails on my site. http://wordpress.org/extend... - Carl Boettiger
Got a basic citation system working in wordpress at least: http://www.carlboettiger.info/archive... - Carl Boettiger
My thoughts on this are here: http://blogs.plos.org/mfenner.... Briefly, we should integrate citations as Wordpress links, this would give us a lot of interesting features for free. - Martin Fenner
Thanks Martin, that's an excellent piece. Yes, I agree citations should be put in as links, though I'm not sure what links: as @rmpage points out, doi based links might make more sense than those pointing to a particular publisher? What track-back tools are available that could determine how many incoming links a paper has? How do these cope with multiple potential link urls to the same paper? - Carl Boettiger
Carl, you point a big problem that goes beyond managing citations for a blog. I'm a big fan of DOIs, and I'm always confused why so many places prefer their own internal identifier (PubMed is a prime example). - Martin Fenner
Rajarshi Guha
Supercomputer sets protein-folding record : Nature News - http://www.nature.com/news...
What a story! Academia --> hedge fund --> ridiculous wealth --> self-funded academic research - Andrew Su
And I remain completely in awe of DE Shaw - Deepak Singh
Wow, what would you do in science if you had that amount of money available? - joergkurtwegner
Shaw is not doing this for commercial reasons. He has the money, which gives him the luxury to try interesting problems that don't make commercial sense. Although as Vijay Pande says, even Shaw acknowledges that Anton only goes so far - Deepak Singh
Anyone done an Anton vs. Folding@Home comparison? - Matthew Todd
Wonder how long that'll hold up with Blue Waters around the corner. http://gladiator.ncsa.illinois.edu/vidcast... - Christopher Fields
edythe
A Minimalist Lifestyle Does Not Make You a Better Person - http://lifehacker.com/5663045...
A Minimalist Lifestyle Does Not Make You a Better Person
"It is not possible, nor is it desirable, to own nothing. In fact, a point comes when not owning critical stuff (a bed, a toilet, a room) starts becoming stressful again, in a whole different way from "too much stuff" stress. "Simplicity" is a relative term, and perhaps inapt; try "convenience", which has more useful connotations. Fitting my life into a small number of boxes tucked under my bed makes me happy. Fretting over the precise enumeration of the items in those boxes would completely defeat the object of the exercise." - edythe from Bookmarklet
RAPatton
2 Brothers Await Broad Use of e-Medical Records - NYTimes.com - http://www.nytimes.com/2010...
2 Brothers Await Broad Use of e-Medical Records - NYTimes.com
2 Brothers Await Broad Use of e-Medical Records - NYTimes.com
"There is no silver bullet for reforming America’s health care system, but medical experts have long agreed that digital patient records and electronic prescribing can help improve care and curb costs. It seems straightforward. Just combine technology skills with investment money, and then develop innovative products. But to date, the push for a digital revolution in doctors’ offices has brought mostly frustration for the many companies big and small that are trying to conquer the field. Just ask the Doerr brothers — John Doerr, the well-known venture capitalist who was an early backer of Google and Amazon, and Dr. Tom Doerr, a physician and software designer. Dr. Doerr founded a software company in 1999, beginning with an electronic prescribing product and later adding electronic health records. His brother is the largest investor. After more than a decade, the venture has fewer than 500 doctors using its software." - RAPatton from Bookmarklet
"The Doerrs’ software company is only one of many hoping to cash in on the national mandate for digital medical records. The companies range from giants like General Electric to specialists like Athenahealth that cater to small physician practices. They, like the Doerrs, are betting that the law will help create a turning point for the economics of digital health records, opening the... more... - RAPatton
Christopher Sacca
Donald Duck Meets Glenn Beck in "Right Wing Radio Duck" - http://www.youtube.com/watch...
Donald Duck Meets Glenn Beck in "Right Wing Radio Duck"
Play
Deepak Singh
http://codequarterly.com looks like something to follow
"Greetings. Code Quarterly is a new publication that intends to publish in-depth articles of interest to hackers. Readers will be able to read them on the web or buy DRM-free PDFs, Kindle and iPad versions, and print-on-demand paper copies. Subscribers to our print journal will receive a beautifully typeset quarterly containing all the articles from the past three months." - Deepak Singh from iPhone
Deepak Singh
I think an anti-academia rant on bbgm is long overdue :) - Deepak Singh
It's been festering. Need to find time to type. Maybe on the flight to Hong Kong :) - Deepak Singh
Yeah, that one makes my fingers twitching, too. - joergkurtwegner
Hmm, these things are bad topics for generalizations. In a lot of cases, once the research plan is set, you need to generate data and sometimes lots of it. When you then see graduate students or postdocs without family come to the lab after yourself and when you leave, their labs are dark and locked, you know it's time for a talk... - Björn Brembs
I'm with Björn and slightly conflicted on this. You get the people who you can't stop working (indeed I am going to have force one staff member to take a holiday this year) and at the same time you get those who head off at 1715 on the dot regardless of anything else. On the other hand I leave work at a regular time to get a bus so I can get home at a reasonable time. What its about is... more... - Cameron Neylon
But none of that is particularly peculiar to academia - Cameron Neylon
Well, except that in academia the people who are being expected to work in this fashion are not getting paid at the same level as they would be in other careers with this kind of work ethic. - Matt Leifer
Actually I'm not really convinced that's true any more. I know plenty of people working similar kinds of hours and intensities to plenty of scientists on pretty ropey salaries. And academic salaries (in the UK at least) are nowhere near as bad as they were a few years back (e.g. when I started as a lecturer we had students going out of our degree program into industry on higher salaries... more... - Cameron Neylon
Of course, if anyone wants to prove me wrong on that last point I'm happy to listen ;-) - Cameron Neylon
I recommend reading the book Rework by Jason Fried from 37Signals for a different perspective. From the book: "fire the workaholics" - Martin Fenner
I've come to abhor the referral to PhD candidates as graduate students. You are not students once you're past your qualifiers or equivalent. You are producing researchers, who could be making significant contributions to society. The idea of busting your butt in a lab when you could be making way more money, get benefits, actually think about having a life, etc is something that IMO... more... - Deepak Singh
@Deepak: I don't tell my colleagues they need to spend more time in the lab. I tell them their competitors spend, on average, so and so many hours in the lab (currently between 50-55, according to polls) and that average won't cut it. If they want to gamble on beating these odds, it's their informed decision. More importantly, though, I spend these hours in the lab because I know few... more... - Björn Brembs
@Cameron: I wonder if there's a UK/US divide in academic vs industry salaries. I got a 50% raise in moving from academia to industry, and my personal collection of anecdotes says that's on the low end if anything. (Note that it says more about my academic salary than my current one, which I think is fair.) - Bill Hooker
Commenter #56 wins the Pipeline thread, imo: http://pipeline.corante.com/archive... - Bill Hooker
Bjorn, it's not about hours. I worked longer hours at a startup and work 80 hour weeks today. You're in a labor market and there are a lot of opportunities to do creative work, and it was clear to me that we are losing out on many smart people due to the structure and reward system. - Deepak Singh
@Deepak, definitely agree with the last point. And what no-one yet is saying is the role of luck in all of this. You try more you increase your chances of getting lucky perhaps, but only if your brain is still in a state to be prepared to be favoured by fortune. What does annoy me tho is people who don't do an experiment because it would mean staying till 6pm. Largely because I know I'm bad at this form of procrastination myself... - Cameron Neylon
Actually the thing that really beefs me about the original article is the passage that runs "won't anyone think of the patients!" If the f%*@!ing PIs were thinking about the patients they'd be out there communicating more effectively rather than hiding data and conclusions and stabbing each other in the back so as to climb up the greasy funding pole. - Cameron Neylon
Should the patients be put first at the cost of greatly increasing the incidence of stress-related disease amongst your students and postdocs? - Matt Leifer
No, absolutely not. But my point is that there are many things PIs could do to radically increase the effectiveness of their research in terms of patient outcomes (particularly in cancer where Heather Piwowar has shown for some types of data a significant negative correlation with data sharing i.e. the study having to do with cancer is significantly _negatively_ correlated with sharing... more... - Cameron Neylon
Michael W. May
Hermetica: The Greek Corpus Hermeticum and the Latin Asclepius in a New English Translation, with Notes and Introduction - http://www.amazon.com/dp...
Hermetica: The Greek Corpus Hermeticum and the Latin Asclepius in a New English Translation, with Notes and Introduction
Bill Hooker
DigitalKoans » Blog Archive » "Keeping Research Data Safe Factsheet" - http://digital-scholarship.org/digital...
Charles Beagrie Limited has released the "Keeping Research Data Safe Factsheet." Here's an excerpt: This factsheet illustrates for institutions, researchers, and funders some of the key findings and recommendations from the JISC-funded Keeping Research Data Safe (KRDS1) and Keeping Research Data Safe 2 (KRDS2) projects. - Bill Hooker from Bookmarklet
Deepak Singh
Hiding in Plain Sight: The Rise of Amazon Web Services – tecosystems - http://redmonk.com/sogrady...
John Resig
Ran a performance test on the recent .css() changes: http://www.flickr.com/photos... 11-22% improvement across the board.
Bill Hooker
"Readersourcing.org is an independent, third-party, non-profit, academic/scientific endeavour, aimed at quality rating of both scholarly literature and scholars." - Bill Hooker from Bookmarklet
I hope this succeeds. But how will it get critical mass? See also thirdreviewer.com, journalfire. Amassing sufficient comments may require novel functionality or a replacement for existing workflow, as in Connotea, Mendeley etc. - Alex Holcombe
literature comment aggregation sites are popping up like "facebook for scientists" were two years ago. Do any of them have a "secret sauce" that will pull people in, or do they all think they're the only one with the idea? - Mr. Gunn
Wow. And here I thought I've already read every paper/author on the subject of improving peer review/scholarly communication. Yet, I'm somewhat ashamed to admit I've never heard of this guy (behind this site) before. - Wobbler
Bill Hooker
An economic analysis of which journal to choose for your publication - http://dianthus.co.uk/an-econ...
Cool explanation of today's silly decision-making tragedies :-) - Björn Brembs
Deepak Singh
High Scalability - High Scalability - Scaling an AWS infrastructure - Tools and Patterns - http://highscalability.com/blog...
Anne Marie Cunningham
What are the risks in sharing PhD findings before completion? - http://wishfulthinkinginmedica...
I always make the argument that this kind of secrecy is good for the supervisor but bad for the student. They need to get their name out and in front of their next employer probably more than they need that paper at this stage in the career. That's a very broad generalisation but there's an element of truth in it. The other approach is to make the point that they shouldn't make it public if they don't want it public but that isn't as positive and encouraging a tack to take. - Cameron Neylon
don't PhD students normally go on speaking tours before they've defended? Do job talks and all? Some places you get your 3 journal articles before defending instead of afterward. - Christina Pikas
In the UK you're fairly unlikely to get 3 journal articles frankly. Maybe some years later but it would be rare prior to graduation. - Cameron Neylon
In both Aus and US, it's becoming rarer and rarer to graduate without publishing. There's increasing acceptance of the publications-as-thesis method, where you just write an intro essay to your papers and bundle 'em up and call it a dissertation. My (Aus) PhD was not outstanding by any measure and resulted in four papers, all but one published by the time I graduated. - Bill Hooker
Tried to post this comment on your blog, but had problems so adding a comment here instead. Doesn't some of this depend on what the PhD is about. If it's a highly competitive area of research, such a reaction might be understandable but I wouldn't of thought this was the case in Medical Education. I know people who've published papers before completing their PhDs. Medical Education... more... - Natalie Lafferty
I'm with Bill - I went down the "bundle previously published work and call it a dissertation" route. Probably needn't be said that I think scooping is just an academic boogeyman, a story told by profs to younger students to keep their noses to the bench. Like all, there is a grain of truth somewhere, but if you looked at all the ideas that were kept secret by a early stage researcher... more... - Mr. Gunn
Many thanks for all the comments. I think that those on the blog and Friendfeed show the range of thoughts on this issue. I think it does need to be pointed out that medical education research is different to lab-based disciplines. Doctoral researchers are likely to be based in or taking the approaches of social sciences rather than medical sciences. Researchers, like other education... more... - Anne Marie Cunningham
Victor / Mendeley Team
RT @fredemmott: #mendeley one year ago: just moved to colo, 2 servers for live - now 35 running the site, syncing, stats, and our research (+backups ;) )
Daniel Mietchen
ESOF2010 Session: What would science look like if it were invented today? - 4 July, 15.45-17.00, Room 9 - http://www.esof2010.org/schedul... http://friendfeed.com/esof201...
ESOF-session-announcement.png
No slides, but clickstream via http://science-2-0.piratenpad.de/Science... . Please chime in there, or comment here. Thanks! Related older threads: http://ff.im/gaWDe and http://ff.im/9SvED and http://ff.im/8Wiki and http://ff.im/3Zk6I . - Daniel Mietchen
I will meet you there or online ... ;-) - http://www.joergkurtwegner.eu/... - joergkurtwegner
What is more friendly to the audience - a wiki-based or Etherpad-based presentation? Example for the former at http://en.citizendium.org/wiki... , for the latter the one mentioned in the first comment. - Daniel Mietchen
maybe combine an FF group with etherpad (incl. the chat function in the bottom right corner) - Claudia Koltzenburg
even if you're doing your bit remotely, Daniel, are we sure there will be live-streaming outside the room? ;-) - Claudia Koltzenburg
I have been asking the organizers about technical details for months, and called in half an hour ago, but still no response other than "I want to confirm your technical request for Room Dublino on July th 4 at 15.45-17". - Daniel Mietchen
Yes, the Etherpad chat is an interesting option, but there are no feeds from that, so integration with FF or Twitter or whatever people use is difficult. And it's not threaded, and the window may be too small for a real discussion. - Daniel Mietchen
a. this sounds like no live-streaming - so we might want to reconsider the gist of the game, ... Joerg, are you prepared for instant tweets so we know when it is appropriate to place which question? could someone present in Torino organize at minimum a web radio transmission? b. don't think all people would have to use the same tool? maybe let's consider this question: given the pretty... more... - Claudia Koltzenburg
Etherpad works nicely when many authors are contributing to a single document, Friendfeed is hard to beat for discussions though. - Mike Chelen
if we want to hear what is said in the room: given the organizers agree but wouldn't do it themselves, I wonder if, e.g., these two initiatives are able to do live transmission? radio popolare Torino http://www.radioflash.to/ - or La prima radio rumena e multietnica italiana http://www.torinointernational.com/ - Claudia Koltzenburg
Streaming services such as Qik or Ustream can be used even if only for audio. - Mike Chelen
+1 Mike, what exactly do the organizers need to know to get this going? - Claudia Koltzenburg
A laptop with Flash or a cell phone that is compatible with the broadcast sites' applications. Either wired or WiFi internet, or decent cell phone reception. That should pretty much be it. A laptop with external microphone would probably be the best audio quality. - Mike Chelen
I was assured WiFi would be there, and my "request" included questions as to whether video live streaming would be possible, via which platform the two remote talks shall be given, and whether FF/ Twitter can be displayed on a separate screen. - Daniel Mietchen
If the organizers can provide direct line out from a microphone being used by speakers that would be fantastic audio quality. Same applies for video, if they are unable to stream it themselves. - Mike Chelen
It seems that @openvideo will be at ESOF too (cf. http://openvideoalliance.org/event... ) - can you help with streaming this session? - Daniel Mietchen
OK, just got a call from ESOF - Skype will be available to deliver the remote talks, video stream (via a laptop's web cam) to follow online. No 2nd screen for feeds, but possibly two windows on the laptop's screen. There will be a skype test during lunch break, so if anyone could help with that, this would be cool. - Daniel Mietchen
Sounds good, they will be streaming it themselves? Details about which service and URL will be used would be great. - Mike Chelen
It seems that they will organize the streaming, and that service/ URL will not be known before the first sessions start (on Friday 2). I will post details as soon as I get them. One problem not solved yet: If the video streaming and skype are to be handled by the same laptop, people who follow the session online will probably not be able to see the skype talks. Setting up a second... more... - Daniel Mietchen
@Daniel -I will arrive on Friday in Italy, and I have my laptop with me, WiFi, Chrome, Skype ... so if there are any problems I might be able helping out ... we could have a test run, too? Anyway, I assume this will be done with the chair-man, right? - joergkurtwegner
@ Joerg - yes, test run during lunch break. Details fluid. Please DM me your mobile to keep you in the loop. - Daniel Mietchen
re my inquiry of 28 June if I could participate in this session online, I just got a mail saying: "we wish to inform you that a video streaming will be available, however, we are waiting for the confirmation if it will be visible during the meeting or will be published after the event." - Claudia Koltzenburg
@Daniel - mobile number is on the way ... - joergkurtwegner
@openvideo this session at ESOF - see link - Daniel Mietchen
The admin of the ESOF2010 group did not react on request for customization, so I suggest to use http://friendfeed.com/esof201... instead. - Daniel Mietchen
It will be a challenge I was just stitting in the room, again, and had no wireless access, and in front of the room it works ... - joergkurtwegner
Problems solved now - thanks to Joerg and Carlos and whoever else helped! Details via http://science-2-0.piratenpad.de/Science... . - Daniel Mietchen
Stream is working fine.. - Graham Steel
stream is good - is there an active chat going on somewhere or are people just listening? - Cameron Neylon
I think folks are just listening at the mo. - Graham Steel
see the chat window to the right of the UStream window - it is still on Steven's talk, re WAYS - Claudia Koltzenburg
Chat is also available through IRC, chat1.ustream.com #danielmietchenesof2010 - Stream just went down though. - Mike Chelen
well, thanks, happy to hear it's not due to the Swiss mountains heat I am in ;-) - Claudia Koltzenburg
The other place that might be interesting is the Pirate Pad http://science-2-0.piratenpad.de/Science... - Mike Chelen
yes, PiratenPad is being used (was used during Steven's talk) - seems to be a bit difficult to figure out where to write AND have one's most recent lines be seen by the others - if you're looking for the chat feel, that tis - Claudia Koltzenburg
The video is now available via http://nubes.esof2010.org/stored... . Best when viewed with http://science-2-0.piratenpad.de/ep... open in another window, and following the links (and taking notes) in there. - Daniel Mietchen
FAB - will watch after the footie.... - Graham Steel
Cool - looking forward to your feedback! - Daniel Mietchen
I followed the livestream on the day until it went dead. Nice to have now watched it in full. This is a great resource for folks new to the whole concept of 'science online' and '2.0' tools etc. I hope that those who attended on the day are now much better informed in this regard. I think you pretty much covered everything that I can think of that is of relevance. On a technical level,... more... - Graham Steel
A successful cybernaute activity ESOF on Facebook : Invitation to Social Funding tour on ESOF 2010 Torino - Our selection Plan A, B, C. http://www.facebook.com/topic... - project sh feed
Deepak Singh
Christina Pikas
Hey maybe scientists should do more than just wait for their journal to issue a press release on their new fabu article - http://scienceblogs.com/christi...
Paul Bacchus
Legislature Moves to Make Funded Research Public - http://www.readwriteweb.com/archive...
Legislature Moves to Make Funded Research Public
Not sure whether the bill really holds what this heading promises. Have not seen detailed text yet, though (let alone understand its precise implications). - Daniel Mietchen
Deepak Singh
Testing for traces of Neanderthal in your own genome - http://www.genomesunzipped.org/2010...
Should be fun to see someone just rustle up a simple service for this. Some day there will be enough of a developer ecosystem where such stuff just shows up cause developing software and making it available is a good thing - Deepak Singh
Agreed. I suppose I am hoping for a day where all of that will happen, but this also speaks to the thread that Pawel started around Open Data. That's why the data is so important. Without that, the ability of smart dev/bioinformaticians to build the software is severely restricted - Deepak Singh
Pawel Szczesny
Open data and open source. Incompatible? - http://www.pawelszczesny.org/2010...
We should make a list of people working in industry and people working in academia ... especially for any comments flying in on this ;-) I am an industry person with a strong believe in some "open" aspects, clearly not all. - joergkurtwegner
I'd turn it round the other way - the only way the business of science can succeed is by doing our best to provide the best possible return. The question is whether open foo is the way to achieve that. In the case of government funders I think the evidence is pretty clear that the losses from not commercialising research are much less than the losses from not effectively exploiting the... more... - Cameron Neylon
Thinking about it - all these kinds of arguments hinge on an unspoken assumption - that the major returns on investment in research come from the results of that funded research. If that is shown to not be true - if for example the major economic benefit is through the generation of human capital and capacity - then all these scarcity based arguments need to be reassessed. The British... more... - Cameron Neylon
Spinning back in time/history. A quick search on Wikipedia. Open Source:- http://en.wikipedia.org/wiki... (started in 1911), Open Access Publishing:- http://en.wikipedia.org/wiki... (started in the 1960's) and Open Data:- http://en.wikipedia.org/wiki... is rather interesting !! - Graham Steel
Cameron, actually I am arguing (talking on open science with Open Society Institute right now) that one of the benefits of opening up science in transition countries (such as Poland) is exactly building human capital and capacity. I'm not sure if that is also true for all research (closed academic or industrial) and in all countries - because of local law regulations and traditions this might differ between countries. - Pawel Szczesny
Agreed - one of the most interesting things about Willetts' speech was the comment that only 3% of economic returns from academic research come from patenting and spinouts - the classic scarcity based approach and that there were bigger returns in building that "absorptive capacity" as he termed it to apply research done in other places. The key question is whether this is true for... more... - Cameron Neylon
@Cameron - commenting on "if government funders have a long term strategy of locking up data then they won't have a long term future" ... I think it is important that people learn being more flexible with their licensing terms and with offering multiple options on how and to which degree data can be accessed, and at which time point. If this could help preventing endless discussions and... more... - joergkurtwegner
Graham, nice comparison of dates of adoption. Joerg, I wanted to reply that maybe instead of relying on people becoming more reasonable, we should go for implementation of automated contracts (see Michael Nielsen's post http://michaelnielsen.org/blog... )? Michael Heller in "Gridlock economy" claims that "quick"... more... - Pawel Szczesny
@Pawel, @Michael - Are there any practical examples of automated contracts, especially in a life science context? - joergkurtwegner
There's not a lot out there at the moment but this is the kind of thing that Creative Commons have been at with generic patent licensing and such like I think. The aim is to have well understood terms that are designed to be compatible and predictable so that people can get on and do stuff with confidence. - Cameron Neylon
Its a chicken-egg-problem and it would be good seeing some examples on this for making this discussion easier for all parties;-) - joergkurtwegner
I haven't seen any examples either. Automated contracts in open digital media would be something like "DRM meets Creative Commons". In life sciences we don't have DRM nor CC (SC is trying to fill the niche in the latter). It's harder to build a system from the scratch. - Pawel Szczesny
"Do not go where the path may lead; go instead where there is no path and leave a trail." [Ralph Waldo Emerson] and yes, at some point we will get it ... http://www.joergkurtwegner.eu/... - joergkurtwegner
Very interesting. We've never run into such a conflict (the idea that these conflict had not even occurred to us). - Ruchira S. Datta
Joerg - high-speed algorithmic trading (on Wall St and elsewhere) relies on having an infrastructure in place that allows for automated contracts to be carried out. Many extremely interesting things become possible in that context. (I don't know of really good single reference on what's being done, unfortunately.) Aside from that, I'm not aware of much that's been done in other fields, although I'm sure it will come. The ability to automate contracts will be incredibly powerful. - Michael Nielsen
Not that unknown. Enterprise Service Buses are often required to fulfill and automate data contracts used in BI, other market intelligence ops, and of course for algorithmic trading. A lot of companies in the creative space and yield analytics also have similar "contracts" - Deepak Singh
One of the confusions in the use of the term "open source" was described by Richard Stallman in a CACM Viewpoint (http://doi.acm.org/10...) on open source and free software: "Open source is a [software] development methodology; free software is a social movement." "Open data" is not a data development method; it's a data sharing practice, and one that can be supported by policies and procedures. It is helpful to avoid conflating this with a software development practice. - Bill Anderson
lukask
Royal Library of The Netherlands and Google sign agreement for digitising more than 160.000 public domain books http://www.kb.nl/nieuws...
“The partnership with the KB is another step in helping make the world's books searchable and accessible for anyone with a connection to the Internet. We're delighted to be able to help accelerate the work that the KB is already doing to make Dutch cultural heritage digitally accessible - via Google Books, via their own website, and at a later date, via the work they do with the European Union's Europeana portal.” - Dan Brickley
this sounds promising, I wonder what the license terms will be for the results of this work... - Dan Brickley
Daniel Mietchen
"I believe there is a real need for a communal effort in making academic theses more Open and would like the OKF to set up a project along these lines." - brainstorming via http://open-thesis.okfnpad.org/initial... . - Daniel Mietchen from Bookmarklet
This site http://nzresearch.org.nz/index... ran by the New Zealand National Library harvests local open access content (including thesis that are under CC licences, like my student who opted in without mandate). As far as I know, University of Canterbury has an OA mandate on thesis, and it is my understanding that several Australian Universities have that too. Not sure whether this is an example that would be useful to you guys. - Kubke
+1 Kubke - Claudia Koltzenburg
Found this page at my Uni Site: http://www.library.auckland.ac.nz/instruc... There amay be useful links in there. - Kubke
Thanks, Kubke - found http://www.ndltd.org/ there which seems to be a good hit. - Daniel Mietchen
Is there any university in which PhD theses (incl. data and code etc.) are published under an open license by default? - Daniel Mietchen
Check out the ROARMAP site, http://www.eprints.org/openacc... it has a list (including 'thesis mandates' with links to the specific wording for each - Kubke
I think ROARMAP must be updated, cause I now see that my Uni (Auckland NZ) has an OA mandate on thesis (funny how I didn't know about it!) which wasnt there last time I check (less than a year ago) - Kubke
What I meant by "open" was not merely "providing free access" but rather as at http://www.opendefinition.org/ : "A piece of knowledge is open if you are free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and share-alike." Further background on this definition:... more... - Daniel Mietchen
I see what you mean, and I thought that is what ROARMAP was providing. I went back into my University site and I also cannot find such clear definition for theses. So you are right, each link would have to be checked individually (Bugger!). - Kubke
D0r0th34, for a start, we are looking out for the one that is Libre. And if there is none, the next ones to look for would be those willing to give it a try. - Daniel Mietchen
University of São Paulo requires students to provide a digital copy of theses (you can ask for a delay, though), but indeed there is no mention about licensing... besides the standard "all rights reserved" in the footer www.teses.usp.br Just sent a question to them about that. - Bruno C. Vellutini
Just relicensed my PhD thesis under CC-BY. http://scidok.sulb.uni-saarland.de/volltex... - Daniel Mietchen
I didn't have money to copyright my thesis, I would assume that would automatically make it a CCZero? - Kubke
In my case, it had been simply linked to the repository's default copyright notice ( http://scidok.sulb.uni-saarland.de/doku... ) which basically states CC-BY-NC-ND and disallows sharing. Don't think money was involved. In many countries, anything that does not have an explicit copyright statement automatically falls under copyright, though I agree CC0 would be more appropriate. - Daniel Mietchen
D0r0th34, I would actually prefer them, or at least the links to their theses, to be alive ;-) - Daniel Mietchen
Oh my, feeling really old since I am pre-digital age thesis. I managed to burn my thesis on a 1X CD burner for a personal copy and people were shocked I had access to such sophisticated technology! - Kubke
@Daniel Back then, the way it was explained to me is that by not 'buying' copyrighting, contents were not 'protected' and that at most I could fight for attribution, but otherwise no legal protection. (i.e., pretty much a CC0). The argument didn't make much sense to me, but I didn't care, since I felt 'publicly funded' thesis should belong to the tax payers as much as to the author. - Kubke
Proquest (the main US supplier/vendor for dissertations) has an option to license a thesis/dissertation for OA. There is a PQDT Open Database that has all of the OA theses/dissertations: http://pqdtopen.proquest.com/#. I would call these open theses. - Elizabeth Brown
here's another ProQuest link for more info on the project: http://www.proquest.com/en-US.... I'm a little surprised Proquest has not promoted this more but of course it would affect the revenue they get from the non-OA content. - Elizabeth Brown
What PQDT offers is free to the reader, not open in the sense discussed above (comment #9). When downloading a pdf from there, you have to pass a screen stating "Copyright in each Dissertation and Thesis is retained by the author. All Rights Reserved. Terms & Conditions of Use apply." - Daniel Mietchen
I think you could get around the copyright issue by posting it in the library repository with a CC license. But you're right - the PQDT database doesn't state you can reuse and share the work. I agree Dorothea that getting students to get a CC or more open license for a dissertation is a lot of work. - Elizabeth Brown
Marcin Wojnarski
My small attempt to comment on scientific papers on the blog - http://blog.tunedit.org/2010... - Papers come from RSCTC 2010 conference
I've never done this before, but must say it's an extremely insightful experience, to summarize someone else's papers, in straight words. I recommend it to everyone - Marcin Wojnarski
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