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Walter Jessen › Likes

Lisa Green
Sage Congress starts in 20 minutes! You can watch the webcast live at http://fora.tv/live...
Also, there is a super cool tool for discussing the ideas raised at Sage Congress called DiscoveryCast. If you would like to participate in DiscoveryCast just send an email to support@discoverycast.com and they will make an account for you right away. - Lisa Green
Thanks for this, Lisa. Anyone know if it's being microblogged in a FF room? - Michael Nielsen
This room should have all tweets with #sagecon hashtag. I will see if I can get that set up properly and if not I will start a new room. - Lisa Green
all tweets with #sagecon hashtag are now fed to the Sage Congress room http://friendfeed.com/sage-co... - Lisa Green
Deepak Singh
"Jaw-dropping" verdict against Myriad in BRCA patent case - http://scienceblogs.com/genetic...
"The decision invalidates patents held by Myriad on the BRCA1 and BRCA2 genes, mutations in which are associated with increased risk of breast and ovarian cancers, and casts doubt on the validity of thousands of gene patents." - Michael Kuhn
This is long overdue. I will note, though, it really casts doubt on the validity of thousand gene sequence patents. It does not address 'composition of matter', what can be made from the sequences such as insulin or bioengineered derivatives. - John Hogenesch
'Like' does not even begin to describe this :) - Lars Juhl Jensen
looks like a good start :) - Pedro Beltrao
+1 Pedro: a good start. Onwards to invalidating thousands of ridiculous over-reaching patents that are blocking innovation. - Bill Hooker
Hope Leman
Hi, all. I am delighted to announce that we have finally officially launched ResearchRaven http://www.researchraven.com/ It is designed to save researchers time and effort in finding calls for papers for conferences and journals and announcements of meetings. It is a little light on some categories so far and I am still populating it.
Jan Wessnitzer
Bill Hooker
Comments from respondents: "I'd also want really good stability, equivalent search, and archives from a paid FF clone." ($10); "Maybe not FriendFeed itself, but a similar service that I actually trusted? Would definitely pay a small fee." ($10); " It would need to improve, though!" ($50); "Even a $0.01 fee will stop people signing up." ($0) - Bill Hooker
I'm one of the $100 datapoints. - Bill Hooker
I was a $10 datapoint, but so much depends on the details. I could go higher, but it would have to be pretty damn cool to justify me spending $100 on it. - Mr. Gunn
Just noticed, there are two datapoints missing. Those are the totals Surveymonkey gave me, but they add up to 26 and it claims n = 28. - Bill Hooker
Just wanted to clarify my $10 vote was based on friendfeed exactly as it is now, with search that goes back further into the archives, and with assured stability. I'd pay more for something more tailored to research and with more professional analytics features. - Mr. Gunn
The missing two datapoints are both $200 -- either I simply missed them the first time I looked, or they have just caught up between the counter and the analysis page. - Bill Hooker
So, $1030/28 approx = $37 per person if we let everyone pay what they think is fair. TLS has about 1300 users, so 1300 x 37 is around $48K per year. This is, of course, nonsense for many reasons, not least of which is n=28, but still. I'm getting the impression that we couldn't raise enough to roll our own, but maybe we could get buyin to an existing service? I'm not sure how that would... more... - Bill Hooker
This is just a hunch, but I figure that a much larger percentage of the non-respondents would be in the $0 camp due to increased likelihood of apathy about which services they use. Also, don't forget the non-TLS scientists, e.g. 878 subscribers to Science2.0 who don't completely overlap. - Matt Leifer
I agree about the apathy -- if they can't be arsed to respond they're not likely to be willing to pay! It's probably just silly to do calculations like mine up there without at least gathering a much larger sample. I can't bump the survey because that seems to have stopped working, so I'll post updates with links back to the OP every so often this week, and see just how many respondents we can get. - Bill Hooker
I would not pay - I think any charge would kill the participation to a level below critical mass for proper networking. I think we could find free hosted alternatives if necessary - Jean-Claude Bradley
This is the problem in a nutshell. Unfortunately, it takes money to support the service. ($100 datapoint) - Walter Jessen
I was one of the lazy buggers who didn't get around to answering - I'd be prepared to pay for some form of service but my suspicion is that a more imaginative business model is required. Some form of freemium or pay for privacy system might work. Other suggestions include paying for archive access or paying to make your archive available...but I'm not sold on any of these I have to... more... - Cameron Neylon
@Cameron I didn't think of this before, but your comment made me think of the Evernote business model. I think that could work quite well. The basic service would be free; additional features such as analytics and archiving would require a monthly or yearly fee. Article here: Using ‘Free’ to Turn a Profit: http://www.nytimes.com/2009... - Walter Jessen
I think if we want (master/PhD) students and post-docs involved (which I think we do), we should also consider institutional fees... - Egon Willighagen
@Egon, or "lab" fees (such as 10 licenses for substantial discount). I sort of lean towards agreeing with everyone (ha ha). It's worth more than $100 to me right now. But as Jean-Claude says, FF wouldn't be anywhere near as good as it is now if it had had a fee originally. A big grant (such as the NSF one OpenWetWare obtained) would be appropriate. But even those aren't stable enough. So, probably commercial or private foundation would seem best ownership. - Steve Koch
It's also worth somehow making a very clear presentation to facebook as to how valuable friendfeed is for scientists around the world. It's not impossible that they couldn't keep it running, perhaps in collaboration with scientists. I'd tolerate instrumentation-related and other ads around this site. - Steve Koch
Considering that social networks for scientists are often labeled "Facebook for scientists", I think asking Facebook directly to let this one turn into one that fits this description may have chances of success. And, as Steve points out, manufacturers of scientific instrumentation might well be willing to advertise in this space, thus providing a way to cover the operational costs. - Daniel Mietchen
I think Steve and Daniel are onto something there. How about a letter to Facebook making exactly that case? -- i.e. you have got something here that scientists are using and don't want to lose, that could grow into a real "Fb for scientists", and that we'd be willing to let you stick some advertising on; if you make a commitment to it we'll help spread the word. - Bill Hooker
So another concept that has been kicking around is the idea of a non-profit foundation that is supported by and integrated at some level with a range of commercial suppliers who build on an open source(ish) base to provide paid for services but where users could choose to run up their own installation(s) or if that's not appropriate use a hosted service. So Wordpress.com/org Apache or... more... - Cameron Neylon
I'm liking the sound of Cameron's idea much more than the idea of making a plea to Facebook. I worry about Facebook being so in bed with marketers and not respecting privacy. - Mr. Gunn
I hear you on the privacy concerns, MrG, and I also like Cameron's idea a lot. A whole lot. That non-profit could do other things besides run our FriendFeed replacement... - Bill Hooker
I worry about Facebook being curators of a site that is widely used by the science community. In the past, they have shown themselves to be purely driven by the profit motive, with concessions to users only being made under duress. If we were talking about Google then that would be one thing, but I don't think we'll hear a peep out of Zukerberg if we write to Facebook. - Matt Leifer
I worry about the Facebook/google approach in two ways. One is that in such a big pond you'd only ever get a small voice. The other is the risk of disappearing under the need to make money as Matt mentions. Something that can leverage the high quality work done and vast resources committed to consumer services but that balances that against the need for researchers to have a strong (but not necessarily the only!) voice would be the aim or whatever we can put together. - Cameron Neylon
I agree with your comments, Matt and Cameron, but still think it may be good to contact them and point out that there is a sizable community of researchers who would like to run (and improve) their own installation of Friendfeed and whether they could (a) make it open source entirely (don't think they will, but asking is probably OK) or (b) give the code to a scientific institution -... more... - Daniel Mietchen
Agreed. Worst case is there's no response. - Walter Jessen
My experience with getting site sponsors is that biotech companies do not like to sponsor sites unless they have significant reach. I'm only now starting to get people interested in advertising on LabSpaces. I don't know what kind of support you're looking for from instrument companies, but my pleas for $100 a month to host on a dedicated server and support a minor ad budget were turned... more... - Brian Krueger - LabSpaces
Brian, that's very useful feedback, thanks. - Bill Hooker
I agree site sponsors or advertising isn't either going to pay enough nor be reliable enough to give people confidence. I would certainly agree if the question to Facebook/Friendfeed is "would you give us the/some source code and if so under what circumstances" - I'd be happy with the code as it was prior to the UI change even - I can think of a few ways it might be possible to get it hosted - few different organizations probably under different conditions. - Cameron Neylon
I also wonder how much money you'd need from the get-go. My site is hosted on a $10 a month virtual host box and although they say its unlimited bandwidth it can only handle 30 simultaneous connections. Bandwidth has only ever been a problem for me when the site gets hammered by Reddit, Fark, et al. So at the outset, you guys could definitely run this off of a small budget, assuming... more... - Brian Krueger - LabSpaces
Its the setup and maintenance costs (I'm kind of assuming this is a full time job for one person at minimum) that are the big issues. - Cameron Neylon
@Cameron, what kind of maintenance are you expecting? Once the site reaches critical mass, then maybe it will require constant attention, but if it stays on the sub 1000 users level I don't think it would be a huge effort. I maintain my site all by myself. It takes an hour every morning before work and an hour every night to set-up the news queue and clean up the spam. Most of the... more... - Brian Krueger - LabSpaces
Would US$50k do for a start? http://ff.im/gXoNX - Daniel Mietchen
That's a fantastic offer, Brian. I guess we should check into that. - Mr. Gunn
I thought I would just mention that AOL has a friendfeed like service at http://lifestream.aol.com I don't think it has been mentioned yet in our "what to do if friendfeed implodes discussions". It's pretty similar to Google Buzz in that it allows you to import from a limited number of services and doesn't support anything like groups/rooms yet. Still, playing with it for a while I found it to be a better user experience than Buzz, so it is another one worth watching. - Matt Leifer
It's hard to take anything.aol.com seriously - Mr. Gunn
I know, but post Time-Warner, AOL actually has one or two good sites, e.g. http://spinner.com. Most of their successes are not branded AOL for obvious reasons. - Matt Leifer
Bumping this as a reminder that two weeks are left to put in a proposal for US$50k on an Open Friendfeed, see http://ff.im/gXoNX . - Daniel Mietchen
@Brian -- how about that $50K? Would that buy six months of your time, plus trimmings, to set up and maintain an Open Friendfeed? If so, I think the proposal could be put together on that basis: we have someone willing to be Benevolent Dictator for the coding and do the maintenance, we have X users who want this NOW, we think it's worth doing to get FF out of the hands of the for-profits and into the hands of the user community... - Bill Hooker
That would be more than enough money to run the site for a couple of years. I can probably use a lot of the labspaces backend for authentication, so it shouldn't take more than a week or two of coding to get off of the ground. Let me know if you need help writing the proposal! - Brian Krueger - LabSpaces
Actually, it looks as though they require institutional backing. Also, I registered for the site but cannot find any mechanism for submitting an application -- the "apply" links all take you to the privacy statement. - Bill Hooker
Bill, I had reported that problem a while ago and it appears to have been fixed. I am stuck at a different step - getting a Grant ID - because the form would not accept any phone number I entered. The likelihood of small bugs like these seems to be one of the reasons why they start out small, and I consider it a Beta anyway, as long as the review process is not open. - Daniel Mietchen
Update on the fineprint: It's basically like the usual NIH grant application. Specifically, affiliation with a US institution is required (any volunteers?), and so is agreement with a "no indirect cost" stipulation once an award is being made. More via https://apply.fundscience.org/user_ap... . - Daniel Mietchen
That same FAQ page, however, also states a severe thematic restriction: "we encourage doctoral students to apply for FundScience support of projects pursuing hypotheses related to the pathogenesis or modeling of diseases including Crohns and Familial Mediterranean Fever, and diseases predominantly affecting the developing world." Bye-bye, FF clone? - Daniel Mietchen
Daniel - yes I ran into the same problem - Jean-Claude Bradley
We could probably work around the institutional affiliation part, but given the disease focus my feeling is that they would not be interested in funding a FF clone. - Bill Hooker
OK, so we will have to say good bye on this one. Another option for a grant is at http://ff.im/hGFHZ - Europe and Global Challenges - and I think we could give the transition to open science a try. Funds up to Euro 1M are possible, so the FF clone may fit in as part of a broader concept. - Daniel Mietchen
Alexey
Brain cancer stem cells are no match for killer T cells - http://www.cityofhope.org/about...
Brain cancer stem cells are no match for killer T cells
The researchers focused on cytotoxic T cells, or CTLs, which are specialized white blood cells that seek out and destroy bacteria and other invading pathogens. Reporting in the Dec. 1, 2009, issue of Cancer Research, the team found that CTLs could be “trained” to recognize and destroy brain cancer stem cells resistant to other treatments. - Alexey from Bookmarklet
Andy Maloney
I came across the words "lifestream" and "aggregator" recently. I know, I'm behind the times. And, I came across Cameron Neylon's blog entry on science lifestreaming. http://blog.openwetware.org/science... Very cool and informative.
I have been in contact with a web designer that I went to school with and he seems to be interested in making a science lifestreamer. The big questions about doing this project would be; would anyone use it and how important would it be to open scientists? - Andy Maloney
I have been literally jonesing for something that would logically contain the projects I work on that use the services like friendfeed, YouTube, and OWW. It seems that I'm not alone but, with no web design knowledge, this task seems pretty daunting. - Andy Maloney
Heh, there's been quite a bit of discussion about this recently, and from my perspective many of those who initially made "social networks for scientists" are now trying to jump on the "lifestreaming for scientists" bandwagon, but it worth considering how open and how successful their initial efforts were when considering how useful their new lifestreaming services will be. In terms of standard formats for sharing data, they all fall pretty short right now IMO - Mr. Gunn
Mr. Gunn: So far lifestreaming and aggregators are all very new to me. I had no idea people tried to create lifestreams geared towards scientists. If you have examples, I'd love to see them. - Andy Maloney
This is where things get a bit tricky with the idea of a lifestream for scientists. I think a lifestream would be pretty useless if you want to show multiple data from multiple projects in the stream. Lifestreams aren't setup with the ability to organize posts in a logical manner. If I tweet about project A and then about project B, a lifestream would show both tweets in the stream as... more... - Andy Maloney
What you describe in the previous comment, Andy, is just the "groups"/"lists" concept in Friendfeed: You would have Group A and Group B and could bundle them under a list "Projects" (others might be "Literature", "Tools" etc.). I find this pretty handy, and we are discussing to set up an Open Friendfeed at http://ff.im/gLtCJ and http://ff.im/gXoNX . - Daniel Mietchen
Mr. Gunn
Dear friends: What's a good way to scan for conferences, meetings, and other events in my area? I'm aware of eventful/upcoming, but they miss many things. I'm looking for something along the lines of a well-tweaked Google Alert that would find local science/tech events.
interdok is not fabulous, but it's ok.http://www.interdok.com/mind... - it looks ugly. there was one for CS that had promise and there was a subscription one from CSA, but I don't know what happened with that. In general,this is a very hard problem, IMHO, even though it shouldn't be - Christina Pikas
http://upcoming.yahoo.com/ is more about entertainment but maybe there's some utility. - Bill Hooker
Thanks, Christina, Interdok is pretty useful for conferences. Now I'd like to add something that incorporates local meetups and user groups as well. - Mr. Gunn
Nature Events seems pretty good too, for those events big enough to have PR people that publicize them. The hard thing is to find the local smaller stuff. - Mr. Gunn
I've used upcoming, and I think they do some spidering for things that look like events, but they also pick up a lot of science night at the Zoo stuff. I think a combo of these and a tweaked google alert should get me mostly there, though. Thanks everyone! - Mr. Gunn
Twitter search? It seems there's always someone tweeting about events (especially for tech-ier ones), so maybe it's just a matter of finding the right search terms/hashtags. And then parsing webpages for location and date details if not in the message... hmm, maybe not so simple... - Shirley Wu
I've had success with wikiCFP for conferences: http://www.wikicfp.com/ For events, if you have any relevant university departments in your area, subscribe to their event RSS feeds? They often post stuff of interest to their students. - Heather Piwowar
WikiCFP looks OK for IT-related stuff, confabb has no results for San Diego this year :-( - Mr. Gunn
Getting in contact with people in the area who are interested in the same topic is the most effective method. Finding events through automated systems becomes more efficient when they are shared by individuals. - Mike Chelen
Bill Hooker
In the wake of the Facebook buyout and the recent outage and the Buzz debacle and so on, lots of folks are considering exit strategies. I'm wondering whether we could fund a user-owned version, probably based on Tornado. Would you pay for FriendFeed? If so, how much/year? Survey here: http://www.surveymonkey.com/s....
related thread, and impetus for this one: http://friendfeed.com/neilfws... - Bill Hooker
Should distinguish using FF for groups such as this one, and using it for aggregating and sharing personal content? How important is it that the same platform provides both functions? - Eric Jain
Eric, I think you are absolutely right. FriendFeed seems to fulfill two different roles for many of us at the moment: discussion among users and aggregation of content. In my view, the two do not necessarily have to go together. Once content has been aggregated, it can be forwarded to other services, which could be where the discussion happens. I don't see why both jobs would necessarily have to be done by the same tool. - Lars Juhl Jensen
Actually, I personally love to have it all in one place. I display my feed on my homepage and without discussion, there would be less of a reason to display it there. - Björn Brembs
Björn, my point was that you could have one tool that aggregates, and a second tool that is used for discussing the aggregated stream. You would obviously want to put the latter on your home page, but that does not mean that this tool would itself have to do the aggregation. For example, I could imagine using Yahoo pipes to aggregate a bunch of RSS feeds and then have Buzz import the aggregated feed to allow discussion. - Lars Juhl Jensen
My read is that the aggregation is good, that the aggregation feeds the discussion, which is good. However, the discussion is separate from the source (possible with its own discussion), which is bad (but perhaps fixable through a back feed like Disqus). Also, there seem to be a bunch of folk who are "nominally" on FF and whose content gets aggregated here, but who never turn up to... more... - Chris Rusbridge
I think you have a point, Dorothea, because the number of comments an item (a blog post or even a tweet) gets here is greater than the number of comments you'll tend to get on the post or tweets you'll get in reply - not to mention that having a three or more person discussion on twitter is annoyingly inconvenient and hard to follow - the conversation always fractures into a bunch of... more... - Mr. Gunn
Repeating a comment from the original thread: "I was figuring one full-time pro with crowdsourced help from the community could maintain a Tornado install. Better IT minds than mine might want to beat on that assumption, but what would that (or a better assumption) cost? What would hosting and bandwidth cost?" Let's toss some numbers around and compare those with the results of the survey (a whopping 25 responses so far, but it is the weekend after all). - Bill Hooker
Costs are heavily dependent on the number of users, so we need a good estimate for that before we can really say anything. Note: Tornado is just a webserver. You still need someone to write a FF-like application on top of it. That is most of the job and it will cost money. I am only a dabbler in web-coding, but it is not clear to me that we even need Tornado because it is designed to... more... - Matt Leifer
Here's a Life Science group for cliqset for those wishing to try it out. http://ff.im/gI1ov - Mr. Gunn
I can't even log in to cliqset at the moment. Edit: yes I can, it just took several minutes and then a reload. Blech. The holdup seems to be at s3.amazonaws.com. This is a pretty fundamental flaw. - Bill Hooker
He did say in the other thread (or maybe his profile) that they did some hardware upgrades recently. Amazon S3 is highly scalable, so maybe he just needs to turn the crank there a little to meet increased demand? - Mr. Gunn
For me, aggregation and discussion are important, but so is the possibility to keep several separate information streams (multiple groups, e.g. those housing my HubMed alerts) in one convenient environment that can be blended into the aggregation and discussion streams (e.g. by posting something to multiple groups at once, and by hierarchically structured lists). No idea to what extent this would be possible elsewhere. - Daniel Mietchen
Speaking for myself, I would. However, only if everything (and I mean everything) was archived, downloadable in a sane format and accessible by date / user. I'd possibly pay what I pay for flickr yearly. But it also depends on whether other people I interact with also would. FF is not its technology, but its users. The ability of the site to fade into the background (unlike facebook) is, for me, one of the qualities that make it special. - Goran Zec
JJ
Who owns the copyright of the reviews? Are we allowed to post the full text of the email from the editor on our website with our papers? Journals don't want to publish the reviews but may authors post them on their website on a voluntary basis? Do you think that this step might make science more open.
These questions arose earlier today around the lunch table. The idea would be to post the whole story of the reviews, even when rejected from journals and not only the last email from the editor... People would then be able to judge how good the review process is in a journal before deciding where to submit their manuscript. - JJ
I like this idea. If the reviews are simply posted (and not commented on), there wouldn't be any trashing involved. Remember, names aren't on the reviews, so the scrutiny wouldn't be on individual reviewers per se, but on the types of reviewers the journal employs. It would go a long way towards holding journals accountable for their reviewers. - Walter Jessen
The name of the reviewers will not be displayed since the reviews are always anonymous... - JJ
hmm, hadn''t considered the copyright question.. I've actually done this a few times via my blog. In one case I was venting, in another I actually agreed with them. I personally think the reviews should be linked to the articles when they are published. Most importantly, it helps to extend the conversation. - Benjamin Good
Beyond any legal issues, I don't think it's a good idea to publish on a website a review that was made under confidential terms, unless you have the reviewer's consent (perhaps the consent could be obtained via the journal editor?). If you wish to make public the reviews for your papers, I would suggest either submitting to journals with open peer review, or communicating your intentions to the journal editor at the time of submission. - Cesar Sanchez
Interesting idea! I always sign my reviews and include my email; perhaps I will start including a CCZero notice. - Bill Hooker
+1 Bill! - Cesar Sanchez
You could also post your review as a comment on the published paper, if the journal has that set up (e.g. PLoS ONE). I think P.1 comments are automatically CC-BY but an embedded CCZero would override that. - Bill Hooker
Initially, I do not see a problem with putting up anonymous reviews but if only the text is posted, then some people may end up posting fake reviews (anonymity basically invites that) along with papers. The best way out that I see is public peer review in the sense that it is the publisher who puts up the peer review conversation along with the paper, ideally without delay. Example at http://www.biogeosciences-discuss.net/4... . - Daniel Mietchen
Iddo Friedberg
Thanks to all who contributed - Iddo Friedberg
Damn - I forgot all about it. Oh well, I'll happily read this one and contribute next time. - Chris Miller
Ricardo Vidal
I must be pinging the GEO database too much because I'm getting connection refused errors via BioPython's Entrez parser.
Mr. Gunn
Science in the Open » Blog Archive » “Friendfeeds for Science” pt II – Design ideas for a research focussed aggregator - http://cameronneylon.net/default...
"One thing that really annoys me is seeing an interesting title and a friendly avatar on Friendfeed and clicking through to find something written by someone else. Not because I don’t want to read something written by someone else, but because my decision to click through was based on assumptions about who the author was." - Mr. Gunn from Bookmarklet
When I click, whether or not the post was authored by the poster, I'm clicking based on the reputation of the poster, and also of the author, if it's apparent. What annoys me is clicking through to find a post on a site like Digg, that further references another site. I haven't tried it out yet, but apparently Cliqset can pull in comments on a blog as comments on the item in Cliqset, so maybe it could pull in post author as well? - Mr. Gunn
Presumably if things are marked up properly with reasonably standard RSS or Atom tags (or even better dublin core) it shouldn't be too hard to capture this information. I'd be less fussed about trying to disambiguate in the short term. But yes, you click through based on presumed context and I don't think any service is really getting that right yet - and I think right for researchers... more... - Cameron Neylon
Incidentally if the above link breaks (my fault for tagging it wrong) then this is the right one: http://cameronneylon.net/blog... - Cameron Neylon
agreed, the service icons issue was what really kicked off the whole train of thought for me. And distinguishing between Flickr posts and Flickr favourites seems to me like something that is important - and perhaps more so for researchers. - Cameron Neylon
Yeah, that was my issue with the service icons too. All a service would need to do is capture the post author when it aggregated an item, but if the intervening site in the case of a favorite didn't capture that, then it would be harder. - Mr. Gunn
Sounds like cliqset is starting to gain momentum as the front-runner alternative to FriendFeed. - Michael Barton
I think they're among the best, but there remain some issues, and none meet the ideal from Cameron's latest post. Buzz would have been my pick due to the built-in network, but since the developer of Cliqset has already joined the discussion it seems like they are probably going to be more responsive. I don't see the Buzz developers joining this thread anytime soon. The third best... more... - Mr. Gunn
Cliqset is absolutely out of the running as far as I can see, but as MrGunn notes, that conversation is in this thread: http://friendfeed.com/neilfws.... - Bill Hooker
Bill, I think nothing is available that works for us right now, so I'm just trying to think of the shortest route to getting there when the time comes. In my shortlist of "least crappy" services I have Buzz and Cliqset, but I realize that either or both of them might not realize their potential and become what we need by the time we need it. Writing our own might be the best, given we can find the resources as a group and also assuming it doesn't turn out to be way harder than we think. - Mr. Gunn
Have been trying to think whether there might be a funding scheme that could help to kickstart something but drawing a blank. Also just has the potential to leave us where we started...with np business model - Cameron Neylon from Android
It may be worth drawing up a business plan and presenting it to facebook via blogs from the most eloquent of us (that wouldn't include me, except as an endorsee). Related to other threads around here, many of us are willing to pay for what we have now, but many aren't. Perhaps we could patch together some "donations," which would prove that we're serious. Then we could present Facebook... more... - Steve Koch
Particularly since we're people in pursuit of making science better, it would be good PR for Facebook at a minimum. - Steve Koch
A proper business plan would be a really valuable thing...I need to look into that for something related anyway so I could try to make that available (might be difficult because it would be done by out tech transfer people and they might object to making to it freely available) - Cameron Neylon
I think there is a business model here. Have a 'open and free' platform for 90 days of postings/comments and thereafter the comments/post are archived. This is valuable information, so academic libraries could subscribe to this database? It's something I have been thinking about for a while. Imagine a freemium model of F1000 for instance... - Chris Leonard
@Chris: not sure I'm following. Do you mean a model where after 90 days everything gets locked up behind a paywall? - Bill Hooker
I think that's essentially the idea - although a micropayments approach would be an alternative or an author pays model for archiving and availability - but if its a diverse model then you can't rely on availability which doesn't really fit with the open aspects... - Cameron Neylon
@Bill: Yes. As a pragmatic approach to getting payment for a service, this is what I suggest (in clearer terms). 1 - All posts with no comments are archived behind a paywall after 90 days. 2 - All posts with comments are archived 90 days after last comment. 3 - Archived posts are only available to those with a subscription, probably through an academic institute. Now, I acknowledge this... more... - Chris Leonard
Speaking as a non-scientist and pseudo-librarian, I'm guessing that getting academic libraries to subscribe to/pay for a formalized version of gray literature, basically a forum, is going to be a very tough sell. - Walt Crawford
Just brainstorming here, but what about other organizations or non-profits such as Science Commons (http://sciencecommons.org/), the Open Knowledge Foundation (http://www.okfn.org/) or OpenWetWare (http://openwetware.org/)? - Walter Jessen
@Chris, I'm unlikely to participate in a "public" forum which then takes my comments, intended for the public domain in case they are ever useful to anyone, and locks them away behind a paywall. I suspect many here would feel similarly. - Bill Hooker
I agree that I'm uneasy with comments going behind a paywall - but arguably a pay for archiving "or take responsibility for it yourself" might work - in a sense subscription vs pay for storage is not so different. Walter - I could imagine folding a project like this into OpenWetWare, I don't think Science Commons or OKF have the interest or the resources to support something like this... more... - Cameron Neylon
Jan Aerts
Data Mining with R: learning by case studies - http://www.liaad.up.pt/~ltorgo...
Khader Shameer
Cameron Neylon
Friendfeed for Research? First impressions of ScienceFeed - http://cameronneylon.net/blog...
I have long been an advocate of Friendfeed as a great tool for researchers. Here I discuss the new Friendfeed clone built for researchers, ScienceFeed, suggest what it is good for and what its weaknesses are. - Cameron Neylon
Thanks for the post. ScienceFeed has potential, and being focused on science can be an advantage. It is for example probably easier than with FriendFeed to make ScienceFeed work closely with CiteULike, Connotea, Mendeley, Nature Network, etc. ScienceFeed will not work if it is simply the microblogging part of ResearchGate. - Martin Fenner
Nice post, Cameron. Agree with Martin - if Sciencefeed integrates services well it could work very well. - Sally Church
Definitely agree Martin, there is potential here, particularly if we can build an effort that really takes our best current knowledge and pushes the potential of federation. Maybe this also solves the business model problem? Less sure of that. I am going to try and follow up with some design suggestions. But the social issues are a biggy as well.. - Cameron Neylon
Sciencefeed interface is an exact clone of friendfeed down to the "my discussion", "best of the day". Surprising it doesn't allow you to add RSS feeds. - aaron
I like your take, Cameron--even without seeing ScienceFeed. As a nonscientist/"library person" interested in *some* issues related to science, I'd never think to approach ScienceFeed...and that may be a good thing for some scientists who'd just as soon avoid the great unwashed. Not so great for those (like you) seeking broader discussions. - Walt Crawford
Just played with Sciencefeed for half an hour... good to see the usual suspects there :>}. It's much clunkier than Friendfeed, you can only connect up Twitter, FB and FF that I can see, no RSS so that would force aggregation to FF and then import it to ScienceFeed. Fine if FF is still alive but no rooms as yet that I can find. For now, I think FF has more utility but am wondering who the owners/developers of ScienceFeed are? - Sally Church
Sally -- SF is from the same people who run ResearchGate. I don't care for ResearchGate and I particularly dislike this hamstrung FF knockoff with its "scientists only" gatekeeping. Science is insular enough, let's not make it worse. - Bill Hooker
ScienceFeed wants to add special features to support conference microblogging. For now they only automatically import using the conference hashtag. - Martin Fenner
Hi guys,thanks for discussing sciencefeed. From now on I will participate on this discussion. Thanks for your initial feedback. When we created sciencefeed, it was pretty clear that it is not smart to build something which is completely new. Friendfeed proved to be a place for referencing easy and fast to scientific content and to discuss it. We want to add features to sciencefeed based on your feedback. I am looking forward to your new ideas, how we can improve sciencefeed in the future. Best Ijad - Sciencefeed
Ijad - It sounds like the consensus is 1st - change the name. 2nd - add services 3rd - clarify if this is intended to be a replacement for friendfeed or the microblogging part of ResearchGate - Mr. Gunn
I'm with Mr Gunn, I think positioning is really important. There is a balance between not scaring off the non-professionals and encouraging the professionals but that the core issue is finding that balance. - Cameron Neylon
Hello Mr. Gunn, and Cameron, our intention is that it should be at one point a replacement for friendfeed and it should connect the various Science 2.0 platforms as mendeley, academia, researchgate in a dynamic way. We will add features, but I do not want to do that without communicating with the community. That's why we launched it early and with just small additions (compared to... more... - Sciencefeed
Ijad, after having touched the service, I agree with many others that by itself sciencefeed is not so compelling (you know my usual arguments). I think as part of something else, where this kind of information sharing is part of the offering, it becomes more compelling, especially if the right services are supported. I think Mr. Gunn is on the right track. - Deepak Singh
Ijad, am working on a post looking at what I think such a service should include. Don't know when I will get to post it though. Hopefully by the end of the weekend. - Cameron Neylon from twhirl
Deepak, thanks for the feedback. Yes, I think also that this is a good idea and I hope that we can specify together what these "right services" are. Cameron, cool. I am looking forward to it. - Sciencefeed
@Ijad: I've sent a couple of messages via the ScienceFeed contact form regarding features and issues. Hope they're getting through to you. - Walter Jessen
We are using a ScienceFeed group for a workshop today and tomorrow. Some observations: messages can't be edited after posting, can't link to messages, COinS support is a great addition (but only finds the first reference), a bookmarklet to import content (including references) would be great. And of course automatic importing of RSS feeds into groups and personal accounts. - Martin Fenner from iPhone
@Walter yes, thank you. I replied to you. Did you get my message? They are all on our To Do List. Martin thank you for testing and you are absolutely right with your ideas. We will work on that. Good feedback. Thanks again. - Sciencefeed
@Ijad: No, I never received your message. - Walter Jessen
Added a few comments (most of them minor software glitches) at the ScienceFeed feedback group http://www.sciencefeed.com/feedbac... - Martin Fenner from iPhone
Anyone figured out if a post can be pointed to/opened in its individual page (as in http://friendfeed.com/cameron...). I find that feature good to point to comments on a conference session. - Kubke
Some more suggestions have been collected at http://friendfeed.com/ff-for-... . - Daniel Mietchen
@neil, If you click on the time stamp it takes you to the twitter or the friendfeed individual post. But if you want to link to a post plus comments that live inside sciencefeed, I cannot see a way of pointing to an individual SF post (and the embedded comments) - Kubke
@neil indeed... - Kubke
A huge update with lots of bugfixes and updates is on its way. I hope we can review then together, what we changed. A lot of your feedback was included. THanks for your ideas. Best Ijad - Sciencefeed
here we go: today an update was launched at sciencefeed. In groups you can now define hash tags, which then automatically getting imported from twitter. More is on its way. Several bugfixes went online as well, like friendfeed webpages etc. Thanks for your feedback. - Sciencefeed
Iddo Friedberg
Bioinformatics blog carnival - http://bytesizebio.net/index...
I remember that :) ... there should more blogs around these days, but with all the microthingys there might be less incentive. - Pedro Beltrao
How many did you get, Pedro? (starting to sweat here a bit) - Iddo Friedberg
Great idea Iddo ... but Pedro's right. In my experiences on Highlight HEALTH, submissions can be sparse. - Walter Jessen
A little less conversation and a little more action... send me your posts! - Iddo Friedberg
Iddo .. you can also act as editor and pick a bunch of posts you like. I ended up doing a few times when there were few submissions. - Pedro Beltrao
Well, I am actually getting a nice trickle of submissions. - Iddo Friedberg
I've submitted a couple. A good editor trumps an aggregator every time. - Maria Hodges
Jan Wessnitzer
Good introductions (and I think generally useful resources) to R
R search engine http://rseek.org/ - Jan Wessnitzer
I have collected many more and a number of PDF introductions. I am happy to put links to these up too if you want me to. Also, I would be interested in knowing about your favourites and day-to-day resources.... - Jan Wessnitzer
Comments and complaints welcome ;) - Jan Wessnitzer
I hadn't come across crantastic.org before. Thanks for the link. - Jan Wessnitzer
More?! ;) - Jan Wessnitzer from iPod
Jason Winget
"Citation can scale where attribution can't" - John Wilbanks #scspn
Science Commons Symposium
"don't underestimate the complexity of making the transition [to open data]" - Stephen Friend #scspn - http://twitter.com/plausib...
Jan Aerts
Small collection of useful vim tricks | Awesomeful - http://awesomeful.net/posts...
I think this is the part where I'm supposed to bash vim and extol the virtues of emacs </holywar> - Chris Miller
Attila Csordas
"Importantly, a social network centered on genes facilitates biological serendipity. When you create a new BioGPS gene list, wouldn't it be great to see that your colleague Jane has another list with a significant overlap to yours? When you search for resources on SNPs, maybe John just registered a plugin for a SNP annotation site he's developed. When you search BioGPS for "diabetes", wouldn't it be useful to see all the relevant genes, gene lists, plugins, layouts and data sets that are shared in your network?" - Attila Csordas from Bookmarklet
Neil, I think I need to troll through the archives of your blog more often for inspiration... ;) A key thing I wanted to emphasize is that many people already use BioGPS for exploring gene annotation (150k pageviews, 23k visits in Jan), and if you use/like BioGPS then the social features tag along without doing anything new. This is unlike many other "facebook for scientists" sites where you sign up and add personal content in the *hope* you'll reap value later on. - Andrew Su
Liking this: no overhead to the social part, just use the resource. - Walter Jessen
the BioGPS iPhone app was the 1st serious biology-related app that 'made' me spend a significant time with science on the iPhone - Attila Csordas
Fantastic Attila, great to hear! Honestly we haven't spent too much time/effort on the iPhone app, so hearing the positive feedback may encourage us to develop that further... (Having said that, the majority of our development effort will probably always be on the web UI...) - Andrew Su
When you hear it from someone who gets it, it just sounds so obvious. Yea Andrew! - Mr. Gunn
Andrew, is there an android app in the pipeline? - Walter Jessen
Walter, to play devil's advocate for a moment, we've considered that _any_ serious app development might not be worth it for BioGPS. Unless we take advantage of a phone feature aside from the browser (shake the phone for a random gene?) then it's essentially a glorified mobile interface. If that's the case, then why not focus on a dedicated mobile interface (sneak peak http://biogps.gnf.org/m) with better cross-browser/device support and less headache of dealing with the plugin framework? Thoughts? - Andrew Su
Agreed, a dedicated mobile interface is all that's really necessary. I'm more interested in that than an app. - Walter Jessen
Oh well. Scientifically that's the way I'm thinking, but part of me is disappointed no one seems to like my shake-phone-random-gene idea... - Andrew Su
@Andrew shaking is cool. How about an app that let's you "feel" an entire chromosome by sliding fingers across the screen. Haptic feedback will let user know when they encounter genes or other features. In high-res mode, haptic feedback will reveal highly positioned nucleosomes, paused polymerases, other DNA binding proteins. Or perhaps higher-ordered chromatin tangles. Sort of like a... more... - Steve Koch
Anne PAJON
Why sharing data between scientists is still mainly done via emails? What's wrong with blogs, wikis, and other existing social web tools?
Theoretically, this is something Wave could excel in. - Mr. Gunn
There is an element of the need for push notification bizarrely enough. Its the most effective and general way of bringing people back into a service to interact with a document. Its not an accident that GoogleDocs provides email notification mechanisms of changes. This was indeed one of the things that appealed to me about Wave, that it has the potential to mix the Wiki collaborative... more... - Cameron Neylon
Exactly. Expecting Wave to be the initial point of entry for wave-related stuff isn't realistic. That said, remember the current client is just a demo client - the true power of Wave is the underlying protocol, which could be woven into all kinds of things on the web invisibly. - Mr. Gunn
I've always wanted a feature to convert an email into a discussion forum. Unfortunately wave doesn't do that. Basecamp and Campfire actually do a better job of that kind of interaction (as an example) - Deepak Singh
I think there are several factors, among them are: 1. Getting used to new mediums 2. People do not understand what tool is good for what 3. People get confused about the features and objectives each tools provides 4. People do not wanna share with everybody/privacy issues - marianaº
Facebook page of drunk son of co-worker? - Egon Willighagen
Email remains the ONLY ubiquitous social medium. Non-FF-ers will not read this. Wave, FB, Mendeley, Connotea, Cite-U-Like, even twitter, are social islands. Only half my team uses twiiter; if I need to talk to them all, I have to use email. - Chris Rusbridge
Incorporating email alerts to changes in documents makes wikis (at least the one I use) and Google Spreadsheets work well in my experience. Curiously GoogleDocs don't have that option - but the technology is so good that it works well for private proposals, papers and other text based projects. - Jean-Claude Bradley
(I'll try not to make my point without turning it into a sales pitch) We have a PI in a sabbatical in the states, her lab is in Israel, she uses our platform to follow and review every progress made in her lab. the system allows her to know when new results are posted and she can comment and make sure her researchers are on the right track. this is just one example. The key in my... more... - Jonathan Gross
That's right, Johnathan, and a lab can manage its own projects with a project management tool such as BioKM, but what about distributed collaboration between labs or teams? This is where top-down hierarchical systems break down, because the investment of getting into the project itself is a barrier. For example, how would a team using your system share results with another team using a wiki or different system? - Mr. Gunn
Within my field (philosophy), blogs are used primarily as a gossip medium and a way of getting calls for papers, conference announcements and funding information and the like out, and only a little bit as a kind of pre-peer-review pre-press where people can frankly exchange ideas. There's a few people using Wave, but we're sorting of flailing around in the dark with it trying to find a problem for the solution. - Tom Morris
It's interesting actually - I've just come recently across a whole bunch of "not the usual suspects" using Wave who have had almost no introduction and just found it useful for distributed lab communication and similar things. Two interesting facts - they are just using the vanilla client with essentially no Robots or Gadgets - its the underlying real time nature that is important - and... more... - Cameron Neylon
Or perhaps they started with a problem that Wave addressed, whereas we're starting with the solution and looking for the problem. - Walter Jessen
I think its an element of both - I think Google Docs didn't really work for them because it was too document like - dropbox was a much better solution in one case, which fits with the "must go into the work flow" theory. Wave they are using in a journal like way, although in one case in a very sophisticated journal-like manner. Limited data points but it is interesting. As you say, it seemed to solve the problem they had. I think this is still true of us but that we expect too much to be solved at once.... - Cameron Neylon
Allyson Lister
Live Coverage of Scientific Conferences Using Web Technologies - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 6, No. 1. (29 January 2010), e1000563. Allyson Lister, Ruchira Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider - Allyson Lister
That blog post now has more citations than some of my papers ;-) - Cameron Neylon
:D Glad we could help, @Cameron! - Allyson Lister
Martin Fenner
Scientists and librarians: friend or foe? - http://network.nature.com/people...
I think you meant "siezed the opportunity" rather than "ceased"? Though on context the latter is ironic... - Cameron Neylon
Yes, of course I meant "seized". And "friend or foe" in the title is also not really the best description, because this is rather about the disconnect of scientists and librarians. - Martin Fenner
The word is "seized". "Neither leisured foreigner seized the weird heights." - Ruchira S. Datta
[stupid comment deleted] Pay me no mind, I've not had my coffee yet. - Bill Hooker
Martin: What I was trying to get at in my muddled tweet was that users want to get directly to specific resources that they use frequently. That's good; nothing from either publisher or library should intervene in that space where you are trying to get something done. To me, it is a good thing that you go directly to PubMed and to specific journal pages. I am aware that the library... more... - Jill O'Neill
Jill, completely agree. But maybe libraries should put up more valuable resources so that researchers go to their webpages. And publishers and other information providers should think more about libraries and not just users. An invisible library works for many things but this might be dangerous in the long run. - Martin Fenner from iPhone
I agree with your points in your post that there are constraints on the services and databases we offer. I should probably post a blog response to this, as there are several different reasons why. Libraries have to serve a wide variety of people, and if you happen to be in a group that's outside the "mean" you'll get less service and/or attention. The mean can be an audience (undergrad... more... - Elizabeth Brown
Growing list of blog posts about scientists and librarians. (Incomplete) list here: http://network.nature.com/people... - Martin Fenner
More blog posts on scientists and librarians: http://undergraduatesciencelib... and http://kraftylibrarian.com/... - Martin Fenner
I really really love that there's so much discussion about this. - Stephan!e•CogSc!L!brar!an
Jonathan Eisen
ISI - late to index #PLoS One but now marketing that they do so - http://phylogenomics.blogspot.com/2010...
ISI - late to index #PLoS One but now marketing that they do so
Honestly, PLoS ONE has already made ISI obsolete, they just refuse to admit it. We should start a Dead Pool for when they will go out of business... - Bill Hooker
But should the dead pool be "open"? - Jonathan Eisen
Sure, ISI employees welcome! :-) - Bill Hooker
@bill not so fast. There are still 100,000 promotion and tenure committees that use ISI metrics exclusively. Article level metrics are still quite obscure, nad and not adopted by most publishers. The fate of grants and careers will rest with ISI metrics for still some time. - Iddo Friedberg from Android
@iddo that's included in the "refuse to admit it" part :-) - Bill Hooker
I think, for the Open Access movement, a full verbal and other assault on the idiotic processes people use for promotion, tenure and hiring is in need. The more we make public how inane the whole thing is the better. - Jonathan Eisen
"The more we make public how inane the whole thing is the better" -> Then you have an "internal" version of the communication problem. - pn
Paulo - not sure what you mean - Jonathan Eisen from iPhone
How to change the perception the IF, ISI and all idiotic processes are really idiotic? How do we communicate that to people that they are the best metrics? - pn
1. Just telling people in the world that many hiring processes are not based on evaluating quality of people but instead on numbers with no established proof that they measure quality 2. There are many things in science like this -- where we have systems that do not measure quality as well as we pretend - anothr good example is peer review - it is important but it should not be viewed in as glorified a manner as it is portrayed - Jonathan Eisen from iPhone
@Jonathan and Paulo: Shameless plug for my most in-demand presentation http://www.slideshare.net/brembs... will be presented again tomorrow at the Charite university hospital Berlin.. - Björn Brembs
I agree wholeheartedly with you, Jonathan, but how do we break this barrier? - pn
Not sure Paulo - but I think it should be a major new front on the move towards more Open Science - Jonathan Eisen
It has to be the first front, IMHO. - pn
Two thoughts: publish and promote PLoS ONE as much as possible, and demand other journals to adopt the same types of metrics. - Walter Jessen
Fight the views with science: Studies have shown that the IF is poorly correlated with eventual citations and that other measures do better. - Mr. Gunn
True mr gunn but also important to point out that success and IF can be falsely positively correlated if people use IF to give people resources and power and positions - Jonathan Eisen from iPhone
@Mr. Gunn: you got a reference to these studies? I'd be very interested... would be giving a talk about this here soon. @Jonathan you are right in saying that hiring a postdoc with a paper in a high IF journal to a resource rich department is a self-fulfilling prophecy. which would make the studies referred to about by Mr Gunn even more interesting. - Iddo Friedberg
Iddo: start here: http://www.simpy.com/user.... There's a whole journal of this stuff: http://www.springerlink.com/content... - Bill Hooker
Funnily enough - that journal used to be under me (in a formal life at Kluwer) - Peter Binfield from iPhone
Thanks, Bill. You always do have your finger on the trigger. - Mr. Gunn
@Jonathan, agree that making public the crazy process of tenure and promotion is a good thing. Example: I was on a faculty search committee here. Candidates A & B both came out for interview. Candidate A was delightful, gave a great presentation, and seemed like would be a wonderful colleague. Candidate B was an a-hole, and essentially told people at dinner, "I'll take your job if I... more... - Steve Koch
Last night I convinced another ~20 colleagues. One of them exclaimed "this impact factor stuff is so ridiculous, it's beyond any discussion" (that person has two papers with around 1000 citations). - Björn Brembs
Seems to me that if you have 1000 citations you can rise above the system. The system drags down younger authors though who are forced to play the game. - Peter Binfield from iPhone
Yes, it is the younger researchers in particular who are in trouble from this. But it is both younger and older who "enforce" this system. We need to break out of it. At UC Davis I have been both impressed and saddened by some of the promotion and review things I have been on. In some cases, we have meetings (e.g., in particular in one of the departments I am affiliated with) where many... more... - Jonathan Eisen
Sally Church
Cancer biology is becoming very complex #AACR - http://www.pharmastrategyblog.com/2010...
Say that again? Is becoming? - pn
Believe me, this is not only true for cancer, but for many other research areas, too. I think this every single day when working on drug design and research. The more you know, the more you realize how little you know actually ;-) - joergkurtwegner
Sally is the mistress of understatement. - Mr. Gunn
It will become "simpler" again only when the whole process is understood completely. Until then, I only see the complexity growing. - pn
Mike Chelen
The Spread of Scientific Information: insights from the web access statistics in PLoS Article-level Metrics Dataset #plosalm - http://homes.gersteinlab.org/people...
The Spread of Scientific Information: insights from the web access statistics in PLoS Article-level Metrics Dataset #plosalm
The Spread of Scientific Information: insights from the web access statistics in PLoS Article-level Metrics Dataset #plosalm
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"We studied the number of html access a paper received after publication using the PLoS ALM dataset. Figure 1 shows the variation of access statistics in time. Here we include 7000 publications that have been published for at least one year. As expected, in average, the older is a paper, the less attention it receives. However, an interesting observation is, there are two phases of decay: a fast decay period during the first 3 months, and a slow decay period afterward. Of particular interest is the decay patterns are the same for three different PLoS journals: PLoS Computational Biology, PLoS Biology and PLoS One." - Mike Chelen from Bookmarklet
an interesting result "we found that the decay of pdf download and html access are very similar, while the decay of xml download is actually slower. This is probably because xml download is performed by machines, and thus the decay profile follows a different characteristics time scale" - Mike Chelen
Can you explain the machine difference a bit more? Different info spread assumption? - Bill Anderson from twhirl
Machines (aka automated scripts) are sometimes run across our content (e.g. to get an entire copy of the corpus) and so they may be expected to do this for articles of any age (as they just want 'everything' as opposed to humans who mainly want 'recent stuff'). Not really sure though whether those scripts go after XML in favour of HTML/PDF (or all 3) but given the low number of XML... more... - Peter Binfield
Steve Koch
I also want to try out another idea discussed at #scio10 ScienceOnline2010: fully-attributed, non-anonymous peer review.
For maybe ten years now, I've thought that the value of anonymous peer review is overstated. During that time, I've heard other people, much more eloquent than me also express this opinion. Just briefly, I think fully-attributed, non-anonymous peer review would solve many problems that exist with today's science, and I discussed this a bit at the meeting. Two of these problems are: (a) good referee work is difficult, and good referees are not credited for the work and the original ideas, and (b) a whole lot of incomplete and sloppy work is submitted and much of it is published due to ineffective referees / editors. The solution I like is for every aspect of the peer-review process to be published, including the original manuscript submitted, all subsequent revisions, and all communication between authors, editor, and referees. Clearly this solves problem (a). As for problem (b), people often say, "but people aren't going to say negative things if their name is on it!" First of all,... more... - Steve Koch
I sign all my reviews; always have. I include a note to the editor saying that I'm happy for the authors to have my name and email, and I include that information in the body of my review (where a journal will have to actively edit it out, if that's their policy). Mainly I do this because doing things in public keeps me in line. I once had a reviewer call a section of my paper... more... - Bill Hooker
I'd go one step further and say that journals should have to publicly own up to rejecting papers. Arguments over priority are only going to get more bitter (and probably more underhand). Journals should provide a date stamped record or hash of the submitted manuscript that shows gives the authors a firm date of submission and what was submitted (and rejected) - Cameron Neylon
Note there have been experiments with open peer review and I don't know of many (if any) successes. Ditto open commentary. I think people are reluctant to be seen criticising. Brain and Behavioural Science "the internationally renowned journal with the innovative format known as Open Peer Commentary" has been going for >10 years, and does appear to be bucking the trend by still working, but I believe it was a lot of effort to change the culture. - Chris Rusbridge
Chris, yeah, I know they tend to fail. But examples of successes in many fields would be nice. Sure, many of the benefits would only be realized if open peer review were the rule. But small examples (such as I want to try) would be valuable, I think. - Steve Koch
@Bill, Yes, and you're my hero for your referee efforts. But you're not getting enough credit! Would be nice if all of your reviews were posted, along with the original manuscript you were commenting on. - Steve Koch
I think PLoS gives referees the option of publishing their reviews alongside papers, at least for some of their journals. - Bill Hooker
Yes, definitely PLoS ONE does and encourages it. So, I think in combination with Nature precedings (for versioning, as suggested by Deepak, I think), all the necessary pieces are there. Just need willing authors, AE, and referees. - Steve Koch
We used to post all reviews alongside the published papers (as a Comment) and did so for about 6 months. We had to stop as this was a manual process and we ran out of resources. :( - Peter Binfield
Why not just make the review PDFs downloadable and link to them? - Walter Jessen
Still too manual. We publish 25 papers a day and they all have at least 2 reviews, plus any reviews on any revisions. Therefore, that's a lot of PDFs to create. load, link to etc. Plus, we need to check we have the reviewer's permission etc and that we arent posting anything sensitive or wrong etc - more time. Then we have to deal with responses from the authors / reviewers who may not have been fully aware that this was going to happen and may not appreciate it etc. It all adds up... - Peter Binfield
Matthew Todd
tldr - Interfaces for Large-Scale Online Discussion Spaces - http://demaws.net/project...
tldr - Interfaces for Large-Scale Online Discussion Spaces
First example I've seen of a visualisation tool for handling large and cumbersome linear discussion threads. Relies on user ranking of comments, rather than some inherent assessment of activity. - Matthew Todd from Bookmarklet
very interesting - Mr. Gunn
Very cool. - Bill Hooker
I'd like to see how that compares to the social filtering here on FF... - Björn Brembs
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