Walter Jessen - Comments

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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...

October 22 from twhirl - Comment - Like - Share

Abhishek Tiwari, Anders Norgaard, suelibrarian and 15 other people liked this

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

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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

I tried a site like this a few years ago. ResearchFire, or something like that? Never heard of it again. - Neil Saunders

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... - Bill Strathearn

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

Mr. Gunn

An anonymous source has informed me that the ASCB has banned “replication of data” by visitors, but has presented Twitter as the poster child of conference data... - http://synthesis.williamgunn.org/2009...

December 6 from Synthesis - Comment - Like - Share

Mike Chelen, Daniel Mietchen, Benjamin Tseng and 5 other people liked this

Sad, just sad - Deepak Singh

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"forms of communication involving replication of data" - pretty much invalidates the entire conference? - Neil Saunders

I wonder if people are allowed to talk - Deepak Singh from IM

Natural selection in action. Either another set of organizers, or another conference, will take over as this one dies off. - Bill Hooker

What is the point of scientific conferences again? - 'Mummi' Thorisson

What was the point in science again? - Cameron Neylon

What was the point of life again? [descending into pessimism...and trip to the pub] - 'Mummi' Thorisson

Bill, another source reports that attendance seems way off this year from what it has been in the past. - Mr. Gunn

As I see it, the problem is one of copyright. All the biologists I know (and to a degree, myself included) are alright with presenting pre-publication data at a conference as long as it isn't digitally recorded or disseminated. If there were a way to enforce "first presentation rights", less people would worry about getting scooped and be more willing to share unpublished data. - Walter Jessen

It'd be nice if the talk were publicly available, either during or very soon after the talk. Then, this public record, combined with the tweets, blogs, etc. would provide pretty good evidence of who did the work and presented it first. At least for me it would. Even as it stands now, though, if scooping is a worry, it seems to me that allowing the audience to tweet & blog will make it... more... - Steve Koch

Walter, you might be right, but surely it has been disseminated in the form of conference abstract prior to someone tweeting about it. If they have copyright concerns, they're simply not understanding things. - Mr. Gunn

I disagree - abstracts are much different than data. I like Steve's idea .. let's get the status quo to swing in the opposite direction and make everything publicly available following conferences and meetings. - Walter Jessen

what is so harmful about having your research referenced by another? if it is cited, it can bring attention and acclaim to the original. if it is not properly cited, then that is itself the problem - Mike Chelen

Cameron Neylon to Cameron's feed, scienceapps, The Life Scientists

I'm going to do a round of looking at some of the Science Social Networking sites again. Is anyone active on ResearchGate, Epernicus etc. and interested in testing functionality?

November 20 - Comment - Like - Share

John Delacruz, Jack H. Pincus, Dan Hagon and 24 other people liked this

I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though. - Daniel Mietchen

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I'm willing to keep an open mind but so far FF surpasses these in terms of networking and ease of use. But if you want to experiment I have accounts in many of these and I would be willing to try. - Jean-Claude Bradley

I'm really just looking to make sure that things haven't moved on and improved significantly, particularly in the light of the NIH projects. - Cameron Neylon

I tend to migrate to social networking sites based on "pull" - virtually the only time I go on LinkedIn or Facebook is when I get an email alert to something relevant to my interests. I would assume that if there was anything really cool going on in these new sites I would get these alerts generated by actions by you and my other friends. - Jean-Claude Bradley

BTW Cameron - that is one of the issues I'm finding with Wave - I tend not to check it because I don't get alerts that there are updates - is there a way to get an email alert for Wave updates? - Jean-Claude Bradley

Yes, there is an email alerter. I'll add you and it to Wave... - Cameron Neylon

Agreed to the general point though - if there isn't a pull, I'm not going there really. And I think that is a big issue with Wave - people just aren't checking in. - Cameron Neylon

@Jean-Claude I don't think there's currently a way of doing this with the current interface without adding a robot but I saw there's a robot on the Haskell public wave which has similar support http://wave-xmpp.appspot.com/public... - Dan Hagon

I'd be interested in testing (I recently started looking over Epernicus for an article on NGS). Where is the email alerter for Google Wave? Currently, I'm using Waveboard (Mac), which alerts you when there's activity. However, it needs to be running in order to do so. - Walter Jessen

Just added you to a Wave with the email notifier Walter... - Cameron Neylon

New SNS from American Institute of Physics, got email invite today: http://www.aipuniphy.org/ - Andrew Lang

I have accounts on Epernicus, SciLink, Laboratree, and maybe could consider BenchFly a social networking site too, but like JC, I don't go to any sites besides FF and Twitter (and those are typically through 3rd-party apps), not even Facebook or LinkedIn, unless I get some alert. But I would be happy to see if anything's changed in those science-oriented sites I mentioned - Shirley Wu from twhirl

I do get alerts that new people have joined the organic chemistry group in Research Gate but there is no discussion and my questions have not been answered there by anyone so not much motivation to check in. - Jean-Claude Bradley

I have accounts at NN, Epernicus, BioCrowd and SciLink. I have begged for account deletion at the latter for months, to no avail and have not visited most of the others for as long as I can recall. So: active - no, interested - no. It's all FF/Twitter for me. - Neil Saunders

It's alright - this is a benefit of the doubt exercise - making sure that things haven't changed or that we've missed something. My brief look around yesterday suggested that nothing much has but I wanted to make sure I'm not missing something. - Cameron Neylon

What about the criteria for comparison other than some "pull" functionality (which they all seem to have, to different extents)? Does usability boil down to feed import/ export and (hierarchically) threaded conversations ordered by novelty and importance, as at FF? - Daniel Mietchen

When considering the usefulness of the individual platforms, perhaps discipline-specific ones should also be on the list? Besides http://polymathprojects.org/ (maths), these would include, for instance, http://openanthcoop.ning.com/ (anthropology), http://www.apecs.is/ (polar research), or this very life science group at http://friendfeed.com/the-lif.... - Daniel Mietchen

It would be worth doing a compare and contrast - also things like Math Overflow and even some of the chemistry blogs act more like community sites. Seems particularly apposite with respect to Pawel's blog post yesterday about the idea to set up a next generation sequencing community site. - Cameron Neylon

I have a ResearchGate account but don't actively use it. I currently do some FriendFeed, Nature Network (where my blog is hosted) and Google Wave, but mostly Twitter. - Martin Fenner

The last issue (November 23) of the German computer magazine c't has an article on social networking for scientists. They like ResearchGate and Mendeley, but also include ResearcherID, Scholarz (a German network), Nature Network, SciLink and Scientist Solutions: http://www.heise.de/ct... - Martin Fenner

That c't article (which shall come out in some OA fashion soon) may serve as guidance but I found the choice of networks therein rather arbitrary, and the comparison between sites was done on a more general level rather than on the basis of specific criteria. - Daniel Mietchen

The article makes two obvious omissions: a) no mention of CiteULike (or Connotea), b) no mention of the recent $12 Mio social networking NIH grant to U of Florida/Cornell University. There are some more things in it I don't like, so I wrote a letter to c't magazine. - Martin Fenner

Cameron, what criteria were you thinking of using? - Mr. Gunn

Key questions: a) What is the immediate impression on signing up? Is there a pull for people to come back? b) What functionality is being offered? Is it immediately available? How dependent is it on having a network in place? c) Funding model and stability d) User numbers, ideally active users and accounts, but whether we can get those is another question. Those aren't very objective criteria and they are built on my biases but nonetheless - Cameron Neylon

Sorry if this is slightly tangential to the discussion, but I was imagining a new kind of social network for publication of research results here: http://virtualchrisleonard.co.uk/blog... - Chris Leonard

Chris - when you talk about "credit" are you expecting tenure and promotion committees to count it or do you have some other system in mind? If you set something up I have content that might be suitable to play with. As for citability - in our last few papers we have used blog posts and wiki pages as references and have not had any problems with that - so I think the system is quite flexible and can accommodate the types of activities you are proposing. - Jean-Claude Bradley

I think Chris means system credit or karma. The idea as I understand it is somewhere between Friendfeed and Stack Overflow - Cameron Neylon

Thanks Cameron, yes, that's what I meant by 'credit' - however, by quantifying and metricising that credit, there is a possibility that one day tenure and promotion committees may want to use it as another measure of a scientists influence in a field. Apologies to Cameron for hijacking his thread. There is another discussion on this blog post here: http://friendfeed.com/chrisle... - Chris Leonard

That's fine, it's not my thread, it the communities thread :-) Pointers are good, they link up the information. - Cameron Neylon

Blog postings to replace (journal) papers and (in-depth) peer review a luxury that can only be acquired if paid for and to be replaced by blog comments instead? Weakening both readability and certification? That does not sound like a healthy idea. - Wobbler

Wobbler: why should blogs lack any aspect of peer review? the standard of any publication depends on how editorial powers are used - Mike Chelen

...and we already pay for peer review. It just isn't a cost transferred as actual cash. - Cameron Neylon

But blogs do not have any editorial powers? What advantage do blog postings have over (journal) papers? They lack format = lack of consistency = lack of efficiency = lack of scalability. Are you seriously suggesting that blogging/blog posts have the potential to replace journal publishing/ (journal) papers as the primary scholarly communication model/channel? Upgrading the traditional... more... - Wobbler

@Cameron: that's true, but now peer review is at least mandatory for the primary scholarly communication model i.e. scholarly publishing. Replacing that with something else and having peer review only on request/payment is a very different story. - Wobbler

Wobbler - there is a difference between requiring the peer review to be performed before making some information public and allowing it to take place after that. I do not see why the latter option would generally fare worse than the former. In fact, we already practice it here at FF, with numbers of likes and comments roughly indicating the popularity of a topic, while the quality has to be sought in the individual comments (and of course the source item that started the thread). - Daniel Mietchen

... it isn't a cost transferred BY YOU as actual cash. Yet. It should be, in my not-terribly-humble opinion, however, because the market disconnect in the current system has proven ridiculously unsustainable. Wobbler, some of my blog posts have had more measurable impact than anything I've ever written. Sure, it's a lightning-strike sort of thing, and most of my blog posts languish in... more... - D0r0th34

@Daniel: I'm not talking about post-"publication" peer review. That's still different from random blog commentary on blog posts. There's no evidence that what we're doing here isn't just a "niche" thing that works well because we're a niche. There's certainly no consistency in quality in our blog postings (well, at least not in mine :p ). Not to mention a lack of consistency in... more... - Wobbler

@D0r0th34: No, we should absolutely not ignore lighting strikes. But we should see them as lightning strikes and consider them to be an exception more than a rule and focus our attention on something that provides that level of quality more as a rule than an exception. Blogs as a complement to (journal) papers is great. But once you start to see it as a primary source, a replacement for... more... - Wobbler

We don't know about our OA bets. As for slow-and-steady, a well-run blog isn't? Lightning strikes aside, building a reputation and a readership is hardly an immediate thing. - D0r0th34

@D0r0th34: That's one more reason why blogging as the primary scholarly communication model is a broken idea. "Popularity" and "building a readership" will be important for blogs (and other post publication peer review models) to be visible/significant. But aren't we going after journals for using their JIF to attract peeps to read their stuff? How is "blog (poster) popularity" to get a... more... - Wobbler

I think the most important property of non peer-reviewed scientific communication is that the content be easily indexed and searchable. Relying on comments and rankings can be very misleading indicators for utility in long tail systems. For example we get over 100 searches a day for our solubility data via Google and Wikipedia but we have never had a comment or any type of feedback from the people who searched for and found information. - Jean-Claude Bradley

Shrug. System-gaming goes on everywhere; there are a number of studies of citation-impact gaming, if you look. Also, why is connectivity a bad thing? We are talking about scholarly *communication* after all, right? Restricting "what counts" only to what goes through the baroque serials-publishing process is IMO an extraordinarily blinkered and limiting view of how knowledge really advances. Sure, it's not easy to come up with more inclusive views -- but that doesn't mean it's not worthwhile. - D0r0th34

The problem is that I'm not sure we can talk about "gaming the system" rather than "an intrinsic part of the system that everybody will be forced to play or greatly risk invisibility" when it comes to blogs and other models relying on postpublication "peer review". PLoS ONE is, intentionally or not, already trying to stake their claim on an as large a readership/community as possible.... more... - Wobbler

@D0r0th34: And connectivity can be unfair if your serious/scientific works are getting more attention than others simply because you've managed to draw a bigger crowd through non serious/scientific stuff. On a slightly more personal note: for someone who occasionally complains about the (lack of) readability of (journal) articles, I had expected that you, of all people, would appreciate... more... - Wobbler

I have to say reading down this I am unsure of whether the complaints apply to blogs or journal articles. Consistent structure and copy editing would be nice but it is rare for both blogs and journal articles. Quality is an issue across the board. Going back to peer review - it's only mandatory for the author, refusal rates for reviewers are going through the roof and unless we acknowledge that cost the system will collapse sometime soon. - Cameron Neylon

@Cameron: Consistent structure and copy editing are rare for journal articles? They are? Not entirely sure about copyediting, but surely most, if not all, journal papers have a recognizable structure? And I don't think they're as rare or rarer than for blog postings. I also think the issue is with peer review, and not with the (journal) paper (format). As such, we should find ways to... more... - Wobbler

Of my recent papers, only one received close copy editing by anyone but me. And that was the Nature piece for which to be honest I would have been happier if the editor had got a co-credit. And formats are all over the place - maybe consistent for a single journal but that's not use to me. The costs of both peer review and publication are so high we need to find a way to lower them -... more... - Cameron Neylon

@Cameron: I'm not sure that's a convincing enough argument for me. Maybe your other papers were written clearly enough already? You're a prolific blogger/writer, Cameron. It's not weird to assume that your ability to communicate concepts clearly is higher than the average scholar. Maybe high enough to not warrant copyediting (in a lot of journals)? My impression of journals is that... more... - Wobbler

Well others can pitch in but perhaps a different anecdote. Until I started getting into arguments with Maxine Clarke I didn't even realise that journals might do copy editing. Nature and similar are very different beasts to the average of course. - Cameron Neylon

So, generally speaking, only the high profile/impact journals provide copyediting services? Hmm, that is definitely not what I expected. If you had to estimate the % of journals that provide copyediting services, what % would that be? The (top) 10% of all journals? - Wobbler

I have the same experience as Cameron - the only time my manuscript was copyedited was when I published in Nature - Jean-Claude Bradley

So far as I'm aware, no-one here wants to replace peer-reviewed journals entirely by blogs. Yet that seems to be what you're arguing against, Wobbler. For some functions, journals are a lot better than blogs. But for other functions, blogs are a lot better than journals. At the least, I really can't imagine how, say, DHJ Polymath or Galaxy Zoo or the Open Dinosaur Project or [fill in... more... - Michael Nielsen

Most of this is as a response to an FF comment by Chris Leonard on the 23th of November in this thread, who is arguing for exactly that. - Wobbler

Cameron, any progress on the roundup? Is there any information I can provide from Mendeley? - Mr. Gunn

Right - getting there slowly! Have set up a wiki page (ignore the state of the rest of the site I am working on it!) at http://wiki.cameronneylon.net/index... You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I... more... - Cameron Neylon

Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability. - Daniel Mietchen

I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point! - Cameron Neylon

Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not... more... - Steve Koch

I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who... more... - Steve Koch

Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a... more... - Steve Koch

Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data. - Steve Koch

Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is... more... - Cameron Neylon

Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that? - Steve Koch

If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what... more... - Cameron Neylon

Should we include some discipline-specific ones or are we going for general-purpose only? - Daniel Mietchen

Neil Saunders

Much as I love FriendFeed, its real-time nature is starting to take up too much of my work day. Same goes for Twitter. Any tips for regular, but less frequent ways to use it? For example, if I wanted to check/contribute once or twice a day, what would be a good strategy? I tend to check GReader in this way - how about the FF atom feed?

November 24 - Comment - Like - Share

JoeCamel, Richard Akerman, Anders Norgaard and 11 other people liked this

I'd recommend checking it out at the end of your day. Things will likely be slower, allowing you to catch up and comment as you will. Turn email updates off if you don't want to be tempted to come back to answer what someone posts outside of your allotted FF visit time. - Spidra Webster

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Try the pause button. - Raphael, Raphael

Try putting people/groups you want to specifically check on in a special list, that way when you do make your way to FF you can quickly check on the things that interest you most. - FFing Enigma (aka Tina)

The FF feed is one way to do it, but you'll just end up clicking through to friendfeed, so it'll only save you time if you need to screen through lots of posts. I'm also not sure what order things will come out in. My strategy is just to install the Cleaner Friendfeed Widescreen stylesheets and make liberal use of "Best of Day". - Mr. Gunn

Sounds like I need a better client. Something that will show only changes since my last visit (like a feed reader), but also allow post, comment and like. - Neil Saunders

FF needs a good client. Let me know if you find anything. - Mr. Gunn

We need real-time filtering in my opinion, real-time feeds are becoming just like stocks, they become addictive and eat a lot of your time! - Alvin

I'm scrolling through everything frontpage in the morning, then "best of day". Same again in the evening. Not too much time. - Björn Brembs

check fewer times, make groups, and start out with surfing thru "best of day/wek/month" first - chaz2b

I suggest you write a script that changes your Host file at certain times of the day. The alternative host file will point friendfeed.com to some horrible site that you would never go to while at work. - Santa CW™

Neil, I can sympathize as my work has recently picked up in intensity. I wind up checking once or twice and just skimming, but in the evening (when I have more time), I use the "Best of Day" to really focus what I spend my time reading. - Benjamin Tseng

Use Best of day / week / month. - Joe from iPod

Ration yourself - check in, check out. - AJCann

Screen the people you follow mercilessly. Keep only low-volume, high-signal people. Someone may post great stuff, but if they publish 20 tweets a day and 18 of them are useless to me, I'll pass. If the idea is *that* great, you'll hear about it from a dozen different people reposting it. - Chris Miller

I have the same problem with "real-time" social networks. I've piped FF into my Twitter account and keep a client open all the time, but I've faced up to the fact that there's a lot I miss. @Chris Based on your point, I've revised my FF services to reduce the amount of noise and redundancy. Thanks. - Walter Jessen

Also, make use of the search operators to filter by service (which you can still do with a userscript or in adv. search) - Mr. Gunn

Walter Jessen

Grant writing would be so much easier if I didn't share space with someone who talks on the phone all the time! Where's the consideration?

November 13 from Twitter - Comment - Like - Share

Mickey Schafer liked this

I have this challenge working at home! - Mickey Schafer

My challenge at home is a four and a half year old! - Walter Jessen

Aah -- it gets easier when they get into school (providing you're not home schooling!). I never got people who can work at home with kids. My kids will do anything to get attention! - Mickey Schafer

Michael Barton

The Way I Work: Jason Fried of 37Signals - http://www.inc.com/magazin...

November 3 - Comment - Like - Share

Mickey Schafer, Adam Kraut, Konrad Förstner and 3 other people liked this

QUOTE "We rarely have meetings. I hate them. They're a huge waste of time, and they're costly. It's not one hour; it's 10, because you pulled 10 people away from their real work. Plus, they chop your day into small bits, so you have only 20 minutes of free time here or 45 minutes there. Creative people need unstructured time to get in the zone. You can't do that in 20 minutes." - Michael Barton

I wouldn't complain if one day I was part of a company with the 37Signals mentality working in the field of bioinformatics. - Michael Barton

Love this: "Creative people need unstructured time to get in the zone. You can't do that in 20 minutes." No kidding! - Walter Jessen

Shirley Wu

BBC NEWS | Technology | Science enters the age of Web 2.0 - http://news.bbc.co.uk/2...

October 26 from Bookmarklet - Comment - Like - Share

Dan Hagon, Jean-Claude Bradley, Khader Shameer and 6 other people liked this

"Tweeting scientists can exploit this to quickly pass on that hot new paper to their peers with minimal effort yet maximum effect." - that's funny. Why do we need twitter for this? So far Twitter is really useless for scientists - Alexey

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I know you're down on twitter for scientists, Alexey, but I know that it is widely used in some fields. Medicine is just slow on the uptake - how long did it take for PCR to make it to the clinic? - Mr. Gunn

@Mr. Gunn - agreed, i'm still trying to oppose Twitter to FF - Alexey

I wouldn't say that twitter is either essential or useless for scientists. I get some benefits from it: alerts, useful URLs, corporate communications and as IM. Like many tools, it's about effective usage and we're all still learning what that entails. - Neil Saunders

@Neil - Agreed. I also see more articles and useful URLs using Twitter, but it's clearly not an "essential" app for my work. I think it's useful because of how easy it is for someone to broadcast something they find interesting rather than email people directly. - Walter Jessen

The Life Scientists: Chris Lasher

I need to make a hop from mouse genes to human genes. What's your suggested pre-calculated ortholog database for this?

October 22 - Comment - Like - Share

Andrew Perry, Chris Miller, Paulo Nuin and 5 other people liked this

It seems there's InParanoid (http://inparanoid.sbc.su.se/), roundup (http://roundup.hms.harvard.edu/site...), and TreeFam (http://www.treefam.org/). Any others? - Chris Lasher

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Mine, of course. ;-) Berkeley PHOG: http://phylofacts.berkeley.edu/ortholo... See in particular the Downloads page http://phylofacts.berkeley.edu/ortholo... which includes orthologs between human and mouse. We're in the midst of library construction which will greatly expand the number of genes for which we find orthologs. - Ruchira S. Datta

More generally, see this paper: http://genomebiology.com/2009... and references therein for an up-to-date list of methods and databases. - Ruchira S. Datta

@Ruchira I didn't realize you worked with Sjölander. She spoke at the VBI symposium a year or two ago. - Chris Lasher

So I heard! You're at VBI? Please say hello to Reinhard from me. :) - Ruchira S. Datta

I was; I changed groups. Other VBI-ers on FriendFeed: http://friendfeed.com/bryanle..., http://friendfeed.com/aswarren, and http://friendfeed.com/behindt... - Chris Lasher

I've had a ton of trouble every time I tried to use that phylofacts site for anything. Maybe it's just not intended to do what I wanted... - Donnie Berkholz

@Donnie, I'm sorry to hear that. What did you want to do? - Ruchira S. Datta

I'll let you know next time something comes up, I don't remember exactly what things it was anymore. One example of something I've done recently is, given a residue number in a PDB file, find the sequence, find all homologous sequences (given some cutoff), their % identity to the original, and the equivalent residues (a per-residue mapping of input:result) in an automated fashion. By the way, say hi to John Davidson! - Donnie Berkholz

Yes, I can see how that would be hard to do in the current site. We've been thinking of making per-residue information more evident for the site redesign that's in progress, but I at least had been thinking more about the display rather than doing it "in an automated fashion"--I presume you want to script it? It's good to know what people are interested in, thanks. I'll tell John you said hi! - Ruchira S. Datta

Chris : MGI is providing mammalian orthology information based on literature reports. For example for Myod1, list of mammalian orthologs : http://www.informatics.jax.org/searche... . - Khader Shameer

@Ruchira: Yeah. I had a set of 150 or so proteins I wanted to do that with, comparing each one with all of its homologs. Not reasonable to do it manually. - Donnie Berkholz

Second the MGI resource. Mammalian Orthology: ftp://ftp.informatics.jax.org/pub/reports/index.html#orthology - Walter Jessen

Walter Jessen

Watching an interview with Richard Smith (former BMJ editor) discussing the trouble with medical journals http://www.cbc.ca/mansbri...

October 24 from Twitter - Comment - Like - Share

John Dupuis and Graham Steel liked this

Dang, I really must watch this one again. - Graham Steel

4 more comments

I'm trying to rip it (unsuccessfully at the moment), since I think it would be useful for readers of Highlight HEALTH. - Walter Jessen

Have you read the book? - Walter Jessen

No I've not. I'm a REALLY slow book reader. - Graham Steel

Some of the book content is OA http://jrsm.rsmjournals.com/cgi... - Graham Steel

Cool, I'll read over it this evening. - Walter Jessen

Graham Steel

"Open Science" talk by John Wilbanks 20th Oct 'Open Source Science Commons' video/slides http://seraph.cchmc.org/mediasi... #oaw09

October 22 - Comment - Like - Share

Walter Jessen, Richard Akerman, Daniel Mietchen and Jean-Claude Bradley liked this

is there a SlideShare version or do we really have to install Microsoft software to view for purposeful irony? - Jean-Claude Bradley

15 more comments

Just checked, the slides of this one aren't yet on SlideShare. It played fine for me without downloading software here.... - Graham Steel

hmm - still can't change slides - using Firefox - Jean-Claude Bradley

Not working for me either, FF3.5/WinXP. Not even for a Wilbanks talk will I install more M$ bloatware. - Bill Hooker

Dang. This worked for me earlier but I'm now getting blank screens 'ere. Hum ho..... - Graham Steel

I like the way he reframes "open science" as "distributed science" (at 6:50). - Daniel Mietchen

"PDF is a digital version of paper with all of the technical benefits of paper." (ca. 10:00) - Daniel Mietchen

On business models: "Be number one or be open." (ca. 24:00) - Daniel Mietchen

"It is hard enough to integrate the data technically and scientificaly. If you add legal complexity to that, it becomes nearly impossible." (ca. 49:40) - Daniel Mietchen

Google Map functionality for scientific images (ca. 54:00) - Daniel Mietchen

"Now it is easier to find shoes, pornography, hotel reviews than it is to do science on the web." (ca. 1:02:00) - Daniel Mietchen

Quotes Merton "i propose the seeming paradox that in science, private property is established by having its substance freely given to others who might want to make use of it" (ca. 1:03:00), as Cameron did recently at http://blog.openwetware.org/science... . - Daniel Mietchen

"If we create an open scientific system, it will be abused - the question is how we deal with that" (ca. 1:08:00) - Daniel Mietchen

Discussion concludes with an encouragement to bring journal clubs online, as has been recently discussed at http://ff.im/ajIdm . - Daniel Mietchen

Daniel - I have not watched it but if reframing "open science" as "distributed science" implies the terms are interchangeable that isn't right. I suspect most science is distributed to some extent between collaborating groups. Open means absolutely nobody is kept out. - Jean-Claude Bradley

A copy of the talk can be viewed on Next Generation Science (without slides): http://www.nextgenerationscience.com/open-ac... - Walter Jessen

thanks Walter! - Jean-Claude Bradley

Mr. Gunn

October 12 from Flickr - Comment - Like - Share

Neil Saunders, Brian Krueger - LabSpaces, John Dupuis and 9 other people liked this

Awwwwwwwww. - Bill Hooker

4 more comments

Congratulations Dr father Gunn - Nils Reinton

Congratulations! - Chris Lasher

Congratulations! - Yann Abraham

Congrats William! - Walter Jessen

So cute! - Stephen Francoeur

References Wanted: Paulo Nuin

I would appreciate anyone sending me this ref:http://www.landesbioscience.com/journal.... Please send to paulo.nuin at gmail. Thanks in advance.

October 2 - Comment - Like - Share

Sent! - Walter Jessen

Thanks a lot! - Paulo Nuin

Walter Jessen

Want to connect on LinkedIn? http://www.linkedin.com/in...

September 28 from Twitter - Comment - Like - Share

Your LinkedIn page is impressive -- detailed, informative, enough info to help someone make a decision. Mine is not! Part of the difficulty is that I still seem to be deciding what I want to be when I grow up -- some people by sports cars for their mid-life crisis; I'm trying to define what the next 20 years of my prof. life should be dedicated to. - Mickey Schafer

Don't let my profile fool you. My road is far from linear. - Walter Jessen

Bora Zivkovic

Happy to announce I got on the Editorial Board of the Journal of Science Communication: http://jcom.sissa.it/

September 24 from Twitter - Comment - Like - Share

Pedro Beltrao, Mickey Kosloff, Nils Reinton and 22 other people liked this

Congratulations! - Admiral Anika

17 more comments

eeeeeeeeeexcellent. World domination continues apace... - D0r0th34

Congratulations! - Joe Bonner

Congrats! - FFing Enigma (aka Tina)

congratulations! - Sofia @ SoMaFusion

Very nice. Congrats! - Dave Slusher

Congrats, Bora! :) - Ayşe E.

congrats! that's quite an accomplishment! - sean808080

Nice one. Also, +1 D0r0th34... - Bill Hooker

Congratulations, Bora! Very well-deserved! - Benjamin Tseng

Congratulations! - NeuroWhoa

Congratulations! - John (a.k.a. dendroica)

As Bill says !! - Graham Steel

Congrats! - Walter Jessen

Congratulations, Bora! - Mo

yay! - Stephanie_Thankful

Hopefully you will help internationalize the authors (they are mostly Italian) and the public (mostly European) of this OA journal! - Enro

Congrats, Bora! :-) - Kol Tregaskes

w00t! - Kubke

Walter Jessen

RT @BoraZ: RT @ccziv What writers still need ... (it's the editor, stupid) http://www.good.is/post...

September 17 from Twitter - Comment - Like - Share

Mickey Schafer liked this

yes yes yes yes -- just had a student say "wow, I really like the way you took those two paragraphs and made them into one. Makes much more sense now -- can I actually use that?" My answer? Yes, please use that! My goal isn't to change style; it's to improve how well the writer's style accomplishes the writer's objectives. - Mickey Schafer

I'm spending more time as an editor on Highlight HEALTH and NGS, so I can really relate to the article. - Walter Jessen

Walter Jessen

Want to connect on LinkedIn? http://www.linkedin.com/in...

September 14 from Twitter - Comment - Like - Share

Join the FriendFeed Life Scientist group! http://www.linkedin.com/groups... - Benjamin Tseng

I didn't know about this - thanks Benjamin. - Walter Jessen

laura

iHOP - Information Hyperlinked over Proteins - http://www.ihop-net.org/UniPub...

September 6 from delicious - Comment - Like - Share

Walter Jessen, joergkurtwegner, Tristan Hambling and 2 other people liked this

My favourite example of a wonderful idea crippled by the lack of access. iHOP does excellent work using only PubMed abstracts... imagine what it could do if it could access full text. - Bill Hooker

Very true Bill, nonetheless, it's still a great resource. I use it all the time. - Walter Jessen

Cameron Neylon

Call for JCOM papers on participative media - http://jcom.sissa.it/call

March 31 - Comment - Like - Share

Claudia Koltzenburg, joergkurtwegner, Antonella and 19 other people liked this

I know this has been posted a couple of times but does anyone think that it is worth trying to write a "Friendfeed for Science" paper for this (or somewhere else even)? - Cameron Neylon

98 more comments

Absolutely. I'd say it's the first SM application that's truly been utilized by researchers. - Walter Jessen

Is Cameron the lead author? Someone needs to lead and we'll all follow and jump in and try to be generally helpful. - Bora Zivkovic

Sure, it's worth it. I repeat Bora's question: who's lead? - D0r0th34

I can write an abstract by the deadline and probably an outline. I can coordinate I guess and probably write an outline but would need a reasonable number of people committed to helping writing before going too far down the road. - Cameron Neylon

Is there an example of "citizen science" on FF? Not scientists collaborating, but non-scientists or amateur scientists pulling data about some aspect of nature together here? - Bora Zivkovic

Count me in .. I'll commit to writing. - Walter Jessen

What kind of writing help do you need, Cameron? I can maybe pitch in a few paragraphs. It seems to me that comparisons with e.g. academia.edu would be in order, f'rinstance. Can also offer to take other sections in, do basic grammar/sense check, integrate into a smoother paper. - D0r0th34

Dorothea that would definitely help. My experience of the crowd sourced grant proposal as that editing and sensemaking was a big part of the headache at the end. Just pulling all the pieces together and making sense of them. - Cameron Neylon

Bora - I'm not aware of "citizen science" per se but definitely examples of crowdsourcing (e.g. the comment categorization on PLoS ONE). Comparison with other networking sites would seem to fit with the call at some level - Cameron Neylon

Well, if you get enough buy-in to go for it, definitely count me in. - D0r0th34

Okey dokey - wiki set up at http://ff4s-paper.wikidot.com/ I've tried to set it up so that anyone can get in reasonably easily. If you get asked for a password for access then it is the name of our most prolific blogger all lower case twice no spaces - Cameron Neylon

Vivian Siegel and I have a manuscript in press that touches on the subject of FF in science; I started the research for it with a FF conversation http://bit.ly/1ZpfMJ Wanted to mention it so that it can be part of the discussion. Will post a link to this thread when we have a DOI URL. (If I forget and folks are interested, please remind me.) - Chris Patil

@Cam, xlnt but looks like I'm only the first through the gate other than you. Hint to others, *first name only* of our most prolific blogger x 2 ;-) - Graham Steel

@Chris - I just so happened to bump into Vivian over the weekend on Fb. Thanks for flagging up that other FF thread, which I don't think I'd seen before. - Graham Steel

Cmon Graham, he's only got one name :-) Like Madonna remember... - Cameron Neylon

Also pages are actually set to allow anonymous editing at the moment (I think) but obviously better if you do it under some name that can be credited. - Cameron Neylon

And now with a friendly cc0 at the bottom :-) - Cameron Neylon

Posted very quick paragraph for people to dissect as a starting point. - Matthew Todd

If you still need people, I'm up for it, too! - Björn Brembs

More the merrier... - Cameron Neylon

I already made some edits on the wiki... - Björn Brembs

Sounds like fun - I think the focus should just be on FF. Are we putting suggestions/questions in [.....] for Cameron to decide? Maybe we should tag them with our initials, like [..... -AL]. - Andrew Lang

I think we should be able to track who wrote what using the wiki functionality as long as people are logged in (see other comments for password) but tagging with initials is helpful. My thought was to let it run for a few days and then try to cut down to an abstract and save the rest of the text for the (hopefully) full paper. My experience of these things is that people don't like cutting other people's text out so we'll probably end up with lots of stuff that can then be re-used - Cameron Neylon

mmm ok wikidot isn't quite as functional in display as one might home but its ok. Certainly got a list of contributors but if you want to make a point about some specific writing or to propose a significantly re-written version then feel free to initial it. - Cameron Neylon

I probably cannot be an author, but I like your idea. I changed your first sentence to include "initiation" of collaboration...my first read-through it seemed to focus more on "carrying out" collaboration, which implied to me that the relationship existed prior to friendfeed. - Steve Koch

Part of the original call that's most relevant is perhaps: "How web tools are changing and widening this way of participating in the production of scientific knowledge. Do[es] this increase in participation consist in a real shift towards democratizing science or on the contrary is merely a rhetoric which do not affect the asymmetrical relationships between citizens and institutions?" FF is a case study in wideing participation. So, yes, we should discuss initiation as well as extension of collaborations. - Matthew Todd

Still only 183 words without the references. Perhaps need to select one or two examples. Also suggest we tone down how great FF is, and take an analytical approach - is it any good? - Matthew Todd

I agree with Matthew and suggest embedding the toned-down FF blurb into a solid description of the social media currently available (blogs, wikis, microblogging services, social networking sites are already mentioned in the abstract), pointing out for each the pros and cons in comparison to traditional means of communication (for wikis, I have started to compile such a comparison at... more... - Daniel Mietchen

This sounds like a good plan - compare and contrast and then try to pull out what the key features are. Will try to look at this tomorrow if I can find time. - Cameron Neylon

Ok, I'm bumping this up for another round. I think the abstract looks pretty good (less sure about the word "peripherality" but I get the idea at least). Two questions. 1) Is it time to start fleshing this out a bit more for the actual paper? 2) I am wondering about whether JCOM is the right place. No harm in putting the abstract in but what about somewhere like Nature Methods? Or both for that matter? But that involves writing two papers... - Cameron Neylon

Actually, we have two abstracts there now since the two paragraphs are basically paraphrases of each other. 1) probably yes. 2) The purpose of the article is to describe science 2.0 through FF glasses, ideally in an updatable way, to people who do not know either, i.e. to those who prefer paper-based journals. Neither of the two options allow for both, but that could be ok for this initial shot. Alternatives? A community page at PLoS Biology perhaps? - Daniel Mietchen

To see existing PB community pages, run this search: http://biology.plosjournals.org/perlser... (the resulting url is horrible which is why I'm not linking directly to the result) This option might require some kind of formal community, rather than the loose affiliation of the biogang. - Bill Hooker

I think the point of this paper is to lay down some markers in the conventional literature so I was thinking of it as as fairly conventional paper. I haven't checked the JCOM copyright arrangements but if it goes to somewhere with liberal pre-print approach then we can re-use and put up the pre-print version at least on a website for updating (OWW? Some other Wiki). I'd be inclined not to go to PLoS just because the impression could be that "of course PLoS would publish that but it's not a _real_ paper" - Cameron Neylon

Which is NOT my view I should add - just don't want to give people any excuses... - Cameron Neylon

the references i put there aren't really for the abstract submission - they're for later... i think we should have a new paragraph talking about what friend feed is and another maybe outlining some examples - Christina Pikas

A good wiki place for updated versions would be near http://openwetware.org/wiki... . As for people who do not see PLoS papers as _real_, I share Camerons concerns, so we should go that extra step in their direction to pick them up near their home base. But where are suitable _real_ journals that allow reuse in a wiki? JCOM use CC-BY-NC-ND ( http://creativecommons.org/license... ) which would prohibit it. - Daniel Mietchen

Another way to go might be to start out on-wiki directly (not at wikidot - at the "final" destination), get one version published on paper and continue updating. Nature Physics may be open to that, judging from things like http://www.nature.com/nphys... and http://www.nature.com/nphys... . - Daniel Mietchen

Any NPG journal is ok with a pre-print and that includes writing the paper completely openly and leaving the presubmission version on a Wiki. The only license allowed for a preprint on Nature Precedings is CC-BY so for that version, re-use is perfectly allowed. It is only the peer reviewed published version that has a six month embargo on re-use. - Cameron Neylon

I'm thinking more and more that a real practical "Web2 tools for the active and busy researcher" could be a worthwhile Nature Methods paper. We could get David Crotty to referee ;-) - Cameron Neylon

I had a closer look at Nature Methods now and think the topic would fit (closest match I found is at http://www.nature.com/nmeth... ). However, who of the "tactile" readers are actually subscribed to the print edition of this one? I found only two Nature Methods papers in my electronic database and have never actually seen it in print. - Daniel Mietchen

Interesting development. I would definitely agree that a submission to a NPG journal would be an excellent idea. I used to get Nature Methods in print, but no longer. It was very good last time I saw it. Something on Web 2.0 tools would be excellent. That leaves the JCOM paper. Still worth submitting an abstract, but we need to emphasise the 'democritisation' of research, rather than FF itself. - Matthew Todd

Someone want to start a Web 2.0 tools paper on a wiki, and we can flesh out something and ask Nat Methods if they would be interested? - Matthew Todd

15th May deadline approaches. The way the abstract currently looks includes mention of peripherality. JCOM itself is interested in participation in science of non-scientists, e.g. those at peripheral institutions (I guess) but surely more importantly those who do not have access to the hardware of science, so the public, librarians, curators, journalists. I think this is a slightly... more... - Matthew Todd

[And why is this whole thread not appearing at the top of my feed, despite my commenting on it afresh?] ugh - Matthew Todd

Bump - 5 days left. - Graham Steel

Two days left for this one now but I think we had agreed that Nature Methods would be a better location anyway. Still, without some sort of plan and deadlines, http://ff4s-paper.wikidot.com/ probably won't go too far but by means of http://friendfeed.com/ff-for-... we might actually get some concrete things to report about. - Daniel Mietchen

One day left, folks. - Graham Steel

One or two days? 15 May isn't it? I have received Nature Methods in the past, comes out monthly, got lots of good stuff in it. I agree with Mat that the focus of the current abstract is perhaps slightly off from the JCOM call but no harm in putting something in. I think we can talk about including people beyond research scientists and how that could lead to the general public. I was thinking of a NMeth paper as more of a "how to" than anything else. - Cameron Neylon

Looking at it it is actually well under 500 words even if we combine both versions. Can add some more but does anyone have a feel for what would be optimal? I've been caught out by funny cultural things about lengths of abstracts before... - Cameron Neylon

Chipped in a little more. Still around 400 words. Am still concerned about mentioning Friendfeed so much. Imagine in 10 years, and FF is no longer with us (I know, I know, but just imagine for a second), then this article will look terribly dated. We should mention FF, but try to also keep broadly mentioning aggregators as the central idea - the functionality is the key thing -... more... - Matthew Todd

I think the abstract is in good shape now, and with 459 words it's not too far off the mark. In case of a submission to JCOM, however, we should perhaps ask whether they agree for this article to remove the "ND" (possibly along with the "NC") from their default CC-BY-NC-ND license - otherwise there will be problems with updating the stuff the wiki way. - Daniel Mietchen

I also need a list of all the people who feel they've contributed. Unfortunately the free settings only give us the last twenty edits and I have a feel there were more people who made some contributions at the beginning. I'm not so keen on upgrading to see whether I can recover those names...will draft up an email that says something about the ND bit - but as the license on the current piece is cc0 anyway they can't restrict our re-use anyway... - Cameron Neylon

And the word count is now 486.... Agree with Daniel re. dropping ND and possibly NC too. - Graham Steel

Just did another minor edit (anonymously by mistake)- 496 words! Again made FF an *example* of an aggregator, to try to make the article more general. - Matthew Todd

The deadline has been extended to June 1st - I just got an e-mail about it. http://jcom.sissa.it/call - Bora Zivkovic

i think it's pretty good right now. it's just an abstract and not the whole article so.. @Matthew - I like your edits making FF an example of a type of service. i'm fine with dropping the ND and NC and just keeping the by. how about we add a place for the authors on the page - with the names, e-mails and affiliation info we want to use (i use UMD for this not my place of work, btw) - Christina Pikas

Really like the new paragraph and additions to the first one. A call again. Anyone else in this conversation made contributions that they feel should be recognized by authorship at this stage (presumably can change later anyway if accepted)? I want to interpret that generously as well. Have put up a draft submission letter at http://ff4s-paper.wikidot.com/submiss... - Cameron Neylon

Ok so realized I can get a free upgrade for 30 days which lets me see all the revisions. So Dorothea, Graham Steel, Romney, and Walter made additions early on and aren't listed as authors currently. If you would like to be included (even if you just want to keep a hand in for potentially writing the paper) can you add your name/affiliation to the front page? - Cameron Neylon

Looks like you have plenty of help! Not sure another cook in the kitchen is needed. - D0r0th34

Am I just confused or has the deadline just shifted by two weeks in the last couple of hours? Now seems to be June 1. Still I'm pretty happy with abstract as stands and would be willing to put it in. - Cameron Neylon

+1 Cameron. Great submission letter (BTW). I say SHOOT and let's see what happens. - Graham Steel

If everyone is happy then I will submit it tomorrow. Speak now, or forever hold your pieces... - Cameron Neylon

i say shoot - but do we need a catchy title first? (agree with G.S. - like the submission letter) - Christina Pikas

Ah woops. Title. Mmmm. "Design Patterns for the Succesful Implementation of Web 2.0 Tools for Research: Does FriendFeed point the way for online tools that will enable and support widespread collaboration?" That's a bit unwieldy but it's a start... - Cameron Neylon

"A friend in feed is a co-author indeed" was/is the working title and I say keep it at that unless anyone comes up with a better one. - Graham Steel

+1 for Graham's -1 for Cameron's (bcs design patterns might be too hard to live up to in an article) - Christina Pikas

Do we need something a bit more explanatory though? Or is that the right style for this kind of journal? I agree design patterns is probably too much to get into this article. Guess that one will be further down the track. - Cameron Neylon

We're talking about collaboration, rather than co-authoring necessarily, so "A collaborator in need is a friend in feed" comes to mind (though now a bit of a mouthful!), then maybe followed by ": Democritisation of Research Through New Web 2.0 Tools." ?? Agree whole things looks good, and thanks for putting together the covering letter Cameron. You happy to submit, finally? Nice that deadline is extended, but don't think we need it unless we can't decide what to call it :) - Matthew Todd

I'll sit on it for the moment until we have had a bit more time to think about titles I think. Could benefit from a few cycles of discussion. I like Mat's but agree it is a bit more of a mouthful. My only concern with the Friend in Feed is a co-author indeed is that we probably won't write that much about authoring. Although that will be how the thing is put together so I'd be happy with it. - Cameron Neylon

Not having seen the latest discussion here, I have just put in "The social aggregator as a tool for user-led collaborative science" as a placeholder until we have agreed on a final phrasing. - Daniel Mietchen

How do people feel about double barreled titles. I find I do them by default but I know they irritate some. Thinking that "A friend in feed is a co-author indeed: The social aggregator as a tool for user-led collaborative science" might work? - Cameron Neylon

Fine with me. - Daniel Mietchen

And with me. - Graham Steel

Fine. Really hate double-barreled titles, but feels right here. - Matthew Todd

I would hate to impose my double-barreled tendencies on others ;-) - Cameron Neylon

it's been proven in a seminal article by L. Puppybreath that increased titular colonicity means increased citation: I agree :) - Christina Pikas

Ok peoples. Final draft version I propose to send off is available at http://dl.getdropbox.com/u... - Cameron Neylon

And submission letter at http://dl.getdropbox.com/u... - Cameron Neylon

Top man, Cameron =) - Graham Steel

Would I be right in thinking that if I could avoid submitting it by email then email will have played no part in the preparation process? - Cameron Neylon

Yes, absolutely. - Graham Steel

minor edit. on the draft version, 4. Patient Advocate, Scotland 5. University of Sydney, Australia should read:- 5. Patient Advocate, Scotland 6. University of Sydney, Australia - Graham Steel

fixed. Also minor edit to submission letter - Cameron Neylon

Will send at end of day today - Cameron Neylon

or tomorrow...but it's gone now... we see what happens - Cameron Neylon

Danka very much. - Graham Steel

just our affiliations alone are cool - what a diverse set! how exciting - Christina Pikas

Awesome, Cameron, thanks for sending it in, and for catalysing this whole (very interesting) process. - Matthew Todd

Well thankyou all for writing it! Now all we've got to do is turn it into a paper.. - Cameron Neylon

Can I add a paragraph about a commercial view on this? I will probably do it as free-citizen (private person), not as the employee of the company I am working for. - joergkurtwegner

This is cool: http://tinyurl.com/l98lwp - Bora Zivkovic

Just to keep the conversation together: Just received this back from the editor "I'm the editor of the JCOM's special issue about User-led, P2P Science. We hereby inform you that your abstract unfortunately has not been selected for publication. There was strong competition, several applicants for the limited places, and we wanted to strictly respect the topic of the call." - I guess... more... - Cameron Neylon

Yes, I think a Nature Methods paper would actually be the more interesting possibility in any case. Scope being Web 2.0 Tools for Scientific Collaboration? - Matthew Todd

Yes, that's what I was thinking, with some use cases and examples of "how to" effectively. probably still focussing on friendfeed - Cameron Neylon from twhirl

Yes, "Web 2.0 Tools for Scientific Collaboration" for Nature Methods sounds good to me too. - Daniel Mietchen

ok - best get on and write it then :-) Will try and get some sections put up over the next week - Cameron Neylon

Was wondering what has or has not happened since the last update in June. Any clues?? - Graham Steel

Ummm not a great deal I'm afraid. It is currently No 4 on my list of papers I really must do something about...Daniel has been regularly updating the bibliography section - Cameron Neylon

Thanks, Cameron. - Graham Steel

References Wanted: Walter Jessen

Looking for http://cancerpreventionresearc... Please send to wjjessen at gmail .. thanks!

September 1 - Comment - Like - Share

Sent. - Torfinn Nome

Thank you. - Walter Jessen

Walter Jessen

Psychological Profiling Via Twitter: http://TweetPsych.com?name=wjjessen

August 31 from Twitter - Comment - Like - Share

Jackye Chan, Mr. Gunn, joergkurtwegner and 2 other people liked this

I like how it provides links to people with similar profiles - Jean-Claude Bradley

2 more comments

how about users who will provide a rousing good argument?! - Mickey Schafer

I told me I have pretty much exactly the same profile as you, Walter. - Mr. Gunn

Cool. No surprise we're socially connected then, eh? Funny though ... I don't see your profile, only see the same 5 people I was shown when I first ran the tool this morning. - Walter Jessen

Walter Jessen

Who's using Google Reader? Let me know so I can follow you there.

August 19 from Twitter - Comment - Like - Share

Daniel Swan liked this

I am! - Sandeep Gautam

7 more comments

I am. - Günther Mulder

me2 - Nils Reinton

who's not? - Paulo Nuin

Paulo, good question :) - Deepak Singh

You'd be surprised. As I'm digging through FF contacts, many don't list Google Reader. - Walter Jessen

I haven't used Reader for a long time, so have no clue at the moment how it would fit into my online agregation/presence activity. - Jan Aerts from Android

I am!! - Nikhil Kadadi

I use Google reader extensively. 90% of shared links are science related. - Kevin Z from twhirl

Neil Saunders

So, there are other lifestream applications which aggregate feeds and allow comments. Profilactic, Storytlr, to name two. Are there others? Are they any good? What would it take for you to migrate to them? Or are we all off to Facebook?

August 10 - Comment - Like - Share

chrisofspades, M F, Morton Fox and 29 other people liked this

Which ones are OpenSource? If the FriendFeed software was OpenSource, then that would be a certain guarantee for future freedom, as people would set up alternatives in no time, forcing any provider to play friendly with the users... (not implying FF is not doing that!) - Egon Willighagen

35 more comments

are we being a bit quick off the mark? do we know for sure that FF is going away? And maybe it will but take awhile and something else will come along in the mean time. Unless I have missed news that says otherwise I am not rushing into anything. - suelibrarian

It's conceivable, but unlikely, that FF will be maintained. Even just leaving the servers running takes money, staff and time. And very similar services have come (and in some cases, gone) already. I'm not rushing out of here either, but the time will come to look at other options. - Neil Saunders

I think it's safer to assume right now that FF is not going to continue in it's current form. I agree with Neil, other options need to be explored. I don't want to have to sign into Facebook (an increasingly rare event) to keep in touch with everyone here. - Daniel Swan

God no. I had nicely partitioned Facebook into being mostly for family and RL friends. Adding the "friends" I have here would just confuse the conversations such as they are. The main issues I have with FB is that the "groups" are so closed. As soon as the news from the groups are enabled into the news streams they will become more active. I mostly inhabit FB to find out what my 17yr old is up to. Increasingly she isnt on there either. - suelibrarian

It seems unlikely that FF would be maintained - particularly just for us. I'm with Sue, its less the privacy issues that bother me as the mixing of conversations that benefit from being (gently) partitioned. I don't know whether FF might consider open sourcing an earlier version of their code but I don't think anything else really has the functionality. What we do have is the community and critical mass to make it work if we can find the right place... - Cameron Neylon

Noserub is the main Open Source lifestreaming app that I know of. It is not as feature rich (e.g. no groups at the moment) nor as fast as FF, but you can follow someone's FF from a noserub installation as well as following people from other noserub installations. See http://noserub.com and http://identoo.com for an example of a public installation. - Matt Leifer

Noserub looks potentially interesting as an open source platform. Would be interested to know what people with web management expertise think of it as a tool? - Cameron Neylon

Facebook is a big NO for me. Thanks for telling alternatives, I'll surely try them all... - Marcos Marado from fftogo

The gov. agency I work for has been developing a FF-like application for a while now. See my profile at http://me.edu.au/p/nlothian. We do aim to open source it, but that's probably a way off at the moment. But if anyone is looking at trying to develop this from scratch, DM me, because I'd love to try and make something happen. - Nick Lothian

One problem with noserub is that it is ridiculously slow at the moment, especially if you are used to FriendFeed levels of performance. However, it is the closest to FF of any of the open source social media projects that I know of. Also, the federated approach is definitely something I would like to see in a future FF replacement. - Matt Leifer

Streamy. - Meg v. Meg v. 1.0.0.1

Streamy certainly has a better demo video ;) - JSNFLMNG

Hmm. Streamy looks nice but I just tested it for 10 mins, around 9 of which were spent staring at an unresponsive browser, waiting for my CPU fan to stop howling. - Neil Saunders

I was playing with http://noserub.com / http://identoo.com some month ago - I think this will be the place to be. Elgg.org might be also an alternative that I will test soon. - Konrad Förstner

I wonder if elgg is close enough that the community could make it what we want? http://elgg.org/about.php - Richard Akerman

I have installed both Elgg and noserub. Elgg is not really very close to FF because it is trying to be an all-purpose social networking engine. It is more flexible than noserub but would take quite a lot of coding to turn it into a FF clone. - Matt Leifer

Maybe AmpliFeeder? http://amplifeeder.com/index... Haven't tried it, and I think it is missing the comments part. - Endre Sebestyen

@Matt - maybe some plugins could fill the gap http://elgg.org/plugins.php - Konrad Förstner

Agree that noserub seemed unresponsive, didn't try streamy. But presumably enterprise levels of responsiveness takes enterprise level investment? Please prove me wrong, I'd be delighted. - Cameron Neylon

Are you talking about http://identoo.com? Works okay for me. The general advantage of the noserub protocol is the fact that it is decentralized so it's scalable http://noserub.com/quick-f... - Konrad Förstner

Does anyone know how many regular users FF have? - Ola

I don't think facebook will work for the kind of info sharing we have here. It would be too much noise for existing facebook friends, which tend to be more personal friends and less professional acquaintances, and the personal stuff would be too much noise for our science-focused group here. As most of you know, I am a big fan of the federated approach, but has it improved enough in usability to make it feasible if FF shut down tomorrow? - Mr. Gunn

I'd be willing to put cash into a pool to pay someone with serious web scaling credibility in this community (Matt Wood? Neil Saunders? there are people out there, I'm just not really sure who is best qualified) to assess the scalability and suitability of Noserub/Elgg or any other appropriate framework to actually work for the general research community and to cost development pathways. I'd really like a professional opinion on the options. - Cameron Neylon

I'd say Matt is your man for web scaling credibility/development from our community. Today, I find myself hopeful that FF might just be maintained "as is" and we can stop worrying, since Paul writes "I don't want to see it disappear". - Neil Saunders

I'm hoping that too, Neil, but it just seems like too much of a "buy and bury" move to me. - Mr. Gunn

I will be interested to see what happens. I've enjoyed FF, but perhaps I'm showing my age by finding the excitement over it (and the anxiety over its removal) to be a little overblown. As a Usenet veteran, I find the lack of threaded comments rather primitive; the feed aggregation is interesting and the Ajax is great, but I'd be surprised if they aren't replicated elsewhere. IMO, worries that the community will dissipate are excessive: communities rise and fall all the time. - Ian Holmes

Despite my many posts to the contrary, I'm not too concerned either :-) I like FF, I think it's a great demo of how the right technology can enable conversation within/between communities. But it's only a website. There are multiple ways to find people and information - FF is just a particularly effective one. - Neil Saunders

For me identoo is winning: it lacks "hide" to be a usable replacement, and then lot's of features that will come with time. Being opensource, we can easilly affect its roadmap even if not with code ;-) - Marcos Marado from fftogo

I believe that the FF team honestly wants to keep FF around, but it no longer matters what they want -- and what FaceBook doesn't want is another site that makes them look bad, even if they own it. FF is doomed, mark my words, doomed. Dooooomed. I'm with Cameron, I'd happily contribute to a fund to pay for a professional opinion on how to build and pay for a science-centric FF clone. If... more... - Bill Hooker

what about Google Wave? Will it be replacement of FF? - Alexey

ReadWriteWeb article on Streamy: http://www.readwriteweb.com/archive... - Walter Jessen

Nick Lothian - I'd be interesting in talking with you about what neds to be built. Cameron Neylon - I know a few things about web scaling and I would be happy to help evaluate frameworks. - Jordan M

Tons of options out there people http://lifestreamblog.com/create... Covering Lifetreaming services, scripts, and apps has been my passion for over two years. You got questions? I should have answers. - Mark Krynsky

what? no mention of Lifestream.fm?. shocking. - Avatar X

You could just add Lists to Facebook just like you do in here and add FF people into that list. - Manuel Mas

Liking that identoo at least has all the same services. - Mr. Gunn

The Life Scientists: Jan Aerts

Much of #friendfeed alternatives are about aggregating your online you. But my priority is to facilitate using peers as information filters.

August 11 - Comment - Like - Share

Benjamin Tseng, Lisa Green, Tom Walsh and 9 other people liked this

Agreed. Ego-casting is a lot less interesting than having a place to swap news and ideas with other bio-geeks... - Andrew Clegg

3 more comments

Is there a viable FriendFeed alternative? - Walter Jessen

Not yet but see http://friendfeed.com/clonefe... . But they perhaps suffer from the same mis-focus that Jan identifies. Maybe FB will take heed of all this and let it live on, you never know... - Andrew Clegg

Actually... Not pushing for yet-another-service, but wouldn't there be a business model for a service that is specifically focussed on filtering-by-peer? I know that I wouldn't mind paying some yearly subscription fee if it helps me as much as FriendFeed helps (has helped?) me. - Jan Aerts

I don't think that would work -- see experts-exchange.com in the IT world which just pollutes Google search results with answers you can only see with a subscription. And is full of idiots asking silly questions. And you can't judge the quality of the answers without paying. And has been superseded by Stack Overflow and Server Fault which are much better, and free :-) - Andrew Clegg

The Life Scientists: Walter Jessen

Looking for a list of commercially available antibodies, preferably in table format.

August 11 - Comment - Like - Share

Paul Bacchus and Mr. Gunn liked this

Antibodies in tables? :-) - Jan Aerts

Table format ... you know, a spreadsheet. As opposed to a website with pages and pages of information. - Walter Jessen

Walter, I spent some time looking for this, too. The best idea we came up with was screen-scraping http://exactantigen.com The issue with doing that is that different categories have slightly different names, like "Host" or "Species" and some are missing clonality or isotype information. Concentrations are also reported in different formats, etc, etc. It's easily doable, but would require a couple days for tweaking your script and so on. - Mr. Gunn

The Life Scientists: Jan Aerts

Has anyone tried out socialthing.com?

August 11 - Comment - Like - Share

Yep, thought it was pretty good until I got a message a few months ago saying the site was being discontinued. It still appears to work ok but the message about being shut down is still at the top of the site. - Mick Adams

2 more comments

Never got an invite :( - Colby

It's been in private beta since I started looking at lifestream apps, 1.5 - 2 years ago. Not holding my breath. - Neil Saunders

This looks interesting (albeit, a self-hosted solution): http://amplifeeder.com/ - Walter Jessen

References Wanted: Walter Jessen

Future Oncology review: Inflammation and prostate cancer, http://www.futuremedicine.com/doi... Please send to wjjessen at gmail .. thanks!

June 25 - Comment - Like - Share

no access, sorry. - Björn Brembs

8 more comments

Does anyone have access? - Walter Jessen

Not me, sorry. - Bill Hooker

Sorry, Walter. One is hit with - "You are logged into the Athens service, but you do not have permission to access this particular resource. Your session has now been terminated". - Graham Steel

Why not write to the lead author requesting an e-copy? I find that approach helpful when no one has access to an article. Most send within a week with a nice note. - Sally Church

I emailed one of my prostate cancer buddies and asked if he has access for you :) - Sally Church

sent - Torfinn Nome

Thanks Torfinn! - Walter Jessen

Torfinn, can I have a copy too please? - Sally Church

Sally; sent. - Torfinn Nome

Deepak Singh

Switched over the keynote. Most of the powerpoint import works fine enough to start from my existing decks

June 9 from Twitter - Comment - Like - Share

'Mummi' Thorisson and Walter Jessen liked this

I've done the same. Keynote is simply better that PowerPoint. I've also dumped Word for Pages. Now if only there was a good Excel replacement ... - Walter Jessen

5 more comments

Heck, I wish Excel for Mac was half as good as Excel for Windows. But Keynote ... yummmmmm - Deepak Singh

Re: Excel sub for Mac, admittedly I only rarely use a spreadsheet, but Numbers works ok for me. - tim

Tim, Numbers just doesn't have the power for the advanced stuff I need to do and neither does Excel for Mac. For all it's flaws, Excel for Windows is one good piece of software - Deepak Singh

+1 for Keynote, way better than sodding PPT - 'Mummi' Thorisson

Keynote's just good. Forget comparisons. Actually enjoying making slides - Deepak Singh

Agreed! But frustrating because of the need to export to powerpoint for some meetings. - Mark Strom

References Wanted: Walter Jessen

Could someone please send me a copy of http://www.ncbi.nlm.nih.gov/pubmed... European Journal of Human Genetics, July 2008 - wjjessen at gmail.com

June 1 - Comment - Like - Share

Sent. - Bill Hooker

Thanks Bill! - Walter Jessen

Science 2.0: Mickey Schafer

A question about Linked In -- a former student has invited me to join her LinkedIn professional network -- I know there have been discussions about Linked In, but I find myself leery of joining simply because I'm satisfied with my current on-line profile/relationships. What does it mean to be part of someone's "professional network"?

May 19 - Comment - Like - Share

Gladstone, Steve Koch, suelibrarian and 2 other people liked this

Specifically, what should I expect (if anything) in terms of new people trying to get in touch? - Mickey Schafer

18 more comments

LinkedIn is the de-facto leading professional networking (not collaboration) platform. Anyway, if you join, you might get contacted for a job, discussion, or conferences. If you do not join, you will never know what will not happen. Humans are pretty bad in predicting the unknown unknown ;-) - joergkurtwegner

LinkedIn allows you to adjust your contact settings and what types of opportunities (e.g. personal reference requests, requests to reconnect, etc.) you would like to receive. IMHO, if you join any network on the web, it should be LinkedIn. - Walter Jessen

LinkedIn is a social network that is well-established(mostly just because it was first in its area). Lots of recruiters and such use it. It's worth joining. It's also great for seeing who works where. - Mr. Gunn

Thanks much for the feedback -- it helps! - Mickey Schafer

I joined precisely for that reason - though I don't think I will ever glean much personal benefit, you don't know how your own network might help others, including former students, get that life-changing internship or job. It's pretty intuitive to set up and indeed is not bad when your colleagues or students start moving around from place to place, as you can set things to be notified (or not). - Heather

I really like LinkedIn. It's professional, no spam, a good place to keep my resume up-to-date, to keep a list of my contacts, a nice place to find 'who know who' , etc... - Pierre Lindenbaum

I hate Linkedin! It spams my address book and sends out invites repeatedly. I have whole series of "invites" that repeat, I cannot stop them, and when I contact the "sender" he or she also has no idea how to do this. Certainly it is a long-established service but I thoroughly regret joining it. (I joined it once, eventually cancelled membership, was persuaded by some at Friend Feed to... more... - Maxine

Maxine, if you want to turn off all those alerts: home -> account and settings -> receiving messages -> No Email - Pierre Lindenbaum

Maxine, I thought you might have that idea -- I found an earlier entry of yours on FF regarding LinkedIn. It's interesting to me b/c it may be a way to help students -- this particular student worked with me to start a "career" in freelance editing, which has more or less worked out for her. I will be sure to take Pierre's advice, though! - Mickey Schafer

Maxine, Mary Canady(@comprendia) is a heavy user of LinkedIn, so much that they called her on the phone about something the other day. If you like, I'll see if she can get a hold of someone for you. LinkedIn did that to me, too, but just once, not repeatedly. Sounds like something's going really wrong there. - Mr. Gunn

I've never had any trouble with LinkedIn alerts, invites etc. Until MrGunn just now, Maxine was the only person I'd heard complain. - Bill Hooker

LinkedIn is both my online resume and rolodex. It's got me at least one job, and has helped me many many times professionally. It just stays out of the way. I've used it to research people who might be interviewing me, potential candidates, collaborators, partners, etc. - Deepak Singh

Maxine, that's essentially why I hate Plaxo and refuse to use it. LinkedIn's been pretty good in those departments - Deepak Singh

Strange you mention Plaxo, because I had read about its tendencies, and was able to successfully avoid them. LinkedIn got me by re-selecting everyone on the "to invite" list when I had only selected a few, whereas I knew better than to let Plaxo get at my address book in the first place. - Mr. Gunn

I find LinkedIn fairly unobtrusive and as others have said, there are plenty of controls on what gets sent to you. I've yet to get any utility from it whatsoever but then I don't move in the US business world, which seems to be the larger part of the network. - Neil Saunders

I find linkedin pretty harmless - it's just a step or two beyond exchanging business cards. Since I don't allow work connections in my facebook and not many people have friendfeed, it gives an easy connection point. If you already have a professional blog and web presence I think it's less valuable. Probably good for students looking to establish a basic professional web presence. - Richard Akerman

Just to echo Richard, a lot of the people in my LinkedIn network are people who give me business cards at conferences, etc - Deepak Singh

Yeah, Deepak, that's pretty much what I do - look up people on linkedin after getting a business card and wanting to follow up with them later. - Mr. Gunn

Thanks for the advice- turning off "my" email alerts will not stop me getting spurious repeat invitations from "other people" who when I contact them directly about it say they have no idea LinkedIn is sending them. Why should I put in the time to control LinkedIn when I haven't made a single new contact there (plenty of people I know contact me) and have not had one single useful interaction there? Unlike Friend Feed, Nature Network, my blog etc, all of which have led to interesting new opportunities. - Maxine

Walter Jessen

Ideally, I'd like to use Yahoo Pipes (and presumably Regex) to replace the description with the pubdate. Any suggestions from a Pipes guru?

May 20 from Twitter - Comment - Like - Share

I think I'm missing the obvious here. It should be simple to replace <description>[^<]*</description> with <description/> but I'm not sure how to implement it in Yahoo Pipes. - Walter Jessen

Walter Jessen › Comments