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Pedro Beltrao › Comments

Graham Steel
POLL. As a direct result of this FF thread http://friendfeed.com/science... I've created a one question poll. The question is "Is it appropriate to raise the visibility of the References Wanted room outwith FriendFeed?". The possible answers are "yes", "no", or "unsure". I would be really grateful if subscribers to this room would participate.
Poll is here:- http://www.micropoll.com/akira... Thank you in advance. - Graham Steel
Just to expand briefly on Graham's intro: I think the RW room is covered by Fair Use (nota bene, ianal). Nonetheless, the likely result of any legal challenge by publishers would be that FF would shut the room down as a precaution, and we'd have to fight to re-open it. I doubt we have the resources for that fight, so as a matter of realpolitik I'm voting to continue to fly under the... more... - Bill Hooker
^^What Bill said. Yes, the world absolutely needs access to the scientific literature, but we need to work to reform the publishing process and the laws. All things considered, this is a very small room, which is why it hasn't attracted the ire of the publishers. If we advertise and it gets large, the industry will start playing the same whack-a-mole lawsuit game that they do with music or movie sites. - Chris Miller
I voted "No" - Pierre Lindenbaum
Please keep voting folks. A dozen in so far, thanks. - Graham Steel
The referenced thread is about a letter to the journal Cell in which we promote FriendFeed. The RW room will be the single most attractive feature for people who have never used social media. I also think it helps to show a large readership what kinds of hoops we will jump through to get access - and the RW has a great record of people not having access. So in the end, all publicity... more... - Björn Brembs
I'd love to read that Cell paper if possible! http://is.gd/5fQ0D I voted 'unsure' on the poll, perhaps not very helpful, but I thought that my 'yes' might not be as strong as the poll's yes might be demanding. I would like more people to be aware of this helpful service, but to hear of it as word of mouth rather than a 'one to many' broadcast in a journal article. I suppose I'm voting for the status quo (of this room), but with gradual increases in numbers. #fencesitting ;) - Jo Brodie
I would be more concerned about publishers cutting off access to individuals known to be supplying papers in the room for breech of TOS. It has happened to one of our researchers but for other reasons. - suelibrarian from iPhone
Here is the draft of the letter: http://etherpad.com/Microbl... Note that we do not need to spell out the name of the room in the letter, as we do now, just the functionality. I can only re-word my argument from above: cowering before the possible reprisals of 'big publishers' is definitely not the best way to change the current publishing model. In fact, anybody who... more... - Björn Brembs
I voted no. As I see it, the role of RW is to provide a service, not to instigate a revolution or provide a soapbox for change in the publishing industry. I don't think it's fair to create the potential for unpleasant repercussions through wider publicity for a "cause", certainly not without the full knowledge and agreement of everyone who has ever used the room. - Neil Saunders
@Bjoern, it's not "no big deal" to open another room -- that simply won't work, corporate copyright lawyers are quite good at whack-a-mole and we cannot expect FriendFeed to fight our Death To Toll Access battle with us. As I said above, the fight you are spoiling for is worth having, but I don't want to pick it and then get my ass kicked. If you really want people to fight, you'll need... more... - Bill Hooker
The purpose of the room is explicitly "to document the harm caused by closed/toll-access publication". What's the purpose of collecting this data if we're not going to publish it? Voted yes, apparently against the consensus, whose arguments I'm sympathetic to, but it seems to me like even if we did mention the RW room in a letter it would still only have visibility to a quite small audience. Perhaps the poll choices should have been "yes, publish the RW room/No, don't publish yet"? - Mr. Gunn
28 votes so far, with "no" currently in the lead. - Bill Hooker
What about mentioning the functionality but not the room? If we include a link to the etherpad in which the letter has been prepared, interested people would find the information. - Daniel Mietchen
A few thoughts. 1) It is possible to vote multiple times, I noticed. 2) @Neil: as Mr. Gunn pointed out, the explicit purpose of the room is to document, not to provide a service. What's the point to document, when the document remains secret? 3) @Bill: point taken. However, the mere fact of multi-billion dollar corporations (who, unlike the RIAA, make their money from tax-dollars!!)... more... - Björn Brembs
Also unlike the music industry, the three major publishers have had increasing profits for at least the last five years, with 2008 (of all years!) being a record year with double-digit growth rates for some and a total of almost 5 billion dollars in profits for the three largest corporations alone - and that when other large publishing businesses seem not to have such a great time... more... - Björn Brembs
Couple things. 1) researchers are not the only people here; publishers have shown no compunction in going after librarians. 2) in the library literature, it's fairly well-established that researchers are asking other researchers for copies of articles, rather than (sometimes in addition to) going through ILL and document-delivery services. - D0r0th34
I don't know if this has been studied, but the reasons for that, D0r0th34, have to do with the overhead. To ask a colleague, all you have to do is send them an email. ILL requires forms and accounts and waiting periods and follow-up and so on. - Mr. Gunn
yes, that's the usual reason given :) - D0r0th34
Procedural suggestion - I don't use the RW room for reasons I can go into elsewhere but I voted I don't know because I didn't. I actually take Bjorn's point though - what is the point if it doesn't change things? Anyway the suggestion - rather than people posting that they've sent stuff I suggest people post when they receive a copy. It would even be possible to set up a dead letter... more... - Cameron Neylon
I am behind Bjørn on this, I voted yes and at the time the yes -side was winning. In my opinion, this is a fight worth taking and if that happens, worth loosing. - Nils Reinton
+1 Neil and +1 Cameron. A simple change in the etiquette of the room would protect those sending papers from liability. To fully protect them, though, you'd also have to scrub the archives, something that isn't easy to do on the internet. - Chris Miller
Changing the etiquette in that way is a tacit admission that we are doing something wrong, OR that we are doing something we don't believe is either wrong or illegal but that we fully expect we could be punished for anyway (because the system is unjust). If we are going to fight the good fight as above, we would be better off not handing our opponents the opportunity to argue for the... more... - Bill Hooker
I'll admit to not following the 'fair use' argument very closely, but I'm under the impression that sharing such articles is a clear violation of an institution's TOS with the publisher. I'll readily agree that something can be just but illegal, but that doesn't change the fact that there could be repercussions against those providing articles. Every movement needs its zealots, but I'm more of a casual supporter, and certainly am not willing to go down for the cause. I suspect there are many others like me. - Chris Miller
Chris, it does appear that our use of References Wanted falls under fair use as I figure it: http://www.utsystem.edu/OGC... - Mr. Gunn
Yes, I also think it is fair use, though I am aware that just the suspicion of this not being the case may be enough to shut down the room. Besides, we have Harvard law professor Lawrence Lessig on our sides: http://ff.im/9xiRN . - Daniel Mietchen
Chris's point is a good one - fair use is one thing but its definitely a technical violation of most TOS. On the other hand its not clear that library users sign up to the TOS, the librarians do, which takes us back to Dorothea's point. I take Bill's point though. If you think its a fight worth fighting then it should be done out in the open. The question is both strategic and tactical.... more... - Cameron Neylon
A very kind person sent me a copy of the letter to Cell - unfortunately it was picked up by my mail system's quarantine and instead of rerouteing it safely to my inbox I have to admit I pressed the wrong button and deleted it. Might I trouble them to resend it to me? http://is.gd/5fQ0D <embarassed> - Jo Brodie
Given that you can vote multiple times and only 40 votes have been cast, does that mean that about 75% of the subscribers to this room don't care enough to vote? - Björn Brembs
well, you have to figure on some attention attrition, there -- I have a lot of FFeeps who don't seem to actually use the service - D0r0th34
Jo, in case it wasn't clear -- that link from Bjoern goes to the Cell letter. - Bill Hooker
@Björn, that was only the second online poll that I've created and realised shortly after creating it that there _might_ be a potential issue with multiple votes. Can't drill the stats so will have to work on trust. Many of the subscribers to RW don't frequent that often in terms of posting, so I think it's unlikely that the "n" of 40 on the poll is likely to increase much further than as it stands. Moving forward, I guess we'll have to rely on the stats of 57% no 30% yes and 13% unsure. - Graham Steel
Sorry for just posting the link, was in a hurry! - Björn Brembs
@Graham: The question now is, what do we do with the poll? I don't think it really tells us all that much. Moreover, I think none of the arguments for publishing have seen any serious refutation. On the other hand, I don't want to dismiss the counter arguments completely. I suggest we go ahead and describe the functionality without mentioning the room name, even though I think it would be much more effective to mention it explicitly. Any comments/suggestions? - Björn Brembs
I for one agree with that suggestion. What do others think... - Graham Steel
I voted to mention the name but since the majority of votes are against I think Bjorn s suggestion is a good balance. - Pedro Beltrao
+1 Pedro - Nils Reinton
Presumably the letter's authors will give links to their FF accounts, then it's just a matter of scrolling through their posts until, aha!, "Refs Wanted" must be the room they were talking about. So is there really much difference between describing and naming the room? - Bill Hooker
@Bill: You're right, of course, in that it is more a token of appreciation of the other arguments than an effective step towards concealing the room. Alas, it is the only 'middle ground' I could think of. - Björn Brembs
Thank you Björn and Bill :) - Jo Brodie
Iddo Friedberg
Wow, that's really weird. - Ruchira S. Datta
yeah ... I never thought about fake structures. I wonder how exactly was fake about them. - Pedro Beltrao
Built a plausible homology model and shake a bit I would guess...you know of course what will happen now when we discover someone has faked genomics/proteomics data? Omics-gate! The two most overused cliches in media and science finally united together! - Cameron Neylon
Wow. Here's a link to an Evernote summary of the structure pages on Pub Med. I think I did all of them: http://www.evernote.com/pub... - Steve Koch
thanks Steve .. at quick glance the common name seams to be last author in many of the papers ... that is even weirder. - Pedro Beltrao
A posting Kevin Karplus to the pdb-l (possibly) expanding the list to 1bgx 1ay1 1hef 1heg 1sbg 1hps 1hos. Also, it seems that RosettaHoles which assesses core packing did not like 1bgx (it's in the RosettaHoles paper, linked from Kevin's posting. https://lists.sdsc.edu/piperma... - Iddo Friedberg
From the RosettaHole paper (published online 2-DEC-2008): "Eight of the outliers, (checking for anomalous core packing, IF) (PDB codes 2A01, 1BEF, 1RID, 1Y8E, 1BGX, 1G44, 2QID, 1G40) are from the Murthy group.[9]" - Iddo Friedberg
What is strangest to me about this story is how did a supervisor get all the other authors to go with the fake results ? - Pedro Beltrao
Oliver Hofmann
Anyone attending the RECOMB Satellite meeting (http://compbio.mit.edu/recombs...) next week?
Yay. RECOMB wants to follow the ISMB/ISCB model from this year. Guess I'll need help. - Oliver Hofmann
Regulatory genomics track about to begin - Oliver Hofmann
thanks - Pedro Beltrao
Going to be.. interesting. Very, very fast talks. Still trying to recruit folks to help :) - Oliver Hofmann
Using Cameron's 'blogging permitted' slides and a simple sign at the podium that says 'blogging' or 'no blogging'. So far no speaker declined coverage - Oliver Hofmann
Morning session, chaired by Ron Shamir, actually starts on time :) - Oliver Hofmann
Meeting is completely booked out. And this is supposed to be Winter in Boston: http://compbio.mit.edu/recombs... - Oliver Hofmann
First batch of full length papers coming online, more tomorrow and Monday: http://compbio.mit.edu/recombs... - Oliver Hofmann
Next up: Systems Biology track - Oliver Hofmann
First synthetic biology talk I've actually been convinced by (Jef D Boeke on Yeast 2.0) - Oliver Hofmann
Oliver do you mean there are physical versions of the signs that people can choose from? If so could you take a picture? - Cameron Neylon from Android
@Cameron, sorry, no -- I just grabbed your slides, added them to the blogging announcement slide that is on rotation during breaks, and made them available to presenters. The physical sign is just a big green/red cardboard that says blogging/no blogging. I'll try the physical signs next time :) - Oliver Hofmann
That's still very cool. Well done on raising visibility of the issue! - Cameron Neylon from Android
@Cameron: the iPhone version at http://www.flickr.com/photos... - Oliver Hofmann
Cool - have you got any interesting responses to it? I would guess its probably a pretty open community in that regard at least. - Cameron Neylon
Manolis (Kellis) keeps advertising. Lots of good feedback, particular from folks stuck in the lab while their PIs are downstairs attending the talks ;) So far not a single person has declined coverage despite lots and lots of unpublished results - Oliver Hofmann
That's really good to hear! Some sectors aren't so precious as others - Cameron Neylon
First two groups making use of the 'no blogging' side of the sign. About time, I needed a break :) - Oliver Hofmann
Thanks for all the great coverage, it must be exhausting all by yourself! - Ruchira S. Datta
@Ruchira, thanks! Lots of fun, though, and getting good feedback even at the conference. Well worth it. - Oliver Hofmann
What not to do: be in the process of starting a new lab, giving a neat talk, looking for great postdocs.. and asking for the talk not to be blogged. - Oliver Hofmann
Aaand that's it. Instant feedback on a survey taken by 200+ participants: http://compbio.mit.edu/recombs... - Oliver Hofmann
(never seen that high of a feedback rate on a survey, seems everyone is indeed very interested in this Satellite) - Oliver Hofmann
Too much biology: correlated with CS background. To much CS? Yep, those were the biologists :) - Oliver Hofmann
That's among the most positive conference feedback I've seen in a long time I have to say. - Cameron Neylon
Oliver Hofmann
Mandatory group picture
RecombSat2009GroupMid.jpg
looks like a good size for a meeting - Pedro Beltrao
Pedro Beltrao
Warren L. DeLano 21 June 1972-3 November 2009 : Article : Nature Structural & Molecular Biology - http://www.nature.com/nsmb...
Warren L. DeLano 21 June 1972-3 November 2009 : Article : Nature Structural & Molecular Biology
"Warren L. DeLano 21 June 1972–3 November 2009" - Pedro Beltrao from Bookmarklet
Michael Kuhn
If I have my story right I think this came out of a criticism from a review panel that the structures and computational bio department was not collaborating enough. They came up with the mycoplasma collaboration that Luis Serrano in particular was very excited about. 3 science papers is not a bad way to show results :). I still have to read them. - Pedro Beltrao
News and Views at MSB: http://www.nature.com/msb... - Pedro Beltrao
Editor's choice at Science Signalling http://stke.sciencemag.org/cgi... - Pedro Beltrao
Bruno Afonso
Pubmed returns 1721 reviews for "Synthetic Biology". Just sayin'
lol ... the field with more reviews than actual research papers :) - Pedro Beltrao
this could be a good measure of hype reviews/research papers - Pedro Beltrao
We could have a hype factor per field/keyword/buzzword :-) - Bruno Afonso
Pedro Beltrao
Cloud computing, circa 1965 - http://www.roughtype.com/archive...
Check also the video link in the comments where a guy connects to wikipedia with a 1964 modem. - Pedro Beltrao
Cameron Neylon
Does anybody know if any of the "dropbox like" online storage services provide an RSS feed for public folders?
Dropbox does, and Mendeley Web does as well. I don't use any other services, so don't know about others. - Mr. Gunn
does dropbox? Haven't been able to find it... - Cameron Neylon
You get a feed from folders you're sharing. Not actually public, I guess. - Mr. Gunn
No, not quite what I want. I'm looking to lash up something quickly where I drop a data file into a folder and then have it immediately available to link into from Wave or similar, so what I want is a public RSS feed off that public folder. Ideally without having to write anything or cheat by knowing what the names are in advance or something like that. - Cameron Neylon
And you'd like it to be any filetype? - Mr. Gunn
Ideally, but for the purpose of a demo I can live with something simpler. Text would be fine for demo. - Cameron Neylon
Mendeley provides a public collection feed, but you'll get citation details and stuff, not just filenames. Hmm..let me think for a sec.. - Mr. Gunn
I think box.net might have something like this. I remember Lars was sharing box.net files in his blog at some point. - Pedro Beltrao
You could try http://drop.io/ it does have RSS for your drop content. But in this case the whole drop would be the "public folder", I think you can't create a folder within a drop and only get the RSS from it. - Bruno C. Vellutini
ah cool, that's fine - public is good for a simple demo, I'll check out box.net and drop.io tomorrow. Thanks! - Cameron Neylon
Proposed this as a feature for DropBox. Feel free to vote up the item titled: "Public RSS feed for the public folder" :-) - Cameron Neylon
Evernote feed for public folders worked well for me (very basic use). Maybe with pay version of evernote, you can embed files? Or maybe with free version even and limited bandwidth? I've had a good vibe from endnote for these kinds of things, but haven't tried much out. - Steve Koch
PS: Here is a feed for my test public notebook: http://www.evernote.com/shard... - Steve Koch
Update thus far: The feed given in dropbox does work if you remove the https from a separate account. Box.net has functionality which is very close to what want but the RSS feed points at the secure version of the file...haven't checked out drop.io yet. mmmm Evernote - I can see Steve's notes and images from links in the rss...will look closer - Cameron Neylon
Drop.io seems the best long term option as it has a proper API but that would require writing something...guess I should check it out anyway. - Cameron Neylon
Text Savvy
E-mail is jaydamion@gmail.com - Text Savvy
no access. :-( - Björn Brembs
on the way - Pedro Beltrao
Much appreciated! - Text Savvy
Pierre Lindenbaum
This might look interesting in 5 years or so - Pedro Beltrao
Michael Barton
Visa, viva, vici! I've got my visa and just passed my viva.
congratulations! - Simon Cockell
Thanks everyone. I'm in the pub making the moat of it. Being mocked for going online too. - Michael Barton from iPod
Drinks all around ;) - Pedro Beltrao
@Michael Congratulations! - Duncan Hull
Congratulations^2! - Bill Hooker
Congratulations - Frank from iPhone
Congratulations Michael ! - Pierre Lindenbaum
What they all said. So where are you off to and to do what? - Neil Saunders
Congratulations! All the best! - Ricardo Vidal
Thank you everyone, was nice to read this morning. - Michael Barton
electronic congrats as well... - Max
Pedro Beltrao
The genome of the cucumber, Cucumis sativus L. - http://www.nature.com/ng...
the genome we have all been waiting for :) - Pedro Beltrao
Michael Kuhn
Not sure how to describe this brilliant answer on StackOverflow on parsing HTML w/ regex - http://stackoverflow.com/questio...
Superb - Rajarshi Guha
very good :) - Pedro Beltrao
fidel ramirez
Last week: One paper accepted and a new grade in Aikido. Now I need to get a hakama.
are these connected ? did you pay a visitor to the editor ? ;) - Pedro Beltrao
Mickey Schafer
A tech question -- is anyone using web-based file storage? If so, what company would you recommend as host?
What do you want to store? Bits and bobs or lots of stuff? I use google doc for bits and prices dropbox is useful as it has an iPhone app. - Jo Badge from iPod
How big of files are you thinking about? - Holly Rae, FFer
Hell yes. For me, photos -> flickr, audio -> divshare, video -> youtube/vimeo, PDF's -> Mendeley/scribd and google docs for various other bits 'n bobs. - Graham Steel
SlideShare, SciVee (vids), Scribd (pdfs), Flickr, YouTube, lots of GoogleDocs and Wikispaces will take up to 10Meg misc files - Jean-Claude Bradley
favorites are dropbox (good file sync) box.net (webdav standard support) drop.io (quick, easy) and wuala (free limit is high). specialized storage by file type such as flickr for images or gdocs for docs is also a good option, and there are some utilities that can help synchronize with these services - Mike Chelen
Google docs for documents, Mozy for backup, dropbox for sync across computers - Pedro Beltrao
Junlgedisk for archival, dropbox for "hot" content. - Deepak Singh from iPhone
Jungle disk for big files, documents etc. I also use google docs and dropbox for convenience. - ashish
Ooh - dropbox seems rather handy. Thanks. On Desktop now..... - Graham Steel
Any specific suggestions for podcasts/sharing? - Allan Besselink
I use ADrive for pretty much everything. If sharing, will host things on Slideshare, Scribd, Flickr, YouTube, etc. But if it is just for me ... ADrive. Free accounts get something like 50 GB. Podcasts get hosted with Archive.org. - Miss Elle
Allan, I use vanilla S3 for all my podcasts in combination with Cloudfront for edge delivery. - Deepak Singh
Dropbox for a collaborative document share. Wiggio.com for inter-institutional share and collaboration tool. I belong to a group that uses a pogoplug, too, which has been a boon (the trick is where to host it). - Jason Miller
JungleDisk on the Mac - off-site backups of docs + family photos - 'Mummi' Thorisson
Also a Jungle Disk user -- have a workgroup account with all partners and customers having partitions. Use it for backup, transfer of large files (audio, video, lesson packages) to and from internal people and customers. - Brian Sullivan
Dropbox for keeping the contents of a directory sync'd across computers & sharing private pics, Flickr for public pics, slideshare from PPTs and Mendeley for docs. - Mr. Gunn
Thanks so much! Here's a link (though most of you don't need it:-)) that reviews some of these products: http://www.consumersearch.com/online-... -- For me, I am looking to back up everything on 3 computers at home. "Kids" computer used to be mine, and has all the family photos on it -- just 2005 is in excess of 4GB (or so says the flash drive which is full). It seems as... more... - Mickey Schafer
mediafire - ffcode
thanks Mickey you had a good subscriptions list, subscribed to a few of the active folks - ffcode
Miss Elle: ADrive looks kind of cool, FTP can come in handy - Mike Chelen
Mickey: if there is 4gb this year, how much data is there in total? it may be worthwhile to also keep local backups, since 8gb or 16gb memory sticks only cost $20-$30, and external hard disk drives are coming down in price too - Mike Chelen
Mickey - From what it sounds like you want to do, a pogoplug (hardware) might be really great for you. http://www.pogoplug.com - Jason Miller
Thanks, Mike -- that's basically what I was thinking. Maybe a larger GB flash drive for each year, but a combo of external hard drive and online back up for everything. The kids' computer needs ghosting...I'll be able to get Windows 7 for about $12.00 in a few weeks (faculty price) and will likely use it to restore that computer to better functioning. - Mickey Schafer from email
Jason, what a totally cool device! - Mickey Schafer from email
For those who'd still like to explore, the suggestions made here are at http://delicious.com/msscha... -- features to look for seem to be amount of free space (ranges from 1GB to 50GB), share features, file syncing (only a couple do that), upgrade service cost (in all, much less expensive than I expected), mobile apps, and whether there's a desktop component (I don't get this... more... - Mickey Schafer
it is a mistake to keep you personal dta on servers on web first it is very difficult to delete that data and other there is a possibility that data can be stolen - ffcode
@Jason is there a pogo plug available in UK? - Anna Croft
@AnnaCroft - Not sure. Id' poke around on their site to see. On it, I saw what looked like a portal to twitter, and I saw some German tweets. That would make me hopeful that the product is available outside the US. Please post what you find out. - Jason Miller
Anna -- I've also seen French tweets -- here's the product spec page: http://www.pogoplug.com/meet... -- voltage specs are "Power requirements: 100-240V, 50/60HZ" -- the rest relates to OS, internet, browsers, etc so should cross the ocean just fine. - Mickey Schafer
@Jason/Mickey ace - although I'll probably wait until next year to get one, when I'm in the US ... Update: just read on one of the websites that it will ship to Europe in 2010 ... http://www.pogoplugged.com/forum... - Anna Croft
ffcode: it's important to keep multiple backups on local and remote systems, as well as on several company's servers if possible. a good backup service should include client-side encryption (wuala does for example) and if not then it is worthwhile for users to learn how encrypt data themselves - Mike Chelen
Jason: does pogo plug have much built-in storage or is it best to attach an external drive as well? - Mike Chelen
Mickey: flash drives are great for portability, still external hard disks are the best value for the size, for example 500gb for $100 http://www.newegg.com/Product... though online copies are important since a single drive could get lost or damaged at any time - Mike Chelen
Neil Saunders
Hmm. CiteULike user survey rather suggests plans for targeted ads from scientific suppliers.
That would be fine by me and it makes a lot of sense. - Pedro Beltrao
I don't mind (I have AdBlock!). But they phrased the question in a rather underhand way - "help support CiteULike" - when the survey had nothing to do with the CiteULike user experience and everything to do with "what do you buy for the lab and from whom". - Neil Saunders
On the CiteULike forums I explain WHY it helps citeulike. My colleague is writing a more detailed post as I type... - Fergus Gallagher
Bosco Ho
The bioinformatic-journal/software hydrid - http://boscoh.com/protein...
Yes, yes. Very much like. - Neil Saunders
Bosco, this is a superb idea. Along with starting up a new journal/software hybrid, it will be great if existing journals insist users to submit source code, executable or VM of a bioinformatics software / database / server to a centralized repository like 'biohub.org'. - Khader Shameer
This is a good idea. - Michael Barton
While not linked to an actual repository (but rather, provides a snapshot of the s/w and data for the article), Journal of Statistical Software, does pretty much this - Rajarshi Guha
I would take this further and the article text remains in the revision repo. The reviewers are sent to the article, not the other way around and it can be forked in just the same way the software can - Frank from iPhone
@Frank, this makes sense, since otherwise the paper would be static and refer to old versions. But then this assumes that as the s/w is updated, so is the paper - Rajarshi Guha
@Rajarshi not neccessarily the paper should state which version/revision it refers to. It does not have to keep up with the sw. That is what documentation is for :) - Frank from iPhone
me likey too - Deepak Singh
The more I think about it, the more I think some big-wig bioinformaticians should do a deal with Google Code to edit a journal. That might even align with Google Scholar. - Bosco Ho
@Frank, in that case, why bother with a VCS? Why not just put a tarball with the source code for the version that goes with the paper? - Rajarshi Guha
Great idea, but I can't see it working for data sets. Yes data sets evolve and should track provenance somehow, but having been in and around standards groups for some time now, this is an impossible task for a publishing group to take care of, especially considering the nature of big-data bioinformatics. Plus if goes against best practices for software source control (use factories, don't store your database...) - delagoya
There are some interesting and non-trivial questions around this kind of idea as to what peer review should look like. Should such a journal provide virtualisation environments so that the code can be run? Example data should be a requirement presumably? Are peer reviewers expected to evaluate code "quality". Anyone thoughts on this would be extremely useful...and help guide a project like this into reality. - Cameron Neylon
My answers to Cameron's points: (1) no, (2) yes, sample data would probably be used to run tests which should pass, (3) quality is somewhat subjective - minimum requirement should be that code runs and generates output as expected - but reviewers could certainly suggest code improvement where appropriate. - Neil Saunders
So if the answer to 1) is no, does that mean that you can't necessarily expect referees to actually run the code? Or compile it? Or just that you pick referees appropriately? Or conversely that "refereeing" becomes a process of building up enough positive comments or karma points in the repository...? It seems to me that you want to bring the best of versioning systems and best practice... more... - Cameron Neylon
Referees should certainly be able to run code - I'm just not sure that virtualisation through the web interface is the way to do it. Seems like an additional layer of complexity that might get in the way of making this idea work. - Neil Saunders
@Cameron & Neil: If it could be figured out how to to handle the virtualization (or having remote access to machines), I think that'd be a highly valuable addition to peer review. Easy for me to say (not knowing how to implement it), but I think it's a great goal to strive for. It doesn't seem too crazy to have the journal have a bunch of machines on hand so the authors can remotely upload / install code and referees could then remotely log in to look at and try out code. - Steve Koch
I can't figure out where to jump into this thread. Personally, I think we just need a place to publish locations, i.e. the code is here, data is there and this is the version we used, etc. That must be maintained and being able to maintain that should become part of the funding process. Since funding agencies are the ones who are funding this research they need to include the ability to... more... - Deepak Singh
My feeling is that being able to run the programs somewhere on a server without downloading them is important - but that is very much a user's perspective. I often look at useful things that are made available and just have no clue how to actually make them work. A good range of downloadable executables would probably do the job for me though. Additional question: what are the standards for web services? - Cameron Neylon
Which is why VM's and cloud services are such a big deal for demo's and provenance now. You can package up a VM with the exact stack that you want and make it available, either as a service or a VM you can launch yourself. It's too easy not to do it - Deepak Singh
@Deepak : Cloud + VM is an an interesting combination, but should have an accessible pricing that is affordable to a larger research community - Khader Shameer
I think there should be strict guidelines while reviewing bioinformatics software / database / servers to test the resource. I had a recent experience : a reviewer wrote extensive list of points to reject a server that we developed with out trying what exactly it is doing or to know how does it differs from other existing resources. I strongly support the hybrid journal model, also it... more... - Khader Shameer
Let's talk specifics. VM images are great, but you are tying your release to a particular release of a particular platform. A better approach is to start from a base OS (like a linus distro ISO) and have a set of build instructions for system set up and application building. My favorite of the moment would be Chef. - delagoya
Second, academics love to solve a problem with a novel algorithm and then move on. In fact it is in their best interest to move on after milking a project for all it's worth, publication wise. Maintenance, or even robust testing (couch... Tophat ... cough ... Bowtie .. cough ) is not even on the radar. Frankly I am not so sure it should be. Maintenance requirements may slow the pace of... more... - delagoya
@delagoya, good point. If I have made significant improvements, why update the old paper? better to try for a new paper! - Rajarshi Guha
delagoya, chef's fine too. Find a common medium/mechanism that works for the community. The resources are certainly there. It's a matter of trying things out. As someone I know says, start simple, and iterate - Deepak Singh
Khader, that's where the funding agencies come in. They need to provide mechanisms for sustainable funding here. - Deepak Singh
The nice thing about a hybrid journal is that it might be possible to have new dois/database entries for "significant" updates. Not perhaps just place holding papers as is the case sometimes in the NAR database issue but when something has changed significantly you can get a new paper without needing a new algorithm or service. I like the idea of funding to support "orphan" code and services as well. Make it worth money and people will do it. - Cameron Neylon
Delagoya - as a naive user I disagree. I really don't want to have to build, I want to use in the lowest stress way possible and a hosted VM seems like a good way to enable that - as well as allow for longer term preservation. We may not be able to run linux on future hardware but will probably be able to handle VMs for longer (actually having written that I'm not sure its true - would be interested in more expert perspectives) - Cameron Neylon
I almost missed this discussion. I really like the idea but I wonder how discovery type projects fit in. I mostly use code to look for trends. If anything I might make some predictor to enhance existing data. For these reasons most of what I do is one off scripts around perl and R. Maybe this sort of project does not belong in a bioinformatics journal at all. - Pedro Beltrao
Pedro, great question. Personally, if we included all glue code, small scripts, etc this would be unsustainable and defeat the purpose of peer review as well - Deepak Singh
@Pedro, I don't see a journal/software hybrid as replacing all bioinformatics journals. I think there's a place for journals that discuss pure algorithms and ideas. These would do exploratory type programming. Normal journals service these papers quite well. For me, a hybrid model targets specifically those papers that describe a program that is meant to be used by other people. In that... more... - Bosco Ho
Bosco, you're thinking along the lines of a communications journal aren't you. And then people can go to work on the code if it is on github or something - Deepak Singh
@Deepak. Yep. The disconnect I see is that pragmatically, it's the open-source project that counts. The article in the bioinformatics journal is so that we can get a place-holder to collect citations that contribute to our academic CV. The journal/software hybrid provides the most efficient way to this goal. - Bosco Ho
Very nicely summary of the problem. Really, the whole concept of a journal article about software is stupid. What does an academic article do? Alert people to a new finding/discovery. But in the case of software - well, the software is the finding. And people are "alerted" by finding it on the web, downloading it and using it. As Bosco says, the sole role of an article here is a CV tick - hence the hybrid approach. Non-academic programmers must find all of this very odd. - Neil Saunders
Michael Nielsen
Rough Type: Nicholas Carr's Blog: Does my tweet look fat? - http://www.roughtype.com/archive...
"...it becomes kind of annoying when somebody actually uses the full 140 characters. Jeez, I'm going to skip that tweet. It's too long. The same thing has happened, of course, with texting. Who sends a 160-character text? A 160-character text would feel downright Homeric. And that's what a 140-character tweet is starting to feel like, too. I think our alphabetic system of writing may be doomed. It doesn't work well with realtime communication. That's why people are forced to use all sorts of abbreviations and symbols - the alphabet's just too damn slow. In the end, I bet we move back to a purely hieroglyphic system of writing, with the number of available symbols limited to what can fit onto a smartphone keypad. Honestly, I think that communicating effectively in realtime requires no more than 25 or 30 units of meaning. " - Michael Nielsen
Holy crap, can others on twitter corroborate this? My immediate reaction: Nick Carr has jumped the shark. - Kartik Agaram
Kartik - He has tongue firmly in cheek, but beneath it there's an interesting point, I think - that's Carr's style. (I rarely agree with him, but usually find him interesting.) And since you ask: no, 140/160 characters certainly isn't feeling spacious, at least to me! - Michael Nielsen
I also rarely agree with his viewpoints on .. lets call it web culture, but I like the way he writes and it helps me to put some of these changes in perspective. Even if the tweet length trend is not true I think the move from blogging to microblogging is very real in general. At least for me I tend to blog a lot less and discuss things on friendfeed instead. - Pedro Beltrao
Agreed, it's more about the shift to microblogging. My attention span has dropped off in recent years but if my response to 140 characters were "tl;dr", I think I'd just quit reading anything :-) - Neil Saunders
tl;dr :-P - Bill Hooker
I think I'm actually quite good at hitting 140 right on the nose. - Mr. Gunn
:-) I believe a 140-character tweet is called a "twoosh". Is that worth knowing? I don't know. - Neil Saunders
Michael: Hmm, I've been following roughtype for a while, can't remember a tongue-in-cheek Carr. But it does fit with his 'making us dumber' schtick. I guess this takes on renewed relevance: http://blog.inklingmarkets.com/2009.... He had sure me :) - Kartik Agaram
I read a lot of Carr as being slightly tongue-in-cheek. And sometimes not even slightly - this was hilariously over the top (check out the second and third comments also): http://www.roughtype.com/archive... - Michael Nielsen
Touche. I guess I haven't been following him as well as I thought if I missed that. My feedreader is *so* broken.. - Kartik Agaram
Neil Saunders
STITCH 2: an interaction network database for small molecules and proteins - http://www.citeulike.org/user...
Nucl. Acids Res. (6 November 2009), gkp937. Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. 10.1093/nar/gkp937 Michael Kuhn, Damian Szklarczyk, Andrea Franceschini,... - Neil Saunders
I didn't expect the paper to come out this quickly, I was quite surprised to see it in my feed reader on the weekend. I have now activated STITCH 2 as public website ... hope it's not too buggy :) - Michael Kuhn
this looks like it could be quite useful for our cheminfo retrieval class - I added it to our resources and will let you know if any students make use of it for their term projects http://getcheminfo.wikispaces.com/resourc... - Jean-Claude Bradley
umm .. you are going to make me re-do some work :p - Pedro Beltrao
@Michael - quick questions: I don't think I ever saw homology evidences in the drug-gene interactions. Do you guys avoid doing this or it is just not reported in the evidence info ? - Pedro Beltrao
Congrats Michael! - Ruchira S. Datta
@Pedro: going from STITCH 1 to 2 will change the identifiers of proteins and chemicals, so check first if you run into trouble there - Michael Kuhn
re transfer: if you are in human or mouse, you probably won't see so much transfer. but if you go to e.g. chimp, you'll see a lot of transferred evidence - Michael Kuhn
Thomas Lemberger
Direct cell reprogramming is a stochastic process amenable to acceleration - http://www.nature.com/nature...
Alexander van Oudenaarden keeps looking for randomness everywhere :) - Pedro Beltrao
Jo Badge
Anyone using using social referencing for journal clubs? - http://twitter.com/actuala...
Alex is : Exploring social referencing apps to deliver training about using them for an online journal club. Anyone used them for this purpose? - Jo Badge from Bookmarklet
I was pretty sure someone on here would have done this before - anyone? - Jo Badge
Well, we're going to do it via CiteULike next term... - AJCann
I'm thinking of using Mendeley to store the docs and google mailing lists to host and manage the discussions.... I'm not sure I can work with the built in "notes" section in Mendeley or CiteUlike etc.... - Alex (ActualAl)
I wish something like this would exist: http://bjoern.brembs.net/comment... - Björn Brembs
Alex, did you know you can also annotate PDFs within Mendeley and share the annotated versions (full text) with a limited group? - Mr. Gunn
@ Mr. Gunn: Can everyone in the limited group edit the same doc simultaneously? - Steve Koch
Steve, version control and conflict resolution for concurrent editing is under development. The dev preview (0.9.5 http://www.mendeley.com/downloa... release notes http://www.mendeley.com/release...) has some of these features like conflict resolution already. I haven't tried that feature out, but if you want to give it a go, I'll mark up a couple docs with you. - Mr. Gunn
You can also have a shared reference list in Zotero and pipe the RSS feed to a Friendfeed group for discussion. - Pedro Beltrao
Pedro Beltrao
lazyweb: what is the best (free) set up to try out ligand docking in large scale. Any recent good reviews on the methods ?
I am going to try autodock. Anyone here on friendfeed has a better suggestion ? - Pedro Beltrao
Autodock would be my recommendation as well unless there is something new out there that I haven't tracked. - Deepak Singh
Autodock seems to be widely-used and well-regarded. Could also try zdock - more lightweight and good for command-line scripting, parsing. - Neil Saunders
zdock is more protein-protein centric. Did they add small molecule stuff? - Deepak Singh from IM
Ah, that's true. Haven't used it in a while. Autodock would be better for ligands. - Neil Saunders
wondering how difficult it would be to integrate #autodock into #bioclipse or with the #cdk ... - Egon Willighagen
can Autodock actually be scripted from the command line? Or am I restricted to using their GUI to create input files? - Egon Willighagen
I believe they had developed a python based framework - Deepak Singh from IM
they have command line tools but I am still wrapping my head around the basics - Pedro Beltrao
FRED (not Open Source) is very easy to use, but maybe not as accurate as others. If accuracy is the goal it seems that Glide does a good job. - Rajarshi Guha
Glide is definitely state of the art. The one thing about docking though is no one tool is good enough. Pretty much every company I know that does a lot of virtual screening uses two tools - Deepak Singh from IM
Thanks for the suggestions. Does anyone know if Glide free for academics ? - Pedro Beltrao
Pedro Beltrao
Edgetic perturbation models of human inherited disorders - http://www.citeulike.org/user...
from the people that brought you "party" and "date" hubs .. we have now "edgetic" - Pedro Beltrao
Pedro Beltrao
DRYGIN: a database of quantitative genetic interaction networks in yeast. - http://www.ncbi.nlm.nih.gov/entrez...
umm .. everything is password protected. Not a very useful database if you cant actually use it. - Pedro Beltrao
they might have been aiming for January 2010, when the NAR db issue officially comes out - Michael Kuhn
It makes sense, since the data they have on this database is part of paper that Boone talked about and that I assume is currently under review. Still .. annoying :) - Pedro Beltrao
yep, I just got the email response back. They will remove the password protection when the other paper describing the data is published. Bummer :) - Pedro Beltrao
Pierre Lindenbaum
RT @pansapiens Nodalpoint is dead !! http://www.nodalpoint.org/ ... Long live NodalPoint !! http://archive.nodalpoint.org/
but what is the "something new" :-) - Neil Saunders
I am glad it was archived :) ahh the good old days - Pedro Beltrao
Where many of us started, really. And then to personal blogs and now, microblogs ;-) - Neil Saunders
Alexey
NPG shut down Nature Reports Stem Cells and blog "the Niche". Not sustainable business-model for publisher? Analytical professional content can not be for free? So sad that the excellent idea died. http://blogs.nature.com/reports...
Nature really gone bad! I'm pissed off. Instead of acquiring tons of small useless journals they should realize the real thing - online community and its impact. It was under-under-underestimated. - Alexey
It would be very interesting to find out what criteria were used by the NPG to evaluate "Nature Reports Stem Cells" and "the Niche". Not enough visitors? If so, how many visitors would be enough? - Jim Till
You can make a comment at The Niche blog if you have any questions for the editors. (Go to link above). - Maxine
I did make a comment at "the Niche". The comment has been posted, but, so far, no response. - Jim Till
Monya Baker and Natalie DeWitt commented, in their final post to "the Niche", that they "are sad". So, I suspect that the decision was a business one. Other blogs will need to fill the gap left by the closing down of this high-quality contribution to the stem cell field. - Jim Till
Here is a link to another frindfeed thread about this (http://ff.im/ajDua). As I mentioned there I think this was an interesting experiment in online community building. It had the things I though were important to stimulate user participation but users were not really participating. I wish they had a bit more detailed explanation about this closing down. Particularly about the numbers of users reading/participating on the site over time. - Pedro Beltrao
commenting section under the final Niche post is updated http://blogs.nature.com/reports... @Jim - I'm sure that decision was a business one. I suspect based on budget NPG decide to cut off something. Of course it was freely available online resource - it doesn't make money. @Pedro it was great experiment which actually reach the... more... - Alexey
for a sec I was thinking about the option that a community (like us) could continue&maintain NRSC & the Niche in a freely rebranded way...here's a post I made for the Niche back in 2007 http://blogs.nature.com/reports... - Attila Csordas
It was great Attila! Other "members of community" also participated in making of Niche - http://blogs.nature.com/reports... or NRSC - http://www.nature.com/stemcel... Professors and freelancers wrote for NRSC, but not only NPG journalists. So it was made by community and for community finally. - Alexey
I wrote the necrology - http://hematopoiesis.info/2009... - Alexey
HI Everyone, It would be really amazing to see the community pick this up. You might be able to do this through Nature Network. I can make some introductions for you if there's interest. (Though I think you likely know the relevant players already). Thanks so much for your enthusiasm. Monya - Monya Baker
If one searches, using the key words "stem cell", for all of the Forums currently using Nature Network, 13 Forums match these key words. None of these Forums appears to be very active. See: http://network.nature.com/forums... For example, the "cancer stem cells (CSC) forum" currently has 25 members (one of whom is Alexey), but 0 topics and 0 replies: http://network.nature.com/groups... - Jim Till
Jim, I gave up discussions on NN about 2 years ago, because it was zero interest to the topic and all discussions were dead. I don't know maybe something changed now, but i'm doubt about it. I think NRSC+Niche was the best model for unite community and discuss online. Even so, Niche commenting was not as active as me and editors wanted. - Alexey
I too am sad the shut down The Niche. This just shows the downsides to letting business interests host the discussions. It would cost me absolutely nothing to host a blog and stem cell news discussion forum at my web host, and I could leave it running indefinitely because I don't need to answer to anyone in terms of return on investment. If the community were to run it, we'd be more free to innovate and try new things, getting away from Nature's static and (to me) somewhat unsightly look-and-feel. - Mr. Gunn
@Mr Gunn sounds like a plan! ;) To be fair it does take a lot of work over and above the initial setup (and cheap webhosting) to get a contributing community going and somebody has to bear the time / money cost, right? There are lots of examples of sites started by people in their spare time and guiding it into something successful and sustainable - and an equal number where the tumbleweed has taken over. - Euan
And just so that people don't think Euan is being a homer, I was about the write much the same. - Deepak Singh
Noah Gray
*Cell* wonders out loud... Scientists, Should You Be Tweeting? - http://www.cell.com/fulltex...
*Cell* wonders out loud... Scientists, Should You Be Tweeting?
With mentions of @phylogenomics, @girlscientist, @sciencebase and @dgmacarthur - Noah Gray from Bookmarklet
I really hope David Crotty tells us his opinion on this. - Mr. Gunn
*snerk* - D0r0th34
*fluff* - Graham Steel
too bad they did not mention friendfeed - Pedro Beltrao
You mean Facefeed, don't you? - Noah Gray
Mr Gunn wins the thread. - Bill Hooker
He's written about social networks, anyway, http://www.cshblogs.org/cshprot... - Maxine
Yes, Maxine, he certainly has. He didn't link to the earlier posts, but he used to be quite firmly in the "blogging is a waste of time, now get back to the bench" camp. - Mr. Gunn
Pedro Beltrao
'Edgetic' perturbation of a C. elegans BCL2 ortholog - http://www.citeulike.org/user...
Not sure if I like the (made-up) word 'edgetic' though ;-) - Neil Saunders
Vidal lab is buzzword heavy :) - Pedro Beltrao
Attila Csordas
The final issue of Nature Reports Stem Cells http://www.nature.com/stemcel... they're shutting down,sadly
It was an interesting experiment. I though it had everything I would suggest to build a topic portal. It has editorial content that does not require user participation and then tools to let users participate if they want to. I guess this tells you that even if you always have fresh content and user participation tools that this is not enough to create a web community. - Pedro Beltrao
I wonder if they got any lessons from it about how to do it better. - Pedro Beltrao
It would be a very interesting post mortem - Deepak Singh
it was a top-down effort and building a community is harder that way - Attila Csordas
See also another FF thread at: http://ff.im/akFhF - Jim Till
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