Walter Jessen › Likes

I thought the whole point of science3point0 was to take over part of this functionality? - Brian Krueger - LabSpaces

liking so I can remember I don't need to worry about this tool anymore. It's too bad - cliqset had pretty good functionality - though not quite as good as FF. - Elizabeth Brown

Hhmm. - Graham Steel

s30 still far away from FF, though... - Björn Brembs

That's what were trying to do, we're growing steadily, half the people who have commented so far are members so what's stopping the others and what would you like to see? - science3point0 from iPhone

One needs to be able to set up a personal starting page where all the news are ordered the way they are here (with best-of functionality). Now I have to log in, click on activity to see the news. I'd need to be able to set 'activity' as the starting page. Last I looked, all comments were visible, this needs to be more like here. Finally, It seems the buttons are larger than the text, which makes it difficult to take in large amounts of info quickly. - Björn Brembs

Moreover, liked items need to move to the top. Also, 'liking' is not an activity that gets reported, what for, when the liked items appear at the top of my stream? In all, neither functionality nor the functional design is quite there, yet. - Björn Brembs

Thanks Bjoern, this is precisely the kind of feedback we were looking for. I'll get to work on all of them. From what I'm hearing, people want an exact replica of friendfeed along with the additional features and the opportunity to ask for developments. We already have the groups option and additional features operating that I think makes us more useful in other ways such as the... more... - science3point0

Thanks a lot for that, Mark. - Graham Steel

One aspect that shouldn't be neglected (and is probably quite difficult, because it involves psychology) is a design that somehow (and I can't tell you how to do that) maximizes the flow of information. With FF, I can scroll quickly over my page and the important and most active threads 'jump out' at me, sort of. Here's a screenshot of what my FF page looks like:... more... - Björn Brembs

This is all very true Bjoern, this is the standard we at S3.0 are working towards and beyond. Its a very achievable goal. As mentioned before, this is only one aspect of the site but in terms of the constant developmement of this element, I would argue against the statement of facebook or nothing. - science3point0

I think you all should really get behind Mark if this is something that you don't want to see die. He's very passionate about it and willing to make the website exactly how you'd like to see it. Google isn't going to waste its time creating a niche site for scientists. Mark will. Help him do that. - Brian Krueger - LabSpaces

http://www.scriptsiparis.com/ - 404notfound

Something I noted about Friendfeed that might be important... the Dunbar number may figure more than it does with Twitter. The latter has a strictly time-oriented list (at least on Tweetdeck), so I can go back as far as I like and catch up. The FF approach of promoting popular stuff is great, but if the number of my contacts grows too great, then stuff popular with my friends (but less so with me) may completely overwhelm stuff I would have liked... - Chris Rusbridge

Isn't the FF code open source? Called Tornado or something? Since we all like FF, why not just do a local install of that (or run your own Diaspora pod)? - Mr. Gunn from YouFeed

+1 Brian, but I just think custom-coding a site is a waste of time when there's good code avail. Design is hard, too. - Mr. Gunn from YouFeed

win!! - $tephanie•Cog$ciLibrarian

Fabulous !! - Graham Steel

Had the meeting a couple hours ago. Went OK, but UNM is not as far along as I'd hoped. So, currently our lab can use the dSpace IR for our preprints and perhaps zip files of data (a good thing and we'll do it), but dreams of hosting data not a reality yet. Good news is that she told me her Associate Dean, Johann van Reenen is leading a faculty search for two new slots, both of which... more... - Steve Koch

Thanks for the update, Steve. - Mr. Gunn

I met van Reenen at the IEEE eScience conference I attended - need guy and it would definitely be a good idea to touch base with him. Those job descriptions are very cool, but I'm not sure if our workforce is up for them yet... - Christina Pikas

Yeah I understand it's going to take time. Overall, it's still very good to have made that connection, and the upcoming van Reenen (I sent him an email). Amazing that I can get this kind of advice and feedback so quickly from you -- FriendFeed still rocks! - Steve Koch

Met with Johann van Reenen today to talk about data curation. Overall quick comments: I am very optimistic about our partnership with the library! He's got the UNM's library on a very good track and is leading dramatic changes. There is a new hire coming in the fall, with whom we're going to work on our open data and even ONS. Johann feels like our lab is the perfect lab for the new... more... - Steve Koch

but I can't like this again :) - excellent! - Christina Pikas

What Christina said. I'm gonna go like the other post, because I can't like this one again. Need a "+1" button for when things on FF keep getting better! - Bill Hooker

Just only met him today and am not well-informed. My impression, though is that he's been working hard for fifteen years here at UNM to transform the library for the future. Looks like he's fought and won a bunch of battles, and the library is poised to be essential for us going forward. Like I said, based on limited info and gut instinct but I think UNM and my lab are lucky. - Steve Koch from Android

Met with Johann and the new assistant professor for data curation at UNM, Rob Olendorf, yesterday. It was a great meeting. Johann kicks ass, and Rob seems like the perfect person to work with on our open data projects. Rob has a background in molecular biology, too, so he easily understands our science. We're going to start pretty much right away with a test data curation project. The... more... - Steve Koch

The thinking is we'll start small, with just one set of conditions. Then Rob will work with Andy to figure out how the UNM library can permanently host the following: the raw data along with meta data describing the raw data; possibly some means for viewing the raw data; our software for processing the raw data; the processed data, x&y position versus time for all the microtubules... more... - Steve Koch

That's just sort of my understanding. We'll have to see how things play out as Rob works with Andy and me on this project. - Steve Koch

Oh, also we'll try to figure out how to archive Andy's open notebook on OWW. Johann (I think) mentioned the Memento project as potentially useful for that http://www.mementoweb.org/ - Steve Koch

I think Johann also mentioned use of DataCite http://www.datacite.org/ Rob mentioned that it would be great to be able to link to each of the images individually by DOI. However, that's probably not do-able in this first go-round, and instead the entire data set, or maybe big chunks will get DOI. - Steve Koch

Rob visited our lab today for 2 hours and met with Andy and me to discuss our first data curation test project. I think the meeting went really well. Rob's background in molecular genetics is very useful I think and he understands our data and workflow very well. We showed rob how Andy collects and analyzes data, from start to finish for one chunk of data. This chunk of data was a... more... - Steve Koch

We collected all this data and put them into a folder for Rob to start fiddling with to see how to best archive things. This folder is here: http://kochlab.org/files... - Steve Koch

In the processed data folders in this directory, it points to license and readme files. Rob will also look at these readme files to see where the software is and how to best archive it http://kochlab.org/files... - Steve Koch

Another component that's important is Andy's lab notebook. Use of the wayback machine may be useful here. For example, here is Andy's description of the objective heater he built for these assays: http://openwetware.org/wiki... - Steve Koch

So, there's a lot of work we need to do to. In terms of making sure we've linked all of the lab notebook entries, and also in terms of creating some new software that will turn our binary *.ini files into more readable text files which describe the software settings. I'm also going to introduce Rob to my contact at National Instruments to see if they can have discussions about how to deal with the issue that LabVIEW is a proprietary and moderately expensive platform. - Steve Koch

We were hopeful that the Wayback Machine would be of some help for archiving but it completely failed. That's one reason we spent so much time working on code to archive. http://onsarchive.wikispaces.com/ Maybe some of that can be useful - let us know. - Jean-Claude Bradley

Thanks, Jean-Claude. I had missed your bad experience with Wayback. I have previously introduced Rob to your work, and I'll send him that specific link. Please keep telling me when I'm repeating your mistakes or ignoring other good ideas :) Thank you! - Steve Koch

The lab team is not too web-savvy or web-based so there should be one site/app through which he can manage the workflow and not the lab (schedule meetings, marking milestones of PhD projects, follow developments, etc.) - Berci Mesko, MD

I'm sure it would be impossible to get everyone online, but he is a regular web user and is open to such things (in case I can find the right tool for this). - Berci Mesko, MD

Yes, the one site thing is important - things need to look integrated of have a single gateway at least. A blog that brings elements from other services into a central place could work well for this. Lots of good Wordpress plugins for creating content. Pull in IM/twitter feeds and get everyone to write a brief post at least once every second day. Use the comments for communication via... more... - Cameron Neylon

If you want a one-stop solution... I think a wiki is the best approach. - Egon Willighagen

You can also take the opportunity and lead the troops into the Web2.0 era, all in light of your PhD supervisor's ability to monitor things... - Egon Willighagen

Google groups is not bad. Especially if you email through that interface. You can store documents, have a calendar, edit a wiki, as well as have threaded messages. By leveraging email, your boss doesn't have to learn no "wiki" interface. - Bosco Ho

My supervisor uses Google Calendar for scheduling meetings (each of us will Skype him every second week) and the lab uses Google Groups for group e-mails but I wanted to centralize things somehow. - Berci Mesko, MD

Anyway, thank you for the great suggestions! - Berci Mesko, MD

I haven't tried it yet, but posterous has a group blog feature that might be useful for that. You just need one person to create the blog and add other collaborators' emails. With this set you (and everyone else) can send emails to a specific address to communicate and everything (including attached files) are aggregated into the blog. Might work for the not web-savvy since all you need is to write and reply emails. - Bruno C. Vellutini

how non-public do you want the exchanges to be, Berci? I mean: gpg-style wanted/needed? or are digital postcards fine? - Claudia Koltzenburg

Absolutely non public. - Berci Mesko, MD

Just check the CMS list for features you need and like, integration options with other tools might be one of the corner stones - http://en.wikipedia.org/wiki... As usual there is no one size fits all solution for all needs, so happy digging and taking it from there. Depending on the possible investment options you might find more information and insights out there. P.S.: I like Drupal, but are biased and not fully informed about other options ! - joergkurtwegner

Great list, thank you for sharing! - Berci Mesko, MD

Berci: also check out Open Atrium (http://openatrium.com), a pretty sleek intranet/collaboration-focused CMS based on Drupal. Our group is looking at this for a couple of projects in our group. Disclaimer: we're fairly Drupal-biased; we use it as a base for a production community portal site (http://www.gen2phen.org). Still, Atrium might make a great base for a group website and can be customized ad infinitum if desired. - 'Mummi' Thorisson

Thank you, Mummi, for the suggestion! - Berci Mesko, MD

My lab uses 37signals' Basecamp to manage and monitor most of the daily activity (ordering reagents, sending out announcements, internal communications, etc). I'd highly recommend looking into it, as it's inexpensive and the learning curve is very small for those who are not very web-savvy. - Ben Ferguson from iPhone

You can make posterous non-public and it's pretty easy to just email things into posterous and let it handle it. Basecamp is another solution, but you'll have to pay for it for your level of use and it's not brain-dead easy like posterous (of course, you can do a lot more, like manage projects, with Basecamp but hey, a lesser tool people use is better a great one people don't, right?)... more... - Mr. Gunn

I don't see why not, Heather. Regardless of the license, it would be a clear violation of community norms for someone to re-use a chunk of your text or any of your ideas or data without attribution (including, if appropriate, citation). I doubt that it would occur to 99.999% of researchers to use something without citation, even if (as most of 'em won't be) they are aware that a CCZero license makes it legal to do so. - Bill Hooker

And if I'm wrong, we (open foo types) need to know about it -- although it would suck to be the guinea pig in that case. - Bill Hooker

CC0 - why not? @Bill, you say on your blog re "you_cannot_steal_this_weblog": "To the extent possible under law, I have waived all copyright and related or neighboring rights to this weblog. This work is published from the United States. Further information." http://www.sennoma.net/ - what made you add this note of caution (asks someone non-US-based), also seen it on Cameron's blog... more... - Claudia Koltzenburg

I think CCZero may scare people. I would suggest: "All copyright material in this work is made available under a CC-BY 3.0 licence. For avoidance of doubt all shown data and graphs are made available under a CCZero Public Domain Waiver. The author asserts their moral rights to be identified as the creator of this work." - Cameron Neylon

And you can always suggest that people could make the whole thing CCZero if they choose. Point them at my BL collection piece for an argument for that if you like...http://cameronneylon.net/blog... - Cameron Neylon

I really like that combined version, Cameron, thanks - Claudia Koltzenburg

The CCZero bit is a little clumsy but what I'm trying to say is. All non-copyright stuff is public domain (which should be obvious) and just to be clear we're making a wide intepretation of what is data (essentially any data, table, or graph - but probably not including images or figures which people are more sensitive about I suspect). - Cameron Neylon

v2 "All copyright material in this work is made available under a CC-BY 3.0 licence. For avoidance of doubt all data, graphs, and tables, and their contents are made available under a CCZero Public Domain Waiver. The author asserts their moral rights to be identified as the creator of this work." - Software should be separate as well probably but I'm assuming that's a relatively small issue here. - Cameron Neylon

Helpful. I think "moral rights" will scare and confuse people. How about "All copyrightable material in this work is released under a CC-BY 3.0 licence. All data in the article and supplementary material, interpreted inclusively, is naturally available under a CCZero waiver. Please attribute according to academic norms." - Heather Piwowar

You think moral rights might scare people? Interesting - never occurred to me because its quite common in a lot of books. The only problem with your text is that in many jurisdictions if you don't explicitly assert moral rights you don't get them (I think, I'm getting more and more confused about this...) - Cameron Neylon

I don't even know what "moral rights" are in this context, I'm ashamed to admit. I do think mentioning them instills fear and doubt though, and chills the "yup, do what you want with it, you don't have to second-guess yourself" message. So maybe I'm happy to not assert them and not get them as part of that tradeoff. Now off to go look up what they are. - Heather Piwowar

Moral rights are mainly the right to be credited as the author and creator and not to have your work misrepresented (except for the purposes of satire or irony which are protected I believe). So here people are actually protecting the right to be credited for the data (although it may not actually apply - what is not clear to me is whether you can only have moral rights in copyrightable material) even tho it is being made available under a CCZero - Cameron Neylon

I love examples: "Moral rights in Canada were famously exercised in the case of Snow v. The Eaton Centre Ltd. In this case Toronto Eaton Centre, a large shopping mall, had commissioned the artist Michael Snow for a sculpture of Canada Geese. Snow successfully stopped Eaton's from decorating the geese with bows at Christmas." http://en.wikipedia.org/wiki... - Heather Piwowar

So people's big concerns are usually being credited and not having stuff misrepresented or taken out of context. In principle asserting moral rights creates some protections from that without screwing around with people's ability to use stuff. - Cameron Neylon

Hang on, is this a recommendation for the conference in general or just for your own paper? I may have this backwards. If you're just doing this for yourself then feel free to go the full blown CCZero route and tell people you can do whatever they like. I was thinking this was something you had to sell to a whole conference of people...hence the prevaricating around protecting things... - Cameron Neylon

Just my own paper. Though useful thought experiment for the whole conference, in this case just my paper. I want to be the change I want to see... I just don't know for sure what that change is. There is something to be said for modelling a non-extreme approach there too. will think. thanks for comments, very helpful. - Heather Piwowar

It would certainly be nice to have a clear form of words that would be the kind of thing a lot of people could sign up to. I see using CCZero on the blog as aiming to shift the Overton [sp?] window - Cameron Neylon

I'm leaning towards this. "All copyrightable material in this work is released under a CC-BY 3.0 licence. All data in the article and supplementary material, interpreted inclusively, are naturally available under a CCZero waiver. Please attribute according to academic norms." Critiques welcome if it is misleading or unclear? - Heather Piwowar

ok, and maybe a sentence about "moral rights" grrr I wish it had a less scary name :) - Heather Piwowar

I don't think its necessary. I've just been wondering whether it could help assuage some fears. I think your reaction shows that it might well not... ;-) Academic norms is good to as it references some of the CC work on norms and creating them. - Cameron Neylon

phewph! The unfamiliarity might be a regional thing... reading wikipedia, it sounds like moral rights have low visibility in the US compared to Europe. Now re-read that... see it totally needs a new name. heh. - Heather Piwowar

Well that explains it. thx! Cameron, good to know though that even with your across-the-pond hat on you wouldn't think it necessary. - Heather Piwowar

I think that, for U.S. work, mentioning "moral rights" at all will just confuse the issue--as Dorothea says, there's no such thing in U.S. copyright or patent law, and I (for example) haven't the vaguest idea how they would apply: Can I stop you from using my CC-BY material in a manner I find offensive? CC0 for data, CC-BY for text should (I would think) handle almost everything. - Walt Crawford

@Claudia, the text of my CC0 waiver declaration is taken directly from the Creative Commons site -- that's how they recommend that you word it. My best guess is that, because things like moral rights and database rights and so on are so very variable from jurisdiction to jurisdiction, the wording is designed to make things as obvious as possible. I include the "further info" link to the... more... - Bill Hooker

Heather, we planned to do CC-BY on our ASIS&T paper as well. However, a closer look at the rights form made me think that this can't work. They require that before and for 90 days after publication you "promise not to publish this Work elsewhere...*or grant permission to others to publish this Work*...without our advance permission." - Jason Priem

So as I understand it, they give you the copyright, but make you temporarily sign away some of those rights--rights that you need in order to make it CC. Our plan is to play that game, then change the copyright to CC after the 90 days are up. IANAL, so I may have it all mixed up. I'd love to hear if I'm missing something. - Jason Priem

Useful, Jason, thanks. I hadn't got that far yet. I wonder if it is legit to write something like "Effective Jan 1, 2011 this work is released under CC-BY" etc? - Heather Piwowar

Yeah, that's not a bad idea. Wish I'd have thought of that. Oh well, I'll have the self-archived one that'll be CC, so as least it's free somewhere. And it'll be in the ACM digital library this year, which at least makes it somewhat more accessible... - Jason Priem

I don't think you need to worry too much. If you put CC-BY on the copy they publish then _that copy_ is CC-BY (and people can re-use as they wish). If you have a separate contractual agreement with them not to publish it separately for six months that is an entirely different issue to copyright. For instance, you could later release a copy that was all rights reserved (why you'd do that... more... - Cameron Neylon

@Bill <-- thanks - Claudia Koltzenburg

@Cameron, thank you, that clarifies a great deal. Would you think it is still fair game to put CC-BY on the copy they publish if I also must agree agree *not to grant permission to others to publish this Work* for 90 days? Putting CC-BY on any copy is granting that permission? - Heather Piwowar

It is. I hadn't noticed that little corner. Not sure. Put it in as ccby and see what the response is? Seems strange they would ask you to think about copyright and then prevent you from using the best licenses... - Cameron Neylon from Android

Wonder about studies that have measured the relative quality of various review processes? - Mike Chelen

"The full podcast, originally created for the Journal of Participatory Medicine, is hosted here." http://www.patientpower.info/JoPM... (Podcast with transcripts) -- Peer Review and Reputation Systems: A Discussion -- 1. Defining the Problems and Issues with Peer Review Today -- 2. Light Versus Heavy Peer Review -- 3. Transparency in Peer Review -- 4. Wikipedia-Style Peer Review…and Rating/Reputation Systems -- 5. Crowdsourcing Research/Peer Review -- 6. Building a Community - Claudia Koltzenburg

Hmm, I don't know if peer-review improves papers but it has so far often improved *my*papers... - Björn Brembs

what's your take, Björn, does review quality depend on anonymity? should we say blind or non-blind should be up to the reviewer? - Claudia Koltzenburg

btw, have not seen this idea voiced before ;-) - Claudia Koltzenburg

I am with Bjoern here, I see improvement of papers on peer review (mine and others'). Both on substantial issues as much as smaller things. But i also don't think that peer review is a bulletproof system. - Kubke

I think the point of peer review is not to improve papers but to prevent the publication of truly shitty ones. We really should judge the system on the true negatives. Kind of like democracy - democracy is great, not because it helps you choose great leaders, but because it helps you get rid of shitty ones. - Bosco Ho

if publications were wiki documents then... +1 - Claudia Koltzenburg

Yes, like Kevin Kelly proposed (wikiscience): http://www.edge.org/3rd_cul... Additionally micro-contributions like comments and corrections should be measured and added to the overall reputation of a person. - Konrad Förstner

I'm going to offer counter examples. I've had several papers that were damaged by peer review in my opinion and several more which were severely delayed to publication and not significantly improved by the process, leading to potential opportunity costs (one paper which took nearly two years to get published subsequently has got around 50-80 citations depending on what you count). but... more... - Cameron Neylon

Bosco, I disagree. Firstly the evidence suggests that most of the shitty papers get published anyway eventually and secondly, like I argued here (http://cameronneylon.net/blog...) actually the more rubbish is out there, the easier it will be to find what you want. - Cameron Neylon

Bosco. While Cameron may be right on arguing against the papers part of your argument, I think the democracy part is a true gem...... - Nils Reinton

Yep Nils, I don't think search is going to do much to improve our parliamentarians unfortunately... - Cameron Neylon

In both cases, though, bringing in transparency has lots of potential to improve the system. By the way, I listened to the podcast last night (not knowing about this thread then) and took my notes at http://ff.im/oVHcb . - Daniel Mietchen

Not sure I've done this before, but -- I disagree with Cameron here. The assumption that more data = better search just doesn't convince me at all. I've seen a lot of papers that were basically trash, but that would appear as hits in any search that would also find good work on the same topic. I think the figure that gets bandied about is that only 30% of papers fail to find a home... more... - Bill Hooker

There's a step missing there. My argument was more that we need more data to build better search systems to enable better search. Putting out more stuff with today's Google won't help but it could help build tomorrows was the idea. In terms of the 70/30 figure the thing we don't have any real data on whether papers are improved, delayed, or made worse - most scientists say it improves... more... - Cameron Neylon

Well, we've had this part of the conversation too -- if reviewing were seen as part of a researcher's job and being good at it were properly rewarded, then studies like the BMJ one might not find such rampant slack-arsery. I guess part of this is failure of imagination compounded by lack of knowledge on my part -- I don't see how any search algorithm is going to be able to distinguish... more... - Bill Hooker

Imagine two papers, reporting the same experiments but in paper A the obvious control was omitted in each case, whereas paper B included proper controls. A and B may even draw the same conclusions! Both are going to be hits on any search I can imagine, and then you have to read 'em to know that A is rubbish. Scale that up, and you pretty quickly get beyond the point where you can read... more... - Bill Hooker

I begin to think that what we need most is more data... - Bill Hooker

I don't really buy the opening crystallography example as an argument that peer review is broken. Okay, one reviewer suggested something unnecessary. There should have been more than one reviewer, and the editor (or his/her minions) should have reviewed the reviewer's comments, either omitting any blatantly ridiculous ones in correspondence back to the author or easily accepting the author's note that it did not need to be addressed. - Rachel Walden

Bill, agree that more data is required to draw any sensible conclusions but in response to your point about paper A and B, as far as I'm aware we have absolutely no credible evidence that this is _not_ the case and some examples of dreadful peer review at the top of the pile. So should we be spending billions a year on something we have no evidence does any good? - Cameron Neylon

In any case, my argument would be that unless you have both papers A and B then there is no way anyone can develop tools to distinguish between them, whether they be social or technical. Also surely the argument must be that both support the same conclusion and it is only by reading them together that you get the fullest possible picture...even without the control paper A strengthens paper B's case. - Cameron Neylon

Bill: Why should the concept of search be limited to keywords? Consider Friendfeed for example, where results are highlighted by number of Likes. If anyone considers one paper better than the other, it would appear higher in the search results. - Mike Chelen

Mike, may be a matter of semantics but when you get into "likes" etc, to me that's post-publication review -- in other words, a filter. I love the idea, but a glance at PLoS journals (and other experiments) will show that it hasn't taken off: people just don't interact with the research literature (yet?) in a way that makes social filtering effective. - Bill Hooker

Cam, if A really is going to get published without the controls (70% of the time), then I'd have to conclude that peer review is a waste of time and money. I'm finding that hard to believe, but as you point out -- I have no evidence. I've made fun of other people for falling into the trap where "I can't imagine it" == "it's not possible", and now it seems I am hoist on my own petard...... more... - Bill Hooker

A different way to consider peer review: it's as much a psychological barrier as a real one. So, consider paper A -- it may be shite but the authors thought it was good enough to pass peer review. If they didn't even have to consider that hurdle, what might they be pushing out? Is there a mountain of substandard work that would be dumped into the knowledge base but for fear of the Peer... more... - Bill Hooker

That argument I'd agree with more. One of the things I've not seen a discussion of is the extent to which the citation advantage in high IF journals is a result of author selection bias (i.e. authors are probably pretty well placed to say which of their papers will be most successful and send them to 'appropriate' journals on the basis of that). There's a flip side to this tho. What... more... - Cameron Neylon from twhirl

see also http://journalology.blogspot.com/2010... (e.g., "CNS" disease explained) thx to http://ff.im/oZdka - Claudia Koltzenburg

Welcome in the "real" world ! Now what would your "open" access advocate say to security issues? Right ... *blank* ... as well, but at least he knows what a web-service is (maybe). - joergkurtwegner

the sysadmins are overwhelmed and understanding but there is always some new problems with this firewall. :-/ - Pierre Lindenbaum

That's a great news Andrew. Congratulations! Open science ftw !! - Khader Shameer

Wow, wonderful news! :) - Ricardo Vidal

That's great news! - Mr. Gunn

Great news, congrats! - Walter Jessen from FreshFeed

Yay! - Oliver Hofmann

Great news indeed - congrats! - Lars Juhl Jensen

Congratulations! - Bill Hooker

Wonderful! Well done. Can I start exhorting more genome annotators to head your way? I think I convinced an archaeal person a few weeks ago. Gene Wiki is certainly gaining more attention from the Sanger/EBI crowd. - Paul Gardner

Congratulations to them! - Tyson Key

Second R01, you're on your way... - John Hogenesch

The pharma drug development pipeline is broken. - Ruchira S. Datta

Standards of care are inadequate: people are getting treatments that aren't appropriate for them, with concomitant side effects. - Ruchira S. Datta

We need to look in the mirror for blame: many of the blocks are in academia. - Ruchira S. Datta

Oswald Avery found that DNA is the substance of genes, Watson & Crick solved the structure. - Ruchira S. Datta

We used to focus on single genes. Gene regulation circa 1990: everyone looked at single gene pathways. - Ruchira S. Datta

1996: See interconnecting pathways in Wnt gene regulatory network. - Ruchira S. Datta

2002: See very complex system with many different genes. But now very confusing: for therapeutics, which is the correct target? - Ruchira S. Datta

How is genomic data used to understand biology? GWAS identifies causative DNA variation but provides NO mechanism. Profiling approaches (microarrays) at genome scale provide correlates of disease, but what is cause and effect? - Ruchira S. Datta

Biological systems are very flexible. They work around single perturbations. - Ruchira S. Datta

Looking at integrating genetics approaches and clinical data. - Ruchira S. Datta

Steven Friend started Rosetta Informatics, which was acquired by Merck. Integrate multiple Bayesian models to make predictive models of where to perturb for effective therapeutics. - Ruchira S. Datta

Computationally intensive: keep updating Bayesian networks. - Ruchira S. Datta

>60 publications over 5 years substantiating probabilistic causal bionetwork models. Use these to make detailed priority lists of what is important. - Ruchira S. Datta

Cancer and metabolic diseases are very diverse among patients. Opportunity for individual medicine. - Ruchira S. Datta

Mission of Sage Bionetworks is to create a Commons where integrative bionetworks are evolved by contributor scientists. - Ruchira S. Datta

New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center. - Ruchira S. Datta

Small, plan to stay small. Rather, work with partners including commercial groups. - Ruchira S. Datta

Many of the commercial groups are actually some of the best partners for open access sharing. E.g., Merck, Lilly have found very early stage research should be open--very difficult to value very early stage research. - Ruchira S. Datta

See The Sage Commons website. Get highly annotated, globally coherent data with multiple layers of data. - Ruchira S. Datta

Have datasets stratified in different stages. - Ruchira S. Datta

Challenges from Sage Commons Congress (scientists, funders, policy experts, publishers): workgroups on Standards (data, annotation), Tools (combining, analyzing), Citation (recognition), Internationalization, Public Engagement - Ruchira S. Datta

especially, how to engage patient advocacy groups - Ruchira S. Datta

Many barriers to openness, trying to work through with partners - Ruchira S. Datta

Problem: 'Accessible' data often isn't. - Ruchira S. Datta

Checked the scientific social network of attendees at the Congress. Many hubs. - Ruchira S. Datta

IT experts tended to collaborate w/ everyone; media, policy, funders weren't as interested in talking with them! - Ruchira S. Datta

Biomedical research developed as a Cottage Industry. - Ruchira S. Datta

Resulted in current complex ecosystem w/ FACULTY and TENURE. - Ruchira S. Datta

Have rapid information transfer within labs, very slow between labs. This is costing lives. - Ruchira S. Datta

Incentive issues. The Federation Experiment: fuse four research labs. - Ruchira S. Datta from Android

What about Stanford & The Mission Bay Campus? "New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center" - Attila Csordas

Attila, are they there too? Got no indication from the talk or their website. - Ruchira S. Datta

Surprised that among all the meanings of SAGE from which Sage Bionetworks distinguishes themselves, no one mentioned the OSS math system http://www.sagemath.org Slogan similar in spirit: "instead of reinventing the wheel, let's build the car". Founder William Stein also now Seattle-based (fellow Berkeley math PhD). - Ruchira S. Datta

I don't think they published it, but the slides will be up later (so they say) - Mr. Gunn

I've just read the transcript http://gnusha.org/transcr... - Pawel Szczesny

I thought they didn't use real data (from questionaire). Will look for slides later.Thank you. - Pawel Szczesny

Yeah, the time between the time something starts and the message actually gets through to the bigger audience does not really to have changed with the introduction of the internet :( - Egon Willighagen

Interesting analysis. Companies getting involved is good (speed) and bad (different priorities to academic partners. Includes this quote about the problem of scaling large projects: "Managing the complexity of collaborations that occur when large numbers of institutions and individuals collaborate creates another twist in the road toward open participation. This is particularly... more... - Matthew Todd

@Matthew Todd Do you have a link to Jonathon Cummings study ? I couldn't track it down via google. My own experience is that large scale *research* collaborations are difficult to manage and more importantly take forever (lumbering is the right word). - Greg Tyrelle

No, sorry, never seen it. Large CAN mean lumbering, depending on how you do it. - Matthew Todd

My fault missed the double quotes, thought you were referring to it rather than the article. - Greg Tyrelle

There are different studies on communication efficiency and group size, the best investigations are probably available in the software engineering area, since code development contributions can be measured easily (lets not get into the quality question, which is a another topic). Anyway, two notable readings might be "Drug discovery: new models for industry–academic partnerships"... more... - joergkurtwegner

Would the interaction model stand up on a desktop. - Deepak Singh from iPhone

Likewise... whos behind this? It's not Apple, right? This should scare FaceBook if FlipBoard indeed start supporting any RSS input, like FriendFeed does... and I hope to see other clients too... this would be a killer web app... (like Cameron says) - Egon Willighagen

As I commented elsewhere ... "as it's content filtered by your social network, I can see some value in Flipboard as a concept! But it'd be more compelling if it was a browser-based web app rather than an iPad app. - Chris Jobling

Don't know how well it would work on a desktop, but I can see it on a phone and I think you could make it work on a desktop with a bit of redesign. It's the hooking into and cleverly redisplaying information from social contacts that got me. - Cameron Neylon from twhirl

Wow indeed. Seems like Flipboard was only launched on Tuesday. This review from PC Magazine went out two hours ago:- http://www.pcmag.com/article... They are on Twitter http://twitter.com/flipboard - Graham Steel

Nice idea, but I wish they would have shown more about how the app actually works, instead of how a touchscreen interface works. </rant> - Mr. Gunn

I have been using Flipboard for a few days and I really like it. The reading experience on the iPad is very nice, wouldn't work on a notebook, desktop computer or phone. Because the system is totally overloaded, couldn't connect y Twitter and Facebook accounts yet. Would like to see a FlipScience channel. - Martin Fenner

http://www.esajournals.org/doi... - Bruno C. Vellutini

hmm... tit for tat works under some circumstances quite well, but this pubcreds would assume that only people who are good at contributions AND reviewing have an advantage whereas people very good at the one and not the other are discouraged from the system. would this work? what if the core problem of the scientific publication culture is somewhere else? - Damir Perisa

See also http://www.plosbiology.org/article... . - Daniel Mietchen

I remember that peer-review session on ESOF very well http://picasaweb.google.com/joergku... and I was asking at the end if anyone of Elsevier or Nature has ever looked into MicroPayment systems, especially because some of them are busy with a ResearchIdentifier. ... I got a hand-waving (aka no) answer on this. - joergkurtwegner

Here's the video: http://nubes.esof2010.org/stored... . - Daniel Mietchen

I have been suggesting this to editors a couple of time... also in questionaires of publishers... radical idea? No, not really, and it sounds pretty fair to me. For every 5 (10?) (serious) reviews I make, one free BMC submission? I'm all for it. - Egon Willighagen

Interestingly, the ESA journal does not allow to leave post-publication reviews :) - Egon Willighagen

Not sure that this is a terribly new idea. Jeremiah Faith proposed something not dissimilar about four years ago. And at some level its not so different to how stack overflow works (kind of in reverse - you earn the right to review and curate through adding content but principle is the same). With a growing proportion of author side charges tho this might actually work - the journal would have to get an economic benefit though e.g. would have to get a reputation for rapid high quality review - Cameron Neylon from twhirl

BMC-series already give 20% APC discount to people who have reviewed (not cumulative & expires after a year -- argue amongst yourselves about how good a deal that is). Trouble is, people most likely to need a discount -- people very early in their careers, publishing their first papers -- are also the least likely to even be asked to review anything. To me, though, this all looks like another "inventing a better horseshoe" idea. These are problems that need a revolution, not another incremental tinker. - Joe Dunckley

Joe, never seen that before... got a link with details? I guess the 20% does not add up? 5 reviews is a free submission? - Egon Willighagen

Egon, I don't have a link but I will verify as a BMC Assoc Editor that I am offered a 20% APC discount every time I review. I don't remember the terms as I never read that part of the email. - Bill Hooker

Or satellites (perhaps even as an un-conf) - Kubke

Interesting...however we'd like to get more interdisciplinary action going on. For example, if we did a satellite of the SfN meeting coming up, it would be all Neuro people--unless we could convince locals in other disciplines to come. Not to say people shouldn't consider doing unconferences as satellites to life science conferences--interesting idea! - Mary Canady

Haven't tried it focused on social media, but have organised interdisciplinary advisory boards across several medical functions focused around a particular medical theme or issue. The challenge is making the topic interesting and compelling to people. Most physicians are not interested in social media (no time, don't see any value), while the number of cancer scientists interested is... more... - Sally Church

Hi Sally--it's not meant to be focused on social media, the topics would be all science or biotech related. We just group social media and unconferences as being similar in that they're more open and life scientists seem reticent to adopt. - Mary Canady

I think it would be interesting to do both and see what differences might occur. My inclination is to start with and probably focus on all the genes annotated with GO regardless of species though. If 2 concepts end up disjoint across all organisms that provides the strongest evidence. - Benjamin Good from email

Given the current sparsity of GO annotations with experimental evidence, it would be premature to try to do this. With the current state of knowledge, the most likely explanation of why two GO annotations with experimental evidence don't both occur is that no one has done those two kinds of experiments on that gene. I would definitely *not* try to do this on GO annotations without... more... - Ruchira S. Datta

You provide a good reminder that not all the annotations we will be computing over are going to be 100% correct. I don't think this is a good enough reason to "*not* try to do this" though.. If we waited for perfect databases before running experiments in bioinformatics we would have very boring, fruitless jobs.. What you correctly point out is that we will need to keep the certainty of... more... - Benjamin Good from email

I guess you are looking for something like this one: http://www.biomedcentral.com/1471-21... Applying negative rule mining to improve genome annotation. Rules are not in GO format, but surely it's possible to convert them, or eventually repeat the procedure. See also http://bioinformatics.oxfordjournals.org/cgi... apparently from the same group. BTW, I am working on something remotely similar. :) - Pawel Szczesny

Thanks for the references, really interesting work. Different goals, but could indeed be very useful for this project. Thanks! Don't suppose you'd like to mention what you are working on?? - Benjamin Good from email

In case anyone is interested, we (John Pinney and I) have some data now.. You can view a list of pairs of GO concepts that are very unlikely to be used to annotate the same gene (with associated p value) here -> http://sites.google.com/site... - Benjamin Good

Very interesting on a quick scan. I wonder what it would look like if you partition the pairs by the main GO classes (# CC-CC, CC-BP, CC-MF, BP-BP, BP-MF, MF-MF). The top of the list seems dominated by CC-CC (which makes sense, and is perhaps less interesting?). - Andrew Su

Hey, aren't you supposed to be not-working?? I'll add columns for the ontology roots and add another file (want to lower the p value threshold too). - Benjamin Good

Ben, this isn't working, it's called taking a break... ;) (...from baby care, for everyone else...) - Andrew Su

New file is up at same location http://sites.google.com/site... . Definitely plenty of non-CC-CC pairs with very low P values in the list. Here are a couple examples: "sensory perception" <--> "intracellular", "regulation of transcription" <--> "transport", "metabolic process" <--> "receptor activity" - Benjamin Good

I work at a small biotech company and as Neil said, access to journals is the biggest issue. We are associated with a university so when I'm there I can access journals, however normally from the company building I can't. The delay is frustrating. In terms of commercial tools/databases, currently I would like access to Genelogic gene expression database and Biobase transcription factor database and analysis tools. - Greg Tyrelle

Another small biotech here, and yes, access to journals is a huge pain. - Bill Hooker

I'm currently at a university, but was considering being an independent scholar for year or two (= a homeschooling mom with a research rather than a knitting hobby). Resource problems I anticipated: access to journals, Scopus subscription, Web of Science subscription. - Heather Piwowar

Thank you all - just as I expected: access to journals (and ways to find journals/papers) is the most expensive and most difficult to get thing if one is outside of University. How about space for office (lab?), equipment (poster printer?), software - if you were a researcher at home (freelance scientist) what would you need that costs? - Bora Zivkovic

Depends what kind of research. I'd need a biosafety hood, liquid nitrogen storage, glassware, balances, electrophoresis equipment, culture incubators, autoclave, chemical store... :-) - Bill Hooker

Software is the other bit. Biotech's tend to be a lot more budget constrained than many academic labs. - Deepak Singh

Access to journals and availability of equipment are both big deals, but whereas some equipment can be obtained from ebay or a local lab equipment company, academic literature database subscriptions can't be obtained at a discount rate. (AFAIK) - Mr. Gunn

For journal access, try getting yourself an unpaid appointment as affiliate faculty (aka courtesy appointment) at your local university. I've known a couple of people who have done that. - Donnie Berkholz

Lab space outside of a university or big company is very difficult to find. The so called "incubators" are expensive. It is still unclear to me what the rules are for running labs in commercially-zoned properties. - Jeremy Leipzig

Access to journals is a huge issue. My biggest expense for freelance science (computational biology) is the computing equipment; second would be software. - Walter Jessen

As I'm considering becoming an independent scientist (again!), some time ago I did back-of-the-napkin calculations and it turned out that I might need ca. $100 (reliable internet connection) + $500-1000 (per article payments, no subscriptions) + $500-1000 (computing cloud, storage and calculations) a month to work comfortably outside of academic infrastructure (without spamming all my... more... - Pawel Szczesny

Access to journals is the biggest issue. Obtaining this access by being an adjunct faculty is much more valuable than the salary they pay for your services. Obtaining funds to attend scientific meetings and to cover publication costs isn't far behind. Not always trivial to convince business types there is value in publishing your basic research. - Jeff Habig

Donnie, good to know re: affiliate positions, thank you. - Heather Piwowar

Downgrading is part of the plan. You can get a $15 plan if that's how much you use. I've never spoken to anyone who uses over 2GB from their phone unless they're tethering 24/7 and don't have internet at home. - Mr. Gunn

If my phone & plan supported tethering, then unlimited data would probably be useful, otherwise $15 is a far better value than $30 for the current level of bandwidth usage. - Mike Chelen