Heather › Likes

@Pranab, the point and purpose of this 'room' on FriendFeed is outlined above (in the References Wanted Room). Since you are new to this, I would suggest browsing through earlier entries which will give you a flavour for 'how things work' in terms the unintended/unplanned use of it !! That aside, it's always been important from the onset to collect hard data in the manner in which we do here. - Graham Steel

@Graham Feeling much more at home on this site now! I have a question: What data are you collecting here? The citations people ask for? And how are you interpreting them? Forgive me if these sound stupid, but I am a little confused! Thanks! :-) - Pranab Chatterjee

Sorry for not replying sooner, been at work. The data gathered here are in the form of hundreds and hundreds of posts from people around the globe who don't have access to the literature they would like to study because of STM Publishing pay walls. Again this goes back to the wording at the top of this page on FF. As far as I know, it's not about interpreting the data, but mainly about collecting it. Does that make sense to you? - Graham Steel

In that case you should have had some more folks like me, who have absolutely nowhere to go except open access sources, because the whole world is closed off for us! :-) Just going to post my first request now! Wondering why I hadn't found this group earlier! - Pranab Chatterjee

@Pranab Quite. Folks here have discussed at great length the "visibility more widely of this group" issue more than once. Main discussions are documented at http://ff.im/beKZB and http://ff.im/cCto1 both in 2009. - Graham Steel

Re. "Don't worry, won't be long before I start bombarding requests" Cool, keep 'em coming. http://www.youtube.com/watch... BOMBS AWAY. Sorry that I couldn't help out personally on your first two even armed with this:- http://www.earlham.edu/~peters... - Graham Steel

Cool song! :-) Didn't these guys also sing "don't stand so close to me?" :P - Pranab Chatterjee

You should have stressed on the GREAT bit... ;) Would it be ok if I spread word of the group on my small email lists? - Pranab Chatterjee

BTW, read the special access rights you have on Peter Suber's page. That is soooo cool! :-) But it is a little disappointing in that you do not have access to NEJM, one of the big guns out there! - Pranab Chatterjee

http://ontogenesis.knowledgeblog.org/ and http://taverna.knowledgeblog.org/ are 'blogged books' using Wordpress as a commodity platform for rapid publication. There are a number of posts on knowledgeblog.org detailing the motivations for this and the advantages it can bring. Blogs can be particularly useful in situations where a subject is too niche for a publisher to be especially interested, or when writing about a fast moving field where traditional publishing is simply too slow to keep up. - Simon Cockell

These are excellent examples! Thank you very much! I especially like the Taverna collaboration. I found Engelbart Book http://engelbartbook.com/ and Seaside programming text http://book.seaside.st/book but still looking. - Patricia F. Anderson

"I want to make an announcement that my book entitled The P=NP Question and Gödel’s Lost Letter is now published. It is available here at Amazon.com, for example. I started writing a book that became a blog. Now the blog has become a book." http://rjlipton.wordpress.com/2010... - JoeCamel

These are awesome! I am still working on that collection of books born as blogs / born digital for a blogpost. Need to get my Yahoo Pipes alternatives post out first ... - Patricia F. Anderson

Students/postdocs propose three or four papers, PI has input into final choice. PI present at every JC and presents at least once. Papers chosen for intrinsic interest ("holy shit that's cool") or applicability to current projects in the lab. Honestly, I've always found JC to be a great idea in theory but a dismal failure in practice. Even with well chosen papers, if the presenter... more... - Bill Hooker

We had three themes, and alternated the themes. PI picks; once every few weeks, in-depth discussion. Students write up review in blog post. - Egon Willighagen

We're currently revamping our journal club due to much of the same problems mentioned here, so please keep the descriptions of your particular method coming! - Björn Brembs

@Bill It is not only the JC that would benefit if the research environment would change it's pace - or at least would acknowledge that there are other important things but mere papers. - Oliver Schuster

Here, the JC is attended by several research groups and the number of people attending varies between 5 to 30 people. Clearly, the presented paper and the presenter determined the number of people in the audience. Sometimes, the paper does not seem relevant to most of the researcher so almost nobody shows up, sometimes the paper is appealing or the presenter is known to present well so... more... - JJ

We had similar issues, mostly due to people either not picking good papers, not preparing for JC, just not being good presenters, or all three. In grad school we had an assessed JC class which had all the same problems, except people prepared a little more. People did come out of the class a little better at public speaking but not better at picking good papers. I still think they're good practice. Previous JCs where papers were assigned were much worse that when people pick their own. - Mr. Gunn from YouFeed

every Friday ,we have JC meeting. We discuss two paper in an hour and we have to send the paper at least 2-3 days before. Every one is supposed to read the paper beforehand.The person talking about the paper give the gist and others are supposed to ask question if there is any doubt about any part of the paper. At the end Paper is critiqued. The paper is chosen by Grad student and the... more... - sushant

No formal journal club for our lab, and I like not having to block of a chunk of time to discuss paper(s) that may or may not be interesting. Instead, PI and lab members are usually around and informal discussion of relevant papers happens randomly, as needed. That said, I was recently visiting another lab and their journal club brought together several labs from different disciplines... more... - Jason Snyder

Once a week one person chooses a paper and each student/postdoc gets a figure. PI is present, but just interjects when things are not being explained properly. I decided on this course after sitting through several miserable journal clubs where the presenter struggled mightily to explain the whole paper. When we started everyone involved was a 1st year masters student. It was made more... more... - Walton Jones

There is a journal club rota, and that person emails round a PDF. They give 10 min intro to the paper at the start, then it's a free for all. Much better for scientific development than someone presenting a paper formally, and much more fun. - Dave Lunt

"...as professional measurers and analysts of the world we should be embarrassed to use JIFs to measure people and papers. It is quite simply bad science." Hear, hear! - Bill Hooker

Totally OT - I would gladly pay to watch Aussies, Bill and Cameron play tennis (other games may be applicable) and all the proceeds be donated to a worthy cause. #anyonefortennis? - Graham Steel

Ironically enough, just yesterday I filled in a form required for an application for a professorship, where they wanted to know how many papers I had in which IF journals. Should I be interviewed, this particular position would be so important for me, that for the first time ever, I would probably not say anything about this embarrassing use of the IF, which would normally disqualify them as employers immediately. - Björn Brembs

Björn, was that Göteborg? I was trying to find the details, but they are apparently using that as part of the officiel job application process... did not find those details yet, though... - Egon Willighagen

Now, and that makes it even more embarrassing, it was here in Berlin. When I interviewed in Uppsala I did not see any of this nonsense. If I get the professorship, you can be sure there'll be a lecture or two about IFs. And there will be figures with forms from certain universities... - Björn Brembs

This whole sad discussion reminds me: why isn't there a tool available, that allows people to construct their own citation list??? I've been doing this by hand for years now: http://bjoern.brembs.net/citatio... - Björn Brembs

Bjoern, have you tried PoP http://www.harzing.com/pop.htm? - Bill Hooker

Yes, I use it, but it only pulls from GS which is neither as user friendly nor as 'accurate' as WoS/Scopus. So I use all three, de-duplicate by hand, copy and paste into an HTML editor and format (also by hand). I don't know of any other way to do this. To stay on topic: I think this is currently the best way to replace IF counts when evaluating people: use actual citations. - Björn Brembs

In Poland JIF is used every single time scientists are evaluated (whether it's a grant or a new position). Also, quite often a lecturer on a science seminar is introduced with mentioning her/his "total IF points". We have also "ministry points" (from Ministry of Science). These are awarded in the same manner as IF - per publication (points are also awarded for writing a syllabus for a... more... - Pawel Szczesny

@Björn We're working on something with the intention of delivering this and PM-R has been arguing a lot recently for open citations and open metrics. - Cameron Neylon

I would have thought that using JIF in a job application process would open an organization up to being sued... - Cameron Neylon

@Pawel - that was kind of the basis of the prestige vs outcomes riff that I most recently wrote about in the interview with Michael. It's a perfectly reasonable decision for a country, particularly a small country to go for prestige as a way of making a mark. But they shouldn't expect that to lead to either a viable, stable, or particularly valuable research community. If you want those things then you need to optimise for them (which is harder to measure obviously, but most important things are) - Cameron Neylon

I was thinking the other day about changing my cv and instead of listing 'my publications' start listing the papers that cite my papers (first order) and those that cite those first order papers (second order)) (or some quantification of that sort based on 'order'). A visualization of it could be fun to do too. Then I start wondering whether I should wait until I am out of my continuation period .... - Kubke

@Kubke... agreed... if your research published in a low ranking journal but used significantly in Nature X publications, what JIF should you fairly take... should we perhaps make a black list of universities where JIFs are used? it seems that SHOUTING is the only way to get things changed these days... :( - Egon Willighagen

@Egon :) I am on the advisory board for creative commons Aotearoa New Zealand, and one thing that came up is that 'opening up' requires a serious change in assessment policies. One example: Lets say someone gets 1000 citations on nature preceedings (not peer reviewed) shouldn't that count more than zero or 1 citation on a 'peer reviewed' nature? Should we move from 'peer reviewed' to 'peer accepted'? - Kubke

Tres interesting, Kubke. >>> "Should we move from 'peer reviewed' to 'peer accepted'?" - Graham Steel

@Graham or 'peer uptake' - Kubke

And depending on who your peers are, we could have top peer, instead of top tier. - Noel O'Boyle

What if the citing papers all cite the paper to dismiss it, or because it was shown to be fraudulent? You'd need either a citation typology or he possibility to retract papers from the record, the latter being difficult in non-peer-reviewed archives. - Björn Brembs

@Cameron: Looking forward to that tool! - Björn Brembs

@Björn It's not so much the tool. That's pretty trivial. It's getting hold of the data that is the problem.... but that's what the project is about. - Cameron Neylon

Similar issue here as what Bjorn mentioned in the beginning: about to start a tenure-track, and one of the items on my checklist to be eligible for tenure in 5 yrs is "x papers/yr in a journal with IF >= y". Which obviously completely bypasses my open-source work... But at this point in my career there is nothing much that I can do. - Jan Aerts

I think there are two things I would say to that. One is don't assume that tenure process in 5yrs will look like tenure today. Things are shifting, slowly admittedly, and perhaps too slowly but they are shifting. "Impact" and demonstrated income potential will be very important, both of which your prominence in the Open Source community will help with. Secondly, yes you need some good... more... - Cameron Neylon

@Björn wrt. citation typology: here's a recent paper on this very topic: Shotton. CiTO, the Citation Typing Ontology. Journal of Biomedical Semantics 2010, 1(Suppl 1):S6 http://dx.doi.org/10... "..ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. .." - 'Mummi' Thorisson

It's relevant to ask whether people who work at hosting companies feel like they're being watched regarding what sites they put up at that host. AFAIK, they don't. So why do people at Nature blogs feel this way? Maybe blogs should be independent? - Mr. Gunn from Android

@Mr Gunn or do like sciblogs.co.nz does: we were able to choose whether to build our blogs 'inside' or outside. For those of us that have our blogs outside, the content gets sucked into and reposted on sciblogs site with the sciblogs 'look'. I think it is a nice balance of 'independence' and 'aggregation'. - Kubke

Agreed. Aggregators are great, but you can have aggregators without a conflict of interest - those that provide pure hosting, for example. I think #pepsigate is an example of why this is valuable. - Mr. Gunn

Ok, since there is heaps being written about blogging/aggregation etc, here is an idea: What if we were to start an account (or a group) called e.g. science blogs in FF. How a blog gets fed into it could be decided for some sort of 'filtering' or 'quality control' (or not): for example, can the owner of the blog ask to be added, or should someone else nominate them, or does the blogger... more... - Kubke

Nice idea. My problem is that the way FF aggregates RSS feeds is poor - title and link only, no images, no text. This makes it an unattractive solution, but I fully support the principle. OTOH, I'm not in favour of setting up another destination (such as a BuddyPress site) - aggregation needs to happen within existing networks, not split attention. - AJCann

I agree with the ff issue with rss, but if my blog were to be aggregated I might make the effort to provide full title and first paragraph in the comments. (but no big deal if I don't). It would be up to the blogger to make that effort. One nice thing of FF is being able to pull it into wherever you want. - Kubke

True, but few people would bother to annotate the FF page. For sustainability, aggregation should be an automated process, not aggregation + manual editing. - AJCann

So you think it might be worthwhile doing but it in a place that shows more info? Do you know of one? - Kubke

OK, give it a try. The catchy title of the FF group is? However, I'd like to use the science tag from my blog rather than the base feed so I can filter content appropriately. - AJCann

OK, added 2 blogs in, invited you both (AJ and Neil). Let me know what you think. - Kubke

Well, one may see that as an incentive to make titles more informative? :-) - Björn Brembs

Or very attractive. Where is the group? I haven't had an invitation yet. - AJCann

Good point Björn, but this sort of formatting http://www.facebook.com/Microbi... (forget the sidebars, just the article summaries) is much more attractive than the standard FF RSS aggregation. - AJCann

Made AJCann and Neil admins, invited Bjoern (let me know if you want me to add/remove admin) - Kubke

OK, I'm in. - AJCann

Just a note that if you use 'custom RSS' rather than blog import you can get the first paragraph in automatically, particularly if there is an abstract element in the RSS feed - Cameron Neylon from twhirl

Thanks Cameron, I am inviting you and customising a few to see how it works - Kubke

Still can't get custom RSS to work for Blogger tags, works fine for WordPress. - AJCann

this is what cameron's look like on custom rss http://feeds.feedburner.com/Science... - Kubke

OK, done transferign all existing feeds into custom feeds. The only one that doesn't seem to work is AJCann's. (anyone has an idea). Right now it is closed, any of the members can invite others, and I have been making you admins as you popped in (can remove you from that role if you want). So, also any of you can make any other an admin (I think) and change the settings of the group. I have to do laundy and pack to go stalk intelligent people in California. - Kubke

@AJCann: here are example RSS feeds for tagged posts in my blog: https://bugs.eclipse.org/bugs... - Egon Willighagen

e.g. one of your labels: http://scienceoftheinvisible.b... - Egon Willighagen

Let me know whenever the group is public. will like to join! - Sandeep Gautam

BTW, ResearchBlogging has done a very good job of aggregating peer-reviewed research; cant we extend the same concept / have a parallel diluted version of ResearchBlogging , say ScienceBlogging , which has equally rigorous inclusion criteria, but does not necessarily needs the posts to be peer-reviewed (only the blogger, herself, to be peer-reviewed:-) ; having all the good science blog... more... - Sandeep Gautam

@Sandeep Research Blogging is great, but there is a lot of blogging that does not go in there. The problem with trying to set up something like research blogging is... well... trying to set up and host something like research blogging! A FF group tha taggregates blots would automatically move posts to the top based on likes and comments of the readers. The community would eventually end... more... - Kubke

We've been thinking about doing something like what Sandeep suggests at ResearchBlogging. The nice thing about that is that we already have a huge database of blogs and their RSS addresses, and they are already roughly categorized. The difficulty would be getting bloggers to tag individual posts when they don't fit into the broad categories they have chosen for the blogs (and, of course, administering the whole thing). - Dave Munger

The problem with I see with a friendfeed group would be managing the huge flow of information. I would guess that you'd be easily talking about hundreds of posts per day. Can the FF group organize all this by category? - Dave Munger

There are no sub-groupings in FF groups, but the architecture of FF is designed to filter large amounts of information. Personally, I'm not convinced FF is the best solution to this, but it might be the best available at present? We are looking for alternatives here. - AJCann

@Dave not sure you can do that but one could create 'groups' (blogs of Neuroscience, Blogs of microbiology, etc). Also remember that you can always opt of not having the group feed come into your home page, and just go open it at your leisure. What got me frustrated with all this #pepsigate was the idea of thousands of people changing each RSS feed by hand. That is a lot of wasted time! - Kubke

I agree FF is a 'dirty' solution but one that has some advantages in my view: commenting and likes (which move the good blogs up) the best of week/best of day feature and that you can opt out of bringing it into your home page, easy updates when URLs change, and being able to import into the group the odd blogpost that may be of interest (but not worth aggregating as a whole). What sucks is the mess and the lack of categories/tagging. - Kubke

Okay folks, here's a group for you. This is all the anthropology feeds from ResearchBlogging.org that were in blogger or wordpress (since I had easier access to their RSS feeds). Would something like this be useful? http://friendfeed.com/science... - Dave Munger

Yes, lets start with blog feeds that are already present in ResearchBlogging feed/DB and add them to diff FF groups- built around subjects like anthropology/psychology/neuroscience etc . for now this can be a valuable seed DB (BTW, no pun on seed here:-) with which to start and we can then decide on more rigorous exclusion/inclusion criteria as we go. - Sandeep Gautam

Here's a more extended blog post with my thoughts about setting up a system on FriendFeed http://wordmunger.com/?p=1378 - Dave Munger

I made the group public (I am off in a few hours on a trip) and posted this message http://friendfeed.com/blogs-a... . Lets see how the experiment works. If it doesn't the group can be destroyed :). I also pointed to the RSS and FB feeds at the bottom of the page (on the description) for those that aren't in FF. - Kubke

Ding, ding, ding. Cool! - Jeff Habig

That's awesome! - Alejandro Montenegro

"Ding, ding, ding. Cool!" Gotta love comments like that. We have an address so we'll ship some cool OA stuff out to Jeff in the next 24 - 48 hours. #openaccess - Graham Steel

(I should confess that this is all Graham's doing, I'm just free-riding on his generosity and imagination here.) - Bill Hooker

(Thanks, Bill.) - Graham Steel

Very cool! Welcome Jeff! - Björn Brembs

Graham and Bill, I'm still curious which side of the line to toe, here. Should I be attracting attention to RW by publicizing it, or not? Currently I just transmit occasional colleague's requests I can not satisfy myself. And I occasionally am able to satisfy someone else's need. What with Simon Singh's ordeal (for different reasons) I am worried that the room will be made an example of, though. Have we thought more about this than a year or two ago? - Heather

Heather. There were lengthy discussions about this on FF a few months back. There are two threads http://ff.im/cCto1 and http://ff.im/beKZB If you don't mind, I would much prefer NOT to continue these on this one which was posted solely for the purpose of welcoming the 200th member. I hope you understand. - Graham Steel

Awesomesauce! - Sally Church

Hey Jeff. Been busy playing with my new phone for the last few evenings but have now packaged up this lot for you:- http://steelgraham.posterous.com/oa-pack... Next stop - The Post Office !! - Graham Steel

Sweet...seems like there should be an app for that:) - Jeff Habig

For the record, I am reliably informed that the swag reached Jeff who of his own accord, decided to distribute it accordingly. A big thanks to Jeff from myself and Bill !! - Graham Steel

Can I still apply?? please? - Carlos Leiva Burotto

No application needed, Carlos, just join on in. :-) - Bill Hooker

evet - moda endüstrisi üzerine suçlarlar. [google tarafından tercüme verilen cevap] - Mickey Schafer

Mickey, that almost made sense. I blame Google. Seyyarat, erkeklerin dunyasi oyle renklidir iste. - mkz

:) Madem oyle, buyrunuz, "more geekery" (kimi kadinlarin renkli dunyalari hakkinda): "This principle of trichromacy is in need of reexamination in view of molecular genetics results suggesting that a substantial percentage of women possess more than three classes of retinal photopigments. [...] Women with four-photopigment genotypes are found to perceive significantly more chromatic... more... - mkz

Renk koru olmadigini nasil anladiniz? - mkz

Bu konu beni kesin çok ilgilendiriyor ama bunu okumadan önce herkesi çok güzel bir belgesel izlemeye davet ediyorum: http://www.youtube.com/watch... - Cagla

Yani ben de daha birinci bölümdeyim ama kesin çok güzeldir. Sevgiler, deli komşunuz - Cagla

:) Isyerinden Yutubunu acamiyoruz, eve gidince ilk is olsun. - mkz

..Belgesel hakikaten çok güzel çıktı. Kadınların en sevdiği renkler neden tuvalet renkleri? Baj rengi en iyi taşıyan erkek her zaman Erol Evgin olmuştur. http://vthumb.ak.facebook.com/vthumb-... - Cagla

Bir de: http://userserve-ak.last.fm/serve... Ay ortalığı çöpe çevirdim, gidiyorum - Cagla

FA, pek enteresanmis, isimlerini ogrenememis olmasi mumkun mu gercekten? Acaba ansiklopedideki testler mi yetersizdi? Kunthar, sen olayi eskimolarin kar cesitlerine verdigi isimler muhabbetine baglayacaksin gibi geldi. Pre-emptive link vereyim hemen: http://158.130.17.5/~myl... - mkz

Eheh, yok estagfurullah, ne coplugu, pek nadide bir parcaymis o. - mkz

@Cameron... can I help? With the procrastination, that is ;) - Egon Willighagen

Heh, yes, I'm sure there is some code we ought to be discussing in great detail :-) Actually I have made reasonable progress. I just have to write about all my failures for the year now... - Cameron Neylon

not failures, MAYBE temporary setbacks that provided valuable info/experience and enabled you to make better plans for next year? :) - Christina Pikas

absolutely - the heading is actually "Problems (and lessons learned), opportunities and areas for improvement." - 1. Days (and weeks) are too short 2. Travel leaves me significantly sub-par for extended periods. 3. I need to get by with less sleep... - Cameron Neylon

...it would play hell with unique researcher ID systems and citation tho ;-) - Cameron Neylon

Three separate people have said to me today that they plan to clone themselves as soon as possible to deal with their workload. I suspect this may also trouble researcher ID ;-) - AJCann

Oh, and don't forget the traditional ending by asking for money ;-) - AJCann

It could be an AF joke. But if so, that's an opportunity the LoC is missing. And if not, congrats to them for initiative and vision. - Michael Nielsen

Can anyone confirm this is for real? - Michael Nielsen

LOC blog looks real enough, confirms story: http://www.loc.gov/tweet... - Bill Hooker

Hari, you must be joking. This is a very smart move (if indeed it's real... still not convinced). Predicting box office take (http://news.slashdot.org/story...) is just the tip of the iceberg, once people start really mining that dataset. - Bill Hooker

Thanks for that, Bill, that pretty much seals it. Matches well with their archiving of law blogs, too. Good stuff. - Michael Nielsen

On mining: twitter limits access to their feed, unless you're willing to pay big $. I'd be very interested to know who is paying for access. The published literature on data mining Google's search data is already pretty interesting - shows you can predict influenza spread, house prices, unemployment, and who knows what else. Eric Schmidt said at a media conference that they'd figured you could also predict stock prices, but thought it was illegal, so they weren't doing that(!) - Michael Nielsen

Definitely real http://blog.twitter.com/2010... - Deepak Singh

Wonder if it includes private tweets? - Nick Lothian

It only includes public tweets. - Deborah Fitchett

We (!) will be part of Neurology and housed in the new Immunobiology space. We'll effectively be a post-GWAS group, trying to discover the pathogenic processes being perturbed by genetic variants conferring risk to diseases. Primary focus will be autoimmune and inflammatory diseases. Activities will include small molecule screening; expression studies; network approaches to risk and liability; and sundry other stuff that I'll make up as I go along. - Chris Cotsapas

Congratulations. Way way cool - Deepak Singh

thanks guys. It must have been a slow year on the circuit ;) - Chris Cotsapas

Congrats & good luck! - Attila Csordas from iPhone

One valid question would be: "is there a point to the wiki?" I'm thinking not a whole lot, right now I'm just using it as an easy way to place in a few iframes of the friend feed threads. A really advanced mindmap that I could drag and drop FriendFeed threads around, and then describe relationships between feeds would be very cool. Of course, I'm biased that way because I learned how mindmaps work last night and looked into them today. - Steve Koch

Breakin' the law! I'm so cool. Here's some non-science for you: http://friendfeed.com/steveko... - Steve Koch

I would say that there is a point to the wiki. Mainly because you can embed video, use LaTeX, Google spreadsheets, etc. Plus the wiki markup allows for greater structure in a post (headings, links...). Now if we use the power of the wiki with the flexibility for posting things via Friendfeed, that's spectacular. The ability to post relevent conversations on Friendfeed to a notebook entry is pretty awesome. I actually can't wait to try this. - Andy Maloney from iPhone

I also like the wiki because I am more of a wet lab person, and it more resembles a lab notebook to me - way to paste in various pieces of information as Andy wrote. Will follow this with much interest. - Heather

I've been using the wiki within our institutional VLE for over a year (giving up the paper notebooks was v. difficult!;) The flexibility is key: got to be able to post / upload anything. Am working on a "parts list" for diagrams that are used frequently (sequence maps, pcr primers etc) mostly generated spontaneously by students. Anybody know of an online source of such things? - Richard Badge from Nambu

Ant also asked this question, "do you need OWW?" I think if OWW can transform to make this work, then it'd be a "yes," since it could be very flexible. I had to create this example page manually. The next version of OWW (or other VLE or whatever) needs to be able to create pages automatically. So, when I create a new gel photo it automatically goes in my "gels" section of that day's page. It's OK if I need to do some setup work, but I shouldn't have to manually do stuff every day. - Steve Koch

I do not think imagining a FF widget is too far off: http://openwetware.org/wiki... . - Daniel Mietchen

It's times like this I feel the lack of a DropBox API - but we do have a grant in to develop a really lightweight, "drop it in the appropriate folder and have it go to the right place" system. That could work with the MediaWiki API (or anything else) to enable a bit of this kind of thing. But agree with Richard, its nice if a system knows what to do with a particular file type, but the important thing is that you can upload anything at all. - Cameron Neylon

Here's Carl's friendfeed: http://friendfeed.com/cboettig - Steve Koch

Carl says that KochLab students' ONS on OWW partly inspired him to start his own open notebooks. That makes me happy! Props to Carl & Anthony, Larry, Andy, Brian, ... - Steve Koch

One of us! One of us! :-) :-) This makes me very happy. - Bill Hooker

"I'm an Open Scientist and this is what I do!" I agree with Bill. This makes me very happy! - Anthony Salvagno

nice! Are these examples of theoretical notebooks? http://en.wikipedia.org/wiki... - Jean-Claude Bradley

I added his two notebooks under the theory section. As I understand it, it's theory + computational modeling. Computational modeling can be in either in my opinion--the kind of results generated are probably more like lab experiments than theory. So, probably there's need for far more than two categories. Plus, that section of notebooks examples is getting too big! That's a good thing,... more... - Steve Koch

Thanks for adding Steve. I think computational is more closely related to theoretical since there isn't a clear tradition of what constitutes an "experiment" and how to record it like there is in experimental sciences. I don't think the Wikipedia editors will allow the creation of a separate page just for examples of ONS but we certainly can put them at the end if some more examples get collected. - Jean-Claude Bradley

I'm surprised that wikipedia editors have been harassing you, Jean-Claude! I've started many articles of questionable significance and never had anyone mark them for deletion. (For example: http://en.wikipedia.org/wiki...) Someday I think the article would have to be changed to "notable open notebook science practitioners," but I don't see why we... more... - Steve Koch

Carl, you should pipe in on whether your computational work is more similar to theory or experiment! I think the whole spectrum of science is much harder to put into categories than Jean-Claude or I expect. I see computational as "experiment" often. For example, I collaborate with some people doing molecular dynamics (MD) simulations. It surprising how much like experiments it is.... more... - Steve Koch

Steve - it was actually not that easy to get the ONS entry on Wikipedia to not be deleted or redirected - it took 2 tries and lots of documentation to appease the editors - see the discussion page. I guess you don't know how it will play out until you try. - Jean-Claude Bradley

Sounds like an overly-aggressive guy was obsessed with deleting your article? No rush for anything, but if you think it'd be better with a sub-page of practitioners, I'll create the page someday. - Steve Koch

Steve - I think it is actually much more difficult to capture the information for computational experiments because it is so easy to generate immense amounts of data. If every tweak is "an experiment" you would end up spending more time documenting what you do than actually doing work. When we did docking we did approach documenting it like a physical experiment so that there is enough... more... - Jean-Claude Bradley

Interesting, Jean-Claude. And I hadn't been thinking of the legal definition (and I also don't feel like thinking about that now :) ). The MD simulations I was thinking of actually took significant time on a supercomputer for each tweak (I think). So, that would be practical to record everything and treat it as an experiment. Clearly, though, as you say there are cases where it would be... more... - Steve Koch

And perhaps another dimension for how much tacit knowledge there is. I think tacit knowledge may be what I had in mind when I said computational science may be easier to do as ONS. Certainly there is tacit knowledge in computational science. But listening to John Hogenech at ScienceOnline2010, I learned that it's possible for one group to exactly replicate another group's computations,... more... - Steve Koch

For Andy's gliding motility assays in our lab, I'd rate it (1) solidly in experiment, (2) low/moderate amounts of information (GBs of image data), (3) moderate/high amounts of tacit knowledge. (Or tacit knowledge that is difficult to capture. Maybe that's what the 3rd dimension is: how difficult to capture the tacit knowledge) - Steve Koch

Interesting discussion! In my mind they are both. In the phyologenetics notebook, I am trying to extend the theory of comparative methods beyond linear models. This field is moving very quickly, and it's no use to suggest new theory without providing software that implements it, or no one will be able to use it. I also find that saving all the data from all the runs I do can be... more... - Carl Boettiger

The reason I mention the legal definition of a lab notebook is that it leads to an expectation in the scientific community that students will be trained to record their experiments in a fairly consistent way. Perhaps I have the wrong impression here but it seems that there is not a standard way to record computational/theoretical work. [In fact as a postdoc I wanted to change the format... more... - Jean-Claude Bradley

Carl - one of the benefits I'm finding from the researchers who keep Open Notebooks is learning how science is done in different fields and different groups. This is something that has traditionally been difficult to assess because notebooks are traditionally very private. Over time we're gathering data that will prove handy for discovering how the scientific process actually works - as opposed to the ideal of hypothesis -> experiment design and execution -> evaluation which is widely taught. - Jean-Claude Bradley

Jean-Claude, that's an excellent point. I've also found that most of my colleagues in wet labs are taught to keep lab notebooks in a rather precise way. I know of only a few theorists in my department who keep any kind of regular notebook, and I've never had that kind of instruction or even encouragement. In computational sciences I'm surprised how few scientists use version management... more... - Carl Boettiger

Re SL, bandwidth can be a significant issue at conferences and voice seems to be one of the first services to fail. Having said that, it appears that my voice held up even though the indicator wasn't showing it. On the other hand, I was asked to use text chat when showing people round so they could listen to the scio2010 ustream! Overall though, I would probably have used canned video given the time available. - Peter Miller

Peter - I had the speakers up the whole time and could not hear anybody while I was on the network - dot or no dot - except for a 1-2 min period about 45 min before the session. Others were reporting problems with voice. At least the ustream was working. - Jean-Claude Bradley

JC - I had the ustream feeds (Rooms D & E) open all weekend - only about 1.5 hours of the event was streamed, unfortunately. Waiting for the uploads later this week. - Graham Steel

I could never get the ustream to work - "Off Air". Posts on twitter suggested that they kept "running out of tape." - Andrew Lang

Graham - I heard there were problems with the ustream but didn't realize how bad. Hopefully the vids will be posted soon. It would be nice to have an option with the streaming site to just make every session available immediately after it is done. - Jean-Claude Bradley

I'm curious, have you asked anyone about archiving your ONS data at Drexel? Does your department have a server, the computer center, the library? - Elizabeth Brown

Elizabeth - yes I have contacted our library but the time isn't right for them. We'll probably end up using our own server but I think the participation of librarians would add a lot of value to the archiving project. - Jean-Claude Bradley

Thanks - I think it will take some time for libraries to deal with supporting data. Many traditional archivists are not familar with scientific data and lab practice. They're trained to deal with paper and more "traditional" documents. - Elizabeth Brown