Euan › Likes

Yes, Neil, and thanks. I was asking a bit in the other direction because the Neanderthal genome paper was already on our list. If anyone knows of a supplement exceeding these 175 pages (which includes 51 figures and 58 tables), though, please share it here. - Daniel Mietchen

Thanks for pointing me to the Neanderthal paper. Used the info in a presentation today. - Martin Fenner

Just noticed that the above comment by @neilfws is gone. I was sad to see him leave, but I understood the reasoning behind that. I do not understand why he deleted the account. For the record, the paper he mentioned is at http://www.sciencemag.org/content... . - Daniel Mietchen

What happened to neilfws? - Björn Brembs

yeah, only html but as this is a totally public & important project there's incentive to make it obviously better & faster by the ... public if the official people behind are lagging a bit ... behind - Attila Csordas

sounds good, yesterday when I had 20 minutes I tried to utilize web-harvest and jsoup as java html parsers but haven't seen the plateau I needed for the job from the bottom of the learning curve I reached, so today when I had 10 minutes I wrote a primitive java parser to get the age information out, with that I will probably be able to get some stats I'm interested in but still the data should be much more accessible programmatically for a public project like this. - Attila Csordas

given that it's all consistently formatted, it looks like the data is stored in a structured manner somewhere. Can't you just ask them for the raw data? - Rajarshi Guha

time to do some open networking then, just tweeted Jason Bobe about this, who is a PGP guy https://twitter.com/#!... shall see - Attila Csordas

update: emailed Jason Bobe - Attila Csordas

We're working on an API, so people can programatically access the data. Obviously html is of little use for developers. We have a few items ahead in the queue, but we're working on it. - Jason Bobe

Regarding the weight issue of 14kg in the vital signs section, its related to this known bug: http://groups.google.com/group... - Jason Bobe

That particular individual has organized their medical history dating back to the age of 5 years old (when weight was 14kg). Neat. - Jason Bobe

thanks for the answer, Jason, I wonder what kind of API do you have in mind? - Attila Csordas

Man, check out the Usual Suspects lineup! Brilliant. - Bill Hooker

Awesome! err.. Is there an RSS feed for this one? I'm not seeing it.. - Carl Boettiger

Carl: http://www.openresearchcomputation.com/rss - Deepak Singh

brilliant, didn't know that worked. Now in my google reader. How about an rss icon on the front page? - Carl Boettiger

I always wondered if a social media savvy editorial board could project a journal above the rest ... I guess I will see :) - Pedro Beltrao

Who is Keyser Sozer? - Bosco Ho

I'm more than a little surprised Greg Wilson isn't on the board, but there are certainly a lot of recognizable names on it already. RSS feeds++. - Chris Lasher

Nope, I can confirm there are at least three people who aren't on the list, Neil, Arfon Smith, and Peter Murray-Rust, and we're still planning to build the board up some more. I did approach Greg Wilson but he's got some other big projects on the go so understandably didn't want to take more on. - Cameron Neylon

Should also note that the website has a lot of stock text in it still that will be being replaced with some more relevant material as soon as I get access to the ed board mailing list and we start figuring out how to get our hands into the website itself... - Cameron Neylon

It would be nice to see people associated with the physiome project in there http://www.abi.auckland.ac.nz/uoa... - Kubke

The plan is to expand the Ed Board reasonably organically so very happy to speak to people who would have an interest. It will take us a while to get there but always happy to talk to people. - Cameron Neylon

I'll send them that way then. Cheers. - Kubke

Honestly, I seem to be a bit confused - how's ORC positioned against Source Code for Biology and Medicine? - Pawel Szczesny

Yes! it's an example from the 16th century, there weren't many refereed papers available :) http://www.evidencechart.com/charts... - Alex Holcombe

the most surprising thing I read about the heliocentric/geocentric debate is that in Galileo's time, supposedly noone brought up parsimony as a factor. So apparently people didn't consider all those epicycles of geocentrism to be a point against geocentrism. Even tho that's what I always assumed http://alexholcombe.wordpress.com/2008... - Alex Holcombe

Minor niggle - but the site gives the impression on the landing page that you need to login before you can see anything which is slightly offputting for someone just wanting to look around. Would be good to see the list of charts from the landing page so you can explore what's been done already. - Cameron Neylon

thanks Cameron. And unfortunately there's a lot more niggly user-interface imperfections beyond that one ;) we'll use your suggestion and others to improve it little by little - Alex Holcombe

Just thinking off the top of my head, for scientific issues, would it be interesting to ask the question, what papers are not included on this list? Again trying to tackle the selection bias you mention in the post... - Cameron Neylon

Since when do review papers tout theory? Maybe there is a class of them that do -- and perhaps this varies across scientific disciplines -- but the majority of reviews I read and allow students to use (and teach to write!) are NOT arguments supporting a theory -- they aren't even particularly biased. They do offer a personal perspective through selection of articles, organization of... more... - Mickey Schafer

"It allows one to create systematic reviews of a topic, without having to write many thousands of words, and without having to weave all the studies together with a narrative unified by a single theory." -- Alex, how have you created a systematic review if all you've done is categorized data? Or, simply gathered all the articles into one place? What's the basis for understanding one... more... - Mickey Schafer

Alex, totally agree with you on the experience reading reviews as it relates to expertise. But I think the conclusion that reviews are thus biased is incorrect; expertise so changes perspective that relatively little one reads as an expert feels "unbiased" -- the science has to be phenomenally well done for us to be convinced. I read language stuff done by neuroscientists sometimes and find it frustratingly distant from what happens in fields of linguistics. But the bias in this case is mine. - Mickey Schafer

I absolutely agree that the requirement for the narrative format in review articles is as constraining as it is for communicating experimental results. Lets hope more people start experimenting with more modular formats such as this and share them on the open web. - Jean-Claude Bradley

From a discourse linguistic perspective, Jean-Claude, I find that statement really interesting. Maybe b/c I come from a humanities background way back when, I do not experience reviews as narratives, nor do I teach them that way. But I very much agree that the IMRD is narrative in feel b/c an idealized sequence is implied that may never have happened (and I tell this to students as... more... - Mickey Schafer

Mickey - I think that reviews are expected to be narratives in the sense that there is a "story" to be told. Reviewers will expect an historical perspective, key people involved, an exhaustive review of different aspects of the topic, etc. That is why it is annoying to read reviews in one's own field because we always find missing components. However just sharing information in a modular way as is shown here can be done because there are no such expectations. - Jean-Claude Bradley

Jean-Claude, it's the contention that one is "just sharing information in a modular way" that I'm disagreeing with -- not b/c it's a bad idea, but b/c it is not value-neutral. No chart is without a bias; it cannot exist without terms defining where entries go, so by definition, is not "merely" sharing. That would be the exchange of raw data; charts are a form of filtering. As for... more... - Mickey Schafer

this is an interesting organizational tool. I agree with Mickey - non-scientists may not find it useful and might event mock such an attempt to "pidgeonhole" ideas or see the format as a way to structure an argument to achieve a desired result. As a librarian with a lot of colleagues in the humanties and social sciences I am routinely surprised by how different I think about concepts or... more... - Elizabeth Brown

Mickey- I believe that any format will involve its own biases, so I didn't mean to imply that evidence charts are always better than reviews; just different in sometimes-useful ways. Any form of discourse has its own norms and perhaps even implicit assumptions. My own experience of writing articles is that to make it 'work' with the word limit provided and to get the 'story' to slot nicely into the reader's head, I am pushed to ignore certain difficulties and even to sweep things under the rug. - Alex Holcombe

Hi, Alex -- yep! I discuss these struggles with students all the time, and show them how it can change the interpretation from a reading point, too. The thesis students in particular struggle with this as PIs push them to condense 2 years of research into 10 pages or less. One student nearly cried 2 years ago when a single graph covering 1/2 page was the result of 2 years of life with... more... - Mickey Schafer

Hi, Alex. I've just spent the afternoon reading several reviews written in various areas of biology. I think I must amend at least some of my previous comment: I read several papers that were clearly making arguments. This is quite different from what I usually read in medicine where a review is more, well, review-like. Could have something to do with the place I was reading (the... more... - Mickey Schafer

Mickey yes, now that you mention it, it's also my impression that medical reviews tend to be more "just the facts, ma'am". I haven't been expert enough in a medical topic to judge whether they might somehow be just as biased, but being more subtle about it. - Alex Holcombe

Alex -- I am not qualified as a medical expert, but from a linguistic standpoint, I think the bias is there, but represented in the selection of materials rather than in how language is used. Frankly, I found much of the stuff I read today refreshing insofar as authors weren't hiding their agendas; I don't mind bias when the writer says "Look, I think this is what we should be doing and... more... - Mickey Schafer

Mickey- this is interesting; I have seen a lot of tables in papers, but rarely or never one with each column representing a theory and each row evidence. In a systematic review for example, each row might be a study and each column a methodological trait of the study, with other columns representing the results. If you could send me the references, I'm very interested to have a look at the ones you're referring to. - Alex Holcombe

I will need to go back to web site and see if I can locate a good example -- the "Trends" journals published by cellpress seem to require "boxes" of information -- usually 3-4 per 8 page pub. A few of those were charts. I'm not at a VPN enabled computer at the moment, so this may need to wait until Monday. - Mickey Schafer

This is awesome. I wish I knew it existed when I pushed my students to make this: http://pharmacomicrobiomics.com/papers... - Ramy Karam Aziz

Sure it is awesome, i like this idea, new vision and interesting! @ Dr. Ramy as u know when one do things from the ground up he learns more:), so it is still good experiment for me^_^ - len hat

Alex, here is a link to one paper that seemed to be using an evidence chart of some kind -- see Table 1, "Evolutionary hypotheses..." -- http://bit.ly/d15jVQ (sorry for the pdf -- wasn't sure if you had sub or not, and just seemed faster). - Mickey Schafer

Congrats! - Heather Piwowar

Thank you. And please thank FriendFeed and Claudia Koltzenburg. - Martin Fenner from iPhone

75k authors... how many Nature print pages is that? - Egon Willighagen

@Egon hahaha, but a bloody good point. One for @timohannay and now @kaythaney to sort out. - Graham Steel

If this one is not #OA then...... - Graham Steel

And they all get equal credit when that paper is cited a gazillion times... - Just Joe from iPod

I've tried this (or possibly a previous version of it) out. Very nice, except you keep needing to specify more memory to the JVM. - Ruchira S. Datta

This seems a common issue for many Java applications that crunch data ... very common to see the suggestion to use the java -Xmx flag in README files. - Andrew Perry

BTW, Knime or RapidMiner are large packages for data mining that incorporate all Weka libraries and are more user friendly. - Pawel Szczesny

I love Weka (and +1 Ruchira). - Euan

Weka is perhaps the largest and most notable library of machine learning algorithms, developed since mid-90s. I recommend it to everyone. There's indeed a problem with memory sometimes. I've tried to build a software platform, Debellor, which solves this problem by pipeline processing of data. Debellor incorporates some algs from Weka. It's a work in progress but those interested can find it at http://www.debellor.org - Marcin Wojnarski

@Ruchira: well, many papers just describe the use of blogs and roles as observational, and do not reflect on it in relation to theoretical models from the pedagogical literature that tell us what features are needed for optimal communication, education, etc... - Egon Willighagen

If you want many of the theoretical details and underlying principles, please check the KFTF book (definitely **+ see references therein) - http://www.keepingfoundthingsfound.com It is not about blogging alone, it is about a much broader concept of finding, making sense, re-finding, and sharing information with yourself over various locations and with others, this is why this book is so important, since it discusses PIM (Personal Information Management) and learning. - joergkurtwegner

10.1109/eScience.2008.30 not so much theory there but in my unpublished piece i at least have a decent lit review and conceptual framework http://terpconnect.umd.edu/~cpikas... - Christina Pikas

@joerg - it's interesting you mention kftf or personal information management - i cover that in the unpublished piece but a lot of people had trouble with that part. maybe it's how i explained it. - Christina Pikas

@Christina - Nice work! 1. Any more conclusions in Shakar2007? besides "Electronic laboratory notebooks have not been well received because they force a rigid external structure on the record-keeping process (page 10)"? 2. As a KFTF reader I clearly like: "The blogs act as a learning tool as well as a tool for personal information management. Two participants post lists of links of... more... - joergkurtwegner

@Christina: is the unpublished piece published now? Can you perhaps post it to Nature Preceedings? - Egon Willighagen

It's still unpublished - I just saw this note (sorry!) and posted it to Nature Preceedings... it has to be reviewed by curators before it goes live. - Christina Pikas

No worries! I just posted the comment an hour or two ago ;) Thanx for uploading to NP! BTW, can you read the wave in my blog? Do you have a wave account? If not, please email you, so that I can request one for you. - Egon Willighagen

I can see it - my google wave account is also cpikas - Christina Pikas

It's just a first draft now... I'm new to this stuff, but think I found in Miller1998 a theoretical framework I was looking for :) Will continue tomorrow... - Egon Willighagen

Is there a link to this Nature Preceedings content? - joergkurtwegner

No, not yet. It was posted yesterday, and the Nature offices don't open until tomorrow... - Egon Willighagen

it's the exact same article as was posted previously on my UMD website, but the link will probably be more stable on precedings: http://precedings.nature.com/documen... - Christina Pikas

Thanx! The DOI did not make what I submitted to our course, but will it to a later version. The wave has the current version... still draft, but a full story now. - Egon Willighagen

Thanks, Pierre. Been working hard to make the jump between experimental biology & bioinformatics - Attila Csordas from iPhone

Congrats! Sounds like a great opportunity. - Heather Piwowar

congrats! - imabonehead

Congrats! Great news: welcome to the Silicon Fen. - Matt Wood

congrats, Attila! What will you be working on? - Mr. Gunn

Congrats Attila !! - Khader Shameer

Thanks, appreciate the support, it's definitely a proteomics job, exciting horizon - Attila Csordas from iPhone

Congratulations! Where will you be based? - Berci Mesko, MD

Congratulations!! - Yann Abraham

congrats :) - Pedro Beltrao

Congratulations! - Ruchira S. Datta

Woot - glad to see that the mass take over of EBI continues apace... - Cameron Neylon

How so take over? Is there anything you do not like about the EBI that requires take over? - Egon Willighagen

No, no. Just that we seem to be gradually getting people we know into positions there. Duncan, Nico, now Attila...not so much a takeover as an _enhancement_ - Cameron Neylon from twhirl

Congrats - Abhishek Tiwari

Thank you all! (Berci: EBI is @ the Genome Campus in Hinxton, we'll be based in Cambridge) Looking forward to meet all the Cambridge/Sanger/EBI people there - Attila Csordas

Congratulations! - Kubke

Congrats Attila :) - John Cumbers

Great! Congratulations! - Konrad Förstner

And of course my congratulations too, Attila.....looking forward to meeting you in person (finally)... - Nico Adams

thanks again to everyone, accepted the offer today with an April start date. - Attila Csordas

Congrats Attila! Read this on my handheld and thought you said the "FBI" instead. Does this mean the next BioBarCamp will be in the UK? - Jim Hardy

Nice, congrats! - Sung W. Lim

HI/congrats!--I think my friend John Tate works there...if so tell him I said hi! - Mary Canady

+1 Andrew! - Björn Brembs

Well that's a given... ;) Any others that you use? If not, any that you'd _like_ to use? For example, I've wanted to use NCBI resources in a seminar/meeting before, but the interface right now is pretty poor on my blackberry. - Andrew Su

I'm so sorry deepak :-) But you have to know that before erlang, I unsuccessfully tried to play with ruby, python, clojure, scala,(...) but nothing was as interesting/fun/fast/new as erlang. I'm currently reading Joe Armstrong's "Programming Erlang" which is a well written and intelligible book. Worth reading. - Pierre Lindenbaum

:-) I am just wholly devoting myself to becoming a Rubyist (although I do find Clojure fascinating). You live on a different planet. By the way, have you read the Prag Prog Clojure book. It's really nice - Deepak Singh

I read the beta version of the Clojure Book. But , just like Scala, I was somehow disappointed that soon or later, a knowledge of the Java VM was required. - Pierre Lindenbaum