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Piotr Byzia › Likes

Michael Barton
GitWrite - blogging for nerds - http://gitwrite.com/
looks like a potentially great platform for a lab notebook... - Carl Boettiger
Sounds an awful lot like http://pages.github.com/ GitHub Pages is an awesome platform for hosting documentation. For example, we use it to host http://gunicorn.org from this GitHub branch: http://github.com/benoitc... - Paul J. Davis
There's a great desktop/cloud notebook app to be written using git as a back end. Anybody got into the guts of this and seen what is different if anything under the hood? - Cameron Neylon from twhirl
I know that the Mercurial vs. Git debate seems to have been won by git in the Open Science community, but if you want a saner life you should look at http://hatta-wiki.org/ (Also see http://www.mzlinux.org/node... for a list of Mercurial/Git backed wiki engines.) True nerds should consider an Emacs Org mode backed blog or wiki http://orgmode.org/worg... which can also be combined with revision control. - Matt Leifer
Just thought about an Emacs org-mode + git solution, too. Especially as it can include executable code snippets via Babel: http://orgmode.org/worg... (at the bottom of this page you can find a description how this can be used for reproducible research). - Konrad Förstner
The server software used for display must be available for the content to be truly portable. Would be happy to see even if only basic features were available so far. - Mike Chelen
Hatta looks good, wonder how difficult it is to get set up? - Mike Chelen
Ended up using Github's Git-backed wikis https://github.com/blog.... Now if only there were a way to allow comments similar to blog posts... - Mike Chelen
Simon Cockell
Stack Exchange and the future of BioStar - http://blog.fuzzierlogic.com/archive...
Over the weekend I saw this tweet from Stack Overflow/Exchange founder Joel Spolsky. The content of the link he posted has served to crystallise some of my thinking of the last couple of weeks with relation to the Bioinformatics question and answer site BioStar. The link Spolsky posted in the tweet was to a failed [...] - Simon Cockell
Now with feedback from Jeff Atwood. Encouraging. - Simon Cockell from iPhone
Pawel Szczesny
How many times you can publish the same service? http://www.ncbi.nlm.nih.gov/pubmed...
All three articles are describing slightly different aspects of the service, but it's still _the same_ service (!). - Pawel Szczesny
Well papers are academic currency. Any way to increase your wealth (utility be damned) :) - Rajarshi Guha
But three? Within six months? 200% inflation rate is going to kill this system... :) - Pawel Szczesny
@Pawel... agreed. This is the same paper. It is not uncommon for biology groups to publish the 'tool' separetely from the 'science', but this sounds ridiculous... plagiarism it is... actually, all journals I have been reviewing for in chemistry, do not allow results to be published before... I can't believe there are so many angles to this tool that those journals would have allowed it... within 6 months... that means they must have been submitted simultaneously :) - Egon Willighagen
Actually they're doing themselves a major disservice. By publishing the same thing 3 times they effectively divide their citations by 3, which harms their H-index. - Paul Gardner
And none of these 3 papers cite Jmol! Or even mention it... - Egon Willighagen
I've also heard of a rejection to the NAR webserver issue b/c of a Bioinformatics Application Note. But I'm not sure if this is a general policy. Once you're in the NAR db / webserver issue, you can re-submit after 2 years. - Michael Kuhn
I'll play devil's advocate. Apart from the reaction against CV stuffing is there any good reason not to do multiple publications for a service? If the argument were, for instance, to reach a series of different audiences? - Cameron Neylon
multiple pubs in multiple venues are fine. But pubs are currently a currency and basis of competition (amongst other things); from this POV, spamming journals with multiple articles devalues the individual articles - Rajarshi Guha
Agreed but surely its the author's choice to balance that devaluation against potential value gain of reaching new people? I guess what I find interesting is that people feel that protecting against publication inflation is a bigger concern than getting information out efficiently. Similar case where a piece in PLoS Currents was subsequently published elsewhere and everyone got their... more... - Cameron Neylon
I checked the website, and the have an attribution clause... I could not find the attribution requirements, but nothing stops them from asking people to cite all *3* papers... - Egon Willighagen
@Cameron... I think it's a problem of inflation, and devaluation. 3 papers is simply more rewarding, and everyone not publishing more or less the same thing trice is effectively punished. - Egon Willighagen
Perhaps, but is that not a symptom of measuring the wrong thing? If we actually measured re-use (e.g. citations) and three papers meant the number of citations were cut in three for each paper and the total number was the same then we'd be ok right? No devaluation? The problem here is not that its being published three times but that we value the wrong things (number of papers) in a system that enables (or even encourages) cheating. - Cameron Neylon
What @egon said. My basis for this argument is that, in principle, multiple pubs in different venues are fine (I'm not sure how different the venues were for this case). And in a world where the nuances (or lack thereof) of these multiple pubs are taken into account, this would be fine. But in the real world, where jobs/grants/promotions are (unfortunately, frustratingly) based on a... more... - Rajarshi Guha
@cameron - absolutely! We are measuring the wrong thing. But, that's what we're measuring. So to stay in the race, we (well, not me, it doesn't matter to me much anymore) play the game, whose apparently best strategy is to publish as much as we can. I'm sure that with your and others' efforts this will change one day - but people still want to get their jobs/grants/promotions ... - Rajarshi Guha
Agreed - and this isn't a case where I'd argue much in their favour. But the thing with PLoS Currents was a bit different but got a very similar response. Interested whether people feel that's as egregious a case. - Cameron Neylon
is there a link to the PLoS Currents discussion? - Rajarshi Guha
Not sure if these particular 3 papers are what I usually think of as duplicate papers. The "Acta Crystallographica Section F" one is part of a special issue about the JCSG pipeline, so I think it's reasonable there even if it's duplicating things. And my opinion is that the NAR database/server issues are also a special case - as they provide a resource to the community and often describe websites that have been published elsewhere. In short, not the most straight forward example of duplicate publications. - Mickey Kosloff
Cameron, if you're playing devil's advocate, don't forget to send an invoice to NPG, because they will profit the most from perceived inflation of papers outside of Nature* ecosystem. :) But let me play the game as well - if we allow for such marketing strategy, it gives yet another advantage to people who use English natively and have no problems to write five different stories on the same discovery. Yet another penalty for not being British? Thank you so much, Cameron ;). - Pawel Szczesny
Pawel++ - Egon Willighagen
Mickey, while I agree these are "special cases", not clear duplications, I still don't really get it why it's allowed in a first place. When I was reviewing a manuscript for NAR special issue I'd asked authors to improve the service in comparison to the original (published few months earlier) despite clear policy on allowing duplicates. Today, probably I would refuse to review for NAR special issue at all... - Pawel Szczesny
Incredible how people behave like you expect them to behave in these comments. Very revealing and eye opening. - pn
Pawel Szczesny
FigShare in beta! Congratulations to Mark! http://blog.okfn.org/2011...
Although I get a feeling Mark borrowed spelling of my name from Cameron :) - Pawel Szczesny from iPhone
Apologies, apologies, its correct on the http://FigShare.com post! I blame OKFN! - science3point0
It's quite characteristic spelling so I assumed it's his influence. ;) No worries, it's not an issue. Google is aware of polymorphisms in weird sounding names. - Pawel Szczesny from iPhone
Congratulations! - Catherine Anderson
Pawel Szczesny
Systems Institute is officially supporting FigShare (backstage story) http://www.pawelszczesny.org/2011...
A lesson from deciding to support Mark's FigShare. - Pawel Szczesny
I love that Figshare is launching and has support from Systems Institute. Thank you! However, not even an "about us" page on the website? The support is surely essential to sustain Figshare. But confidence in that support will be key to people contributing figures and the service gaining popularity. As of now, I think the placeholder website wouldn't sway many people outside of this FF circle, right? - Steve Koch
Steve, in essence you're right. But on the other hand, lack of website has never been an issue since launch. We were initiating large international consortium and closing gaps on other two and nobody cared if we have a website. It might be also the mode of operation of SI - we're working within networks of personal connections (where online presence doesn't really matter). As for... more... - Pawel Szczesny
Actually, I had the same doubts as Steve before making the announcement, but Mark's response was in line what we were already doing. - Pawel Szczesny
Pawel Szczesny
Systems Institute is officially supporting FigShare (backstage story) - http://www.pawelszczesny.org/2011...
Bill Hooker
Publish and perish: why the current publication and review model is killing research and wasting your money - http://ubiquity.acm.org/article...
tldr (yet) but thought folks around here might be interested - Bill Hooker from Bookmarklet
Fabio Casati is doing some interesting stuff... - Cameron Neylon
"Highly Inefficient Publishing Process. This model is incredibly inefficient under every perspective, and results in a colossal waste of public funding, and forces researchers worldwide to waste countless hours that could be devoted to better research (or to have fun with family and friends). It is a system deeply rooted in the past, oblivious to the advent of the Web and related new... more... - Daniel Mietchen
It is interesting that the ACM Digital Library entry (http://portal.acm.org/citatio...) for this article has a broken DOI number and requires an account for full text access. The authors note that: "this is preliminary work (version 1.0, or rather 0.9). We release it anyway according to the concepts proposed in this document." This is a nice illustration of the point that the ACM Digital Library does not handle versioning well. - Don Pellegrino
Lars Juhl Jensen
The scientific social network - http://www.nature.com/nm...
Joint statement from 17 funding agencies: "The widespread adoption of social networks, wikis and blogs has fostered an environment of sharing and collaboration. For scientists, this provides the opportunity to generate and curate content more seamlessly and dynamically than ever before. Web 2.0 applications targeted at researchers are gaining in popularity but need to be adopted more widely to stimulate a more collaborative and open research environment." - Björn Brembs
it's behind a paywall, though. - Elizabeth Brown
Oh, and guess what their solution is... (focus on guess; I have no prior knowledge here)... it will be another silo that doesn't allow interaction with general tools... who's here to take on that bet? - Egon Willighagen
(Participants of the project are uninvited for that bet :) - Egon Willighagen
@Egon: you forgot the brand. It will be a Nature-branded silo that, etc. :-) - Bill Hooker
Pierre Lindenbaum
Champagne ! Our paper is accepted in "Nature Genetics" :-)
Congrats! What's it about? Or doesn't that matter? :) - Egon Willighagen
@Egon, I'm going to wait for the publication of this article before talking about it :-P - Pierre Lindenbaum
Congrats!! - Björn Brembs
I'm glad you got a paper out, but I'm sorry you couldn't get it published in a real journal. - Bill Hooker
@Pierre... ah, embargoed... obviously increases dissemination of scientific results :) - Egon Willighagen
Congrats !!! - Mitsuteru N
Egon Willighagen
released my first book ... about the #cdk -> http://www.lulu.com/product...
Groovy! - Noel O'Boyle
Great! - Pawel Szczesny
Make sure to check my blog post on what (and what not) is covered in the book... I list the full ToC... - Egon Willighagen
Just for reference, the post is at: http://chem-bla-ics.blogspot.com/2011... - Egon Willighagen
Lars Juhl Jensen
Chris Miller
Yesterday I successfully defended my thesis and had a paper go live at PLoS One. Kind of a big day. http://www.plosone.org/article...
Double congratulations! - Bill Hooker
Congrats! Good job! - Björn Brembs
Jonathan Eisen
Cool paper, & winner of "worst new omics word award": Predatosome - http://phylogenomics.blogspot.com/2010...
Perhaps authors are now deliberately baiting you in order to get publicity for their paper :) - nlomioni
Yes, sure that would be a good strategy. May have to rethink whether I write about the paper in the future. - Jonathan Eisen
Eisenome: the set of all papers profiled in the "worst new omics word" series... - Andrew Su
Oh man, I can't believe I never thought of Eisenome before --- I am definitely going to find a way to use that - Jonathan Eisen
Liking for "Eisenome". :-) - Bill Hooker
Wouldn't that be the "ironome" ... i.e. all genes involved in iron metabolism? Someone is already researching "you", Jonathan: http://www.chem.tamu.edu/faculty... - Iddo Friedberg
perfect Iddo - my baseball nickname for years was "Ironman" - Jonathan Eisen
Graham - not anymore. - Mr. Gunn
Mr. Gunn you are in deep trouble if that was you - Jonathan Eisen
I was kidding, but is it really not avail. anymore? Could be the evil speculative domain parking stuff practiced by the likes of GoDaddy et al. - Mr. Gunn
Despite my use of twitter for the #scio10 meeting, I continue to be amazed by how awesome friendfeed is --- friendfeed - I am back - Jonathan Eisen
Not that I wont still tweet - but I do love friendfeed - Jonathan Eisen
Make good use of it. It's a rare scientist that can play this trick of a self-named -ome. "Suome" doesn't quite roll off the tongue. "Lindenbaumome"? "Steelome?" "Szczesnyome"? None quite have the same ring. "Hookerome" is close, but I'm sure that's just putting a nerdy spin on a third-grade playground taunt (just a guess Bill)... - Andrew Su
@Andrew "Iddome"? Going back to the hiring and P&T discussion, an inner joke in my department says I was hired only because one of the senior researchers there is working on indoleamine 2,3-dioxygenase (IDO). Hey, it's as good a metric as the ISI impact factor... - Iddo Friedberg
+1 Iddo - thanks for a hilarious discussion Andrew, Graham, Johnathan.... - Mr. Gunn
Andrew, even the judge at our wedding made fun of my name, pointing out that well, of course my wife wasn't going to take *that* name. I'm just wondering how I get a grant to study my own -ome... :-) - Bill Hooker
The Koch a doodle doo -ome is unveiled http://kochadoodledoo-ome.blogspot.com/2010... - Steve Koch
Thank you all for this great discussion. Just changed my name in all public registers to "Nils Reintome". - Nils Reinton
"Lindenbaumome" may not work, but surely it would be the "Lindenbome", which kinda does.. I'm not even going there for my own name... - Simon Cockell
@Steve Koch... kochpostulates.blogspot.com is still free... - Iddo Friedberg
Maybe we should do homeopathomics - Jonathan Eisen
@Iddo -- good idea. I snapped it up, and tried to use it for good, not evil :) Maybe someday I'll know what to do with it http://kochspostulates.blogspot.com/ - Steve Koch
As requested, I'm officially adding the Björnome: http://bjoern.brembs.net/news... - Björn Brembs
Pedro Beltrao
Episode 02 – Systems Biology with Pedro Beltrao - http://nodalpoint.org/2011...
its so weird to hear my own voice :) - Pedro Beltrao
Wow, I didn't realize nodalpoint was revived (and in podcast form). Love! - Chris Lasher
Jonathan Eisen
Just submitted my first data set to Dryad http://www.datadryad.org/repo/ - seems like everyone should do this ...
Rufus from the Open Knowledge Foundation was asking for datasets too...is there any coordination on this...? - Noel O'Boyle
All datasets in Dryad are CC0, so he is welcome to any and all data in Dryad, for any purpose! - Heather Piwowar
Simon Cockell
I’m giving a lecture next week to the Bioinformatics Masters students here about protein structure prediction. As part of the introduction to this topic, I have a traditional ‘data explosion’ slide, to illustrate the gap between the quantity of protein sequence data available versus the number of solved protein structures in the PDB (hence the [...] - Simon Cockell
Nice work! - joergkurtwegner
Carl Boettiger
I've written a post as an introduction to my open lab notebook, explaining how I view it and how it's organized and integrated with my github, flickr, and mendeley accounts. Still figuring things out, but think I've learned a lot about notebook workflow over the past 6 months. Feedback welcome! - Carl Boettiger from Bookmarklet
Awesome explanation of what you are doing with ONS! - Jean-Claude Bradley
Deepak Singh
Jan Aerts
Jan Aerts
Dear lazyweb. Looking for a good RSS reader for mac/online. Which do you prefer? And why?
Hard to compete with Google Reader these days. I didn't like it at first, coming from Bloglines, but it won me over pretty quickly. - Chris Miller
GReader. Reason: keyboard shortcuts - Deepak Singh from iPhone
GReader: The GUI, sharing, flagging - Pierre Lindenbaum
GReader + Better Google Reader extension + Snow Leopard extension - Adam Kraut
GReader. Reason: it sucks but there aren't any others. Like Chris, I moved from Bloglines; unlike Chris, I still hate Greader. But seriously, I haven't found anything (online; I try to stay away from desktop solutions) that even works properly, let alone competes. - Bill Hooker
GReader because I've got my fingers taped to the j and k keys. - Matt Leifer
I've seen quite a bit about NewsBlur this week. Not yet tried it myself on my own set of feeds but sounds like one to watch. http://www.newsblur.com/ http://news.ycombinator.com/item... http://github.com/samuelc... - Dan Hagon
newsblur does look interesting - Deepak Singh from IM
http://www.guardian.co.uk/technol... - some interesting options there. I use Reeder (http://reederapp.com/) on the iPhone, and I see they're developing a Mac Desktop App. The iPhone version is really, really good. - Simon Cockell
Pawel Szczesny
Launching Polish fork of Science 3.0 portal - http://www.pawelszczesny.org/2010...
I get interesting feedback from the students - some of them use OpenWetWere (as a help in designing experiments), some know more about virtual conferences than I do, some already use FriendFeed and Twitter. Given that the other side of the spectrum are people who seem never experience online interactions other than sending an email, it's going to be interesting to see how such group is going to collaborate on notes from the lectures. - Pawel Szczesny
Egon Willighagen
new journal online, which I hope will make a difference: http://www.openresearchcomputation.com/
Editorial Board reads like a list of favourite bloggers. :) - Pawel Szczesny
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
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
Focus is a bit different and there is no disciplinary restrictions. The instructions for authors stuff on the ORC website is very generic at the moment. We're waiting for more specific stuff to go up. Basically ORC will focus more on the software quality side, with documentation and testing (including provision of test data) being an important part of the process. - Cameron Neylon
Euan
Got another request to use webapp from 2003 paper. I, er, don't have it any more. Where can you "freeze" webapps and host permanently?
I think standalone AMI's (a la galaxy) are always a good idea, and with micro instances might be even cheaper - Deepak Singh
Has anyone built an app/webapp archiving service? Something that makes it nice and easy to roll an AMI? Or is it so easy that anyone providing an app _should_ be able to do it? - Cameron Neylon from twhirl
If you have an existing app and it's got a fairly well defined environment should be relatively trivial with some docs. Launch AMI with the right security group, log into URL. - Deepak Singh
Or make the code available so that it can be re-instantiated. - Deepak Singh
I should have a go at it. I think I'm probably fairly typical of the "might write some code but not done it before so find it a bit scarey" type. I can see a case for a service but can't really see what the long term business model for preservation would be... - Cameron Neylon from twhirl
"...can't really see what the long term business model for preservation might be." That made me LOL. You aren't the only one ;-) - Mr. Gunn
Marius, that's my argument, especially in forms that don't need to be "hot", but provisioned as required. Alternatively, it is an interesting "library of the future" problem - Deepak Singh
Our webapps are not hosted on an old machine, they're hosted on a cluster with an infrastructure for queueing jobs from the webserver to compute nodes, updating the database (on another node) and the filesystem, etc. We have two full-time programmers working on them along with myself, plus we get sysadmin support from LBL. I don't think it would really be reasonable to ask the publisher to host that, they're not in the web application development business. - Ruchira S. Datta
I would like to roll AMIs some time, hopefully sooner rather than later, but I'm rather skeptical it's going to be "trivial". - Ruchira S. Datta
I once believed that virtualization could help solve the impermanence challenge of scientific resources but was ultimately stymied by all the problems pointed out by @Ruchira. Neil points out another inherent problem, that funding for specific projects is often connected to specific personnel and once they move on, the resource is sure to break with the next reboot and security update.... more... - Todd Harris
I'm glad people are warming to the idea of packaging up code+databases as a working VM to be included 'supplementary data'. I can remember suggesting something like this on Friendfeed a long while back and being somewhat shouted down .. which was probably fair in the case of apps like Ruchira's. But for single node apps with databases in the order of 10s of gigabytes, I think it's... more... - Andrew Perry
There are always apps that don't fit the bill (e.g. Porting Galaxy was non-trivial), but for many apps, it's not that hard. In the future, Todd's suggestion is the right one, in that we should think about it at the start of the project and it should be part of the process for larger projects (where there is significant investment into developing the app or service). I do think that... more... - Deepak Singh
Björn Brembs
Dear colleagues: how do you organize your journal club? With or without PIs? Who choses the papers? Journal Blitz or alphabetical list? What works for you?
Every student is assigned several journals he is 'responsible' for. Once a week each student sends an email to the group with relevant abstracts. Every other week there is a JC meeting in which a student chooses an interesting paper (on his own) presents it and lead a discussion about it. In the week between a student gives a 'research progress' meeting instead. PI is present in all of... more... - Nir London
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
Our JC is organised centrally and informally. Papers are either picked by the three organisers (all non-PI) or suggested by any of the participants. Articles are then circulated via a closed mailing list and (should be) read by all. Discussion is moderated by the organisers who also give an informal summary in the beginning. Afterwards, conclusions are published on the JC's website.... more... - Arnulf Koehncke
Deepak Singh
Hacker News thread on a blog post on the future of R http://news.ycombinator.com/item... (original post http://www.r-bloggers.com/%E2%80%...
A lot of good points in the original post. I'd love to see a rewrite, but it's hard to get momentum away from something so entrenched and with such a huge ecosystem of packages. - Chris Miller
rpy2 provides great access to R from Python:http://rpy.sourceforge.net/rpy2.... It's really useful to do the data manipulation bits in Python, and then only delve into R when you need libraries or statistics. The best thing about the R language itself is data tables; now I miss them when writing in any other language. - Brad Chapman
agree with Brad, data.frame's are great for keeping heterogenous data together. I've creted many half baked mimics in Java just to have some similar functinality - Rajarshi Guha
Jan Aerts
This scares the hell out of me. http://twitpic.com/2k6fx1
This scares the hell out of me. http://twitpic.com/2k6fx1
What is it? - Egon Willighagen
"Now you can go crazy with BioInformatics" ?! - Cass Johnston
That's scary indeed... seems to depend on closed source platforms... but the graphics are cool, and that's what matters, right? - Egon Willighagen
Are we all scared of how poorly this is aligning or am I missing something? - Rutger Vos
what alignment? that's not supposed to be aligned yet, is it? No, I'm scared of more vendor-lock-in... MS plays the game brilliantly, though... hat off for that. - Egon Willighagen
I guess I did read the picture incorrectly. Sorry :) - Rutger Vos
Yes, that's what we need. More people using excel for bioinformatics *facepalm* - Chris Miller
FWIW, one of the pieces of code mentioned, NodeXL, is actually open source, though Excel-only. I'm not sure how they are using it in this demo though. - Mike Chelen
Egon Willighagen
Anyone here who knows a cool tool to analyze and/or visualize the tweet stream around a particular hashtag, say #acs_boston? Perhaps show a wordle of the tweets of the past hour or so? That kind of stuff...
worldle is pretty slow for real time apps - Rajarshi Guha
No permalink :( - Egon Willighagen
I'm not sure if 140kit is capable of this, but it's worth a shot! - Alex
got a solution coming up - Rajarshi Guha
Alex: that hashtag is #acs_boston... please give it a try... - Egon Willighagen
Rajarshi... sounds promising... - Egon Willighagen
quick hack at http://rguha.net/atv/atv.html - could do with some prettifying. Makes use of http://johannburkard.de/blog... - Rajarshi Guha
put the HTML in a GitHub repository? Then people can hack on layout... and send pull requests? - Egon Willighagen
there is a patch in my github fork - Egon Willighagen
Twapper Keeper is usually a great aggregator for multi day events. Here's the one I followed back in June for the annual oncology meeting, ASCO. Hashtag was #ASCO10. Scroll down to read the whole feed. - Sally Church
You can then download the tweets to excel and import them into other tools for analysis or use other online tools from the hashtag such as this using the same data: http://summarizr.labs.eduserv.org.uk/... - Sally Church
I imported the excel file into wordle, for top words used, but can't find the output. Melanoma was one of the hot words of the meeting, for example, owing to the ipilimumab data in the plenary. - Sally Church
Rajarshi... hey that's wicked cool! How can I see what the top words from #ASCO10 were? - Sally Church
@sally, http://rguha.net/atv/asco.html but not very useful since the twitter php code doesn't let me retrieve *all* tweets. It was a quick hack during a committee meeting, so has limited functionality. focus was on live updates of the conversations - Rajarshi Guha
@daniel, nice summary tool - Rajarshi Guha
Andrew Su
Boy, wouldn't it be cool if there was an easy way to translate a pubmed search into a wordle of the abstracts?
you could ask on BioStar, maybe someone will bite ;-) - Michael Kuhn
There's an interesting deeper question here which is how best to display a set of results from a literature search to make it easier to start organising the results and collecting what you need. We often think too much about "finding the right paper" rather than optimising the search/discovery process to get us the knowledge that we need...and if that sounds waffly its because I have no... more... - Cameron Neylon
Far from where you want to go, but still a step in the right direction: http://biosearch.berkeley.edu/index... . - Daniel Mietchen
That's certainly kind of neat... - Cameron Neylon
http://biostar.stackexchange.com/questio... -- will include a bounty if someone actually implements it! - Andrew Su
Okay, every once in a while I have to convince myself that I can program . So check it out: http://pubmed2wordle.appspot.com. (Only works on small queries < 100 due to GAE timeout issues, I think. executing on my localhost works fine...) - Andrew Su
Andy Maloney
Question to the community: Where do you draw the line with what you post in your open notebook? For instance, do you keep your notebook focused and only post results/failures with your experiments, or do you make a point to post things that are tedious lab necessities such as "mixing solutions, analyzing data, or cleaning..."?
It makes sense to catalog everything you do in the lab so that you can see how your time is appropriated. That way when you return to your notebook, you can see how much time it takes to do things. But, is it necessary? I'm on the fence about this one since there are pluses and minuses to both sides of the argument. - Andy Maloney
I try and just keep notes as I go. It's always the minor detail you don't think work recording that is the critical piece of information you want six months down the track. The mixing solutions one has bitten us a few times when one lot of buffer was good and one was bad. I've certainly never regretted putting too much in the notebook. On the other hand those details probably aren't... more... - Cameron Neylon
Cameron: I know exactly what you mean about mixing buffers as I'm making one right now that doesn't seem to be working. Perhaps I should make a category in my notebook that I tag things that I think are "lab drudgery". - Andy Maloney
Taking Cameron's idea a little further: top layer = homepages for each project, featuring an intro and any published work; second layer = lab notes focused on experiments; third layer = everything that happened in the lab and was recorded, by a human or by a machine. That way readers could choose their own level of detail. In my daydreams every lab links to this kind of layered notebook directly from their own homepage... - Bill Hooker
Steve Koch pointed out that I have been lax lately with posting to my notebook. I agree with him completely. However, what I have been doing lately seems to me more along the lines of engineering necessities and not science. Thus, no postings as of late from me. But it seems that even posting the engineering nightmares I have to go through to make science is important as well. - Andy Maloney
Bill: I've tried to implement your idea in my notebook. This is not trivial and is proving to be quite time consuming to try and tag my entries properly so that there is some sort of layering affect. Both for my own sanity and those that may come across my page. http://www.openwetware.org/wiki... - Andy Maloney
One negative idea I have about posting everything to my notebook probably has to do with how I feel about Twitter. No one cares (or at least they shouldn't care in my opinion) about how I had to order more vials. Of course, I may be taking that sentiment too far when it comes to my notebook. - Andy Maloney
Not to say Twitter is bad. It's great for those that want to use it. - Andy Maloney
"it seems that even posting the engineering nightmares I have to go through to make science is important as well" -- absolutely. This is exactly the kind of tacit knowledge that gets lost, and rediscovered, and lost, and rediscovered, and so on. If you solved a problem, engineering or scientific, then you did something that someone else might be able to use. Perhaps running out of vials... more... - Bill Hooker
+1 Bill and the challenge remains how to make it both easy to record all of that detail effectively and to make the right thing easily discoverable when someone somewhere wants it. - Cameron Neylon
I would not log 'making solutions', never logged that on books. But what I do is put the date on which a solution was made (date and maker's initials) and that gets logged in the experiment. Same with chemicals like antibodies: when I aliquot I tape the bottle label to the notebook and the 'internal' tag/batch that identifies the tubes in the freezer. The internal reference is what I... more... - Kubke
In my imagination we have a little web widget which is part recipe and buffer calculation engine and part logging in of buffer making. This serves two purposes, it makes it appealing to log the creation of the buffer because you get that as a side effect of bringing up/calculating the recipe and it also allows you connect other automatic logging of e.g. a balance that could let you go... more... - Cameron Neylon
I ask my students to keep a time log of what they do and observe. Invariably new students don't record enough detail. But that comes out naturally when I step through their logs and can't recreate exactly what they did - and I will comment on this directly in their notebook. Maybe they will remember a critical missing detail or maybe all that was learned from the experiment was what... more... - Jean-Claude Bradley
This is a terrific discussion -- one that I plan to use with students when discussing the practice/ethics of recording science. From a social science perspective, the mere existence of thoroughly noted lab notebooks is quite interesting... - Mickey Schafer
Sure D :) - BTW there is a recent paper in J Chem Ed about using wikis for chem lab - unfortunately none of them are public - via Brent Friesen http://ff.im/olji7 - Jean-Claude Bradley
Great discussion! My work is all theory and I don't get all my blackboard scraps into the notebook, though often I wish i had (learning that a camera is faster than LaTeX), while git records all the micro-level changes in the code so I just comment on the larger ones. I try and use tags to avoid the most useful stuff getting buried in the details but haven't found OWW Categories or search to be quite good enough for me. Open to suggestions for that one. - Carl Boettiger
Carl: Using OWW categories is a pain but, it is nice to have a page that links dynamically to all my notebook entries with specific category tags. I include a template in my notebook that allows me to write a short description about the entry and that description is visible in my DPL page. It's just a shame that I learned how to do this a year after I started my notebook, so I have a... more... - Andy Maloney
Chris Miller
The private beta of the Stackexchange Q/A site for Statistics has opened, and there are already some great contributions. If you signed up, go here to check out the site: http://stats.stackexchange.com/ If you didn't sign up, no worries - it'll open to the public in a week.
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