Piotr Byzia › Likes

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

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

NAR often includes previously published databases and software. - Matt Hodgkinson

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

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

Ha ha @Mark, but can you pronounce it ;-) - Graham Steel

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

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

Catchy URL: http://www2.innocentive.com/pavilio... :) - science3point0

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, 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

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

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

Eisenome. Brilliant !! :-)) - Graham Steel

Liking for "Eisenome". :-) - Bill Hooker

@Jonathan The geek element in me can confirm that http://eisenome.blogspot.com is freely available. Just sayin' ;-) - Graham Steel

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

"It Wasn't Me" - Shaggy :- http://www.youtube.com/watch... - Graham Steel

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

I am now the proud owner of http://eisenomics.blogspot.com/ and http://eisenome.blogspot.com/ - - Jonathan Eisen

1 Gazillion points to Mr/Dr./Prof J. Eisien for creating these soon to be, infamous Eisenome and Eisenomics blog sites via this humble FriendFeed thread !! - Graham Steel

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, I think we all have to hand this one to you for coming up with the idea in the first place :-) - Graham Steel

@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

To keep the fun/discussion going, I have commenced http://prionomics.blogspot.com/2010... - Graham Steel

Maybe we should do homeopathomics - Jonathan Eisen

Absolutely :-)) Now't on goog so far in that regard !! - Graham Steel

@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

Ideally, you'd want your own lab after 1 maybe 2 postdocs - if you eventually want to get a tenured position that is. The reason: they'll ask for senior author papers and you usually don't get them as a regular postdoc. - Björn Brembs

Sure you do... (well, perhaps I'm an exception...) - Egon Willighagen

Sometimes you do - my thesis advisor let me have a senior authorship during my PhD thesis - but that's pretty rare, I guess... - Björn Brembs

I have an undergrad (HHMI research scholarship recipient) who is getting first authorship on a publication, or so he claims on this resume. I haven't looked up the citation, but was impressed nonetheless. - Mickey Schafer

~3 years into my 1st postdoc and this question is also on my mind these days. My plan is to start looking after this postdoc. I also wonder how many years one should do before moving again. Any tips ? - Pedro Beltrao from Android

I don't think there's any one correct answer. It so very much depends on the field, the CV, what kind of position one is looking for (e.g. "highly ranked" research U. vs. a position with more emphasis on teaching), the particular year. etc. etc. - Mickey Kosloff

The Nobel Prize winner in economics, Joseph Stiglitz, says that his advisor in graduate student told him once, "You can't remain a promising young man forever." - Hope Leman

I'm with Neil and Bjoern: no more than 2, preferably one. Beyond that you are being treated as a fungible data-collection unit in someone's factory, a small stone at the bottom of a large pyramid. (I did 4, though one was so abortive I try to pretend it didn't happen, over 11 years.) - Bill Hooker

@pedro: I don't think it matters much if you spent 3 or 5 years on your first postdoc, as long as you've been productive. I'd definitely start looking for independent positions (in the widest sense) after five years, especially with your track record. They don't have to be tenure-track, but ideally they would. - Björn Brembs

Hmm... I'm currently in an odd position in so far as that I'm coming to the end of my first PostDoc, which I got before I had done a PhD. I'm now (hopefully) going to get a PhD via the work that I've published over the last five years. I've also got ~10 years industrial experience. So does this make me a newly awarded PhD, a one-PostDoc or a washed-up drifter?!? - Neil Swainston from iPhone

Why, the last option, of course :-) - Björn Brembs

It makes you uniquely qualified and uncategorizable. Bottom line no-one's going to care much beyond your publication list and any evidence of being able to bring in funding (industrial experience always looks good in the UK). To be honest in the current climate in the UK I would say all bets are off. There will be opportunities and there will be a lot of pain both institutional and personal so take a look at Deepak's post on serendipity. - Cameron Neylon

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

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

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

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

"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

http://tagcrowd.com/ - 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

http://github.com/rajarsh... - Rajarshi Guha

there is a patch in my github fork - Egon Willighagen

what about something like http://summarizr.labs.eduserv.org.uk/... ? - Daniel Mietchen

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

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

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