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The Life Scientists

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Matt Wood posted a link

Failcamp

4 minutes ago - via Bookmarklet - Link

Embrace the fail. - Matt Wood via Bookmarklet

Pierre posted a message on Twitter

“OK, rails installed”

8 hours ago - Link

Michael Nielsen and Matt Wood liked this

Good luck! - Matt Wood

Deepak posted a message on Twitter

“Seriously thinking of moving of shared hosting and onto my own slicehost account (and moving to Dekiwiki as well for the personal wiki)”

8 hours ago - Link

Is there any reason to choose slicehost over other vps hostings? AFAIK, they are not the cheapest option available. - Pawel Szczesny

Good experience with bioscreencast and other anecdotal opinion. Cost is the only reason I haven't moved yet (that and the headache) - Deepak

and I just tweeted myself. Thought I was awake - Deepak

I've heard good things from Slicehost. I'm with (mt) at the moment - good so far too. - Matt Wood

I've found slicehost reliable and good value. - Michael Nielsen

PauloNuin shared an item on Google Reader

Writing An Hadoop MapReduce Program In Python

7 hours ago - Link

Thomas Brox Røst and Deepak liked this

And for the Rubyists, take a look at Skynet: http://skynet.rubyforge.org/ - Matt Wood

Roger Pettett posted a message on Twitter

“Another successful NPG release”

Friday at 2:12 am - Link

Matt Wood liked this

Congrats, Rog. - Matt Wood

Neil Saunders posted a message on Twitter

“is it wrong that the phrase "independence day" just makes me think of the whitehouse exploding in the movie of same name?”

Thursday at 9:30 pm - Link

Hassan Ibraheem and Pierre liked this

nope, thats the image I always get too. With Bill Pullman saying "Today we celebrate our Independence Day! " - Andrew Perry

Just makes me think of my birthday! - Matt Wood

Well then, happy birthday - Neil Saunders

Happy Birthday, Matt! Mine is tomorrow. - PauloNuin

The Life Scientists: Neil Saunders posted a message

“What interests you more: doing research or enabling research?”

Thursday at 5:57 am - Link

Alexey, Ntino, Attila Csordas and dekay liked this

Enabling! I'm so done with doing research right now. Too slow, too frustrating. It's fun now that I'm writing up my thesis, but every chapter was two years of work and I was unhappy and stressed and suppressed 99% of my time at the bench. - Eva

doing research. But mother Nature said "NOOOOO!!!!, the bench is not a safe place for Science when you're using your pipetman" :-) - Pierre

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enabling. I like the variety of challenges that brings as opposed to the microfocus of research - Daniel Swan via twhirl

Doing it, definitely. I've been a patch clamper a long time now, but I still get a thrill when I see currents up on the screen. There's nothing like it. - NatBlair

I loved doing research myself, but as a career, definitely the latter. - Deepak

Enabling: adding value to anything which helps the scientific method. Always different, emerging and interesting. - Matt Wood

Enabling it. I have the same feeling as Eva and Matt. - PauloNuin

both, but like to walk on the computational side - Attila Csordas

occasional bench research + running lab as a PI + teaching students - 2/3 of the current hellish grant burden = perfect - Maureen

enabling. greater variety, plus I still get to do all the original thinking I want to. Also I was a danger with P32. - Simon Cockell

I love doing research, but I hate writing it up. I enjoy writing well-crafted Ruby code to answer scientific questions, but I'm utterly useless at communicating the results. - Michael Barton

Haven't had much experience enabling yet, but I have the feeling I'd enjoy enabling research more consistently than doing research. But doing research does give a thrill if it goes well and you can keep the interest alive. - Shirley Wu

I do lots of "research" -- on the internets... - Eric Jain

Enabling & Connecting Minds. In doing my focus seems to move towards empirical work, statistics, anything in highly complex macro-systems. Ah, science in industry is cool. - dekay

It used to be research but then it got to a point where there were no tools available that could meet my needs, so now it has turned to enabling and trying to develop those tools. - Paul Bacchus

maybe I'm on the enabling side? Well fact is I've developed my share of computational methodologies and software so far, and it was fun!, but when it comes to thinking about the biological theories/hypotheses/paper writing from the data the software spit out, I kind of hate it. So I guess I'm no into "doing research", but more for hacking the heck out of it... - Ntino

I just don't know. I'm having a really hard time with that exact question right now. I'm nearing my use-by date as a postdoc and not sure I really want to try to scramble up the faculty food chain. - Bill Hooker

I'd say 60:40 - Ricardo Vidal

@Bill - hard time with that exact question is precisely my feeling and reason for the post. - Neil Saunders

the answer is "translate the the clinic!!!!!" not from bench to the bench - Alexey

Deepak shared an item on Google Reader

Intel Says to Prepare For "Thousands of Cores"

Wednesday at 4:00 pm - Link

err ... folks .. better start re-writing your code now - Deepak

parallelizing legacy code is a tremendous challenge; the tools suck and we aren't really training future programmers to do it; what will happen? - Adam Kraut

I thought we were hitting the limits of silicon semiconductors. What happened to "optical/quantum computing is the future"? - Neil Saunders

Having worked in the molecular electronics field in the past, I've heard the "this is the future of computing" all too often. Definitely fall in the "silicon has more legs than you think" camp - Deepak

Good overview of some of these threads from Pat Helland: http://is.gd/L5q - Matt Wood

One core per Twitter clone.. - Nick Lothian

Deepak posted an entry on business|bytes|genes|molecules

Wanted: Disruptor

Wednesday at 10:04 pm - Link

Pawel Szczesny, Mitchell Tsai, mike "glemak" dunn and Matt Wood liked this

Couldn't agree more. Love it. Should we wait for someone, or just start pushing the boundaries? - Matt Wood

I was just about to get around to that blog post about SNP profiling being a disruptive technology. Was even going to use that phrase, too. We must be reading the same people, Deepak! - Mr. Gunn

Neil and I have made a habit of telepathic blog posts. I should add that for a moment I was tempted to put a picture of a Klingon disruptor there :) - Deepak

I'll add that the technological disruptions are there (I was pretty much focused on SNP profiling in the clinic for the past six months), but how people use those technologies. Also, even with SNPs, the actual clinical utility is still limited (see Eric Schadt's work on needing network analysis etc to supplement GWAS) - Deepak

I've got into a habit of no blog posts; hopefully that will change on return from ISMB. So other than "just go for it", how would someone (practically) begin to drive a disruptive process? Let's say my goal is "revolutionise drug development". Academia is out - such a grant will never fly. So I need to think startup. Write a business plan, win over a wealthy philanthropist? - Neil Saunders

If I knew, I'd be on a beach somewhere :) - Deepak

Matt Wood posted a link

Gnip

July 1 at 10:35 am - via Bookmarklet - Link

Making data portability suck less, apparently. - Matt Wood via Bookmarklet

Matt Wood posted an item on Tumblr

Science Blogging 2008: Conference programme

July 1 at 5:54 am - Link

Jean-Claude Bradley, Duncan Hull, Deepak, Michael Barton and mike "glemak" dunn liked this

Hey, Matt, if you are talking on FF and Twitter on the conference you should set up a FF room for the conference to prove it! :))) - Attila Csordas

I can only prove my presence on the conference if I call it the Science (micro)Blogging 2008 conference. :) - Attila Csordas

Attila - excellent idea! http://friendfeed.com/rooms/sc... - Matt Wood

Matt Wood posted a slide show on SlideShare

Genomes On Rails

June 25 at 11:44 pm - Link

Heather, arek, Jan Aerts, Neil Saunders and Pawel Szczesny liked this

A repost due to the World's Best Presentation competition, now on over at Slideshare. - Matt Wood

Matt Wood posted a message on Twitter

“Another excellent day at Microsoft”

June 25 at 10:20 pm - Link

Michael Barton and Deepak liked this

Sounds like you're having fun with the MS folk - Deepak

Absolutely - smart cookies, one and all - Matt Wood

Neil Saunders posted a message on Twitter

“dropped a few project ideas on OWW biogang”

June 22 at 9:45 pm - Link

Andrew Perry, Cameron Neylon, Pawel Szczesny, Pierre and 2 other people liked this

Is the LIMS idea yours? I like that one. I think a killer app in that arena could make a huge difference to science, because once you get a majority of labrats using an electronic notebook you're halfway to getting them to do real science online. Think of it as a gateway drug for Open Science. - Bill Hooker

Left a comment on the LIMS system bit - our blog is going into major re-write over the summer and if we could get it talking programmatically to other services I think it could handle a lot of what is suggested there. Equally if people have views that it needs to change in a specific way (or you want to get in to have a look so that you can see what needs to change) then now would be a great time to tell us - also added a recent changes section to the front biogang page - Cameron Neylon

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I wrote a Joomla-based LIMS once: http://groups.google.com/group.... We use it in our lab. The code is terrible, it's unmaintained and unloved and I'd really like to redo it in a modern web framework, if I had the time. - Neil Saunders

The generic/modular Structural Genomics platform reminded me of a Synaptic Leap subproject that is wanting to do the target selection part: http://www.thesynapticleap.org... ... it seems the idea there is to use the 'traditional' target selection techniques alongside a social target selection scheme that uses collective knowledge (crowdsourcing, with a small, smart crowd I guess). Looks like there is a real need ... - Andrew Perry

We actually have a reasonable LIMS, written in RoR, for the UQ SG project. The problem is that target selection is not built in: it requires that you use a bunch of external scripts then upload a CSV file. What I'd like to see is an SG LIMS that starts with the gene and automates both the selection and construct design as far as possible. We need someone who knows RoR and bioruby or alternatively, Django/GAE and biopython. - Neil Saunders

Where's the URL to the ideas? I'd be interested in seeing them :) - Andreas Matern

http://openwetware.org/wiki/Bi... - Neil Saunders

I also have a vague, half-formed notion that Google Maps + geotagged genes would be cool; http://openwetware.org/wiki/Bi... - Neil Saunders

At the first DIYbio meeting here in Boston there was a similar project mentioned called Plant Genome Project with the help of http://www.metacarta.com/ Genomes of specific plants where mapped out geographically - Ricardo Vidal

Added a quick comment about the soon-to-be-open LIMS we use for next gen sequencing at Sanger. - Matt Wood

I think the LIMS idea is great, but dare I propose some integration with Outlook? Cut and paste ease with images, word docs, and excel files would be a must have for the aim of getting novice users to start using it. - Mr. Gunn

Nooooooo!!!!1111 Outlook is the spawn of Satan!!!1111 Though I absolutely agree that bringing novices on board will require integration with the tools with which they are already familiar. I just don't think anyone should encourage Outlook use. - Bill Hooker

I have to agree with Bill - with Gmail, Outlook can't compete with speed, convenience and reliability - and it is free to boot. Even our university is switching students over to Gmail because they can't compete with the offerings of storage space. - Jean-Claude Bradley

the Gmail thing is particularly close to me because a month after I switched from Outlook I had a massive crash and was hardly affected - Jean-Claude Bradley

I re-route all mail to GMail. Our uni has 200MB storage and rubbish spam filtering - so why would I bother with them? Wish they were as far-sighted as Drexel. - Neil Saunders

A while ago I hunted around for the Sargasso Sea datasets, hoping to find sequences with GPS coordinates to do a Google Maps mashup. I couldn't find any longitude + latitude data at the time, but maybe I missed it ... does anyone know if that is available now ? - Andrew Perry

@Andrew - don't know about the original Sargasso data, but the Global Ocean Surveyor data at NCBI is annotated with lat/long/depth. Search NCBI all databases for "global ocean surveyor" or here's an example: http://www.ncbi.nlm.nih.gov/en... - Neil Saunders

Neil: Nice ! That might be a project for the weekend then :) - Andrew Perry

I'm seeing a simple search form to the left; a Google map panel to the right; clickable markers that appear to indicate search hits; click marker -> display more fields and links. Mmm yes, could be rather nice. - Neil Saunders

Neil Saunders posted a message on Twitter

“one skill I have learned in academia is whipping up a bullshit abstract in no time :)”

June 19 at 10:16 pm - Link

Deepak, Euan, Pawel Szczesny, Lars Juhl Jensen and 5 other people liked this

someone should write up a generator for those things :D - Ricardo Vidal

One should start with ... "The sequencing of the human genome ... " - Deepak

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:) "plethora of data", "tsunami of information", etc. etc. - Neil Saunders

"information overload", "web services", "semantic .*" - Lars Juhl Jensen

"complex systems", "high throughput", "nano-bio" "systems biology" ^H^H^H^H^H^H^H^H^H :) - Cameron Neylon

"Exponential data explosions", "era of personalised genomics", "exabytes", etc - Matt Wood

Thank you all for the inspiration :) - Pawel Szczesny

upregulates, generates, contributes to, affects, induces - pick your weasel word - Mr. Gunn

Maybe the BioGang can complement the impact factor with a bullshit-abstract factor, based on the occurrence of those weasel^Wbuzz words? - Egon Willighagen

Maybe something a bit like one of the Readability indicies ( http://www.standards-schmandar... ) mashed up with Lars' BuzzCloud buzzword extraction method ? - Andrew Perry

I can pretty much take all the words here, add some more for structure and have a short abstract - Deepak

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Pellentesque ultricies, elit a iaculis suscipit, turpis turpis aliquet dui, quis facilisis orci ipsum id lectus. Vivamus a urna. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Fusce at felis. Sed rhoncus lorem et metus. Curabitur eget lectus vulputate libero tristique viverra. Aenean ullamcorper justo ut mi. Cras mollis nunc sed leo. Sed iaculis eleifend nisi. Phasellus sem eros, ullamcorper at, pretium ac, rutrum ac, odio. Praesent nec quam congue mauris aliquet condimentum. Fusce dui dui, faucibus vel, eleifend vitae, tristique a, pede. Proin ante ante, volutpat vel, lacinia ac, feugiat sagittis, sem. - Brian Daniel Eisenberg

Yes, I was thinking along the lines of defining a BS Index (which of course is short for "Buzzword Similarity Index"), but I never got around to doing it. I think it could have many (politically incorrect) uses: the most obvious is to be able to rank abstracts based on their BS Index, but one could also consider averaging across all papers by a given author to obtain the author's BS Index ;-) - Lars Juhl Jensen

That would be _solid gold_ Lars. - Andrew Perry

Lars, maybe Bullfighter could be adapted for this purpose http://scilib.typepad.com/scie... - Richard Akerman

Abstract generator, circa 1997: http://toddot.net/projects/fun... - Todd Harris via twhirl

Todd - that is great. I put in some realistic and some bogus terms and got, pretty much, something we REALLY did in the lab! - Bora Zivkovic

Bora Zivkovic and Herbert Underwood NCSU Despite ten years of intensive efforts, little is known about the molecular mechanisms that underlie circadian rhythms. Recent observations have implicated cryptochrome, a photolyase, in this process, but to date no perturbation studies of this gene have been conducted. We tested the hypothesis that cryptochrome functions in circadian rhythms by cloning the Japanese quail cryptochrome homolog. The homolog encodes a predicted protein of 1000 amino acids with 96% overall identity to the vertebrate cryptochrome. Japanese quail cryptochrome is highly expressed in all retinal ganglion cells and colocalizes with period, a protein known to be essential for circadian rhythms. Mutations in cryptochrome substantially disrupt circadian rhythms and cause Japanese quail to become clock-blind. These observations 1) confirm a role for cryptochrome in circadian rhythms and 2) suggest that cryptochrome and period form part of a core complex mediating circadian rhythms. - Bora Zivkovic

The Life Scientists: Martin Fenner posted a link

RailsConf Europe 2008 - O'Reilly Conferences, 02 September - 04, 2008, Berlin, Germany

June 20 at 3:17 am - via Reshare - Link

Matt Wood liked this

Is anybody planning to attend this conference? - Martin Fenner

I'll be there: was also thinking of arranging some kind of scientific software summit around there, too. - Matt Wood

I went last year, but haven't decided on going again. But I would be around to do something. - Martin Fenner

Jeremy Zawodny bookmarked a page on del.icio.us

It Gets Worse: Joshua Schachter Leaving Yahoo

June 19 at 7:20 pm - Link

Harvey Simmons, Isaac Hepworth, marcel weiss, Ron Emrick and 9 other people liked this

I saw this coming a mile away... - Jeremy Zawodny

This is what they call an exodus - Deepak

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Joshua always copies Flickr! :^) - Christian Crumlish via Alert Thingy

For me this one is particularly sad. del.icio.us remains my most used web service, and despite Yahoo neglecting it for so long, I've never found anything to replace it. - Deepak

My question is: what's going to happen to my Flickr, del.icio.us data? - l0ckergn0me

It is all looking a bit ominous. I like del.icio.us, but there are very similar alternatives to turn to. Flickr is a different story; IMO it's by far the best photo manager out there. - Neil Saunders

@l0ckergn0me : read yahoo's TOS :) - directeur

... delicious isn't being neglected by Yahoo. - Dave Dash

Excuse me while I go and back up my bookmarks - Adewale Oshineye

@Dave - as a user of delicious all the publically available evidence points to it being completely ignored... - Andy Davies

Interesting: http://www.techcrunch.com/2008... - Matt Wood

Del.icio.us could have become anything if Yahoo had put resources behind it. You can see the genes of delicious in things like Digg & FriendFeed now - but delicious itself has gone nowhere. - Nick Lothian

Delicious has in a way fulfilled its historical mission: spreading the tagging meme. - benedikt

Good call benedikt!! Tags as touching points born on del.icio.us, next stop mento.info ;-) - cbgreenwood

Nick Lothian is right. del.icio.us could have become something huge. but they went nowhere with it. it's pretty unbelievable actually - marcel weiss

another sad day on the internet. - andre

Duncan Hull posted an entry on CiteULike: dullhunk's library [1292 articles]

Digital identifiers work for articles, so why not for authors?

June 18 at 2:49 pm - Link

Jill O'Neill, Tom Morris, Sean McBride, Mr. Gunn and 5 other people liked this

If it is possible to have DOIs for objects (or, so they say, enough IPv6 addresses for every molecule on Earth), why is it so difficult to implement DAIs for authors? - Duncan Hull

Because everyone wants their own ;-) - Cameron Neylon

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ask NCBI... - Pierre

I'm not sure NCBI see it as their problem: although they are clearly best suited to fix it. There is Spock, but that doesn't seem to have gathered much traction: http://www.spock.com/ - Matt Wood

I think biomednetwork has probably implemented this the best - at least in terms of figuring out who is who - but all of these things seem to be limited to abstracts in PubMed which is a bit limiting really. Need something that publishers actually want to implement and which is an 'opt-in' system. And who gets to assert who the authors on a paper are - the corresponding author - the poor student actually doing the submission? - Cameron Neylon

This is one of those issues that everyone agrees on and that comes up once in a while but for some reason it still is not implemented. NCBI would be the best place to start. Is there any argument against an universal author ID number for science ? The only questions would be when does someone get recognized as an author ? Who certifies the authorship? - Pedro Beltrao

I think all the efforts will be vain as long as pubmed/NCBI , the leading player, will not add an author-id in the pubmed records. It needs a database of author with their name, their location, their... hey... we already suggested this yesterday, didn't we ? :-) http://friendfeed.com/e/5a1a4d... - Pierre

The technology is there to do it http://en.wikipedia.org/wiki/O..., I think the main barriers are sociological and political. The NCBI is not necessarily the best place to start, like DOI's, it needs to work outside (as well as within) biomedical and life sciences. If you like commercial companies being in charge of your identity then there is http://www.researcherid.com, http://www.scilink.com and hundreds of other people eager to take on your digital identity for you... - Duncan Hull

Online identity is probably the next big thing on the web. Whether it is you as an individual, or you as a scientist, or you as a furry, there needs to be some control of who you are and what you can claim. Maybe the future is some kind of marriage between openid + researcherid type system, i.e. one where you can claim a domain specific id, via some global ID system. - Deepak

This is actually kinda a gnarly thing, when you think about it. Theoretically, ICANN or DOI could have a little side-business assigning identifiers, but do we really all want permanent unchangeable serial numbers? - Mr. Gunn

SciPhu posted a message on Twitter

“Any downside to upgrading to Firefox 3 right away ?”

June 18 at 4:11 am - Link

Tom Morris liked this

No and it's much faster! - Sally Church via fftogo

Unbelievably faster and better memory usage. Used to assume FF2 page rendering was slow due to slow networks, but it was FF2. - Neil Saunders

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Only downside is some of your favourite extensions might break. - Neil Saunders

i upgraded to FF3 and it is great so far! - Morgan

Firefox 3 has been great for me on a Mac. Prefer it to safari - Michael Barton

Favourite plugin not migrated yet though http://tinyurl.com/6ekbch - Michael Barton

Really very fast: any killer 3.0 plugins that I should take a look at? - Matt Wood

@Mike - lol. Most if not all of my favourites have a 3.0 version (del.icio.us, greasemonkey, adblock, better gmail 2, gears, google notebook...many more) - and some new FF3 features make some extensions obsolete. - Neil Saunders

How often do you use Google Noteook? Do you find it useful for keeping information? - Michael Barton

I use GNotebook quite a lot. It's great for just quickly grabbing a link to a page with some text to come back to later; e.g. for writing a blog post, answering a question, recording the URL of a database search. Also non-work stuff: recipes, travel plans. I think the collaborative features have potential too, but of course can never get the colleagues to try it out. - Neil Saunders

Almost all of my plugins are still working great. "It's All Text" being the one I can't live without, being a Mac-bound TextMate addict. Firefox 3 is officially very good. - Tom Morris

FF3 installed and I am an even happier camper - SciPhu

Tom - I LOVE it's all text, too. - Mr. Gunn

Pawel Szczesny posted a message on Twitter

“Convinced half of my colleagues to join FF and The Life Scientists room. Now back to writing PhD thesis...”

June 18 at 3:44 am - Link

Pierre and Neil Saunders liked this

Best of luck! What's the page count so far? - Matt Wood

Thanks a lot Matt. It's around 40-50 at the moment (it would be more, if I didn't use LaTex :) ). There's something like 20 left (another week) and I'm done. Or rather I have to be done before end of next week, as I have another project due in July. - Pawel Szczesny

Neil Saunders posted a message on Twitter

“I want to like Nature Network, I really do, but it can't progress without a total redesign from bottom up”

June 18 at 3:23 am - Link

Michael Nielsen, Mr. Gunn, Eva, Kambiz Kamrani and 5 other people liked this

My dreamed NN would be just a repository of FOAF profiles ( http://xmlns.com/foaf/spec/ ) including publications, geo-loc , interests, accounts , etc... :-) - Pierre

Seconded. Some ideas: ditch the big banners on each page, but the content front and centre, optimise the common paths and network features and make it much easier to jump to current 'hot' discussions. - Matt Wood

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Fix up the RSS - still haven't got it quite right. Thread the comments. Enforce tagging. Roll out the API so some smart person can rustle up a Firefox extension and we don't have to visit the actual site. - Neil Saunders

Why APIs are important #6728 - because at least half your potential users will always think your interface sucks - Mr. Gunn

Pierre, you just made my day. I don't think we need more networks, we need something like Friend Connect with support for pubs, etc. For connecting with people we already have LinkedIn and the like, many of which are begging to support hCard and FOAF, etc - Deepak

get yer FOAF here, if you don't already have it: http://www.ldodds.com/foaf/foa... - Mr. Gunn

FYI: Years ago I wrote SciFOAF http://www.urbigene.com/foaf/ a tool building a FOAF profile from pubmed and FOAFExplorer (http://www.urbigene.com/foafex...) to browse a FOAF file. Both are somewhat old, at that time I didn't fully mastered RDF, and many TODO on my list (I should rewrite this using the Jena API....). - Pierre

My #1 wish for Nature Network is an API. Support for OpenSocial would also be great. - Martin Fenner

all good ideas, I think total redesign is a bit strong though. Also FOAF has a tiny usage outside of sem web circles. Rss bug already noted, it is a valid feed, but it is lacking ids, so isn't as compatible as it might be. - Gavin Bell

Pierre, I spent a while with your SciFOAF, getting fascinating results. Turns out I'm 4 degrees removed from George Daley of iPS cell fame. Also turns out that this little corner of my field is quite inter-linked, but has few external connections. I'd love to see an updated version of this. - Mr. Gunn

Matt Wood posted a message on Twitter

“Big queries in BioMart: 28,094,448,845,195,421 rows returned, 10 ExaBytes of data.”

June 18 at 2:44 am - Link

Nick Lothian, Benson Miller, Brandon Werner, Piotr Byzia and 7 other people liked this

Insane! And BioMart handles that? What sort of run time? - Neil Saunders

A single, popular transcript on the MHC viewed through BioMart's 'cartesian product' query. "Handles" is a strong word: let's just say we didn't let it complete. ; ) - Matt Wood

I'd love to see my network admin's face if I called up 10 EB of traffic :) - Neil Saunders

Got any example queries? Just curious... - Duncan Hull

Jan Aerts posted a message on Twitter

“After trying git-cvsimport and cvsparse without any luck, I bumped into fromcvs/togit. But guess what: doesn't work either.”

June 18 at 2:25 am - Link

Ouch - cvs -> svn -> git may be your only salvation! - Matt Wood

I tried to do a CVS->Git import a while back and it took about eight or nine hours to run, then failed. Running it again would take another nine hours. I was very tempted to just take the latest snapshot. Really quite annoying. - Tom Morris

The Life Scientists: Shirley Wu posted a message

“Clustering question for the informaticists: out of the half a dozen or so ways of calculating intra- and inter-cluster distances, is there one that is most widely accepted? For hierarchical clustering, is there a linkage method that is preferred over others?”

June 17 at 4:48 pm - Link

Andrew Perry, Pawel Szczesny, Pierre and Deepak liked this

clustering of what? - PauloNuin

Yeah, that was my question :) - Neil Saunders

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Depends on what type of data you are looking at. Average and complete linkage are probably common, but I've noticed a lot of people move to other forms of clustering lately, especially SOMs (for gene expression data) - Deepak

I'd like to see a method that clusters all the different clustering methods out there :-) - Eric Jain

Meta-clustering. Well if we can have meta-programming, why not - Deepak

Well, nominally I'm talking about binary vectors, but it's possible I will work with non-binary vectors too. The vectors are features derived from sites in protein structures. Perhaps the answer is totally dependent on the nature of the data? - Shirley Wu

I just realized you work for Russ Altman. Didn't they publish a k-means clustering paper on protein microenvironments last year? Is there a reason you wouldn't use that? Going back to your original question, I suppose Pearson Correlation might be a good place to start and apply on a test set to see if you get some decent clusters - Deepak

K-means seems to be pretty popular, and is relatively easy to implement. From that, you should get some idea as to whether additional clustering approaches would be useful. - Matt Wood

Pearson is a good distance measure for variables in a dataset. An example would be clustering stats about a group of people such as height and weight, you cannot compare these directly, but you might be interested in how one variable changes with the other. Euclidean distance on the other hand would be useful for clustering the records (each person) based on their height and weight i.e. sum of the difference between height/weight of person A and person B, where you can compare variables on the same scale. - Michael Barton

You could also think about row/column normalising a data set to prevent over-variation biasing the clustering method. This wouldn't be applicable to a correlation based distance measure, but would be for a euclidean based distance measure. One possible way to normalise is to scale each row/column to have the same mean and variance. - Michael Barton

I realise I didn't answer your original question. I like centroid based linkage because it's median-based and is a little more robust to outliers. However this might not be as useful if the data is non-globular. As Deepak mentioned SOMs are good, as well as Neural Gas, and Growing Neural Gas. If you're using Matlab I think there's a good package with all these things in. - Michael Barton

If you're using R, Mclust is pretty good. You don't have to decide the number of clusters before hand, the model calculates the number of clusters in the data based on maximising a byesian information criterion. - Michael Barton

@Deepak, yes, we published a paper with k-means, and now we're going back to those clusters and would like to do a "better" clustering within them - idea being that k-means got us into a reasonable ballpark, now we want to have more refined clusters. - Shirley Wu

The last two days I've been using Cluster 3.0 (with TreeView to visualize) which offers probably half a dozen distance metrics and 4 or 5 linkage methods. I'll look into Mclust for if we decide to recluster everything, but we're talking 2 million vectors here - can SOMs or Mclust handle data on that scale? - Shirley Wu

Use Dendroscope for visualization. Better, more powerful. - PauloNuin

I've never used Cluster unfortunately. Two million vectors is large data set, I'm not sure how R would cope with that, I guess the only way to find would would be to give it a go if you have the time. As for SOMs I guess it would depend on which platform, I think Matlab should be able to handle such a sized dataset. - Michael Barton

Two million vectors in R would take quite a while and good amount of memory. - PauloNuin

Deepak posted a link

Wordle - mndociondelicious

June 16 at 8:55 pm - via Bookmarklet - Link

PauloNuin, Mr. Gunn, Matt Wood, Andrew Perry and 2 other people liked this

Coolness - Deepak

Blogged mine wordle: http://chem-bla-ics.blogspot.c... - Egon Willighagen

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Funny ! here is mine ( phew ! Bioinformatics is the biggest word !) http://wordle.net/gallery/pier... - Pierre

I get "applet not started". Whatever. - Neil Saunders

Posts from Green is Good: http://wordle.net/gallery/Gree... - Matt Wood

pretty cool - Mr. Gunn

Can you say I am a biologist? http://wordle.net/gallery/nuin... - PauloNuin

Matt Wood posted a message on Twitter

“Quitting and uninstalling Flock 2”

June 17 at 4:06 am - Link

4 minutes only? - PauloNuin

Yeah - and 3 minutes of that was it spinning the beach ball at me! - Matt Wood

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I love that "additional plugins" are required to show the getting started page. - Neil Saunders

I also respect the eagerness to become my default browser. RealPlayer from 1992 is calling, he wants his nag window back. - Matt Wood

I think I need to check Flock 2, seems kinda fun - PauloNuin

I gave it a quick run; it is quite fun but eats CPU on my system. Apart from a few cool features, don't see how it differs from FF + extensions. - Neil Saunders

I am trying http://xerobank.com/xB_Browser... - PauloNuin

Pierre posted a message on Twitter

“@mza currently whatching your presentation http://www.viddler.com/explore...”

June 16 at 8:16 am - Link

Awesome. Enjoy! - Matt Wood

The Life Scientists: Jason Stajich posted a link

Google Trends: bioinformatics, computational biology, genomics, genome

June 12 at 5:29 pm - via Bookmarklet - Link

Chris Lasher, Matt Wood, Duncan Hull, Attila Csordas and 3 other people liked this

hmm, is it all losing steam - Jason Stajich

Lincoln Stein's prediction is coming true :) http://www.oreillynet.com/pub/... - Neil Saunders

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check the top country, India, and the longest bar is bioinformatics -- haven't searched the matter, but is there outsourcing of bioinformatics application coding there like with the other types of software ? - Ntino

They changed the scaling algorithms in the new version right ? I cant seam to make a query that results in an upward trend. Maybe buggy ? Alternative .. a lot more people getting online and therefore reducing the relative number of science related queries (its a relative measure). Or just even pople doing a lot more queries in general, most of them just to find a website, etc - Pedro Beltrao

Agree with Stein's writing... it's a tool, even though to do, but will become a field generated by the next stage in the evolution of the biology field... cause biology is becoming more and more data intensive. Do you think in 2012, anybody will be going to the lab to do cultures on Petri dishes and observe colonies changing colors (sorry wet lab people in the room). Sure there'll be labs, but Core labs with the data spitting instruments, like array scanners, sequencers, auto-protein gel scanners etc. - Ntino

... to continue the rambling: all data out of those machines sucked into computers (well we hope for e-lab notebooks, or better for the data in the open) and then that 's where the discovery will be... that's how I see the future of biology, which is currently happening, turning into a data-intensive discipline. - Ntino

Note that the news volume (bottom chart) has actually increased. The search stats tend to be a bit weird (except for very popular search terms, which bioinformatics is not), so I wouldn't use that information for investment advice :-) - Eric Jain

I sense debate brewing :) I think there will always be a place for people looking at things in labs. I like bioinformatics but I don't think it ever has been, is, or will be a field. The sole reason for bioinformatics journals is to give academic bioinformaticians a place to publish: because that's the sole output recognised by academia. Academia doesn't know how to employ tool-builders, or recognise their skills. - Neil Saunders

One reason "bioinformatics" collapsed as an industry was for some of the same reasons listed above. It was never an industry by itself, just got subsumed by the broader scientific process (by and large) - Deepak

To blame: Leona Lewis? http://is.gd/wAp ; ) - Matt Wood

To be honest, that was a joke: but what's going on towards the end of 2006? A big spike for Leona and a big corresponding dip in science searches! She _is_ to blame! - Matt Wood

:) I blame twitter, same observation. - Neil Saunders

Matt ... lol :) - Deepak

Attila Csordas posted a message

“The 8GB model is going to be $199, 16GB will be $299. There’s also going to be a white model. WHITE.”

June 9 at 11:47 am - Link

It's going to be a maximum of $199 USD in any country, according to Leo Laporte. With 3G and GPS builtin, impressive. - Chris Lasher

Remember me to tell you the price in Brazil after the release date. Everything there has at least 100% premium. - PauloNuin

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I find it difficult to believe that there won't be a 100% markup for the UK market - Cameron Neylon

Chris, it's only impressive compared to itself. Newer model Nokias have had 3G and GPS and Wifi for years, and they're not any more expensive. You also don't have to pay $10-25 extra for unlimited data. Oh, and the screens are higher res. - Mr. Gunn

yeah, but that UI and the web browsing. I don't have one, but it's been cause of the price - Deepak

My Nokia E51 feels dated now. At least it's a single-handed phone, one of my decisions not to get an iPhone (or Blackberry). - Roland Krause

Deepak - Did you know that the N and E series Nokias (Symbian smartphones) use the same browser as the iphone? iphone sites/apps generally work on the Nokias, but you can also install local apps when you need speed, like for maps and gmail, etc. - Mr. Gunn

I've heard already approximate price in Poland for 8GB model - ca. $270 when signing two year contract. Still it's pretty OK, I would expect much more. - Pawel Szczesny

Mr Gunn - it's the same rendering engine, WebKit, rather than the same Browser, Safari. It's _all about_ the pinch zoom. ; ) - Matt Wood

I'll be surprised if they don't have a huge mark up in Australia. My prediction: 8GB=US$300, 16GB=US$400, only available on 24 month $50+ contracts (at least for the first few months while the hype subsides). Lets see how close my prediction is. I'll be thrilled if I'm wrong, since that means I may get one (after closely comparing the Nokias ... I agree with Mr Gunn [ http://www.thebestpageintheuni... ]) - Andrew Perry

LOL, Andrew, I thought about posting that, and I do have PuTTY on my phone. - Mr. Gunn

Jeremy Zawodny posted an entry on Jeremy Zawodny's blog

Leaving Yahoo!

June 12 at 6:42 am - Link

accesine, Jeremiah Owyang, My Blog Posts, Gabor Cselle and 72 other people liked this

Good luck at your new gig! - J. Phil

From somebody who's Internet experience has been heavily influenced by you (you were one of the first blogs I ever followed), best of luck and I look forward to seeing the results of your new opportunity! - Damon via twhirl

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yahoo won't be the same without you.. :( - Augusto Becciu via twhirl

Just to hope you all good to your new work, whatever it is. - Daniel Schildt

Where are you going? Anywhere we've heard of? - Tony Ruscoe

Jeremy. Good luck. I can only echo what Damon said above - Deepak

good luck - Andreas Gohr

shocked to know that u'r leaving. good luck. - Jansen Lu via twhirl

:) - Sarath via Alert Thingy

shocked. And happy for you :) - John Mueller

woo. crazy. all the best to you. - Josh via twhirl

Congrats on a huge move, and all the best, Jeremy. You'll be deeply missed as a Yahoo, even by those of us that don't work there. - DeWitt Clinton

Welcome to the ex-Yahoo club, Jeremy, and congratulations on the move. Looking forward to seeing what comes next for you. - Ryan Kuder

Congrats! - Ginger Makela

Best of luck! - Mike Reynolds

Who's the next lucky one to hire you!? :) - directeur

Good luck! - Matt Wood

Reading this in Friendfeed. Doesn't seem appropriate to "like" it. More "ackknowledge that it is news". You seemed like a force for good in a good company Jeremy. - Scott Koon via twhirl

Congratulations ;) What's next ? Google or Own project ;) - David Berrebi via twhirl

@Jeremy startup please!! ;-) - Erhan Erdogan

He said a 'smaller' company. So that rules out Google. - Adewale Oshineye

Best of luck Jeremy ! - Charlie Anzman

Good luck Jeremy, can't wait to see what your up to next. - Barry Schwartz

Wow! All the best man! - Robert Cooper via twhirl

Wow! Good luck Jeremy! - Niranjan Tulpule

The problem with having an ! in your company name is people always sound so excited when they write about leaving - Christian Anderson