arek › Comments

I see nothing. Any chance we'll see a FF version? - Egon Willighagen

What tool are you using on the backend for entity extraction? Out of curiosity (I don't have IE handy) how many terms does it highlight in that text? - Rajarshi Guha

here's something that also works in Firefox: http://reflect.ws/Reflect... ( http://reflect.ws ). Although I'm on a Mac and so I don't know what actions are linked to the colored items in the posted URL - Michael Kuhn

Works here. What tool is used to extract the terms? - Rajarshi Guha

Michael, cool! That works for me too! But that's not ChemMantis, or is it? Where does this come from? And a very cool TLD, btw! - Egon Willighagen

Oh, and does it use semantic markup, like microformats or RDFa? Would love to see our Userscripts work on it! - Egon Willighagen

I noticed the class="reflect_chemical"... I'll update my userscript to support that (soon) - Egon Willighagen

Reflect is using the STRING/STITCH text-mining engine, plus lots of Java/browser plug-in magic by Evangelos Pafilis et al. I'm sure that if you contact Evangelos or Sean O'Donoghue with an idea about microformats etc. they might be able to embed something. - Michael Kuhn

(the approach is dictionary based, so no fancy recognition of IUPAC names etc.) - Michael Kuhn

Pawel I don't have any experience with CouchDB and HBase. They are quite fresh projects so there might be some troubles with support (correct me if i'm wrong). I was using mysql for some Uniprot data and with good indexation there were no problem at all to effectively find and fetch few thousands of rows at once. - arek

Depends on the structure of the data... if the XML reflects a simple RDBS design, then RDBS; if you have, instead, unpredictable structures in the XML, or very many fields in general which are only sparsely filled, you either have to carefully think about normalization (etc), or just use a XML db. The latter situation is where XML is really paying off: multiple namespaces. - Egon Willighagen

Thanks a lot guys! Amount of data isn't really an issue, but their structure indeed is, so I'll have a look at XML dbs. Uniprot was just an example of dataset that doesn't have all fields filled in (probably not the best one). I didn't want to suggest anything, but I was blown away by the new Parallax interface to Freebase - I'm aiming at something partially similar to it. - Pawel Szczesny

Postgres recently added XML support in the DB, so you can do XPath queries right in the SQL I think - Rajarshi Guha

Pawel: I'm curious to see what solution you come up with and how well it works ... I had to parse Uniprot/Trembl XML last week - I only needed one quick and dirty pass, so I used the Python SAX parser. Silly idea ... it took many hours to run over all 26 Gb. - Andrew Perry

Thanks Rajarshi, I'll have a look on Postgres (it was my favourite rdbms some time ago). Andrew, I'm going to share whatever I find useful - in theory dumping biodata into Freebase would be the fastest solution, but it's not that simple due to various licensing issues... - Pawel Szczesny

Yeh, the complexities of dealing the the licensing really put me off Freebase. Many many months ago (when I first got Freebase access) I was disappointed with the protein data in there. I decided rather than complaining, I'd just remedy the situation and import some large, freely available datasets. The definition of "freely available" was the problem. It was enough to make me give up on the idea in the short term ... it seems you must be allowed to re-license any data you put into Freebase as CC-BY. - Andrew Perry

UniProt has ID mapping service: http://www.uniprot.org/mapping... but it's limited to 1000 entries. Similar tool has EBI (PICR) and it has even RESTful API: http://www.ebi.ac.uk/Tools... - Pawel Szczesny

Wow what a marvellous response time ;-). Pawel and Duncan, Real thanks :) - arek

Prompt http://www.geneinfo.eu/prompt... is also interesing tool as far as not only protein id's mapping but also retrieval, analysis, and comparison are concerned (software described in publication recommanded by Duncan) - arek

It's worth to mention that PICR enables automation of resolving mapping problems (implemented by the means of SOAP and REST protocols) - arek

fingers crossed :) - arek

just occurs to me - can we do anything cool with a linkup to ISMB? Was going to use the coverage there as one of my examples... - Cameron Neylon

Cameron - Just to confirm, you'll be on at 12:45 UTC? Not sure whether I'll be able to watch it live (it's a bit early, here in Toronto!), but good luck! - Michael Nielsen

Cameron, I think FF cut your link short. Here's where some extra info can be found: http://bit.ly/3jIXnu - Ricardo Vidal

documentation http://code.google.com/apis... - arek

Don't see much benefit for large files that are streamed (gzip does a good job there)? But could be great for storing or transferring large quantities of small bits of data -- e.g. when using Google's App Engine datastore! - Eric Jain

I suppose the PC will be both alive and dead -- at least until the box is opened... - Eric Jain

Liking Eric's comment :) - Deepak Singh

admission time - I'll start. Win XP - PC - Graham Steel

I am a full Mac guy, but I am not a bioinformatician, so all my demands are fulfilled. at home: latest black MacBook 4GB RAM, at work: oldest white MacBook 1.25 GB RAM Oh, yeah and there is a new HP Compaq official XP PC on the top of my desk, somebody turned it on/off once. - Attila Csordas

Linux on PCs. - Chris Lasher

Vista Box, Linux (virtual machines at home, box at work), iBook, iMac, XP as virtual machine in Vista and iMac. - Paulo Nuin

Since our data acquisition is all controlled by Windows based software, it's a Windows box for me. But that doesn't bother me; I'm agnostic when it comes to operating systems. - NatBlair

Win XP PC, thinking of moving to Mac or Ubunto. Linux on clusters - Pedro Beltrao

Macbook Pro (recently acquired) + Linux VMs + Windows at work - Deepak Singh

Linux ! I can't imagine doing bioinformatics, programming without it !! - Pierre Lindenbaum

XP PC at work and home and additional PC Linux mint at home, had Vista, got rid of it thank god, hoping to find new PC laptop with XP on it, but hard to find.... - Nils Reinton

Mac OS X for most things at work, but it's an old box so for some stuff I have to use the new XP PCs. Win/XP at home because the spousal unit used to do Win-based IT for a living. Have a Red Hat install disc somewhere and all kinds of good intentions -- probably be better off with Ubuntu now though? Vista eats babies. - Bill Hooker

Mac OS X Leopard on iMac and laptop. I have an old Dell on XP Pro but it is almost dead and crawls at the pace of a snail. - Sally Church

At work, *nix for big machines and clusters; my workstation is an 8-core Mac Pro. At home, the PC I built runs Ubuntu/WinXP and I have an older Macbook. I prefer to develop for Linux, but I'm OS agnostic otherwise. - Adam Kraut

I've noticed that this is a question many people like to answer but they don't really like it. :) The statistics is interesting. - Attila Csordas

Now, I would be curious to know who is working at the bench and still analyzes the 'omics' data with microsoft excel .... - Pierre Lindenbaum

That's a question many people would NOT like to answer - Deepak Singh

No, Deepak, people answer to this question just don't like it. (How many people liked this message?) That's a difference. :) - Attila Csordas

@attila :-) - Pierre Lindenbaum

Mac OS X (Used to be PC Win NT also) - Mitchell Tsai

Does it really matter? All heavy tasks are done on remote machines which are always *nix based, so even if sb uses win, putty is a must. Personally, I use OS X on Mac, about 30% in Terminal. - Piotr Byzia

Vista at home, Ubuntu mostly for development. - Michael Nielsen

after a few years with OSX, switched to Linux / PC for cheaper hardware... Linux blade servers at work for the heavy stuff... lately 've been checking out BSDs, amazed by the lightweight-ness yet full power of NetBSD and contemplating a transition towards that direction (who needs multimedia ?!!? ) :-) - Ntino

After reading this I was curious about how using the old Dell would go, so I cranked it up (zzzzzz) alongside a PB of the same genre and boy, what a difference! I wouldn't go back to a PC and Windoze if you paid me - too slow and clunky and Firefox mysteriously closed twice. Hi hum. - Sally Church

Linux (Ubuntu these days). I also have a (rarely used) Vista partition on my laptop ... it's hard to buy one with the hardware specs you want without being forced to also absorb the cost of the bundled Windows installation. - Andrew Perry

OS X on my laptop, Linux on our servers. VMWare for cross browser testing. - Matt Wood

100% Linux at home and work, mostly Ubuntu. Quit Windows about 6-7 years ago, never looked back. Like the idea of OS X but haven't used it much. - Neil Saunders

Linux (Ubuntu at work and Debian on laptop). Virtualbox for some nice soft on Win XP. - arek

Ubuntu Hardy Heron 8.04 - Kyle Weller