Rajarshi Guha › Likes

"matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala matlab or mathematica), web application servers, and six graphical user interface toolkits. matplotlib tries to make easy things easy and hard things possible. You can generate plots, histograms, power spectra, bar charts, errorcharts, scatterplots, etc, with just a few lines of code. For a sampling, see the screenshots, thumbnail gallery, and examples directory" - Mike Chelen from Bookmarklet

thanks to this post for mentioning the library: http://biostumblematic.wordpress.com/2009... - Mike Chelen

I've found matplotlib to be one of the more mature plotting libraries out there. It's also a great reason to use tools like f2py to bring data into Python. - Christopher Granade

#qotd "I'm playing my part in the slow strangulation of innovative blue-skies research - but hey, I've got to eat, right? " - Duncan Hull

View the Universe in seven different wavelengths: gamma ray (Fermi), X-ray (ROSAT), H-alpha (WHAM), optical (DSS), infrared (IRAS),microwave (WMAP) and radio (Haslam). Developed by Stuart Lowe (Manchester), Chris North (Cardiff) and Rob Simpson (Cardiff) - Sarah Kendrew

Anyone interested in a webinar on Bioclipse2 plugin development? If so, please send email to the bioclipse-devel@ mailing list... - Egon Willighagen

"he credit card data read from the magnetic stripe is not stored on the iPhone at any point. The magnetic data is converted to audio and input through the headphone jack, where it is encrypted and transmitted to Square for processing" - Attila Csordas from Bookmarklet

Except for the minor point that most places in the first world don't use the magnetic strip any more because it's inherently unsecure :-) That said I heard that phones would be shipping with RFID readers in 2010 recently which solves the same problem potentially. - Cameron Neylon

great - Jorko Jorkov

all of their slideshare stuff is worth a look - Neil Saunders

Two weeks ago, I released CDK 1.2.4. Anay reported fails with generating the JavaDoc from the packages, which I think I both fixed now; the uploaded 1.2.4.1 packages on SourceForge include these fixes. The 1.2.4 release was soon followed by 1.3.1. Unfortunately, uploading the packages to to SourceForge over 3G with Chrome did not work well, so only finished that today. CDK 1.3.1 is the second release in the development branch, and brings in new functionality but also API changes. Here are the changes since the 1.3.0 release:Bumped version for 1.3.1 release c341095Added some extra lines, hopefully fixing the conflicts all the time 6dab943 Fixed param name 743bad3 Updated the makefp3d target to work with the current build system bbb78ee Set up a branch for the 1.2.4 release 4801d79 Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H. Also...

Well worth the download. Focuses on the theory, rather than the R code. - Neil Saunders

Maybe Springer finally realised that *no-one* buys their stuff because it's so expensive ;-) - Neil Saunders

Strangely similar in some ways to a discussion on the Java Posse - Deepak Singh

lol ... the field with more reviews than actual research papers :) - Pedro Beltrao

this could be a good measure of hype reviews/research papers - Pedro Beltrao

We could have a hype factor per field/keyword/buzzword :-) - Bruno Afonso

That was the last one folks - we're looking for further sponsorship for next year - let me know if interested - Jean-Claude Bradley

We use BerkeleyDB here (key=snp, value=array of genotypes). Last year, Deepak suggested to use HDF5 too http://twitter.com/mndoci... - Pierre Lindenbaum

HDF is nice because scaling up is relatively straightforward, haven't tried BerkeleyDB for comparison though - Mike Chelen

@Mike I just read the doc of HDF5. I understand it is a good choice for storing structured data but it it isn't clear for me how it can be used for querying the data. e.g. find a genotype=f(sample, snp) - Pierre Lindenbaum

Did you know you can run remote computations from your Windows/Mac/Linux box without any special client software installed, just by dragging and dropping? And it even doesn’t matter if it’s not online all the time… The trick uses Dropbox, which is software that syncs your files across your computers. This is incredibly handy – as time goes on we all use more PCs, laptops (and indeed iPhones!) and Dropbox synchronises the contents of your Dropbox folder across all these for you. Note this is quite different from having some centralised filestore (or WebDAV drive) mounted on everything – it doesn’t need you to be online at time of use and it doesn’t need a sysadmin to set it up. Dropbox is very easy to install and incredibly easy to use – there really is no need to read a manual and the benefits are immediate. (Other synchronising software exists, but Ian prefers the simpliciity and ease of Dropbox.) - Duncan Hull

Anyone tried this? - Duncan Hull

We've not tried the compute side, but have been using dropbox to move stuff between our compute machines. Looking forward to trying this - thanks for flagging it up ... - Anna Croft

Qian at Indiana wrote a little service that does linear regression for JC and I. - Andrew Lang

thanks - Rajarshi Guha

Rzepa applies the anthropic principle to amide bond rotation. [Note to self - how do dipoles help explain the Me inequivalence of dimethylformamide?] - Matthew Todd from Bookmarklet

It is interesting that we sometimes see rotamers for our Ugi products in the H NMR spectra - an example 173G containing and alkyne bond http://usefulchem.wikispaces.com/Exp173 - Jean-Claude Bradley

Couldn't you change the parameters in the model he mentions to see what chemistry would be like in a 'different' universe? I think that would be very interesting. - Andrew Lang

ouch! That hurt! - Björn Brembs

The stupid... it burns. - Bill Hooker

with the notable exception of dataspora.com - Neil Saunders

Dataspora rocks. Normally I access R through Python with rpy2 (http://rpy.sourceforge.net/rpy2...). It's a nice way to work as you get all of the web frameworks and what not with Python and still do your statistical work on the backend. Galaxy does this as well with several of their integrated tools (http://main.g2.bx.psu.edu/). - Brad Chapman

I think Brad (and the Dataspora PDF) have a point - R is used but as a backend tool. I think RApache and RWeb are the only packages that make R a web app directly. rpy2 is a great approach. JRI and Rserver are also excellent if you have to work with Java - Rajarshi Guha

PDF presentation on R, web apps, big data from Dataspora - Neil Saunders

This is a wise step... I hope it is in time, and I hope it is not a hollow promise... time to act, I'd say. - Egon Willighagen

It strikes me that I still have the other half of my pork belly...is the complete recipe online somewhere? - Cameron Neylon