tag:blogger.com,1999:blog-8401274931342779902009-10-23T17:41:09.203-02:00Scientific adventures with Python.Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.comBlogger49125PythonInSciencehttp://feedburner.google.comtag:blogger.com,1999:blog-840127493134277990.post-34308924665125801522009-10-22T09:05:00.001-02:002009-10-22T09:05:55.295-02:002009-10-22T09:05:55.295-02:00

I have recently come across an interestng problem while working on my random variable implementation for BIP. Any type in Python is expected to have a __str__(self) method which returns an adequate and expressive string representation of the object. Well, as far as I could think, the most straightforward representation of a random variable is its probability distribution. Probability

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com4http://pyinsci.blogspot.com/2009/10/ascii-histograms.htmltag:blogger.com,1999:blog-840127493134277990.post-12758953385080743302009-09-29T10:11:00.001-03:002009-09-29T10:11:56.793-03:002009-09-29T10:11:56.793-03:00

This document is a must read (see link at the end).I want to add my own items to it:1. Net Neutrality is not only protecting Internet content provider corporations' profitsWe need to defend net neutrality in a way which goes beyond what is currently done: We need to establish fixed ip addresss for every private individual so that publishing rights don't have to be gatekeeped by large corporations

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com3http://pyinsci.blogspot.com/2009/09/internet-manifesto.htmltag:blogger.com,1999:blog-840127493134277990.post-24873396637085225362009-09-28T06:49:00.001-03:002009-09-28T06:49:09.725-03:002009-09-28T06:49:09.725-03:00

I recently came across, this interesting, opensource Python Scientific Distribution for Windows. I normally don't pay too much attention to windows tools, but it's good to have something to recommend to windows users when you want them to try out some Python code. For Linux users, it's not really relevant, because we all have powerfull package managers to help us get most Python packages

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com1http://pyinsci.blogspot.com/2009/09/pythonxy-scientific-python-distribution.htmltag:blogger.com,1999:blog-840127493134277990.post-74324761789699520202009-09-24T07:51:00.001-03:002009-09-24T07:51:55.879-03:002009-09-24T07:51:55.879-03:00

I have just created a Scientific Python Group at LinkedIn. I was actually surprised that there wasn't one already.Python is quickly becoming a major tool in scientific computing and we should all do our best to advertise its capabilities.referente a: Scientific Python Group | LinkedIn (ver no Google Sidewiki)

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com0http://pyinsci.blogspot.com/2009/09/scientific-python-group-at-linkedin.htmltag:blogger.com,1999:blog-840127493134277990.post-34325216219671144192009-09-17T11:41:00.008-03:002009-09-17T12:24:15.501-03:002009-09-17T12:24:15.501-03:00

One of the things I sorely missed from matplotlib for a very long time, was a violin plot implementation. Many a time, I thought about implementing one myself, but never found the time.Today, browsing through Matplotlib's documentation, I found the recently added fill_betweenx function. Finally it seemed to have become a piece of cake to implement a violin plot. I Googled for violin plot and

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com4http://pyinsci.blogspot.com/2009/09/violin-plot-with-matplotlib.htmltag:blogger.com,1999:blog-840127493134277990.post-19396017552985518302009-09-11T11:52:00.002-03:002009-09-11T11:55:40.267-03:002009-09-11T11:55:40.267-03:00

I recently came across a repository of jewels in the form of the unpublished manuscripts of E.W. Dijkstra. I just finished reading one entitled "Some Meditations on Advanced Programming". It is amazingly well written and still so relevant to present-day computer science, that I recommend anyone with at least a passing interest on the subject to read it. I was pleasantly surprised to find in the

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com1http://pyinsci.blogspot.com/2009/09/why-python.htmltag:blogger.com,1999:blog-840127493134277990.post-35671869647426705722009-09-02T10:27:00.003-03:002009-09-02T10:49:34.864-03:002009-09-02T10:49:34.864-03:00

The recommended new way (since 2.6) of doing string formating in Python is to use the format method of string objects instead of the % operator and %s (and variants) placemarks.I decided to check it out to generate some LaTeX tables programatically. Bad Idea. the method expects placemarks like this: "some string {key}".format(key=123) and that is a big problem when formatting LaTeX strings.

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com5http://pyinsci.blogspot.com/2009/09/new-style-string-formatting-and-latex.htmltag:blogger.com,1999:blog-840127493134277990.post-7805975184304197762009-07-10T16:28:00.002-03:002009-07-10T16:56:40.765-03:002009-07-10T16:56:40.765-03:00

The web platform is starting to get annoying in its attempt to re-invent and re-create everything that previously existed in the Desktop space.Finally, Desktop developers are beginning to wake up to this problem.For years, browser-developing companies have tried to turn the Browser into an operating-system-like autonomous system. While the rest of us were trying to figure out how to get our

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com11http://pyinsci.blogspot.com/2009/07/chrome-os-and-google-world-domination.htmltag:blogger.com,1999:blog-840127493134277990.post-83159210671624632682009-04-17T09:29:00.003-03:002009-04-17T10:00:58.724-03:002009-04-17T10:00:58.724-03:00

A few months back I blogged about my implementation of the Gillespie SSA algorithm for solving stochastic differential equations. I have now improved the code allowing for parallel execution on SMP systems. If you don't know what this is all about, please refer the the first post for a quick intro to what a stochastic differential equation is and what it means to numerically solve a system of

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com2http://pyinsci.blogspot.com/2009/04/parallel-version-of-gillespie-solver.htmltag:blogger.com,1999:blog-840127493134277990.post-87792438711803871872009-03-05T08:46:00.002-03:002009-03-05T09:13:27.775-03:002009-03-05T09:13:27.775-03:00

Rkward is a Nice IDE project for R based on standard KDE components such as Kate, etc.However, most people wanting to try it (version 0.5b) have come across a startup bug, where Rkward says it can't find some plugins, resulting in a useless interface since some plugins are required for proper operation.After spending quite some time looking for the solution to this problem, and finding it, I

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com0http://pyinsci.blogspot.com/2009/03/fixing-rkward-startup-problems.htmltag:blogger.com,1999:blog-840127493134277990.post-70463921073598007882009-02-27T08:00:00.005-03:002009-02-27T08:24:51.548-03:002009-02-27T08:24:51.548-03:00

Complex numerical simulations usually take a long time to run while using full CPU(s). If something goes wrong during such a run, we generally only find out in the end of the run when the traces of what went wrong are no longer available, debugging such codes is also not an easy task, because the code gets even slower running through the debugger, and when we don't know where the code is going to

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com3http://pyinsci.blogspot.com/2009/02/real-time-plotting-from-numerical.htmltag:blogger.com,1999:blog-840127493134277990.post-86295031515535097832009-02-27T07:06:00.002-03:002009-02-27T07:59:44.454-03:002009-02-27T07:59:44.454-03:00

I have found myself using multiprocessing more and more these days, especially since it has been backported to Python 2.5.x.I can no longer remember what was the last computer I owned, which had a single core/processor. Multiprocessing make me much happier as I know I can milk my hardware for all it has to offer. I numpy, scipy and related packages find ways to build parallelization into their

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com4http://pyinsci.blogspot.com/2009/02/usage-pattern-for-multiprocessing.htmltag:blogger.com,1999:blog-840127493134277990.post-23310063228459710062009-02-19T06:45:00.004-03:002009-02-19T07:32:07.297-03:002009-02-19T07:32:07.297-03:00

The title of this post is intentionally the same as this one by Greg Wilson. His post brings up the important issue of the lack of efficient collaborative science tools, and asks for opinions on the subject. Here is my personal view:Though science has invented collaborative open-source development centuries ago, it is currently not the best example of such practices, being surpassed on many

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com4http://pyinsci.blogspot.com/2009/02/computer-supported-collaborative.htmltag:blogger.com,1999:blog-840127493134277990.post-42578651921367969262008-10-30T15:04:00.020-02:002008-11-04T12:37:02.312-02:002008-11-04T12:37:02.312-02:00

Today I took the day off to implement the Gillespie SSA algorithm. For those of you who have never heard of it is a solver for stochastic equations. There is no implementation of it in Python (to my knowledge) and the only other easily accessible implementation I found was the one on the GillespieSSA package for R.To help the unfamiliar to understand the application and relevance of this

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com9http://pyinsci.blogspot.com/2008/10/fast-gillespies-direct-algorithm-in.htmltag:blogger.com,1999:blog-840127493134277990.post-72907582273721118572008-10-05T18:47:00.002-03:002008-10-05T19:02:11.361-03:002008-10-05T19:02:11.361-03:00

I am quite busy at the moment. But I recently got some inspiration for pushing forward with the development of my object-oriented Bayesian-inference package. The inspiration came in the form of the recently released R-packages rv By Kerman and Gelman. A technical report by the same authors provided me with the initial idea for starting this package. The rv package implements part of what intend

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com6http://pyinsci.blogspot.com/2008/10/further-bayesian-adventures.htmltag:blogger.com,1999:blog-840127493134277990.post-3217262191284474642008-09-30T07:15:00.007-03:002008-09-30T08:08:22.774-03:002008-09-30T08:08:22.774-03:00

In this era of multiple cores everywhere, it kind of makes me nervous to see one of my computer cores siting idle as the other crunches away at some numerical simulation. Running heavy numerical simulations is the bread and butter of my work, so I am always on the lookout for ways to extract as much  computational juice as I can from my CPUs.Over last couple of years I have played different

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com12http://pyinsci.blogspot.com/2008/09/python-processing.htmltag:blogger.com,1999:blog-840127493134277990.post-20295114689685594152008-08-07T03:33:00.001-03:002008-08-07T03:33:59.809-03:002008-08-07T03:33:59.809-03:00

My experiments with AppEngine keep expanding. One thing they got rightwas the incentive to use other google services through google dataAPIs also known as GData.The first step towards that was forcing us to use Authsub by defaultin appEngine. Noticing that, I am thinking about taking advantage ofthat to aleviate the usage of the tiny storage quota offered by Googleat AppEngine.I'll post more

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com1http://pyinsci.blogspot.com/2008/08/appengine-and-google-base.htmltag:blogger.com,1999:blog-840127493134277990.post-91635115365488956262008-08-05T17:46:00.004-03:002008-08-05T18:08:02.857-03:002008-08-05T18:08:02.857-03:00

Editra is a relatively new (at least for me) text editor written in Python/GTK.I have been working extensively with it recently, and although I am not ready to leave behind my currently favorite Python IDE, Eric, Editra doesn't make me miss it too much. One thing that it does that Eric still does not, even though it could, is to provide a code browser for a source file which is not part of a

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com6http://pyinsci.blogspot.com/2008/08/editra-great-new-python-editor.htmltag:blogger.com,1999:blog-840127493134277990.post-82623120843085770642008-08-04T15:46:00.002-03:002008-08-04T16:00:52.878-03:002008-08-04T16:00:52.878-03:00

I have spent quite a lot of time lately developing for google appengine. I must admit that it is really a great package, especially considering that is still in beta.The development cycle is a breeze. One thing I would add though, would be a decent source code management system. This could take the form of an integration with google code. The appEngine dashboard does a good job keeping track of

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com2http://pyinsci.blogspot.com/2008/08/google-appengine.htmltag:blogger.com,1999:blog-840127493134277990.post-14739468919584874462008-07-23T17:21:00.002-03:002008-07-23T17:38:21.021-03:002008-07-23T17:38:21.021-03:00

I am rather busy at the moment pushing my new company forward. Yes, for those of you who don't know yet, I have just started up my own company.It has been very rewarding so far, even considering all the hassle of tasks such as fund-seeking, registering the company, creating a website, develop the products, and making sure that everything work. Wow!, it's been a great challenge.The focus of this

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com2http://pyinsci.blogspot.com/2008/07/metamodellers.htmltag:blogger.com,1999:blog-840127493134277990.post-86205494655667360242008-05-12T15:45:00.003-03:002008-05-12T16:21:42.382-03:002008-05-12T16:21:42.382-03:00

A while ago, I blogged about a little piece of code I had written as an example for my book.Back then, it was a fun exercise for me, but it was clearly unfinished (and it still is) but worth as an example of how to model a mathematical object, a Bayesian random variate, as a python class.Despite its simplicity and incompleteness, that example, still attracts attention, and people contact me

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com6http://pyinsci.blogspot.com/2008/05/object-oriented-bayesian-inference-ii.htmltag:blogger.com,1999:blog-840127493134277990.post-19951128028706256852008-04-13T19:17:00.000-03:002008-04-13T19:19:41.606-03:002008-04-13T19:19:41.606-03:00

It's been a while since i last posted about python in science. I apologize to my readers, but it has been a very busy couple of months. As a matter of fact it still is (i am writing this on my cell phone while I comute), but let's get to the point.The reason for this crazyer than usual months is that I switched jobs. I have been offered a job in a private research company called Intelekto. It is

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com1http://pyinsci.blogspot.com/2008/04/new-job.htmltag:blogger.com,1999:blog-840127493134277990.post-60880463170944816652008-03-03T20:27:00.004-03:002008-03-13T12:46:40.300-03:002008-03-13T12:46:40.300-03:00

I just found this incredible video (animation) depicting what goes on continually within our own cells. Reminds me of why I became a biologist.We should never cease to let ourselves be amazed by the great machine that is the living cell and the organisms they are part of. Enjoy!

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com3http://pyinsci.blogspot.com/2008/03/incredible-video-of-intracellular.htmltag:blogger.com,1999:blog-840127493134277990.post-24338859913286276132007-12-09T22:01:00.000-02:002007-12-09T22:14:37.312-02:002007-12-09T22:14:37.312-02:00

I am a big fan of ZODB and use it standalone (without Zope) on many projects of mine. One of the things I miss, is a community around it. I don't care much about Zope (though I admire it as a project) and have not being able to find a ZODB focused community. Is there one?I think ZODB is a great product, the best Object-Oriented database for Python. It's a shame it does not have an active and

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com7http://pyinsci.blogspot.com/2007/12/free-zodb.htmltag:blogger.com,1999:blog-840127493134277990.post-62876908413791195962007-11-05T13:13:00.000-02:002007-11-05T15:19:33.775-02:002007-11-05T15:19:33.775-02:00

I have finally found a justification to work on Epigrass again. I am publishing a paper on it and I want to have a fresh version out by the time he paper goes to press. It was a good thing since my wish list for the next release was becoming too long.So here are the the things I have done so far and some I expect to get done before the new release:Port to Qt4: Done. Not as hard as I suspected it

Flavio Coelhohttp://www.blogger.com/profile/02885581033966597420noreply@blogger.com2http://pyinsci.blogspot.com/2007/11/new-release-of-epigrass-coming-soon.html