tag:blogger.com,1999:blog-4195135246107166251.post6686408606508944888..comments2023-05-08T07:04:09.641-07:00Comments on Neopythonic: Python in the Scientific WorldGuido van Rossumhttp://www.blogger.com/profile/12821714508588242516noreply@blogger.comBlogger35125tag:blogger.com,1999:blog-4195135246107166251.post-17861124586758387222010-08-04T18:58:00.808-07:002010-08-04T18:58:00.808-07:00@Tenzig Norgay: please voice your support on the A...@Tenzig Norgay: please voice your support on the App Engine tracker!<br /><br />http://code.google.com/p/googleappengine/issues/detail?id=190Guido van Rossumhttps://www.blogger.com/profile/12821714508588242516noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-80549654938362747732010-08-04T18:46:17.803-07:002010-08-04T18:46:17.803-07:00Just found Guido's post now. The biggest thin...Just found Guido's post now. The biggest thing you could do to advance the use of Python in science is to get Numpy installed on Google's AppEngine platform.<br /><br />AppEngine is a wonderful thing, an creation of genius, really, but its lack of efficient numerical computation means that almost everyone in science ignores it. Put Numpy on AppEngine, and you will see a flowering of usage of both Numpy and AppEngine.Tenzig Norgayhttps://www.blogger.com/profile/07443932114772501933noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-15678371884281204982010-01-06T03:25:18.904-08:002010-01-06T03:25:18.904-08:00Hi evryone,
I am developing a major project in py...Hi evryone,<br /><br />I am developing a major project in python 2.5 version now and it will complete in a month. <br /><br />I don't want any code changes till 2012. <br /><br />Is it ok to just stick to 2.5 v rather than 3.0v? (Somehow I amn't convinced of using 2.6v.)<br /><br />please reply.<br /><br />Many Thanks.Sivahttps://www.blogger.com/profile/00163412795871824599noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-11178483825098471922009-12-07T16:56:43.669-08:002009-12-07T16:56:43.669-08:00Hi,
I wrote a post (in portuguese) discussing Pyt...Hi,<br /><br />I wrote a post (in portuguese) discussing Python in Scientific World.<br /><br />The culture of Python is very weak where I live, but some people (including me) are trying to make this reality a bit different.<br /><br />You can see the post here: <a href="http://herberthamaral.com/2009/11/python-e-computacao-cientifica/" rel="nofollow">http://herberthamaral.com/2009/11/python-e-computacao-cientifica/</a><br /><br />See ya!Herberth Amaralhttps://www.blogger.com/profile/14102559990909946517noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-6606650547734418082009-11-29T09:20:02.301-08:002009-11-29T09:20:02.301-08:00The structural biology world has embraced python s...The structural biology world has embraced python since its inception. Pymol( http://www.pymol.org), the phenix project (http://www.phenix-online.org/) , coot, the list is quite big. It would be almost impossible to practice crystallography today without using at least one tool or the other which incorporates python.harijayhttps://www.blogger.com/profile/13670079204332523637noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-41777573678973536942009-11-15T11:32:25.308-08:002009-11-15T11:32:25.308-08:00@Alejandro I know the PySKI authors -- I'll as...@Alejandro I know the PySKI authors -- I'll ask them if they are ready to post links here.HilbertAstronauthttps://www.blogger.com/profile/11443786031975040593noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-81352038533692295492009-11-15T08:01:39.152-08:002009-11-15T08:01:39.152-08:00It is very exciting to see a free open-source pyth...It is very exciting to see a free open-source python becoming the new standard language used and taught in science. <br />In my opinion the lack of two things prevent python from being already the de-facto standard: 1) documentation/ standard operating procedures and 2) an uniform interface for the download/installation of modules.<br /><br />1) Environments such as MATLAB maintain their central role mostly because they are easy to start working with. Little customization is necessary and, most importantly, the documentation is in a single place, it's extensive and contains lots of *basic* examples for *novices* (basically SOPs for the most common tasks). <br />Ipython makes a wonderful step in the right direction with the ? magic operator, but a centralized and well-organized repository containing documentation of all scientific py modules would save much googling to the beginning user. <br /><br />2) I second the comment about a CPAN-like repository. The lack of an uniform interface to install scientific modules is a big barrier for the average scientific user, who wants things that "just work" and can't be bothered in working out installation procedures and dependencies.<br /><br />Thanks for all the great work..elihttps://www.blogger.com/profile/15590020541017470180noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-44885245035430289542009-11-08T02:08:57.458-08:002009-11-08T02:08:57.458-08:00I would like to add another scientific tool under ...I would like to add another scientific tool under development that will heavily use Python: The Molecular Dynamics simulation package <a href="http://www.espresso-pp.de" rel="nofollow">ESPResSo++</a>. The predecessor ESPResSo used Tcl/Tk as a scripting frontend language. Thanks to Guido for the great advantages that Python has over Tcl/Tk!Anonymoushttps://www.blogger.com/profile/06074144980846801894noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-91830917852068471752009-11-06T18:38:14.973-08:002009-11-06T18:38:14.973-08:00Thanks for continuing to engage the Scientific Com...Thanks for continuing to engage the Scientific Community. I haven't had nearly the time I would have liked to continue to help push the Python/NumPy linkage. Fortunately, there are other great people continuing the work.Travis Oliphanthttps://www.blogger.com/profile/04514536132317233988noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-25647106379074153282009-11-06T17:34:34.347-08:002009-11-06T17:34:34.347-08:00Did you see any reports about using PyMPI or other...Did you see any reports about using PyMPI or other MPI versions of Python to control large parallel jobs?Ted Sternhttps://www.blogger.com/profile/15298055747984752174noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-48995301976987260382009-11-06T16:44:41.953-08:002009-11-06T16:44:41.953-08:00Python's also gaining increasing momentum in n...Python's also gaining increasing momentum in neuroscience, where it's competing mainly with MATLAB. See for example the recent <a href="http://www.frontiersin.org/neuroinformatics/specialtopics/8/" rel="nofollow">special issue of Frontiers in Neuroinformatics</a>, as well as <a href="http://www.cnsorg.org/meetings/2009/workshops/CNS2009%20Python%20workshop.pdf" rel="nofollow">workshops</a> at major conferences and <a href="http://www.g-node.org/Teaching/" rel="nofollow">summer schools</a> in the field.Unknownhttps://www.blogger.com/profile/04903969847912039998noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-44693060386542796622009-11-06T16:39:42.433-08:002009-11-06T16:39:42.433-08:00This comment has been removed by the author.Unknownhttps://www.blogger.com/profile/04903969847912039998noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-6989751943661966772009-11-06T09:13:59.878-08:002009-11-06T09:13:59.878-08:00I'm Bryan Catanzaro, one of the authors of the...I'm Bryan Catanzaro, one of the authors of the Copperhead project. It was great to be able to talk briefly about our work during Guido's visit, and thanks for the interest expressed in the comments. We are planning on releasing the source code for Copperhead in the next few months, when it's not quite so raw. Feel free to email me directly with any questions.Recession Conehttps://www.blogger.com/profile/04288371918529972744noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-88633090979562054872009-11-06T08:01:19.777-08:002009-11-06T08:01:19.777-08:00Python is suffering a lot in the scientific word, ...Python is suffering a lot in the scientific word, because it has not a CPAN-like repository.<br /><br />PyPI is fine, but it is still far from the level of CPAN, CRAN, Bioconductor, etc..<br /><br />Scientists who use programming usually have a lot of different interests and approaches, therefore it is really difficult to write a package that can be useful to everyone. <br />Other programming language like Perl and R have repository-like structure which enable people to download packages easily, and to upload new ones and organize them withouth having to worry about having to integrate them into existing packages.<br /><br />This is what is happening to biopython now: it is a monolitic package that it is supposed to work for any bioinformatic problem; but this is so general that to accomplish that you would need to add a lot of dependencies, to numpy, networkx, suds, any kind of library.<br />However, since easy_install is not as ready yet as the counterparts in other languages, if the biopython developers add too many dependencies, nobody will be able to install it properly, and nobody will use it.dalloliogmhttps://www.blogger.com/profile/11230528124875348719noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-86648794430237734082009-11-06T07:23:45.478-08:002009-11-06T07:23:45.478-08:00Python over C++ on massively parallel supercompute...Python over C++ on massively parallel supercomputers -- who would have believed it 15 years ago? I am so proud of this community. And thank you, Guido, for listening to what we needed.Paul F. Duboishttps://www.blogger.com/profile/07669741315922671782noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-67342888808148952132009-11-06T06:29:07.796-08:002009-11-06T06:29:07.796-08:00Our group is currently porting our open-source sof...Our group is currently porting our open-source software projects to Python, making heavy use of SciPy and NumPy. We have been pleased with the process and the results. Our software is used in biomedical research for a wide variety of applications, most notably identifying the genetic basis and chemical treatments for diseases, based on screening microscopy images (www.cellprofiler.org). <br />* CellProfiler software for high-throughput image analysis (formerly Matlab-based)<br />* CellProfiler Analyst software for data exploration (formerly Java-based)Unknownhttps://www.blogger.com/profile/08198759498497197072noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-37565095079020555702009-11-06T03:56:58.363-08:002009-11-06T03:56:58.363-08:00Thanks again for the visit, Guido, it was fantasti...Thanks again for the visit, Guido, it was fantastic and the feedback I've received locally has been very good.<br /><br />I've posted on my blog my take on the event:<br /><br />http://fdoperez.blogspot.com/2009/11/guido-van-rossum-at-uc-berkeleys.html<br /><br />and I also have now on my site all the slides from the presentations:<br /><br />http://fperez.org/py4science/2009_guido_ucb/index.html<br /><br />Finally, I should note that the whole session is available on video:<br /><br />http://www.archive.org/details/ucb_py4science_2009_11_04_Guido_van_RossumFernando Perezhttps://www.blogger.com/profile/12945463674195535011noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-43147578634686698202009-11-06T02:29:49.118-08:002009-11-06T02:29:49.118-08:00This comment has been removed by the author.Père de Jumelleshttps://www.blogger.com/profile/05318661938344116057noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-67722399336749282382009-11-05T23:48:48.744-08:002009-11-05T23:48:48.744-08:00I work in s tructural bioinfomrtics and may add to...I work in s tructural bioinfomrtics and may add to the list:<br />The molecular modeling toolkit (MMTK): http://dirac.cnrs-orleans.fr/MMTK/<br />BioPython: http://biopython.org/wiki/Main_Page<br /><br />I'd also like to mention Rpy, which I sometimes use for leveraging Rs plotting-packages from within python.<br /><br />Personally I develop methods in structural bioinformatics and it is really great to have a language that minimize coding time when new ideas are to be tested out. I also like that I can develop code on my Macbook, yet my coworkers can check out and run without any hazzle on their linux-boxes and I can very easily move things over to our linux cluster whenever I need to run larger-scale analysis.Edvinhttps://www.blogger.com/profile/18164114010601090967noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-50861077505894711902009-11-05T18:36:50.206-08:002009-11-05T18:36:50.206-08:00Rpy seems interesting too.http://rpy.sourceforge.n...Rpy seems interesting too.http://rpy.sourceforge.net/<br />A python extension over R statistical programming languagekoolhead17https://www.blogger.com/profile/15627699270866975540noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-27882379973963600502009-11-05T18:19:52.746-08:002009-11-05T18:19:52.746-08:00There will be a tutorial on "Python for High ...There will be a tutorial on "Python for High Performance and Scientific Computing" at Supercomputing 2009 and there are 112 registered participants already. We use Python for most of the analysis of Lattice QCD data.Maxhttps://www.blogger.com/profile/09623275440139063403noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-49448349435706550602009-11-05T15:21:06.929-08:002009-11-05T15:21:06.929-08:00I'm also working on a Python project in scient...I'm also working on a Python project in scientific computing, <a href="http://garlicsim.org" rel="nofollow">GarlicSim</a>.<br /><br />It's a framework for working with simulations. If you do any sort of work with simulations, I urge you to check out the <a href="http://garlicsim.org" rel="nofollow">readme</a> (and the <a href="http://dl.getdropbox.com/u/1927707/Introduction%20to%20GarlicSim.doc" rel="nofollow">Introduction</a>.)cool-RRhttps://www.blogger.com/profile/09525756972721680643noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-47632897901720302772009-11-05T14:39:33.540-08:002009-11-05T14:39:33.540-08:00At the meeting I misrepresented Antoine Pitrou'...At the meeting I misrepresented Antoine Pitrou's newgil work. His code is here: http://svn.python.org/view/sandbox/trunk/newgil/ and his original description of the work is here: http://mail.python.org/pipermail/python-dev/2009-October/093321.html . The work does not remove the GIL or make Python multi-threaded or add more fine-grained locks. However it vastly improves the efficiency of the existing GIL code, removing the so-called "Dave Beazley effect" (see the post for details).<br /><br />I don't know any links about PySKI, but it is an offshoot of something called OSKI (Optimized Sparse Kernel Interface): http://bebop.cs.berkeley.edu/oski/Guido van Rossumhttps://www.blogger.com/profile/12821714508588242516noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-22586721019917960762009-11-05T14:28:16.883-08:002009-11-05T14:28:16.883-08:00Related to http://live.sympy.org are the larger &q...Related to http://live.sympy.org are the larger "code notebook" projects, like http://sagenb.org and http://codenode.org.<br /><br />Both projects are like "Google docs for programming" and I think represent a missing piece in the Python scientific community.Alex Clemeshahttps://www.blogger.com/profile/17949962033823551918noreply@blogger.comtag:blogger.com,1999:blog-4195135246107166251.post-32151054467714527902009-11-05T14:24:16.237-08:002009-11-05T14:24:16.237-08:00Copperhead seems to be a very interesting project....Copperhead seems to be a very interesting project. After few presentation that I found on the web, I think it works smoothly with the map function, lambdas, and etc not so much in the rest of the Python language. Cython already has a good coverage in what Copperhead is lacking right now. It would be very EXCITING to see Copperhead to be integrated with Cython.Unknownhttps://www.blogger.com/profile/10126201233447745896noreply@blogger.com