I am considering using pubmed class of BioPython to access Pubmed. I have a question for using this. Is there any limitation for using this class? I am afraid too much use of this class would recognize as traffic attack to ncbi site from my company. I heard ncbi would limit the internet access if there are too much access. Sincerely, Hisahiko Sato
Finally, I found out how to update the Biopython web page. On the download page, you will now find a Windows installer for Biopython 1.30 for Python versions 2.2, 2.3, and 2.4. Sorry for the delay. Please let me know if there are any problems. --Michiel. Michiel Jan Laurens de Hoon wrote: > There *is* a Windows installer for Biopython 1.30, for some reason it is > not visible now on the Biopython website. I have updated the biopython > webpage in CVS, but I cannot find the setup.py on the biopython > webserver to install the new webpage. Does anybody know what happened > with this setup.py? > > --Michiel. > > Peter wrote: > >> I'm trying to build and/or install BioPython 1.30 on Windows XP. >> >> I would guess that since there isn't a Windows installer for Biopython >> 1.30 (yet) that most development occurs on linux/unix. >> >> Furthermore, the only instructions in the documentation are for >> Borland's free C++ compiler: >> >> http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial001.html#sec:windows_install >> >>(Continue reading)
As far as I know/believe, PubMed.py, which handles communication with Entrez/PubMed, imports Bio.WWW.RequestLimiter. It seems to limit your access to NCBI based on time delay. The default delays are 5.0 seconds for Dictionary(), 2.0 seconds for search_for(), 120.0 seconds for download_many(). Those delays are injected just *before* each iterative request (even in single query) by RequestLimitter so that your program will sleep before retriving individual entry every time. Thus, if you write your program in well-behaved manner (no parallelize of requests by threading, no use of broken system timer, etc.), there should be no problem. If you are interested in reading Python code doing it, please take a look into $pythonlib/site-packages/Bio/WWW/__init__.py or $ptyhonlib/site-packages/Bio/PubMed.py. "Hisahiko Sato" <hisahikosatou <at> hotmail.com> wrote: > I am considering using pubmed class of BioPython to access Pubmed. > > I have a question for using this. > Is there any limitation for using this class? > I am afraid too much use of this class would recognize as traffic attack to > ncbi site from my company. > I heard ncbi would limit the internet access if there are too much access. --- Yasushi Masuda http://www.cubelab.com/ymasuda/(Continue reading)
I have tried the following code (see at the end).
It is a function that retrieves information about a given SNP from pubmed.
I use:
snpInfoFile = eutils.efetch_using_dbids(...)
and then:
snpInfoFile.readline()
and store this in a list (local memory).
My problem is that I do it for several SNPs and each time some <urllib2.OpenerDirector instance at
0x01435F30> is stored in the RAM. At the end the system hungs up.
Do you know how to free this memory?
I have tried to snpInfoFile.close() and del snpInfoFile but seems not to work!!!!
Help please!!!!!
Regards,
Julio Bonis Sanz
def getSNPInfo(self,rs): #
"""
given a rs return the contig and the position in it
(Continue reading)
Hi, I just started browsing around what you can do with Biopython, for some educational interest. I'd like to try and implement an Open GL Viewer for molecules in Python. In my wild days (before studying veterinary medicine) I acquired a solid grasp of Open Gl. In case you wonder, if Python is fast enough for this task. It is. Or better: it's not, but Open Gl does all the work with hardware acceleration, circumventing the speed draw-back of python. First task would be to obtain the structure of the molecule by linking 3D coordinates together. I browsed in the biopython documentation, but I did not really get a clue. I suspected the neccessary functionality in the PDB module, but could not find a way on how to get to 3D coordinates out of a pdb file or whatever data object is neccessary for that. The widget would then be used something like this, in fictional code without caring for module importing / referencing. >>> model = model_from_data(something) >>> window = gl_window(model) >>> window.show() A window would popup now, with a slowly rotating molecule in it. One tricky part will be to open a window on different platforms, but that's pretty simple. At first, pygame will be enough, since it runs on Linux, Windows and Mac, but that's a bad dependency (in my opinion). The module could check for availability of pyGTK, win32 or wxPython bindings and use them. The core of the open gl representation would not care a bit about the underlying windowing API.(Continue reading)
Hi all, Would the biopython community have any interest in a C/API wrap of rasmol (the classic Sayles version 2.6.4) as a python extension module? I made this a few years ago and it is just sitting in my garage. So it has low mileage, was only driven on Sundays, but may need some tinkering. It has python functionality to control the molecule view, read and write to the molecule data, put 'artificial' objects into the molecule view, etc etc. Comes with all source, a setup.py build script and even python style documentation and some python demo scripts. Ciao, Dick -- -- Dick Madden Home: 2708 rue Prospect Bioinformatics Coordinator Sherbrooke, QC, Canada J1L 2V2 RNA Group Room 7410-5 Phone: (819) 562 1040 Departement de microbiologie Faculte de medecine Universite de Sherbrooke 3001, 12e Avenue Nord Sherbrooke, QC, Canada J1H 5N4 Phone: (819) 820-6868 poste 12324 _______________________________________________ BioPython mailing list - BioPython <at> biopython.org http://biopython.org/mailman/listinfo/biopython
Richard Madden wrote: >Hi all, > > Would the biopython community have any interest in a C/API wrap of >rasmol (the classic Sayles version 2.6.4) as a python extension module? >I made this a few years ago and it is just sitting in my garage. So it >has low mileage, was only driven on Sundays, but may need some >tinkering. It has python functionality to control the molecule view, >read and write to the molecule data, put 'artificial' objects into the >molecule view, etc etc. Comes with all source, a setup.py build script >and even python style documentation and some python demo scripts. > >Ciao, Dick > > > Dick, Sounds interesting, thanks for the offer. Would you like to email me a tarball, and I'll work this into CVS. Thanks, Iddo -- -- Iddo Friedberg, Ph.D. The Burnham Institute(Continue reading)
not biopython-based, but open source and seems to fit the rest of your requirements - why not start here: http://pymol.sourceforge.net/ On Thursday 16 December 2004 2:51 am, Andreas Klostermann wrote: > Hi, > > I just started browsing around what you can do with Biopython, for > some educational interest. I'd like to try and implement an Open GL > Viewer for molecules in Python. In my wild days (before studying > veterinary medicine) I acquired a solid grasp of Open Gl. In case > you wonder, if Python is fast enough for this task. It is. Or > better: it's not, but Open Gl does all the work with hardware > acceleration, circumventing the speed draw-back of python. > > First task would be to obtain the structure of the molecule by > linking 3D coordinates together. I browsed in the biopython > documentation, but I did not really get a clue. I suspected the > neccessary functionality in the PDB module, but could not find a > way on how to get to 3D coordinates out of a pdb file or whatever > data object is neccessary for that. > > The widget would then be used something like this, in fictional > code without caring for module importing / referencing. > > >>> model = model_from_data(something) > >>> window = gl_window(model) > >>> window.show()(Continue reading)
Hi to all, does anyboy know if is possible to handle PDB files of structures obteined via NMR spectrometry? E.G. obtein models of various conformers in a file? thnks Edoardo -- "Raffiniert ist der Herr Gott, aber boshaft ist Er nicht." --- Dr. Edoardo Saccenti FiorGen Pharmacogenomics Foundation CERM Nuclear Magnetic Resonace Research Center Scientific Pole - University of Florence Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) tel: +39 055 4574193 fax: +39 055 4574253 saccenti <at> cerm.unifi.it www.cerm.unifi.it _______________________________________________ BioPython mailing list - BioPython <at> biopython.org http://biopython.org/mailman/listinfo/biopython
Andreas: Although not part of Biopython, UCSF Chimera is another python/open GL based structure analysis application. I use it to prepare graphics for my lectures, do comparative modeling, surface analysis, etc. It is supposed to be extensible, but I haven't explored that side of it. Citation and link: Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. "UCSF Chimera - A Visualization System for Exploratory Research and Analysis." J. Comput. Chem. 25:1605-1612 (2004). http://www.cgl.ucsf.edu/chimera Best, Kael At 02:51 AM 12/16/2004, Andreas Klostermann wrote: >Hi, > >I just started browsing around what you can do with Biopython, for some >educational interest. I'd like to try and implement an Open GL Viewer >for molecules in Python. In my wild days (before studying veterinary >medicine) I acquired a solid grasp of Open Gl. In case you wonder, if >Python is fast enough for this task. It is. Or better: it's not, but >Open Gl does all the work with hardware acceleration, circumventing the >speed draw-back of python. > >First task would be to obtain the structure of the molecule by linking >3D coordinates together. I browsed in the biopython documentation, but I(Continue reading)
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