From idoerg at burnham.org Fri Nov 5 12:50:42 2004 From: idoerg at burnham.org (Iddo) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Re: Contribute to BioPython In-Reply-To: <200411041643.43001.jstroud@mbi.ucla.edu> References: <200410291743.19336.jstroud@mbi.ucla.edu> <4182EB80.4070203@burnham.org> <200411041643.43001.jstroud@mbi.ucla.edu> Message-ID: <418BBD72.3050405@burnham.org> James, I'm cc-ing your email to the lists, I think it's important other Biopythoneers comment on this. James Stroud wrote: >Hi Iddo, > >Thanks for your tips. I looked at Jeff Chang's cpairwise2module.c and its >associated pure python implementation pairwise2.py. They look like nothing >too special was done for the python module, except that the code is pretty >clean. The C-code was barren of doc-style comments, but I think that is >because he also had the python implementation to document the API. I'm mostly >looking for how I should mark up my C code (namely the API code for python) >to produce automated documentation. I'm not yet ready to make a pure python >implementation, but I am happy to contribute my C-based python module to >biopython once its a little more complete. I'm thinking of using doxygen to >mark the C, but first I wanted to get an idea of what would be best for the C >code to communicate with python. > > Probably the best way would be to learn how to extend Python with C. It's a pretty standard procedure, although there are several ways of going about it. I use SWIG, which has the advantage of writing the Python extension code and the C wrapper for you. I never quite got the hang of how to do it with distutils (see JC's code for that), but I confess I am lazy in that department. However, distutils has the advantage that code is easier to install from source, as the users do not need to install SWIG on their machine, on top of everything else. Bottom line: learning curve on SWIG is easier, but distutils is probably the way to go because it is "pure Python". http://www.swig.org http://docs.python.org/ext/ext.html >Incidentally, the module I'm making is for scanning sequence information and >looking for islands of things, such as high or low complexity, CpG, etc. The >user will be able to pass arrays of values (as python lists) to the C code >and islands can be found from the data given certain cutoff and window >parameters and such. If the user takes one step back, he or she can just tell >the module to look for certain types of islands. So far, I have the code for >sequence complexity written as well as the data structures and functions that >handle islands themselves (separate from any particular type of island). Soon >I will do Q/N islands (for protein), and in the future I will add to that >(probably CpG, at least). Because the island-handling code is separate from >any type of island, it will allow (once the API is written for this part) the >user to write python to generate values for properties they are interested in >and pass it to the island API to build the islands. Currently I have a >nascent API to several of the more higher-level C functions. > > > Wow! Biopython is entering epigenomics. This sounds like a very hefty contribution. I can't wait to see it. (CpG islands are methylation sites.. what are Q/N islands? Some sort of glutamine repeat variation?) >Anyway, I'm looking forward to any thoughts on how I might best document this >for biopython. > > > Look at the Python tutorial/cookbook. Then write your own chapter! This would be for the users of your modules. Latex source is best, but if you don't do Latex, just send over a text file. As for the code documentation: the more the merrier. Try putting cookbook-like documentation in the docstrings (those are the bits that start & end with """), as they are automatically placed in the __doc__ attribute of the classes/modules you write. This means they are easy to harvest by third party programs which write up automatic documentation, such as HappyDoc. Then, sprinkle your documentation liberally in the code, you can never overdocument! (Well theoretically you can, but no I've never seen it). Thanks again for your efforts. Iddo > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 North Torrey Pines Road La Jolla, CA 92037 USA T: (858) 646 3100 x3516 F: (858) 713 9930 http://ffas.ljcrf.edu/~iddo From hawaii2005 at vreme.yubc.net Fri Nov 5 20:56:51 2004 From: hawaii2005 at vreme.yubc.net (IPSI-2005 France and Spain) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Invitation to France and Spain, c/bba Message-ID: <200411060156.iA61upW7017272@vreme.yubc.net> Dear potential speaker: On behalf of the organizing committee, I would like to extend a cordial invitation for you to attend one or both of the upcoming IPSI BgD multidisciplinary, interdisciplinary, and transdisciplinary conferences. They take place on two consecutive weekends, in two nearby locations (only about 200km away from each other, in the hills of France and on the coast of Spain). The first one will be in Carcassonne, France (near Toulouse): IPSI-2005 FRANCE (Carcassonne is a UNESCO World Heritage City) Hotel de la Cite (arrival: 23 April 05 / departure: 26 April 05) Deadlines: 20 December 04 (abstract) & 20 January 05 (full paper) The second one will be in Costa Brava, Spain (near Barcelona): IPSI-2005 SPAIN (S'Agaro is the Pearl of Costa Brava) Hostal de la Gavina (arrival: 28 April 05 / departure: 1 May 05) Deadlines: 27 December 04 (abstract) / 27 January 05 (full paper) All IPSI BgD conferences are non-profit. They bring together the elite of the world of science; so far, we have had seven Nobel Laureates speaking at the opening ceremonies. The conferences always take place in some of the most attractive places of the world. All those who come to IPSI conferences once, always love to come back (because of the unique professional quality and the extremely creative atmosphere); lists of past participants are on the web, as well as details of future conferences. These conferences are in line with the newest recommendations of the US National Science Foundation and of the EU research sponsoring agencies, to stress multidisciplinary, interdisciplinary, and transdisciplinary research (M.I.T. research). The speakers and activities at the conferences truly support this type of scientific interaction. Topics of interest include, but are not limited to: * Internet * Computer Science and Engineering * Mobile Communications/Computing for Science and Business * Management and Business Administration * Education * e-Medicine * e-Oriented Bio Engineering/Science and Molecular Engineering/Science * Environmental Protection * e-Economy * e-Law * Technology Based Art and Art to Inspire Technology Developments * Internet Psychology If you would like more information on either conference, please reply to this e-mail message. If you plan to submit an abstract and paper, please let us know immediately for planning purposes. Sincerely Yours, Prof. V. Milutinovic, Chairman IPSI BgD Conferences * * * CONTROLLING OUR E-MAILS TO YOU * * * If you would like to continue to be informed about future IPSI BgD conferences, please reply to this e-mail message with a subject line of SUBSCRIBE. If you would like to be removed from our mailing list, please reply to this e-mail message with a subject line of REMOVE. From bugzilla-daemon at portal.open-bio.org Sat Nov 6 07:34:34 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1709] New: Not using -fPIC to build shared lib. Message-ID: <200411061234.iA6CYYgu028962@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1709 Summary: Not using -fPIC to build shared lib. Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: mail@philipp-benner.de Biopython is now part of the Debian distribution, but we had to fix some bugs before submitting. The most recent is that "-fPIC" is not used to compile KDTree and Affy. Therefore compilation failes at some arches. See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=278959 I fixed this bug as follows: --- python-biopython-1.30.orig/setup.py +++ python-biopython-1.30/setup.py @@ -448,10 +448,12 @@ ["Bio/KDTree/KDTree.cpp", "Bio/KDTree/KDTree.swig.cpp"], libraries=["stdc++"], + extra_compile_args=["-fPIC"], language="c++" ), CplusplusExtension('Bio.Affy._cel', ['Bio/Affy/celmodule.cc'], + extra_compile_args=["-fPIC"], language="c++" ), ] Apart from this bug I had to change the following: 1. /usr/lib/python*/site-packages/Bio/EUtils/DTDs/*dtd These files should have mode 644 as permission. (http://www.debian.org/doc/debian-policy/ch-files.html#s10.9) 2. Many site-package modules include a special first-line comment (script magic) after installation. I had to remove all of these. 3. The following files were not deleted after cleaning the source tree: MANIFEST Makefile Martel/*.pyc build The clean target must undo any effects that the build target may have had. Best regards, Philipp Benner --------- http://packages.qa.debian.org/p/python-biopython.html ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Nov 12 10:11:40 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1704] problem with Bio.Blast.NCBIStandalone Message-ID: <200411121511.iACFBeuw000668@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1704 ------- Additional Comments From gebauer-jung@ice.mpg.de 2004-11-12 10:11 ------- Created an attachment (id=175) --> (http://bugzilla.open-bio.org/attachment.cgi?id=175&action=view) BLAST output file This BLAST output file was created using a database generated with a gi list. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Nov 13 14:20:57 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1704] problem with Bio.Blast.NCBIStandalone Message-ID: <200411131920.iADJKvOT025668@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1704 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2004-11-13 14:20 ------- Thanks for the attachment. I have made a fix to the source code. Please get the most updated NCBIStandalone.py from the CVS. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From peter at maubp.freeserve.co.uk Tue Nov 16 12:48:08 2004 From: peter at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV Message-ID: <27816144.1100627287997.JavaMail.www@wwinf3001> 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 I have Microsoft Visual C++ 6.0 (MSVC) which I have successfully used to compile other python extensions (both a simple install, and creation of a windows installation program). In theory using MSVC 6.0 should actually be easier, but it looks like no-one has tried this recently as there is a library problem of some sort. If I try this for BioPython 1.30: python setup.py bdist_wininst After a few warnings, it fails here: building 'Bio.PDB.mmCIF.MMCIFlex' extension C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG -IBio -Ic:\Python23\include -Ic:\Python23\PC /TcBio/PDB/mmCIF/lex.yy.c /Fobuild\temp.win32-2.3\Release\Bio/PDB/mmCIF/lex.yy.obj lex.yy.c Bio/PDB/mmCIF/lex.yy.c(12) : fatal error C1083: Cannot open include file: 'unistd.h': No such file or directory error: command '"C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe"' fail ed with exit status 2 Before I can too carried away, does anyone on the list have any experience of building BioPython on windows? Thank you Peter -- Whatever you Wanadoo: http://www.wanadoo.co.uk/time/ This email has been checked for most known viruses - find out more at: http://www.wanadoo.co.uk/help/id/7098.htm From hoffman at ebi.ac.uk Tue Nov 16 12:53:49 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV In-Reply-To: <27816144.1100627287997.JavaMail.www@wwinf3001> References: <27816144.1100627287997.JavaMail.www@wwinf3001> Message-ID: On Tue, 16 Nov 2004, Peter wrote: > Before I can too carried away, does anyone on the list have any > experience of building BioPython on windows? I don't. But you probably already know that a Cygwin build might be a little easier than a MSVC build. -- Michael Hoffman European Bioinformatics Institute From peter at maubp.freeserve.co.uk Tue Nov 16 12:58:31 2004 From: peter at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV Message-ID: <15721034.1100627911709.JavaMail.www@wwinf3001> >> Before I can too carried away, does anyone on the list have any >> experience of building BioPython on windows? > > I don't. But you probably already know that a Cygwin build might be a > little easier than a MSVC build. Thanks Michael, I also have used Cygwin, but this time last year the Cygwin-Python was not as stable or usable as the native Windows Python. Also, I doubt it is possible to create a Windows Installation program using cygwin. Peter -- Whatever you Wanadoo: http://www.wanadoo.co.uk/time/ This email has been checked for most known viruses - find out more at: http://www.wanadoo.co.uk/help/id/7098.htm From peter at maubp.freeserve.co.uk Tue Nov 16 13:41:40 2004 From: peter at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV Message-ID: <11183264.1100630500323.JavaMail.www@wwinf3001> I have a partial solution. Acording to some old posts on the mailing list back in May 2004: http://portal.open-bio.org/pipermail/biopython-dev/2004-May/001998.html the Bio/PDB/mmCIF/lex.yy.c file is generated automatically using something called lex, which complicates making the file windows friendly, for example by conditional compilation of the include unistd.h statement. Editing setup.py to remove Extension('Bio.PDB.mmCIF.MMCIFlex', ...) from the definition of EXTENSIONS list allows me to compile a windows installation program (which appears to work fine) with just the command: python setup.py bdist_wininst (There are still a selection of compiler warnings...) Would the BioPython team like the resulting file biopython-1.30.win32-py2.3.exe to make available to end users? Peter -- Whatever you Wanadoo: http://www.wanadoo.co.uk/time/ This email has been checked for most known viruses - find out more at: http://www.wanadoo.co.uk/help/id/7098.htm From mdehoon at ims.u-tokyo.ac.jp Tue Nov 16 21:25:01 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV In-Reply-To: <27816144.1100627287997.JavaMail.www@wwinf3001> References: <27816144.1100627287997.JavaMail.www@wwinf3001> Message-ID: <419AB67D.7050703@ims.u-tokyo.ac.jp> 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 > > I have Microsoft Visual C++ 6.0 (MSVC) which I have successfully used to compile other python extensions (both a simple install, and creation of a windows installation program). > > In theory using MSVC 6.0 should actually be easier, but it looks like no-one has tried this recently as there is a library problem of some sort. If I try this for BioPython 1.30: > > python setup.py bdist_wininst > > After a few warnings, it fails here: > > building 'Bio.PDB.mmCIF.MMCIFlex' extension > C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox /MD /W3 > /GX /DNDEBUG -IBio -Ic:\Python23\include -Ic:\Python23\PC /TcBio/PDB/mmCIF/lex.yy.c /Fobuild\temp.win32-2.3\Release\Bio/PDB/mmCIF/lex.yy.obj > lex.yy.c > Bio/PDB/mmCIF/lex.yy.c(12) : fatal error C1083: Cannot open include file: 'unistd.h': No such file or directory > error: command '"C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe"' fail > ed with exit status 2 > > Before I can too carried away, does anyone on the list have any experience of building BioPython on windows? > > Thank you > > Peter > -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From P.Taschner at lumc.nl Wed Nov 17 04:22:01 2004 From: P.Taschner at lumc.nl (Taschner, P. (HKG)) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Biopython-1.30.win32-py2.3 executable Message-ID: Dear Sir/Madam, Some time ago I have downloaded the Biopython-1.30 executable for windows. When I directed a student to your site to download this version, he told me that it was not available and that he would have to compile it. A search on the internet revealed that the executable is still present in the biopython.org/files directory, which makes me wonder what the reason for the removal of its link on the download page is. I would appreciate it very much if you would be able to clarify this. Thanking you very much in anticipation. Best regards, Peter Taschner Dr. Peter E.M. Taschner Department of Human Genetics Center for Human and Clinical Genetics Sylvius Laboratories Leiden University Medical Center Wassenaarseweg 72 P.O. Box 9503 2300 RA Leiden The Netherlands Tel. +31-71-5276093 Fax: +31-71-5276075 E-mail: P.Taschner@lumc.nl From mike at maibaum.org Wed Nov 17 07:33:42 2004 From: mike at maibaum.org (Michael Maibaum) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] KEGG Gene Parser Message-ID: From: mike@maibaum.org Subject: KEGG Gene Parser Date: 17 November 2004 11:23:08 GMT To: biopython-dev@biopython.org Hi, I've been working on a KEGG Gene parser attached and wondered if it would be of use to the project as a whole. It is based on the existing Bio.KEGG.Compound/Enzyme modules. I'm still in the process of testing the parser against more kegg files but it I believe it parses all the current kegg gene files successfully (except c.hominis). Known bugs and missing features: A method for outputting a record as straight text (__str__) Properly parsing the CODON_USAGE section. More refinement of expressions for POSITION section. Methods to handle CODON_USAGE and POSITION callbacks Parsing c.hominis aa_sequences (I'm not sure this is exactly a bug, see below) I'm not really interested in codon usage, position and returning a record in string form (for my current needs), so I haven't spent the time handling this stuff. It should be fairly easy to add if someone cares enough. Otherwise I may get around to it one day. I know c.hominis parsing is broken because they have very odd aa_seq entries and I'm trying to figure out if they have a broken program creating the file, mean something sensible, or it is just another dumb stretching of an inadequate flat-file format designed to test the patience of people writing parsers. I think it could do with some polishing and the parsing regexes could probably be optimised a fair bit but it is useful as it is. The files are available at I'm continuing to work on the module to fix any parsing errors I come across with further testing/usage and will post updates soon. I'd be grateful for any comments or suggestions (be nice, I've only been using Python a little while ;) ) cheers Michael -- Dr Michael Maibaum Department of Biochemistry and Molecular Biology, UCL email: maibaum@biochemistry.ucl.ac.uk From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:12:56 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] Enhancements to Bio.SCOP module Message-ID: <200411171612.iAHGCuU2020707@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-11-17 11:12 ------- Created an attachment (id=176) --> (http://bugzilla.open-bio.org/attachment.cgi?id=176&action=view) Code enhancements A patch for the new code I generated with 'cvs diff -u'. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:13:59 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] Enhancements to Bio.SCOP module Message-ID: <200411171613.iAHGDxQx020737@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-11-17 11:13 ------- Created an attachment (id=177) --> (http://bugzilla.open-bio.org/attachment.cgi?id=177&action=view) test suite for the new Astral class ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:16:35 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] Enhancements to Bio.SCOP module Message-ID: <200411171616.iAHGGZA0020827@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-11-17 11:16 ------- Created an attachment (id=178) --> (http://bugzilla.open-bio.org/attachment.cgi?id=178&action=view) test case for SCOP using SQL Probably shouldn't go in the test suite as it requires mysql to work, and I haven't worked out a principled way of testing SQL (this has a database connection hard coded in). But still it might be useful! ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:18:43 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] Enhancements to Bio.SCOP module Message-ID: <200411171618.iAHGIhUS020856@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-11-17 11:18 ------- Created an attachment (id=179) --> (http://bugzilla.open-bio.org/attachment.cgi?id=179&action=view) test case for Astral using SQL Again SQL test, so probably should be left out of distribution ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:21:12 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] Enhancements to Bio.SCOP module Message-ID: <200411171621.iAHGLCxI020921@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-11-17 11:21 ------- Created an attachment (id=180) --> (http://bugzilla.open-bio.org/attachment.cgi?id=180&action=view) test data for Bio.SCOP new test data to live in /Tests/SCOP/ ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Nov 17 11:11:47 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1711] New: Enhancements to Bio.SCOP module Message-ID: <200411171611.iAHGBl25020682@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1711 Summary: Enhancements to Bio.SCOP module Product: Biopython Version: Not Applicable Platform: All OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: j.a.casbon@qmul.ac.uk I have coded up some stuff for Bio.SCOP that you might want to include in the distribution. A few new methods for Scop class, a new Astral class for ASTRAL data and support for dumping to and using SQL backends. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From shameer at macfast.org Thu Nov 18 05:16:18 2004 From: shameer at macfast.org (Sameer Khader) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Request from India, Message-ID: <20041118101618.24454.qmail@macfast.org> Dear BioPyhton Team, Am a graduate student in Bioinformatics from India. Currently am preparing a review article about the languages which are meant for the exclusive use of Computational Biology/Bioinformatics community. I have gone through your "BioPython" website. I need your co-operation to explain more about your language in my review. So please send me the following details as soon as possible. 1.Potential applications of BioPython. 2.Tools/software developed using BioPython. 3.Develomenmtal history with short descroption (up to till-date) 4.Lead developers/contributors. By providing the above information, you will be entitled as the Contributor of the review article. Hope you care to reply, Wishing you great success with BioPython. Mr.SHAMEER PK Systems Bio Lab MACFAST Bioinformatics & Computational Biology Group (MBCBG) Department: Of Bioinformatics & Biosciences Mar Athanasios College for Advanced Studies (MACFAST) TIRUVALLA - 689 101 - KERALA - INDIA ----------------------------------------------------------- http://bio.macfast.org/ From nanotech at nsti.org Wed Nov 17 21:37:47 2004 From: nanotech at nsti.org (Nanotech 2005) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Friday Abstract Deadline - Nanotech 2005 Message-ID: Nanotech 2005 The Nanotechnology Conference and Trade Show Anaheim Conference Center, May 8-12 2005 http://www.nanotech2005.com ABSTRACT DEADLINE, THIS FRIDAY, Nov. 19th - 423 abstracts already submitted - SUBMIT YOUR ABSTRACT TODAY http://www.nsti.org/Nanotech2005/authors Inter-Disciplinary, Multi-Industry, Technology to Business: - 2500+ Attendees - 600+ Research, business, investment presentations - 130+ Exhibiting companies and demos - 50+ Early stage nanotech companies, Investment forum Industrial Participants Include: GE, IBM, Intel, Hewlett-Packard, Honeywell, Freescale Motorola, ST Microelectronics, Molecular Diamond Technologies, Proctor & Gamble, Nestl?, Chiron, Ciphergen Biosystems, ChevronTexaco, DuPont, Daimler-Chrysler, Kodak, Samsung, Boeing Accelrys, Nanophase, NanoInk, Molecular Imprints, Synopsys Veeco, Zygo, Keithley, Heidelberg, Carl Zeiss, ... (many more) EXHIBIT & SPONSOR TODAY - space is rapidly filling http://www.nsti.org/Nanotech2005/exhibit_sponsor.html SUBMIT YOUR ABSTRACT TODAY http://www.nsti.org/Nanotech2005/authors - text announce x3427 - --- You are currently subscribed to nanotech as: biopython-dev@biopython.org To unsubscribe send a blank email to leave-nanotech-6195156B@spirit.sparklist.com From ymasuda at ethercube.com Thu Nov 18 19:59:27 2004 From: ymasuda at ethercube.com (Yasushi MASUDA) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Japanese translation of Tutorial & Cookbook Message-ID: <200411190059.iAJ0xVtx098236@www216.sakura.ne.jp> Dear biopyhon-dev Team, I am a biopython user in Japan and pleased to tell you that a draft version of Japanese translation for "Biopython Tutorial & Cookbook" has been finished by Japanese uses (Takashi Ishida, Toshiya Sakai and me). Currently we are releasing HTML/PDF versions of the document at: http://www.cubelab.com/ymasuda/python/biopython/ under the Biopython Licence Agreement. (since I could not find copyright and licence notice in the original document, I put that on Introduction chapter in our translated version.) If you have any problems, or any idea for better place of the doucment and its source, please let me know. Biopython is very cool and powerful, and I hope it catches much more Japanese users (and worldwide, of course!) :) Sincerely, --- Yasushi Masuda http://www.cubelab.com/ymasuda/ From idoerg at burnham.org Thu Nov 18 20:12:19 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Japanese translation of Tutorial & Cookbook In-Reply-To: <200411190059.iAJ0xVtx098236@www216.sakura.ne.jp> References: <200411190059.iAJ0xVtx098236@www216.sakura.ne.jp> Message-ID: <419D4873.60506@burnham.org> Too cool! As a co-author of the BP T&B, let me be the first to congratulate and thank you guys for what must have been a great effort. And thank you for your kind words. I don't believe that there are any Copyright/Licensing issues, as long as you take care to name names.. which you did :) Thanks again, Iddo Yasushi MASUDA wrote: >Dear biopyhon-dev Team, > >I am a biopython user in Japan and pleased to tell you that a draft >version of Japanese translation for "Biopython Tutorial & Cookbook" >has been finished by Japanese uses (Takashi Ishida, Toshiya Sakai and >me). > >Currently we are releasing HTML/PDF versions of the document at: > >http://www.cubelab.com/ymasuda/python/biopython/ > >under the Biopython Licence Agreement. (since I could not find >copyright and licence notice in the original document, I put >that on Introduction chapter in our translated version.) > >If you have any problems, or any idea for better place of the >doucment and its source, please let me know. > >Biopython is very cool and powerful, and I hope it catches much more >Japanese users (and worldwide, of course!) :) > >Sincerely, >--- >Yasushi Masuda >http://www.cubelab.com/ymasuda/ > >_______________________________________________ >Biopython-dev mailing list >Biopython-dev@biopython.org >http://biopython.org/mailman/listinfo/biopython-dev > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From biopython-dev at maubp.freeserve.co.uk Fri Nov 26 10:56:36 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Biopython-1.30.win32-py2.3 executable In-Reply-To: References: Message-ID: <41A75234.6010401@maubp.freeserve.co.uk> Taschner, P. (HKG) wrote: > Some time ago I have downloaded the Biopython-1.30 executable for windows. > When I directed a student to your site to download this version, he told me > that it was not available and that he would have to compile it. A search on > the internet revealed that the executable is still present in the > biopython.org/files directory, which makes me wonder what the reason for the > removal of its link on the download page is. I would appreciate it very much > if you would be able to clarify this. The Biopython-1.30 installer for windows is available from the website, but there is no link to it. You have to guess the address: http://www.biopython.org/files/biopython-1.30.win32-py2.2.exe http://www.biopython.org/files/biopython-1.30.win32-py2.3.exe Or go here: http://www.biopython.org/files/ Are there any web masters reading this list? This has been mentioned before: http://www.biopython.org/pipermail/biopython-dev/2004-November/002711.html Peter From j.a.casbon at qmul.ac.uk Fri Nov 26 11:39:20 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Biopython-1.30.win32-py2.3 executable In-Reply-To: <41A75234.6010401@maubp.freeserve.co.uk> References: <41A75234.6010401@maubp.freeserve.co.uk> Message-ID: <200411261639.20344.j.a.casbon@qmul.ac.uk> > Are there any web masters reading this list? This has been mentioned > before: > > http://www.biopython.org/pipermail/biopython-dev/2004-November/002711.html Pretty much everyting I've posted to this list gets ignored. James From mike at maibaum.org Sun Nov 28 16:02:07 2004 From: mike at maibaum.org (Michael Maibaum) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Biopython-1.30.win32-py2.3 executable In-Reply-To: <200411261639.20344.j.a.casbon@qmul.ac.uk> References: <41A75234.6010401@maubp.freeserve.co.uk> <200411261639.20344.j.a.casbon@qmul.ac.uk> Message-ID: On Nov 26, 2004, at 16:39, James Casbon wrote: > >> Are there any web masters reading this list? This has been mentioned >> before: >> >> http://www.biopython.org/pipermail/biopython-dev/2004-November/ >> 002711.html > > Pretty much everyting I've posted to this list gets ignored. Yep, same here - I posted code for parsing a file format but got no feedback - not even a "no thanks, you suck". partly the complete bias on this list to spam over useful content is part of it... Why isn't this list subscriber only. I can (just about) understand the users list being open, but the people posting to dev are motivated enough to subscribe. Also, the users list is swamped with spam to the point I question it's usefulness. Michael -- Michael Maibaum internet: mike@maibaum.org | http://mike.maibaum.org voice: [m] 07958 604025 | From biopython-dev at maubp.freeserve.co.uk Mon Nov 29 07:13:45 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Spam on this the mailing lists (Was: Biopython-1.30.win32-py2.3 executable) In-Reply-To: References: <41A75234.6010401@maubp.freeserve.co.uk> <200411261639.20344.j.a.casbon@qmul.ac.uk> Message-ID: <41AB1279.1080102@maubp.freeserve.co.uk> Michael Maibaum wrote: > > James Casbon wrote: > >> Pretty much everyting I've posted to this list gets ignored. > > Yep, same here - I posted code for parsing a file format but got no > feedback - not even a "no thanks, you suck". > > partly the complete bias on this list to spam over useful content is > part of it... Why isn't this list subscriber only. I can (just about) > understand the users list being open, but the people posting to dev are > motivated enough to subscribe. Also, the users list is swamped with > spam to the point I question it's usefulness. I was also shocked by the amount of spam on the list, and looking back at the archives its been like this a while. It can't be very helpful for BioPython's development. I would second the call to make this list subscriber only. [Note I am "just" a biopython user, not a developer] Peter From ajoshi at cse.unsw.edu.au Mon Nov 29 07:24:10 2004 From: ajoshi at cse.unsw.edu.au (Ajinkya Joshi) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Spam on this the mailing lists (Was: Biopython-1.30.win32-py2.3 executable) In-Reply-To: <41AB1279.1080102@maubp.freeserve.co.uk> References: <41A75234.6010401@maubp.freeserve.co.uk> <200411261639.20344.j.a.casbon@qmul.ac.uk> <41AB1279.1080102@maubp.freeserve.co.uk> Message-ID: On Mon, 29 Nov 2004, Peter wrote: > Michael Maibaum wrote: >> >> James Casbon wrote: >> >>> Pretty much everyting I've posted to this list gets ignored. >> >> Yep, same here - I posted code for parsing a file format but got no >> feedback - not even a "no thanks, you suck". >> >> partly the complete bias on this list to spam over useful content is part >> of it... Why isn't this list subscriber only. I can (just about) >> understand the users list being open, but the people posting to dev are >> motivated enough to subscribe. Also, the users list is swamped with spam >> to the point I question it's usefulness. > > I was also shocked by the amount of spam on the list, and looking back at the > archives its been like this a while. It can't be very helpful for > BioPython's development. > > I would second the call to make this list subscriber only. And a third > > [Note I am "just" a biopython user, not a developer] > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > Ajinkya Joshi 3rd Year Bioinformatics Engineering Student Mobile Phone: 0417063485 CSE login/email: ajoshi From james.casbon at a4internet.com Mon Nov 29 07:28:01 2004 From: james.casbon at a4internet.com (James Casbon) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Spam on this the mailing lists (Was: Biopython-1.30.win32-py2.3 executable) In-Reply-To: <41AB1279.1080102@maubp.freeserve.co.uk> References: <41AB1279.1080102@maubp.freeserve.co.uk> Message-ID: <200411291228.04896.james.casbon@a4internet.com> > > partly the complete bias on this list to spam over useful content is > > part of it... Why isn't this list subscriber only. I can (just about) > > understand the users list being open, but the people posting to dev are > > motivated enough to subscribe. Also, the users list is swamped with > > spam to the point I question it's usefulness. > > I was also shocked by the amount of spam on the list, and looking back > at the archives its been like this a while. It can't be very helpful > for BioPython's development. > > I would second the call to make this list subscriber only. > > [Note I am "just" a biopython user, not a developer] It seems this was discussed here: http://portal.open-bio.org/pipermail/biopython-dev/2004-January/001829.html and Chris Dagdigian resolved to check the filters. Maybe he's the person to ask to restrict the list? To be honest, spamassassin filters this list fine for me so filtering could work. James From mike at maibaum.org Mon Nov 29 08:09:31 2004 From: mike at maibaum.org (Michael Maibaum) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Spam on this the mailing lists (Was: Biopython-1.30.win32-py2.3 executable) In-Reply-To: <200411291228.04896.james.casbon@a4internet.com> References: <41AB1279.1080102@maubp.freeserve.co.uk> <200411291228.04896.james.casbon@a4internet.com> Message-ID: <20041129130931.GC30404@remote.gene-hacker.net> On Mon, Nov 29, 2004 at 12:28:01PM +0000, James Casbon wrote: >> > partly the complete bias on this list to spam over useful content is >> > part of it... Why isn't this list subscriber only. I can (just about) >> > understand the users list being open, but the people posting to dev are >> > motivated enough to subscribe. Also, the users list is swamped with >> > spam to the point I question it's usefulness. >> >> I was also shocked by the amount of spam on the list, and looking back >> at the archives its been like this a while. It can't be very helpful >> for BioPython's development. >> >> I would second the call to make this list subscriber only. >> >> [Note I am "just" a biopython user, not a developer] > >It seems this was discussed here: >http://portal.open-bio.org/pipermail/biopython-dev/2004-January/001829.html >and Chris Dagdigian resolved to check the filters. > >Maybe he's the person to ask to restrict the list? > >To be honest, spamassassin filters this list fine for me so filtering could >work. I have to work to stop my bayesian filter from learning to equate biopython == spam ;) >From what I can see of the archives, this is a topic that comes up again and again... Michael -- Dr Michael A. Maibaum internet: mike@maibaum.org http://mike.maibaum.org/ voice: [m] 07813 713 952 [w] (020) 7679 3890