From johann@egenetics.com Tue Nov 7 14:52:36 2000
Date: Tue, 7 Nov 2000 16:52:36 +0200
From: Johann Visagie johann@egenetics.com
Subject: [BioPython] Paper in Bioinformatics
Scott T. Kelley on 2000-10-24 (Tue) at 12:00:40 -0700:
>
> I just ran into a recent Python reference in Bioinformatics about object
> oriented parsing of biological databases that I thought members of the list
> might find interesting (if you don't already know of the ref).
Just busy reading it myself.
> If they aren't already aware and members of Biopython, they might be worth
> contacting...
Indeed. The authors state (under "Future developments") that they would like
to "incorporate bioperl/biopython efforts to standardize the sequence
object".
Frankly, as far as creating parsers are concerned, I think they'd benefit
from having a look at Martel. :-)
-- Johann
From jchang@SMI.Stanford.EDU Wed Nov 8 21:57:21 2000
Date: Wed, 8 Nov 2000 13:57:21 -0800 (PST)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] biocorba IDL
Hello Biopythoners,
Alan Robinson has made the Biocorba IDL version 0.2.0 is available at:
http://industry.ebi.ac.uk/~alan/BioCorba-0.2.0/
While it hasn't been implemented yet in the bio* projects, it's a good
roadmap for the directions in the near future. This is important for
biopython because as we develop our sequence object model, we'll know what
features we'll need to support.
Anyone using the biopython-corba module should definitely take a look at
this. Discussions will occur on the biocorba list!
Jeff
From chapmanb@arches.uga.edu Wed Nov 8 23:02:24 2000
Date: Wed, 8 Nov 2000 18:02:24 -0500 (EST)
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] biocorba IDL
Jeff wrote:
> Alan Robinson has made the Biocorba IDL version 0.2.0 is available at:
> http://industry.ebi.ac.uk/~alan/BioCorba-0.2.0/
Thanks for pointing this out, Jeff! I think Alan et al. have really
done a great job on the object model (at least, I like it :-), and I
really got a lot out of taking some time to sit down and go through it.
> While it hasn't been implemented yet in the bio* projects, it's a good
> roadmap for the directions in the near future.
>
> Anyone using the biopython-corba module should definitely take a look at
> this.
Yup, I'm planning to move the biopython-corba module to this as soon
as I have some time to do it. If anyone else is using biopython-corba
besides me and has concerns about moving over to this, please let me
know! Or if anyone has a burning desire to help (I can always dream,
can't I? :-), I'm more than open to working with other people on this.
Brad
From pa_wilki@gene.concordia.ca Thu Nov 9 15:32:21 2000
Date: Thu, 9 Nov 2000 10:32:21 -0500 (EST)
From: Peter pa_wilki@gene.concordia.ca
Subject: [BioPython] Biopython and python 2
Has anyone started to develop with b2 or used it to run the biopython
package?
Any quirks?
Peter
._______________________________________________________________________.
| Peter Wilkinson |
| mailto:pa_wilki@gene.concordia.ca |
| |
| |
[ The Center for Structural and Functional Genomics ]
From jchang@SMI.Stanford.EDU Thu Nov 9 19:08:24 2000
Date: Thu, 9 Nov 2000 11:08:24 -0800 (PST)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] Biopython and python 2
I know of a few people using python 2 with biopython and haven't heard
reports of anything broken. However, we are planning on supporting python
2, so please send in bug reports and/or patches!
Jeff
On Thu, 9 Nov 2000, Peter wrote:
> Has anyone started to develop with b2 or used it to run the biopython
> package?
> Any quirks?
>
>
> Peter
>
> ._______________________________________________________________________.
> | Peter Wilkinson |
> | mailto:pa_wilki@gene.concordia.ca |
> | |
> | |
> [ The Center for Structural and Functional Genomics ]
>
>
>
>
>
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
From thomas@cbs.dtu.dk Mon Nov 20 15:24:40 2000
Date: Mon, 20 Nov 2000 16:24:40 +0100 (CET)
From: thomas@cbs.dtu.dk thomas@cbs.dtu.dk
Subject: [BioPython] scriptcentral
Hej Biopythoneer's,
Finally our paper describing PYPHY (Python Phylogenomics) has been accepted
(NAR) - who should I mail concerning a Hall of Fame entry at ScriptCentral???
thx
-thomas
Sicheritz Ponten Thomas E. CBS, Department of Biotechnology
thomas@biopython.org The Technical University of Denmark
CBS: +45 45 252485 Building 208, DK-2800 Lyngby
Fax +45 45 931585 http://www.cbs.dtu.dk/thomas/index.html
De Chelonian Mobile ... The Turtle Moves ...
From chapmanb@arches.uga.edu Tue Nov 21 17:41:13 2000
Date: Tue, 21 Nov 2000 12:41:13 -0500 (EST)
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] scriptcentral
Hi Thomas!
> Finally our paper describing PYPHY (Python Phylogenomics) has been accepted
> (NAR) - who should I mail concerning a Hall of Fame entry at ScriptCentral???
Sounds really interesting. I for one am very interested in checking
this out!
I'm not sure if anyone responded to your privately, but I would be
happy to add the info to script central (since I just discovered
recently I can update the web site :-). If you want, just send the
relevant info (contact author + URL + short description) either to
the list or to me personally, and I'll add it ASAP.
Looking forward to playing with the code!
Brad
From jchang@SMI.Stanford.EDU Mon Nov 27 03:08:56 2000
Date: Sun, 26 Nov 2000 19:08:56 -0800 (PST)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] Biopython 0.90d04 now available
Hello everyone,
Biopython release 0.90d04 is now available.
Added support for multiple alignments, ClustalW
BLAST updates, bug fixes, and BlastErrorParser
Fixes for PSI-BLAST in master-slave mode
Minor update in stringfns, split separators can be negated
Added download_many function to PubMed
xbbtools updates
Prodoc parser now accepts a copyright at the end of a record
Swiss-Prot parser now handles taxonomy ID tag
Also, an elaboration from Iddo Friedberg:
SubsMat: a module for generating substitution matrices from user data.
Documentation is available on
http://biopython.org/wiki/html/BioPython/SubsMat.html Accepted replacement
matrices (the initial input for a substitution matrix) may be generated
using the Align module.
FreqTable: a module for generating alphabet (amino-acid/nucleotide)
frequency tables from user data. Documentation is available on:
http://biopython.org/wiki/html/BioPython/FreqTable.html
Note: this release requires Python 2.0. Most older code will continue to
work with Python 1.52, however. If you need continued 1.52 compatibility
with a specific module(s), please let us know!
Download and enjoy!
Jeff
From jchang@SMI.Stanford.EDU Mon Nov 27 03:21:58 2000
Date: Sun, 26 Nov 2000 19:21:58 -0800 (PST)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] plans for next release
Hello everybody,
We've been getting a lot of functionality into the core package. Things
are starting to become useful!
Unfortunately, we've also started to pick up some "cruft", as Ewan Birney
likes to call it. Most of it is my fault, though. :( Thus, the next
release will mainly be for refactoring and technology upgrades. Here are
my thoughts:
- Since Martel is maturing and becoming useful (used in Clustalw code),
we'll integrate that with the release and installation process. In
addition, we'll pull mxTextTools in as well, since its host (starship)
doesn't seem to be reliable and also for simplicity of installation.
- Deprecate Sequence.py. The functionality is superceded by Seq.py.
- Move more code into __init__.py. This is cosmetic and will prevent code
like:
from Prosite import Prosite
Unfortunately, this will break code. Hopefully, the changes will be minor
and easy to fix.
Please send mail if you have any more structural changes, or if you
disagree with these plans.
Thanks,
Jeff
From katel@worldpath.net Tue Nov 28 06:21:22 2000
Date: Mon, 27 Nov 2000 22:21:22 -0800
From: Cayte katel@worldpath.net
Subject: [BioPython] plans for next release
----- Original Message -----
From: "Jeffrey Chang" <jchang@SMI.Stanford.EDU>
To: <biopython@biopython.org>
Sent: Sunday, November 26, 2000 7:21 PM
Subject: [BioPython] plans for next release
> Hello everybody,
>
> We've been getting a lot of functionality into the core package. Things
> are starting to become useful!
>
.> Please send mail if you have any more structural changes, or if you
> disagree with these plans.
>
In the future, I think we should use wxPython guis to provide
visualization, such as using colors and fonts to emphasize regions with high
information content or to show hydrophilic amino acids, etc.
. Cayte
From jchang@SMI.Stanford.EDU Tue Nov 28 16:48:36 2000
Date: Tue, 28 Nov 2000 08:48:36 -0800 (PST)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] plans for next release
Thomas Sicheritz-Ponten is working on visualization with his xbbtools,
using Tk instead of wx, though.
Jeff
On Mon, 27 Nov 2000, Cayte wrote:
>
> ----- Original Message -----
> From: "Jeffrey Chang" <jchang@SMI.Stanford.EDU>
> To: <biopython@biopython.org>
> Sent: Sunday, November 26, 2000 7:21 PM
> Subject: [BioPython] plans for next release
>
>
> > Hello everybody,
> >
> > We've been getting a lot of functionality into the core package. Things
> > are starting to become useful!
> >
> .> Please send mail if you have any more structural changes, or if you
> > disagree with these plans.
> >
> In the future, I think we should use wxPython guis to provide
> visualization, such as using colors and fonts to emphasize regions with high
> information content or to show hydrophilic amino acids, etc.
>
> . Cayte
>
>
From katel@worldpath.net Wed Nov 29 04:35:16 2000
Date: Tue, 28 Nov 2000 20:35:16 -0800
From: Cayte katel@worldpath.net
Subject: [BioPython] plans for next release
----- Original Message -----
From: "Jeffrey Chang" <jchang@SMI.Stanford.EDU>
To: "Cayte" <katel@worldpath.net>
Cc: <biopython@biopython.org>
Sent: Tuesday, November 28, 2000 8:48 AM
Subject: Re: [BioPython] plans for next release
> Thomas Sicheritz-Ponten is working on visualization with his xbbtools,
> using Tk instead of wx, though.
>
> Jeff
>
>
> On Mon, 27 Nov 2000, Cayte wrote:
>
> >
> > ----- Original Message -----
> > From: "Jeffrey Chang" <jchang@SMI.Stanford.EDU>
> > To: <biopython@biopython.org>
> > Sent: Sunday, November 26, 2000 7:21 PM
> > Subject: [BioPython] plans for next release
> >
> >
> > > Hello everybody,
> > >
> > > We've been getting a lot of functionality into the core package.
Things
> > > are starting to become useful!
> > >
> > .> Please send mail if you have any more structural changes, or if you
> > > disagree with these plans.
> > >
> > In the future, I think we should use wxPython guis to provide
> > visualization, such as using colors and fonts to emphasize regions with
high
> > information content or to show hydrophilic amino acids, etc.
> >
> > . Cayte
> >
> >
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
>
From katel@worldpath.net Wed Nov 29 04:38:07 2000
Date: Tue, 28 Nov 2000 20:38:07 -0800
From: Cayte katel@worldpath.net
Subject: [BioPython] plans for next release
----- Original Message -----
From: "Jeffrey Chang" <jchang@SMI.Stanford.EDU>
To: "Cayte" <katel@worldpath.net>
Cc: <biopython@biopython.org>
Sent: Tuesday, November 28, 2000 8:48 AM
Subject: Re: [BioPython] plans for next release
> Thomas Sicheritz-Ponten is working on visualization with his xbbtools,
> using Tk instead of wx, though.
>
>
I'm not sure its supported on Windows. The web description mentioned
Linux but didn't mention Windows. It imports posix.
Cayte
From chapmanb@arches.uga.edu Wed Nov 29 23:58:24 2000
Date: Wed, 29 Nov 2000 18:58:24 -0500 (EST)
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] Biopython 0.90d04 now available
Jeff wrote:
> Biopython release 0.90d04 is now available.
Looks great Jeff! Thanks for getting this together.
For anyone who is interested, I just uploaded some "package" type
distributions for various platforms:
o A Windows installer for those people working on a Microsoft OS
o A RPM installer for LinuxPPC.
These are available at the normal download site:
http://biopython.org/Download/
I don't normally use RPMs or Windows, and am just trying to make these
as a convenience for people who do use them, so any feedback on the
usefulness of these (ie. whether they work properly or not :-) would
be very appreciated.
I'd like to also take a quick chance to plug the documentation
available for this release. If you point your browser to:
http://biopython.org/wiki/html/BioPython/BiopythonCode.html
you can find all of the documentation available right
now. Specifically, we've got API documentation for the release created
automagically using HappyDoc, and a 44 page Tutorial covering how to
do a lot of things with the code.
If anyone is interested in helping out by maintaining one of these
built distributions (or contributing one for additional platforms),
that would be especially super-duper. There is a nice section in
the Tutorial describing how to do this.
Enjoy, and thanks for listening!
Brad
From chapmanb@arches.uga.edu Thu Nov 30 01:20:32 2000
Date: Wed, 29 Nov 2000 20:20:32 -0500 (EST)
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] plans for next release
Jeff:
> > Thomas Sicheritz-Ponten is working on visualization with his xbbtools,
> > using Tk instead of wx, though.
> >
Cayte:
> I'm not sure its supported on Windows. The web description mentioned
> Linux but didn't mention Windows. It imports posix.
Hi Cayte -- I just looked at this using my little bit of Windows/python
knowledge. It looks like Thomas is importing posix/posixpath in all of
the different modules in xbbtools, but never actually using them. I
commented out all of the imports, installed Pmw, and xbbtools seems to
run okay on the machine I was playing on (vanilla Windows 98).
I'm not sure if there is a good reason to import the posix stuff
(Thomas?) but maybe if not, it might be good to get rid of the imports
so it'll run nicely on Windows as well.
Brad
From johann@egenetics.com Thu Nov 30 14:14:53 2000
Date: Thu, 30 Nov 2000 16:14:53 +0200
From: Johann Visagie johann@egenetics.com
Subject: [BioPython] Biopython 0.90d04 now available
Brad Chapman on 2000-11-29 (Wed) at 18:58:24 -0500:
>
> Jeff wrote:
> > Biopython release 0.90d04 is now available.
>
> Looks great Jeff! Thanks for getting this together.
Indeedy! :-)
> For anyone who is interested, I just uploaded some "package" type
> distributions for various platforms:
[ snip ]
As always - and as Brad already knows - I am working on getting the FreeBSD
port of Biopython up to date. This time around I'm also integrating optional
CORBA functionality into the FreeBSD port which will install Brad's
biopython-corba package as well as either omniORBpy or Fnorb (whichever the
user prefers) and all other dependencies. It should be in the FreeBSD ports
tree within the next few days.
-- Johann