Brad Chapman | 6 May 19:22 2003
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BOSC abstract for Biopython

Hey all;
Since many Biopython developers are facing the monetary difficulties 
of making it to Australia for this years Bioinformatics Open Source 
Conference (BOSC), I've been honored again this year with the 
privilege of giving a Biopython talk. As always, I am but a humble 
servant of the Biopython community and want to represent you fine 
folks as best I can (so I'll try not to show up reeking like cheap 
gin (although, no promises :-)).

I've gotten together an abstract for my talk which I've pasted
below. Basically, I'm planning to take the style of stepping through
a problem and showing solutions to it using Biopython, which seems
to have been a decent technique in talks I've given on Biopython in
the past (something useful for people plus the basics of Biopython
thrown in throughout).

I'd appreciate any feedback, good or bad, on it before I submit it
to the fine BOSC organizers. I'm already behind on this (my writtens
are coming up in two weeks -- man, does my life suck right now) so
I'm hoping to get it in as soon as I can. Thanks in advance for any
comments!

Brad

Using Biopython for Laboratory Analysis Pipelines

The Biopython project is distributed collaborative effort to develop Python
libraries to address the needs of researchers doing bioinformatics work.
Python is an interpreted object-oriented programming language that we feel is
well suited for both beginning and advanced computational researchers. Biopython 
(Continue reading)

biopython-bugs | 8 May 08:56 2003

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	Date: Thu, 08 May 2003 07:57:24  0000
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Coleman, Michael | 8 May 18:28 2003

buglet in BLASTX parsing

Parsing by NCBIStandalone.py fails for BLASTX 2.2.5 output, due to a missing 'S2' line.  The current code
seems to assume that either an S2 line or an immediate EOF will be hit.  The 2.2.5 output cleverly defeats
this assumption by including an extra newline before the EOF.  :-)

One solution is to change the read_and_call to an attempt, like so

	attempt_read_and_call(uhandle, consumer.blast_cutoff, start='S2')

I'm not sure whether that's the best solution, though.

Mike

Mike Coleman, Scientific Programmer, +1 816 926 4419
Stowers Institute for Biomedical Research
1000 E. 50th St., Kansas City, MO  64110
biopython-bugs | 8 May 17:59 2003

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	Date: Thu, 08 May 2003 17:00:51  0000
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(Continue reading)

Jeffrey Chang | 8 May 19:01 2003

Re: buglet in BLASTX parsing

Hey Mike,

Thanks for the report.  I have submitted a fix to NCBIStandalone.py.  
The fix I used is to check if the line is blank first.  If it is, then 
the parser does not attempt to parse the S2 line.

         # not in blastx 2.2.1
         # first we make sure we have additional lines to work with, if
         # not then the file is done and we don't have a final S2
         if not is_blank_line(uhandle.peekline(), allow_spaces=1):
             read_and_call(uhandle, consumer.blast_cutoff, start='S2')

Please wait a few hours for the fix to propogate to the anonymous CVS 
server at cvs.biopython.org.  Let me know if there continue to be 
problems!

Jeff

On Thursday, May 8, 2003, at 09:28  AM, Coleman, Michael wrote:

> Parsing by NCBIStandalone.py fails for BLASTX 2.2.5 output, due to a 
> missing 'S2' line.  The current code seems to assume that either an S2 
> line or an immediate EOF will be hit.  The 2.2.5 output cleverly 
> defeats this assumption by including an extra newline before the EOF.  
> :-)
>
> One solution is to change the read_and_call to an attempt, like so
>
> 	attempt_read_and_call(uhandle, consumer.blast_cutoff, start='S2')
>
(Continue reading)

Chris Dagdigian | 8 May 19:08 2003

will the biopython project be willing to be test case for relocating our webserver and mailing lists?


Hi folks,

We need to retire "open-bio.org" which is our ancient 500mhz Alpha box 
running Redhat 6.2.  It's old, has just 128M of memory, small disks and 
is hard to keep secure.

Its also our most important box as it does all of our mailing lists and 
a majority of our high traffic websites.

We have a new machine up online at va1220.open-bio.org that is meant to 
replace the alphaserver. It has Redhat 8.0, lots of memory, a pair of 
80gig disks etc.

Once the machine gets renamed to "portal.open-bio.org" and I can 
generate some SSL certificates I want to start moving projects onto the 
new box. I've spent a ton of time hand-tuning sendmail and building in 
anti-spam and anti-virus scanning

This is complicated because Mailman listserve is so tightly tied to the 
web that we pretty much have to move email, mailman and the website all 
at once to avoid disrupting things.

I'd like to use biopython as the first test case because you folks have 
  a simple website (looks like static HTML plus an old wiki) and three 
low traffic email lists. Plus Brad/Andrew/JeffC all know their way 
around our servers and can quickly notice problems if any occur.

Advantages to the move:

(Continue reading)

biopython-bugs | 8 May 18:22 2003

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Jeffrey Chang | 8 May 19:24 2003

Re: will the biopython project be willing to be test case for relocating our webserver and mailing lists?

No problem with me.

Brad has been working on a new version of the website, that is 
generally more easy to manage and better integrated with the blog.  Is 
this a good time to switch to that?  Or do you want to see if we can 
get a straight migration first?

Jeff

On Thursday, May 8, 2003, at 10:08  AM, Chris Dagdigian wrote:

>
> Hi folks,
>
> We need to retire "open-bio.org" which is our ancient 500mhz Alpha box 
> running Redhat 6.2.  It's old, has just 128M of memory, small disks 
> and is hard to keep secure.
>
> Its also our most important box as it does all of our mailing lists 
> and a majority of our high traffic websites.
>
> We have a new machine up online at va1220.open-bio.org that is meant 
> to replace the alphaserver. It has Redhat 8.0, lots of memory, a pair 
> of 80gig disks etc.
>
> Once the machine gets renamed to "portal.open-bio.org" and I can 
> generate some SSL certificates I want to start moving projects onto 
> the new box. I've spent a ton of time hand-tuning sendmail and 
> building in anti-spam and anti-virus scanning
>
(Continue reading)

Andrew Dalke | 8 May 19:32 2003

Re: will the biopython project be willing to be test case for relocating our webserver and mailing lists?

Jeff:
> No problem with me.

Ditto.

					Andrew
Brad Chapman | 8 May 19:37 2003
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Re: will the biopython project be willing to be test case for relocating our webserver and mailing lists?

Chris:
> >I'd like to use biopython as the first test case because you folks 
> >have  a simple website (looks like static HTML plus an old wiki) and 
> >three low traffic email lists. Plus Brad/Andrew/JeffC all know their 
> >way around our servers and can quickly notice problems if any occur.

Jeff:
> Brad has been working on a new version of the website, that is 
> generally more easy to manage and better integrated with the blog.  Is 
> this a good time to switch to that?  Or do you want to see if we can 
> get a straight migration first?

This is also cool with me. I am willing to do the website switching
this weekend if that works with everyone (Sunday evening would work
good with me).

The new page is a little more complicated since it's not straight
HTML, but also doesn't need the wiki (I don't really think there is
much reason to keep that around) so it's easier in some ways. Plus
I'm willing to do the work in getting it up and running provided I
can get sudo access or whatever. So this makes it lots easier for
ya'll.

So, yeah: +1 for moving to the new server and +1 for using the new
website.

Brad

Gmane