Spiros Denaxas | 1 Feb 12:59 2011
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Re: medperl, something kinda like bioperl

On Mon, Jan 31, 2011 at 11:46 PM, Robert Buels <rmb32 <at> cornell.edu> wrote:

> Hi Spiros,
>
> This is a fine idea.  My most important piece of advice is to keep the code
> loosely coupled and flexible.
>
> Don't try to make big monolithic distributions like Bioperl.  Keep the code
> as loosely-coupled as possible: think carefully before making something be a
> subclass of something else, or have some other kind of direct dependency
> upon it.  Things change.  Coding practices change. Technology changes too,
> both on the bio/med side, *and* on the code side.
>
> For the project to stay healthy for the long haul, it needs to stay easy
> for people to wrap their minds around the codebase, and then work on it:
> developers need to be able to focus their efforts on the code that they are
> interested in without having to worry about huge amounts of other code.  For
> this to be possible, the various parts of the codebase need to stay
> organized and compartmentalized, with minimal, well-characterized dependency
> relationships between them.
>
> Good luck!
>
> Rob
>
>
>
Hello Rob,

thanks for the feedback. It will be definitely a learning experience for me
(Continue reading)

Dave Clements | 1 Feb 06:57 2011

March 2011 GMOD Meeting Registration is now open

Hello all,

Registration is now open for the March 2011 GMOD Meeting (
http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). This meeting will be
held March 5-6, as part of GMOD Americas 2011, which also includes a day of
Satellite Meetings, a GMOD Course (already full), and for the first time, an
"Introduction to GMOD" session the night before the meeting for GMOD
newcomers. GMOD Americas 2011 events are being held at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United
States.

As with previous GMOD meetings, this meeting will have a mixture of project
talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone
of North Carolina State University.  Dr. Stone will talk about his
experience on the "Drosophila Genome Reference Panel," a project that is
sequencing 192 lines.  See
http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda for more.

The agenda is driven by attendee suggestions, and you are encouraged to add
your suggestions now (
http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda_Proposals). For
examples of what happens at a GMOD meeting, see the writeup of the September
2010 GMOD Meeting (http://gmod.oicr.on.ca/wiki/September_2010_GMOD_Meeting),
or any previous meeting. GMOD meetings are an excellent way to meet GMOD
developers and users and to learn (and affect) what's coming in the project.

Registration for the March 2011 GMOD Meeting is
  $80 on or before February 18 <<<<=======
  $95 after February 18

(Continue reading)

Gregory Jordan | 1 Feb 15:21 2011
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Re: nucleotide changes along tree

Hi Nicholas,

PAML is the de facto standard for ancestral reconstruction of DNA
sequences. http://abacus.gene.ucl.ac.uk/software/paml.html

<http://abacus.gene.ucl.ac.uk/software/paml.html>BioPerl contains a
Bio::Tools::Phylo::PAML module for running PAML and parsing the output.
There's a how-to (http://www.bioperl.org/wiki/HOWTO:PAML) and documentation
on the specific methods to access ancestral state reconstructions (
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Phylo/PAML/Result.html#Synopsis)
.

If you're just doing a one-off run and don't need to automate things, you
may be better off running PAML on its own. Extensive documentation is
available from the PAML site (first link above).

Cheers,
 Greg

On Mon, Jan 31, 2011 at 4:30 PM, Nicholas Price <price4890 <at> gmail.com> wrote:

> Hi
>
> I have  three nucleotide sequences from human, chimp and Orangutan and
> the corresponding tree.I want align the sequences and for each column
> in the alignment where there are substitutions, I want to infer on
> which branches the changes occurred using a maximum likelihood method.
> Is there a way to do this in Bioperl??
>
> thank you
(Continue reading)

Frank Schwach | 1 Feb 15:22 2011
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Re: Proposed improvement to to Bio::Tools::Run::Primer3Redux

Hi John and Chris,

I was wondering about the state of affairs with this new
Bio-Tools-Primer3Redux module. I need to run and parse Primer3 v2.xx as
well and I also need the SEQUENCE_PRIMER_PAIR_OK_REGION_LIST function. I
was about to put together a module for my own use when I saw your
messages. So, if there is anything I can do to help with this I would be
happy to do so (instead of re-inventing the wheel). 

Frank

On Mon, 2011-01-24 at 12:41 -0600, Chris Fields wrote:
> John,
> 
> This patch is made off an older version of Bio-Tools-Primer3Redux, which is now hosted in a separate repo
on GitHub:
> 
> https://github.com/cjfields/Bio-Tools-Primer3Redux
> 
> I get one patch failure against the latest code which is easily added (the
SEQUENCE_PRIMER_PAIR_OK_REGION_LIST parameter), but tests now fail (see below).  Can you resubmit
this against the latest code?
> 
> chris
> 
> 
> $ ./Build test --test-files t/Run/Primer3Redux.t --verbose
> t/Run/Primer3Redux.t .. Subroutine p3_settings_file redefined at
/Users/cjfields/bioperl/Bio-Tools-Primer3Redux/blib/lib/Bio/Tools/Run/Primer3Redux.pm line 620.
> 
(Continue reading)

Chris Fields | 1 Feb 15:57 2011

Re: Proposed improvement to to Bio::Tools::Run::Primer3Redux

Frank,

You are more than welcome to look at the code on github and improve it.  In fact, let me know if you have a github
account and I can add you as a collaborator (John, same for you).  I'll probably work on conversion to
Dist::Zilla at some point for easier distribution building, but will keep a stub Build.PL for easy
installation from github if needed.

Key thing I want to make sure we keep up is tests and test coverage.  Could probably improve the backend a bit
more as well, but it works for now.

chris 

On Feb 1, 2011, at 8:22 AM, Frank Schwach wrote:

> Hi John and Chris,
> 
> I was wondering about the state of affairs with this new
> Bio-Tools-Primer3Redux module. I need to run and parse Primer3 v2.xx as
> well and I also need the SEQUENCE_PRIMER_PAIR_OK_REGION_LIST function. I
> was about to put together a module for my own use when I saw your
> messages. So, if there is anything I can do to help with this I would be
> happy to do so (instead of re-inventing the wheel). 
> 
> Frank
> 
> 
> 
> On Mon, 2011-01-24 at 12:41 -0600, Chris Fields wrote:
>> John,
>> 
(Continue reading)

Chris Fields | 1 Feb 15:58 2011

Re: nucleotide changes along tree

+1 on all this, just wish the output were easily parsable from version to version :P

chris

On Feb 1, 2011, at 8:21 AM, Gregory Jordan wrote:

> Hi Nicholas,
> 
> PAML is the de facto standard for ancestral reconstruction of DNA
> sequences. http://abacus.gene.ucl.ac.uk/software/paml.html
> 
> <http://abacus.gene.ucl.ac.uk/software/paml.html>BioPerl contains a
> Bio::Tools::Phylo::PAML module for running PAML and parsing the output.
> There's a how-to (http://www.bioperl.org/wiki/HOWTO:PAML) and documentation
> on the specific methods to access ancestral state reconstructions (
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Phylo/PAML/Result.html#Synopsis)
> .
> 
> If you're just doing a one-off run and don't need to automate things, you
> may be better off running PAML on its own. Extensive documentation is
> available from the PAML site (first link above).
> 
> Cheers,
> Greg
> 
> On Mon, Jan 31, 2011 at 4:30 PM, Nicholas Price <price4890 <at> gmail.com> wrote:
> 
>> Hi
>> 
>> I have  three nucleotide sequences from human, chimp and Orangutan and
(Continue reading)

Jinshun Zhong | 1 Feb 18:16 2011
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Fail to install DBD-mysql

Hi folks,

I followed the instruction to install the program, using GUI, command line
or cygwin. But every time I failed to find DBD-mysql, then I could not
proceed with "make" command. Is there anyone who knew how to deal with this?

Thanks.
Jinshun
Scott Cain | 1 Feb 18:37 2011
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Re: Fail to install DBD-mysql

Hi Jinshun,

What version are you trying to install that involves make?  It must be
very old, so that is a problem to start with.

DBD::mysql is not a required prerequisite for BioPerl, so that
shouldn't be a problem.

Scott

On Tue, Feb 1, 2011 at 12:16 PM, Jinshun Zhong <zsuzjsl <at> gmail.com> wrote:
> Hi folks,
>
> I followed the instruction to install the program, using GUI, command line
> or cygwin. But every time I failed to find DBD-mysql, then I could not
> proceed with "make" command. Is there anyone who knew how to deal with this?
>
> Thanks.
> Jinshun
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
(Continue reading)

pablo marin-garcia | 1 Feb 19:10 2011

Re: medperl, something kinda like bioperl

Hello Spiros,

I have been writing a set of modules and scripts called pmGWAS (perl
modules for genome wide association) and PMG (Perl for Medical
Genetics). They are based in bioperl and ensembl and I was going to
release in github and later in CPAN. They are modules for
visualization and creating report analysis for medical sequencing and
genotyping. Also I have been writing parsers for the common genotype
and SNPs file formats that at some point I would like to 'bioperlize'
following the SeqIO factory style.

Would be nice to use the bioperl wiki for organize and coordinate
these kind of modules. The current view on bioperl development,  I
think, today is more like the unix motto: do one thing, do it well and
interact well with others. As Rob said the trick is to keep things
simple and modular following the bioperl interfaces or defining new
ones and try to convince people to adhere.

Nice to see more people wanting to increase the perl contribution in this area.

  -Pablo

> >
> Hello Rob,
>
> thanks for the feedback. It will be definitely a learning experience for me
> as well. I'm planing on setting up some sort of public resource for people
> to have a look at and discuss / make a plan before actual coding gets done.
> Will keep you posted.
>
(Continue reading)

Dave Clements | 2 Feb 07:25 2011

GMOD Satellite Meetings, March 7, NESCent, Durham, NC

Hello all,

Yesterday, we opened registration for the March 2011 GMOD Meeting (see
http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting).  *That meeting is part
of a larger event, GMOD Americas 2011, that also includes several Satellite
Meetings on March 7*, the day after the meeting ends.

Satellite meetings are smaller groups of people meeting to discuss a common
interest, or work on a common problem (think special interest groups /
birds-of-a-feather).  Unlike the GMOD Meeting, there is *no registration fee
* for the Satellites, and you don't even need to go to any other GMOD
Americas events to participate in the Satellites.  *If you are in the area,
or attending other GMOD Americas events, or are just very interested in the
topic, we strongly encourage you to attend.*

The current list of Satellites (see
http://gmod.oicr.on.ca/wiki/Satellite_Meetings_-_GMOD_Americas_2011)
includes:

   - *GMOD Evo Hackathon
Followup*<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon#March_2011_Satellite>,
   organized by Duke Leto <http://gmod.oicr.on.ca/wiki/User:Dukeleto>.  A
   followup to the GMOD Evo
Hackathon<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon>held at
NESCent in November 2011.  You didn't to participate in the original
   event to participate in this followup.  Also, if there is interest, this
   satellite can extend for more than one day.
   - *Customizing and Extending JBrowse<http://gmod.oicr.on.ca/wiki/JBrowse>
   *, organized by Mitch Skinner<http://gmod.oicr.on.ca/wiki/User:MitchSkinner>
   .  JBrowse <http://gmod.oicr.on.ca/wiki/JBrowse> has a few different
(Continue reading)


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