[Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada

Jason Stajich jason at bioperl.org
Thu Dec 11 18:12:51 UTC 2008


Ian -
I definitely agree - I think the only place the analysis needs to  
happen on the BioC/R side- great to hear your help volunteered Ian.

I was mainly making comments about

a) Whether or not these new commits should live in the "core" or a  
different main bioperl svn sub-repository
b) if we can consider how we'll model this kind of data for  
manipulation in bioperl and also some generic representations that  
could capture Expression in general in terms of RNA-Seq type data
c) semi-offhandly reminding myself and us that there is a dead svn  
repository called bioperl-microarray that we ought to probably  
formally described as deprecated

I'd also be curious if this community wants to work towards some  
common tools for the sequence-based expression (short-read  
technology).  This would certainly go in a separate repository to move  
in this spirit of de-monolithing bioperl.  I like Chris's suggestion  
of bioperl-expression although it might be that we want some common  
solutions for chip-seq and genomic sequencing from ABI/Illumina/454 as  
well.
   I know there are a lot of tools out there already for aspects of  
these sequence-based analyses so I think it would be best focus on  
some specific goals here if we got into it rather than just writing  
parsers, etc.  Certainly a lot of us have home-grown solutions but  
wonder whether there will be enough interest to architect some common  
tools.

-jason
On Dec 11, 2008, at 7:19 AM, Dr. T. I. Simpson wrote:

> Hi guys, I am a newbie on here so  hope this mail is appropriate.
>
> Just thought I would chip in here (sorry for the pun). I would like  
> to echo Marian's comments. I work extensively with R/BioC and Perl  
> taking experimental data from low-level array to lots of different  
> downstream analyses. I made an effort to work with R through Perl  
> about a year ago using RSPerl and it was mighty painful. As Marian  
> suggests it wouldn't be a good idea to compete with R/BioC there are  
> some absolutely gold standard packages like affy, affyPLM and limma  
> to name just three that cope with serious statistics within the R  
> environment. If it were possible to make a good bridge to execute R  
> scripts and access/manipulate R variables (a run wrapper  module for  
> R ?) then that would be a very significant step forward for someone  
> like me. I don't know how skillfully I could contribute to this, but  
> happy to help wherever I can.
>
> Best wishes
>
> Ian.
>
> On Thu, 11 Dec 2008 10:12:42 -0000, Marian thieme <Marian.thieme at klinik.uni-regensburg.de 
> > wrote:
>
>> I also had the impression that "it" was discouraged to use bioperl  
>> for microarray processing.
>> As I know from my colleagues and also I did to good extemt) people  
>> use R (especially Bioconductor) for most of the issues concerning  
>> microarrays. (there are so many supoorted microarray designs,  
>> preprocessing and normalization tools, and complete packages to  
>> perform differential expression analysis). At least for the  
>> expression chips but also for genotyping/SNP chips I think R/BioC  
>> is method of choice. Probably for the resequencing chips they are  
>> not that well supported, because its only a minority that uses this  
>> kind of chips. Therefore I think ReseqChip has its right to exist,  
>> even though it would reach more people if it would a R/BioC  
>> package. (Moreover I believe that this kind of chips wont have  
>> broader interest, because second generation sequencing methods will  
>> probably be more appropriate in the next few years)
>> So to cut a long story short, I find Chris' idea of bridging  
>> bioperl to BioC (or vice versa) very good: Dont compete against R/ 
>> BioC, but make it easier to use both together.
>>
>> marian
>>
>> Marian Thieme
>> Institute of Functional Genomics
>> University Regensburg
>> Josef Engert Str. 9
>> 93053
>> Regensburg
>> Germany
>> P: 0049 (0)941 943 1584
>> F: 0049 (0)941 943 5020
>> E:  marian.thieme at klinik.uni-regensburg.de
>> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik
>>
>>
>>>>> Chris Fields <cjfields at illinois.edu> 12/10/2008 7:59 PM >>>
>> Sounds like a good idea, with one caveat: Allen had pretty much given
>> up on bioperl-microarray last I heard (last significant commits were
>> ~6 yrs ago).  It would be nice to revive with this theme in mind,
>> though maybe bioperl-expression would be better (could focus on other
>> expression-related issues along with microarray data).  Marian, what
>> do you think?
>>
>> chris
>>
>> P.S. An aside: I'm planning on running lots of Illumina data myself
>> and have been thinking about making a BioC-BioPerl bridge, then  
>> seeing
>> how it fits into a bioperl-microarray.  Just need a working perl-R
>> interface (NOT RSPerl).
>>
>> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote:
>>
>>> Since we've started discussing the idea of starting to move things
>>> out into smaller packages, does it make sense to move this
>>> Bio::Microarray into its own package before it gets bigger? What
>>> about the old bioperl-microarray stuff from Allen Day?
>>>
>>> I also know that as we haven't branched for 1.6 Chris we'll have to
>>> make some decisions about new code going in before then?
>>>
>>> Not trying to stifle any of the development with extra work but
>>> trying to see if we should start to make some logical slices of
>>> packages?
>>>
>>> -jason
>>>
>>> Begin forwarded message:
>>>
>>>> From: Marian Thieme <thm09830 at dev.open-bio.org>
>>>> Date: December 10, 2008 6:10:21 AM PST
>>>> To: bioperl-guts-l at bioperl.org
>>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ 
>>>> Microarray/
>>>> Tools: use superclasses initialization and argument processing/
>>>> attribute setting as suggested in styleguide
>>>>
>>>> Revision: 15134
>>>> Author:   thm09830
>>>> Date:     2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008)
>>>>
>>>> Log Message:
>>>> -----------
>>>> use superclasses initialization and argument processing/attribute
>>>> setting as suggested in styleguide
>>>>
>>>> Modified Paths:
>>>> --------------
>>>>  bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
>>>>  bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>>>
>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ 
>>>> MitoChipV2Parser.pm
>>>> ===================================================================
>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>>> 2008-12-10 12:51:47 UTC (rev 15133)
>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>>> 2008-12-10 14:10:21 UTC (rev 15134)
>>>> @@ -78,12 +78,13 @@
>>>>
>>>> sub new {
>>>>
>>>> -  my ($class, $file_name) = @_;
>>>> -  my $self = $class->SUPER::new();
>>>> +  my ($class, @args) = @_;
>>>> +  my $self = $class->SUPER::new(@args);
>>>> +  my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)],
>>>> @args);
>>>> +
>>>> $self->{_frags_hash}=undef;
>>>> $self->{_oligos2calc_hash}=undef;
>>>> $self->throw("Must provide filename as first argument !") unless
>>>> $file_name;
>>>> -
>>>>
>>>> my %max_ins_hash=();
>>>> $self->{_frags_hash}=$self-
>>>> >_parse_Affy_mtDNA_design_annotation_file($file_name);
>>>>
>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>>> ===================================================================
>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10
>>>> 12:51:47 UTC (rev 15133)
>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10
>>>> 14:10:21 UTC (rev 15134)
>>>> @@ -194,8 +194,11 @@
>>>>
>>>> sub new {
>>>>
>>>> -  my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>>> $refseq) = @_;
>>>> -  my $self = $class->SUPER::new();
>>>> +  #my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>>> $refseq) = @_;
>>>> +  my ($class, @args) = @_;
>>>> +  my $self = $class->SUPER::new(@args);
>>>> +  my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)=
>>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE
>>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args);
>>>> +
>>>> $self->{_frags_hash}=undef;
>>>> $self->{_max_ins_hash}=undef;
>>>> $self->{_refseq}=undef;
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-guts-l mailing list
>>>> Bioperl-guts-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
>>>
>>> Jason Stajich
>>> jason at bioperl.org
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> -- 
> Dr T.I.Simpson
> School of Biomedical Sciences
> University of Edinburgh
> Hugh Robson Building
> George Square
> Edinburgh
> EH8 9XD
>
> ian.simpson at ed.ac.uk
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

Jason Stajich
jason at bioperl.org






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