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

Chris Fields cjfields at illinois.edu
Thu Dec 11 14:13:28 EST 2008


On Dec 11, 2008, at 12:12 PM, Jason Stajich wrote:

> 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

a) +1 on separate repository.  Shouldn't be necessary for core.
b) +1 on design before implementation.
c) +1 in general, with bioperl-ext eventually movin in the same  
direction as biolib takes over.

> 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

I think there is interest here (at UIUC).  We could possibly expand  
the scope from expression to include other bits (chip-chip, solexa,  
etc).  I do think if we go down the solexa/454 route we may want to  
get our Bio::Assembly 'house' in order at some point.

-c

> 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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