[Bioperl-l] TFBS databases, Bio::Matrix::PSM suitable?

skirov skirov at utk.edu
Tue Aug 22 14:45:12 EDT 2006

>===== Original Message From Sendu Bala <bix at sendu.me.uk> =====
>skirov wrote:
>>>> Stefan Kirov wrote:
>>>> Sendu Bala wrote:
>>> I'm not sure what you mean. Do you think that before a genbank parser
>>> can be released, all genbank files in existence must be supplied in the
>>> test suite to ensure it really does work on everyone's machine?
> >
>> Did I say that or you infer? What I said is the tests are prepared to make
>> sure the code work properly under specific environment (architecture,
>> compiler, etc.) However, developers must make sure their code does not get
>> choked up by the full data set.
>I would have thought this went without saying. Of course the original
>developer checks to see if his code works on the full data. The question
>is does every user of bioperl need to be able to test the full data? No.
>Until recently, Bio::DB::Taxonomy::flatfile wasn't tested at all. I
>didn't see you complain at my suggestion a subset of the taxonomy
>database be included in t/data for testing purposes.
Taxonomy is not a good example since it is available to anyone. Transfac is 
>> My point exactly- how bioperl contributors can fix a bug if they do not 
>> access to the data? It means the user would have to submit a test set which
>> could be a license violation. I do not know to what extent Transfac would
>> pursue their rights and its implication, but I wouldn't like to try either.
>Look, the TFBS:: module seems to have survived without causing anguish
>and heartache. If /you/ don't have access to the data maybe you can't
>fix some possible future bug. But the nice thing about an open-source
>project like Bioperl is that maybe someone else /does/ have access, and
>/they/ can fix the bug.
I think TFBS is quite different project with different goals and scope. I do 
not think it is fair to make a comparison between TFBS and Bioperl.
My concern is how many people are going to be able to take care of this code.
>>> Who says it won't be maintained? I will maintain it. The very second I
>>> can no longer maintain it and no one else can, it can be deprecated to
>>> avoid clutter. I don't see the problem. But in any case see below -
>>> anyone could probably maintain it.
> >
>> I guess that if you decide you can no longer do that you are going to 
>> it? Go ahead, but do not forget what you are promising now.
>I made no such promise. It is the case that with all modules in bioperl
>that if they are no longer maintained and no longer work, they should be
>deprecated. My proposed module would be different in this regard.
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