[Bioperl-pipeline] Information on development?

[Anelda Boardman]

Dear Juguang and Shawn,

Thanks for your replies!

We are busy developing a sequence analysis pipeline to be integrated to
a local HIV database in a nationwide study in South Africa.  We're also
still in the process of developing the database.

I have been looking at a couple of pipeline generators/ already existing
pipelines and the software that we would have to incorporate into the
pipeline and was wondering if biopipe won't make my life easier...

What we want to do is take the whole project from scratch.. Sequencing,
chromatogram evaluation, vector trimming, assembly, finishing, then
ruling out contamination, and finally annotation of the sequences.

Do you think biopipe can facilitate development of such a pipeline?

One obstacle is that we will be using a single server for running the
pipeline and storing the db (anyways for now).  Seems like biopipe is
meant to do some loadsharing etc.

I'm in the process of installing biopipe on my machine to see how it works
(got some example pipelines to test).

Regards,
Anelda



> Hi Anelda,
>
> We Singapore team, including Aaron and Allison, is working on a
> web-based, biomart-like pipeline project. I hope you have some idea on
> biomart.
>
> The motivation of this project is to ease users' work on create XML
> configuration file by allowing user to click this or that on the web,
> and further provide the bioinformatics service such as protein
> annotation on web interface.
>
> We are in the hope to improve biopipe thought identifying what the
> current biopipe cannot do or is hard to do, in this project. That is
> what I am trying to do here, while my colleague will mainly develop
> the web interface and back-end logic from the user side of biopipe.
> They will be positive feedback providers for us.
>
> Please let us know your expectation or idea on our biopipe, or the
> difficulty or confusion in using biopipe.
>
> Cheers,
> Juguang
>
> On Thursday, May 20, 2004, at 12:29  am, Shawn Hoon wrote:
>
>> Hi Anelda,
>> 	yes, development is still going on, although the number of people
>> involved may not be too many right now.
>> First year in grad school has push biopipe a little down on my todo
>> list. Hopefully, I can work on it more this summer.
>> In anycase, the TLL group in Singapore, Juguang and Bala work on
>> biopipe (although I would love to see more commits :)
>> as well as Kiran at CSHL AFAIK. I wish I could put forward more
>> information. Perhaps you could describe what you would like to do
>> then we can steer you in the right direction.
>>
>> cheers,
>> shawn
>>
>> On May 18, 2004, at 7:30 AM, Anelda Boardman wrote:
>>
>>> Hallo,
>>>
>>> I've heard of the biopipe project and would like to know more about
>>> it,
>>> but fail to find information on the latest development/progress..
>>> Is
>>>  this
>>> project still ongoing?
>>>
>>> Looking forward to your reply!
>>>
>>> Kind regards,
>>> Anelda Boardman
>>>
>>>
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>>
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