[Bioperl-l] question about the nature of bioperl

[Elia Stupka]

> maybe bioperl is biased towards the use-cases of the core developers, who
> often work in big genome centres?

bioper and ensembl have started with maybe some bias in that area, and
this is one of the reasons why we have started working on the bioperl
pipeline, it is to encapsulate in a robust reproducible core
simple-to-complex tasks that people out there in small to medium labs
would like to manage. Running things as part of the pipeline of course
gives you an easy way to a)re-run every time you want with updated data,
b)record sensibly each stage of your analysis for a potential
paper,etc. c)introduces sanity all round.

As part of this effort to make it easier for newbies we are producing XML
"templates" for commonly wanted tasks, eventually we will have one out for
annotation (genome-style) on any input sequence, as well as simple blast
pipelines that can be easily modified, protein clustering,etc.

Elia

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