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Biology Birds of a Feather (BoF) Session

The Biology BoF was organized by Titus Brown.

The following text was scraped from:

The mailing list posting has been duplicated here with slight formatting changes.

Hi All,

Last night we had a biology birds of a feather meeting as part of SciPy 2007. I have included notes below from both Diane and myself. To summarize, there were two general trends during the evening:

  1. Need to establish python/biology community, via website,
    • biology-in-python mailing list, rss, blogs, etc.
  2. Having a core set of "interfaces" for handling basic
    • bioinformatics objects would allow independent projects to share these basic objects. I am sure others will describe this better and in more detail in the near future.

I have agreed to setup the python/biology community site. There are some ideas in the notes below and I will also be posting ideas and requesting ideas for this in a future post.

Enthought has agreed to host our community site. We have the option of using sub-domain such as or we can choose a domain name like Any thoughts or preferences on which one we should use?

I will let others jump and provide some of the details/interests from the meeting in more detail.

-Brandon King

Brandon King's Notes

Birds of a Feather: Biology

Chris: We could use some core package where all Biology Python packages can build off of, but still do there own thing. This would allow for the packages to pass data around in a compatible way.

Share [complex] functionality.

Parsing (Only need one / format).

Large analysis management / parallel / cluster processing.

Other people's databases.

Problems with BioPython:

Parsing Issues:

Where is the community?

Tutorials / entry documentation:

Common Theme:

Core interface so programs can play well together, while the implementations can change. This allows the interface to be independent from the storage.



Diane Trout's Notes

SciPy: SciPy2007/BioBoFNotes (last edited 2015-10-24 17:48:25 by anonymous)