[bip] Python wrapper for the NCBI C++ Toolkit

[Josh Cherry]

Hi Andrew.  Thanks for the feedback.  The C++ Toolkit book is out of my 
control, but I'll pass your suggestions along.  I can offer a summary of 
the Toolkit here.

The NCBI C++ Toolkit provides a variety of general-purpose and 
mission-specific functionality.  This includes reading and writing NCBI 
data model objects in ASN.1 and XML; retrieving sequences, their 
annotations, etc., from NCBI's databases; retrieving other information, 
such as PubMed entries and data from the taxonomic database; reading and 
writing a variety of file formats relevant to biology; and algorithms for 
sequence analysis and related endeavors.

The Toolkit is large (over 3000 classes in the Python wrapper) and the 
work of many people, so no single person is familiar with all of it. 
It's what we use at NCBI for just about anything we write in C++, and 
where we eventually put anything likely to be of general use.

The Python wrapper more or less mirrors the C++ API, but with a few 
important enhancements.  These include simplified 
serialization/deserialization of ASN.1/XML and mechanisms for easy access 
to Toolkit documentation.  It's an open question what role the Python 
wrapper will play outside of NCBI.  I see it, and its Perl counterpart, as 
making the Toolkit much more accessible to the outside world.

Josh


On Mon, 21 Jul 2008, Andrew Straw wrote:

> Hi Josh,
>
> I think you could improve the interest and uptake of the project if you
> included a 1 sentence blurb at the top of the project webpages. This
> sentence should attempt to encapsulate what the software does or is
> intended to do. And then a 1 paragraph blurb giving an ever-so-slightly
> more detailed idea in, for example, the "Part 1. Overview" section of
> the book would be further appreciated.
>
> Also, it's slightly weird that clicking on "The NCBI C++ Toolkit" icon
> at the top of the page sends me to http://www.ncbi.nlm.nih.gov/, which
> tells me nothing about the C++ toolkit.
>
> Still not exactly sure what the high-level mission of the NCBI C++
> Toolkit is after several minutes of clicking around on the website,
> Andrew
>
> Josh Cherry wrote:
>> NCBI is pleased to announce the availability of Perl and Python interfaces
>> to the NCBI C++ Toolkit for Intel Linux platforms.  These interfaces
>> provide access to most of the Toolkit's functionality
>> (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.TOC) from the Perl
>> and Python programming languages.  They are available as binary releases
>> under ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/, in the Perl
>> and Python subdirectories.  We welcome any feedback about these newly
>> available tools.
>>
>> _______________________________________________
>> biology-in-python mailing list - bip at lists.idyll.org.
>>
>> See http://bio.scipy.org/ for our Wiki.
>
>