Re: What is new in Debian-Med Etch ?
Hi all,
On Sun, Apr 15, 2007 at 04:20:49PM +0900, Charles Plessy wrote:
> Increased support of bioinformatics and molecular biology.
> ----------------------------------------------------------
>
> The number of programs available for multiple sequence
> alignment in Debian-Med has more than doubled, giving a broad choice
> of algorithms. Thanks to a collaboration with the upstream author of
> Seaview, we could move this alignment editor in the main Debian
> archive. We also expanded the support for phylogenetic analysis by
> adding to our collection TreeView X, a viewer which can export in SVG
> format. Molecular biologists will find a new primer design program in
> Debian-Med, Primer3, and a new version of perlprimer. These two
> programs nicely complement as the latter a graphical user interface
> and the former is well suited for high-throughput design.
Unfortunately, I have little to add to the list of features of this
release (at least regarding debian-med), but the next release is
codenamed 'Neuro-Lenny' ;)
If things work as expected lenny will feature a nice number of
neuro-imaging packages -- previously not available in Debian. I'm now quoting
the short descriptions of already existing packages (either already in
unstable or still on my local disk):
afni - toolkit for analyzing and visualizing functional MRI data
dicomnifti - converts DICOM files into the NIfTI format
freesurfer - cortical surface reconstruction from MRI data
fsl - analysis tools for FMRI, MRI and DTI brain imaging
mni-autoreg - MNI Automated Linear Registration
mni-n3 - intensity non-uniformity correction of MR volumes
libnifti* - IO libraries for the NIfTI-1 data format [ + some tools ]
pynifti - Python interface to the NIfTI I/O libraries
[ I'm upstream as well ]
Some of those are quite heavy (providing a huge number of tools). Taken
all together the next Debian release provides all tools required to do
neuro-imaging research, without the need to use closed source software.
This list does not include a number of additional new packages required
to satisfy dependencies. Some of them are also useful on there own:
libebtks - C++ library of numerical types and algorithm
fsl-feeds - FSL Evaluation and Example Data Suite
libgetopt-tabular-perl - table-driven argument parsing for Perl 5
libmni-perllib-perl - The MNI Perl Library
mni-autoreg-model - MNI average brain (305 MRI) stereotaxic registration model
vxl - C++ Libraries for Computer Vision Research
Please forgive me if I'm a bit enthusiastic, but the goal is to have only a
single newsline:
'Debian is now the recommend system for neuro-imaging research.'
Don't take me too serious ;)
Cheers,
Michael
PS: If you are interested, all packages are available to the public
(except for Freesurfer which is currently still closed-source). You can
find them either in my private repository or in the SVN repository of
the pkg-exppsy project on Alioth or at mentors.
And yes I need sponsor(s), as for some reason I cannot dedicate
enough time to my NM process (stuck at T&S part 1).
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
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