Biomedical Engineering Reference
In-Depth Information
contribution was the single most signifi cant motivation for making this
suite of tools publicly and freely available. Soon after we decided to open
source our software, we realized that it is one thing to use software
internally, and a totally different thing to actually expose it to public
usage. For example, we understood that for open source to be meaningful,
the developer needs to undertake a variety of tasks, such as documenting
the source code, creating a user's manual, tutorials, a web site, and also
using some version control and a bug tracking system. Overall, we are
convinced that this effort was worthwhile and that the open source trend
is only going to get stronger in the next few years.
8.8 Resources
This chapter described version 2.0 of GenomicTools released in September
2011. The source code, documentation, user manual, example data sets
and scripts are available online at
http://code.google.com/p/ibm-cbc-
genomic-tools/
.
To install GenomicTools, follow these simple instructions:
tar xvzf genomic-tools-VERSION-src+doc.tgz
cd genomic-tools
make
sudo cp bin/* /usr/local/bin
tar xvzf genomic-tools-VERSION-src+doc.tgz
cd genomic-tools
make
sudo cp bin/* /usr/local/bin
There is a dependency on the GNU Scientifi c Library (GSL), which can
be downloaded from
http://www.gnu.org/software/gsl/
.
Examples and associated input fi les and scripts are part of the source
code distribution in the 'examples' subdirectory. The API documentation
is stored in the 'doc' subdirectory.
For details about the options for each tool, the reader is referred to the
User's Manual, which can be downloaded from
http://code.google.com/p/
ibm-cbc-genomic-tools/#Documentation
.
For any questions, suggestions or comments contact Aristotelis Tsirigos
at atsirigo@us.ibm.com.
8.9 References
[1] Margulies M, et al. 'Genome sequencing in microfabricated high-density
picolitre reactors,'
Nature
2005;437(7057):376-80.
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