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A tool is needed to help automating the update of packages. A first rudimentary skeleton was prepared with [http://svn.debian.org/wsvn/debian-med/trunk/community/infrastructure/getData.pl?op=file&rev=0&sc=0 getData.pl] on the Debian-Med subversion repository. | A tool is needed to help automating the update of packages. A first rudimentary skeleton was prepared with [http://svn.debian.org/wsvn/debian-med/trunk/community/infrastructure/getData/ getData.pl] on the Debian-Med subversion repository. |
Introduction
Software changes repeatedly and the package maintainers do the best to keep pace with upstream's progress. It seems inappropriate though to prepare regular Debian packages for large database since
- data is released frequently
- some user demand weekly updates
- others refer to official releases
- some databases are large, e.g. UniProt/Pfam all are beyond the Gigabyte barrier
- updating databases will demand further operations
- update of indices
- ..? which depends on other tools and packages that are installed on the machine
A tool is needed to help automating the update of packages. A first rudimentary skeleton was prepared with [http://svn.debian.org/wsvn/debian-med/trunk/community/infrastructure/getData/ getData.pl] on the Debian-Med subversion repository.
Public Databases that may be considered for Debian
Name |
Contents |
Licence |
Package |
[http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html Genbank] |
Public sequences |
Publicly available |
|
[http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE3/ BAliBASE3] |
Sequence aligments version3, and a c program for scoring |
unknown, but contains a header file from clustalw, which is not free |
|
[http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html OXbench] |
Multiple alignments and scoring system |
|
|
[http://www.pseudogene.org www.pseudogene.org] |
pseudogenes |
unknown |
|
[http://jaspar.genereg.net/ Jaspar] |
Transcription factor bindng sites |
"Freely available" |
|
[http://www.bcgsc.ca:8080/oregano/Index.jsp ORegAnno] |
Regulatory sequences |
LGPL |
|
[http://www.pazar.info Pazar] |
public repository for regulatory data |
Says Open Source but not found |
|
[http://rebase.neb.com REbase] |
Restriction Enzymes |
? |
[http://pdb.finkproject.org/pdb/package.php/embossdb-rebase fink] |
Repeat elements |
Academic, registration needed |
|
|
[http://www.genetics.wustl.edu/fish_lab/repeats Zebrafish repeats] |
Repeat elements (Zebrafish) |
no license |
|
Probably, many free databases can be found in the database issue of Nucleic Acid Research http://nar.oxfordjournals.org/content/vol34/suppl_1/index.dtl
We also need open-source software to warehouse the databases
Name |
Licence |
Package |
Listed on microbio.wml? |
[http://www.biomart.org/ ?BioMart] |
LGPL |
packaged ([http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/martj/ unofficial]) |
yes |
[https://sourceforge.net/project/showfiles.php?group_id=147980 S3DB] |
GPL |
depends on PHP and (My|Postgre)SQL |
no |
[http://biomoby.open-bio.org/ BioMOBY] |
Artistic |
depends on java |
no |
[http://hitkeeper.sourceforge.net/ hitkeeper] |
GPL |
depends on Perl and SQL |
no |
[http://bioinformatics.ai.sri.com/biowarehouse/ ?BioWarehouse] |
MPL 1.1 |
|
no |
4-clause BSD |
complex |
no |
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