Citing BIRCH software
Imagine if you had invented a technique and published a paper
describing
it, and lots of people used it without citing it. The development
and
refinement
of computer software requires as much work as development of a lab
technique,
and has just as much impact on the research community. Not citing
the
programs
you use underestimates the impact of these these programs in their
fields
of research. Particularly when molecular biology programs are
distributed
free, the only return the author gets on their time investment is
your
literature citation. If you use 20 different programs your work,
that's
like using 20 different techniques, and each one of those authors
deserves
a citation.
Even free
software
comes with a price. Citations in the
literature
help authors of free software:
- keep their jobs
- get grant money and institutional support necessary to develop
new software and support existing software
- attract good students, postdocs and research associates
- help funding agencies make a case for supporting
bioinformatics
'Nuff said. Here are some of the papers to cite for programs in
BIRCH.
If you can't find a citation here, look in the documentation for
that
program.
Some programs are not written up in papers, but one should still
give
credit
to the author.
BIRCH
BIRCH: A user-oriented,
locally-customizable, bioinformatics system
Brian Fristensky
BMC Bioinformatics 2007, 8:54 (9 February 2007)
[Abstract]
[PDF]
FSAP Package (NUMSEQ, BACHREST, INTREST, DIGEST, TESTCODE)
Fristensky, B., Lis, J.T. and Wu, R. (1982) Portable microcomputer
software
for nucleotide sequence analysis. Nucl. Acids Res. 10:6451-6463.
P1HOM, P2HOM, D3HOM & D4HOM
Fristensky, B. (1986) Improving the efficiency of dot-matrix
similarity
searches through use of an oligomer table. Nucl. Acids Res.
14,597-610.
FASTA programs (FASTA, TFASTA, ALIGN, LFASTA, GREASE, MRTRANS,
GARNIER)
Pearson, W.R. (1990) Rapid and Sensitive Sequence Comparison with
FASTP
and FASTA. Methods in Enzymology 183:63-98.
ClustalW , ClustalX
Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W:
improving
the sensitivity of progressive multiple sequence alignments through
sequence
weighting, position specific gap penalties and weight matrix choice.
Nucl.
Acids Res. 22:4673-4680.
GenBank Database
Bilofsky, H.S. and Burks, C. (1988) The GenBank genetic sequence
data
bank.
Nucl. Acids Res. 16:1861-1864.
Phylip
Felsenstein, J. (1989) PHYLIP Phylogeny Inference Package.
Cladistics
5:164-166.
PIR/NBRF Database
Sidman, K.E. George, D.G. Barker, W.C. and Hunt, L.T. (1988) The
protein
identification resource (PIR). Nucl. Acids Res. 16:1869-1871.
others
See documentation file for the program.
XYLEM (FETCH, FINDKEY, FEATURES, REFORM, SPLITDB, RIBOSOME)
Fristensky, B. (1993) Feature expressions: creating and manipulating
sequence
datasets. Nucl. Acids Res. 21:5997-6003.