Biomedical Engineering Reference
In-Depth Information
facilitate low-level communications between applications. Most of these niche solutions never leave
the laboratory in which they are developed because the niche solutions can't be generalized to other
laboratories. The few applications that do address general problems in a typical bioinformatics
laboratory may progress to the next phase of standards evolution, tool and data accessibility.
Tool and Data Accessibility
The tool and data accessibility phase of standards evolution involves restricted sharing of the niche
solutions among the members of the bioinformatics R&D community. Applications that have the
greatest general appeal to other researchers are typically either distributed through academic and
government-sponsored consortia or transformed into commercial ventures. In either case, there is a
lack of data uniformity, and applications may be very useful or of no practical value, depending on
the problems that need to be addressed.
This stage of standards evolution represents the status of applications in many areas of
bioinformatics today. For example, consider the many varied file formats in use by the relatively
small number of bioinformatics-specific applications, illustrated in
Table 10-1
.
Table 10-1. Major Bioinformatics File Formats.
ASN.1
DNAStrider
EMBL
Fitch
GCG
GenBank/GBFF
IG/Stanford
MmCIF
MSF
NBRF
Olsen
PAUP/NEXUS
PDB
Pearson/FASTA
Phylip/Philip3.2
PIR/CODATA
Plain/Raw
Pretty
Zuker
The number and variation of file formats used for nucleotide and protein data is an indicator of the
amount of variability in the applications used in bioinformatics computing. Although bioinformatics is
moving toward file format and application standards, there are hundreds of file formats in use. Many
of these formats are application-specific and associated with niche solutions that are designed to
