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The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. [1] It is a free and open standard with widespread software support and a community of users and developers.
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project [1] and then adopted by other sequencing
[2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4] The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them.
Cell-based models are mathematical models that represent biological cells as discrete entities. Within the field of computational biology they are often simply called agent-based models [1] of which they are a specific application and they are used for simulating the biomechanics of multicellular structures such as tissues. to study the influence of these behaviors on how tissues are organised ...
Biological database design, development, and long-term management is a core area of the discipline of bioinformatics. [3] Data contents include gene sequences, textual descriptions, attributes and ontology classifications, citations, and tabular data.
Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED. 5 end Genomic end of the feature, with a 1-base offset. This is the same end coordinate as it is in 0-offset half-open sequence formats, like BED. [citation needed] 6 score
A PDF file is organized using ASCII characters, except for certain elements that may have binary content. The file starts with a header containing a magic number (as a readable string) and the version of the format, for example %PDF-1.7. The format is a subset of a COS ("Carousel" Object Structure) format. [24]
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute , and became widely known through its implementation within the SAMtools ...