Abstract

Genome browsers are widely used tools for the visualization of a genome and related data.
The demands placed on genome browsers due to the size, variety, and complexity of the data produced by modern biotechnology is increasing.
These demands are poorly understood, and are not documented.
Our study is establishing and documenting a clear set of requirements for genome browsers.


Our study reviewed all widely used genome browsers, as well as notable research prototypes of genome browsers.
This involved a review of the literature, executing typical uses of the genome browsers, program comprehension, reverse engineering, and code analysis.


The key outcome of the study is a clear set of requirements in the form of a requirement document
which conforms to the IEEE Std 830-1998 Standard of a Software Requirement Specification.
This contains a domain model of concepts,
the functional requirements as use cases,
a definition of visualizations as metaphors, glyphs, or icons,
formal specification of the system in Z notation
and a specification of all widely used file formats.

Genome browsers share a set of basic features like display, scroll, zoom, and search.
However, they differ in their performance, maturity level and the implementation technologies.
Our requirements also document the major non-functional requirements.

The outcome of our study can be used in several ways:
it can be used as a guide for future developers of Genome Browsers;
it can form the basis of future enhancements of features in existing genome browsers;
and it can motivate the invention of new algorithms, data structures, or file formats for implementations.