A language for comprehensively supporting the in vitro experimental process in silico

One of the challenges for bioinformaticians is to approximate, in silico, tried and tested research methods used in vitro. One of the problems standing in their way is the lack of a concrete framework for designing and expressing in silico experiments that aims at being isomorphic to in vitro experiments. This paper introduces such a framework in the form of a specification language called ISXL. ISXL projects to biologists a model of in silico experiments that approximates the research method they are most familiar with, as follows. An ISXL-specified experiment (1) conforms to a conceptual model that explicitly captures the basic constituents of experiments in the empirical sciences; (2) may be defined in relation to explicit hypothesis formulation and validation rather than simply taking the form of an evidence gathering process as in alternative approaches; (3) may be long-lived and evolve over lime, in the sense that there is built-in support for denoting past versions of specifications, past results, past hypotheses, past validation criteria; (4) may denote other experiments and their constituent parts, thereby reflecting the interrelatedness of scientific processes. Features (1)-(4) above are made possible by endowing ISXL with certain characteristics of a persistent workflow environment This allows ISXL experiments to be rich in metadata without imposing too great a burden on the biologist. The metadata in turn open the way for ISXL experiments to be capable of introspection and reflection. This paper focuses on describing of ISXL conceptually and syntactically, and indicates how ISXL experiments are given a formal semantics.