A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Relational Parametricity for Computational Effects

According to Strachey, a polymorphic program is parametric if it applies a uniform algorithm independently of the type instantiations at which it is applied. The notion of relational parametricity, introduced by Reynolds, is one possible mathematical formulation of this idea. Relational parametricity provides a powerful tool for establishing data abstraction properties, proving equivalences of datatypes, and establishing equalities of programs. Such properties have been well studied in a pure functional setting. Many programs, however, exhibit computational effects, and are not accounted for by the standard theory of relational parametricity. In this paper, we develop a foundational framework for extending the notion of relational parametricity to programming languages with effects.Comment: 31 pages, appears in Logical Methods in Computer Scienc

Facilitating modular property-preserving extensions of programming languages

We will explore an approach to modular programming language descriptions and extensions in a denotational style. Based on a language core, language features are added stepwise on the core. Language features can be described separated from each other in a self-contained, orthogonal way. We present an extension semantics framework consisting of mechanisms to adapt semantics of a basic language to new structural requirements in an extended language preserving the behaviour of programs of the basic language. Common templates of extension are provided. These can be collected in extension libraries accessible to and extendible by language designers. Mechanisms to extend these libraries are provided. A notation for describing language features embedding these semantics extensions is presented

Coinductive Resumption Monads: Guarded Iterative and Guarded Elgot

We introduce a new notion of "guarded Elgot monad", that is a monad equipped with a form of iteration. It requires every guarded morphism to have a specified fixpoint, and classical equational laws of iteration to be satisfied. This notion includes Elgot monads, but also further examples of partial non-unique iteration, emerging in the semantics of processes under infinite trace equivalence. We recall the construction of the "coinductive resumption monad" from a monad and endofunctor, that is used for modelling programs up to bisimilarity. We characterize this construction via a universal property: if the given monad is guarded Elgot, then the coinductive resumption monad is the guarded Elgot monad that freely extends it by the given endofunctor

Lifting homotopy T-algebra maps to strict maps

The settings for homotopical algebra---categories such as simplicial groups, simplicial rings, $A_\infty$ spaces, $E_\infty$ ring spectra, etc.---are often equivalent to categories of algebras over some monad or triple $T$. In such cases, $T$ is acting on a nice simplicial model category in such a way that $T$ descends to a monad on the homotopy category and defines a category of homotopy $T$-algebras. In this setting there is a forgetful functor from the homotopy category of $T$-algebras to the category of homotopy $T$-algebras. Under suitable hypotheses we provide an obstruction theory, in the form of a Bousfield-Kan spectral sequence, for lifting a homotopy $T$-algebra map to a strict map of $T$-algebras. Once we have a map of $T$-algebras to serve as a basepoint, the spectral sequence computes the homotopy groups of the space of $T$-algebra maps and the edge homomorphism on $\pi_0$ is the aforementioned forgetful functor. We discuss a variety of settings in which the required hypotheses are satisfied, including monads arising from algebraic theories and operads. We also give sufficient conditions for the $E_2$-term to be calculable in terms of Quillen cohomology groups. We provide worked examples in $G$-spaces, $G$-spectra, rational $E_\infty$ algebras, and $A_\infty$ algebras. Explicit calculations, connected to rational unstable homotopy theory, show that the forgetful functor from the homotopy category of $E_\infty$ ring spectra to the category of $H_\infty$ ring spectra is generally neither full nor faithful. We also apply a result of the second named author and Nick Kuhn to compute the homotopy type of the space $E_\infty(\Sigma^\infty_+ \mathrm{Coker}\, J, L_{K(2)} R)$.Comment: 45 pages. Substantial revision. To appear in Advances in Mathematic