Automatically linking MEDLINE abstracts to the Gene Ontology

Much has been written recently about the need for effective tools and methods for mining the wealth of information present in biomedical literature (Mack and Hehenberger, 2002; Blagosklonny and Pardee, 2001; Rindflesch et al., 2002)—the activity of conceptual biology. Keyword search engines operating over large electronic document stores (such as PubMed and the PNAS) offer some help, but there are fundamental obstacles that limit their effectiveness. In the first instance, there is no general consensus among scientists about the vernacular to be used when describing research about genes, proteins, drugs, diseases, tissues and therapies, making it very difficult to formulate a search query that retrieves the right documents. Secondly, finding relevant articles is just one aspect of the investigative process. A more fundamental goal is to establish links and relationships between facts existing in published literature in order to “validate current hypotheses or to generate new ones” (Barnes and Robertson, 2002)—something keyword search engines do little to support

A semantics and implementation of a causal logic programming language

The increasingly widespread availability of multicore and manycore computers demands new programming languages that make parallel programming dramatically easier and less error prone. This paper describes a semantics for a new class of declarative programming languages that support massive amounts of implicit parallelism

Datalog as a parallel general purpose programming language

The increasing available parallelism of computers demands new programming languages that make parallel programming dramatically easier and less error prone. It is proposed that datalog with negation and timestamps is a suitable basis for a general purpose programming language for sequential, parallel and distributed computers. This paper develops a fully incremental bottom-up interpreter for datalog that supports a wide range of execution strategies, with trade-offs affecting efficiency, parallelism and control of resource usage. Examples show how the language can accept real-time external inputs and outputs, and mimic assignment, all without departing from its pure logical semantics

A Parallel semantics for normal logic programs plus time

It is proposed that Normal Logic Programs with an explicit time ordering are a suitable basis for a general purpose parallel programming language. Examples show that such a language can accept real-time external inputs and outputs, and mimic assignment, all without departing from its pure logical semantics. This paper describes a fully incremental bottom-up interpreter that supports a wide range of parallel execution strategies and can extract significant potential parallelism from programs with complex dependencies

The JStar language philosophy

This paper introduces the JStar parallel programming language, which is a Java-based declarative language aimed at discouraging sequential programming, en-couraging massively parallel programming, and giving the compiler and runtime maximum freedom to try alternative parallelisation strategies. We describe the execution semantics and runtime support of the language, several optimisations and parallelism strategies, with some benchmark results

Improving the performance of HTTP over high bandwidth-delay product circuits

As the WWW continues to grow, providing adequate bandwidth to countries remote from the geographic and topological center of the network, such as those in the Asia/Pacific, becomes more and more difficult. To meet the growing traffic needs of the Internet some Network Service Providers are deploying satellite connections. Through discrete event simulation of a real HTTP workload with differing international architectures this paper is able to give guidance on the architecture that should be deployed for long distance, high capacity Internet links. We show that a significant increase in the time taken to fetch HTTP requests can be expected when traffic is moved from a long distance international terrestrial link to a satellite link. We then show several modifications to the network architecture that can be used to greatly improve the performance of a satellite link. These modifications include the use of an asymmetric satellite link, the multiplexing of multiple HTTP requests onto a single TCP connection and the use of HTTP1.1

Jumble Java Byte Code to Measure the Effectiveness of Unit Tests

Jumble is a byte code level mutation testing tool for Java which inter-operates with JUnit. It has been designed to operate in an industrial setting with large projects. Heuristics have been included to speed the checking of mutations, for example, noting which test fails for each mutation and running this first in subsequent mutation checks. Significant effort has been put into ensuring that it can test code which uses custom class loading and reflection. This requires careful attention to class path handling and coexistence with foreign class-loaders. Jumble is currently used on a continuous basis within an agile programming environment with approximately 370,000 lines of Java code under source control. This checks out project code every fifteen minutes and runs an incremental set of unit tests and mutation tests for modified classes. Jumble is being made available as open source

Proving the existence of solutions in logical arithmetic

Logical arithmetic is a logically correct technique for real arithmetic in Prolog which uses constraints over interval representations for its implementation. Four problems with the technique are considered: answers are conditional and uninformative; iterative computations may lead to unboundedly large constraint networks; it is difficult and ineffective to deal with negation; and computing extrema is often not effective. A solution to these problems is proposed in the form of "existential intervals" which record the existence of a solution to a set of constraints within an interval. It is shown how to operate on existential intervals and how they solve the four problems