Workshop on Database Programming Languages

These are the revised proceedings of the Workshop on Database Programming Languages held at Roscoff, Finistère, France in September of 1987. The last few years have seen an enormous activity in the development of new programming languages and new programming environments for databases. The purpose of the workshop was to bring together researchers from both databases and programming languages to discuss recent developments in the two areas in the hope of overcoming some of the obstacles that appear to prevent the construction of a uniform database programming environment. The workshop, which follows a previous workshop held in Appin, Scotland in 1985, was extremely successful. The organizers were delighted with both the quality and volume of the submissions for this meeting, and it was regrettable that more papers could not be accepted. Both the stimulating discussions and the excellent food and scenery of the Brittany coast made the meeting thoroughly enjoyable. There were three main foci for this workshop: the type systems suitable for databases (especially object-oriented and complex-object databases,) the representation and manipulation of persistent structures, and extensions to deductive databases that allow for more general and flexible programming. Many of the papers describe recent results, or work in progress, and are indicative of the latest research trends in database programming languages. The organizers are extremely grateful for the financial support given by CRAI (Italy), Altaïr (France) and AT&T (USA). We would also like to acknowledge the organizational help provided by Florence Deshors, Hélène Gans and Pauline Turcaud of Altaïr, and by Karen Carter of the University of Pennsylvania

Alignment uncertainty, regressive alignment and large scale deployment

A multiple sequence alignment (MSA) provides a description of the relationship between biological sequences where columns represent a shared ancestry through an implied set of evolutionary events. The majority of research in the field has focused on improving the accuracy of alignments within the progressive alignment framework and has allowed for powerful inferences including phylogenetic reconstruction, homology modelling and disease prediction. Notwithstanding this, when applied to modern genomics datasets - often comprising tens of thousands of sequences - new challenges arise in the construction of accurate MSA. These issues can be generalised to form three basic problems. Foremost, as the number of sequences increases, progressive alignment methodologies exhibit a dramatic decrease in alignment accuracy. Additionally, for any given dataset many possible MSA solutions exist, a problem which is exacerbated with an increasing number of sequences due to alignment uncertainty. Finally, technical difficulties hamper the deployment of such genomic analysis workflows - especially in a reproducible manner - often presenting a high barrier for even skilled practitioners. This work aims to address this trifecta of problems through a web server for fast homology extension based MSA, two new methods for improved phylogenetic bootstrap supports incorporating alignment uncertainty, a novel alignment procedure that improves large scale alignments termed regressive MSA and finally a workflow framework that enables the deployment of large scale reproducible analyses across clusters and clouds titled Nextflow. Together, this work can be seen to provide both conceptual and technical advances which deliver substantial improvements to existing MSA methods and the resulting inferences.Un alineament de seqüència múltiple (MSA) proporciona una descripció de la relació entre seqüències biològiques on les columnes representen una ascendència compartida a través d'un conjunt implicat d'esdeveniments evolutius. La majoria de la investigació en el camp s'ha centrat a millorar la precisió dels alineaments dins del marc d'alineació progressiva i ha permès inferències poderoses, incloent-hi la reconstrucció filogenètica, el modelatge d'homologia i la predicció de malalties. Malgrat això, quan s'aplica als conjunts de dades de genòmica moderns, que sovint comprenen desenes de milers de seqüències, sorgeixen nous reptes en la construcció d'un MSA precís. Aquests problemes es poden generalitzar per formar tres problemes bàsics. En primer lloc, a mesura que augmenta el nombre de seqüències, les metodologies d'alineació progressiva presenten una disminució espectacular de la precisió de l'alineació. A més, per a un conjunt de dades, existeixen molts MSA com a possibles solucions un problema que s'agreuja amb un nombre creixent de seqüències a causa de la incertesa d'alineació. Finalment, les dificultats tècniques obstaculitzen el desplegament d'aquests fluxos de treball d'anàlisi genòmica, especialment de manera reproduïble, sovint presenten una gran barrera per als professionals fins i tot qualificats. Aquest treball té com a objectiu abordar aquesta trifecta de problemes a través d'un servidor web per a l'extensió ràpida d'homologia basada en MSA, dos nous mètodes per a la millora de l'arrencada filogenètica permeten incorporar incertesa d'alineació, un nou procediment d'alineació que millora els alineaments a gran escala anomenat MSA regressivu i, finalment, un marc de flux de treball permet el desplegament d'anàlisis reproduïbles a gran escala a través de clústers i computació al núvol anomenat Nextflow. En conjunt, es pot veure que aquest treball proporciona tant avanços conceptuals com tècniques que proporcionen millores substancials als mètodes MSA existents i les conseqüències resultants

A TYPE ANALYSIS OF REWRITE STRATEGIES

Rewrite strategies provide an algorithmic rewriting of terms using strategic compositions of rewrite rules. Due to the programmability of rewrites, errors are often made due to incorrect compositions of rewrites or incorrect application of rewrites to a term within a strategic rewriting program. In practical applications of strategic rewriting, testing and debugging becomes substantially time-intensive for large programs applied to large inputs derived from large term grammars. In essence, determining which rewrite in what position in a term did or did not re comes down to logging, tracing and/or di -like comparison of inputs to outputs. In this thesis, we explore type-enabled analysis of strategic rewriting programs to detect errors statically. In particular, we introduce high-precision types to closely approximate the dynamic behavior of rewriting. We also use union types to track sets of types due to presence of strategic compositions. In this framework of high-precision strategic typing, we develop and implement an expressive type system for a representative strategic rewriting language TL. The results of this research are sufficiently broad to be adapted to other strategic rewriting languages. In particular, the type-inferencing algorithm does not require explicit type annotations for minimal impact on an existing language. Based on our experience with the implementation, the type system significantly reduces the time and effort to program correct rewrite strategies while performing the analysis on the order of thousands of source lines of code per second