Scrap your boilerplate with object algebras

htmlabstractTraversing complex Abstract Syntax Trees (ASTs) typically requires large amounts of tedious boilerplate code. For many operations most of the code simply walks the structure, and only a small portion of the code implements the functional- ity that motivated the traversal in the first place. This paper presents a type-safe Java framework called Shy that removes much of this boilerplate code. In Shy Object Algebras are used to describe complex and extensible AST structures. Using Java annotations Shy generates generic boilerplate code for various types of traversals. For a concrete traversal, users of Shy can then inherit from the generated code and over- ride only the interesting cases. Consequently, the amount of code that users need to write is significantly smaller. Moreover, traversals using the Shy framework are also much more structure shy, becoming more adaptive to future changes or extensions to the AST structure. To prove the effectiveness of the approach, we applied Shy in the implementation of a domain-specific questionnaire language. Our results show that for a large number of traversals there was a significant reduction in the amount of user-defined code

Synthesizing Iterators from Abstraction Functions

A technique for synthesizing iterators from declarative abstraction functions written in a relational logic specification language is described. The logic includes a transitive closure operator that makes it convenient for expressing reachability queries on linked data structures. Some optimizations, including tuple elimination, iterator flattening, and traversal state reduction, are used to improve performance of the generated iterators. A case study demonstrates that most of the iterators in the widely used JDK Collections classes can be replaced with code synthesized from declarative abstraction functions. These synthesized iterators perform competitively with the hand-written originals. In a user study the synthesized iterators always passed more test cases than the hand-written ones, were almost always as efficient, usually took less programmer effort, and were the qualitative preference of all participants who provided free-form comments

Aspect-Oriented Programming for Dynamic Web Service Monitoring and Selection

Abstract. In Service-Oriented Application Development, applications are composed by selecting and integrating third-party web services. To avoid hardwiring concrete services in client applications we introduced in previous work the Web Services Management Layer (WSML) and suggested a redirection mechanism based on Aspect Oriented Programming (AOP). Even though this mechanism enables hot swapping between semantically equivalent services based on their availability, this is not enough to create applications that are driven by business requirements. In this paper we introduce a more advanced selection mechanism that allows dynamic switching between services based on business driven requirements that can change over time. Choosing a service may be done based on cost, presence on approved partners list, as well as binding support, quality of service classifications, historical performance and proximity. We introduce a modular monitoring mechanism that is able to observe these criteria and trigger a more advanced service selection procedure. We show how the AOP language JAsCo with its dynamically pluggable aspects is well suited to achieve this. 1

Scrap your boilerplate with object algebras

International audienceTraversing complex Abstract Syntax Trees (ASTs) typically requires large amounts of tedious boilerplate code. For many operations most of the code simply walks the structure, and only a small portion of the code implements the functional- ity that motivated the traversal in the first place. This paper presents a type-safe Java framework called Shy that removes much of this boilerplate code. In Shy Object Algebras are used to describe complex and extensible AST structures. Using Java annotations Shy generates generic boilerplate code for various types of traversals. For a concrete traversal, users of Shy can then inherit from the generated code and over- ride only the interesting cases. Consequently, the amount of code that users need to write is significantly smaller. Moreover, traversals using the Shy framework are also much more structure shy, becoming more adaptive to future changes or extensions to the AST structure. To prove the effectiveness of the approach, we applied Shy in the implementation of a domain-specific questionnaire language. Our results show that for a large number of traversals there was a significant reduction in the amount of user-defined code

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

The Regulation of MS-KIF18A Expression and Cross Talk with Estrogen Receptor

This study provides a novel view on the interactions between the MS-KIF18A, a kinesin protein, and estrogen receptor alpha (ERα) which were studied in vivo and in vitro. Additionally, the regulation of MS-KIF18A expression by estrogen was investigated at the gene and protein levels. An association between recombinant proteins; ERα and MS-KIF18A was demonstrated in vitro in a pull down assay. Such interactions were proven also for endogenous proteins in MBA-15 cells were detected prominently in the cytoplasm and are up-regulated by estrogen. Additionally, an association between these proteins and the transcription factor NF-κB was identified. MS-KIF18A mRNA expression was measured in vivo in relation to age and estrogen level in mice and rats models. A decrease in MS-KIF18A mRNA level was measured in old and in OVX-estrogen depleted rats as compared to young animals. The low MS-KIF18A mRNA expression in OVX rats was restored by estrogen treatment. We studied the regulation of MS-KIF18A transcription by estrogen using the luciferase reporter gene and chromatin immuno-percipitation (ChIP) assays. The luciferase reporter gene assay demonstrated an increase in MS-KIF18A promoter activity in response to 10−8 M estrogen and 10−7M ICI-182,780. Complimentary, the ChIP assay quantified the binding of ERα and pcJun to the MS-KIF18A promoter that was enhanced in cells treated by estrogen and ICI-182,780. In addition, cells treated by estrogen expressed higher levels of MS-KIF18A mRNA and protein and the protein turnover in MBA-15 cells was accelerated. Presented data demonstrated that ERα is a defined cargo of MS-KIF18A and added novel insight on the role of estrogen in regulation of MS-KIF18A expression both in vivo and in vitro