1919715
Statically safe program generation with safegen
SafeGen is a meta-programming language for writing statically safe generators of Java programs. If a program generator written in SafeGen passes the checks of the SafeGen compiler, then the generator will only generate well-formed Java programs, for any generator input. In other words, statically checking the generator guarantees the correctness of any generated program, with respect to static checks commonly performed by a conventional compiler (including type safety, existence of a superclass, etc.). To achieve this guarantee, SafeGen supports only language primitives for reflection over an existing well-formed Java program, primitives for creating program fragments, and a restricted set of constructs for iteration, conditional actions, and name generation. SafeGen's static checking algorithm is a combination of traditional type checking for Java, and a series of calls to a theorem prover to check the validity of first-order logical sentences constructed to represent well-formedness properties of the generated program under all inputs. The approach has worked quite well in our tests, providing proofs for correct generators or pointing out interesting bugs.
15498474
Generating AspectJ Programs with Meta-AspectJ
Meta-AspectJ (MAJ) is a language tool for generating AspectJ programs using code templates. MAJ itself is an extension of Java, so users can interleave arbitrary Java code with AspectJ code templates. MAJ is a structured meta-programming tool: a well-typed generator implies a syntactically correct generated program. MAJ promotes a methodology that combines aspect-oriented and generative programming. Potential applications range from implementing domain-specific languages with AspectJ as a back-end to enhancing AspectJ with more powerful general-purpose constructs. In addition to its practical value, MAJ offers valuable insights to meta-programming tool designers. It is a mature meta-programming tool for AspectJ (and, by extension, Java): a lot of emphasis has been placed on context-sensitive parsing and error-reporting. As a result, MAJ minimizes the number of meta-programming (quote/unquote) operators and uses type inference to reduce the need to remember type names for syntactic entities.
6628850
A qualitative assessment of the efficacy of UML diagrams as a form of graphical documentation in aiding program understanding
Graphical documentation is often characterized as an effective aid in program understanding. However, it is an open question exactly which types of graphical documentation are most suitable for which types of program understanding tasks (and in which specific usage contexts). The Unified Modeling Language (UML) is the de facto standard for modeling modern software applications. This paper describes an experiment to assess the qualitative efficacy of UML diagrams in aiding program understanding. The experiment had participants analyze a series of UML diagrams and answer a detailed questionnaire concerning a hypothetical software system. Results from the experiment suggest that the UML's efficacy in support of program understanding is limited by factors such as ill-defined syntax and semantics, spatial layout, and domain knowledge.
17764116
Identifying transcriptional regulatory sites in the human genome using an integrated computation
Recently, biological databases and analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences. However, users must make the complicated analyses to query the data in various databases, and to analyze the gene upstreams using various predictive tools. Beyond methods for predicting transcriptional regulatory sites, new automated and integrated methods for analyzing gene upstream sequences on a higher level are urgently required. We present an integrated system to predict transcriptional regulatory sites and detect co-occurrence of these regulatory sites after a set of genes are input. The system comprises a biological data warehousing system, pattern discovery programs, pattern occurrence association detectors and user interfaces. User profiles and history pages enable users to trace the sequence analyses for transcriptional regulatory sites.
2797141
Evaluating the reverse engineering capabilities of Web tools for understanding site content and structure: a case study
This paper describes an evaluation of the reverse engineering capabilities of three Web tools for understanding site content and structure. The evaluation is based on partitioning Web sites into three classes (static, interactive, and dynamic), and is structured using an existing reverse engineering environment framework (REEF). This case study also represents an initial evaluation of the applicability of the REEF in the related but qualitatively different domain of Web sites. The case study highlights several shortcomings of current Web tools in the context of aiding understanding to support evolution. For example, most Web tools are geared towards new page design and development, not to understanding detailed page content or overall site structure. The evaluation also identified some aspects of the REEF that might benefit from refinement to better reflect Web tool capabilities that support common evolution tasks. For example, Web server log file analysis as a specialized form of data gathering and subsequence information presentation.
53306687
Identifying the combination of genetic factors that determine susceptibility to cervical cancer
Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent population-based twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, SNP markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer. The web site associated with this study is http://dblab8.csie.ncu.edu.tw/FactorAnalysis/.
31128018
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions
At least 43% of the human genome is occupied by repetitive elements. Moreover, around 51% of the rice genome is occupied by repetitive elements. The analysis of repetitive elements reveals that repetitive elements in our genome may have been very important in the evolutionary genomics. The first part of this study is to describe a database of repetitive elements - RSDB. The RSDB database contains repetitive elements, which are classified into the following categories: exact, tandem, and similar. The interfaces needed to query and show the results and statistical data, such as the relationship between repetitive elements and genes, cross-references of repetitive elements among different organisms, and so on, are provided. The second part of this study then attempts to mine the putative binding site for information on how combinations of the known regulatory sites and overrepresented repetitive elements in RSDB are distributed in the promoter regions of groups of functionally related genes. The overrepresented repetitive elements appearing in the associations are possible transcription factor binding sites. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of Yeast ORFs. The complete contents of RSDB and partial putative binding sites are available to the public at www.rsdb.csie.ncu.edu.tw. The readers may download partial query results.