An Integrated Development Environment for Declarative Multi-Paradigm Programming

In this paper we present CIDER (Curry Integrated Development EnviRonment), an analysis and programming environment for the declarative multi-paradigm language Curry. CIDER is a graphical environment to support the development of Curry programs by providing integrated tools for the analysis and visualization of programs. CIDER is completely implemented in Curry using libraries for GUI programming (based on Tcl/Tk) and meta-programming. An important aspect of our environment is the possible adaptation of the development environment to other declarative source languages (e.g., Prolog or Haskell) and the extensibility w.r.t. new analysis methods. To support the latter feature, the lazy evaluation strategy of the underlying implementation language Curry becomes quite useful.Comment: In A. Kusalik (ed), proceedings of the Eleventh International Workshop on Logic Programming Environments (WLPE'01), December 1, 2001, Paphos, Cyprus. cs.PL/011104

Prototyping a process-centered environment

This paper describes an experimental system developed and used as a vehicle for prototyping the Arcadia-1 software development environment. Prototyping is viewed as a knowledge acquisition process and is used to reduce risks in software development by gaining rapid feedback about the suitability of a production system before the system is completed. Prototyping a software development environment is particularly important due to the lack of experience with them. There is an acute need to acquire knowledge about user interaction requirements for software environments. These needs are especially important for the Arcadia project, as it is one of the first attempts to construct a process-centered environment. Our prototyping effort addresses questions about effective interaction with a process-centered environment by simulating how Arcadia-1 would interact with users in a representative range of usage scenarios. We built a prototyping system, called PRODUCER, and used it to generate a variety of prototypes simulating user interactions with Arcadia-1 process programs.Experience with PRODUCER indicates that our approach is effective at risk reduction. The prototypes greatly improved communication with our customer. They confirmed some of our design decisions but also redirected our research efforts as a result of unexpected insight. We also found that prototyping usage scenarios provides conceptual guides and design information for process programmers. Most of the benefits of our prototyping effort derive from developing and interacting with usage scenarios, so our approach is generalizable to other prototyping systems. This paper reports on our prototyping approach and our experience in prototyping a process-centered environment

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

NiMo syntax: part 1

Many formalisms for the specification for concurrent and distributed systems have emerged. In particular considering boxes and strings approaches. Examples are action calculi, rewriting logic and graph rewriting, bigraphs. The boxes and string metaphor is addressed with different levels of granularity. One of the approaches is to consider a process network as an hypergraph. Based in this general framework, we encode NiMo nets as a class of Annotated hypergraphs. This class is defined by giving the alphabet and the operations used to construct such programs. Therefore we treat only editing operations on labelled hypergraphs and afterwards how this editing operation affects the graph. Graph transformation (execution rules) is not covered here.Postprint (published version

maigesPack: A Computational Environment for Microarray Data Analysis

Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies focused on systems biology. One of its main problem is complexity of experimental procedure, presenting several sources of variability, hindering statistical modeling. So far, there is no standard protocol for generation and evaluation of microarray data. To mitigate the analysis process this paper presents an R package, named maigesPack, that helps with data organization. Besides that, it makes data analysis process more robust, reliable and reproducible. Also, maigesPack aggregates several data analysis procedures reported in literature, for instance: cluster analysis, differential expression, supervised classifiers, relevance networks and functional classification of gene groups or gene networks

A document-like software visualization method for effective cognition of c-based software systems

It is clear that maintenance is a crucial and very costly process in a software life cycle. Nowadays there are a lot of software systems particularly legacy systems that are always maintained from time to time as new requirements arise. One important source to understand a software system before it is being maintained is through the documentation, particularly system documentation. Unfortunately, not all software systems developed or maintained are accompanied with their reliable and updated documents. In this case, source codes will be the only reliable source for programmers. A number of studies have been carried out in order to assist cognition based on source codes. One way is through tool automation via reverse engineering technique in which source codes will be parsed and the information extracted will be visualized using certain visualization methods. Most software visualization methods use graph as the main element to represent extracted software artifacts. Nevertheless, current methods tend to produce more complicated graphs and do not grant an explicit, document-like re-documentation environment. Hence, this thesis proposes a document-like software visualization method called DocLike Modularized Graph (DMG). The method is realized in a prototype tool named DocLike Viewer that targets on C-based software systems. The main contribution of the DMG method is to provide an explicit structural re-document mechanism in the software visualization tool. Besides, the DMG method provides more level of information abstractions via less complex graph that include inter-module dependencies, inter-program dependencies, procedural abstraction and also parameter passing. The DMG method was empirically evaluated based on the Goal/Question/Metric (GQM) paradigm and the findings depict that the method can improve productivity and quality in the aspect of cognition or program comprehension. A usability study was also conducted and DocLike Viewer had the most positive responses from the software practitioners