22222939
Program comprehension with dynamic recovery of code collaboration patterns and roles
Software functionalities and behavior are accomplished by the cooperation of code artifacts. The understanding of this type of source code collaboration provides an important aid to the maintenance and evolution of legacy systems. Normally, legacy systems were developed decades ago using early programming languages such as Cobol, Fortran or C etc., and a huge number of such systems are still in use. Coyle et. al estimate that only the systems written in Cobol have been account for more than 100 billion LOC. Moreover, a large amount of domain business knowledge has been coded in legacy software. After many years of maintenance, the quality of operation and maintainability has deteriorated dramatically due to many reasons, such as lack of up-to-date documents, lost of key personnel, shift of technology of inter-operating peripheral systems etc. The extraction of code artifact collaborations and their roles is therefore an important support in legacy software comprehension and design recovery. However, the original collaboration design information is dispersed at the implementation level. In this paper, we present a novel approach to efficiently recover and analyze code collaborations and roles based on dynamic program analysis technique. We also illustrate the tools that we have developed to support our approach and illustrate the viability of our approach in a case study.
2955650
Caribou: a supporting environment for software e-development
With the rapid progress of Internet technology, more and more software projects adopt e-development to facilitate the software development process in a world wide context. However, collaborative software e-development activity itself is a complex orchestration. It involves many people working together without the barrier of time and space difference. Therefore, how to efficiently monitor and control software e-development in a global perspective becomes an important issue for any Internet-based software e-development project. In this paper, we present a novel approach to tackle this crucial issue by means of controlling e-development process and communication quality. Meanwhile, we also present our e-development supporting environment prototype: Caribou, to demonstrate the viability of our approach.
31598462
A computationally efficient method for nonlinear mixed-effects models with nonignorable missing data in time-varying covariates
Nonlinear mixed-effects (NLME) models are widely used for longitudinal data analyses. Time-dependent covariates are often introduced to partially explain inter-individual variation. These covariates often have missing data, and the missingness may be nonignorable. Likelihood inference for NLME models with nonignorable missing data in time-varying covariates can be computationally very intensive and may even offer computational difficulties such as nonconvergence. We propose a computationally very efficient method for approximate likelihood inference. The method is illustrated using a real data example.
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.
37498905
Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes
Certain structural motifs, like tetra-loops, in ribosomal RNA are known to functionally implicate in virtually every aspect of protein synthesis. Ribosomal RNA molecules were also widely used as a tool in molecular evolutionary studies because of their ubiquity, size and low evolutionary rate. In this study, we adapt a data mining approach to discover common structural motifs, and then we use a machine learning approach to identify discriminating CSMs from groups of organisms. Finally, we construct phylogeneitc trees to investigate the evolution of ribosomal RNA by serving the CSMs discovered as targets, which are used to estimate the evolutionary relatedness between organisms. The aim of this study is to discover common structural motifs (CSMs), i.e., those single-strain regions shared in ribosomal RNA secondary structures by several organisms, which are related to specific domains or functions. We discover a set of common structural motifs from several data sets of Archaea and Bacteria. Significant CSMs are then induced by a decision tree. Furthermore, phylogenetic trees are constructed based on CSMs and primary sequences of SSU 16 S ribosomal RNA.
19540960
Automated multivariate profiling of drug effects from fluorescence microscopy images
Fluorescence microscopy is a useful tool for building quantitative profiles of drug effects. Although features with rich information can be extracted from fluorescence microscopy images, most current profiling methods build profiles from the extracted features using either univariate or non-automated methods. We propose a new multivariate, automated and scalable method for building drug profiles by using a decision hyperplane. The method was evaluated by using 23 compounds belonging to four groups of known mechanisms. We produced quantitative profiles that group drugs with similar mechanisms together, and separate drugs with dissimilar mechanisms from each other. These profiles resulted in better characterizations of the drug effects than profiles obtained from a previous univariate method
9069029
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures
Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability.