15154017
Coping with legacy system migration complexity
During the last three decades, a considerable amount of software has been developed based on obsolete technologies (such as using procedural languages). This type of systems has undergone severe code revisions during a long time period. As a consequence, the high level of entropy combined with imprecise documentation about the design and architecture make the maintenance more difficult, time consuming, and costly. On the other hand, these systems have important economical value; many of them are crucial to their owners (Bennett, 1995). For the high cost of lost former investment and business knowledge that embedded in those systems, in many cases, simply abandon legacy systems and re-develop new systems based on new technology is not the choice. Migrating legacy system toward new emerging technology is an appropriate solution. However, migrating legacy system towards new technology is a complex system engineering work. In this paper, we propose a novel approach to reduce the migration complexity. We apply dynamic program analysis, software visualization, knowledge recovery, and divide-and-conquer techniques to cope with the complexity issue in legacy software migration project.
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.
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/.
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
12480908
Improving the Gilbert-Varshamov bound for q-ary codes
Given positive integers q,n, and d, denote by A/sub q/(n,d) the maximum size of a q-ary code of length n and minimum distance d. The famous Gilbert-Varshamov bound asserts that A/sub q/(n,d+1)/spl ges/q/sup n//V/sub q/(n,d) where V/sub q/(n,d)=/spl Sigma//sub i=0//sup d/ (/sub i//sup n/)(q-1)/sup i/ is the volume of a q-ary sphere of radius d. Extending a recent work of Jiang and Vardy on binary codes, we show that for any positive constant /spl alpha/ less than (q-1)/q there is a positive constant c such that for d/spl les//spl alpha/n A/sub q/(n,d+1)/spl ges/cq/sup n//V/sub q/(n,d)n. This confirms a conjecture by Jiang and Vardy.
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.
18861193
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints
Proteins "work together" by actually binding to form multicomponent complexes that carry out specific functions. Proteomic analyses based on the mass spectrum are now key methods to determine the components in protein complexes. The protein-protein interaction or functional association may be known to exist among the extracted protein spots while analyzing the proteins on the 2D gel. In this study, we develop an agent-based system, namely AgentMultiProtIdent, which integrated two protein identification tools and a variety of databases storing relations among proteins and used to discover protein-protein interactions and protein functional associations, and identify protein complexes and proteins with multiple peptide mass fingerprints as input. The system takes Multiple Peptide Mass Fingerprints (PMFs) as a whole in the protein complex or protein identification. With the relations among proteins, it may greatly improve the accuracy of identification of protein complexes. Also, possible relationship of the multiple peptide mass fingerprints, such as ontology relation, can be discovered by our system, especially in the identification of protein complexes. The agent-based system is now available on the Web at http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/.