1918071
ESTWeb: bioinformatics services for EST sequencing projects
ESTWeb is an internet based software package designed for uniform data processing and storage for large-scale EST sequencing projects. The package provides for: (a) reception of sequencing chromatograms; (b) sequence processing such as base-calling, vector screening, comparison with public databases; (c) storage of data and analysis in a relational database, (d) generation of a graphical report of individual sequence quality; and (e) issuing of reports with statistics of productivity and redundancy. The software facilitates real-time monitoring and evaluation of EST sequence acquisition progress along an EST sequencing project.
18125589
Zerg: A Very Fast BLAST Parser Library
SUMMARY
Zerg is a library of sub-routines that parses the output from all NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx) and returns the attributes of a BLAST report to the user. It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers.


AVAILABILITY
http://bioinfo.iq.usp.br/zerg
32839673
Genomics and Gene Expression Management Tools for the Schistosoma Mansoni cDNA Microarray Project
IV BSB 22 Favor ver os Anais do Simpósio em Springer Verlag, Lecture Notes in Bioinformatics (LNBI número 3594) para este trabalho.
12270268
Mining Web Usage Data for Discovering Navigation Clusters
The analysis of a web site based on usage data is an important task as it provides insight into the organization of the site and its adequacy regarding user needs. This allows the relationship between prior categories and user browsing patterns to be explored. In this paper we propose an approach for discovering the profiles of visitor groups. To this end, we begin by mapping user interests into symbolic objects, which is the basis of the Symbolic Data Analysis and represents here a successful interaction of the user with the web site. We then identify groups of users with similar behavior by means of a dynamic clustering approach applying a context dependent dissimilarity measure. The method was applied to identify visitor groups of a web site in the educational domain and also to analyze the traces of different user behavior.
1719989
Empirical Evaluation of SysML through the Modeling of an Industrial Automation Unit
Industrial automation systems may include people, hardware, software and other elements necessary to produce the desirable results. The SysML modeling language is being proposed, by OMG and INCOSE, as a language that allows the system description correctly and consistently among various participants of the same project (software, mechanical, electrical and others engineers). The objective of this work is to evaluate the SysML proposal as a description language for industrial systems through the modeling of an industrial automation unit. A brief system description of the case study is included, the SysML diagrams will be presented during the system modeling and finally comments and considerations about the models and the modeling task are presented.
19002308
Planning Brazilian Urban Traffic with a Geographic Application Software
Planning and optimizing urban traff ic is a diff icult problem, with considerable economic and social impacts. The development of suitable software tools to aid municipal governments to control and to improve the traff ic flow is urgent due to the increasing number of vehicles in urban areas. However, the development of this kind of software represents a great challenge since the problems to be dealt with in this domain are both computationally and mathematically complex. This article presents a geographic application software as a feasible solution for this problem. The solution is geared towards Brazilian medium to large cities and is based on a mathematical model of the urban traff ic. This model is stored in a geographic database and allows the user of the software (typicall y a traff ic engineer) to search for alternative solutions for traff ic problems. The software can provide optimal solutions for an important family of traff ic problems, namely the Traff ic Equili brium Problem (TEP). This family involves the common hashing problems (e.g. traff ic bottlenecks) as well as more sophisticated problems li ke vehicles’ pollution minimization. We have developed a prototype of the software and its solutions for the TEP were empiricall y validated against real traff ic data from Goiânia, capital of the Brazilian state of Goiás.
12706002
Computer-Assisted Discrepancy Management - A Case Study in Research Transfer to Industry
This paper reports on the “repackaging” and transfer to industry of research results in ViewpointBased Requirements Engineering (VBRE). Our experience, as indicated here, is a particular case of the problems and solutions that small research groups can find in their transfer from theoretical work to practical application. In particular, starting with a formal approach for discrepancy management, we first developed a “light-weight version” of VBRE and empirically validated their most important claims. Then we developed a software tool (discRman) that encapsulates the main points of the approach and, finally, partner organizations used it in small projects. We think that this “theoretical-empirical-light-weight-tool” sequence can be applied in similar situations, especially by small research groups seeking for transfer of their results to industry. ACM Classification: D.2.1 (Software Engineering – Requirements/Specifications – Methodologies, Tools), D.2.8 (Software Engineering – Metrics – Performance measures), D.2.9 (Software Engineering – Management – Productivity)
4598397
Workflow Access Control from a Business Perspective
Workflow management systems are increasingly being used to support business processes. Methodologies have been proposed in order to derive workflow process definitions from business models. However, these methodologies do not comprise access control aspects. In this paper we propose an extension to the Work Analysis Refinement Modelling (WARM) methodology, which also enables to determine workflow access control information from the business process model. This is done by identifying useful information from business process models and showing how it can be refined to derive access control information. Our approach reduces the effort required to define the workflow access control, ensures that authorization rules are directly related to the business and aligns access control with the information system architecture that implements the business process.