A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

Information-dependent processes in incubated and graduated technology-based companies: a comparative case study

Nowadays, competitiveness introduces new behaviors and leads companies to a discomforting situation and often to non adaptation to environmental requirements. A growing number of challenges associated with control of information in organizations with engineering activities can be seen, particularly, the growing amount of information subject to continuous changes. The innovative performance of an organization is directly proportional to its ability to manage information. Thus, the importance of information management is recognized by the search for more competent ways to face current demands. The purpose of this article was to analyze informationdependent processes in technology-based companies, through the four major stages of information management. The comparative method of cases and qualitative research were used. The research was conducted in nine technology-based companies which were incubated or recently went through the incubating process at the Technological Park of Sao Carlos, in the state of Sao Paulo. Among the main results, it was found that in graduated companies information management and its procedures were identified as more conscious and structured in contrast to those of the incubated companies.

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F-i) or individual increases in inbreeding coefficient (Delta F-i) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scro-tal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including Delta F-i can be considered more adequate to quantify inbreeding depression. The inclusion of F-i or Delta F-i in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.

Processos dependentes de informação em empresas incubadas e graduadas de base tecnológica: um estudo comparativo de casos

A competitividade, atualmente, introduz novos comportamentos e leva empresas a uma situação de desconforto e, muitas vezes, a não adaptação às exigências ambientais. Percebe-se um crescente número de desafios associados com o controle de informação em organizações com atividades de engenharia, em particular os volumes crescentes de informação de natureza continuamente mutável. Pode-se afirmar que o desempenho inovador de uma organização é diretamente proporcional a sua capacidade de gerenciar informações. Desta forma, a importância da gestão da informação é reconhecida em detrimento da procura de meios mais competentes para atender demandas atuais. O artigo teve como propósito analisar doze processos dependentes de informação em empresas de base tecnológica, através das principais fases do processo de gerenciamento da informação. Optou-se pelo emprego do método comparativo de casos e pela pesquisa qualitativa, realizada em nove empresas de base tecnológica, as quais se encontravam incubadas ou que passaram recentemente pela fase de incubação no Parque Tecnológico da cidade de São Carlos, do estado de São Paulo. Entre os principais resultados, constatou-se que, nas empresas graduadas, a gestão da informação e seus procedimentos foram identificados de forma mais consciente e estruturados em relação às empresas incubadas.