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The object of the following paper is to present the process of designing and implementing and verifying a new bioinformatics information system containing a biological database. It is designed for collecting and analyzing nucleotide/protein sequence data for scientific research work and educational purposes. The Needleman-Wunsch global alignment algorithm is implemented and verified by conducting experiments using online bioinformatics tools. It is also used to test the performance of the proposed bioinformatics information system. In addition, several test cases, in which the alignment of biological sequences is used for clinical diagnosis, are considered; detecting patient similarity; gene prediction, etc. The paper includes a brief state-of-the-art on online biological databases and bioinformatics systems and tools. [ABSTRACT FROM AUTHOR]

The comparisons of means from biological data require the selection of the right fited model to obtain results compatible with phenomena under study. This work presents an application of comparison of means through statistical models. The authors concluded that in this case the best model was the lognormal, considering the values of AIC, SE, log-likelihood and biological relevance of model coefficients. [ABSTRACT FROM AUTHOR]

In this work we present results obtained in the frame of the BioQuaRT project. The objective of the study was the correlation between the number of radiation-induced double strand breaks (DSB) of the DNA molecule and the probability of detecting nuclear foci after targeted microbeam irradiation of cells with protons and alpha particles of different LET. The former were obtained by simulation with new methods integrated into Geant4-DNA that permit calculating the number of DSB in a DNA target model induced by direct and indirect radiation effects. A particular focus was laid in this work on evaluating the influence of different criteria applied to the simulated results for predicting the formation of a direct SSB. Indeed, these criteria have an important impact on the predicted number of DSB per particle track and its dependence with LET. Among the criteria tested in this work, the case that a direct radiation interaction leads to a strand break if the cumulative energy deposited in the backbone part of one nucleotide exceeds a threshold of 17.5 eV leads to the best agreement with the relative LET dependence of number of radiation induced foci. Further calculations and experimental data are nevertheless needed in order to fix the simulation parameters and to help interpreting the biological experimental data observed by immunofluorescence in terms of the DSB complexity. [ABSTRACT FROM AUTHOR]

There are a large number of web-based biological databases publicly available for scientists. In addition, many private databases are generated in the course of research projects. Web standards have evolved in recent times, and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, the integration and querying of biological databases can be facilitated by semantic web techniques. The key idea is to describe data in the Resource Description Format (RDF) and to query them using the SPARQL language. In this paper, we introduce "BioCarian" an efficient and user-friendly search engine that can be used to perform exploratory searches of biological databases. The search engine acts as an interface for running SPARQL queries in RDF databases. In addition, we also provide a graphical interface based on facets that can be used to create advanced SPARQL queries. The facet interface is more advanced and novel than conventional facets. It allows complex queries to be constructed and includes additional features such as allowing facet values to be ranked based on several criteria, visually indicating the relevance of a facet value, and presenting the most important facet values when a large number of choices are available. We have constructed a prototype database that combines public databases that have gene-level, protein-level, and disease-level information. The search engine can be accessed from www.biocarian.com. [ABSTRACT FROM AUTHOR]

The continuous growth in quantity and diversity of life sciences data is triggering several bioinformatics challenges to be able to integrate and select desired information for later study. The majority of these data are scattered through independent systems disregarding interoperability features, which makes data integration processes not a trivial task. Consequently, several ETL (Extract-Transform-and-Load) frameworks have been developed to make data integrations tasks suitable for later exploration studies, providing better solutions for data heterogeneity, diversity and distribution. However, current advanced data integration tasks depend on large and heterogeneous data sources that must be modelled according to the source specifications and network conditions. Furthermore, these automated tasks are significantly dependent of sequential processes that dramatically increase the global request and processing time. Without estimation of the task completion time, the whole research workflow becomes even more challenging. This paper presents DISim, an ontology for data integration simulation, to estimate large and heterogeneous data integration jobs, in order to provide valuable outputs to enhance decision-making scenarios. [ABSTRACT FROM AUTHOR]

Method of identification refers to the statistics (probability) modeling. And in Your magazine to section «Computational and bioinformatic methods for analysis, modeling or visualization of biological data». The difference is that the step of selecting the formulas we formalized and there-fore it is only the second stage of modeling - the choice of parameter values identified on the initial data of the generalized model or, in the special case of equation. In addition, each parameter of any member has a physical meaning. This dramatically increases the value compared to the linear regression correlation coefficient of 0.9999. History modeling completely given additional information. Here we will show not only advantages of our method, but also possibility of identification according to aprioristic information of essentially new regularities in the form of Seed factor. Because of high definiteness of the first stage of process of statistical modeling essentially new aposteriorny information is shown. As a result «Whole- cell model» method improvement for acceleration of biological opening is possible. The greatest effect gives our method without averaging and other group of basic data. The computing data set receives accurate physical sense and it increases definiteness of forecasting. The group of contradictions1 will decrease, and new opening will appear during modeling. It isn't necessary for data1 of division on categories that was required because of application of linear regression. Therefore "Whole-cell model" addition with our wave equations would allow to give not only qualitative, but also quantitative, essence. Therefore our method of identification will allow to open the mechanism of behavior of populations of any objects. [ABSTRACT FROM AUTHOR]

Object recognition is usually processed based on region segmentation algorithm. Region segmentation in the IT field is carried out by computerized processing of various input information such as brightness, shape, and pattern analysis. If the information mentioned does not make sense, however, many limitations could occur with region segmentation during computer processing. Therefore, this paper suggests effective region segmentation method based on Susceptibility Weighted Imaging (SWI) within the magnetic resonance (MR) theory. In this study, the experiment had been conducted using images including the brain region and by getting up contrast enhancement image of SWI for texture analysis to enable region (white matter) segmentation even when the border line was not clear. As a result, an average area difference of 7.6%, which was higher than the accuracy of conventional region segmentation algorithm, was obtained. [ABSTRACT FROM AUTHOR]

A conference paper about an environment for the production of live research objects presented at the 14th International Conference on Grey Literature (GL14) held at the National Research Council (CNR) in Rome, Italy on November 29-30, 2012. Topics include the environmental data reporting, specialized data management, authoritative data sources and distribution of biological data.