Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Engineering real-time applications with WorldFIP: tools and analysis

WorldFIP is standardised as European Norm EN 50170 - General Purpose Field Communication System. Field communication systems (fieldbuses) started to be widely used as the communication support for distributed computer-controlled systems (DCCS), and are being used in all sorts of process control and manufacturing applications within different types of industries. There are several advantages in using fieldbuses as a replacement of for the traditional point-to-point links between sensors/actuators and computer-based control systems. Indeed they concern economical ones (cable savings) but, importantly, fieldbuses allow an increased decentralisation and distribution of the processing power over the field. Typically DCCS have real-time requirements that must be fulfilled. By this, we mean that process data must be transferred between network computing nodes within a maximum admissible time span. WorldFIP has very interesting mechanisms to schedule data transfers. It explicit distinguishes to types of traffic: periodic and aperiodic. In this paper we describe how WorldFIP handles these two types of traffic, and more importantly, we provide a comprehensive analysis for guaranteeing the real-time requirements of both types of traffic. A major contribution is made in the analysis of worst-case response time of aperiodic transfer requests.

Tools for simulation output analysis

This technical report presents a description of the output data files and the tools used to validate and to extract information from the output data files generated by the Repeater-Based Hybrid Wired/Wireless Network Simulator and the Bridge-Based Hybrid Wired/Wireless Network Simulator.

Cutting forces and wear analysis of Si3N4 diamond coated tools in high speed machining

Si3N4 tools were coated with a thin diamond film using a Hot-Filament Chemical Vapour Deposition (HFCVD) reactor, in order to machining a grey cast iron. Wear behaviour of these tools in high speed machining was the main subject of this work. Turning tests were performed with a combination of cutting speeds of 500, 700 and 900 m min−1, and feed rates of 0.1, 0.25 and 0.4 mm rot−1, remaining constant the depth of cut of 1 mm. In order to evaluate the tool behaviour during the turning tests, cutting forces were analyzed being verified a significant increase with feed rate. Diamond film removal occurred for the most severe set of cutting parameters. It was also observed the adhesion of iron and manganese from the workpiece to the tool. Tests were performed on a CNC lathe provided with a 3-axis dynamometer. Results were collected and registered by homemade software. Tool wear analysis was achieved by a Scanning Electron Microscope (SEM) provided with an X-ray Energy Dispersive Spectroscopy (EDS) system. Surface analysis was performed by a profilometer.

From design-for-test to design-for-debug-and-test: analysis of requirements and limitations for 1149.1

The increasing complexity of VLSI circuits and the reduced accessibility of modern packaging and mounting technologies restrict the usefulness of conventional in-circuit debugging tools, such as in-circuit emulators for microprocessors and microcontrollers. However, this same trend enables the development of more complex products, which in turn require more powerful debugging tools. These conflicting demands could be met if the standard scan test infrastructures now common in most complex components were able to match the debugging requirements of design verification and prototype validation. This paper analyses the main debug requirements in the design of microprocessor-based applications and the feasibility of their implementation using the mandatory, optional and additional operating modes of the standard IEEE 1149.1 test infrastructure.

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

Urban sprawl analysis and modeling in Asmara, Eritreia: Application of Geospatial Tools

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz)

In this study, the metabolomics characterization focusing on the carotenoid composition of ten cassava (Manihot esculenta) genotypes cultivated in southern Brazil by UV-visible scanning spectrophotometry and reverse phase-high performance liquid chromatography was performed. Cassava roots rich in -carotene are an important staple food for populations with risk of vitamin A deficiency. Cassava genotypes with high pro-vitamin A activity have been identified as a strategy to reduce the prevalence of deficiency of this vitamin. The data set was used for the construction of a descriptive model by chemometric analysis. The genotypes of yellow-fleshed roots were clustered by the higher concentrations of cis--carotene and lutein. Inversely, cream-fleshed roots genotypes were grouped precisely due to their lower concentrations of these pigments, as samples rich in lycopene (redfleshed) differed among the studied genotypes. The analytical approach (UV-Vis, HPLC, and chemometrics) used showed to be efficient for understanding the chemodiversity of cassava genotypes, allowing to classify them according to important features for human health and nutrition.

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Analysis and regeneration of hypermedia contents through Java and XML tools

This paper presents a tool for the analysis and regeneration of Web contents, implemented through XML and Java. At the moment, the Web content delivery from server to clients is carried out without taking into account clients' characteristics. Heterogeneous and diverse characteristics, such as user's preferences, different capacities of the client's devices, different types of access, state of the network and current load on the server, directly affect the behavior of Web services. On the other hand, the growing use of multimedia objects in the design of Web contents is made without taking into account this diversity and heterogeneity. It affects, even more, the appropriate content delivery. Thus, the objective of the presented tool is the treatment of Web pages taking into account the mentioned heterogeneity and adapting contents in order to improve the performance on the Web

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies

Background: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLS http://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease"s rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). Results: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. Conclusions: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.