ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo.pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/.

Urban development and traffic accidents in Brazil.

Brazil started to experience high traffic accident rates since the 1960s, when road transportation began to be dominant and the number of motorized vehicles increased sharply. The severity of the problem was also related to the fast and uncontrolled urban growth, which allowed for the organization of an inherently dangerous circulation space, characterized by a complex pattern of traffic conflicts. With respect to traffic accidents, the results have been highly negative: national statistics report about 28,000 fatalities a year, with more than 340,000 injured people. The paper analyses current patterns of traffic accidents in urban areas, using the data from two of the three largest cities in the country. Hospital data is analyzed to understand the true social impacts of such accidents. Several causal factors are identified, at the political, cultural and technical sides. Challenges to change current conditions are also identified. Practical measures are suggested, especially the change of the dangerous environment and the need to improve the technical approach to the problem, education programs and enforcement logistics.