Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Project management: evaluation of the problems in the portuguese construction industry

During recent decades it has been possible to identify several problems in construction industry project management, related with to systematic failures in terms of fulfilling its schedule, cost and quality targets, which highlight a need for an evaluation of the factors that may cause these failures. Therefore, it is important to understand how project managers plan the projects, so that the performance and the results can be improved. However, it is important to understand if other areas beyond cost and time management that are mentioned on several studies as the most critical areas, receive the necessary attention from construction project managers. Despite the cost and time are the most sensitive areas/fields, there are several other factors that may lead to project failure. This study aims at understand the reasons that may cause the deviation in terms of cost, time and quality, from the project management point of view, looking at the knowledge areas mentioned by PMI (Project Management Institute).