Tools-4-Metatool (T4M) is a suite of web-tools, implemented in PERL, which analyses, parses, and manipulates files related to Metatool. Its main goal is to assist the work with Metatool. T4M has two major sets of tools: Analysis and Compare. Analysis visualizes the results of Metatool (convex basis, elementary flux modes, and enzyme subsets) and facilitates… (More)
Agent-based modelling is becoming widely used for studies in Social Sciences. However, its application faces limitations coming from its bias to software development, which precludes a more active involvement of social researchers. In order to deal with this problem, this work proposes using domain-specific modelling languages based on the… (More)
In the last years, the amount of genomic data produced has increased significantly. These data need to be processed and linked to biological information in order to make a meaningful use of them. Automated tools support these tasks, but their results have to be curated by experts, what creates a bottleneck. Although some collaborative community annotation… (More)
Functional annotation is the process that assigns a biological functionality to a deoxyribonucleic acid (DNA) sequence. It requires searching in huge data sets for candidates, and inferring the most appropriate features based on the information found and expert knowledge. When humans perform most of these tasks, results are of a high quality, but there is a… (More)
The matching preclusion number of a graph is the minimum number of neither edges whose deletion in a graph has a neither perfect matching nor an almost perfect matching. For many interconnection networks, the optimal sets are precisely those induced by a single vertex. Recently the conditional matching preclusion number of a graph was introduced to look for… (More)
The whole-genome shotgun sequence of Rhodococcus ruber strain Chol-4 is presented here. This organism was shown to be able to grow using many steroids as the sole carbon and energy sources. These sequence data will help us to further explore the metabolic abilities of this versatile degrader.
Finding the genes that exist within a DNA sequence and assigning them biological features and functions is one of the biggest challenges of Genomics. This task, called annotation, has to be as accurate and reliable as possible, because this information will be applied in other researches. Ideally, each sequence should be annotated and validated by a human… (More)