There are more than two hundred biological data repositories available for public access, and a vast number of applications to process and interpret biological data. A major challenge for bioinformaticians is to extract and process data from multiple data sources using a variety of query interfaces and analytical tools. In this paper, we describe tools that respond to this challenge by providin...

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biologi...

Sarcopenia is characterized by a lower skeletal muscle quantity, higher fat accumulation in the muscle, lower muscle strength, and lower physical performance. The most commonly used, low cost and accessible methods to assess skeletal muscle mass include dual energy X-ray absorptiometry (DEXA), anthropometry and bioelectrical impedance analysis (BIA). Magnetic resonance imaging (MRI), computeriz...

We present here a compact overview of the data, models and methods proposed for the analysis of biological networks based on the search for significant repetitions. In particular, we concentrate on three problems widely studied in the literature: 'network alignment', 'network querying' and 'network motif extraction'. We provide (i) details of the experimental techniques used to obtain the main ...