The following table contains the complete list of the 105 software tools that were considered in the questionnaire plus 24 additional software tools that were mentioned by the respondents. These additional tools are marked with an asterisk behind the name. The table also contains all the comments that were given for the different tools. We did not edit the comments in any way (except for spelli...

Computational Systems Biology, a rapidly evolving field, is at the interface of computer science, mathematics, physics and biology. It endeavours to study, analyze and understand complex biological systems by taking a coordinated integrated systems view using computational methodologies. From the middle of the twentieth century till present, we have been witnessing breakthrough discoveries in b...

The era of computer simulations (CS) started with the development of the first digital computers in ‘40s and ’50s (for example, MANIAC (stands for “Mathematical and Numerical Integrator and Computer) computer in Los Alamos). First Molecular Dynamics simulations were reported in 1956. Now CS are the standard tool for studying diverse set of problems. The need in CS arises because very few proble...

Computational Biology provides a wide range of applications for Multitask Learning (MTL) methods. As the generation of labels often is very costly in the biomedical domain, combining data from different related problems or tasks is a promising strategy to reduce label cost. In this paper, we present two problems from sequence biology, where MTL was successfully applied. For this, we use regular...

Genomic research is experiencing a shift of paradigm. Old reductionistic research methods are largely replaced by methods and technology that make possible conducting global studies of gene products and their interactions in complex networks in living organisms. Computational data analysis and modelling have become an important and necessary part of this research methodology. In this paper we l...

Here's a comprehensive reference covering the computational frameworks and techniques needed to help research scientists and professionals in computer science, biology, chemistry, pharmaceutical science, and physics solve complex biological problems. Written by leading experts in the field, this practical resource gives detailed descriptions of core subjects, including biological network modeli...

The main topic of this lecture is about how gene expression is regulated. The regulation of gene expression is of utmost importance for both unicellular organisms that need to adapt to environmental changes and nutritional stresses, and for metazoa, in which individual cells respond to extracellular signals such as hormones and growth factors by switching their activities from one state to anot...

Bioinformatics algorithms are computationally demanding and most of them are compute intensive. Hence we require huge amount of computing power. High Performance Computing as been traditionally believed to be an expensive affair. In this paper we investigate techniques that have been used to parallelize conventional algorithms, coding patterns and architectural enhancements of platforms for bet...