Related papers: The genome is software and evolution is a software…
Generating molecules, both in a directed and undirected fashion, is a huge part of the drug discovery pipeline. Genetic algorithms (GAs) generate molecules by randomly modifying known molecules. In this paper we show that GAs are very…
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes,…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
Reverse engineering has been a standard practice in the hardware community for some time. It has only been within the last ten years that reverse engineering, or "program comprehension", has grown into the current sub-discipline of software…
Computer science (CS) education needs to evolve to support software and artificial intelligence (AI) systems engineering, and it needs to happen now -- precisely because the core intellectual contributions of CS have never been more…
Evolution by natural selection can be seen an algorithm for generating creative solutions to difficult problems. More precisely, evolution by natural selection is a class of algorithms that share a set of properties. The question we address…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
Model-driven engineering is the automatic production of software artefacts from abstract models of structure and functionality. By targeting a specific class of system, it is possible to automate aspects of the development process, using…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory as developed by Claude Shannon, but there is open debate about whether such language is anything more…
Research software refers to software development tools that accelerate discovery and simplifies access to digital infrastructures. However, although research software platforms can be built increasingly more innovative and powerful than…
The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Scientific code is not production software. Scientific code participates in the evaluation of a scientific hypothesis. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example,…
Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic…