In biology and other experimental sciences, an in silico experiment is one performed on a computer or via computer simulation software. The phrase is pseudo-Latin for 'in silicon' (correct Latin: in silicio), referring to silicon in computer chips. It was coined in 1987 as an allusion to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology (especially systems biology). The latter phrases refer, respectively, to experiments done in living organisms, outside living organisms, and where they are found in nature.
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👉 In silico in the context of Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure determines their structural formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study.
The range of chemicals studied in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but also containing other elements, especially oxygen, nitrogen, sulfur, phosphorus (included in many biochemicals) and the halogens. Organometallic chemistry is the study of compounds containing carbon–metal bonds.
In this Dossier
In silico in the context of Evolutionary robotics
Evolutionary robotics is an embodied approach to Artificial Intelligence (AI) in which robots are automatically designed using Darwinian principles of natural selection. The design of a robot, or a subsystem of a robot such as a neural controller, is optimized against a behavioral goal (e.g. run as fast as possible). Usually, designs are evaluated in simulations as fabricating thousands or millions of designs and testing them in the real world is prohibitively expensive in terms of time, money, and safety.
An evolutionary robotics experiment starts with a population of randomly generated robot designs. The worst performing designs are discarded and replaced with mutations and/or combinations of the better designs. This evolutionary algorithm continues until a prespecified amount of time elapses or some target performance metric is surpassed.
In silico in the context of Bioinformatics
Bioinformatics (/ˌbaɪ.oʊˌɪnfərˈmætɪks/ ) is an interdisciplinary field of science that develops computational methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. This process can sometimes be referred to as computational biology, however the distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
Computational, statistical, and computer programming techniques have been used for computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphisms (SNPs). These pipelines are used to better understand the genetic basis of disease, unique adaptations, desirable properties (especially in agricultural species), or differences between populations. Bioinformatics also includes proteomics, which aims to understand the organizational principles within nucleic acid and protein sequences.
In silico in the context of Computer experiment
A computer experiment or simulation experiment is an experiment used to study a computer simulation, also referred to as an in silico system. This area includes computational physics, computational chemistry, computational biology and other similar disciplines.
In silico in the context of Bacterial artificial chromosome
A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. F-plasmids play a crucial role because they contain partition genes that promote the even distribution of plasmids after bacterial cell division. The bacterial artificial chromosome's usual insert size is 150–350 kbp. A similar cloning vector called a PAC has also been produced from the DNA of P1 bacteriophage.
BACs were often used to sequence the genomes of organisms in genome projects, for example the Human Genome Project, though they have been replaced by more modern technologies. In BAC sequencing, short piece of the organism's DNA is amplified as an insert in BACs, and then sequenced. Finally, the sequenced parts are rearranged in silico, resulting in the genomic sequence of the organism. BACs were replaced with faster and less laborious sequencing methods like whole genome shotgun sequencing and now more recently next-gen sequencing.