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Modeling stochasticity and robustness in gene regulatory networks

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Stochastic

Stochastic (stəˈkæstɪk; ) refers to the property of being well described by a random probability distribution. Although stochasticity and randomness are distinct in that the former refers to a modeling approach and the latter refers to phenomena themselves, these two terms are often used synonymously. Furthermore, in probability theory, the formal concept of a stochastic process is also referred to as a random process.

Gene prediction

In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.

Gene expression profiling

In the field of molecular biology, gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment. Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. Several transcriptomics technologies can be used to generate the necessary data to analyse.

Computational biology

Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s.

Biological engineering

Biological engineering or bioengineering is the application of principles of biology and the tools of engineering to create usable, tangible, economically viable products. Biological engineering employs knowledge and expertise from a number of pure and applied sciences, such as mass and heat transfer, kinetics, biocatalysts, biomechanics, bioinformatics, separation and purification processes, bioreactor design, surface science, fluid mechanics, thermodynamics, and polymer science.

Boolean algebra

In mathematics and mathematical logic, Boolean algebra is a branch of algebra. It differs from elementary algebra in two ways. First, the values of the variables are the truth values true and false, usually denoted 1 and 0, whereas in elementary algebra the values of the variables are numbers. Second, Boolean algebra uses logical operators such as conjunction (and) denoted as ∧, disjunction (or) denoted as ∨, and the negation (not) denoted as ¬.

Boolean algebra (structure)

In abstract algebra, a Boolean algebra or Boolean lattice is a complemented distributive lattice. This type of algebraic structure captures essential properties of both set operations and logic operations. A Boolean algebra can be seen as a generalization of a power set algebra or a field of sets, or its elements can be viewed as generalized truth values. It is also a special case of a De Morgan algebra and a Kleene algebra (with involution).

Modeling language

A modeling language is any artificial language that can be used to express data, information or knowledge or systems in a structure that is defined by a consistent set of rules. The rules are used for interpretation of the meaning of components in the structure Programing language. A modeling language can be graphical or textual. Graphical modeling languages use a diagram technique with named symbols that represent concepts and lines that connect the symbols and represent relationships and various other graphical notation to represent constraints.

Biological network

A biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. In general, networks or graphs are used to capture relationships between entities or objects. A typical graphing representation consists of a set of nodes connected by edges. As early as 1736 Leonhard Euler analyzed a real-world issue known as the Seven Bridges of Königsberg, which established the foundation of graph theory. From the 1930's-1950's the study of random graphs were developed.

Constructive solid geometry

Constructive solid geometry (CSG; formerly called computational binary solid geometry) is a technique used in solid modeling. Constructive solid geometry allows a modeler to create a complex surface or object by using Boolean operators to combine simpler objects, potentially generating visually complex objects by combining a few primitive ones. In 3D computer graphics and CAD, CSG is often used in procedural modeling. CSG can also be performed on polygonal meshes, and may or may not be procedural and/or parametric.