Bioinformatics Definitions and Singularity

[Cornell University]

Bioinformatics, related to genetics and genomics, is the branch of science that involves the collection, storage, analysis, and dissemination of biological data and information, such as DNA and amino acid sequences or annotations about those sequences, using computer technology. Scientists and clinicians use databases that organize and index such biological information to increase our understanding of health and disease and, in some cases, as part of healthcare.

The role of bioinformatics in biological research can be compared to the role of data analysis in the information and Internet age. In the early days, the main challenge was access to information. Advances in reading DNA sequences have greatly lowered this barrier. Looking ahead, the challenge is how to understand and interpret the information that has been collected. 

Because of the large datasets, whether it is website visit information or human genome information, computer-based approaches are the default. Finally, the collaboration between bioinformatics and the human genome aims to discover practical insights about human health and biology and its complexity.

Data science involves the study of large and complex data sets from various types of research projects. With respect to genomic research, such work requires expertise in quantitative science disciplines such as bioinformatics, computational biology, and biostatistics.

Gene regulation is the process used to control the timing, location and amount of gene expression. This process can be complex and occurs through a variety of mechanisms, including through regulatory proteins and chemical modifications of DNA. Gene regulation is central to the ability of organisms to respond to environmental changes.

Amino acids are the basic molecules that make up proteins. There are 20 different amino acids. Proteins are made up of one or more chains of amino acids (called polypeptides), the sequences of which are encoded by genes. Some amino acids can be synthesized in the body, but others (essential amino acids) cannot and must be obtained from a person's diet.

Deoxyribonucleic acid (abbreviated as DNA) is a molecule that carries genetic information for the development and function of an organism. DNA consists of two connected strands that wind around each other, resembling a twisted ladder—a shape known as a double helix. Each chain has a backbone made up of alternating sugar (deoxyribose) and phosphate groups. Each sugar has one of four bases attached to it: adenine (A), cytosine (C), guanine (G) or thymine (T). The two strands are joined by chemical bonds between the bases: adenine is bound to thymine, and cytosine is bound to guanine. The sequence of bases on the DNA backbone encodes biological information, such as instructions for making proteins or RNA molecules.

Singularity can be used to containerize software (and their dependencies) for later use.

Singularity is a container solution that provides some benefits for bioinformaticians:

• allows to install packages and tools without conflicts with the host system
• ensures reproducibility as using the same image should result in the same output

[More to come ...]