Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can some times referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
The Biocomplexity Institute of Virginia Tech was a research institute specializing in bioinformatics, computational biology, and systems biology. The institute had more than 250 personnel, including over 50 tenured and research faculty. Research at the institute involved collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology and medicine. The institute developed -omic and bioinformatic tools and databases that can be applied to the study of human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets.
The completion of the human genome sequencing in the early 2000s was a turning point in genomics research. Scientists have conducted series of research into the activities of genes and the genome as a whole. The human genome contains around 3 billion base pairs nucleotide, and the huge quantity of data created necessitates the development of an accessible tool to explore and interpret this information in order to investigate the genetic basis of disease, evolution, and biological processes. The field of genomics has continued to grow, with new sequencing technologies and computational tool making it easier to study the genome.
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA, RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes – in many cases, an organism's entire genome – in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult – if not impossible – to analyze without the help of computer programs.
lumi is a free, open source and open development software project for the analysis and comprehension of Illumina expression and methylation microarray data. The project was started in the summer of 2006 and set out to provide algorithms and data management tools of Illumina in the framework of Bioconductor. It is based on the statistical R programming language.
Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M and A scales, then plotting these values. Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
Integrated Genome Browser (IGB) is an open-source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
Rmetrics is a free and open-source software project designed for teaching computational finance. Rmetrics is based primarily on the statistical R programming language, but does contain contributions in other programming languages, such as Fortran, C, and C++. The project was started in 2001 by Diethelm Wuertz, based at the Swiss Federal Institute of Technology in Zurich.
Robert Clifford Gentleman is a Canadian statistician and bioinformatician who is currently the founding executive director of the Center for Computational Biomedicine at Harvard Medical School. He was previously the vice president of computational biology at 23andMe. Gentleman is recognized, along with Ross Ihaka, as one of the originators of the R programming language and the Bioconductor project.
GeneNetwork is a combined database and open-source bioinformatics data analysis software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence differences to corresponding differences in gene and protein expression and to variation in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes and phenotypes from groups of individuals, including humans, strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes makes it practical to carry out web-based gene mapping to discover those regions of genomes that contribute to differences among individuals in mRNA, protein, and metabolite levels, as well as differences in cell function, anatomy, physiology, and behavior.
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. Although the BioMart software is primarily used by the biomedical research community, it is designed in such a way that any type of data can be incorporated into the BioMart framework. The BioMart project originated at the European Bioinformatics Institute as a data management solution for the Human Genome Project. Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents.
The phenotype microarray approach is a technology for high-throughput phenotyping of cells. A phenotype microarray system enables one to monitor simultaneously the phenotypic reaction of cells to environmental challenges or exogenous compounds in a high-throughput manner. The phenotypic reactions are recorded as either end-point measurements or respiration kinetics similar to growth curves.
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g. different organism growth patterns or diseases). The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes, which are used for the analysis.
Sorin Drăghici is a Romanian-American computer scientist and a program director in the Division of Information and Intelligent Systems (IIS) of the Directorate for Computer and Information Science and Engineering (CISE) at the National Science Foundation (NSF). Previous positions include: Associate Dean for Entrepreneurship and Innovation of Wayne State University's College of Engineering, the Director of the Bioinformatics and Biostatistics Core at Karmanos Cancer Institute, and the Director of the James and Patricia Anderson Engineering Ventures Institute. Draghici was elected a Fellow of the Institute of Electrical and Electronics Engineers (IEEE) in 2022, for contributions to the analysis of high-throughput genomics and proteomics data. He has also been elected a Fellow of the Asia-Pacific Artificial Intelligence Association (AAIA).
Rafael Irizarry is a professor of biostatistics at the Harvard T.H. Chan School of Public Health and professor of biostatistics and computational biology at the Dana–Farber Cancer Institute. Irizarry is known as one of the founders of the Bioconductor project.
Sandrine Dudoit is a professor of statistics and public health at the University of California, Berkeley. Her research applies statistics to microarray and genetic data; she is known as one of the founders of the open-source Bioconductor project for the development of bioinformatics software.
R packages are extensions to the R statistical programming language. R packages contain code, data, and documentation in a standardised collection format that can be installed by users of R, typically via a centralised software repository such as CRAN. The large number of packages available for R, and the ease of installing and using them, has been cited as a major factor driving the widespread adoption of the language in data science.
