Contents
 | This article needs additional citations for verification .(November 2020) |
| | This article needs additional citations for verification .(November 2020) |
| Name | Description | Site |
|---|---|---|
| GESTALT Workbench | graphical workbench for analysis of large-scale genomic sequence data | |
| N-Browse | interactive graphical browser for biological networks | |
| NetPath | curated resource of human signal transduction pathways | |
| MEGA | free, online, open-source, phylogenetic analysis, drawing dendrograms etc. | |
| REACTOME | free, online, open-source, curated pathway database encompassing many areas of human biology | |
| WikiPathways | curate biological pathways | |
| MetaboMAPS | visualize omics data on shared metabolic pathways [1] |
| Name | Description | OS | License | Site |
|---|---|---|---|---|
| BioTapestry | interactive tool for building, visualizing, and simulating genetic regulatory networks | multiplatform (Java-based) | LGPL | |
| Cytoscape | data integration, network visualization, and analysis | multiplatform (Java-based) | LGPL | |
| GenMAPP | visualize and analyze genomic data in the context of pathways | Windows | Apache License | |
| MATLAB | tool for modeling, simulating, and analyzing dynamic biological systems | Windows, Linux, macOS | Proprietary | |
| MEGA | free, online, open-source, phylogenetic analysis, drawing dendrograms etc. | Windows/DOS-Win/Mac/Linux | Shareware | |
| PathVisio | tool for displaying and editing biological pathways | multiplatform (Java-based) | Apache License | |
| InCroMAP | tool for the integration of omics data and joint visualization of experimental data in pathways | multiplatform (Java-based) | LGPL | |
| Pathview | pathway based data integration and visualization, easy to use and integrate into pathway analysis | multiplatform (R/Bioconductor) | GPL | |
| SBMLDiagrams [2] | Python API to display and edit SBML layout/render extension | multiplatform | MIT | |
| Systrip | analysis of time-series data in the context of biological networks | Windows, Linux | LGPL, GPL |
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 subsequent process of analyzing and interpreting data is referred to as computational biology.
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
DAVID is a free online bioinformatics resource developed by the Laboratory of Human Retrovirology and Immunoinformatics. All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. DAVID can be found at https://david.ncifcrf.gov/
The International Society for Computational Biology (ISCB) is a scholarly society for researchers in computational biology and bioinformatics. The society was founded in 1997 to provide a stable financial home for the Intelligent Systems for Molecular Biology (ISMB) conference and has grown to become a larger society working towards advancing understanding of living systems through computation and for communicating scientific advances worldwide.
Fiji is an open source image processing package based on ImageJ2.
Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.
Lawrence E. Hunter is a Professor and Director of the Center for Computational Pharmacology and of the Computational Bioscience Program at the University of Colorado School of Medicine and Professor of Computer Science at the University of Colorado Boulder. He is an internationally known scholar, focused on computational biology, knowledge-driven extraction of information from the primary biomedical literature, the semantic integration of knowledge resources in molecular biology, and the use of knowledge in the analysis of high-throughput data, as well as for his foundational work in computational biology, which led to the genesis of the major professional organization in the field and two international conferences.
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things, it identifies the locations of genes and all the coding regions in a genome and determines what those genes do.
The International Society for Computational Biology Student Council (ISCB-SC) is a dedicated section of the International Society for Computational Biology created in 2004. It is composed by students from all levels in the fields of bioinformatics and computational biology. The organisation promotes the development of the students' community worldwide by organizing different events including symposia, workshops, webinars, internship coordination and hackathons. A special focus is made on the development of soft skills in order to develop potential in bioinformatics and computational biology students around the world.
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible.
BioJS is an open-source project for bioinformatics data on the web. Its goal is to develop an open-source library of JavaScript components to visualise biological data. BioJS develops and maintains small building blocks (components) which can be reused by others. For a discovery of available components, BioJS maintains a registryArchived 2018-03-13 at the Wayback Machine.
Christophe Dessimoz is a Swiss National Science Foundation (SNSF) Professor at the University of Lausanne, Associate Professor at University College London and a group leader at the Swiss Institute of Bioinformatics. He was awarded the Overton Prize in 2019 for his contributions to computational biology. Starting in April 2022, he will be joint executive director of the SIB Swiss Institute of Bioinformatics, along with Ron Appel.
Manuel Corpas is an Anglo-Spanish biologist and entrepreneur known primarily for his contributions to the field of Bioinformatics and Genomics. Currently Corpas is Chief Scientist of Cambridge startup Cambridge Precision Medicine, a tutor at the Institute for Continuing Education at the University of Cambridge and a lecturer at the Universidad Internacional de La Rioja. Manuel worked on the human genome from the beginning of his career, being one of the first consumers to sequence and his own genome and that of close relatives, which he published as the Corpasome. He has held positions at the Earlham Institute as Project Leader, and the Wellcome Sanger Institute, developing the DECIPHER database, a database that aids in the diagnosis of patients with rare genomic disorders.