The focus of this category is on software used by biologists in any of the fields of biology.
There are branches of biology, including anatomy, biochemistry, biophysics, biotechnology, botany, cellular biology, ecology, evolution, genetics, immunology, marine biology, microbiology, molecular biology, mycology, parasitology, photobiology, phycology, physiology, plant physiology, radiobiology, structural biology, theoretical biology, virology, and zoology.
There are several different types of biologists, and some of their roles overlap.
Biochemists seek to explain life processes in terms of physical and chemical reactions and properties. Among the activities they are involved in is the analysis of samples of air, animal tissues, drugs, food, water, and wastes.
Computational biologists use computers and mathematical algorithms to analyze and process data relating to biomechanics, DNA, natural and agricultural systems, protein structures, neuroscience, and other systems.
Conservation biologists are interested in the restoration and protection of ecosystems and wildlife habitats, including the conservation of endangered species.
Also known as evolutionary biologists, ecologists study the processes that are fundamental to an understanding of the ecology and evolution of living things.
Marine biologists study aquatic organisms and how they interact with the environment. Specialties in marine biology might focus on a single species.
Microbiologists study living organisms that are invisible to the naked eye, such as fungi, bacteria, and viruses.
Molecular biologists are involved in the study of living things at the molecular level, such as how genetic information is encoded in DNA molecules, how it can be changed, and the effects of these changes.
Physiologists study the internal functions of living organisms, including the processes of reproduction, metabolism, and respiration.
Also known as botanists, plant biologists study plant life. They might identify and evaluate new species, develop new plants through biotechnology, or study the way in which pollution affects plants.
Wildlife biologists observe and study the behaviors of animals and their environment. They observe and analyze the features of certain wildlife, determining their role in a specific ecosystem.
As stated at the outset, the primary interest of this category is on the software that is used by biologists. Software that has been designed primarily to teach biology should be listed in the Education & Training section.
Recommended Resources
The Biochemical ALgorithms Library (BALL) project is an application framework implemented in C++. It was designed to provide an extensive set of data structures, as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structure, file import/export, and visualization. Distributed under the terms of the Lesser GNU Public License, it may be freely downloaded. Documentation, citations, and publications are included.
https://ball-project.org/
Developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign, BioCore offers a seamless interface to a wide range of local and remote technologies, including discipline-specific, general tools, data, and visualization solutions. An overview of the program is given, including its features, screenshots, and installation instructions. A BioCore server is also available, along with the server source code, and licensure.
http://www.ks.uiuc.edu/Research/biocore/
The BioPerl Project produces an open-source bioinformatics toolkit that includes a large set of Perl modules intended to help biologists write their own scripts to meet their specific needs, such as gene and protein sequences, sequence analysis with BLAST, and others. Available for Linux, Unix, and macOS, installation instructions are given, along with extensive documentation, instructions for BioPerl developers and maintainers, and common DNA and protein sequence formats.
https://bioperl.org/
Distributed by the Systems Biology Institute, CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks, based on the process diagram, with graphical notation system by Kitano, and stores using the Systems Biology Markup Language. Free to download and use, its features are listed, and a tutorial, manuals, developers documents, graphical notations, licensure, and links to models built with CellDesigner are included.
http://www.celldesigner.org/
Originally distributed in desktop format, but now as cloud-based applications, DNAS produces DNA diagnostic design and analysis software, including primer design multiplexes, detecting DNA copy number from PCR curves, determining complete modified nucleotide predictions, and predicting rate kinetics from a sequence, along with others. Its products are highlighted, testimonials are posted, acknowledgments, and citations from various publications. A trial offer is available.
https://www.dnasoftware.com/
Headquartered in Wisconsin, DNAStar develops and distributes DNAStar Cloud, which covers the most popular life science workflows, and can be operated on a laptop or desktop computer, although the ability to tap the DNAStar Cloud, powered by Amazon Web Services, is available for those who need faster speeds. Its products include DNAStar Lasergene, Lasergene Molecular Biology, Lasergene Protein, and Lasergene Genomics. Its pricing, training, and technical requirements are posted.
https://www.dnastar.com/
Developed by Pande Laboratory, Sony, Nvidia, ATI, Joseph Coffland, and Cauldron Development, Folding@home is a distributed computing project for disease research, simulating protein folding, computational drug design, and other types of molecular dynamics. By downloading the software, computer owners allow the use of their computing power in a manner like SETI@home. An overview of its projects is given, along with statistics, and news.
https://foldingathome.org/
From Geneious Biologics, the software application is used to screen and manage antibody sequence data in the cloud. The cross-platform program works on Linux, Mac, and Windows platforms, offering molecular cloning and primer design, and NGS analysis and genomics, featuring a shared database, built-in workflows, API and plugin development, and data import and export functions. It offers student/personal, non-commercial personal, and commercial personal plans via subscription.
https://www.geneious.com/
Offered as free software, Molbiotools includes several software tools for DNA sequencing, as well as text and data tools, including WebDSV, a DNA sequence editor, PCR Primer Inspector, Restriction Analyzer, Restriction Comparator, Silent Mutator, Random Sequence Generator, Target Text Extractor, Multiple List Comparator, List Operations, Table Operations, Two-table Operations, and Random Gene Set Generator, each of which is described, with user guides.
http://molbiotools.com/
SBW is a software program that enables various modeling programs to communicate with one another and to provide or use specialized analysis services. There are more than two hundred and fifty different packages for simulating cellular networks, each using its own format, often undocumented, and many of the tools duplicate each other’s capabilities. The SBW provides model exchange and code reuse so that developers can more easily build upon previous work.
http://sbw.sourceforge.net/
