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 often referred to as computational biology, though the distinction between the two terms is often disputed.
Autodesk, Inc. is an American multinational software corporation that provides software products and services for the architecture, engineering, construction, manufacturing, media, education, and entertainment industries. Autodesk is headquartered in San Francisco, California, and has offices worldwide. Its U.S. offices are located in the states of California, Oregon, Colorado, Texas, Michigan, New Hampshire and Massachusetts. Its Canada offices are located in the provinces of Ontario, Quebec, and Alberta.
Ansys, Inc. is an American multinational company with its headquarters based in Canonsburg, Pennsylvania. It develops and markets CAE/multiphysics engineering simulation software for product design, testing and operation and offers its products and services to customers worldwide.
In September 2021, Synthetic Genomics Inc. (SGI), a private company located in La Jolla, California, changed its name to Viridos. The company is focused on the field of synthetic biology, especially harnessing photosynthesis with micro algae to create alternatives to fossil fuels. Viridos designs and builds biological systems to address global sustainability problems.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, then a project under the Apache incubator. Taverna allowed users to integrate many different software components, including WSDL SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench.
CLC bio was a bioinformatics software company that developed a software suite subsequently purchased by QIAGEN.
Biological 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.
OpenSCAD is a free software application for creating solid 3D computer-aided design (CAD) objects. It is a script-only based modeller that uses its own description language; the 3D preview can be manipulated interactively, but cannot be interactively modified in 3D. Instead, an OpenSCAD script specifies geometric primitives and defines how they are modified and combined to render a 3D model. As such, the program performs constructive solid geometry (CSG). OpenSCAD is available for Windows, Linux, and macOS.
Knome, Inc. was a human genome interpretation company based in Cambridge, Massachusetts. Launched in 2007, Knome focused on improving quality of life by applying insights gained from the interpretation of human genomes. They helped identify and classify the variants, genes, and gene sets that are likely to govern or underlie a specific disease, tumor, or drug response. Their clients included academic, pharmaceutical and medical researchers. In 2015, it was acquired by Tute Genomics.
GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores.
GrabCAD, Inc. is a Cambridge, Massachusetts-based startup that created a free cloud-based collaboration environment that helps engineering teams manage, view and share CAD files.
geWorkbench is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data.
Tute Genomics is a genomics startup that provides a cloud-based web application for rapid and accurate annotation of human genomic data. Built on the expertise of ANNOVAR, Tute assists researchers in identifying disease genes and biomarkers, and assists clinicians/labs in performing genetic diagnosis. Based in Provo, Utah, Tute was co-founded by Dr. Kai Wang, an Assistant Professor at the University of Southern California (USC); and Dr. Reid J. Robison, a board-certified psychiatrist with fellowship training in both neurodevelopmental genetics and bioinformatics.
C3D Toolkit is a proprietary cross-platform geometric modeling kit software developed by Russian C3D Labs. It's written in C++. It can be licensed by other companies for use in their 3D computer graphics software products. The most widely known software in which C3D Toolkit is typically used are computer aided design (CAD), computer-aided manufacturing (CAM), and computer-aided engineering (CAE) systems.
Clear Labs, Inc. is a private genomics testing company headquartered in San Carlos, California, United States. It offers a fully automated, next-generation sequencing (NGS) platform for turnkey diagnostics, including SARS-CoV-2 genomic characterization and detection of foodborne pathogens such as listeria and salmonella. It can also verify a food's ingredients, its GMO status, or conduct other tests.
Color Health, Inc. makes population-scale cancer detection and care accessible, convenient, and cost-effective for employers, health plans, and unions. With nearly a decade of experience, Color has served millions of patients and partnered with innovators such as the National Institutes of Health, the CDC, large public health departments, and more.