Miranda NG is an open-source multiprotocol instant messaging application, designed for Microsoft Windows. Miranda NG is free software distributed under the GNU GPL-2.0-or-later.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
NASA WorldWind is an open-source virtual globe. According to the website, "WorldWind is an open source virtual globe API. WorldWind allows developers to quickly and easily create interactive visualizations of 3D globe, map and geographical information. Organizations around the world use WorldWind to monitor weather patterns, visualize cities and terrain, track vehicle movement, analyze geospatial data and educate humanity about the Earth." It was first developed by NASA in 2003 for use on personal computers and then further developed in concert with the open source community since 2004. As of 2017, a web-based version of WorldWind is available online. An Android version is also available.
OpenSceneGraph is an open-source 3D graphics application programming interface, used by application developers in fields such as visual simulation, computer games, virtual reality, scientific visualization and modeling.
A GIS software program is a computer program to support the use of a geographic information system, providing the ability to create, store, manage, query, analyze, and visualize geographic data, that is, data representing phenomena for which location is important. The GIS software industry encompasses a broad range of commercial and open-source products that provide some or all of these capabilities within various information technology architectures.
Quartz Composer is a node-based visual programming language provided as part of the Xcode development environment in macOS for processing and rendering graphical data.
Graph Modeling Language (GML) is a hierarchical ASCII-based file format for describing graphs. It has been also named Graph Meta Language.
ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation. Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multiple imaging system data comparisons to automated hematology systems. ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing.
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
BioPAX is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
Fiji is an open source image processing package based on ImageJ2.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
The National Center for Integrative Biomedical Informatics (NCIBI) is one of seven National Centers for Biomedical Computing funded by the National Institutes of Health's (NIH) Roadmap for Medical Research. The center is based at the University of Michigan and is part of the Center for Computational Medicine and Bioinformatics. NCIBI's mission is to create targeted knowledge environments for molecular biomedical research to help guide experiments and enable new insights from the analysis of complex diseases. It was established in October 2005.
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.
Icinga is an open-source computer system and network monitoring application. It was created as a fork of the Nagios system monitoring application in 2009.
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.
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.
Flutter is an open-source UI software development kit created by Google. It can be used to develop cross platform applications from a single codebase for the web, Fuchsia, Android, iOS, Linux, macOS, and Windows. First described in 2015, Flutter was released in May 2017. Flutter is used internally by Google in apps such as Google Pay and Google Earth as well as by other software developers including ByteDance and Alibaba.
Obsidian is a personal knowledge base and note-taking software application that operates on Markdown files. It allows users to make internal links for notes and then to visualize the connections as a graph. It is designed to help users organize and structure their thoughts and knowledge in a flexible, non-linear way. The software is free for personal use, with commercial licenses available for pay.
