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BioTapestry
BioTapestry is an open source software application for modeling and visualizing gene regulatory networks (GRNs). History BioTapestry was created at thInstitute of Systems Biologyin Seattle, in collaboration with that thCalifornia Institute of Technology The project was initiated to support the ongoing development of the model of the GRN regulating the development of the endomesoderm in the sea urchin Strongylocentrotus purpuratus. BioTapestry was initially made public in late 2003 as a web-based, read-onlinteractive viewer for the sea urchin network with the first fully functional editor released in August 2004 (v0.94.1). The current version, 7.0.0, was released in September 2014. Development Development work on BioTapestry is ongoing. For more information about version 7.0, see th Usage BioTapestry is an interactive tool for modeling and visualizing gene regulatory networks. Interactive examples from the Davidson Lab. from the Davidson Lab. Mouse ventral neural ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Platform
Java is a set of computer software and specifications developed by James Gosling at Sun Microsystems, which was later acquired by the Oracle Corporation, that provides a system for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. Java applets, which are less common than standalone Java applications, were commonly run in secure, sandboxed environments to provide many features of native applications through being embedded in HTML pages. Writing in the Java programming language is the primary way to produce code that will be deployed as byte code in a Java virtual machine (JVM); byte code compilers are also available for other languages, including Ada, JavaScript, Python, and Ruby. In addition, several languages have been designed to run natively on the JVM, including Clojure, Groovy, and S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LGPL
The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own components. However, any developer who modifies an LGPL-covered component is required to make their modified version available under the same LGPL license. For proprietary software, code under the LGPL is usually used in the form of a shared library, so that there is a clear separation between the proprietary and LGPL components. The LGPL is primarily used for software libraries, although it is also used by some stand-alone applications. The LGPL was developed as a compromise between the strong copyleft of the GNU General Public License (GPL) and more permissive licenses such as the BSD licenses and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visualization (graphic)
Visualization or visualisation (see spelling differences) is any technique for creating images, diagrams, or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and concrete ideas since the dawn of humanity. Examples from history include cave paintings, Egyptian hieroglyphs, Greek geometry, and Leonardo da Vinci's revolutionary methods of technical drawing for engineering and scientific purposes. Visualization today has ever-expanding applications in science, education, engineering (e.g., product visualization), interactive multimedia, medicine, etc. Typical of a visualization application is the field of computer graphics. The invention of computer graphics (and 3D computer graphics) may be the most important development in visualization since the invention of central perspective in the Renaissance period. The development of animation also helped advance visualization. Overview The use of visu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Regulatory Network
A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). The regulator can be DNA, RNA, protein or any combination of two or more of these three that form a complex, such as a specific sequence of DNA and a transcription factor to activate that sequence. The interaction can be direct or indirect (through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Strongylocentrotus Purpuratus
''Strongylocentrotus purpuratus'', the purple sea urchin, lives along the eastern edge of the Pacific Ocean extending from Ensenada, Mexico, to British Columbia, Canada. This sea urchin species is deep purple in color, and lives in lower inter-tidal and nearshore sub-tidal communities. Its eggs are orange when secreted in water. January, February, and March function as the typical active reproductive months for the species. Sexual maturity is reached around two years. It normally grows to a diameter of about 10 cm (4 inches) and may live as long as 70 years. Role in biomedical research The initial discovery of three distinct eukaryotic DNA-dependent RNA polymerases was made using ''S. purpuratus'' as a model organism. While embryonic development is still a major part of the utilization of the sea urchin, studies on urchin's position as an evolutionary marvel have become increasingly frequent. Orthologs to human diseases have led scientists to investigate poten ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. History Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Regulatory Network
A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). The regulator can be DNA, RNA, protein or any combination of two or more of these three that form a complex, such as a specific sequence of DNA and a transcription factor to activate that sequence. The interaction can be direct or indirect (through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionist, reductionism) to biological research. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph Drawing Software
Graph drawing is an area of mathematics and computer science combining methods from geometric graph theory and information visualization to derive two-dimensional depictions of graphs arising from applications such as social network analysis, cartography, linguistics, and bioinformatics. A drawing of a graph or network diagram is a pictorial representation of the vertices and edges of a graph. This drawing should not be confused with the graph itself: very different layouts can correspond to the same graph., p. 6. In the abstract, all that matters is which pairs of vertices are connected by edges. In the concrete, however, the arrangement of these vertices and edges within a drawing affects its understandability, usability, fabrication cost, and aesthetics. The problem gets worse if the graph changes over time by adding and deleting edges (dynamic graph drawing) and the goal is to preserve the user's mental map. Graphical conventions Graphs are frequently drawn as node–li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cross-platform Software
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software requires a separate build for each platform, but some can be directly run on any platform without special preparation, being written in an interpreted language or compiled to portable bytecode for which the interpreters or run-time packages are common or standard components of all supported platforms. For example, a cross-platform application may run on Microsoft Windows, Linux, and macOS. Cross-platform software may run on many platforms, or as few as two. Some frameworks for cross-platform development are Codename One, Kivy, Qt, Flutter, NativeScript, Xamarin, Phonegap, Ionic, and React Native. Platforms ''Platform'' can refer to the type of processor (CPU) or other hardware on which an operating system (OS) or application run ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
