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List Of Systems Biology Visualization Software
Online software Applications References {{Reflist Systems A system is a group of interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its environment, is described by its boundaries, structure and purpose and express ... Systems biology Data visualization software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MEGA, Molecular Evolutionary Genetics Analysis
Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phylomedicine. It is licensed as proprietary freeware. The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the Pennsylvania State University in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura.Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.0, The Pennsylvania State University, University Park, PA. Nei wrote a monograph (pp. 130) outlining the scope of the software and presenting new statistical methods that were included in MEGA. The entire set of computer programs was written by Kumar and Tamura. The personal computers then lacked the ability to send the monograph and software electron ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WikiPathways
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool (PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems. Pathway content Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of Website, websites use JavaScript on the Client (computing), client side ...-centric sister project nameCytoscape.jsthat can be used to analyse and visualise graphs in JavaScript environments, like a browser. History Cytoscape was originally created ... [...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] |
GenMAPP
GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open-source team based in an academic research laboratory. GenMAPP maintains databases of gene identifiers and collections of pathway maps in addition to visualization and analysis tools. Together with other public resources, GenMAPP aims to provide the research community with tools to gain insight into biology through the integration of data types ranging from genes to proteins to pathways to disease. History GenMAPP was first created in 2000 as a prototype software tool in the laboratory of Bruce Conklin at the J. David Gladstone Institutes in San Francisco and continues to be developed in the same non-profit, academic research environment. The first release versi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MATLAB
MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems. As of 2020, MATLAB has more than 4 million users worldwide. They come from various backgrounds of engineering, science, and economics. History Origins MATLAB was invented by mathematician and computer programmer Cleve Moler. The idea for MATLAB was based on his 1960s PhD thesis. Moler became a math professor at the University of New Mexico an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PathVisio
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. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. : History PathVisio was created primarily at Maastricht University and Gladstone Institutes. The software is developed in Java and it's also used as part of the WikiPathways framework as an applet. Starting from version 3.0 (released in 2012) plugins are OSGi compliant and plugin directory describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PV ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systrip
Systrip is a visual environment for the analysis of time-series data in the context of biological networks. Systrip gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process. It had been used to analyze various real biological data. Presentation Systrip is developed in C++ and is based on Tulip Tulips (''Tulipa'') are a genus of spring-blooming perennial herbaceous bulbiferous geophytes (having bulbs as storage organs). The flowers are usually large, showy and brightly coloured, generally red, pink, yellow, or white (usually in war ..., an information visualization framework dedicated to the analysis and visualization of relational data. The Model-View-Controller architecture of Tulip allows Systrip to support multiple and synchronized views. Any interaction on a view (e.g. selection of an element) implies the automatic update of all views displaying this data. In addition to the alg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
