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JSBML
JSBML (Java Systems Biology Markup Language) is an open-source Java (API) for the SBML (Systems Biology Markup Language ) format. Its API strives to attain a strong similarity to the Java binding of the corresponding library libSBML, but is entirely implemented in Java and therefore platform independent. JSBML provides an elaborated abstract type hierarchy, whose data types implement or extend many interfaces and abstract classes from the standard Java library. In this way, JSBML integrates smoothly into existing Java projects, and provides methods to read, write, evaluate, and manipulate the content of SBML documents. __TOC__ Development In May 2009 the SBML team conducted a community survey for requests of potential further software development. It turned out that, even though the library libSBML provides a generated binding for the programming language Java, its internal C code makes it difficult to implement platform independent or Web Start applications. Around th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Andreas Dräger
Andreas Dräger (; born 20 September 1980) is a German bioinformatician who leads the research group for Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens at the University of Tübingen. Education In high school, Dräger was fascinated by computer science and recent advancements in genetics and biotechnology in the late 1990s. When he learned about a new degree program that allowed combining those technologies, he was immediately inspired. So, Dräger studied bioinformatics at the Martin Luther University of Halle-Wittenberg in Halle (Saale) from 2000 to 2006. He worked as an intern for genome sequencing at the Max Planck Institute for Molecular Genetics, Berlin. He prepared his thesis about heavy-metal-resistant bacteria at the microbiology department of the University of Illinois at Chicago. Dräger earned his doctorate at the Center for Bioinformatics in Tübingen (ZBIT), focusing on the dynamic simulation of metabolic networks in a virt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LibSBML
LibSBML is an open-source software library that provides an application programming interface (API) for the SBML (Systems Biology Markup Language ) format. The libSBML library can be embedded in a software application or used in a web servlet (such as one that might be served by Apache Tomcat) as part of the application or servlet's implementation of support for reading, writing, and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++; the library provides API for many programming languages via interfaces generated with the help of SWIG. The libSBML library is free software released under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or any later version. LibSBML was developed thanks to funding from many agencies, particularly the National Institute of General Medical Sciences (NIGMS, USA) as well as the Defense Advanced Research Projects Agency ... [...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] |
Library (computer Science)
In computer science, a library is a collection of non-volatile resources used by computer programs, often for software development. These may include configuration data, documentation, help data, message templates, pre-written code and subroutines, classes, values or type specifications. In IBM's OS/360 and its successors they are referred to as partitioned data sets. A library is also a collection of implementations of behavior, written in terms of a language, that has a well-defined interface by which the behavior is invoked. For instance, people who want to write a higher-level program can use a library to make system calls instead of implementing those system calls over and over again. In addition, the behavior is provided for reuse by multiple independent programs. A program invokes the library-provided behavior via a mechanism of the language. For example, in a simple imperative language such as C, the behavior in a library is invoked by using C's normal func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Tübingen
The University of Tübingen, officially the Eberhard Karl University of Tübingen (german: Eberhard Karls Universität Tübingen; la, Universitas Eberhardina Carolina), is a public research university located in the city of Tübingen, Baden-Württemberg, Germany. The University of Tübingen is one of eleven German Excellence Universities. The University of Tübingen is especially known as a centre for the study of plant biology, medicine, law, archeology, ancient cultures, philosophy, theology, and religious studies as well as more recently as center of excellence for artificial intelligence. The university's noted alumni include presidents, EU Commissioners, and judges of the Federal Constitutional Court. The university is associated with eleven Nobel laureates, especially in the fields of medicine and chemistry. History The University of Tübingen was founded in 1477 by Count Eberhard V (Eberhard im Bart, 1445–1496), later the first Duke of Württemberg, a civic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java APIs
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's most populous island, home to approximately 56% of the Indonesian population. Indonesia's capital city, Jakarta, is on Java's northwestern coast. Many of the best known events in Indonesian history took place on Java. It was the centre of powerful Hindu-Buddhist empires, the Islamic sultanates, and the core of the colonial Dutch East Indies. Java was also the center of the Indonesian struggle for independence during the 1930s and 1940s. Java dominates Indonesia politically, economically and culturally. Four of Indonesia's eight UNESCO world heritage sites are located in Java: Ujung Kulon National Park, Borobudur Temple, Prambanan Temple, and Sangiran Early Man Site. Formed by volcanic eruptions due to geologic subduction of the Austral ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Example Output When Reading An SBML File From The SBML Test Suite With JSBML
Example may refer to: * '' exempli gratia'' (e.g.), usually read out in English as "for example" * .example, reserved as a domain name that may not be installed as a top-level domain of the Internet ** example.com, example.net, example.org, example.edu, second-level domain names reserved for use in documentation as examples * HMS ''Example'' (P165), an Archer-class patrol and training vessel of the Royal Navy Arts * ''The Example'', a 1634 play by James Shirley * ''The Example'' (comics), a 2009 graphic novel by Tom Taylor and Colin Wilson * Example (musician), the British dance musician Elliot John Gleave (born 1982) * ''Example'' (album), a 1995 album by American rock band For Squirrels See also * * Exemplar (other), a prototype or model which others can use to understand a topic better * Exemplum, medieval collections of short stories to be told in sermons * Eixample The Eixample (; ) is a district of Barcelona between the old city (Ciutat Vella) and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tree (graph Theory)
In graph theory, a tree is an undirected graph in which any two vertices are connected by ''exactly one'' path, or equivalently a connected acyclic undirected graph. A forest is an undirected graph in which any two vertices are connected by ''at most one'' path, or equivalently an acyclic undirected graph, or equivalently a disjoint union of trees. A polytreeSee . (or directed tree or oriented treeSee .See . or singly connected networkSee .) is a directed acyclic graph (DAG) whose underlying undirected graph is a tree. A polyforest (or directed forest or oriented forest) is a directed acyclic graph whose underlying undirected graph is a forest. The various kinds of data structures referred to as trees in computer science have underlying graphs that are trees in graph theory, although such data structures are generally rooted trees. A rooted tree may be directed, called a directed rooted tree, either making all its edges point away from the root—in which case it is call ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Virtual Machine
A Java virtual machine (JVM) is a virtual machine that enables a computer to run Java programs as well as programs written in other languages that are also compiled to Java bytecode. The JVM is detailed by a specification that formally describes what is required in a JVM implementation. Having a specification ensures interoperability of Java programs across different implementations so that program authors using the Java Development Kit (JDK) need not worry about idiosyncrasies of the underlying hardware platform. The JVM reference implementation is developed by the OpenJDK project as open source code and includes a JIT compiler called HotSpot. The commercially supported Java releases available from Oracle are based on the OpenJDK runtime. Eclipse OpenJ9 is another open source JVM for OpenJDK. JVM specification The Java virtual machine is an abstract (virtual) computer defined by a specification. It is a part of java runtime environment. The garbage-collection algorit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, incl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Caltech
The California Institute of Technology (branded as Caltech or CIT)The university itself only spells its short form as "Caltech"; the institution considers other spellings such a"Cal Tech" and "CalTech" incorrect. The institute is also occasionally referred to as "CIT", most notably in its alma mater, but this is uncommon. is a private research university in Pasadena, California. Caltech is ranked among the best and most selective academic institutions in the world, and with an enrollment of approximately 2400 students (acceptance rate of only 5.7%), it is one of the world's most selective universities. The university is known for its strength in science and engineering, and is among a small group of institutes of technology in the United States which is primarily devoted to the instruction of pure and applied sciences. The institution was founded as a preparatory and vocational school by Amos G. Throop in 1891 and began attracting influential scientists such as George Ellery ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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