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CompuCell3D
CompuCell3D (CC3D) is an open source software problem solving environment for constructing two- and three-dimensional multiscale agent-based models of multicellular biology, including morphogenesis, homeostasis, disease, therapy and tissue engineering. CompuCell3D was designed to make the development, execution and analysis of complex biological models accessible to non-experts. CompuCell3D is written in C++ and Python. CC3D supports a number of different object classes and modeling methodologies including the Cellular Potts model (CPM) or Glazier-Graner-Hogeweg model (GGH) (originally developed by James A. Glazier, François Graner and Paulien Hogeweg) of the dynamic reorganization of generalized cells (clusters of cells, volumes of extracellular matrix (ECM), cells and their subregions) which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling the diffusion equation a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Cellular Potts Model
In computational biology, a Cellular Potts model (CPM, also known as the Glazier-Graner-Hogeweg model) is a computational model of cells and tissues. It is used to simulate individual and collective cell behavior, tissue morphogenesis and cancer development. CPM describes cells as deformable objects with a certain volume, that can adhere to each other and to the medium in which they live. The formalism can be extended to include cell behaviours such as cell migration, growth and division, and cell signalling. The first CPM was proposed for the simulation of cell sorting by François Graner and James A. Glazier as a modification of a large-Q Potts model. CPM was then popularized by Paulien Hogeweg for studying morphogenesis. Although the model was developed to describe biological cells, it can also be used to model individual parts of a biological cell, or even regions of fluid. Model description The CPM consists of a rectangular Euclidean lattice, where each cell is a subse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Open Source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentralized software development model that encourages open collaboration. A main principle of Open-source software, open source software development is peer production, with products such as source code, blueprints, and documentation freely available to the public. The open source movement in software began as a response to the limitations of proprietary code. The model is used for projects such as in open source appropriate technology, and open source drug discovery. Open source promotes universal access via an open-source or free license to a product's design or blueprint, and universal redistribution of that design or blueprint. Before the phrase ''open source'' became widely adopted, developers and producers used a variety of other terms, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Chemotaxis
Chemotaxis (from ''chemical substance, chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell organism, single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (e.g., glucose) by swimming toward the highest concentration of food molecules, or to flee from poisons (e.g., phenol). In multicellular organisms, chemotaxis is critical to early development (e.g., movement of sperm towards the egg during fertilization) and development (e.g., migration of neurons or lymphocytes) as well as in normal function and health (e.g., migration of White blood cell, leukocytes during injury or infection). In addition, it has been recognized that mechanisms that allow chemotaxis in animals can be subverted during cancer metastasis, and the aberrant change of the overall property of these networks, which contro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Energy
Energy () is the physical quantity, quantitative physical property, property that is transferred to a physical body, body or to a physical system, recognizable in the performance of Work (thermodynamics), work and in the form of heat and light. Energy is a Conservation law, conserved quantity—the law of conservation of energy states that energy can be Energy transformation, converted in form, but not created or destroyed. The unit of measurement for energy in the International System of Units (SI) is the joule (J). Forms of energy include the kinetic energy of a moving object, the potential energy stored by an object (for instance due to its position in a Classical field theory, field), the elastic energy stored in a solid object, chemical energy associated with chemical reactions, the radiant energy carried by electromagnetic radiation, the internal energy contained within a thermodynamic system, and rest energy associated with an object's rest mass. These are not mutual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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. This multifaceted research domain necessitates the collaborative efforts of chemists, biologists, mathematicians, physicists, and engineers to decipher the biology of intricate living systems by merging various quantitative molecular measurements with carefully constructed mathematical models. It represents a comprehensive method for comprehending the complex relationships within biological systems. In contrast to conventional biological studies that typically center on isolated elements, systems biology seeks to combine different biological data to create models that illustrate and elucidate the dynamic interactions with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
GNU General Public License
The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first copyleft license available for general use. It was originally written by Richard Stallman, the founder of the Free Software Foundation (FSF), for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. The licenses in the GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. The GPL is more restrictive than the GNU Lesser General Public License, and even more distinct from the more widely used permissive software licenses such as BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software (FOSS) domai ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Project Jupyter
Project Jupyter (pronounced "Jupiter") is a project to develop open-source software, Open standard, open standards, and services for interactive computing across multiple Programming language, programming languages. It was spun off from IPython in 2014 by Fernando Pérez (software developer), Fernando Pérez and Brian Granger. Project Jupyter's name is a reference to the three core programming languages supported by Jupyter, which are Julia (programming language), Julia, Python (programming language), Python and R (programming language), R. Its name and logo are an Homage (arts), homage to Galileo Galilei, Galileo's discovery of the moons of Jupiter, as documented in notebooks attributed to Galileo. Jupyter is financially sponsored by the Jupyter Foundation. History The first version of Notebooks for IPython was released in 2011 by a team including Fernando Pérez, Brian Granger, and Min Ragan-Kelley. In 2014, Pérez announced a spin-off project from IPython called Project J ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Conda (package Manager)
Conda is an open-source, cross-platform, language-agnostic package manager and environment management system. It was originally developed to solve package management challenges faced by Python data scientists, and today is a popular package manager for Python and R. At first, Anaconda Python distribution was developed by Anaconda Inc.; later, it was spun out as a separate package, released under the BSD license. The Conda package and environment manager is included in all versions of Anaconda, Miniconda, and Anaconda Repository. Conda is a NumFOCUS affiliated project. Features As a package manager, Conda allows users to install different versions of binary software packages and their required software dependencies appropriate for their computing platform from a software repository. Conda checks everything that has been installed, any version limitations that the user specifies (for example, the user wants a specific package to be at least version 2.1.3), and determin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Stuart Newman
Stuart Alan Newman (born April 4, 1945 in New York City) is a professor of cell biology and anatomy at New York Medical College in Valhalla, NY, United States. His research centers around three program areas: cellular and molecular mechanisms of vertebrate limb development, physical mechanisms of morphogenesis, and mechanisms of morphological evolution. He also writes about social and cultural aspects of biological research and technology. Career Stuart Newman graduated from Jamaica High School in Queens, New York. He received an A.B. from Columbia College of Columbia University in 1965, and a Ph.D. in chemical physics from the University of Chicago in 1970, where he worked with the theoretical chemist, Stuart A. Rice. He was a postdoctoral fellow in the Department of Theoretical Biology, University of Chicago and the School of Biological Sciences, University of Sussex, UK, and before joining New York Medical College was an instructor in anatomy at the University of Pennsy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Gabor Forgacs
Gabor Forgacs is a Hungarian theoretical physicist A physicist is a scientist who specializes in the field of physics, which encompasses the interactions of matter and energy at all length and time scales in the physical universe. Physicists generally are interested in the root or ultimate cau ... turned bioengineer turned innovator and entrepreneur. He was educated in Hungary, where he earned a MS and a PhD in theoretical physics at the Lorand Eotvos University in Budapest, respectively, in 1972 and in 1976. He started his scientific career at the Central Research Institute for Physics in Budapest in condensed matter physics under the supervision of Alfred Zawadowsky. In 1978 he became the Candidate of Physical Sciences title awarded by the Hungarian National Academy. in 1978 he joined Dr. Harry Frisch at the State University of New York in Albany as a Postdoctoral Fellow and in 1979 moved to the University of Illinois at Urbana-Champaign as a Postdoctoral Fellow in the group ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Indiana University, Bloomington
Indiana University Bloomington (IU Bloomington, Indiana University, IU, IUB, or Indiana) is a public research university in Bloomington, Indiana, United States. It is the flagship campus of Indiana University and its largest campus, with over 48,000 students. Established as the state's seminary in 1820, the name was changed to "Indiana College" in 1829 and to "Indiana University" in 1838. Indiana University is a member of the Association of American Universities and is classified among "R1: Doctoral Universities – Very high research activity". Its schools and programs include the Jacobs School of Music, Kelley School of Business, School of Education, Luddy School of Informatics, O'Neill School of Public and Environmental Affairs, School of Public Health, School of Medicine, School of Nursing, Hutton Honors College, The Media School, and Maurer School of Law. The campus also features the Lilly Library, Eskenazi Museum of Art, and the Indiana Memorial Union. Indiana athlet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
University Of Notre Dame
The University of Notre Dame du Lac (known simply as Notre Dame; ; ND) is a Private university, private Catholic research university in Notre Dame, Indiana, United States. Founded in 1842 by members of the Congregation of Holy Cross, a Catholic religious order of priests and brothers, Campus of the University of Notre Dame, the main campus of 1,261 acres (510 Hectare, ha) has a suburban setting and contains landmarks such as the Main Building (University of Notre Dame), Golden Dome main building, Basilica of the Sacred Heart (Notre Dame), Sacred Heart Basilica, the Grotto of Our Lady of Lourdes, Notre Dame, Grotto of Our Lady of Lourdes, the Word of Life (mural), Word of Life mosaic mural, and Notre Dame Stadium. Notre Dame is Carnegie Classification of Institutions of Higher Education, classified among "R1: Doctoral Universities – Very high research activity". The university is organized into seven schools and colleges: Notre Dame College of Arts and Letters, College of Art ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
