All Topics
.NET
Computational platforms / 3 projects
The Microsoft .NET Framework is a software framework for Microsoft Windows operating systems. It includes a large library, and it supports several programming languages which allows language interoperability (each language can utilize code written in other languages.) The .NET library is available to all the programming languages that .NET supports. (Source: http://en.wikipedia.org/wiki/.NET_Framework))
3ds Max
Visualisation and data handling software / 1 project
Abaqus
Simulation software / 2 projects
Acoustics
Physical Systems and Engineering simulation / 9 projects
Acoustics is the interdisciplinary science that deals with the study of sound, ultrasound, infra-sound (all mechanical waves in gases, liquids, and solids). This topic covers the development or the use of computational methods for predicting the production, propagation, absorption and perception of acoustic waves. This has many applications including transport noise (aircraft, trains), musical acoustics as well as medical applications (ultrasound and lithotripsy). For more information see http://en.wikipedia.org/wiki/Acoustics
Actran
Simulation software / 1 project
Actran is a suite of general purpose CAD software for acoustical engineering developed by FFT (http://www.fft.be). It includes different modules for vibro-acoustics, aerodynamic noise sources, and flow acoustics. And it can be interfaced with a variety of meshing tools as well as pre- and post-processing tools. Its main applications include aircraft noise (including nacelle design), automotive engineering, helicopter turbine noise, air conditioning systems and ducted cooling systems (electronic devices). More information can be found at http://www.fft.be.
Agents
Algorithms and computational methods / 19 projects
An agent-based model (also sometimes related to the term multi-agent system or multi-agent simulation) is a class of computational models for simulating the actions and interactions of autonomous agents (both individual or collective entities such as organizations or groups) with a view to assessing their effects on the system as a whole. It combines elements of game theory, complex systems, emergence, computational sociology, multi-agent systems, and evolutionary programming. Monte Carlo Methods are used to introduce randomness. ABM's are also called individual-based models. (More from Wikipedia).
Image shows an ant trail.
Aimsun
Simulation software / 1 project
Aimsun is a commercially available transport microsimulation package developed by TSS, Transport Simulation Systems. Like other traffic microsimulation tools, Aimsun provides a temporospatial simulation of vehicle behaviour in road networks - meaning that vehicles are modelled moving through the network obeying existing models of car following, lane changing and gap acceptance behaviour. Barcelo (2010) provides a useful overview of the intrinsic models used by Aimsun in comparison to other available tools and is recommended to anyone reviewing approaches to traffic simulation.
From a modelling and simulation perspective, the exceptional aspect of Aimsun is the powerful API which allows modellers to vary individual vehicle routes, speeds and lanes. This means that new route choice or car following models can be easily inserted in to a traffic microsimuation.
Air-traffic Control
Socio-technological System simulation / 1 project
AMBER
Simulation software / 5 projects
Amber, an acronym for Assisted Model Building with Energy Refinement, is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals. (Read more on Wikipedia).
Amira
Visualisation and data handling software / 2 projects
Amira is a visualisation and data analysis tool. Data can be from many modalities, from image stacks to mesh surfaces.
Ansys
Simulation software / 3 projects
Antimicrobial Interaction with Cell Membranes
Visualisation and data handling software / 6 projects
Antimicrobial peptides (AMPs) are known to disrupt the membranes of bacterial cells such as E. coli. I work on investigating the nature of these interactions using molecular dynamics (MD) simulations.
AnyLogic
Simulation software / 1 project
AnyLogic is able to include Agent-based, discrete-event and systems-dynamics logic easily. Also features pedestrian, road and train libraries. See http://www.xjtek.com.
ArcGIS
Visualisation and data handling software / 5 projects
ArcGIS is a suite of Geographic Information System software produced by ESRI. It is one of the most commonly used pieces of GIS software, and includes various components which can run on desktops, servers and PDAs.
ArcGIS provides a large number of processing tools for dealing with spatial data, in both raster and vector formats. These processing tools can be extended by the use of models created in the ArcGIS Model Builder, or by writing extensions in a number of programming languages including Python and any .Net language.
Archaeology
Socio-technological System simulation / 3 projects
Archaeology is the study of past human societies, primarily through the recovery and analysis of the material culture and environmental data which they have left behind, which includes artifacts, architecture, biofacts and cultural landscapes. Renfrew, C. & Bahn, P. G. (1991), Archaeology: Theories, Methods, and Practice, London: Thames and Hudson Ltd
Artificial Neural Networks
Algorithms and computational methods / 4 projects
Astrophysics
Physical Systems and Engineering simulation / 5 projects
Astrophysics is broadly characterized as the physics of non-terrestrial objects. This could include small objects in our solar system or, through cosmology, the study of the entire universe. At present most projects here study extreme astronomical objects such as black holes, neutron stars and accretion disks.
Avizo
Visualisation and data handling software / 3 projects
Bioinformatics
Life sciences simulation / 15 projects
Bioinformatics is the storage, manipulation and processing of biological data using computers. This topic includes all modelling of "omics" data - genomics (DNA), proteomics (protein), transcriptomics (mRNA), metabolomics (metabolites) etc. - as well as "classical" sequence analysis (multiple sequence alignment, homology searching, phylogenetic etc.). Bioinformatics projects will usually make use of in vitro and/or in vivo experimental data.
Biomathematics
Life sciences simulation / 4 projects
Biomathematics deals with applying mathematical and computational techniques to synthesize new scientific knowledge about biological systems. The areas which we are working on range from modelling cancer growth and chemotherapy to mathematical modelling of soil-plant-atmosphere continuum.
Biomechanics
Physical Systems and Engineering simulation / 7 projects
Biomedical
Life sciences simulation / 17 projects
The Biomedical topic covers all projects modelling medical or disease processes in order to develop or improve treatments and therapeutics. This topic includes rational drug design, clinical trials and modelling the molecular basis of disease, inlcuding genetic and epigenetic contributions.
Biomolecular Organisation
Life sciences simulation / 6 projects
Biomolecular simulations
Life sciences simulation / 13 projects
Blender
Visualisation and data handling software / 1 project
Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License.
Built Environment
Socio-technological System simulation / 2 projects
C
Programming languages and libraries / 30 projects
C is a imperative programming language developed in 1972 by Dennis Ritchie at the Bell Telephone Laboratories. It is one of the most popular languages of all time and influenced deeply other popular programming languages such as C++ and Java. The language was designed to reduce the need for assembly language: it can be compiled to fast binary code and allows low-level control of the machine, still being portable among very different computer architectures. For this reason, it is still widely used in high performance computing. A good review of the language, its features and design goals are provided here.
C#
Programming languages and libraries / 4 projects
C++
Programming languages and libraries / 30 projects
C++ is a general-purpose, strongly-typed programming language, with notable support for object-oriented and generic programming. C++ has an ISO standard, and the current version is C++03, which is C++98 with very minor revisions. A major rehaul, provisionally termed C++0x, is planned for 2011.
A good overview (and more) of the language can be found in Bruce Eckel's Thinking in C++, the PDF of which can be downloaded for free HERE. Another recommended read is The C++ Programming Language by Bjarne Stroustrup who created the language. This book cannot be downloaded for free, but for anyone with a serious interest in the subject, I highly recommend having a paper copy.
CAESAR
Simulation software / 1 project
CAESAR (The Cellular Automation Evolutionary Slop and River Model) is a two dimensional flow and sediment transport model, developed by Professor Tom Coulthard in the University of Hull. It can simulate morphological changes in river catchment or reaches, on a flood by flood basis, over periods up to several thousands of years.
CASTEP
Simulation software / 1 project
CFD
Physical Systems and Engineering simulation / 32 projects
The approaches of Computational Fluid Dynamics (CFD) have been developing very fast within the recent decades. Now CFD as a tool is used in many areas, for example, see the list of the projects below.
Note the CFD surgery session provided by Dr Xie.
Chroma
Programming languages and libraries / 4 projects
From the project's webpage:
The Chroma package supports data-parallel programming constructs for lattice field theory and in particular lattice QCD. It uses the SciDAC QDP++ data-parallel programming (in C++) that presents a single high-level code image to the user, but can generate highly optimized code for many architectural systems including single node workstations, multi-threaded SMP workstations, clusters of workstations via QMP, and classic vector computers.
Classification
Algorithms and computational methods / 3 projects
Classification is the method of assigning items to groups (known as classes) based on information about the items. This can be done manually, but is often done automatically by algorithms such as K-Means or Maximum Likelihood, based upon quantitative information about the items.
Classification techniques can be split into two types:
Unsupervised classification can be performed with no a-priori knowledge of the data. For example, a satellite image could be classified into different land-cover classes based entirely on the spectral information inherent in the image, without any human input about what the classes should be.
Supervised classification requires some input about the classes into which the data should be split. For example, the supervised classification equivalent of the example above would be to give the classification routine a list of classes, with examples of the spectra of pixels that fit into those classes. The classification algorithm would then use this training data when classifying the rest of the data.
Classification is a technique that is used in many areas of research. Some fields, such as Remote Sensing/Earth Observation, use classification as a fundamental processing technique, whereas in many other fields data is classified to enable easy visualisation and statistical analysis.
Climate
Physical Systems and Engineering simulation / 5 projects
Climate science covers the physics of the atmosphere, oceans and ice sheets, along with chemistry and biology of the land surface and the oceans, from the surface to the abyss. A fundamental challenge is to understand the basic processes of the modern climate system alongside the evidence for different past climates on Earth and the prospects for future climate change. The study of climate has been transformed through a growing appreciation of the integral role that climate plays in our lives, and in particular the prospect of substantial climate change during a human lifetime. The socio-economics of climate change is increasingly important as evidence mounts for both anthropogenic influences on climate and climatic impacts on economies and societies. A wide range of computational models are used to study climate processes, climate change, and climate impacts. Due to the multi-disciplinary nature of climate problems, a correspondingly wide range of individuals and groups across the university are engaged in this topic.
Combustion
Physical Systems and Engineering simulation / 2 projects
Complex fluids
Physical Systems and Engineering simulation / 5 projects
Complex Systems
Transdisciplinary tags / 36 projects
Complexity Science is an attempt to better understand systems in which aggregate, system-level behaviour arises from the interactions between component parts in a way that is not straightforward. Whereas the temperature of an ideal gas is just a simple average over the kinetic energy of its component molecules, the "temperature" of a football crowd or the temperature of the earth do not behave in the same way. Adding some more energy to some of the gas molecules will increase the macroscopic temperature proportionally. By contrast, adding a little more "heat" to a few members of a football crowd can result in a disproportionate, or non-linear, change in behaviour, sometimes bringing about macroscopic surges, songs, and even Mexican waves. This kind of interesting relationship between the individual components of a system and the system's global behaviour is characteristic of many important and intriguing domains: ecosystems, brains, cities, markets, the internet, etc.
The growing significance of understanding and managing such systems means that Complexity Science is increasingly being recognised as a critical area of enquiry by industry, government and science itself.
For more information, click here.
Computer Science
Transdisciplinary tags / 12 projects
Computer Science covers a wide range of research in addition to Software Engineering, Programming and Scientific Computation.
This topic tag is intended to be used for seminars that are too generic to be described by more specific tags, but fall into the Computer Science remit.
COMSOL
Simulation software / 6 projects
Condor
Computational platforms / 1 project
CVS
Software Engineering Tools / 13 projects
CVS is a simple revision control system for managing large projects. Freely available and robust - included as standard in typical Linux and Mac distributions, and a standard Windows implementation would be TortoiseCVS. Alternatives with some advantages include subversion, git, or Mercurial.
Data Management
Visualisation and data handling methods / 5 projects
Both experimental measurements and simulation results can produce substantial amounts of data that need to be postprocessed, analysed, and stored for archival or subsequent analysis at a later point. Databases are good at storing relatively small amounts of data with logical connections but often simulation or experimental data sets are very large (of the order of gigabytes (GB) or terabytes (TB)).
Depending on the cost of an experiment of the cost of performing a computer simulation, the resulting data need to be stored and made available, using different hardware, software and networking technologies.
Image: 512MB Harddisk source
Database
Visualisation and data handling methods / 6 projects
Research on databases and data storage, including linking metadata to flat files and other datastores, management of large datasets, distribution, access and security.
Density functional Theory
Algorithms and computational methods / 6 projects
Design
Transdisciplinary tags / 5 projects
Developmental Biology
Life sciences simulation / 4 projects
Developmental biology is the study of how organisms grow and develop throughout their life. Topics include the genetic and epigenetic influences on cell growth/differentiation and morphogenesis.
Distributed computing
Algorithms and computational methods / 1 project
Distributed computing involves spreading a computational task across multiple processors, nodes, or agents, each with some degree of autonomy. The idea is that "many hands make light work", and there can also be advantages in terms of robustness when compared to traditional centralized architectures. Message-passing systems are employed so that nodes can communicate with each other as required, but excessive levels of communication will negate the speed advantage of the distributed computing approach. Major research challenges include the design of algorithms that effectively break a problem into sub-tasks that can be worked on with a minimum of inter-node communication, and optimizing the way in which sub-tasks are allocated to particular nodes.
e-Research
Transdisciplinary tags / 3 projects
E-Research/E-Science is computationally intensive science and research that is carried out in highly distributed network environments, or research that uses immense data sets that require grid computing; the term sometimes includes technologies that enable distributed collaboration, such as the Access Grid.
The term eScience was created by John Taylor, the Director General of the United Kingdom's Office of Science and Technology in 1999 and was used to describe a large funding initiative starting in November 2000. Examples of the kind of science include social simulations, particle physics, earth sciences and bio-informatics. (Source: eScience on Wikipedia)
Earth Observation
Physical Systems and Engineering simulation / 2 projects
This topic consists of research on analysing and processing data from Earth Observation systems, typically satellite and airborne imagery platforms. One particular area of focus is atmospheric correction techniques, which aim to remove the effect of the atmosphere on satellite and airborne imagery. Analysis of the efficacy of these correction techniques can involve significant computer modelling, data assimilation and statistical visualisation.
Much other research within Earth Observation/Remote Sensing involves significant computer modelling, often including the processing of extremely large datasets.
Software which is frequently used in Earth Observation research includes ENVI (a remote sensing data processing package), IDL (a scientific programming language linked with ENVI) and Erdas Imagine (another remote sensing data processing package).
Earth surface dynamics
Physical Systems and Engineering simulation / 5 projects
Earth surface dynamics is the study of geomorphic patterns and landforms, along with their interactions with each other and the surrounding environment. This topic includes projects examining environments dominated by aeolian, coastal, fluvial, glacial, periglacial, volcanic, etc. processes, or a combination of these.
Eclipse
Software Engineering Tools / 10 projects
Ecology
Life sciences simulation / 9 projects
Ecology is the study of organisms, populations and their interactions with each other and the environment. This topic includes projects on biogeography, ecosystems (the combined physical and biological components of an environment), animal behaviour and food webs.
Economic Networks
Socio-technological System simulation / 4 projects
Networks can be used to represent the interaction patterns between different entities. This topic includes projects modelling the categorisation of economic interaction structures, their formation and how they can affect the overall system.
Related Links:
Economics
Transdisciplinary tags / 1 project
Economics refers to the production, distribution and consumption of goods and services. It investigates how economies work and how economic agents interact. It is most typically associated with the study of finance and business, but covers a wide range of topics including health, politics, crime and education.
Elasticity
Physical Systems and Engineering simulation / 3 projects
Elastic matter is a mathematical description of solid matter such as rubber, steel, or a neutron star crust. Like fluid mechanics, it is a continuum theory which assigns a density, velocity, and (for example) internal energy density to each point in space.
However, in addition to fluid mechanics, there is a also a memory of an unstressed state at each point in space. The internal energy is lowest in this unstressed state, and so there is an elastic force that wants to return the matter to this state.
Fluid mechanics can be seen as a limit of elastic matter where there is no memory and where the stress tensor is the unit tensor times the pressure.
Electromagnetism
Physical Systems and Engineering simulation / 6 projects
Emacs
Software Engineering Tools / 13 projects
Energy
Physical Systems and Engineering simulation / 9 projects
ENVI
Visualisation and data handling software / 2 projects
ENVI is a commercial remote sensing and image processing software package. It is developed by ITTVIS, and is currently at version 4.7. It provides an environment for displaying and processing remotely sensed data, and includes a large number of processing tools (such as image filtering, topographic modelling and image classification), all of which are accessible through a graphical user interface.
ENVI is written in IDL, and has an extensive IDL application programming interface, thus allowing ENVI's processing tools to be called from IDL programs. This then allows processing to take place with no user input, making these batch processing tasks suitable for use on High Performance Computing systems such as Iridis.
ENVI can be extended by writing IDL code, and a number of extensions (some of which have been developed by members of the University of Southampton) have been released for free at the ITTVIS Code Library.
At the University of Southampton, ENVI is available on all staff UDE machines (it can be installed from Start->All Programs->Additional Software), and a number of student workstation clusters.
Environmental hazards
Life sciences simulation / 4 projects
Environmental hazards manifest themselves in a variety of forms and as such research into the causes and effects of them is often multidisciplinary in nature, requiring some understanding of the terrestrial, aquacultural, or environmental impact and system function. A diverse suite of technical tools from geospatial data analysis to complex numerical models can be used to solve practical problems in watershed modelling, ecosystem science, wildlife ecology, water resource management, landscape ecology, pollution control, conservation biology and land use or land cover dynamics.
Epidemiology
Life sciences simulation / 1 project
Epidemiology is concerned with studying illness and disease in populations. Major concerns of epidemiology include modelling the spread and control of infectious diseases (e.g. flu), and identifying risk factors for common diseases (e.g. heart disease and cancer).
For more information, see the Epidemiology page on Wikipedia.
Epigenetics
Life sciences simulation / 3 projects
Epigenetics referes to the study of biological processes that regulate gene transcription within the cell that are heritable mitoticaly and/or meioticaly but that do not involve changes in the DNA sequence. This include regulation of DNA packaging within the nucleus through chromatin remodelling involving histone modifications and chemical changes to the DNA itself such as cytosine methylation.
Within the Faculty of Medicine there are several groups generating large data sets assessing DNA methylation genome-wide utilising both array based platforms and direct sequencing of bisulphite converted DNA. Analysis of DNA methylation variation between individuals in relation to disease state adds an order of magnitude in complexity to genome wide association analysis of DNA sequence variation as methylation values are quantitative rather than binary and vary over time, between tissues and with environmental exposure.
Evolution
Life sciences simulation / 9 projects
Evolution is the change of replicating entities through time due to descent with modification. This topic includes projects modelling the fundamental processes and forces that drive evolution itself, as well as projects that make use of evolutionary theory to make predictions and inferences about current organisms and biomolecules, particularly DNA and protein. This topic also covers Population Genetics. Evolution is not to be confused with morphogenesis, which can be a gradual change with time but does not involve replication.
Evolutionary Algorithms
Algorithms and computational methods / 6 projects
FFT
Algorithms and computational methods / 13 projects
Finite volume
Algorithms and computational methods / 12 projects
Flight simulation
Physical Systems and Engineering simulation / 3 projects
FLOWer
Simulation software / 1 project
Block-Structured Navier-Stokes Solver FLOWer
- solution of RANS equations for arbitrary moving bodies
- well adapted for external flows around aircaft-like configurations in subsonic, transonic and supersonic flow region
- efficient solver on vector & parallel computers
- computer platform independent
- high flexibility through discontinous block interfaces and overlapping grid technique (Chimera)
- inverse design option, adjoint solver for aerodynamic optimization
- development performed by a joined team from DLR, universities, Airbus Germany and EADS-M
- comprehensively validated
- routinely used by German Aircraft Industry, DLR and several Universities
Fluent
Simulation software / 1 project
Fortran
Programming languages and libraries / 34 projects
Game Theory
Algorithms and computational methods / 6 projects
Game theory is a branch of mathematics that describes rational or optimal conduct in strategic situations, i.e., situations in which more than one agent is involved and the payoff for a particular strategy employed by one agent is dependent on what the other agent (or agents) will do. As such, game theory has been particularly useful in economics, evolutionary biology, ecology, and artificial intelligence.
General Relativity
Physical Systems and Engineering simulation / 3 projects
We study the gravitational wave forms that radiate from either single or merging compact objects.
Geographic Information Systems
Algorithms and computational methods / 8 projects
Geographic information systems (which are sometimes known as geospatial information systems) are a set of tools that allow researchers to capture, store, analyse, manage, and present many types of data that are linked to geographical locations. They are extremely powerful systems for analysis of spatial data and are often used to support policy formulation and decision making from local to international scales. A typical visual output from a GIS is shown to the right, where flood model output data for the Meklong River has been overlaid on Landsat satellite imagery so that the flood extent and potential impacts can be analysed.
Git
Software Engineering Tools / 4 projects
Git is a distributed version control system.
Some useful documentation can be found on the Git website. For those familiar with SVN this guide may be useful.
Gnuplot
Visualisation and data handling software / 16 projects
Gnuplot is a command line plotting program to generate 2-D and 3-D plots of mathematical functions and data. Gnuplot can be used to visualise results directly on the screen or to create figures in a wide variety of output formats (from vectorial formats such as EPS, PDF, SVG to raster formats such as PNG and JPG). When launched, Gnuplot offers a prompt where commands can be entered interactively. Commands can be abbreviated, making Gnuplot a valuable tool for quick-plotting. Example. "p x" can be used as an abbreviation for "plot x" to plot the function f(x) = x. Example. "plot 'data.dat' using 1:2 with lines" can be abbreviated as "p 'data.dat' u 1:2 w l".
GPU
Computational platforms / 6 projects
GPU-libs
Programming languages and libraries / 3 projects
Graph Theory
Algorithms and computational methods / 3 projects
Gromacs
Simulation software / 8 projects
GSL
Programming languages and libraries / 6 projects
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.
The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
Unlike the licenses of proprietary numerical libraries the license of GSL does not restrict scientific cooperation. It allows you to share your programs freely with others.
For more information, follow this link: http://www.gnu.org/software/gsl/
HDF5
Visualisation and data handling software / 7 projects
HDF5 is a technology suite that makes possible the management of extremely large and complex data collections through:
A versatile data model that can represent very complex data objects and a wide variety of metadata.
A completely portable file format with no limit on the number or size of data objects in the collection.
A software library that runs on a range of computational platforms, from laptops to massively parallel systems, and implements a high-level API with C, C++, Fortran 90, and Java interfaces.
A rich set of integrated performance features that allow for access time and storage space optimizations. Tools and applications for managing, manipulating, viewing, and analyzing the data in the collection.
Heat transfer
Physical Systems and Engineering simulation / 2 projects
HECToR
Computational platforms / 16 projects
HiPSTAR
Simulation software / 3 projects
The High-Performance Solver for Turbulence and Aeroacoustic Research (HiPSTAR) is currently being developed as part of the Royal Academy of Engineering/EPSRC research fellowship. The code is tailored to be particularly efficient for axisymmetric flows by employing generalized cylindrical coordinates and making a significant effort to minimize the memory requirement of the code in light of severe bandwidth limitations imposed by current multi core architectures. The code includes the following features: i) highly (wavenumber resolution) optimized 4th-order accurate compact differences, ii) a spectral method for the azimuthal direction (enabling a state-of-the-art axis treatment that exploits parity conditions of individual Fourier modes), iii) ultra low-storage 4th-order Runge-Kutta time integration, iv) skew-symmetric splitting of the nonlinear terms, v) non-reflective characteristic boundary conditions, and vi) domain decomposition in the streamwise and radial directions using an MPI parallelization. The parallel efficiency of HiPSTAR has been extensively tested on various computing platforms and excellent performance was achieved on HECToR for up to 14,208 cores. In a current CRAY centre of excellence project, the code is being converted to a hybrid OMP/MPI parallelisation.
HPC
Transdisciplinary tags / 27 projects
High Performance Computing (HPC). There are at least two ways of interpreting HPC: either as the computational hardware that is used, or as the process of simulating things using a lot of computational power.
We use this tag as a general reference to HPC which is useful for events and work that is too generic to be associated with more particular HPC-relevant tags such as MPI, etc.
The main computational HPC resource at the University of Southampton is Iridis 3 as shown in image (Picture Ash Bennette).
HPCx
Computational platforms / 5 projects
Human environment interaction
Socio-technological System simulation / 5 projects
Throughout history, the establishment, development, interaction and migration of civilizations have been significantly shaped by availability of appropriate climate and natural resources. However, since the industrial revolution human societies increasingly impact and – in many cases – effectively dominate (and often diminish) capacities of the Earth System to regulate climate, biogeochemical cycles and biodiversity in ways that are essential to human life itself. This has recently raised considerable concerns relating to sustainable use and conservation of natural resources. These can be attributed to: (i) insufficient understanding of essential ecological processes acting across multiple time- and spatial scales – which can result in a disparity between those scales of ecological processes and scales of human resource use; and (ii) the fact that human behaviour is traditionally based on narrow and conflicting short-term interests and goals, resulting (inter alia) in high discount rates for future environmental costs and temporal mismatches and disruptions between ecological, social and economic processes. Human societies and their constitutive economic, legal and political institutions drive (both directly and indirectly) changes in our environment and the crucial ecological services that we depend upon. However, the linkages and feedback mechanisms are not always well defined.
Human population
Socio-technological System simulation / 3 projects
The understanding of human population characteristics and behaviour lies at the heart of many of the biggest challenges facing society. Important aspects of human populations are not directly measurable at every point in time and space, hence typical sources are a mix of census-type data, administrative records and incomplete observational data. These measurements may often be sufficient to describe some aspects of population (for example the geographical distribution of residential population on census day) but do not provide sufficient insight into other essential dimensions (for example daytime population distributions, travel behaviour, patterns of wealth or wellbeing). Better representation of the population underlies many research and policy challenges such as resource allocation, service delivery, transportation planning and the calculation of prevalance rates. Computational modellign work in this field ranges across data collection, representation and modelling of population, particularly simulation and computation of those characteristics which cannot be directly measured. It includes computational methods for the design of optimal zoning systems and the creation of time-specific probabilistic geographical population distributions, microsimulation of individual-level characteristics and future projections.
IDL
Visualisation and data handling software / 2 projects
IDL is a commercial scientific programming language originally created by RSI, and now developed by ITTVIS. It is an array-based language, and provides functionality similar to that of Matlab and Numpy.
It is frequently used for projects in Remote Sensing/Earth Observation and Astrophysics as it is particularly good at image processing, and has a very close integration with ENVI.
IfLS
Transdisciplinary tags / 1 project
The Institute for Life Sciences represents a University-wide multidisciplinary collaboration drawing together expertise in science and engineering, with a shared goal to apply scientific discovery to the grand challenges of the day. The Institute's mission is to facilitate fusions of expertise in education and research from a range of disciplines, in order to broaden scientific opportunities.
For more information, please visit: http://www.soton.ac.uk/ifls/
ImageJ/Fiji
Visualisation and data handling software / 1 project
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.
It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
Inverse problems
Algorithms and computational methods / 3 projects
Iridis
Computational platforms / 74 projects
The University of Southampton Major HPC facility is Iridis 3 with more then 8000 processing cores capable of over 72 TFlops. Iridis was ranked 74th in the world in the semi-annual independent ranking of the TOP 500 Supercomputers.
To add your research project to this list, follow these instructions and select the Iridis tag (under "Computational Platforms").
Jaguar
Computational platforms / 1 project
The Jaguar Cray XT5 is a leadership class supercomputer run by the National Center for Computational Science at Oak Ridge National Laboratory, on behalf of the US Department of Energy. It is highly ranked in the top500 list of the world's fastest supercomputers. Very large allocations of computing time can be obtained through competitive application processes such as the ASCR's annual INCITE awards. Note that allocations are available for world leading open scientific research, and applicants do not need to be from US institutions.
Java
Programming languages and libraries / 17 projects
Java is an object-oriented programming language originally developed by Sun Microsystems. Through the use of a "virtual machine" approach, Java allows programs written on one computing architecture (e.g., Linux) to be run on another (e.g., Windows). Java also has a relatively simple and clean syntax and has been a popular language on introductory programming courses.
Jung
Visualisation and data handling software / 2 projects
JUNG — the Java Universal Network/Graph Framework--is a software library that provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network. It is written in Java, which allows JUNG-based applications to make use of the extensive built-in capabilities of the Java API, as well as those of other existing third-party Java libraries.
Read more at http://jung.sourceforge.net/
Landscape evolution
Physical Systems and Engineering simulation / 4 projects
Landscape evolution encompasses a wide range of simulated environments, from purely geomorphic systems, to biological systems or a combination of these. Importantly it examines how these systems change through time, with different environmental forcings.
Lattice Field Theory
Algorithms and computational methods / 4 projects
Lattice QCD (QCD is a field theory) is a non-perturbative approach to compute physical observables from first principles. It can be viewed as way of computing path integral correlation functions numerically and is based on Monte Carlo simulations.
The appeal is not only that it is a method from first principals, but also that it is possible to access information that cannot be obtained by experiments. Simple results like particle spectra are always a starting point before tackling more complicated observables like distribution amplitudes or form factors that may provide insights into fundamental parameters like CKM matrix elements.
Wikipedia claims: "Lattice QCD has also been proposed as a possible benchmark for high-performance computing."
Linux
Computational platforms / 65 projects
Linux is the free, UNIX-like operating system consisting of a kernel, originally written by Linux Torvalds, and the GNU utilities.
Today, there are many popular Linux distributions available, to run on devices from mobile phones to supercomputers, including Iridis. They typically provide a rich variety of software in addition to the base operating system. Examples include ubuntu and Red Hat Enterprise Linux.
Liquid crystals
Physical Systems and Engineering simulation / 1 project
Physics textbooks normally identify as the three phases of matter, the solid, liquid and vapour phases. Liquid Crystals are a different state of matter which exhibit a degree of order between that of a fluid and a solid: its molecules are not in a fixed position, as is the case of liquids, but may have very similar orientations, as is the case of crystals.
The ordered orientation makes these material birefringent, the change the polarisation of the light travelling through them. This property gives rise to beautiful patterns of light when thin liquid crystal layers are seen through cross-polarisers, as in the photo on the right. The different colours are caused by the fact that the liquid crystal is a liquid and so, the average orientation of its molecules, changes across the sample. The change of orientation can be controlled by applying an electric field: at the flick of a switch the alignment can change drastically and, for example, change the thin layer from transparent to opaque. This is the principle at the heart of liquid crystal displays.
For more information on liquid crystals see
http://www.southampton.ac.uk/maths/research/projects/Classicaloptics.page?
Lyceum
Computational platforms / 6 projects
Lyceum is one of High Performance Computing facilities in the University of Southampton aimed for student projects. It is a Linux Cluster composed of the head node and 16 compute nodes, which can reach 1.3 TFlops performance.
You can find more information on getting started and available software on iSolution's Lyceum page. Current usage of Lyceum is reflected on Status page.
Mac OS X
Computational platforms / 23 projects
Mac OS X is the current operating system that is shipped with Apple Macintosh computers (see Wikipedia entry on Mac OS X).
It is based on UNIX and popular with some computational scientist as it provides the power of the Linux/UNIX terminal well integrated with a graphical interface.
Many GNU Linux tools and applications have been ported to Mac OS (see for example the finkproject and macports).
Magnetohydrodynamics
Physical Systems and Engineering simulation / 1 project
Magnetohydrodynamics (MHD) studies electrically charged fluids. It is a continuum theory and hence most useful for studying the interaction of large scale electrical or magnetic fields with objects that can be described by the Navier-Stokes or Euler equations.
Magnonics
Physical Systems and Engineering simulation / 1 project
Magnonics studies travelling excitations (waves) in magnetic materials. As in phononics and photonics, periodic variations in material properties can be used to design waveguides through bandgaps. Potential applications include data processing and communication.
Maple
Programming languages and libraries / 3 projects
Marine Renewable Energy
Physical Systems and Engineering simulation / 4 projects
Wave and tidal energy systems offer a considerable energy resource if suitable systems that are robust and cost-effective can be developed. Computational design methods associated with structural analysis, system dynamics and fluid dynamics are required. It is in the complex interaction between these computationally intensive analysis techniques and their surrounding environment that is of considerable relevance to CMG
Materials
Physical Systems and Engineering simulation / 10 projects
Theory, methods and computational algorithms for simulating matter at lenghtscales (and relevant timescales) from atomic to nano to meso at levels of detail ranging from full ab initio quantum mechanics, to classical atomistic, to coarse-grained to continuum models.
Problems we study using these techniques include molecules (e.g. drugs, catalysts, fuels), crystalline and amorphous materials (e.g. semiconductors, alloys), nanostructures (e.g. carbon nanotubes, nanocrystals), biomolecules and biomolecular assemblies (DNA, protein-drug complexes, cell components).
Mathematica
Programming languages and libraries / 3 projects
Matlab
Programming languages and libraries / 39 projects
Mayavi
Visualisation and data handling software / 5 projects
Mayavi (version 1, version 2) is a tool for easy and interactive visualization of (mostly 3d) data, providing seamless integration with Python scientific libraries.
It uses the Visualisation ToolKit (VTK) for the actual 3d rendering, and allows to create visualisations interactively and script based.
The Mayavi logo (as used on the Mayavi2 home page http://code.enthought.com/projects/mayavi/) has been produced by members of the Southampton Computational Modelling Group.
Medical Imaging
Life sciences simulation / 1 project
Medical imaging plays a vital role in analysing, modelling and understanding biological systems. Technologies such as computed tomography (CT), magnetic resonance imaging (MRI), and a wide range of associated techniques (DEXA, RSA, etc) play a major role in clinical diagnosis and planning. Researchers at Southampton use medical imagining techniques and data for a wide range of modelling purposes. With the computational modelling group, researchers are concerned with the challenges of processing this large volume of medical imaging data, filtering and sampling to handle data artifacts, and processing to extract useful information from these data sets.
MEMS
Physical Systems and Engineering simulation / 2 projects
Mercurial
Software Engineering Tools / 5 projects
Mercurial is a cross-platform, distributed revision control tool for software developers. It is mainly implemented using the Python programming language, but includes a binary diff implementation written in C.
Mercurial is primarily a command line program but graphical user interface extensions are available. All of Mercurial's operations are invoked as keyword options to its driver program hg, a reference to the chemical symbol of the element mercury.
Mercurial's major design goals include high performance and scalability, decentralized, fully distributed collaborative development, robust handling of both plain text and binary files, and advanced branching and merging capabilities, while remaining conceptually simple. It includes an integrated web interface. (Read more from Wikipedia.
Metals
Physical Systems and Engineering simulation / 4 projects
Micromagnetics
Physical Systems and Engineering simulation / 7 projects
Micromagnetics (also called Micromagnetism) is a continuum description of the behaviour of the magnetisation vector field in ferromagnetic structures of the size of micrometres and below.
Major applications are the study and design of magnetic storage media. Ferrogmagnetic nanostructures also play an important rule in emerging fields such as spintronics, where the spin of electrons is used to convey information, and not the charge (as is the case in "electronics").
Microsoft Azure
Computational platforms / 1 project
Molecular Dynamics
Algorithms and computational methods / 14 projects
The molecular dynamics method.
Molecular Mechanics
Algorithms and computational methods / 4 projects
Molecular Mechanics (also known as Newtonian Mechanics) is one of the simplest methods of calculating the total energy of a molecular system, by combining the attractive energy of electrostatic and non-polar interactions, with the repulsive energy of steric geometry. Its speed of calculation makes it both a good candidate for multi-scale simulations, biomolecular dynamics and as a precursor to more advanced calculations, such as Quantum Mechanical methods.
Image taken from http://www.chem.ucla.edu/c125/NIH/MolMechanics.htm
Monte Carlo
Algorithms and computational methods / 18 projects
The Monte Carlo simulation methods (MC methods) are a class of computation algorithms which rely on the use of random number sampling and probability statistics to investigate problems. They are particularly useful in exploration of problems which are too complicated to solve analytically. The algorithms may vary, but there is a general pattern they follow; first the inputs are defined and are further generated randomly from a probability distribution, a deterministic computation on these inputs are performed, and finally the results are collected.
Applications include, among others, applied statistics and games, computational biology, mathematics, physics and astrophysics, as well as finance and business, and risk analysis.
Figure: MC method used to approximate the value of number PI. (Example source: http://en.wikipedia.org/MCintro).
MPI
Programming languages and libraries / 27 projects
The message passing interface for parallel execution.
MS Office Access
Visualisation and data handling software / 2 projects
Microsoft Office Access is the (pseudo-)relational database application for Windows that is part of the Microsoft Office suite of applications.
Multi-scale
Algorithms and computational methods / 18 projects
Multi-scale simulations and multi-scale simulation methodology.
A recurrent pattern in materials simulation is that the smallest length scale simulation (ab-initio in the extreme case) provides the highest accuracy but can only be used for very small systems (i.e. small physical dimensions and short periods of time). Larger scale represenatations (such as atomistic modelling like Molecular Dynamics up to continuum descriptions of matter) are used to describe larger and macroscopic systems. The major challenge of multi-scale modelling is how to bridge between the model descriptions at different length scales.
Similar multi-scale modelling challenges arise in modelling of other systems ranging from production processes and complete devices to social systems.
Multigrid solvers
Algorithms and computational methods / 3 projects
Multipole methods
Algorithms and computational methods / 1 project
Fast multipole methods were introduced in Greengard and Rokhlin's seminal paper in the Journal of Computational Physics in 1987, in which they reduced an O(N-squared) evaluation of the potential and force fields in N-body systems with Coulombic or gravitational potentials to an O(N) computation. They have since become a popular tool in many fields of computational science and modelling, having applications to N-body problems with various potential functions as well as electromagnetic scattering and incompressible fluid dynamics.
MySQL
Visualisation and data handling software / 3 projects
Nanoscale Assemblies
Life sciences simulation / 3 projects
NetLogo
Simulation software / 1 project
NetLogo is a programmable modelling environment for simulating natural and social phenomena. It is particularly well suited for modelling complex systems developing over time. Modellers can give instructions to hundreds or thousands of agents, all operating independently. This makes is possible to explore the connections between the micro-level behaviour of individuals and the macro-level patterns that emerge from the interaction of many individuals.
Written in Java, NetLogo was developed by Uri Wilensky in 1999, and has been in continuous development ever since at the Center for Connected Learning and Computer-Based Modeling. http://ccl.northwestern.edu/netlogo/
Neuroscience
Life sciences simulation / 5 projects
Neuroscience is an interdisciplinary science that studies the nervous system. Neuroscience projects range from electrophysiology on single nerve cells to complex biological and physcological interactions. More information on the breadth of Neuroscience activities at the Univseristy of Southampton can be found at the Southampton Neuroscience Group (SoNG) homepage: http://www.southampton.ac.uk/song/.
NextGen Sequencing
Life sciences simulation / 4 projects
Next Generation Sequencing (NextGen or NGS) covers all the high-throughput nucleotide sequencing technologies and applications that are replacing traditional Sanger sequencing. Applications of NGS include genome/exome sequencing or resequencing, digital transcriptomics, metagenomics and various RNASeq applications. Sequencing capacity is exploding at a rate that far out-strips increases in computational capacity; NGS has shifted the bottleneck for many of these applications from one of data generation to one of data management and processing. This topic is for all CMG members with interests in facilitating, generating or exploiting NGS data.
Local Wiki and Forums (restricted access).
Nmag
Simulation software / 7 projects
The Nmag micromagnetic simulation framework has been developed at the University of Southampton since 2005, and has been made available as open source in November 2007.
Noweb
Software Engineering Tools / 1 project
Noweb is a literate programming tool. Its main advantage over alternative tools is independence of the programming language being used. For details see this paper.
Oceanography
Physical Systems and Engineering simulation / 3 projects
Onetep
Simulation software / 3 projects
ONETEP is a linear-scaling density functional theory software package able to run on parallel computers[1]. It uses a basis of non-orthogonal generalized Wannier functions (NGWFs) expressed in terms of periodic cardinal sine (psinc) functions, which are in turn equivalent to a basis of plane-waves. ONETEP therefore combines the advantages of the plane-wave approach (controllable accuracy and variational convergence of the total energy with respect to the size of the basis) with computational effort that scales linearly with the size of the system [2]. The ONETEP approach involves simultaneous optimization of the density kernel (a generalization of occupation numbers to non-orthogonal basis, which represents the density matrix in the basis of NGWFs) and the NGWFs themselves. The optimized NGWFs then provide a minimal localized basis set, which can be considerably smaller than the unoptimized basis sets used in most approaches.
ONETEP has been developed by a group of UK academics based at Cambridge University, Southampton University and Imperial College London. It is available free to UK academics, and licenses can be obtained for non-UK academic usage from the developers or through Accelrys' Materials Studio package.
Official website: http://www2.tcm.phy.cam.ac.uk/onetep/Main/HomePage Wikipedia entry: http://en.wikipedia.org/wiki/ONETEP
OpenFOAM
Simulation software / 7 projects
OpenFOAM is a free, open source CFD software package produced by a commercial company, OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Read more from http://www.openfoam.com/features/
OpenMP
Programming languages and libraries / 3 projects
Operations Research
Socio-technological System simulation / 2 projects
Optimisation
Algorithms and computational methods / 12 projects
Optimisation is a wide range of approaches, tools and techniques to select the "best" configuration among a set of available alternatives for a given system with respect to a predefined (set of) objective(s). Applications are vast, ranging from telecommunication networks, transportation systems, climate models to biology, economics, mechanics and engineering. Some of the well-known optimisation techniques include mathematical modelling, multiobjective programming, stochastic programming, simulation and (meta)heuristic algorithms and iterative methods.
ParaView
Visualisation and data handling software / 10 projects
ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.
ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
ParaView reads VTK files, and is built on the VTK library.
Cross Wind Fire Simulation. Image courtesy of Sandia Labs.
PETSc
Programming languages and libraries / 4 projects
PETSc (the Portable, Extensible Toolkit for Scientific Computation) is an open source library for scientific computations written in C. It provides a generic framework to manipulate vectors and sparse or dense matrices, solve linear systems, etc. It offers a unified interface to a variety of different algorithms and implementations. In other words, a unique interface is provided as a frontend for different algorithms which can be selected either adding a switch to the command line or by calling an appropriate function. PETSc is built on top of BLAS/LAPACK and MPI to offer high performance and parallelisation capabilities. It comes with built-in monitoring tools to understand and remove the inefficiencies in the user's high performance computing code. Features include: parallel vectors, parallel matrices, several sparse storage formats easy, scalable parallel preconditioners, Krylov subspace methods, parallel Newton-based nonlinear solvers, parallel timestepping (ODE) solvers, support for Nvidia GPU cards, complete documentation, automatic profiling of floating point and memory usage, consistent user interface, intensive error checking, portable to UNIX and Windows, over one hundred examples. See the website: http://www.mcs.anl.gov/petsc/petsc-as/index.html.
Photonics
Physical Systems and Engineering simulation / 9 projects
ProtoMS
Simulation software / 2 projects
ProtoMS is a Monte Carlo simulation package for biomolecular simulations. The code is capable of simulating three different ensembles; NPT, NVT and mVT. In addition, it is capable of performing lambda-dynamics, TI and FEP.
Pylab
Visualisation and data handling software / 3 projects
Matplotlib (also known as Pylab) is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (not too dissimilar from matlab or mathematica), web application servers, and six graphical user interface toolkits.
Matplotlib tries to make easy things easy and hard things possible. It can generate plots, histograms, power spectra, bar charts, errorcharts, scatterplots, etc, with just a few lines of code. For a sampling, see the screenshots, thumbnail gallery with source code, and examples directory. (More from Matplotlib home page.)
The image has been produced using this code
PyTables
Visualisation and data handling software / 2 projects
PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is a Python module and provides a pythonic interface to the HDF5 library.
Python
Programming languages and libraries / 35 projects
Python is a general-purpose high-level programming language. Its design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive. Its use of indentation as block delimiters is unusual among popular programming languages.
QCD
Physical Systems and Engineering simulation / 4 projects
Large scale computer simulations of the strong nuclear force, or Quantum Chromodynamics (QCD) allow us to test the Standard Model of particle physics, understand quark confinement, explore extremes of density and temperature and constrain models of new physics. The fundamental constituent quarks and gluons are not seen experimentally. Instead we must understand how the particles we do detect emerge as complicated bound states of the constituents. Computations on a discretised chunk of space-time, the lattice, are the only known way to establish this connection from first principles and can involve the largest national and international HPC facilities. We are part of the RBC-UKQCD collaboration which designed and built special-purpose QCDOC computers for lattice simulations. QCDOC design features were taken up in IBM's BlueGene systems. Members of our collaboration are now working on successor systems in collaboration with IBM.
Case Study: weak matrix elements
The weak interaction can change the identities of quarks, but because of strong interactions between quarks and gluons the fundamental quark interactions lead to decays of bound-state particles into other particles. Lattice QCD simulations can evaluate the strengths of these decays and thereby probe the underlying quark interactions. Calculations of kaon decays to pairs of pions allow us to test CP-violation, the breaking of the combination of particle-antiparticle and mirror reflection symmetry, whose understanding is bound up with the dominance of matter over antimatter in the Universe. Lattice calculations of weak decays involving bottom quarks will be tested with unprecedented precision at the recently-restarted Large Hadron Collider in Geneva and could provide clues to new physics beyond the current Standard Model.
Quantum Chemistry
Algorithms and computational methods / 2 projects
Quantum Dynamics
Physical Systems and Engineering simulation / 1 project
R
Programming languages and libraries / 8 projects
R is a free, open source, platform independent programming language for statistics and publication quality graphics. It is supported by a highly active user community that develops open source code, much of which is available at the Comprehensive R Archive Network. R is widely used in bioinformatics, with numerous libraries available as part of the BioConductor project.
See the R Project homepage for more information.
Redmine
Software Engineering Tools / 1 project
Redmine is a flexible project management web application. Written using Ruby on Rails framework, it is cross-platform and cross-database. Redmine is open source and released under the terms of the GNU General Public License v2 (GPL).
It supports Wikis, Forums, tickets (issues), Documents, News, links to version control repositories.
Scientific Computing
Transdisciplinary tags / 32 projects
The general area of computation of numerical solutions to mathematical models of systems under investigation. Often read as being related to the mathematics of numerical analysis, but in some parts of the community understood in a similar way as computational modelling.
Sediment transport
Physical Systems and Engineering simulation / 5 projects
Sediment transport simulations examine the movement of solid particles within a liquid or gas. This can include transport within the natural or built environments, for example coastal, marine, fluvial or aeolian transport, or transport within a chemical or water treatment plant.
Semiconductors
Physical Systems and Engineering simulation / 3 projects
Semiconductors, and especially Si, are the basic building block of the transistor and all the processing power that comes with its implementation. Commercial finite element TCAD (Technology computer aided design) software is used from different vendors (Silvaco, Synopsys) to simulate the fabrication and electrical characteristics of individual transistors. Higher up the hierarchy, Electronic CAD shows the behaviour of circuits consisting of millions (billions) of nominal identical transistors with quantisation related parameter fluctuation. On a more fundamental level, density functional theory is used to calculate the intrinisc properties of Si and e.g. its properties undre passivation by hydrogen.
Sensor Networks
Socio-technological System simulation / 2 projects
Sensors
Physical Systems and Engineering simulation / 2 projects
Shelddon
Simulation software / 1 project
Shelddon is a finite element library developped by the french national research centre INRIA. It is part of the Modulef project, an open-source finite element package available at: http://www-rocq.inria.fr/modulef/. Modulef is written in Fortran 77. Even if the core of Shelddon rely upon Modulef, the package is not open-source. Compared to Modulef, major differences are constituted by the implementation of shells MITC non-linear elements and by dynamic Newmark type routines.
Simpleware
Visualisation and data handling software / 1 project
Simpleware offers world-leading software and services for the conversion of 3D image data into high-quality CAD, Rapid Prototype, CFD and Finite Element models.
Social and Socio-economic Systems
Socio-technological System simulation / 8 projects
Social and socio-economic systems are those in which people interact with each other, often within cultural and economic institutions and structures. As individuals, developing an implicit understanding of the systems that we are embedded within is key to our ability to operate as human beings. As academics, developing an explicit understanding of these systems presents a major challenge. How do languages, markets, families, and firms, and systems of care, education and governance come about, interact, change and evolve? What keeps these systems stable? Why do they sometimes fail? By exploring how social and socio-economic systems such as these work, we aim to improve our ability to manage our social world.
Social Networks
Socio-technological System simulation / 9 projects
People are linked by relationships - friendships, animosities, commercial agreements, social contracts, partnerships, familial ties, shared interests, etc. Social scientists of many kinds are interested in understanding the nature of these relationships, how they form, change, dissolve and influence social activity. The importance of these questions is increasing in a world where social behaviour is mediated by an increasing number of technologies and has an impact on an increasing number of
By treating a set of people and the relationships between them as a social network, we are able to approach these research questions using mathematics and simulation modelling in addition to empirical and analytic tools more typical of the social sciences. Combining these methods allows us to explore not only the structure and make-up of the social networks around us, but to understand how those networks arise and evolve over time.
Software Engineering
Transdisciplinary tags / 12 projects
Software Engineering is concerned with the process of designing, implementing and maintaining software efficiently. There is overlap with the Computer Science, Project Management and Systems Engineering. As the field is relatively young, it is still in considerable flux. Good software engineering skills are undoubtedly crucial in developing computational modelling simulation tools.
See also Software Engineering Tools
Image taken from Mercurial Book
SPICE
Simulation software / 1 project
Spitfire
Computational platforms / 2 projects
SQL Azure
Visualisation and data handling software / 1 project
Star CCM+
Simulation software / 4 projects
The two major CFD products of CD-Adapco: Star-CD and Star-CCM+ are used in U Southampton for research and teaching purposes.
Note the CFD surgery session (http://www.personal.soton.ac.uk/zxie/CFD-SURG/CFD-SURG.htm) provided by Dr Xie.
StarCD
Simulation software / 3 projects
Stochastic Pi Calculus
Algorithms and computational methods / 1 project
Developed by Microsoft Research, the Stochastic Pi Machine (SPiM) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems.
Documentation and an on-line simulator can be downloaded from the MSR Stochastic Pi Machine website
Structural biology
Life sciences simulation / 6 projects
Structural biology is concerned with the physical and mechanical properties of biological molecules, including proteins, nucleotides, lipids, drugs and other small molecules. Topics include computational techniques for interpreting experimental data (e.g. NMR and X-Ray crystallography) as well as methods for predicting structure and function in the absence of experimental data (e.g. homology modelling and molecular dynamics).
Image courtesy: Phil Williamson
Structural dynamics
Physical Systems and Engineering simulation / 9 projects
Superconductivity
Physical Systems and Engineering simulation / 4 projects
Superconductors are materials that show no electrical resistance if the temperature drops below a critical value. High temperature superconductors are studied for two reasons: (i) to support the design and realisation of practical systems and devices such as for example magnets for Magnetic Resonanz Imaging (MRI), and (ii) to learn about static and dynamic properties of the vortex matter which are an example of a system of interacting objects with competing interactions, and provided rich and complex behaviour.
Image: System studied in PhysRevB. 67, 174508 (2003)
Superfluidity
Physical Systems and Engineering simulation / 1 project
Superfluidity is a quantum-mechanical phenomenon in which a fluid is able to flow without friction or viscosity. It is realised at low temperatures and densities. They enable the macroscopic study of quantum effects including quantised vortices. Interesting examples include atomic Bose-Einstein Condensates and liquid Helium.
SVN
Software Engineering Tools / 24 projects
In software development, (Apache) Subversion (command name svn) is a revision control system initiated in 2000 by CollabNet Inc. Developers use Subversion to maintain current and historical versions of files such as source code, web pages, and documentation. Its goal is to be a mostly-compatible successor to the widely used Concurrent Versions System (CVS). (More from Wikipedia))
Systems biology
Life sciences simulation / 13 projects
Systems Biology is the study of whole biological systems rather than individual components in isolation. The focus is on discovering emergent system properties that cannot be easily determined using a "sum of the parts" approach. Systems biology typically makes use of high throughput "Omics" technologies. This topic include projects modelling networks of interactions between genes, proteins, cells or whole organisms as well as the interaction between different levels of organisation.
TecPlot
Visualisation and data handling software / 10 projects
TELEMAC
Simulation software / 1 project
Tissue Engineering
Life sciences simulation / 2 projects
Trac
Software Engineering Tools / 1 project
Trac is an enhanced wiki and issue tracking system for software development projects. Trac uses a minimalistic approach to web-based software project management. It's mission is to help developers write great software while staying out of the way. Trac should impose as little as possible on a team's established development process and policies. It provices an interface to subversion repositories.
Transport
Socio-technological System simulation / 7 projects
Tribology
Physical Systems and Engineering simulation / 3 projects
Turbulence
Physical Systems and Engineering simulation / 11 projects
UKHadron
Programming languages and libraries / 4 projects
UKHadron is UKQCD's software package for Lattice QCD. It builds on top of Chroma using it as a library and is meant to provide an easier approach to coding the actual physics.
See for example: link
Value-driven design
Socio-technological System simulation / 3 projects
VG Studio Max
Visualisation and data handling software / 1 project
Vim
Software Engineering Tools / 5 projects
Vim is a text editor released by Bram Moolenaar in 1991 for the Amiga computer. The name "Vim" is an acronym for "Vi IMproved" because Vim was created as an extended version of the vi editor, with many additional features designed to be helpful in editing program source code.
Although Vim was originally released for the Amiga, Vim has since been developed to be cross-platform, supporting many other platforms. It is the most popular editor amongst Linux Journal readers.
Released under a software license compatible with the GNU General Public License, Vim is free and open source software.
Read more from Wikipedia. Image taken from same Wikipedia site.
Virtual Earth
Visualisation and data handling software / 1 project
VisIt
Visualisation and data handling software / 4 projects
VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways.
VisIt is based on the VTK libraries and reads VTK data files.
Image: Courtesy of Visit Documentation
Visual Python
Visualisation and data handling software / 3 projects
Visual Python (VPython) a 3D graphics module for the Python programming language called "Visual" originated by David Scherer in 2000. VPython makes it easy to create navigable 3D displays and animations, even for those with limited programming experience. Because it is based on Python, it also has much to offer for experienced programmers and researchers.
Voxel imaging
Visualisation and data handling methods / 4 projects
Voxel (volume elements) imaging essentially encompasses all truly volumetric imaging modalities. Among many other techniques there is particular high interest in voxel imaging using X-ray computed tomography at the School of Engineering Sciences due to the current formation of the µ-VIS (Micro-tomographic Volume Imaging at Southampton) centre.
VTK
Visualisation and data handling software / 6 projects
The Visualisation ToolKit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python.
VTK is used in visualisation tools such as VisIt, ParaView and MayaVi.
Wave propagation
Physical Systems and Engineering simulation / 5 projects
Waves are disturbances that propagate through space and time. Examples include mechanical waves in solid and fluids (water waves, sound and vibrations), electromagnetic waves (light, radio waves, etc.), gravitational waves. This topic covers any work aiming to understand and/or predict the interference between multiple waves, scattering by obstacles, and refraction by inhomogeneities. Applications are found in many areas of science and engineering, for instance astrophysics, biomedical applications, acoustical engineering, ship science, etc. For more information see http://en.wikipedia.org/wiki/Wave
Windows
Computational platforms / 39 projects
Xmgrace
Visualisation and data handling software / 14 projects
Grace is a free WYSIWYG 2D graph plotting tool, for Unix-like operating systems. The package name stands for "GRaphing, Advanced Computation and Exploration of data." Grace uses the X Window System and Motif for its GUI. It has been ported to VMS, OS/2, and Windows 9*/NT/2000/XP (on Cygwin). In 1996, Linux Journal described Xmgr (an early name for Grace) as one of the two most prominent graphing packages for Linux. (more from Wikipedia)