Computational Modelling Group

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 / 9 projects

Acoustics

Physical Systems and Engineering simulation / 13 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.

Advanced Materials

Physical Systems and Engineering simulation / 5 projects

Advanced materials include nanomaterials and devices, metamaterials, composites and functional materials. Research is conducted, for example, to develop advanced nanoelectronics that combine functional nanomaterials which couple stress, electric polarisation, magnetization, photonic and thermal properties. Similarly, metamaterials in photonics, magnonics and photonics, which can be used for a wide range of applications, including sensors, actuators, tailored waveguides, data storage, and data processing open new opportunities. Advanced materials are a major component of UK exports.

Agent-Based Negotiation

Algorithms and computational methods / 3 projects

Agents

Algorithms and computational methods / 48 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 / 9 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 / 4 projects

AnyLogic

Simulation software / 2 projects

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 / 12 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 / 5 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

ARCHER

Computational platforms / 9 projects

Artificial Neural Networks

Algorithms and computational methods / 10 projects

Astrophysics

Physical Systems and Engineering simulation / 16 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 / 6 projects

AWK

Programming languages and libraries / 2 projects

AWK is a s a small, C-style programming language designed for text processing and typically used as a data extraction and reporting tool. It is a standard feature of most Unix-like operating systems. Many UNIX utilities generates rows and columns of information, AWK is an excellent tool for processing these rows and columns, and is easier to use AWK than most conventional programming languages.

Bioinformatics

Life sciences simulation / 35 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. For informal bioinformatics discussion/networking at Southampton, please visit the UoS Bioinformatics facebook group.

Biomathematics

Life sciences simulation / 12 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 / 14 projects

Biomechanics is the study of the structure and function of biological systems, using methods from engineering mechanics. Areas included under this topic are musculoskeletal modelling, orthopaedics, cardiovascular biomechanics and soft tissue modelling. Since many bioogical systems are complex, it can be beneficial to use engineering methods to calculate approximations of their mechanical behaviour.

Biomedical

Life sciences simulation / 33 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.

Biometrics

Physical Systems and Engineering simulation / 2 projects

Biomolecular Organisation

Life sciences simulation / 11 projects

Biomolecular simulations

Life sciences simulation / 24 projects

Blender

Visualisation and data handling software / 2 projects

Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License.

Boost

Programming languages and libraries / 2 projects

Boundary elements

Algorithms and computational methods / 6 projects

The boundary element method.

Built Environment

Socio-technological System simulation / 4 projects

C

Programming languages and libraries / 64 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 / 5 projects

C++

Programming languages and libraries / 68 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 / 4 projects

Catalysis

Physical Systems and Engineering simulation / 2 projects

Cellular automata

Algorithms and computational methods / 15 projects

Cellular Automata methods

CFD

Physical Systems and Engineering simulation / 60 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 / 8 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 / 14 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.

Cloud computing

Computational platforms / 4 projects

Microsoft Windows Azure provides users with the ability to provision virtual machines, called workers. A worker can be configured to run any code or application supported by the base operating system (Windows Server 2008 R2), other operating systems are available and there are administrator restrictions. Our experience has shown that provisioning a worker takes 15min--30min, but once provisioned it is possible to upgrade the worker in under 5min.

Provisioning a worker is managed by the Azure fabric and involves building a virtual machine, allocating hardware, booting the operating system and starting the user-defined code. Upgrading a worker involves halting the user-defined code, loading new code and restarting the execution, hence it is much quicker than provisioning. Workers come in various sizes and the costs are proportional to capability. We often utilise small workers, but extra large workers with eight times the RAM and CPU capability are available. Currently cloud computing does not support low latency networking such as Myrinet or Infiniband, so often each worker is treated as a standalone piece of computation. Windows Azure provides persistent scalable storage in the form of blob storage which can be accessed by workers. As each worker is independent we are using Azure message queues to coordinate tasks between workers.

We are using Windows Azure for:

  • Space Situational Awareness
  • accelerating the development of algorithms, for example a meshless local weak-strong form method (MLWSFM) for computational electromagnetics
  • and various Windows Phone 7 (WP7) related projects

colour perception

Visualisation and data handling methods / 1 project

How humans perceive colour. This is important in desiging colour maps to accurately display data.

Combustion

Physical Systems and Engineering simulation / 4 projects

Complex fluids

Physical Systems and Engineering simulation / 13 projects

Complex Systems

Transdisciplinary tags / 128 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.

Computational Social Science

Transdisciplinary tags / 4 projects

The use of 'big data' for a wide range of social science research. The term was coined by Lazer et al in Science. 2009 February 6; 323(5915): 721–723.

Computer Science

Transdisciplinary tags / 39 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.

Computer Vision

Algorithms and computational methods / 1 project

COMSOL

Simulation software / 13 projects

Condor

Computational platforms / 1 project

Continuous Integration

Software Engineering Tools / 3 projects

Cosmology

Physical Systems and Engineering simulation / 3 projects

Cosmology, is widely regarded as the scientific study of the origin, lifetime, and ultimate fate of our universe. This includes vast study on models of The Big Bang and inflationary scenarios, as well as the ongoing search for dark energy.

(Image credit: NASA/WMAP Science Team)

Crowdsourcing

Transdisciplinary tags / 1 project

Crowdsourcing is the outsourcing of a task to a large, often distributed, group of people, namely a crowd. This technique if often used in scientific research and aims at capitalising on the different knowledge and expertise a disparate group of people may have, as well as on the access to different resources, including time and a certain geographical location. A task, for example, may require the presence of the executor in very different locations, and may therefore be hard for an individual to perform. On the contrary, a large group of geographically distributed people may complete it in short time and at a very low cost. The term was coined by Jeff Howe in 2006; the practise has become common with the advent of the Internet, which facilitates the creation of online communities of connected users, reducing the effect of geographical, social and cultural bounds. For more information also consult the wikipedia entry on crowdsourcing.

CUDA

Programming languages and libraries / 7 projects

CUDA Fortran

Programming languages and libraries / 3 projects

CVS

Software Engineering Tools / 14 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 Acquisition

Physical Systems and Engineering simulation / 6 projects

Data Acquisition (abbreviated DAQ) is the process of collection of real-world signals and conversion of the resulting samples into digital numeric values that can be manipulated by a computer. Data Acquisition systems can also form part of a process control system, data logging and monitoring.

DAQ systems come in many different technology forms and in a vast range of implementations from small USB device connected to PC to millions of synchronised electronic channels in detectors on Large Hadron Collider at CERN.

Data Aggregation

Visualisation and data handling methods / 4 projects

Summarising data in various ways to reduce size, complexity or to reduce risk of disclosure if the data refers to people

Data Management

Visualisation and data handling methods / 18 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

Data Science

Transdisciplinary tags / 4 projects

Data Science is an interdisciplinary field about processes and systems to extract knowledge or insights from data in various forms, either structured or unstructured,[1][2] which is a continuation of some of the data analysis fields such as statistics, data mining, and predictive analytics, similar to Knowledge Discovery in Databases (KDD). (See more from Wikipedia )

Database

Visualisation and data handling methods / 10 projects

Research on databases and data storage, including linking metadata to flat files and other datastores, management of large datasets, distribution, access and security.

Delft3D

Simulation software / 1 project

Demand Response

Transdisciplinary tags / 1 project

Density functional Theory

Algorithms and computational methods / 15 projects

Design

Transdisciplinary tags / 11 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.

Diffusion

Physical Systems and Engineering simulation / 9 projects

Diffusion is a wide-spread phenomenon with prime examples being the diffusive behaviour of, say, salt or some chemical substance, in a liquid, or the spread of heat through a sample.

Diffusion of heat animation

(Animation has been taken from http://en.wikipedia.org/wiki/File:Heat_eqn.gif)

Digital Economy

Transdisciplinary tags / 2 projects

Digital Humanities

Transdisciplinary tags / 3 projects

Digital Humanities is a transdisciplinary research direction which uses computational and digital media to study culture and history. For more information please visit the SotonDH website.

Distributed computing

Algorithms and computational methods / 7 projects

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.

Docker

Computational platforms / 1 project

Docker is a containerization software that communicates directly with the Linux kernel of the host machine, making unnecessary to simulate a complete operating system. It is therefore widely used in servers as an alternative to virtual machines.

Docker can also be used to speed up the shipping of complex applications and to achieve reproducible computing, as it allows the creation of a common computing environment where everyone has access to the same tools.

A basic introduction can be found here.

e-Research

Transdisciplinary tags / 7 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 / 8 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 / 14 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.

ECCE

Visualisation and data handling software / 1 project

Extensible Computational Chemistry Environment

"The Extensible Computational Chemistry Environment (ECCE, pronounced "etch-ā") provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies."

http://ecce.emsl.pnl.gov/

Eclipse

Software Engineering Tools / 21 projects

Ecology

Life sciences simulation / 25 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 / 6 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 / 8 projects

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.

Education

Transdisciplinary tags / 2 projects

The learning and teaching of computational science.

Computational Modelling requires a wide set of skills: ranging from the analysis of the real-world system and the derivation of a suitable model, to the numerical method of solving the model equations, to the actual implementation to carry out this computation. A substantial effort is often the preparation of a simulation (for example through mesh generation) and the subsequent data analysis and visualisation.

Academics at Southampton University teach all of these aspects (see a selection of computing related modules).

Some have an interested in exploiting information technology to improve the learning experience and in improving the methods with which our students learn about programming and computational modelling.

Elasticity

Physical Systems and Engineering simulation / 6 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 / 18 projects

Electrostatics and electrodynamics underpin a wide range of experiments, measurements, devices, and theories. We use various computational techniques to study such systems, including photonics, magnonics and micromagnetics.

Figure: current density (cones) and electrostatic potential isolines (black).

Emacs

Software Engineering Tools / 31 projects

Emacs is a family of text editors, characterized by their extensibility. One manual describes it as "the extensible, customizable, self-documenting, real-time display editor." Development began in the mid-1970s and continues actively as of 2012. Emacs has over 2,000 built-in commands and allows the user to combine these commands into macros to automate work, in particular with the use of Emacs Lisp, a variant of Lisp, providing a deep extension capability. (More from Wikipedia on Emacs )

Emacs has initially a steep learning curve but is a very powerful tool once the basics are mastered.

Commonly used implementations are Emacs and XEmacs on Linux-like systems, and additionally Aquamacs on Mac OS X.

Emerald

Computational platforms / 3 projects

Energy

Physical Systems and Engineering simulation / 21 projects

ENVI

Visualisation and data handling software / 6 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 / 5 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 / 6 projects

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 / 4 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 / 19 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 / 14 projects

FFT

Algorithms and computational methods / 25 projects

Fiber Optic Communications

Physical Systems and Engineering simulation / 4 projects

Finite differences

Algorithms and computational methods / 50 projects

The finite difference method.

Finite elements

Algorithms and computational methods / 38 projects

The finite element method (often called finite element analysis when used in applications) in is a widespread tool that discretises space into smaller parts of varying shapes (including tetrahedra), and is used to solve partial differential equations (PDEs). The method approximates the PDE with a system of algebraic equations for steady state problems, a system of ordinary differential equations for transient problems.

Image: approximation of a sphere with a set of tetrahedra (known as mesh or grid).

Finite volume

Algorithms and computational methods / 21 projects

Finmag

Simulation software / 5 projects

Finmag is a micro magnetic simulation framework, and the successor software for the open source project Nmag. It is built on the FEniCS project rather than NSim, as the multi physics engine.

Flight simulation

Physical Systems and Engineering simulation / 6 projects

Flow Control

Physical Systems and Engineering simulation / 1 project

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 / 2 projects

Fluent is a simulation software used for Computational Fluid Dynamics (see more from Wikipedia).

Fluid Dynamics

Physical Systems and Engineering simulation / 4 projects

fluid structure interaction

Physical Systems and Engineering simulation / 9 projects

Fortran

Programming languages and libraries / 63 projects

FPGA

Computational platforms / 2 projects

Free surface flows

Physical Systems and Engineering simulation / 3 projects

Game Theory

Algorithms and computational methods / 10 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.

GAMESS(US)

Simulation software / 1 project

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered. Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolplt program (for Macintosh, Windows, or Linux desktops), are available for viewing of the final results, and the Avogadro program can assist with preparation of inputs.

A detailed description of GAMESS is available in the following journal articles: "General Atomic and Molecular Electronic Structure System" M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J. Comput. Chem., 14, 1347-1363(1993). "Advances in electronic structure theory: GAMESS a decade later" M.S.Gordon, M.W.Schmidt pp. 1167-1189, in "Theory and Applications of Computational Chemistry: the first forty years" C.E.Dykstra, G.Frenking, K.S.Kim, G.E.Scuseria (editors), Elsevier, Amsterdam, 2005. The chart below summarizes the program's present capabilities for obtaining wavefunctions, applying correlation treatments, and computing derivatives.

                            SCFTYP= RHF    ROHF   UHF    GVB    MCSCF
                                    ---    ----   ---    ---    -----
            SCF energy             CDFpEP CDFpEP CD-pEP CD-pEP CDFpEP
            SCF analytic gradient  CDFpEP CD-pEP CD-pEP CD-pEP CDFpEP
            SCF analytic Hessian   CD-p-- CD-p-- ------ CD-p-- -D-p--
            MP2 energy             CDFpEP CDFpEP CD-pEP ------ CD-pEP
            MP2 gradient           CDFpEP -D-pEP CD-pEP ------ ------
            CI energy              CDFp-- CD-p-- ------ CD-p-- CD-p--
            CI gradient            CD---- ------ ------ ------ ------
            CC energy              CDFp-- CDF--- ------ ------ ------
            EOMCC excitations      CD---- ------ ------ ------ ------
            DFT energy             CDFpEP CD-pEP CD-pEP  n/a    n/a
            DFT gradient           CDFpEP CD-pEP CD-pEP  n/a    n/a
            TD-DFT energy          CDFpEP ------ CD-p--  n/a    n/a
            TD-DFT gradient        CDFpEP ------ ------  n/a    n/a
            MOPAC energy           yes    yes     yes    yes    n/a
            MOPAC gradient         yes    yes     yes    no     n/a

Here: C= conventional storage of AO integrals on disk D= direct evaluation of AO integrals whenever needed F= Fragment Molecular Orbital methodology is enabled, "F" pertains to the gas phase; for FMO with PCM or EFP see manual. p= parallel execution E= Effective Fragment Potential discrete solvation P= Polarizable Continuum Model continuum solvation A more complete summary of the program capabilities, including all run types and molecular properties can be found in INTRO.DOC, the first chapter of the GAMESS documentation.

gdb

Software Engineering Tools / 3 projects

General Relativity

Physical Systems and Engineering simulation / 10 projects

We study the gravitational wave forms that radiate from either single or merging compact objects.

Geographic Information Systems

Algorithms and computational methods / 12 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.

Geophysics

Physical Systems and Engineering simulation / 4 projects

Geophysics is the physics of the Earth, studying and quantifying geological phenomena, their constituent processes and their physical properties. This can be through gravity, electrical, seismic or magnetic methods, through analogue experimentation or through numerical modelling and simulation work.

Image courtesy of Wikipedia, courtesy of NASA - showing a gravity model of the Earth developed from their GRACE satellite mission.

Git

Software Engineering Tools / 37 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 / 23 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 / 13 projects

Graphical Processing Unit (GPU) computing uses the computational power of modern graphic adaptors for computing, i.e. simulation, data processing etc, and is sometimes referred to as General-purpose computing on graphics processing Wikipedia entry for GPGPU.

A GPU can contain several hundred (or more) computational cores on which computation can be carried out in parallel. For some computational problems a speed up of the order of 40-80 over serial execution (on one core) can be achieved with GPU cards in the price range of ~£150. Good problems that translate well to parallel execution on a GPU require a fair amount of computation on relatively little data: data access is slow in comparison to computation. Typical examples include Molecular Dynamics simulations.

This is an area with rapid change in hardware and software and libraries.

The figure shows results of a GPU accelerated Monte-Carlo simulation (credit Marijan Beg ).

GPU-libs

Programming languages and libraries / 5 projects

Graph Theory

Algorithms and computational methods / 6 projects

Gromacs

Simulation software / 14 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/

h5py

Visualisation and data handling software / 2 projects

h5py is a Python module which provides an interface to the HDF5 library.

HDF5

Visualisation and data handling software / 14 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.

Healthcare modelling

Socio-technological System simulation / 4 projects

Operational Research (OR) has existed as a scientific discipline for over 70 years and has been applied to healthcare for over 50 years. The UK OR Society and the National Health Service (NHS) held a joint Colloquium on hospital appointment systems back in 1962. Since then OR models have been widely and successfully used to assist clinical decision-making, facility planning, resource allocation, evaluation of treatments, and organisational redesign. One of the most commonly used approaches is computer simulation, widely regarded as the technique of choice in healthcare because of its power and flexibility as well as its ability to function at a range of scales from the individual patient up to whole-system models.

Since its inception OR has been a discipline focused on solving real-world problems. Addressing the problems of real hospitals and real patients is paramount. Modellers need to develop new approaches to tackle the tough cultural problems inherent in healthcare systems. Multi-disciplinary working is "de rigeur" - Operational Researchers need to work alongside clinicians and healthcare managers as well as other disciplines such as health services research and health economics in order to exploit the synergies between them.

Healthcare modelling is an endlessly fascinating and challenging area in which to work. It is hard to imagine a more complex organisation than the NHS (the largest employer in Europe and the third largest worldwide, allegedly only exceeded by the Indian Railways and the Chinese Army!). OR models have been used at a patient or population level for modelling epidemics and disease progression, as well as at the micro-level for physiological processes and pharmacodynamics, for example. There are countless research challenges: developing models acceptable to all users, balancing user-friendliness with scientific rigour and validity, capturing human behaviour, understanding the complex links between humans and systems, not to mention all the clinical aspects. New PhD students are always welcome, from any numerate background!

Heat transfer

Physical Systems and Engineering simulation / 10 projects

HECToR

Computational platforms / 23 projects

HiPSTAR

Simulation software / 9 projects

The High-Performance Solver for Turbulence and Aeroacoustic Research (HiPSTAR) was developed as part of a Royal Academy of Engineering/EPSRC research fellowship. The full compressible Navier-Stokes equations are solved on general curvilinear coordinates, with the option of also solving curvilinear cylindrical coordinates. The structured, multi-block code is tailored to be particularly efficient for modern HPC systems by making a significant effort to minimize the memory requirement in light of severe bandwidth limitations imposed by current multi core architectures. The code includes the following features: i) highly optimized (wavenumber resolution) 4th-order accurate parallelized compact differences, ii) a spectral method for the spanwise or azimuthal direction (in the case of cylindrical coordinates 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, vi) characteristic interface conditions for the connection of blocks with metric discontinuities, vii) a time dependent immersed boundary method for the realization of complex and/or moving geometries, and viii) domain decomposition in the two finite-difference directions using an MPI parallelization. The parallel efficiency of HiPSTAR has been extensively tested on various computing platforms and production runs have to date been performed on 14,208 cores. In a CRAY centre of excellence project (http://www.hector.ac.uk/coe/pdf/HiPSTAR_OMP_Report.pdf), the code was converted to a hybrid OMP/MPI parallelisation, where the OMP parallelisation was applied to the direction in which the spectral method is employed.

HPC

Transdisciplinary tags / 49 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 / 8 projects

Human environment interaction

Socio-technological System simulation / 14 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 / 13 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.

Hydrology

Physical Systems and Engineering simulation / 4 projects

IDL

Visualisation and data handling software / 5 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 / 6 projects

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 / 4 projects

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 / 5 projects

IPython/Jupyter Notebook

Programming languages and libraries / 14 projects

IPython and its language agnostic successor Jupyter provides a rich architecture for interactive computing with:

  • Powerful interactive shells (terminal and Qt-based).
  • A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media.
  • Support for interactive data visualization and use of GUI toolkits.
  • Flexible, embeddable interpreters to load into your own projects.
  • Easy to use, high performance tools for parallel computing.

We use IPython/Jupyter for documentation, reporting, data exploration, code development and regression tests.

Iridis

Computational platforms / 147 projects

The University of Southampton Major HPC facility is called Iridis. Currently the University is running two supercomputers at the same time making it one of the top supercomputing sites in the UK. The facility is open to research students and members of academic staff from any Faculty, who has the need for compute resources substantially greater than a standard PC. In addition, we have a dedicated Lyceum cluster intended mainly for undergraduate and MSc project work.

Iridis Documentation and Wikis

More details about Iridis can be found on internal CMG community pages for Iridis 3 and Iridis 4 (accessible to registered users) as well as on iSolutions pages

Acknowledging the use of IRIDIS

When preparing a publication describing work that involved usage of Iridis, please ensure that you reference the Iridis cluster. Such recognition is important for acquiring funding for the next generation hardware, support services, data storage and infrastructure. The following text is suggested as a starting point. Please, feel free to augment or modify as you see fit.

The authors acknowledge the use of the IRIDIS High Performance Computing Facility, and associated support services at the University of Southampton, in the completion of this work.

Research outcome

Scientific projects involving usage of Iridis are listed below.

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 / 27 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.

Jenkins

Software Engineering Tools / 3 projects

Jenkins is an application that monitors executions of repeated jobs, such as building a software project or jobs run by cron. This includes building and testing software projects continuously, just like CruiseControl or DamageControl. In a nutshell, Jenkins provides an easy-to-use so-called continuous integration system, making it easier for developers to integrate changes to the project, and making it easier for users to obtain a fresh build. The automated, continuous build increases the productivity.

More from https://wiki.jenkins-ci.org

Julia

Programming languages and libraries / 4 projects

The Julia language is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. The library, largely written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace.

Julia programs are organized around multiple dispatch; by defining functions and overloading them for different combinations of argument types, which can also be user-defined.

For a more from the Julia home page continue at http://julialang.org.

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/

Kinetic Monte Carlo

Algorithms and computational methods / 1 project

The kinetic Monte Carlo (KMC) method is a Monte Carlo method of computer simulation used to simulate the time evolution of processes. The algorithms underlying the KMC algorithm are known by a variety of other names such as residence-time, n-fold way or the Bortz-Kalos-Liebowitz (BKL) algorithms. KMC is particularly useful for investigating the dynamics of systems in which there are rare events occurring, because the computational speed of the simulation is limited by the slowest event. Hence, KMC can reach much longer time scales than using other simulations techniques that proceed linearly with time, such as classical Molecular Dynamics simulations. KMC also offers the advantage over traditional Monte Carlo approaches that it can be used to study non-equilibrium processes as they evolve through time. The key disadvantage of the technique is that it provides no information of the timescale of the elementary processes; these timescales must be parameterised either from ab initio calculations or experiments.

Labview

Visualisation and data handling software / 1 project

Landscape evolution

Physical Systems and Engineering simulation / 6 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 / 10 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 / 134 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 / 2 projects

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 / 8 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.

Documentation and Support are available for registered users

Mac OS X

Computational platforms / 50 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).

Machine learning

Algorithms and computational methods / 10 projects

Even amongst practitioners, there is no truly well accepted definition for machine learning. So, I’ll to provide two:

  • Pioneer machine learning researcher Arthur Samuel defined machine learning as: “the field of study that gives computers the ability to learn without being explicitly programmed”. This definition is beautiful in its simplicity though lacks a little formality. So, with a little more structure,..
  • Tom Mitchell states that “a computer program is said to learn from experience E, with respect to some task T, and some performance measure P, if its performance on T as measured by P improves with experience E”.

A classic practical application is the email spam filter. The email program watches which emails the user does or does not mark as spam and, based on that, learns how to better filter future spam automatically. In the parlance of Tim Mitchell’s definition, classifying the emails as spam or not span is the task, T, watching the user label emails as spam or not spam is the experience, E, and the fraction emails correctly classified could be the perform measure, P.

There are a great number of machine learning algorithms and, as such, they are often divided into three main types: supervised, unsupervised and reinforcement learning algorithms.

Magnetohydrodynamics

Physical Systems and Engineering simulation / 2 projects

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 / 7 projects

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 / 4 projects

Marine Renewable Energy

Physical Systems and Engineering simulation / 5 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

MASON

Simulation software / 2 projects

Materials

Physical Systems and Engineering simulation / 30 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 / 16 projects

Matlab

Programming languages and libraries / 67 projects

MATLAB (matrix laboratory) is a numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran. (More from Wikipedia on Matlab ).

Matlab is widely spread in engineering and fairly widely used in Science in general.

(Figure source: http://en.wikipedia.org/wiki/File:Matlab_Logo.png)

Maximum Likelihood

Algorithms and computational methods / 1 project

Mayavi

Visualisation and data handling software / 13 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 / 3 projects

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.

Medicine

Transdisciplinary tags / 4 projects

The Medicine tag covers all projects that are carried out in cooperation with the Faculty of Medicine.

MEMS

Physical Systems and Engineering simulation / 3 projects

Microelectromechanical systems (MEMS) are integrated devices that incorporate mechanical functionalities on a chip. They range in size from the sub-micron to the millimetre regime and a particular chip may contain any number of elements from a few to millions. MEMS are employed in a rapidly growing range of applications, such as printer cartridges, accelerometers in cars, biosensors and optical switches in telecommunication networks.

Mercurial

Software Engineering Tools / 20 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.

Meshless methods

Algorithms and computational methods / 3 projects

Meshless methods

Metals

Physical Systems and Engineering simulation / 6 projects

Microbiology

Life sciences simulation / 4 projects

Micromagnetics

Physical Systems and Engineering simulation / 20 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 / 3 projects

Minimum Energy Paths

Algorithms and computational methods / 2 projects

ModelSim

Software Engineering Tools / 1 project

ModelSim is a simulation tool for hardware description languages (HDL) such as Verilog, VHDL and SystemC. ModelSim can be used standalone or in conjunction with Altera Quartus or Xilinx ISE. It has 3 modes of operation: interactive mode with graphic user interface, interactive mode from the command line and non-interactive batch script where standard input and output are redirected from and to files.

Molecular Dynamics

Algorithms and computational methods / 28 projects

The molecular dynamics method.

Molecular Mechanics

Algorithms and computational methods / 9 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 / 42 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 / 48 projects

The message passing interface for parallel execution.

MS Office Access

Visualisation and data handling software / 4 projects

Microsoft Office Access is the (pseudo-)relational database application for Windows that is part of the Microsoft Office suite of applications.

Multi-core

Algorithms and computational methods / 21 projects

Multi-physics

Algorithms and computational methods / 29 projects

Multi-physics simulation method.

Multi-scale

Algorithms and computational methods / 26 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 / 7 projects

Multipole methods

Algorithms and computational methods / 2 projects

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 / 4 projects

Nanoscale Assemblies

Life sciences simulation / 4 projects

NEMO

Simulation software / 1 project

NetLogo

Simulation software / 5 projects

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/

NetworkX

Visualisation and data handling software / 1 project

Neuroscience

Life sciences simulation / 11 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 / 14 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).

NGCM

Transdisciplinary tags / 35 projects

Next Generation Computational Modelling (NGCM)

The Centre for Doctoral Training in Next Generation Computational Modelling brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK, and studentships are available.

Computational Modelling

Computational modelling is emerging as a "third pillar" of science and engineering alongside theory and experimentation. Computer simulations bridge between theory and experiment, generating hypotheses, forecasts and predictions about real-world systems. This reduces the number of experiments that need to be carried out in the real world and the number of design prototypes that have to be built, thereby reducing cost, encouraging innovation, optimising system design and enabling the study of systems for which experimental work is infeasible (for example due to prohibitive cost or risk of endangering lives, the environment, etc).

As a consequence of this increasingly key role, computational modelling is now recognised as a priority area by industry, government and science itself.

NGS

Computational platforms / 2 projects

Nmag

Simulation software / 10 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.

NWCHEM

Simulation software / 3 projects

OCaml

Programming languages and libraries / 4 projects

The Objective Caml language.

OCaml, originally known as Objective Caml, is the main implementation of the Caml programming language, created by Xavier Leroy, Jérôme Vouillon, Damien Doligez, Didier Rémy and others in 1996. OCaml extends the core Caml language with object-oriented constructs.

OCaml is a free open source project managed and principally maintained by INRIA. In recent years, many new languages have drawn elements from OCaml, most notably F# and Scala.

(More from Wikipedia)

Oceanography

Physical Systems and Engineering simulation / 11 projects

Octave

Programming languages and libraries / 1 project

Onetep

Simulation software / 11 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

OpenACC

Programming languages and libraries / 1 project

OpenCL

Programming languages and libraries / 2 projects

OpenFOAM

Simulation software / 12 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/

Local Wiki page

OpenGL

Programming languages and libraries / 1 project

OpenMP

Programming languages and libraries / 22 projects

Operations Research

Socio-technological System simulation / 4 projects

Refer to http://de.wikipedia.org/wiki/Operations_Research .

Optimisation

Algorithms and computational methods / 30 projects

Pandas

Programming languages and libraries / 1 project

Pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

Pandas is one of the big data analytics tools, in particular for the Python community.

ParaView

Visualisation and data handling software / 24 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.

Particle Collisions

Physical Systems and Engineering simulation / 4 projects

Perl

Programming languages and libraries / 6 projects

Perl is a general-purpose programming language originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and more. The language is intended to be practical which means easy to use, efficient and complete. It supports both procedural and object-oriented (OO) programming and has powerful built-in support for text processing (http://www.perl.org).

PETSc

Programming languages and libraries / 6 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 / 15 projects

Photonics is the science concerned with the study of light. It encompasses all of the generation, emission, transmission, detection, control and processing of light. This topic includes a broad range of photonics research, which involves both numerical modelling and the fabrication and testing of photonic devices.

PostGres

Visualisation and data handling software / 1 project

Povray

Visualisation and data handling software / 2 projects

Povray is an open source program for ray tracing, a technique in computer graphics which allows to create a three dimensional image of a scene from a specification of its geometry. The technique is based on an accurate calculation of light paths, which takes into account the characteristic of the light sources, the propagating medium and the surfaces of the objects in the scene. Consequently, the result is often highly realistic: good ray-traced images can be confused with photographs.

Example image from http://commons.wikimedia.org/wiki/File:Glasses_800_edit.png

ProtoMS

Simulation software / 4 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.

Psychology

Life sciences simulation / 3 projects

Pylab

Visualisation and data handling software / 24 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 / 3 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 / 109 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 / 11 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.

QFT

Physical Systems and Engineering simulation / 1 project

Quantum field theory (QFT) provides the theoretical framework for models of quantum mechanics for subatomic particles. The premise of QFT is to treat each of these particles as excitations in underlying fields which interact with one another. Such interactions are described using Feynman diagrams (pictured right).

Quantitative Biology

Transdisciplinary tags / 9 projects

Quantitative Biology represents an interdisciplinary initiative under the umbrella of the Institute for Life Sciences. The remit is broad and targets applications of mathematical, computational and bioinformatics techniques to experimental biology and biomedicine, with a particular initial focus on Systems Biology and protein networks.

Quantum Chemistry

Algorithms and computational methods / 11 projects

Quantum Computation

Algorithms and computational methods / 5 projects

Quantum computation, following the postulates of quantum mechanics, unlocks powerful capabilities in computing.

The smallest unit of information is a quantum bit or qubit. In contrast to the classic bit which may take the values 0 or 1, a qubit may also be in any superposition of 0 and 1 as long as it has not interacted with its environment. It may be thought as a spinning coin in a black box. The coin is simultaneously Heads and Tails, until we open the box after it has settled down and we observe it to be either Heads or Tails. The capabilities of computing that are offered by taking many of these spinning coins at the same time and interacting with them while they are spinning are vast.

The capabilities of quantum computation, such as quantum parallelism, tunnelling and quantum entanglement, do not exist in our every day world, verifying the non-intuitive nature of quantum computation. Quantum computation has already found various applications in quantum error correction, quantum cryptography and quantum search and combinatorial optimization problems. In 2011, the quantum computing company D-Wave Systems announced the creation of a task specific quantum processor, which employs an adiabatic quantum optimization algorithm, the quantum annealing algorithm, to find the index of a function that minimizes it.

Quantum Dynamics

Physical Systems and Engineering simulation / 9 projects

R

Programming languages and libraries / 39 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.

Raspberry Pi

Computational platforms / 1 project

The Raspberry Pi is a credit-card-sized single-board computer developed in the UK by the Raspberry Pi Foundation with the intention of promoting the teaching of basic computer science in schools.

Uptake of the Raspberry Pi was beyond expectations - the machine is a small, cheap, and not very energy hungry computer which runs the Linux operating system.

Find more details at Wikipedia.

The University of Southampton has put together the first supercomputer based on Raspberry Pi machines (see http://www.southampton.ac.uk/~sjc/raspberrypi).

Redmine

Software Engineering Tools / 2 projects

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.

Repast Simphony

Simulation software / 3 projects

Robotics

Physical Systems and Engineering simulation / 1 project

RStudio

Software Engineering Tools / 4 projects

Schrodinger Suite

Simulation software / 1 project

Scientific Computing

Transdisciplinary tags / 83 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 / 10 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.

Self Organized Networks

Socio-technological System simulation / 7 projects

Semiconductors

Physical Systems and Engineering simulation / 9 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 / 4 projects

Sensors

Physical Systems and Engineering simulation / 6 projects

Sentaurus TCAD

Simulation software / 1 project

Sentaurus is a Technology Computer Aided Design (TCAD) software by Synopsys used to simulate semiconductor device fabrication and operation.

Sexual Health

Physical Systems and Engineering simulation / 1 project

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.

Ship Hydrodynamics

Physical Systems and Engineering simulation / 4 projects

Simpleware

Visualisation and data handling software / 2 projects

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.

Smoothed Particle Hydrodynamics

Algorithms and computational methods / 2 projects

Smoothed Particle Hydrodynamics is a computational method that uses Lagrangian physics such that the coordinates move with the fluid elements. It implements a smoothing length that applies different levels of interaction from nearby particles that are relative to the spacing. This means that the algorithm can “smooth” all of the properties of the fluid making it possible to resolve various computationally difficult situations. It was originally developed in 1977 by Gingold and Monaghan and Lucy independently for use in modeling protostar formation and has since become quite popular not only in further astrophysics applications, but in various fields such as ballistics and oceanography.

Social and Socio-economic Systems

Socio-technological System simulation / 19 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 / 17 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 / 25 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

Sourcesafe

Software Engineering Tools / 1 project

Space debris

Physical Systems and Engineering simulation / 1 project

SPICE

Simulation software / 1 project

Spintronics

Physical Systems and Engineering simulation / 5 projects

Spintronics, meaning "spin transport electronics", also known as magnetoelectronics, is an emerging technology that exploits the intrinsic spin of the electron and its associated magnetic moment, in addition to its fundamental electronic charge, in solid-state devices. More from Wikipedia

Image courtesy of Dr Matteo Franchin.

Spitfire

Computational platforms / 2 projects

SQL Azure

Visualisation and data handling software / 1 project

Star CCM+

Simulation software / 6 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 / 5 projects

Stata

Programming languages and libraries / 1 project

Stats package

statistical analysis

Algorithms and computational methods / 22 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 / 11 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 / 12 projects

Sublime Text

Software Engineering Tools / 8 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.

Support Vector Machine

Algorithms and computational methods / 4 projects

Surface imaging

Visualisation and data handling methods / 9 projects

Surface Imaging

SVN

Software Engineering Tools / 32 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))

Swarm Behaviour

Life sciences simulation / 6 projects

Symbolic calculation

Algorithms and computational methods / 2 projects

Symbolic computation -- this is the manipulation of mathematical expression (in contrast to the numerical computation of solutions to given equations). This is useful to support paper-based transformations of expressions, and increasingly used to generate code on the fly that is specialised for the given problem.

The figure shows some simple examples (using Python's 'sympy' package, see http://www.sympy.org):

  • We ask for the expansion of (x+y)^2 (which in Python notation is (x+y)**2 using the 'expand' command
  • differentiate x^2 with respect to the variable x
  • integrate x^2 with respect to x from 0 to 1.5
  • integrate x^2 with respect to x

There are a large number of packages providing these capabilities, including the well know Maple, Maxima, derive and many others.

Systems biology

Life sciences simulation / 19 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.

Tcl

Programming languages and libraries / 4 projects

Multi-platform and multi-purpose scripting language. Python & Perl are probably quicker (and everyone argues about which is best) but tcl is probably easier to learn :-)

TecPlot

Visualisation and data handling software / 17 projects

TELEMAC

Simulation software / 1 project

Thin film flow

Physical Systems and Engineering simulation / 1 project

Thin film flow is extremely viscous flows, where a discrepancy between the dimensions exist. This flow is governed by the lubrication approximation of the Navier-Stokes equation.

Tissue Engineering

Life sciences simulation / 3 projects

Trac

Software Engineering Tools / 3 projects

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 / 8 projects

Tribology

Physical Systems and Engineering simulation / 6 projects

Turbulence

Physical Systems and Engineering simulation / 24 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

Vagrant

Computational platforms / 2 projects

Vagrant is an open source tool for creating, configuring and distributing virtual development environments. It is often described as a wrapper around other virtualisation software such as Virtualbox and VMware, and around configuration management software such as Ansible, Puppet, Chef and salt.

Vagrant provides a workflow that focuses on automation to reduce the set-up time for development environments and multiple virtual machines. It allows for source control of setup files, is highly portable, and can be used to try a wide variety of platforms, quickly.

View the calendar of events relating to this topic.

valgrind

Software Engineering Tools / 2 projects

Value-driven design

Socio-technological System simulation / 4 projects

Verilog

Programming languages and libraries / 2 projects

Verilog is a hardware description language (HDL) used to model electronic systems. It is most commonly used in the design and verification of digital circuits at the register-transfer level of abstraction. It is also used in the verification of analog circuits and mixed-signal circuits.

It can be used to write hardware code which is then synthesised into electronics on an FPGA (field programmable gate array) or ASIC (application specific integrated circuit).

SystemVerilog is the newest version of the Verilog HDL.

VG Studio Max

Visualisation and data handling software / 1 project

VHDL

Programming languages and libraries / 2 projects

VHDL (VHSIC (Very high speed integrated circuit) Hardware Description Language) is a hardware description language used in electronic design automation to describe digital and mixed-signal systems such as field-programmable gate arrays and integrated circuits. VHDL can also be used as a general purpose parallel programming language.

It can be used to write hardware code which is then synthesised into electronics on an FPGA (field programmable gate array) or ASIC (application specific integrated circuit).

Vim

Software Engineering Tools / 16 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

VirtualBox

Computational platforms / 5 projects

VirtualBox is one of several virtualisation technology softwares available. It is free and allows to simulate a computer, and the execution of an operating system and applications inside that operating system on the virtual computer.

A basic introduction is available here.

Virtual machines are increasingly used to provide testing environments, portable environments, and better utilisation of hardware, with applications in general software engineering, high performance computing, service provision and cloud computing.

VisIt

Visualisation and data handling software / 7 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 / 5 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.

Instructional videos

Visual Studio

Software Engineering Tools / 1 project

MS Visual Studio is an IDE for developing software applications. It has built in support for languages such as C, C++ and C#, and can be used to develop in many other languages with specific plugins (e.g. Python).

Visualisation

Transdisciplinary tags / 14 projects

Visualisation -- of data gathered from experiment as well as simulation -- is key to extract insight and understanding.

The figure shows simulation data of space plasma flow. The scalar entity plotted here on a 2d domain is visualised through (i) the chosen colour and (ii) a displacement of the 2d-plane in the third dimension, where the displacement is proportional to the value of the scalar. Here, the scalar is the density of the plasma and the system studied is related to jets from active galaxy nuclei studies.

VMD

Visualisation and data handling software / 18 projects

Voxel imaging

Visualisation and data handling methods / 6 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 / 17 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 / 10 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 / 73 projects

Wireless Communications

Physical Systems and Engineering simulation / 3 projects

Xeon Phi

Computational platforms / 4 projects

Xmgrace

Visualisation and data handling software / 19 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)