Software and Tools
Here are some software and tools available for scientific research.
- Synthesizing Biological TheoriesThis tool enables biologists and modelers to construct high-level theories and models of biological systems, capturing biological hypotheses, inferred mechanisms, and experimental results within the same framework. Among the key features of the tool are convenient ways to represent several competing theories and the interactive nature of building and running the models using an intuitive, rigorous scenario-based visual language.
- Stochastic Pi MachineThe 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.
- A programming language for composable DNA circuitsRecently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their compilation to nucleotide sequences.
- A Programming Language for Genetic Engineering of Living CellsSynthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesised and put to work in living cells.
- Scientific Dataset
Scientific DataSet (SDS) is a managed library for reading, writing and sharing array-oriented scientific data, such as time series, matrices, satellite or medical imagery, and multidimensional numerical grids.
- Disease Model Simulator
This tool enables the user to investigate the theoretical disease model used in the paper "Host-pathogen time series data in wildlife support a transmission function between density and frequency dependence" by Matthew J. Smith, Sandra Telfer, Eva R. Kallio, Sarah Burthe, Alex R. Cook, Xavier Lambin and Michael Begon to be published in Proceedings of the National Academy of Sciences of the United States of America (pending acceptance).
- Plant Competition Model Simulator
A Windows Presentation Foundation application that enables a user to experiment with the Crawley-May plant-competition model, a spatially explicit model that investigates the conditions under which two plant species can coexist. At present, this application runs SLOWLY and we will soon rectify the problem.
- WPF Dynamic-Data-Display
A set of WPF components for interactive visualization of scientific data.
- Density-Dependent Dispersal in Cyclic Populations Simulator
This software tool allows the user to view animations of the dynamics illustrated in the paper “The effects of density-dependent dispersal on the spatiotemporal dynamics of cyclic populations.” by Smith, Sherratt and Lambin, to appear in Journal of Theoretical Biology (doi: 10.1016/j.jtbi.2008.05.034).
- Lambda-Omega Equations Simulator
This software tool allows the user to view animations of the dynamics illustrated in the paper "Convective and Absolute stability of periodic travelling waves selected by Dirichlet and Neumann boundary conditions in reaction-diffusion equations of Lambda-Omega type". Smith, Sherratt & Rademacher, in preparation.
- Mobile Wireless Sensor Network Monitoring and Management Tool
Determining the relationship between an animal's behaviour and its environment is fundamental in assessing how it can be effectively protected. Using a combination of wireless sensor networks, GPS tracking and integrative software solutions, we are developing the tools that allow scientists to work at scales, resolutions and ranges that were previously unavailable. This Windows Mobile based control application has been developed to interactively manage and track the status of the sensor network deployed on Skomer Island.
- NetCDF library for .NET
NetCDF (network Common Data Form) is a software library and a standard binary data format supported by Unidata (http://www.unidata.ucar.edu/software/netcdf/) that enables the creation, access, and network sharing of array-oriented scientific data.
- Environmental Scenario Search Engine (ESSE)
The ESSE search-Engine is a flexible, efficient and easy to use search engine for data mining in environmental data archives. ESSE will help you find useful data even if you don't know exactly what you are looking for.
- ESSE Visualization Plugin for NASA World Wind
ESSE visualization plugins for interactive visualization of scalar fields, vector fields and trajectories on NASA World Wind.
- ScatterWeb .NET SDK
ScatterWeb .NET SDK is a new approach to working with wireless sensor networks. It hides the complexity of embedded programming and makes it easy to handle objects representing wireless sensors.