Earlier this year I was awarded a fellowship from the software sustainability institute, an organization that works to improve all aspects of research software. During their recent collaborations workshop in Oxford, it occurred to me that I was aware of only a relatively tiny number of software projects at my own institution, The University of Manchester. I decided to change that and started contacting our researchers to see what software they had released freely to the world as part of their research activities.
Research software comes in many forms; from small but useful MATLAB, Python or R scripts with just a handful of users and one developer right through to fully-fledged applications used by large communities of researchers and supported by teams of specialist developers. I’m interested in knowing about all of it. After all, we live in a time when even a mistake in an Excel spreadsheet can change the world.
The list below is what’s been sent to me so far and is a mirror of an internal list that’s been doing the rounds at Manchester. I’ll update it as more information becomes available. If you are at Manchester and know of a project that I’ve missed, feel free to contact me.
Faculty of Life Sciences
- antiSMASH – Genome annotation tool for secondary metabolite gene clusters.
- MultiMetEval – Flux-balance analysis tool for comparative and multi-objective analysis of genome-scale metabolic models.
- mzMatch/mzmatch.R/mzMatch.ISO – Comprehensive LC/MS metabolomics data processing toolbox.
- Rank Products – Statistical tool for the identification of differentially expressed entities in molecular profiles.
- openCDMS – The openCDMS project is a community effort to develop a robust, commercial-grade, full-featured and open source clinical data management system for studies and trials.
- ParaFEM – A portable library for parallel finite element analysis. Contributions from MACE, SEAES, School of Materials.
- The Reality Grid Steering Library – A software library for steering and monitoring numerical simulations, APIs available for Fortran/C++/Java and steering clients available for installation on laptops and mobile devices. Developed in collaboration with the School of computer science.
Manchester Institute of Biotechnology
- Copasi – COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
- Condor Copasi – Condor-COPASI is a web-based interface for integrating COPASI with the Condor High Throughput Computing (HTC) environment.
School of Chemistry
- DOSY Toolbox – A free, open source programme for processing PFG NMR diffusion data (a.k.a. DOSY data).
School of Computer Science
- KUPKB (The Kidney & Urinary Pathway Knowledge Base) – The KUPKB is a collection of omics datasets that have been extracted from scientific publications and other related renal databases. The iKUP browser provides a single point of entry for you to query and browse these datasets.
- MethodBox – MethodBox provides a simple, easy to use environment for browsing and sharing surveys, methods and data.
- myExperiment – myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.
- Open PHACTS Discovery Platform – Freely available, this platform integrates pharmacological data from a variety of information resources and provides tools and services to question this integrated data to support pharmacological research.
- OWL API – A Java API and reference implementation for creating, manipulating and serialising OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWL API is open source and is available under either the LGPL or Apache Licenses.
- RightField – Semantic annotation by stealth. RightField is tool for adding ontology term selection to Excel spreadsheets to create templates which are then reused by Scientists to collect and annotate their data without any need to understand, or even be aware of, RightField or the ontologies used. Later the annotations can be collected as RDF
- SEEK – SEEK is a web-based platform, with associated tools, for finding, sharing and exchanging Data, Models and Processes in Systems Biology.
- ServiceCatalographer – ServiceCatalographer is an open-source Web-based platform for describing, annotating, searching and monitoring REST and SOAP Web services.
- Simple Spreadsheet Extractor – A simple ruby gem that provides a facility to read an XLS or XLSX Excel spreadsheet document and produce an XML representation of its content.
- Taverna – Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.
- Utopia Documents – Utopia Documents brings a fresh new perspective to reading the scientific literature, combining the convenience and reliability of the PDF with the flexibility and power of the web.
School of Mathematics
- EIDORS – Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software.
- Fractional Matrix Powers – MATLAB functions to compute fractional matrix powers with Frechet derivatives and condition number estimate
- IFISS – IFISS is a graphical package for the interactive numerical study of incompressible flow problems which can be run under Matlab or Octave.
- Matrix Computation Toolbox – The Matrix Computation Toolbox is a collection of MATLAB M-files containing functions for constructing test matrices, computing matrix factorizations, visualizing matrices, and carrying out direct search optimization.
- Matrix Function Toolbox – The Matrix Function Toolbox is a MATLAB toolbox connected with functions of matrices.
- Matrix Logarithm – MATLAB Files. Two functions for computing the matrix logarithm by the inverse scaling and squaring method.
- Matrix Logarithm with Frechet Derivatives and Condition Number – MATLAB files
- NLEVP A Collection of Nonlinear Eigenvalue Problems – This MATLAB Toolbox provides a collection of nonlinear eigenvalue problems.
- oomph-lib – An object-oriented, open-source finite-element library for the simulation of multiphysics problems.
- Simfit – Free software for simulation, curve fitting, statistics, and plotting.
- SmallOverlap – SmallOverlap is a GAP 4 package which implements new, highly efficient algorithms for computing with finitely presented semigroups and monoids whose defining presentations satisfy small overlap conditions (in the sense of J.H.Remmers)
- Symmetric eigenvalue decomposition and the SVD – MATLAB files
School of Mechanical, Aerospace and Civil Engineering (MACE)
- DualSPHysics – DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics and makes use of GPUs.
- SPHYSICS – SPHysics is a platform of Smoothed Particle Hydrodynamics (SPH) codes inspired by the formulation of Monaghan (1992) developed jointly by researchers at the Johns Hopkins University (U.S.A.), the University of Vigo (Spain), the University of Manchester (U.K.) and the University of Rome La Sapienza (Italy).