## Research Software Made in Manchester

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.

**Last updated: 26th Jan 2015**

**Centre for Imaging Sciences**

- BoneFinder – BoneFinder is a fully automatic segmentation tool to extract bone contours from 2D radiographs. It is written in C++ and is available for Linux and Windows.

**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.

**Health Informatics**

- 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.

**IT Services**

- idiffh – Research software can produce huge text files (e.g. logs). The GNU diff program needs to read the files into memory and therefore has an upper bound on file size. idiffh might only use a simple heuristic but is only bounded by the maximum file size (and free file store).
- nearest_correlation - Python versions of nearest correlation matrix algorithms
- ParaFEM – A portable library for parallel finite element analysis. Contributions from MACE, SEAES, School of Materials.
- Shadow – This is an Apple Mac OS X shell level application that can monitor Dropbox shared folders for file deletions and restore them.
- 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 Chemical Engineering & Analytical Science**

- SurfaceSpectra Identity- is free software that allows you to view and export isotope patterns.

**School of Chemistry**

- DOSY Toolbox – A free, open source programme for processing PFG NMR diffusion data (a.k.a. DOSY data).

- Clinical NERC – Clinical NERC is a simple customizable state-of-the-art named entity recognition, and classification software for clinical concepts or entities.
- EasyChair – EasyChair is a free conference management system.
- GPC – The University of Manchester GPC library is a flexible and highly robust polygon set operations library for use with C, C#, Delphi, Java, Perl, Python, Haskell, Lua, VB.Net (and other) applications.
- HiPLAR – High Performance Linear Algebra in R. A collaboration between Manchester and Imperial.
- iProver – 7 times word champion in theorem proving.
- INSEE – Interconnection Networks Simulation and Evaluation Environment
- 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.
- ManTIME – ManTIME is an open-source machine learning pipeline for the extraction of temporal expressions from general domain texts.
- 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.
- OWL Tools – a collection of tools for working with OWL ontologies
- OWL Webapps – a collection of web apps for working with OWL ontologies
- 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.
- TERN – TERN is a temporal expressions identification and normalisation software; designed for clinical data.
- 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 Earth, Atmospheric and Environmental Sciences**

- ManUniCast – iPad/iPhone app. Weather and Air-Quality Forecasts for the UK and Europe

**School of Electrical and Electronic Engineering**

- Automatic classification of eye fixations - Identify fixations and saccades from point-of-gaze data without parametric assumptions or expert judgement. MATLAB code.
- Bootstrap Threshold Software – Estimate a threshold and a robust SD from stimulus-response data with a normal cumulative distribution. Written in C.
- LDLTS – Laplace transform Transient Processor and Deep Level Spectroscopy. A collaboration between Manchester and the Institute of Physics Polish Academy of Sciences in Warsaw
- Model-Free Psychometric Function Software – Fit a stimulus-response curve and estimate a threshold and SD without a parametric model
- Raspbian – Raspbian is a free operating system based on Debian optimized for the Raspberry Pi hardware.
- Signal Wizard – Digital signal processing software.

**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
- fAbcond – Python code for the condition number of a matrix exponential times a vector
- funm_quad - Quadrature-based Arnoldi restarts for matrix function computations in MATLAB
- IFISS – IFISS is a graphical package for the interactive numerical study of incompressible flow problems which can be run under Matlab or Octave.
- MARKOVFUNMV – An adaptive black-box rational Arnoldi method for the approximation of Markov functions.
- 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.
- rktoolbox – A Rational Krylov Toolbox for MATLAB
- Shrinking (MATLAB) - MATLAB codes for restoring definiteness of a symmetric matrix by shrinking
- Shrinking (Python) – Python codes for restoring definiteness of a symmetric matrix by shrinking
- 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
- testing_matrix_functions - MATLAB files for testing matrix function algorithms using identities such as exp(log(A)) = A

**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.
- FLIGHT – FLIGHT specialises in the prediction and modelling of fixed-wing aircraft performance
- 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).
- SWAB Online – Innovative and User Friendly Web Application in Running Fortran-based 1-D Shallow Water near Shore Wave Simulation Modelling

**School of Physics and Astronomy**

- Herwig++ – Herwig++ is a new event generator, written in C++, built on the experience gained with the well-known event generator HERWIG, which was used by the particle physics community for nearly 30 years. Herwig++ is used by the LHC experiments to predict the results of their collisions and as an essential component of their data analysis. It is developed by a consortium of four main nodes, including Manchester, and its published write-up has been cited over 500 times.
- im3shape - Im3shape measures the shapes of galaxies in astronomical survey images, taking into account that they have been distorted by a point-spread function.
- MAD8/madinput – Mathematica code and MAD8 installer for performing optics calculations for particle accelerator design.
- PolyParticleTracker – MATLAB code for particle tracking against complex optical backgrounds

A great collection. Thanks for the resource, it was worth your efforts.