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Research software development projects

Active projects

GloTraM

GloTraM is a global transport model that combines multi-disciplinary analysis and modelling techniques to estimate foreseeable futures of the shipping industry, forecasting the evolution of a fleet and its activity in response to external stimuli: changing fuel prices, transport demand, regulation, technology availability...  

We are working with Dr. Tristan Smith and Dr. Carlo Raucci at the UCL Energy Institute to improve the status and performance of this model written in MatLab, enabling other projects which will be based on this outcome.

Software
GloTraM
Client Dr. Tristan Smith - The Bartlett UCL Energy Institute
Funding
UCL Innovation and Enterprise
Lead engineer
Raquel Alegre
Languages/technologies Matlab

Modelling and Optimisation of Antibody Purification Processes

Multi-product biopharmaceutical facilities need flexible process configurations that can adapt to products with diverse characteristics and impurity loads so as to avoid bottlenecks and delays, whilst meeting final product specifications and cost targets. In this project we are working with the group to convert existing bioprocess models and optimisers from Excel and C# to Python. The emphasis is on making the model representations clear and easy for the researchers to modify, with robust testing to verify expected behaviour.

Software
Modelling and Optimisation of Anitbody Purification Process
Client Professor Suzanne Farid - UCL Department of Biochemical Engineering
Funding
UCL
Lead engineer
Jonathan Cooper
Languages/technologies C#, Python

Silver Lab: Neuroscience data analysis pipeline

The Silver Lab develops state-of-the-art acousto-optic lens (AOL) two-photon microscopes and uses these to gain understanding of neurophysiology. We are working to integrate and optimise various Matlab analysis scripts developed by lab members into a coherent analysis pipeline, with the data at each stage stored in the open NeurodataWithoutBorders format, based on HDF5. A second line of work is developing some new API libraries for NeuroML2 – a model description language for computational neuroscience.

Software
Silver Lab: Neuroscience data analysis pipeline
Client Professor Angus Silver -  UCL Department of Neuroscience, Physiology & Pharmacology
Funding
UCL
Lead engineer
Jonathan Cooper
Languages/technologies Matlab, Python, C++, HDF5

ORACC

The Open Richly Annotated Cuneiform Corpus (ORACC) supports editing of translations and transliterations of ancient Mesopotamian (Iraqi) texts. The principal aim of this project is to create a local GUI for ORACC.

Software
ORACC
Client
Professor Eleanor Robson - UCL Dept. of Ancient History
Funding
UCL
Lead engineer
Raquel Alegre
Languages/technologies PLY, Jython, Swing, Maven, SOAP/WSDL

BICO: Big data compressive sensing

Collaborating with Dr Jason McEwen of the Mullard Space Science Laboratory, we are working to build a reusable high performance parallel framework for the application of Compressive Sensing to image cleanup, with applications to the Square Kilometre Array.

Software
BICO
Client
Dr Jason McEwen - Mullard Space Science Laboratory
Funding
EPSRC - Software for the future II
Lead engineer
David Pérez-Suarez
Languages/technologies C++11, Python, MATLAB/Mex, cython, cmake, docker, Eigen

Big Data for Critical Care with the National Health Informatics Collaborative

We're excited that we're going to be supporting the UCLH Critical Care team and colleagues at the Farr Institute in their work as part of the NHS Health Informatics Collaborative. "Intensive Care" provides rich, complicated, large, sensitive, high-speed data, with a great deal of data recorded about every patient every moment – as complete an example of the four V’s of big data (Volume, Variety, Velocity and Veracity) as you are likely to get. Together we hope to build tools and systems to allow this data to be used for research, and ultimately, for real-time patient care.

Software
New project
Client
Mervyn Singer, UCLH
Funding
NIHR Health Informatics Collaborative
Lead engineer
James Hetherington
Languages/technologies TBD

Delivering accurate structural bioinformatics to the yeast community with the HHprY data

Progress in cell biology is hampered by the relatively high proportion of proteins for which there is no known function at the molecular level. Such proteins have no domains annotated in the databases. Structural bioinformaticians have for many years been developing profile-profile search tools (such as the HHsearch tool developed by Soeding and colleagues) that are far more sensitive than the standard tools, but due to computational demand these tools have not been widely applied to create fully annotated complete genomes. We are working with Dr Tim Levine at the UCL Institute of Ophthalmology, funded by the BBSRC, to deploy these tools on UCL supercomputing infrastructure, and we are developing an automated pipeline and web interface, to make available a fully augmented annotation of the entire yeast genome.

Software
New project
Client
Tim Levine, UCL Institute of Ophthalmology
Funding
BBSRC
Lead engineer
James Hetherington
Languages/technologies TBD

Completed projects

Ending 2017

RFH-GFR Web Calculator

The Glomerular filtration rate calculator based on research produced at the Royal Free Hospital and UCL. The GFR calculator is a web app for educational purposes that can provide insight on doctors taking care of patients with cirrhosis.

Software
RFH-GR Web-Calculator
Client Emmanouil Tsozhatzis 
Funding
UCL
Lead engineer
Raquel Alegre
Languages/technologies JavasciptBootstrapindigo

Ending 2016

HJCFIT

HJCFIT is a library for the maximum likelihood fitting of kinetic mechanisms to sequences of open and shut time intervals from single-channel experiments. It is a part of the DCProgs suite of tools. In this project, we have transformed HJCFIT from a single-process library running on desktop computers to a multi-precision library that can utilise a full Archer node and is thus 14 times faster than the original serial version. We have implemented multi-precision arithmetic, made the code easier to use on high-performance systems and made several other improvements to the overall codebase.

Software
HJCFIT
Client Prof. Lucia Sivilotti, Dr. Remigijus Lape, UCL Department of Neuroscience, Physiology, and Pharmacology
Funding
Archer eCSE
Lead engineer
Jens H Nielsen
Languages/technologies C++, Python, Swig, OpenMP, MPI, MPI4Py, CMake, Eigen, GMP, MPFR

OPTIMET-3D

We are working with Dr Nicolae Panoiu on the OPTIMET-3D code, a fast and massively distributed electromagnetic solver for advanced HPC studies of 3D photonic nanostructures. The objective is to further scale the code from running efficiently on Legion to running efficiently on ARCHER.

Software
OPTIMET-3D
Client
Dr Nicolae Panoiu
Funding
Archer eCSE call
Lead engineer
Gary Macindoe
Languages/technologies MPI, C

Zacros

Zacros is a Kinetic Monte Carlo software package written in Fortran, for simulating molecular phenomena on catalytic surfaces. The tool enables researchers in the areas of Computational Catalysis and Surface Science to perform dynamic modelling of adsorption, desorption, surface diffusion, and reaction processes on heterogeneous catalysts. We are currently working to add MPI parallelisation to the code to support more detailed simulations.

Software
Zacros
Client
Dr Michail Stamatakis, Dept of Chemical Engineering
Funding
Archer eCSE call
Lead engineer
Jens Nielsen
Languages/technologies openmpcmake

HemeLB

After a successful first round of collaboration we are now working to make further improvements to this open-source computational suite for fluid dynamics simulations of blood flow. We have combined an elastic model of a red blood cell with the underlying Computational Fluid Dynamics simulation of blood flow. Case study

Software
HemeLB
Client
Professor Peter Coveney - UCL Centre for Computational Science
Funding
Archer eCSE call
Lead engineer
Mayeul D'Avezac
Languages/technologies
ParMETIS

Ending 2015

Gaussian Process Emulator

Researchers in the Department of Geography have developed this code to monitor the historical and current state of terrestrial vegetation cover using satellite images. We are working to enable the most computationally intensive aspects of this code to run on GPUs in order to accelerate the analysis of these images.

Software
Gaussian Process Emulator
Client
Dr. Jose Gomez-Dans, Prof. Philip Lewis - Department of geography
Funding
Free call
Lead engineer
Sinan Shi
Languages/technologies Python, C++, CUDA, Python/C API, CUBLAS

Radiance Monte Carlo

The aim of this project is to strike a performance/accuracy balance between Radiance Monte Carlo algorithms that operate on a polyhedral mesh (slow but accurate) and a regular grid (fast but less accurate) by using an Octree.

Software
Radocts
Client
Dr Ben Cox, Medical Physics and Biomedical Engineering
Funding
Free call
Lead engineer
Gary Macindoe
Languages/technologies C++11, MATLAB, Boost, CMake, VTK

ShipViz: AIS Data Visualisation

This project is funded by the European Climate Foundation to substantiate shipping policy debates with high-quality infographics. They need the RSD team to create 4D visualisations of ship tracks, similar to previous work they've done to help researchers analysing the 1 billion records of shipping tracks data.

Software
ShipViz
Client
Dr Tristan Smith - UCL Energy Institute
Funding
European Climate Foundation
Lead engineer
Raquel Alegre
Languages/technologies SQL, PostGIS, Python, JavaScript, HTML/CSS,

Electrical Impedance Tomography

Prof. David Holder's group in the Department of Medical Physics and Biomedical Engineering have been pioneering the use of Electrical Impedance Tomography for imaging brain function. We are helping to identify areas of improvement in the software used to produce 4D EIT visualisations and mentoring the EIT team on how to adopt good software development practices.

Software
EIT
Client
Professor David Holder - UCL Dept. of Medical Physics and Biomedical Engineering
Funding
MRC
Lead engineer
Sinan Shi
Languages/technologies Matlab, C++, Arduino, CGAL, Dune

BEM++

BEM++ is a library for solving partial differential equations using the boundary element method with applications in diverse fields such as acoustics and electrostatics developed in the group of Dr Timo Betcke in the UCL Department of Mathematics. The research software development group has been involved in a number of smaller projects improving and maintaining the BEM++ codebase.

Software
BEM++
Client
Dr Timo Betcke - Dept of Mathematics
Funding
EPSRC Software for the future
Lead engineer
Jens Nielsen
Languages/technologies cython, mako, GreatCMakeCookOff

Dataspring

Funded through the JISC "Research Data Spring" initiative, this project seeks to make it possible to efficiently query a corpus of 81000 out-of-copyright books using UCL's research computing infrastructure, and to thereby understand the issues that arise in using traditional HPC resources for humanities work.

Software
Bluclobber
Client
Professor Melissa Terras - UCL Centre for Digital Humanities
James Baker - British Library
Funding
JISC Research Data Spring
Lead engineer
James Hetherington
Languages/technologies Python, libxml, zip, mpi4py

Ending 2014

abYsis

Abysis is an antibody discovery system supporting the analysis of antibody sequence and structure. We refactored the existing codebase and added new features such as the ability to discover and annotate patterns in antibody protein sequences.

Software
abYsis
Client
Dr Andrew Martin, UCL Structural & Molecular Biology
Funding
-
Lead engineer
Jens Nielsen / Gary Macindoe
Languages/technologies Perl, C, Bash, CGI, Mason, jQuery, PostgreSQL

RapidR

We worked with researchers at Great Ormond Street Hospital and the UCL Institute for Child Health to develop a web interface for a new non-invasive downs syndrome test.

Software
RapidR
Client
Dr Chris Boustred - GOSH
Funding
Free call
Lead engineer
Gary Macindoe
Languages/technologies Django, Celery

EnergyPath

We acted as consultants to advise the UCL Energy Institute and Baringa consulting partners on software architecture for complex multi-scale models of the future of the UK energy and housing infrastructure.

Software
EnergyPath
Client
Mr Andrew Smith - Bartlett School Env, Energy & Resources
Funding
Energy Technologies Institute
Lead engineer
James Hetherington
Languages/technologies Python, C++, ArcGIS, CoinOR

Ending 2013

k-Wave

We worked with Dr Ben Cox of to build a parallel simulation code for propagation of high frequency ultrasound in anisotropic media.

Software
k-Wave
Client
Dr Ben Cox - Dept of Med Phys & Biomedical Eng
Funding
Free call
Lead engineer
Mayeul D'Avezac
Languages/technologies eigen, cmake

LikeLTD

We helped Professor David Balding of the UCL Genetics Institute to prepare his forensic DNA analysis package for submission to CRAN, the online repository for sharing R packages. Case study

Software
LikeLTD
Client
Professor David Balding - UCL Genetics Institute
Funding
Free call
Lead engineer
Mayeul D'Avezac
Languages/technologies R