Software & Websites
Software and websites developed from research
As a result of the protein analysis work carried out for my PhD, I have produced a web-based repository for antigenic peptide data. The link to the site is here -> www.antigens.org.uk
Until the paper is published, the site will require a username and password to access. Please contact me to get access.
The repository databases contain the translated open reading frames with their protein names where known, from the genbank repositories. Additionally, the information from the Cancer Gene Census (Futreal et al 2004) compiled as part of the cancer genome project has been incorporated and cross referenced. The Antigen Finder algorithm has been used to supplement the sequence data with predicted antigenic peptide information, for specific applications in vaccine and diagnostic development.
Species and strains included at this point are:
|
|
This project aims to develop a free crossplatform environment for utilisation of various open source and freely available molecular dynamics and chemistry tools. I haven't developed this for a while now.
Moleculab is all written in Perl with Perl/Tk interfaces. Modules provide a graphical interface to openBabel and Raster3D, as well as modules to perform graphical Kyte Doolittle and Hopp Woods protein hydropathy plots.
Click here to open the Moleculab pages in a new window.
I am just beginning to try and learn more about Molecular Dynamics simulations using the Gromacs package. I am writing helpful scripts as I go along, and I will add them here in case they are useful to anyone else. Eventually these might get incorporated into Moleculab.
First script: to run a basic energy minimisation of a peptide -> minimise.pl
I have recently got involved with the open source development of the Primer3 primer design software originally developed by Steve Rozen and Helen Skaletsky at the Whitehead Institute and the Howard Hughes Medical Institute. From the website ...
"Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers."
"Primer3 -- the C code, the web interface, and the documentation -- are an open source, community-development project hosted by SourceForge." Visit the project pages here -> Primer3
Larcombe IT evolved from Virtua Biomedical Ltd which I formed in January 2002, to provide consultancy and support services to the UK biomedical life science sector. The business specialises in the provision of comprehensive computing and IT support to education, industry or individuals with a particular focus on scientific and technical computing and information management within the biomedical, and bio/chemoinformatics areas.
Previous work for clients has included e-Learning management systems, drug information storage, retrieval and notification systems, small dynamic wap portals, and general website content management systems. Click here for more information on Larcombe IT.