Steve Cobbold's Software for Acorn/RISC-OS.

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There is now a new program from Virtual Acorn that can run RISC-OS on a PC under Windows, emulating an Acorn A5000. I have tested all my programs on this emulator and they all seem to work perfectly: running on Virtual Acorn on an 800MHz Windows 2000 PC they run at about half the speed of my 200MHz StrongARM Acorn RISC-PC.
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All applications are written in BBC BASIC V and will only run on RISC-OS.
(They have been tested on Acorn A4, RISC-PC600 and StrongARM RISC-PC machines, and a variety of Windows PCs running Virtual Acorn.)

All programs are available FREEWARE and "as is", and no responsibility for any outcome resulting from their use is accepted or implied. Please contact me if you wish to modify or further distribute them, and please let me know if you find them useful!

!SAGEClus

!SAGEClus is a complete suite of software for cluster analysis and presentation of SAGE data. It was developed from the !Laws program used for cluster analysis of monoclonal antibodies and CD antigens, but has been optimised for the much larger SAGE datasets, and to be fully usable on Windows PCs running the Virtual Acorn emulator. This software, together with fully annotated tag data from 29 murine SAGE libraries used to analyse regulation within the immune system, is now available to download as the submitted manuscript has been accepted for publication (see below). This is in standard WinZip format and is simple to install on a PC under the Acorn emulator.
The following files are available for download:
Readme File for installation of !SAGEClus software and data (1.7k)
The !SAGEClus software files in Zip format (2.1M)
A Table of the SAGE libraries included with !SAGEClus (PDF file: 182k)
The SAGE data tabulated in Excel file format (5.2M)
A colourful SAGE expression chart for known genes (PDF file: 638k)

For more details and original publications please refer to:
Cobbold, SP., Nolan, K., Graca, L., et al.
Gene Expression Signatures for Regulation in the Immune System.
Immunol. Reviews, in the press. (2003)
Cobbold, SP., Adams, E., Graca, L., Waldmann, H.
Serial analysis of gene expression provides new insights into regulatory T cells.
Seminars in Immunology 15(4): 209-214. (2003)
Zelenika, D., Adams, E. Humm, S., Graca, L., Thompson, S., Cobbold, S*., Waldmann, H*.
Regulatory T cells over-express a subset of Th2 gene transcripts
J. Immunol. 168: 1069-1079. (2002)
Abstract | Article | PDF
(Article and PDF formats only available to JI subscribers)
Laws2 - a self contained package for presentation and cluster analysis of FACS staining as used in the Third Leukocyte Antigen and subsequent workshops. Includes data/clusters from 3rd and 4th workshops (but not 5th or later) as well as murine and canine (CLAW) data. It can be used to perform live cluster analysis at workshops, and will even cope with mixtures of appropriately coded FACS, ImmunoHistology, and ELISA data!

SurvAn - a self contained package for analysing survival data, particularly for bone marrow transplantation, using LogRank methods. Will output survival curves (Draw format) including error bands. Also chi-squared, trend, and power of trial calculations.

CoxSurv - multivariate analysis of survival data using the Cox model. Inputs CSV format data and can output multivariate corrected survival data (in CSV format) for import to graphing packages (eg Fireworks or even Excel!). The progam can output survival curves predicting the interaction of two different variables, whilst still allowing for all the other significant factors, together with error bars and calculations of the P value (trend) of the interaction. This package is not completely user friendly nor fully desktop front ended (it runs in an Edit Task Window, so it does actually multitask, but requires typed input rather than mouse clicks and drags), so please E-mail me if you need any help using it. It almost certainly needs a fast StrongArm RISC-PC for any useful analysis if you have more than a few hundred patients and 10+ covariates in the dataset.

Note: Laws2, Survan and CoxSurv are archived with John Kortink's freeware RISC-OS application "PackDir", which I have included here in !Spark format (sorry - I only have the unpacking version of !Sparkplug).

If you actually wish to use any of the above and need help/improvements/bug fixes etc. then you can E-mail me on stephen.cobbold@path.ox.ac.uk

Steve Cobbold - last updated 27th August 2003.