András Aszódi

Sapere aude!

Software

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I have been developing scientific software for the most part of my career. Some of the packages I have made available here in the hope that they might be useful.

Full packages

These are relatively complex scientific applications.

MULTOVL

MULTOVL is a C++ application that can detect multiple overlaps of genomic regions very quickly. The basic idea of the algorithm is illustrated below.

MULTOVL algorithm

MULTOVL User Guide

The source code (tarred-gzipped archive, 794 kB) and precompiled binaries are freely available from BitBucket and from GitHub. The software is also referenced at OmicTools and at BioTools.

Please cite the following publication when using MULTOVL in your research:

Aszódi, A. (2012): MULTOVL: Fast multiple overlaps of genomic regions. Bioinformatics 28: 3318-3319.

OpenStructure

An object-oriented toolkit for (macro)molecular modelling, initially developed in collaboration between the Novartis In Silico Sciences (ISS) unit which I built up and led, the University of Basel and the Fachhochschule Aargau. When the In Silico Sciences unit was closed down, Novartis kindly released the source so that the other collaboration partners could continue working on it. The code is now available at the OpenStructure website and the package is described in a Bioinformatics paper. You will find my name in the Acknowledgements.

DRAGON

This is a protein structure prediction program package using distance geometry. I developed it between 1992 and 1996 when I was a postdoc in Willie Taylor's lab at the NIMR in London. I have written several papers using DRAGON, here is the main publication describing the algorithms and the software:

Aszódi, A., Gradwell, M. J. and Taylor, W. R. (1995): Global fold determination from a small number of distance restraints. J. Mol. Biol. 251, 308-326.

The DRAGON source code, written in ancient C++, is of historical interest only.

SDPDIST

This application can reconstruct complex 3-dimensional structures from an incomplete set of distance constraints and restraints. I am still working on it. More information will be available after publication.

Small utilities

Other people's code

This is a collection of various packages written by others that I found useful. Please consult the original sources for the authors.

IpOpt easy installation package

The IpOpt nonlinear solver and its supporting libraries (HSL, Metis, Mumps) packaged together for convenience, with installation instructions.