Previous software developed by former colleagues and collaborators include the following packages.

  • RescueNet (links to long dead zombie webpage…) - a neural network package developed by Shaun Mahony to annotate prokaryote genomes using a self organizing map
    • Mahony, S, McInerney, JO, Smith, TJ, Golden, A (2004). Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics, 5:23
  • SOMBRERO (links to long dead zombie webpage…) - a neural network package again developed by Shaun Mahony to characterise/identify transcription factor binding sites, again using self organizing maps
    • Mahony, S, Benos, PV, Smith, TJ, Golden, A (2006). Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Netw, 19, 6-7:950-62
  • BioconductorBuntu - a LAMP bioconductor environment for oligonucleotide/2 color microarray analysis developed by Paul Geeleher
    • Geeleher, P, Morris, D, Hinde, JP, Golden, A (2009). BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server. Bioinformatics, 25, 11:1438-9
  • OpenDDA - a highly optimized Discrete Dipole Approximation to determine the optical scattering properties of geometrically complex particulates, developed by James Mc Donald
    • Mc Donald, J, Golden, A, Jennings, SG (2009). Opendda: a Novel High-Performance Computational Framework for the Discrete Dipole Approximation. International Journal of High Performance Computing Applications, 23, 42-61
  • GMACS - an alignment-free method of clustering of transcription factor binding motifs using genetic-k-medoids, developed by Pilib Ó Broin
    • Broin, PÓ, Smith, TJ, Golden, AA (2015). Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. BMC Bioinformatics, 16:22.
  • AIPSLite - provides a highly powerful means of deploying multiple AIPS routines on distributed computing systems, as applied to large astronomical datasets obtained by radio interferometers, developed by Stephen Bourke
    • Bourke, S, van Langevelde, HJ, Torstensson, K, Golden, A (2013). An AIPS-based Distributed Processing Method for Large Radio Interferometric Datasets’ Experimental Astronomy, Volume 36, Issue 1-2, pp 59-76
  • WASP - an open source environment for managing and analyzing genomic data, the lead developer was Andy McLellan
    • McLellan, AS, Dubin, RA, Jing, Q, Broin, PÓ, Moskowitz, D, Suzuki, M, Calder, RB, Hargitai, J, Golden, A, Greally, JM (2012). The Wasp System: an open source environment for managing and analyzing genomic data. Genomics, 100, 6:345-51
  • GACT - the Genome Annotation Clustering Toolkit, a suite of Java based tools to facilitate the mining of genomic annotations using self organising maps, again developed by Andy McLellan
    • McLellan, AS (2008). Exploring Human Genome Repetitive Elements using Self Organising Maps. MSc Thesis, National University of Ireland, Galway
  • toxoMine - an InterMine instance designed to datawarehouse Omics data on the obligate intracellular parasite, Toxoplasma gondii, developed by David Rhee
    • Rhee, DB, Croken, MM, Shieh, KR, Sullivan, J, Micklem, G, Kim, K, Golden, A (2015). toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. Database (Oxford), 2015:bav066