Cirriculum Vitae - Steven Ness

email : sness@sness.net

phone: (604) 485-7235

address: 4623 Harvie Avenue, Powell River, BC, CANADA, V8A 2K8

Employment History

2003-2006 Scientific Programmer - Leiden University
  • Designed and implemented a free software platform for automated crystallographic structure solution using a wide variety of languages including Tcl, C, Bourne Shell, C shell and FORTRAN.
  • This system, named "Crank" has been used by over 100 crystallographic laboratories and is now included as part of the open source CCP4 Collaborative Computational Project. It is licenced under the GPL.
1995 - 2006 Self-Employed - "sness.net technologies"
  • Scientific consulting programming
  • Linux and Windows setup, administration and consulting
  • HTML design and CGI scripting
  • C/C++ programming
  • Responsible for all aspects of this small business
Major Contracts:
Genome Sequence Centre Washington University at St. Louis
  • Designed and implemented feature additions and bug fixes to the genomics physical map software "FPC".
  • Languages: C, Perl
Neurotech Inc.
  • Developed theory and implementation of a brainwave tool as a plug-in to the popular video compositing tool "After Effects"
  • Languages: C, Perl
University of British Columbia - Department of Biochemistry
  • Designed and constructed a parallel processing farm for high-throughput NMR determination of protein structures.
University of Alberta - Department of Agriculture Food and Nutrition Sciences
  • Helped to administer and install Windows on all computers in the department, including liasing with faculty and on-site troubleshooting.
1997 - 2006 Co-founder Dockvision Inc.
  • Designed and wrote Genetic Algorithm optimatization for drug docking software package
  • Designed and wrote graphical front end for DockVision
  • Responsible for website design, mantenance, and answering of questions from users.
2000 - 2001 Senior Programmer BC Genome Sequence Centre
  • Wrote software for building and analyzing physical maps of large genomes.
  • Helped coordinate efforts to build complete restriction maps of Mouse, Rat and Cow genomes.
  • Added several new features to the industry standard "FPC" software platform, used by all major genome centres for physical mapping.
  • Training and teaching of programmers and genome technicans on software platforms.
  • Custom design of fingerprint analysis tools.
1999 - 2000 Programmer, Stormix Technologies
  • Kernel level and hardware detection programming
  • Responsible for design and implementation of hardware detection system for Storm Linux 2000
  • Implemented splash screen for Linux boot integrated with kernel bootup messages, along with PC speaker programming for boot sound
  • nanoGUI programming - graphics library for embedded devices
1997 - 1999 Programmer, Systems Administrator - UBC
  • Responsible for setup and administration of all computers and software
  • Administered lab computers - 10 heavily used SGI and Linux systems
  • Account setup and UNIX instruction for beginners
  • Design and maintenance of an extensive HTML crystallography program reference library
  • Network admin and accounts officer for Biochemistry department
  • Packages : Apache, sendmail, Samba, NFS, IRIX, Linux
  • Languages: C, C++, F77, bash, csh, perl
1995-1997 Programmer/ Molecular Modeler- University of Alberta
  • Designed and implemented Gamma, a molecular docking program utilizing Genetic Algorithms as an optimization engine.
  • Designed and implemented a GUI to our suite of docking programs, Research, RSDataBase and Gamma.
  • GUI designed as interface to command line tools
  • Designed and implemented 3D molecular viewer using SGI Open Inventor and C++.
  • Languages used - C, C++, Fortran77, bash, csh
1992-1995 Programmer - University of Alberta
  • Designed and implemented Genetic Algorithm general function optimizing program. Designed and implemented data clustering software for data mining of docking results.
  • Language used - C and C++
1987 Programmer - Alberta Environment Research Centre
  • Designed and implemented timekeeping and scheduling software
  • User interface design, Database integration
  • Language used - Turbo Pascal

Papers

Daniel Peter Biro, Steven Ness, Matthew Wright, W. Andrew Schloss and George Tzanetakis Decoding the Song: Histogram-Based Paradigmatic and Syntagmatic Analysis of Melodic Formulae in Hungarian Laments, Jewish Torah Trope, Tenth Century Plainchant and Koran Recitation EMUS Expressivity in MUsic and Speech : IRCAM - Institut de Recherche et de Coordination Acoustique/Musique - Paris, France

Jan Pieter Abrahams, Steven Ness, and Navraj S. Pannu Macromolecular Crystallography conventional and high-throughput methods Chapter 10. Phase refinement through density modification. pp.143-53 - 2007

Skubak P, Ness S, Pannu NS. Extending the resolution and phase-quality limits in automated model building with iterative refinement, Acta Crystallographica D61, 1626-1635. - 2005

Steven R. Ness, Irakli Sikharulidze, R.A.G de Graaff and Navraj S. Pannu Crank, Crunch2 and Bp3: A platform for rapid automated structure determination. Collaborative Computational Project No. 4 on Protein Crystallography. Newsletter Number 42 Summer 2005

Steven R. Ness, Rudolf A.G. de Graaff, Jan Pieter Abrahams, and Navraj S. Pannu Crank: New methods for automated macromolecular crystal structure solution Structure, Vol 12, 1753-1761, October 2004

Simon G. Gregory, Mandeep Sekhon, Jacqueline Schein, Shaying Zhao, Kazutoyo Osoegawa, Carol E. Scott, Richard S. Evans, Paul W. Burridge, Tony V. Cox, Christopher A. Fox, Richard D. Hutton, Ian R. Mullenger, Kimbly J. Phillips, James Smith, Jim Stalker, Glen J. Threadgold, Ewan Birney, Kristine Wylie, Asif Chinwalla, John Wallis, LaDeana Hillier, Jason Carter, Tony Gaige, Sara Jaeger, Colin Kremitzki, Dan Layman, Jason Maas, Rebecca McGrane, Kelly Mead, Rebecca Walker, Steven Jones, Michael Smith, Jennifer Asano, Ian Bosdet, Susanna Chan, Suganthi Chittaranjan, Readman Chiu, Chris Fjell, Dan Fuhrmann, Noreen Girn, Catharine Gray, Ran Guin, Letticia Hsiao, Martin Krzywinski, Reta Kutsche, Soo Sen Lee, Carrie Mathewson, Candice McLeavy, Steve Messervier, Steven Ness, Pawan Pandoh, Anna-Liisa Prabhu, Parvaneh Saeedi, Duane Smailus, Lorraine Spence, Jeff Stott, Sheryl Taylor, Wesley Terpstra, Miranda Tsai, Jill Vardy, Natasja Wye, George Yang, Sofiya Shatsman, Bola Ayodeji, Keita Geer, Getahun Tsegaye, Alla Shvartsbeyn, Elizabeth Gebregeorgis, Margaret Krol, Daniel Russell, Larry Overton, Joel A. Malek, Mike Holmes, Michael Heaney, Jyoti Shetty, Tamara Feldblyum, William C. Nierman, Joseph J. Catanese, Tim Hubbard, Robert H. Waterston, Jane Rogers, Pieter J. de Jong, Claire M. Fraser, Marco Marra, John D. McPherson, David R. Bentley. "A physical map of the mouse genome" Nature 418, 743-750, Aug 15 2002

S.R. Ness, Terpstra, W., Krzywinski, M., Marra M.A. and Jones,S.J.M. "Assembly of fingerprint contigs: parallelized FPC" Bioinformatics 2002 Mar;18(3):484-5

Steven R. Ness, Terence P. Lo, Grant Mauk Structural Models for the Alkaline Conformers of Yeast iso-1-Ferricytochrome c. Israel Journal of Chemistry 2000 - Volume 40(1) 21 - 25

Ness S, Martin R, Kindler AM, Paetzel M, Gold M, Jensen SE, Jones JB, Strynadka NC. Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase. Biochemistry. 2000 May 9;39(18):5312-21

Trevor Hart, Richard Gillilan, Ryan Lilien, Steven Ness, and Randy Read. Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment. High Performance Computing Systems and Applications, pp 299-308. Kluwer Academic Publisher (Summer 1998).

Ness SR, Hart TN. Flexible Ligand Docking for Drug Design Workshop Cornell Theory Center Workshop April 24 - 26, 1997

Hart TN, Ness SR, Read RJ. Critical evaluation of the research docking program for the CASP2 challenge. Proteins. 1997 Supplement 1:205-9.

Read RJ, Hart TN, Cummings MD, Ness SR. Monte Carlo algorithms for docking to proteins. Supramolecular Chemistry, 6 (1-2): 135-140 1995.

Ness SR. GAMMA, an application of Genetic Algorithms to the Docking Problem University of Alberta - Summer Student Research Thesis - 1994

Ness SR. Effects of Temperature Change on the Oscillatory Briggs-Rauscher Chemical Reaction. Lester B. College of the Pacific, November 1990

Ness SR, Ness MM. Designer Genes : Tertiary Structural Analysis of Proteins Canada Wide Science Fair 1988-1989 - Winner Gold Medal 1988 - Gold Medal and Best Senior Project 1989

Programming Languages and Specialties

  • Ruby on Rails
  • C/C++
  • XML
  • Java
  • Tcl
  • Emacs
  • Shell scripting (bash, csh)
  • zsh
  • Perl
  • Genetic Algorithms
  • Neural Networks
  • GUI design and programming
  • AI

Platforms

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  • Linux - RedHat, Fedora, Stormix, Slackware and Debian
  • SGI - IRIX 4.0.5, 5.3, 6.3, 6.5
  • SunOS
  • AIX RS/6000
  • Macintosh
  • Win95/Win98/Win2000/WinXP