Tap to Close  

 Tap to Close

Associate Professor

Intro to ICT Course Co-ordinator
Masters & PhD Co-ordinator

My main research interests are computer architecture, especially understanding industry trends and how to exploit change (e.g., when new form factors become viable), and bioinformatics. I am a member of the Rhodes University Bioinformatics Research Group (RUBi). I am also editor-in-chief of South African Computer Journal. I’ve written two novels, No Tomorrow and The Day it Rained Forever, both with a climate change theme (available from Amazon).

Contact Details

E-mail: P.Machanick@ru.ac.za
Phone: 046-603-8635
Location: Hamilton Building, Room 101

Projects and Student Opportunities

I am currently working on follow-up studies based on the CentriMo algorithm I worked on with Tim Bailey at the Institute for Molecular Bioscience, University of Queensland. I have funding from the NRF to support:

  • MSc and a PhD scholarship
  • Studentships (Honours; final year undergrad is also a possibility)
  • A postdoc, starting 2013

I have some hints for potential graduate students, especially those from outside Rhodes.

Courses

  • CsC302 operating systems
  • CsC202 Object-oriented programming C++
  • Honours Advanced Architecture
  • MSc Bioinformatics
    • Introduction to Linux
    • Basic Genomics

Past lives

  • Research Officer, Institute for Molecular Bioscience, University of Queensland
  • Senior Lecturer and IT Programs director, School of IT and Electrical Engineering, University of Queensland
  • Associate Professor, Department of Computer Science, University of the Witwatersrand
  • sabbaticals: University of Michigan, Stanford University

I’ve also campaigned for various causes:

  • supporting press freedom and freedom of protest in the apartheid era
  • reducing the space where smokers can annoy others and put their health at risk
  • taking on AIDS denial
  • taking on climate change denial

Publications

Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq'', Nucleic Acids Research, published online 18 May 2012 (abstract and pointer to published version).

Jing Yu, M. Todd Valerius, Mary Duah, Karl Staser, Jennifer K Hansard, Jin-jin Guo, Jill McMahon, Joe Vaughan, Diane Faria, Kylie Georgas, Bree Rumballe, Qun Ren, A. Michaela Mayer, Jan P Junker, Rathi D Thiagarajan, Philip Machanick, Paul A Gray, Alexander van Oudenaarden, David H Rowitch, Charles D Stiles, Qiufu Ma, Sean M Grimmond, Timothy Bailey, Melissa H Little, and Andrew P McMahon, "Identification of molecular compartments and genetic circuitry in the developing mammalian kidney'', Development, vol. 139 pp 1863-1873, 2012 (abstract and pointer to published version).

Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets'', Bioinformatics, vol. 27 no. 12, pp 1696-1697, 2011 (abstract and pointer to published version).

Design principles for contactile computing, Proc. SAICSIT-2011, Cape Town, October 2011, pp 306-309 (abstract and published paper).

Timothy L. Bailey, Mikael Bodén, Tom Whitington and Philip Machanick, "The value of position-specific priors in motif discovery using MEME'', BMC Bioinformatics, vol. 11 p179, 2010 (abstract and pointer to published version).

Philip Machanick, Ariel Liebmann and Peter Fritzson. Modeling of CO2 Reduction Impacts on Energy Prices with Modelica, Proc. 6th International Modelica Conference, Bielefeld, Germany, 3-4 March 2008, pp 565-571 (abstract and PDF).

Design Principles for a Virtual Multiprocessor, Proc. SAICSIT-2007, Port Alfred, September-October 2007, pp 76-82 (abstract and published paper).

John Shield, Peter Sutton and Philip Machanick. Dynamic Cache Switching in Reconfigurable Embedded Systems, Proc. 17th International Conference on Field Programmable Logic and Applications FPL07, Amsterdam, August 2007, pp 111-116 (abstract and PDF).

John Shield, Peter Sutton and Philip Machanick. Analysis of Kernel Effects on Cache Reconfiguration in a Soft-core Reconfigurable System, Proc. 17th International Conference on Field Programmable Logic and Applications FPL07, Amsterdam, August 2007, pp 625-628 (abstract and PDF).

Teaching Java Backwards, Computers&Education, vol. 48 no. 3 pp 396-408, April 2007 (draft version – latest, see the journal – abstract and PDF).

A Social Construction Approach to Computer Science Education, Computer Science Education, vol. 17, no. 1, March 2007, pp 1-20 (abstract and PDF).

SMP-SoC Is the Answer If You Ask the Right Questions, Proc. SAICSIT-2006, Somerset West, South Africa, October 2006, pp 12-21 (abstract and PDF).

Kenneth Wilson and Philip Machanick. SecureTorrent: A Security Framework for File Swarming, Proc. Eleventh Asia-Pacific Computer Systems Architecture Conference ACSAC-2006, Shanghai, September 2006, pp 538-544 (abstract and pointer to published version).

The Value of a Small Microkernel for Dreamy Memory and the RAMpage Memory Hierarchy, Journal of Computer Science and Technology, vol. 20 no. 5 September 2005, pp 586-595 (abstract and PDF).

A Distributed Systems Approach to Secure Internet Mail, Computers and Security, vol. 24 no 6 pp 492-499, 2005 (published version).

Peer Assessment for Action Learning of Data Structures and Algorithms, Proc. 2005 Australasian Computing Education Conference (ACE), Newcastle, NSW, January-February 2005, pp 73-82 (abstract and PDF).

Initial Experiences with Dreamy Memory and the RAMpage Memory Hierarchy, Proc. Ninth Asia-Pacific Computer Systems Architecture Conference, Beijing, September 2004, pp 146-159 (abstract and PDF).

Philip Machanick and Brynn Andrew. Latency Improvement in Virtual Multicasting, Proc. Eighth Asia-Pacific Computer Systems Architecture Conference, Aizu-Wakamatsu City, Japan, September 2003, pp 380-394 (abstract and PDF).

Philip Machanick and Zunaid Patel. L1 Cache and TLB Enhancements to the RAMpage Memory Hierarchy, Proc. Eighth Asia-Pacific Computer Systems Architecture Conference, Aizu-Wakamatsu City, Japan, September 2003, pp 305-319 (abstract and PDF).

Principles Versus Artifacts in Computer Science Curriculum Design, Computers&Education, vol. 41 no. 2, pp 191-201, September 2003 (draft version – latest, see the journal – abstract and published version).

What if DRAM is a Slow Peripheral? Computer Architecture News, vol. 30 no. 6 December 2002, pp 16-19 (abstract and full paper).

Philip Machanick and Zunaid Patel. The Effect of First-Level Cache Improvements on the RAMpage Memory Hierarchy, Proc. IEEE Africon 02, George, South Africa, 2002, pp 71-76 (abstract and PDF).

Programming Skills as an Outcome in Panel Discussion: “Programming Early Considered Harmful” [Judith Gersting, Peter B. Henderson, Philip Machanick and Yale N. Patt], Proc. SIGCSE-2001, Charlotte, NC, 21-25 February 2001, pp 402-403 (slides and detailed web site).

[Philip Machanick and Brynn Andrew] Virtual Multicasting as an Example of Information Mass Transit, Proc. SAICSIT-2000, Cape Town, November 2000, pp 252-255 (special issue of South African Computer Journal, no. 26, November 2000) (abstract and full paper).

Scalability of the RAMpage Memory Hierarchy, South African Computer Journal no. 25 August 2000, pp 68-73 (abstract and full paper).

Experience of Applying Bloom's Taxonomy in Three Courses, Proc. Southern African Computer Lecturers' Association Conference, Strand, June 2000, pp 135-144 (abstract and full paper).

Correction to RAMpage ASPLOS Paper, Computer Architecture News, vol. 27, no. 4 September 1999, pp 2-5 (abstract and published paper).

Teaching Programming Backwards, Proc. Southern African Computer Lecturers' Association Conference, Golden Gate, June 1999, pp 69-73. (abstract and full paper).

Curriculum 2020, in Computer Science Education in the 21st Century, editor Tony Greening, Springer, New York, 2000. (abstract and chapter).

Streaming vs. Latency in Information Mass-Transit, Computer Architecture News, vol. 26 no. 5, December 1998, pp 4-6. (abstract and full paper).

The Skills Hierarchy and Curriculum, Proc. SAICSIT '98, Gordon's Bay, South Africa, November 1998, pp 54-62. (abstract and full paper).

[P Machanick and P Salverda] Implications of Emerging DRAM Technologies for the RAMpage Memory Hierarchy, Proc. SAICSIT '98, Gordon's Bay, South Africa, November 1998, pp 27-40. (abstract and full paper).

Design of a Scalable Video on Demand Architecture, Proc. SAICSIT '98, Gordon's Bay, South Africa, November 1998, pp 211-217. (abstract and full paper).

Disk Delay Lines, Proc. SAICSIT '98 (poster session), Gordon's Bay, South Africa, November 1998, pp 142-144. (abstract and full paper).

[P Machanick, P Salverda and L Pompe] Hardware-Software Trade-Offs in a Direct Rambus Implementation of the RAMpage Memory Hierarchy, Proc. ASPLOS-VIII Eighth International Conference on Architectural Support for Programming Languages and Operating Systems, San Jose, October 1998, pp. 105-114. (abstract and published paper).

[P Machanick and P Salverda] Preliminary Investigation of the RAMpage Memory Hierarchy, South African Computer Journal, no. 21, August 1998, pp 16-25. (abstract and full paper).

Socio-Cultural Challenges for the Internet in South Africa, accepted for Multi-Ethnic Cyberworld track: Crossroads in Culture Studies Conference, Tampere, Finland 28 June-1 July, 1998. (abstract and full paper).

The Abstraction-First Approach to Data Abstraction and Algorithms, Computers & Education, vol. 31 no. 2, September 1998, pp. 135-150. (abstract and published version).

The Case for SRAM Main Memory, Computer Architecture News, vol. 24, no. 5, December 1996 pages 23-30. This version has some minor corrections: (PDF 216K).

An Object-Oriented Library for Shared-Memory Parallel Simulations, PhD Thesis, University of Cape Town, 1996. (abstract and PostScript; also available at Amazon).

[P Machanick, R Apteker, P Green, T McWalter] MISANET: The Southern African Press on the Net, Proc. Directions and Implications of Advanced Computing, Cambridge, MA, May 1994 (abstract and full paper).

[DR Cheriton, HA Goosen, H Holbrook and P Machanick] Restructuring a Parallel Simulation to Improve Cache Behaviour in a Shared-Memory Multiprocessor: The Value of Distributed Synchronization, Proc. 7th Workshop on Parallel and Distributed Simulation, San Diego, May 1993, pp 159-162 (abstract and published paper).

[D R Cheriton H A Goosen and P Machanick] Restructuring a Parallel Simulation to Improve Cache Behavior in a Shared-Memory Multiprocessor: A First Experience, Proc. Int. Symp. on Shared Memory Multiprocessing, Tokyo, April 1991, pp. 109-118; update at 1991 Topaz User's Group Conference, DEC SRC, Palo Alto, 1991

Last Modified : Mon, 10 Apr 2017 15:34:16 SAST