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Rhodes > Computer Science > People > Academic Staff > Prof Philip Machanick

Prof Philip Machanick

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

More on research here

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 am also working on a more general-purpose GPU architecture; for that I have funding from the NRF to support:

  • MSc and a PhD scholarship
  • Studentships (Honours; final year undergrad is also a possibility)

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

Courses

More frequently updated here.

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

More frequently updated here.

  • Philip Machanick, “Video on Demand in a High Bandwidth World”, Proc. SAICSIT 2017, accepted (abstract; details to appear)
  • Philip Machanick and Caleb Kipkurui Kibet, “Challenges with Modelling Transcription Factor Binding” Proc. Next Generation Computing Applications (Nextcomp2017), Mauritius, July 2017. In press (abstract and pointer to preprint)
  • Helen Webb, Olga Steeb, Ashleigh Blane, Lia Rotherham, Shaun Aron, Phillip Machanick, Heini Dirr and Sylvia Fanucchi, “The FOXP2 forkhead domain binds to a variety of DNA sequences with different rates and affinities”, The Journal of Biochemistry, vol. 162 no. 1, pp 45–54, 2017 (abstract and pointer to journal)
  • Philip Machanick, “Teaching Operating Systems: Just enough abstraction”, Proc. SACLA 2016, Cullinan, July 2016, CCIS 642, Springer-Verlag, pp 104-111 (abstract and preprint PDF).
  • Caleb Kibet and Philip Machanick, “Transcription factor motif quality assessment requires systematic comparative analysis” [version 2; referees: 2 approved]F1000Research, 4(ISCB Comm J):1429, 2016 doi: 10.12688/f1000research.7408.2 (abstract and pointer to journal).
  • Caleb Kibet and Philip Machanick, “Comparative Assessment Suite for Transcription Factor Binding Motifs” (poster P28), RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges, November 2015 (abstract only).
  • Caleb Kibet and Philip Machanick, “Comparative analysis of transcription factor binding sites assessment approaches”, ISCB Africa ASBCB Conference on Bioinformatics 2015, March 2015 (abstract only).
  • Philip Machanick, “How General-Purpose can a GPU be?” [Viewpoint], South African Computer Journal, no. 57, December 2015, pp 113-117 http://dx.doi.org/10.18489/sacj.v0i57.347 (abstract and PDF).
  • Caleb K. Kibet and Philip Machanick. “Improving transcription factor binding site prediction using a combination of universal protein binding microarray and DNase-seq data”, SASBi-SAGS 2014 (abstract only)
  • Lavious T. Matereke and Philip Machanick. “Examining in vivo representation of PBM-derived sequence affinity to transcription factors”, SASBi-SAGS 2014 (poster)
  • Philip Machanick and Kieran Hunt, “Preliminary Thoughts on Services without Servers”, Proc. SATNAC 2014, Port Elizabeth, September 2014, pp 469-470 (abstract and published version).
  • Tom Lesluyes, James Johnson, Philip Machanick, Timothy L Bailey, “Differential motif enrichment analysis of paired ChIP-seq experiments”, BMC Genomics vol. 15 no. 1, published online 2 September 2014 (abstract and pointer to published version).
  • Philip Machanick, “Teaching Without Technology”, Proc. SACLA 2014, Port Elizabeth, June 2014, pp 20-23 (abstract and PDF).
  • Philip Machanick and Özlem Tastan Bishop, “How to establish a bioinformatics postgraduate degree programme—a case study from South Africa”, Briefings in Bioinformatics , published online 2 May 2014 (abstract and pointer to published version).
  • 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, 07 Aug 2017 15:37:32 SAST