Publications
Recent
Philip Machanick, “Blended Agile Learning of Computer Architecture under COVID”,
Proc. SACLA 2023,
July 2023, Muldersdrift, South Africa, pp 30–45
(abstract and published version)
Philip Machanick, “The Case for a Cray on a Chip”, Proc. SAICSIT 2023,
July 2023, Muldersdrift, South Africa, pp 14–30
(abstract and published version)
Jorge da Rocha, Houcemeddine Othman, Gerrit Botha, Laura Cottino,
David Twesigomwe, Samah Ahmed, Britt Drögemöller, Faisal Fadlelmola,
Philip Machanick, Mamana Mbiyavanga, Sumir Panji, Galen Wright, Clement
Adebamowo, Mogomotsi Matshaba, Michéle Ramsay, Gustave Simo, Martin
Simuunza, Caroline Tiemessen, Sandra Baldwin, Mathias Chiano, Charles
Cox, Annette Gross, Pamela Thomas, Francisco-Javier Gamo and Scott
Hazelhurst, “The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations”
Frontiers in Pharmacology, 12, 2021
doi:10.3389/fphar.2021.634016
(abstract and pointer to journal).
Philip Machanick, “Revisiting early-stage COVID-19 strategy options”
[version 3; peer review: 2 approved]
F1000Research, 9:327, 2021
doi:10.12688/f1000research.23524.3
(abstract and pointer to journal).
Philip Machanick, “A Preliminary Study of Minimal-Contention Locks”, Proc. SAICSIT 2018,
September 2018, Port Elizabeth, South Africa, pp 269–278
(abstract and pointer to published version)
Philip Machanick, “Project CrayOn: Back to the future for a more General-Purpose GPU?”, Proc.
2nd Workshop on Pioneering Processor Paradigms, Vienna, 25 Austria 2018. (abstract and full text)
Philip Machanick, “Video on Demand in a High Bandwidth World”, Proc. SAICSIT 2017,
September 2017, Thaba Nchu, Free State, South Africa
(abstract and pointer to published version)
Philip Machanick and Caleb Kipkurui Kibet, “Challenges with Modelling Transcription Factor Binding”
Proc. Next Generation Computing Applications (Nextcomp2017), Mauritius, July 2017, pp 68-74. (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)
Sexual Violence Task Team. “We Will Not Be Silenced”:
A Three-Pronged Justice Approach to Sexual Offences and Rape Culture at Rhodes University/Uckar (Authors in alphabetic order:
Rod Amner, Dinah Arnott, Charmaine Avery, Kim Barker, Werner Bohmke, Dr Malvern
Chiweshe, Laura de Lange, Natalie Donaldson, Sarah Green, Chelsea Haith, Michael Joseph, Dr Lindsay
Kelland, Jordan King, Philip Machanick: Catriona Macleod, Jabulile Mavuso, Manthipe Moila,
Nomangwane Mrwetyana, Sam Naidu, Yanela Ndabula, Craig Paterson, Jay Pillay, Lynn Quinn,
Esther Ramani, Diale Rapula, Judith Reynolds, Susan Robertson, Alex Sutherland and Pedro Tabensky), December 2016.
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).
Older Publications
A few selected publications from this point on… (more at my ACM author page)
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 PDF; also available at Amazon).
From Data Abstraction to Algorithms, Proc. SACLA 1996, Bakubung, June 1996, pp 65-74
(abstract and preprint PDF).
From Modula-2 to C++: Advanced Programming with Class, Proc. SACLA 1995, Katberg, Eastern Cape, July 1995 pp 175-180
(abstract and preprint PDF).
[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).
SpaceLib: A Library for Shared-Memory Parallel Applications, Proc. 8th National Conference for Masters and PhD Students in Computer Science,
Pretoria, South Africa, July 1993 pp 215-220
(abstract and preprint PDF).
[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 Behaviour, in Shared Memory Multiprocessing, Norihisa Suzuki, MIT Press, 1992, pp 261-286. (abstract).
[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
Philip Machanick p.machanick at [NO SPAM] ru.ac.za
