I am a PhD student in bioinformatics, a first class honours graduate in computer engineering, a computer and electronics enthusiast, an open-source software developer and advocate, an avid traveller, a hiker, a singer and an experimental amateur chef. I have twelve years of industry and academic experience developing software in C++ and a variety of scripting languages, including six years developing high-performance distributed and parallel algorithms for genome sequence assembly, and six years developing embedded and real-time control systems. I have extensive experience developing portable software for POSIX systems such as GNU/Linux and Mac OS X. When developing performance-critical software, I understand the hardware from the transistor up.
NSERC CGS-M and CGS-D scholarship student in bioinformatics. Coursework in bioinformatics, statistics, machine learning and genetics. GPA 4.26 (93%)
Scholarship student in computer engineering. Completed an honours undergraduate thesis and two full years of co-op work experience at three companies. GPA 3.85
Developed the genome sequence assembly software package, ABySS. This heavily parallel and distributed software system, which uses both MPI and OpenMP for parallel computation, was the first system to assemble a human genome using short-read sequencing technology.
Developed the firmware for Pathway's product line of small, low-cost lighting control devices. These small devices, which use Atmel's AVR and ARM microcontrollers, convert between a variety of lighting-control protocols including DMX512, analog, PWM and contact closure. Modernized the lighting control industry in developing a device, the Pathport, to adapt legacy lighting control equipment to Ethernet. This industry-changing product won an award for best new product at the industry trade show, Lighting Dimensions International.
Worked on the rapid thermal processing tool used in the manufacturing of semiconductor devices. Developed the temperature sensor and lamp power control system using the QNX real-time operating system.
Maintain open-source bioinformatics software packages for the Mac OS package manager, Homebrew-science, and the Debian distribution of GNU/Linux.
8 of 19 peer-reviewed publications, h-index 14, over 2000 citations
I Birol, A Raymond, SD Jackman, et al. (2013) Bioinformatics
CI Keeling, MM Yuen, NY Liao, TR Docking, SK Chan, GA Taylor, DL Palmquist, SD Jackman, et al. (2013) Genome Biology
S Haridas, Y Wang, L Lim, SM Alamouti, SD Jackman, et al. (2013) BMC Genomics
G Robertson, J Schein, R Chiu, R Corbett, M Field, SD Jackman et al. (2010) Nature Methods
SD Jackman and I Birol (2010) Genome Biology
I Birol, SD Jackman, CB Nielsen et al. (2009) Bioinformatics
CB Nielsen, SD Jackman, I Birol et al. (2009) IEEE Transactions on Visualization and Computer Graphics
JT Simpson, K Wong, SD Jackman et al. (2009) Genome Research
Techniques for analysis of whole-genome shotgun sequencing and RNA-seq, including de novo sequence assembly (ABySS), sequence alignment (BWA, gmap, exonerate, BLAT, BLAST), variant calling (samtools), genome annotation (MAKER) and visualization and inspection of genome assemblies and rearrangements (IGV)
C++, C, R, Python, Ruby, Matlab, Haskell and assembly
OpenMP, MPI and POSIX threads
Mac OS X, Debian, Ubuntu and other GNU/Linux distributions
- 2013-present Natural Sciences and Engineering Research Council of Canada (NSERC) Canada Graduate Scholarship (CGS-M and CGS-D)
- 2012–2013 CIHR/MSFHR Strategic Training Program in Bioinformatics
- 1999–2004 Open Undergraduate Scholarship
- 1998–1999 Tadeusz Specht Memorial Entrance Scholarship in Science