I am a software developer living in the beautiful city of Vancouver, British Columbia. I have experience with web application design, bioinformatics, database development and more. I've set up this portfolio to showcase some of the projects I have worked on.
I am currently seeking remote employment, download my Resume or contact me via email at .
RECall is a desktop application designed to process HIV chromatogram trace files in an automated manner. It does quality analysis, basecalling, sequence alignment and assembly. As an output it provides a drug resistance interpretation report. This project utilizes a technology stack that includes Ruby, Gtk2, Sinatra, and Sqlite3. The web version can be found at https://recall.bccfe.ca and is now managed by the Centre for excellence in HIV/AIDS.
HCV RECall is a HCV focused version of the HIV RECall web client.
Nano ReCall The Nano ReCall software allows you to process your Oxford Nanopore HIV FASTQ files on the web. On completion, it provides a resistance report, consensus sequences, aligned fasta files and amino acid frequencies for Protease, Reverse Transcriptase and Integrase gene regions. This project utilizes a technology stack that includes Ruby, Sinatra, and Sqlite3.
Barcode Agent is a software tool used for automatic basecalling and manual inspection of aligned chromatogram data for Barcode genes like CO1. This project utilizes a technology stack that includes Ruby and GTK3.
Labosaurus is both a LIMS and a QMS. It was created with the goal to provide a wide range of features for small to medium sized labs at a reasonable price. Labosaurus provides modules for employee records, SOPs, sample management, equipment inventory, reagent inventory, incident reports, and task management. It also includes an API so that software developers can integrate its functionality into their current LIMS systems. This project utilizes a technology stack that includes Ruby, Vue, Sinatra, MySQL, AWS infrastructure, and Webpack. This project was shut down in April 2024 due to lack of interest.
Microcline BioSeq lab is a free tool that lets users align nucleotide and amino acid sequences from their browser. Alignment parameters can be customized as needed, and the software has an option to align to the reverse complement if a sequence has a higher alignment score. Alignments are done with the Needleman-Wunsch algorithm with Gotoh's Affine Penalty optimizations. This project utilizes a technology stack that includes Vue, Tailwind CSS, Webpack and HTML canvases.
Microcline Chromatogram Viewer is a free tool that lets users view their ABI or SCF chromatogram files. It also lets a user extract some of the internal file fields that aren't always visible from other tools. The files are all processed in javascript so that no files are uploaded to us and the web tool itself can be saved locally for offline use. This project utilizes a technology stack that includes just Webpack and HTML canvases.
Microcline Label Maker is a free web application that simplifies the label printing process. Easily print adhesive labels for product IDs, barcodes, asset numbers, inventory tags, sample identifiers, and more onto adhesive label sheets. Customize measurements, margins, rows, and columns to fit your specific requirements. Can print Code 39 or Code 39 extended barcode fonts, QR codes, or plain text. Additionally, you can save and share your settings for added convenience. This project utilizes a technology stack that includes Vue, JQuery and Webpack.
Woods CK, Brumme CJ, Liu TF, Chui CK, Chu AL, Wynhoven B, Hall TA, Trevino C, Shafer RW, Harrigan PR. Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol. 2012 Jun;50(6):1936-42. doi: 10.1128/JCM.06689-11. Epub 2012 Mar 7. PMID: 22403431; PMCID: PMC3372133.
Brumme ZL, Brumme CJ, Chui C, Mo T, Wynhoven B, Woods CK, Henrick BM, Hogg RS, Montaner JS, Harrigan PR. Effects of human leukocyte antigen class I genetic parameters on clinical outcomes and survival after initiation of highly active antiretroviral therapy. J Infect Dis. 2007 Jun 1;195(11):1694-704. doi: 10.1086/516789. Epub 2007 Apr 24. PMID: 17471440.
Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr. 2010 Aug;54(5):506-10. doi: 10.1097/QAI.0b013e3181d0558f. PMID: 20512044.
McGovern RA, Thielen A, Mo T, Dong W, Woods CK, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS. 2010 Oct 23;24(16):2517-25. doi: 10.1097/QAD.0b013e32833e6cfb. PMID: 20736814.
Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis. 2011 Jan 15;203(2):237-45. doi: 10.1093/infdis/jiq030. PMID: 21288824; PMCID: PMC3071057.
Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJ, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis. 2011 Oct;53(7):732-42. doi: 10.1093/cid/cir493. PMID: 21890778.
McGovern RA, Thielen A, Portsmouth S, Mo T, Dong W, Woods CK, Zhong X, Brumme CJ, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial. J Acquir Immune Defic Syndr. 2012 Nov 1;61(3):279-86. doi: 10.1097/QAI.0b013e31826249cf. PMID: 23095934.
Knapp DJ, McGovern RA, Dong W, Poon AF, Swenson LC, Zhong X, Woods CK, Harrigan PR. Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing. J Clin Microbiol. 2013 Feb;51(2):444-51. doi: 10.1128/JCM.00739-12. Epub 2012 Nov 21. PMID: 23175258; PMCID: PMC3553919.
Swenson LC, Chui CK, Brumme CJ, Chan D, Woods CK, Mo T, Dong W, Chapman D, Lewis M, Demarest JF, James I, Portsmouth S, Goodrich J, Heera J, Valdez H, Harrigan PR. Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure. Antimicrob Agents Chemother. 2013 Dec;57(12):6122-30. doi: 10.1128/AAC.01534-13. Epub 2013 Sep 30. PMID: 24080655; PMCID: PMC3837924.
Gonzalez-Serna A, Min JE, Woods C, Chan D, Lima VD, Montaner JS, Harrigan PR, Swenson LC. Performance of HIV-1 drug resistance testing at low-level viremia and its ability to predict future virologic outcomes and viral evolution in treatment-naive individuals. Clin Infect Dis. 2014 Apr;58(8):1165-73. doi: 10.1093/cid/ciu019. Epub 2014 Jan 14. PMID: 24429436; PMCID: PMC3967823.
Swenson LC, Min JE, Woods CK, Cai E, Li JZ, Montaner JS, Harrigan PR, Gonzalez-Serna A. HIV drug resistance detected during low-level viraemia is associated with subsequent virologic failure. AIDS. 2014 May 15;28(8):1125-34. doi: 10.1097/QAD.0000000000000203. PMID: 24451160; PMCID: PMC4278403.
Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CK, Schinkel J, Joy JB, Harrigan PR, Poon AF. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Res. 2014 Jul;42(12):e98. doi: 10.1093/nar/gku355. Epub 2014 May 7. PMID: 24810852; PMCID: PMC4081055.
Lee GQ, Dong W, Mo T, Knapp DJ, Brumme CJ, Woods CK, Kanters S, Yip B, Harrigan PR. Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy. PLoS One. 2014 Jun 6;9(6):e99000. doi: 10.1371/journal.pone.0099000. PMID: 24905411; PMCID: PMC4048224.
Jacka B, Applegate T, Krajden M, Olmstead A, Harrigan PR, Marshall B, DeBeck K, Milloy MJ, Lamoury F, Pybus OG, Lima VD, Magiorkinis G, Montoya V, Montaner J, Joy J, Woods C, Dobrer S, Dore GJ, Poon AF, Grebely J. Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada. Hepatology. 2014 Nov;60(5):1571-1580. doi: 10.1002/hep.27310. Epub 2014 Sep 29. PMID: 25042607; PMCID: PMC4211947.
Poon AF, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JS, Harrigan PR. The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada. J Infect Dis. 2015 Mar 15;211(6):926-35. doi: 10.1093/infdis/jiu560. Epub 2014 Oct 13. PMID: 25312037; PMCID: PMC4351365.
Chui CK, Dong WW, Joy JB, Poon AF, Dong WY, Mo T, Woods CK, Beatty C, Hew H, Harrigan PR, Brumme CJ. Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir. J Clin Microbiol. 2015 Sep;53(9):2942-50. doi: 10.1128/JCM.00650-15. Epub 2015 Jul 1. PMID: 26135875; PMCID: PMC4540893.
Poon AF, Gustafson R, Daly P, Zerr L, Demlow SE, Wong J, Woods CK, Hogg RS, Krajden M, Moore D, Kendall P, Montaner JS, Harrigan PR. Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study. Lancet HIV. 2016 May;3(5):e231-8. doi: 10.1016/S2352-3018(16)00046-1. Epub 2016 Apr 7. PMID: 27126490; PMCID: PMC4853759.
Kamelian K, Lepik KJ, Chau W, Yip B, Zhang WW, Lima VD, Robbins MA, Woods C, Olmstead A, Joy JB, Barrios R, Harrigan PR. Prevalence of Human Immunodeficiency Virus-1 Integrase Strand Transfer Inhibitor Resistance in British Columbia, Canada Between 2009 and 2016: A Longitudinal Analysis. Open Forum Infect Dis. 2019 Feb 12;6(3):ofz060. doi: 10.1093/ofid/ofz060. PMID: 30895202; PMCID: PMC6419991.
Lapointe HR, Dong W, Dong WWY, Kirkby D, Woods C, Poon AFY, Howe AYM, Harrigan PR, Brumme CJ. Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses. 2021 Aug 30;13(9):1721. doi: 10.3390/v13091721. PMID: 34578305; PMCID: PMC8473162.
Delaney KE, Ngobeni T, Woods CK, Gordijn C, Claassen M, Parikh U, Harrigan PR, van Zyl GU. Nano-RECall provides an integrated pipeline for HIV-1 drug resistance testing from Oxford Nanopore sequence data. Trop Med Int Health. 2023 Mar;28(3):186-193. doi: 10.1111/tmi.13851. Epub 2023 Jan 13. PMID: 36599816; PMCID: PMC10230441.