Allen Chi Shing Yu, PhD, is a Chevening Scholar, 2017-18, and an MSc student in computer science at the University of Oxford. He holds a PhD degree in Biochemistry from the Chinese University of Hong Kong, and he has used Python and Matplotlib extensively during his 10 years of experience in the field of bioinformatics and big data analysis. During his research career, Allen has published 12 international scientific research articles and presented at four international conferences, including on-stage presentations at the Congress On the Future of Engineering Software (COFES) 2011, USA, and Genome Informatics 2014, UK. Other research highlights include discovering the novel subtype of Spinocerebellar ataxia (SCA40), identifying the cause of pathogenesis for a family with Spastic paraparesis, leading the gold medalist team in 2011 International Genetically Engineered Machine (iGEM) competition, and co-developing a number of cancer genomics project.
Apart from academic research, Allen is also the co-founder of Codex Genetics Limited, which aims to provide personalized medicine service in Asia through the use of the latest genomics technology. With the financial and business support from the HKSAR Innovation and Technology Commission, Hong Kong Science Park, and the Chinese University of Hong Kong, Codex Genetics has curated and transformed recent advances in cancer and neuro-genomics research into clinically actionable insights.
I wish to thank my fiancée, Dorothy, for her constant love and support, especially during the difficult time in balancing family, work, and life. On behalf of the authors, I would like to thank the wonderful team at Packt Publishing—Mayur, Tushar, Vikrant, Vivek, and the whole editorial team who helped in the creation of this book. Thanks to Tushar's introduction, the authors feel greatly honored to take part in this amazing project. Special thanks and much appreciation to Mayur for guiding the production of this book from the ground up. The authors truly appreciate the comprehensive reviews from Nikhil Borkar. We cannot be thankful enough to the entire Matplotlib and Python community for their hard work in creating open and incredibly useful tools. Last but not least, I would like to express my sincere gratitude to Prof. Ting-Fung Chan, my parents, friends, and colleagues for their guidance in my life and work. Chevening Scholarships, the UK government’s global scholarship programme, are funded by the Foreign and Commonwealth Office (FCO) and partner organisations.
Claire Yik Lok Chung is now a PhD student at the Chinese University of Hong Kong working on Bioinformatics, after receiving her BSc degree in Cell and Molecular Biology. With her passion for scientific research, she joined three labs during her college study, including the synthetic biology lab at the University of Edinburgh. Her current projects include soybean genomic analysis using optical mapping and next-generation sequencing data. Claire started programming 10 years ago, and uses Python and Matplotlib daily to tackle Bioinformatics problems and to bring convenience to life. Being interested in information technology in general, she leads the Campus Network Support Team in college and is constantly keeping up with the latest technological trends by participating in PyCon HK 2016. She is motivated to acquire new skills through self-learning and is keen to share her knowledge and experience. In addition to science, she has developed skills in multilingual translation and graphic design, and found these transferable skills useful at work.
I would like to thank Allen for getting me on board in this exciting authorship journey, and for being a helpful senior, always generous in sharing his experience and insights. It has been a great pleasure to work closely with Allen, Aldrin and the whole editorial team at Packt. I am grateful to everyone along the way that brought my interest in computer to daily practice. I wish to extend my sincere gratitude to my supervisor, Prof. Ting-Fung Chan, my parents, teachers, colleagues, and friends. I would like to make a special mention to my dearest group of high school friends for their unfailing support and source of cheer. I would also like to thank my childhood friend, Eugene, for introducing and provoking me into technological areas. With all the support, I will continue to prove that girls are capable of achieving in the STEM field.
Aldrin Kay Yuen Yim is a PhD student in computational and system biology at Washington University School of Medicine. Before joining the university, his research primarily focused on big data analytics and bioinformatics, which led to multiple discoveries, including a novel major allergen class (designated as Group 24th Major allergen by WHO/IUIS Allergen Nomenclature subcommittee) through a multi-omic approach analysis of dust mites (JACI 2015), as well as the identification of the salt-tolerance gene in soybean through large-scale genomic analysis (Nat. Comm. 2014). He also loves to explore sci-fi ideas and put them into practice, that is, the development of a DNA-based information storage system (iGEM 2010, Frontiers in Bioengineering and Biotechnology 2014). Aldrin’s current research interest focuses on neuro development and diseases, such as exploring the heterogeneity of cell types within the nervous system, as well as the gender dimorphism in brain cancers (JCI Insight 2017).
Aldrin is also the founding CEO of Codex Genetics Limited, which is currently servicing two research hospitals and the cancer registry of Hong Kong.
It is not a one-man task to write a book, and I would like to thank Allen and Claire for their invaluable input and effort during the time; the authors also owe a great debt of gratitude to all the editors and reviewers that made this book happened. I also wish to thank my parents for their love and understanding over the years, as well as my best friends, Charles and Angus, for accompanying me through my ups and downs over the past two decades. Last but not least, I also wish to extend my heartfelt thanks to Kimmy for all the love and support in life and moving all the way to Chicago to keep our love alive.