Basic BioPython Training for Bioinformatics

Topic 1 Introduction to Biopython

• What is Biopython?
• Biopython packages
• Installing Biopython
• Biopython website & resources

Topic 2 Working with Sequences

• Parsing
• Slicing
• Adding
• Concatenating
• Reverse complementing

Topic 3 Annotating Sequences

• FASTA record
• GenBank record
• Chromosomal Location
• Sequence type

Topic 4 Working with Sequence files

• Parsing a file
• Reading from a file
• Writing to file
• Converting file formats

Topic 5 Sequence Alignment

• Parsing an alignment file
• Reading an alignment file
• Writing alignments to file
• Converting file formats
• Manipulating alignments

Topic 6 BLAST

• What is BLAST?
• Running BLAST
• Parsing BLAST output
• Searching within BLAST output

Topic 7 Accessing Entrez Databases at NCBI

• Connect to Entrez
• List accessible Entrez Databases
• Search Entrez Databases
• Upload identifiers for searching
• Return search results
• Parsing results

Topic 8 Simple Plotting (optional)

• Plot %GC 
• Plot sequence similarity (nucleotide dot plot)
• Plot quality scores of sequencing reads

Prerequisite

This is an intermediate level course. The following prerequisite is assumed

• Basic Python
• Bioinformatics

Software Requirement

Please download and install the following software prior to the class

• Python 3.x https://www.python.org/downloads/
• Sublime Text 3 https://www.sublimetext.com/3
• Pycharm https://www.jetbrains.com/pycharm/download/

• Biologists who want to learn basic bioinformatics
• Bioinformatics Scientists who want basic training in Biopython

Ken Yuen: Ken Yuen is a ACTA certified trainer. He has more than 10 years of experience working as an instructor, Application Development Engineer, Technical Consultant and Project Manager. He is an MOE-Registered Instructor teaching STEM programs for past 3 years such as Arduino, Micro:bits and robotics to schools and libraries based on the smart nation initiative roadmap.

He completed his Diploma in Electronic Engineering at Singapore Polytechnic and graduated with Bachelor of Electrical and Electronics Engineering from Nanyang Technological University and certified PMP (Project Management Professional).

Terence Ee: Terence Ee is a ACTA certified trainr that has delivered IT training in Singapore and Myanmar. He has also facilitated faith formation courses for Christians in Singapore and Myanmar. As a trainer, his mission is to co-create insightful and actionable learning experiences with his learners.His current areas of focus include project management, information security management, quality management and office productivity applications.

Terence has more than 25 years of corporate IT experience. He has held senior management roles in the public and private sectors. He holds a Master of Science in Technology Management, a Bachelor of Science in Computer and Information Sciences, a Diploma in Family Education, and the Advanced Certificate in Training and Assessment (ACTA). Part of his spare time goes towards tutoring his children in their studies (while learning a thing or two along the way). He is also imparting to them the essential skills for thriving in a digital world.

Dr Alvin Ang: Dr Alvin Ang is a ACTA certified trainer. Alvin Ang did his Ph.D., Masters and Bachelors from NTU, Singapore. Previously he was a Principal Consultant (Data Science) as well as an Assistant Professor. He was also 8 years SUSS adjunct lecturer. His focus and interest is in the area of real world data science. Though an operational researcher by study, his passion for practical applications outweigh his academic background. He owns a startup externally

Man Guo Chang: Man Guo Chang is a ACTA certified trainer. Man Guo Chang graduated from Nanyang Technological University, School of Electrical and Electronic Engineering, major in Computer Engineering. He has more than 25 years of working experience in the Semiconductor field, specialized in IC Testing, Inline Electrical Testing, Product & Yield Engineering, Data Analysis, System Engineering, and Software Development.

Shahul H. Maricar: Shahul H. Maricar is a ACTA certified trainer. Shahul H. Maricar has been a content developer and  webmaster, building educational websites and applications with HTML, CSS and JavaScript. He then served as an IT analyst, writing programs for automating custom workflows as well as data extraction and analysis in the healthcare field.  

He is currently a freelance educator and is actively involved with development projects in game programming,  computer-aided design and computer graphics.

Noel Lou: Noel Lou is a ACTA certified trainer. Experienced Mentor with a demonstrated history of working in the education management industry. Skilled in IOS, Unity3D, Python, Microsoft Excel, Customer Service, and Microsoft Word. Strong professional with a Bachelor’s Degree focused in Marine offshore engineering from Newcastle University.