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Basic BioPython Training for Bioinformatics

Biopython is a Python package freely available for computational molecular biology. Biopython can parse Blast results (standalone and web); run biology related programs (blastall, clustalw, EMBOSS); deal with FASTA formatted files; parse GenBank files; parse PubMed, Medline and work with on-line resource; parse Expasy, SCOP, Rebase, UniGene, SwissProt; deal with Sequences; data classification (k Nearest Neighbors, Bayes, SVMs); Aligning sequences; CORBA interaction with Bioperl and BioJava; SQL database storage through BioSQL; Neural Networks; Genetic Algorithms; Hidden Markov Models; creating pretty PDF files for posters; format flat files with random access to entries; structural biology PDB, FSSP.

This basic Biopython course includes

  • Sequence manipulation using Biopython
  • Annotating sequences
  • Sequence alignments
  • BLAST
  • Accessing NCBI databases


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Course Code: CRS-N-0035566

Course Booking

$298.00

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Course Cancellation/Reschedule Policy

We reserve the right to cancel or re-schedule the course due to unforeseen circumstances. If the course is cancelled, we will refund 100% to participants.
Note the venue of the training is subject to changes due to class size and availability of the classroom.
Note the minimal class size to start a class is 3 Pax.

Course Details

Module 1 Introduction to Biopython

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


Module 2 Working with Sequences

  • Parsing
  • Slicing
  • Adding
  • Concatenating
  • Reverse complementing


Module 3 Annotating Sequences

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


Module 4 Working with Sequence files

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


Module 5 Sequence Alignment

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


Module 6 BLAST

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


Module 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


Module 8 Simple Plotting (optional)

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

Who Should Attend

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

Prerequisite

  • Basic programming skills
  • Molecular biology
  • Basic bioinformatics (useful but not essential)

Trainers

BioinformaticsTrainerDr Brandon Ooi has a Bachelors degree in Computer Engineering and a PhD in Bioengineering from the National University of Singapore. He has published papers on machine learning, bioinformatics and microarray data analysis. He has six years of teaching experience at the polytechnic level and was also involved in the creation and teaching of modules for adult learners.

Bioinformatics TrainerDr. Marie Wong has a BSc (Biochemistry and Molecular Biology) from the University of Melbourne and a PhD (Structural Biology) from the University of Singapore. She has had more than 18 years in the field of Bioinformatics in both academic and industrial settings.

BioinformaticsTrainerDr Zheng Zejun has seven years’ experience in the data-mining field. Zejun worked as a (Sr.) bioinformatics scientist for six years and currently works as a data scientist manager. Dr. Zheng;s expertise covers machine learning, statistics, algorithm design, bioinformatics and high performance computing. He has published three machine learning algorithms on well-recognized academic journals together with the open source software (CUDA-CRISY, FSOM, DYSC). Zejun is professional with an extensive set of programming languages, including C/C++, Python, R, JAVA and flask for data driven analytics and scalable computing. He has also a broad knowledge of algorithms and mathematical models in the data-mining field.

Bioinformatics TrainerWesley Goi is currently in his final year of his PhD in Bioinformatics at National University of Singapore (NUS) where he previously received his degree in Molecular Biology at NUS (Honours 2nd Uppers). He was the TA for Introductory Bioinformatics LSM2241. He specialises in analysing high throughput DNA and RNA sequencing data of complex microbial communities using network analyses and various functional analyses. In his previous projects he has applied machine learning methods to vaccine discovery.

BioconductorTrainerDwight Nuwan Fonseka have a degree in Biotechnology (from NUS) ,Advanced diploma in Pharamceutical management (from MDIS) and Masters in Education (from NTU). He have 8 years experience of teaching biology at O and A levels/ IB level in international schools in Singapore and overseas.

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