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 a intermediate level course. The following prerequisite is assumed

• Basic Python
• Basic BioinformaticsM

Software Requirement

Pls 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/

HRDF Funding

Please refer to this video https://youtu.be/Kzpd-V1F9Xs

1-     HRD Corp Grant Helper

How to submit grant applications for HRD Corp Claimable Courses

2-     Employers are required to apply for the grant at least one week before training commences.

Employers must submit their applications with supporting documents, including invoices/quotations, trainer profiles, training schedule and course content.

3-     First, Login to Employer’s e-TRIS account -https://etris.hrdcorp.gov.my

Second, Click Application

4-     Click Grant on the left side under Applications

5-     Click Apply Grant on the left side under Applications

6-     Click Apply

7-     Choose a Scheme Code and select HRD Corp Claimable Courses: Skim Bantuan Latihan Khas. Then, click Apply

8-     Scheme Code represents all types of training that suit the requirements provided by HRD Corp. Below are the list of schemes offered by HRD Corp:

9-     Select your Immediate Officer and click Next

10-  Select a Training Provider, then click Next

11-  Please select a training programme from the list, then key in all the required details and click Next

Select your desired training programme.

Give an explanation on why the participant is required to attend the training. E.g., related to their tasks/ career development, etc.

Explain the background and objective of this training.

Select a relevant focus area. For Employer-Specific Courses, select ‘Not Applicable’.

12-  If the training programme is a micro-credential programme, you are required to complete these 3 fields. Save and click Next

Insert MiCAS Application number

13-  Based on the nine (9) pillars listed below, HRD Corp Focus Area Courses are closely tied to support government initiatives towards nation building. As such, courses offered through the HRD Corp Focus Areas are designed to provide the workforce with skills required for current and future demands. Details of the focus areas are as follows:

14-  Please select a Course Title and Type of Training

15-  Select the correct type of training according to the actual type of training, or as mentioned in the training brochure:

16-  Please key in the Training Location and click Next

17-  Please select the Level of Certification and click Next

18-  Please follow the instructions and key in trainee details

19-  Click Add Batch, then click Save

20-  Click Add Trainee Details

21-  Please key in all the required details, then click Add

22-  Click Add if there are more participants. Once done, click Save

23-  Click Next

24-  Please key in the course fees and allowance details, then click Save

25-  Estimated cost includes the course fees/external trainer fees, allowances, and consumable training materials. Please comply with the HRD Corp Allowable Cost Matrix.

26-  Select Upfront Payment to Training Provider and key in the percentage from 0% to 30%. Then, click Save and Next

27-  Complete the declaration form and select a desired officer

28-  Add all the required documents, then click Add Attachment. Then, click Save and Submit Application

29-  Once the New Grant Application is successfully submitted, the Grant Officer will evaluate the application accordingly. The application may be queried if additional information is required.

The application status will be updated via the employer’s dashboard, email, and the e-TRiS inbox.

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

Nero: Nero is dean of Penang School of AI, which is AI learning and sharing community in Northern Malaysia. He is Msc in Computer Imaging in Universiti Sains Malaysia. His research is mainly focusing in Video Analytic and Multiple object tracking. At the same time, he is developing computer vision application in WyseTime, a tech-startup company focus on video analytic application using deep learning technology.

Lee Cheong Loong: Lee Cheong Loong, Manager with 23 years working experience in multiple role and department, He completed HRD Corp Train the Trainer programme, HRD Corp Accredited Trainer, Microsoft Certified Trainer and CPFA Citizen Data scientist Trainer programme. with Professional certificate in Big Data & Analytics, Microsoft Office Specialist -Excel 2016 and Tableau Desktop Specialist. He also deliver training for R & Python programming, Excel Dashboard for Business analysis, Data Visualization with Tableau, and Microsoft PowerBI, and Citizen Data Scientist (OpenCertHub).

Saeid: Saeid  is co-founder of Skymics sdn bhd, he has 8 years experience in field of IOT (Internet of things) and Information Technology. He is a certified IBM IoT Practitioner and instructor and Certified Citizen Data Scientist Train-The-Trainer. He has been co-inventors of 3 inventions during the last 4 years.

He has worked across wide domains such as, data analytics, IoT, social media analytics, smart cities energy management, smart plantations. In addition, 5+ years of experience in data processing, visualization, and analytics. He is expert in Power BI, Qlikview, and Tableau.