Scripting for Biology - Online Virtual Classroom-based Module


Hello all,

I am building a number of online virtual classroom-based modules for researchers working on biological data. The description for the first one is attached below, and I will have a beta test starting Sept 14. Please feel free to pass to anyone interested. The beta test is free, and all course materials (including cloud account) will be provided. I currently have only a small number of spots left for this one. If interested, please email pandora at homolog.us.

This course will be useful for anyone without knowledge of programming, and also for those knowing one language (e.g. python) well, who may want to learn another one (say, golang).

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Scripting for Biology - 1

Time: Sept 14 - Oct 9 (four weeks)

The purpose of this four-week module is to help biology researchers learn scripting languages (python, PERL, GO). You are expected to learn only one language, not all three.

Whether you never programmed or have some programming experience, this course will help you greatly improve your skills. Moreover, our examples are chosen from relevant bioinformatics problems so that you can apply them to understand recent papers. Some of them will be covered in the second scripting module and other modules related to RNAseq, assembly, metagenomics, etc.

How the classes work

I will first give you short introduction to each topic and then let you start writing your own codes to solve problems. When you solve one problem, you will get another more difficult one and so on. If you get stuck at any step, I will help you overcome the obstacle.

We will keep the class size small (~10) so that I can monitor the work done by every student. Each student will be solving problem at his own pace without being impacted by the rest of the class. So, if someone learns fast, he can finish the modules quickly or go on to solve more difficult problems.

The course is primarily based on chat. We will keep the provision for using google hangout for video discussions, but I plan to use it sparingly. Also, I am thinking about preparing some introductory videos, but it also appears that text-based method of delivering content is more effective than video-based method.

We will provide cloud account for each student with relevant programs installed. All other course-related materials will be provided.

Schedule

Week 1 - three 75 minute classes.

D1. i) Introduction to computer hardware, operating system and programming. ii) UNIX practices. iii) Entrance test.

D2. Introduction to python/PERL/GO. ii) Coding practices.

D3. i) Solving the first bioinformatics puzzle. ii) Fun with debugging.

Week 2 - project 1 (k-mer counting).

Week 3 - three 75 minute classes.

D1. i) Strings, ii) Regular expression, iii) Associative arrays.

D2. i) Solving another bioinformatics puzzle.

D3. i) Loops and conditions. ii) Advanced debugging.

Week 4 - project 2 (translation and genetic code) and exit test.


Written by M. //

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