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Thu 15 Mar - Fri 16 Mar 2018
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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An Introduction to Solving Biological Problems with Python
Beginners

Thu 15 Mar - Fri 16 Mar 2018

Description

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites
  • The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor).
  • A very basic knowledge of UNIX would be an advantage, but nothing will be assumed and extremely little will be required.
Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 15 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Fabio Puddu,  G.E. Parada-Gonzalez
2 Fri 16 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Fabio Puddu,  G.E. Parada-Gonzalez
Topics covered

Bioinformatics, Biology, Data handling

Objectives

After this course you should be able to:

  • Edit and run Python code
  • Write file-processing python programs that produce output to the terminal and/or external files
  • Create stand-alone python programs to process biological data
  • Know how to develop your skills in Python after the course
Aims

During this course you will learn about:

  • Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments
  • Different ways to control program flow using loops and conditional tests
  • Writing functions and best-practice ways of making them usable
  • Reading from and writing to files
  • Code packaging and Python libraries
  • How to work with biological data using BioPython
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics Speaker(s)
09:30 - 10:00 Introduction Guillermo Parada-Gonzalez, Mukarram Hossain
10:00 - 10:30 Print and Variables
10:30 - 10:45 Tea/Coffee Break
10:45 - 12:15 Simple data types, Arithmetic and Saving code in files Guillermo Parada-Gonzalez, Mukarram Hossain
12:15 - 13:30 Lunch (not provided)
13:30 - 14:30  Collections: Lists and String Guillermo Parada-Gonzalez, Mukarram Hossain
14:30 - 14:45 Tea/Coffee Break
14:45 - 15:45 Collections: Sets and Dictionaries Guillermo Parada-Gonzalez, Mukarram Hossain
15:45 - 16:00 Tea/Coffee Break
16:00 - 17:00 Wrap Up
Day 2
9:30 - 9:45 Introduction Guillermo Parada-Gonzalez, Mukarram Hossain
9:45 - 10:45  Conditional execution
10:45 - 11:00  Tea/Coffee Break
11:00 - 12:30  Loops  Guillermo Parada-Gonzalez, Mukarram Hossain
12:30 -13:30  Lunch (not provided)
13:30 - 15:00  Files Guillermo Parada-Gonzalez, Mukarram Hossain
15:00 - 15:15  Tea/Coffee Break 
15:15 - 16:15  Delimited Files  Guillermo Parada-Gonzalez, Mukarram Hossain
16:15 - 16:30  Tea/Coffee Break 
16:30 - 17:00  Wrap Up 
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2 days

Frequency

A number of times per year

Related courses
Theme
Core skills

Booking / availability