Python “Zero-to-Hero” Beginner’s Course

This course contains materials for a 1-day beginner’s python course which we have delivered several times now. However, these materials have been developed so that students can work through the materials in their own time and at their own rate. Feel free to download the materials and work your way through the course; you can download the whole course from here.

Binder If you wish to quickly explore the course, you could use Binder (by clicking the button above). However, this won’t save your progress as you go along so we suggest installing locally as described below.

Aim

The overall aim of this course it to:

  1. introduce the basic concepts of programming in Python within the comfort of the Jupyter framework
  2. showcase some of the advanced functionality available in Python by demonstrating (and providing take-home resources) numpy, scipy, matplotlib, seaborn and pandas code

Philosophy

Our general philosophy for this course is

  1. teach in small chunks starting by introducing theory, demonstrating an example, working through a simple case and then setting an exercise. Each exercise is then gone through as a group.
  2. teach through errors, error messages and documentation - so that trainees can debug their own codes after they leave the course
  3. create a safe environment for asking any and all questions.

Contributors

Teaching Yourself Python (12+ hours)

We have designed this course in such a way that it should be easy to follow and work through on your own. Each notebook stands alone and should provide you with all the information needed to complete the tasks (blue boxes) and exercises (yellow boxes).

In order to aid working through the notebooks we have provided short videos for all tasks and exercises. These videos provide complete answers for every task and should be viewed after attempting each task or exercise.

In order to work through the notebooks please follow the instructions in setup.pdf for installing Python and Jupyter Lab on your computer, dowload this repository as a .zip file (using the green button at the top of the landing page), unzip the files and navigate to them from within Jupyter Lab.

We suggest you work through each notebook in turn, attempting at least the tasks on your first run-through. You can then use the exercises to revisit and revise topics when you go through the notebooks again in the future. As with all languages, practice makes perfect.

In-Person Course (1 day)

If you’re interested in taking the course in-person, check out my coming my list of upcoming in-person courses.

In-Person Training Courses

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Bioimage analysis with Python

The aim of this 5 days course is to develop motivated participants toward becoming independent BioImage Analysts in an imaging facility or research role. Participants will be taught theory and algorithms relating to bioimage analysis using Python as the primary coding language. Lectures will focus on image analysis theory and applications. Topics to be covered include: Image Analysis and image processing, Python and Jupyter notebooks, Visualisation, Fiji to Python, Segmentation, Omero and Python, Image Registration, Colocalisation, Time-series analysis, Tracking, Machine Learning, and Applied Machine Learning.

Programming for Biologists

There’s no escaping it - computing is becoming an essential part of the scientist toolkit. From coping with the data deluge by automated analysis or simulating a mathematical model of your system, coding is an essential skill for the modern biologist. This hands-on, one-day course will introduce you to Python, a popular and powerful computer language. You will learn the basics of working with Python through the increasingly popular Jupyter Notebook system. But Don’t Panic - this course is designed for those with no existing coding experience.

Programming for Biologists

There’s no escaping it - computing is becoming an essential part of the scientist toolkit. From coping with the data deluge by automated analysis or simulating a mathematical model of your system, coding is an essential skill for the modern biologist. This hands-on, one-day course will introduce you to Python, a popular and powerful computer language. You will learn the basics of working with Python through the increasingly popular Jupyter Notebook system. But Don’t Panic - this course is designed for those with no existing coding experience.