SWC/GCNU Software Skills

Upcoming dates

• March 20^th 2023. 1pm-5.30pm. SWC Lecture Theatre, UCL.

• May 15^th 2023. 9am-5.30pm. SWC Lecture Theatre, UCL.

• Date and time TBC.

Previous dates

• November 25^th 2022. 11am-12pm. GCNU 3rd floor seminar room.

• December 1st 2022. 10am-5pm. SWC brasserie seminar room.

• Sept 26^th and 27^th 2022. 10am-5pm

• May 6^th and 13^th 2021 10am-4pm

• April 2^nd 10am-11.30am & April 6^th 2020 1pm-2.30pm

• February 25^th 2020

• November 25^th - 26^th 2019

Summary

The course will be split into two sections:

• An introduction to python, and general scientific programming, split over two days (eventually expanded to a one week course). No experience required.
• A series of standalone, more specialist short courses covering specific software skills.

You will be able to come to the entire course without any previous programming experience, but the later specialist courses will hopefully be useful to those with experience.

The focus will be on using Python to develop efficient, reproducible workflows for neuroscience research, while teaching efficient programming and good coding practice.

Two-day introduction

Aims

• Introduce those new to Python (and programming in general) to the language and the vocabulary and show how to install Python and the entire ecosystem (virtual environment, package manager, text editor/IDE).
• Allow new users to feel comfortable carrying out basic data analysis independently.
• To provide a common base level of knowledge for the more advanced, specialist courses that will follow.

Contents

• Bash command line
• Version control using git
• Github (making an account, raising issues, using other peoples software)
• IDEs (what software you use to write your software)
• Working with virtual environments

• Introduction to Python
• Installing Python
• Variables
• Data types
• Loops
• Conditional statements
• Loading and saving data
• Writing your first Python script
• Installing packages with pip
• Using third party libraries from pip and conda
• List comprehensions
• Functions
• Object oriented programming
• Errors and exceptions
• Organising your Python project and importing functions
• Documenting your code

Standalone specialist courses

Future courses to be confirmed, but possible topics include:

• Image analysis (e.g. 2p imaging)
• Timeseries analysis (e.g. neuropixels)
• Plotting
• General data analysis in Pandas
• Data acqusition
• Testing
• Object oriented programming
• Distributing and packaging code
• Profiling, optimisation and packages for efficient computation (e.g. Numba & Dask
• Behavioural analysis using DeepLabCut
• Machine learning

The courses run will depend on enthusiasm and availability of instructors and students. If there's something you want to learn, or tell everyone about, get in touch.