# General software skills for systems neuroscience

## Overview
Held over seven days, this course will provide researchers with some basic computational skills for systems 
neuroscience research. This will include general programming, software development best practices and data analysis 
using leading open-source software tools. This course will also include some general microscopy lectures. 

## Schedule
| Date                  | Time           | Event                                                        | Location                           |
|-----------------------|----------------|--------------------------------------------------------------|------------------------------------|
| **Monday, September 30th** | 13:00-14:00    | Introduction to the course                                    | SWC Brasserie Seminar Room         |
|                       | 14:00-17:00    | Introduction to Python (1)                                    | SWC Brasserie Seminar Room         |
| **Tuesday, October 1st**   | 10:00-11:00    | Data management and sharing (1)                                | SWC Ground Floor Lecture Theatre   |
|                       | 15:00-17:00    | Data management and sharing (2)                                | SWC Ground Floor Lecture Theatre   |
| **Wednesday, October 2nd** | 10:00-12:30    | Introduction to Python (2)                                    | GCNU Seminar Room                  |
|                       | 13:30-17:00    | Version control and software development best practices       | GCNU Seminar Room                  |
| **Thursday, October 3rd**  | 10:00-13:00    | Video-based analysis of animal behaviour (1)                  | SWC Brasserie Seminar Room         |
|                       | 14:00-17:00    | Video-based analysis of animal behaviour (2)                  | SWC Brasserie Seminar Room         |
| **Friday, October 4th**    | 14:00-17:00    | Linux and high-performance computing                          | SWC Ground Floor Lecture Theatre   |
| **Monday, October 7th**    | 11:00-12:00    | General microscopy: basics                                    | SWC Brasserie Seminar Room         |
|                       | 13:00-14:30    | General microscopy: applications                              | SWC Brasserie Seminar Room         |
|                       | 14:30-18:00    | Histology analysis (1)                                        | SWC Brasserie Seminar Room         |
| **Tuesday, October 8th**   | 10:00-11:00    | Histology analysis (2)                                        | SWC Ground Floor Lecture Theatre   |
|                       | 14:00-17:00    | Histology analysis (3)                                        | SWC Brasserie Seminar Room         |


## Introduction to Python
The aim of the course is to introduce basic concepts of programming in Python, and establish a community of Python users. It is a hands-on course, in which we will guide you 
through the process of writing your first Python script and teach you some best practices.

The course will run over two days, 2.5-3h per day with a break in between.

Full details can be found on the [course webpage](https://software-skills.neuroinformatics.dev/courses/intro-software-dev.html)

Instructors: Igor Tatarnikov, Sofía Miñano

## Data Management and Sharing

 This course will introduce best-practices in neuroscience data management 
 and cover recent standardisation initiatives. The primary take-away from this course 
 will be to leave with a strong schema in mind for clean organisation of experimental data.

Full details can be found on the [course webpage](https://software-skills.neuroinformatics.dev/courses/data-management.html)

## Version control and software development best practices

The aims of the course are
* to learn how to keep track of changes to your code with Git and GitHub, 
* to learn how to work with others on code
* and to get an initial idea of how structure, document and test your code.

[Git and Github slides for 2023/2024 course](https://docs.google.com/presentation/d/1HmTqmgB34deJILvPOQtwuaQR_iwGp5AwEwGf7tmx5hE/edit?usp=sharing)
[Site for software development best practice](collaborative-coding)

Instructors: Stephen Lenzi, Laura Porta, Alessandro Felder

## Video-based analysis of animal behaviour

This course will introduce the theory and practice of tracking animals in videos to quantify their behaviour.
Participants will get to train pose estimation models
with [SLEAP](https://sleap.ai/), analyse pose tracks
with [movement](https://movement.neuroinformatics.dev/), and extract behavioural syllables with [keypoint-moseq](https://keypoint-moseq.readthedocs.io/en/latest/index.html). 

Full details can be found on the [course webpage](video-analysis).

Instructors: Niko Sirmpilatze, Chang Huan Lo, Sofía Miñano

## Linux and high-performance computing
This course will introduce some basic principles of using Linux, and high-performance computing in general. Most of 
the course will be centered around learning to run a specific workflow (pose estimation) on the SWC HPC system. 

Full details can be found on the [course webpage](hpc-behaviour).

Instructors: Niko Sirmpilatze, Igor Tatarnikov, Adam Tyson

## General microscopy
This course will introduce some basic concepts about microscopy (optics, fluroescence etc.) to help better understand 
the following course on histology analysis.

Instructors: Rob Campbell, Adam Tyson, Alessandro Felder, Igor Tatarnikov


## Histology analysis

Full details can be found on the [course webpage](https://brainglobe.info/community/courses/scheduled/oct-2024/index.html).