Molecular Basis of Bacterial Infections course, computer practical

The lessons use the Software Carpentry and Data Carpentry lesson template and are partially based on the Data Carpentry Genomics lesson.

Schedule

Thursday: Setup

Tuesday: Intro cloud computing and shell, assembly, protein prediction

Data

Escherichia coli strain K-12 holds a key position as a model organism in studies of molecular biology, biochemistry, genetics and biotechnology. We will be using reads available from the European Nucleotide Archive. In addition, we will be using a pre-assembled genome from Staphylococcus aureus subsp. aureus USA300_FPR3757.

We are using this collaborative document. A cheatsheet can be found here.

Schedule

		Setup	Download files required for the lesson
Day 1	09:00	1. Introduction	What are the goals of this practical training? What data do we work on?
	09:10	2. Logging onto Cloud	How do I connect to a cloud instance?
	09:20	3. Introducing the Shell	What is a command shell and why would I use one? How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer?
	09:50	4. Navigating Files and Directories	How can I perform operations on files outside of my working directory? What are some navigational shortcuts I can use to make my work more efficient?
	10:40	5. Working with Files and Directories	How can I view and search file contents? How can I create, copy and delete files and directories? How can I control who has permission to modify a file? How can I repeat recently used commands?
	11:25	6. Redirection	How can I search within files? How can I combine existing commands to do new things? How can I get rid of sequence data that doesn’t meet my quality standards?
	11:55	7. Trimming	How can I get rid of sequence data that doesn’t meet my quality standards? How can I organize a file system for a bioinformatics project?
	12:15	8. Sequence assembly	How can the information in the sequencing reads be reduced? What is the effect of k-mer size on assembly?
	13:15	9. Lunch	Break
	14:15	10. Annotation	How are proteins predicted from a DNA sequence? How many proteins are found in E.coli?
	15:15	11. Prediction of secreted proteins	How can I predict proteins that are secreted? How do I get my analysis results back to my computer?
	15:55	12. Wrapup	Do my findings match the published data?
	16:05	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.