Course Schedule

Week 1 - Course Organisation and Setup

Tuesday 16th September
Course Introduction & Setup Lecture Background
Slides · Video
Thursday 18th September
Working with Notebooks & Git Lecture Coding
Slides · Video
Introduction Notebook · Practice Notebook

Week 2 - Navigating Data Sources & Retreiving Data

Tuesday 23rd September
Introduction to the Biomedical Dataverse Lecture Background
Slides · Video
Thursday 25th September
Bulk FTP Download & APIs Lecture Coding
Slides · Video
Introduction Notebook · Practice Notebook
FTP Snippet · API Snippet

Week 3 - Data Inter-operability

Tuesday 30th September
Mapping & Harmonisation Lecture Background
Slides · Video
Thursday 2nd October
Data Integration & Summary Analysis Lecture Coding
Slides · Video
Numpy Notebook · eUtils Notebook · Thursdays’s Live Notebook
BioMart Snippet Notebook · NCBI eUtils Snippet Notebook

Week 4 - Exploiting Domain Knowledge

Tuesday 07th October
Biomedical Evidence Lecture Background
Slides · Video
PubMed Basic · PubMed Temporal
Thursday 9th October
Mining & Analysing the Biomedical Literature Lecture Coding
Slides · Video
Week3 Assignment Solution · Lecture Notebook (blank) · Lecture Notebook (completed) · PubMed Citations · PubMed GenCC Example · Open Citations Example

Week 5 - Break

There are no lectures this week

Week 6 - Working with Gene Expression Data

Tuesday 21st October
Measuring Gene Expression Lecture Background
Slides · Video
Thursday 23rd October
Differential Gene Expression Lecture Coding
Slides · Video
PyDESeq2 Toy Example Notebook · PyDESeq2 Real World Example Notebook · Week 6 Assignment Model Notebook

Week 7 - Modeling with Networks

Friday 1st November
Assessed Coursework Released Coursework
GitHub Classroom Assignment Invite
Tuesday 28th October
Biological Networks Lecture Background
Slides · Video
Thursday 30th October
Network Construction Techniques Lecture Coding
Slides · Video
Simple Network Notebook · TCGA Network Analysis Notebook
Accompanying Graph Functions Python File · TCGA Expression Data File

Week 8 - Analysing Networks

Tuesday 4th November
Essential Network Methods Lecture Background
Slides · Video
Thursday 6th November
Network Analysis in Practice Lecture Coding
Slides · Video
Clustering & Functional Enrichment Analysis Notebook · Week 8 Optional Assignment Solution Notebook

Week 9 - Working with Structured Domain Knowledge

Tuesday 11th November
Strusturing Biomedical Data with Ontologies Lecture Background
Thursday 13th November
Functional Analysis Lecture Coding

Week 10 - Integrating Data

Monday 17th November @12pm
Assessed Coursework Submission Deadline Coursework
Tuesday 18th November
Working with multiple data modalities Lecture Background
Thursday 20th November
Modelling at the patient level Lecture Coding

Week 11 - Revision Session

Tuesday 25th November
Revision and Q&A