Course Schedule

Week 1 - Course Organisation and Setup

Tuesday 16th September

Course Introduction & Setup Lecture Background

Slides · Video

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Thursday 18th September

Working with Notebooks & Git Lecture Coding

Slides · Video

Introduction Notebook · Practice Notebook

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Week 2 - Navigating Data Sources & Retreiving Data

Tuesday 23rd September

Introduction to the Biomedical Dataverse Lecture Background

Slides · Video

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Thursday 25th September

Bulk FTP Download & APIs Lecture Coding

Slides · Video

Introduction Notebook · Practice Notebook

FTP Snippet · API Snippet

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Week 3 - Data Inter-operability

Tuesday 30th September

Mapping & Harmonisation Lecture Background

Slides · Video

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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

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Week 4 - Exploiting Domain Knowledge

Tuesday 07th October

Biomedical Evidence Lecture Background

Slides · Video

PubMed Basic · PubMed Temporal

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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

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Week 5 - Break

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There are no lectures this week

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Week 6 - Working with Gene Expression Data

Tuesday 21st October

Measuring Gene Expression Lecture Background

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Thursday 23rd October

Differential Gene Expression Lecture Coding

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Week 7 - Modeling with Networks

Monday 27th October

Assessed Coursework Released Coursework

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Tuesday 28th October

Biological Networks Lecture Background

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Thursday 30th October

Network Construction Techniques Lecture Coding

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Week 8 - Analysing Networks

Tuesday 4th November

Essential Network Methods Lecture Background

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Thursday 6th November

Network Analysis in Practice Lecture Coding

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Week 9 - Working with Structured Domain Knowledge

Tuesday 11th November

Strusturing Biomedical Data with Ontologies Lecture Background

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Thursday 13th November

Functional Analysis Lecture Coding

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Friday 14th November @12pm

Assessed Coursework Submission Deadline Coursework

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Week 10 - Integrating Data

Tuesday 18th November

Working with multiple data modalities Lecture Background

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Thursday 20th November

Modelling at the patient level Lecture Coding

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Week 11 - Revision Session

Tuesday 25th November

Revision and Q&A

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