Course syllabus

Overview

Lectures take place on Mondays, Tuesdays, and Wednesdays from 1-2pm in Mac 2 seminar room 106-113.

Labs are Tuesdays 2-5pm in computer lab room 106-014. 

Section 1: Genomics and transcriptomics (Dan Jones)

A description of this section can be found here: Section 1: Genomics and transcriptomics.

Lectures

• W1 L1: Sequencing technologies
• W1 L2: Genomics (assembly, annotation, gene-prediction)
• W1 L3: Genomics (assembly, annotation, gene-prediction)
• W2 L4: Genomics (assembly, annotation, gene-prediction)
• W2 L5: Genomics (assembly, annotation, gene-prediction) [student-led publication reviews]
• W2 L6: Transcriptomics
• W3 L7: Transcriptomics
• W3 L8: Transcriptomics
• W3 L9: Transcriptomics [student-led publication reviews]

Labs

• W1: 
• W2: 
• W3:

Assessements

Assessment 1A
Presentation of a research paper, to take place in either the Genomics Section (Week 2) or Transcriptomics section (Week 3)

Assessment 1B
Write-up of a practical lab (Due in week 4 [TBC])

Section 2: Metagenomics and community genomics (Kim Handley)

A description of this section can be found here: Section 2: Metagenomics and community genomics

Lectures

• W4 L10: Introduction to metagenomics
• W4 L11: Metagenomics
  
• W4 L12: Metagenomics
  
• W5 L13: Metagenomics + journal presentation
  
• W5 L14: Metagenomics + journal presentation
  
• W5 L15: Metagenomics + journal presentation
  
• W6 L16: Metagenomics + journal presentation
  

Labs

• W4
• W5
• W6

Assessements

Assessment 2
Presentation of a research paper, to take place in Week 5-6, and lab report completion Week 6.

Section 3: Graphs and graph algorithms (Matthew Egbert)

A description of this section can be found here: Section 3: Graphs and graph algorithms

Lectures

• W6 L17: Introduction to graphs.
• W6 L18: Degree distributions
• W7 L19: Graph Models (Erdos-Renyi and Power-Law graphs)
• W7 L20: Small-world networks, clustering and average path length
• W7 L21: Centrality
• W8 L22: Guest lecture: Identifying the important parts of a graph: Beyond topology

Labs

• W7: 13 September: Programming self-directed session. A few Python programming tips are collected here.
• W8: 20 September: Session for working on graph lab

Assessements

Assessment 3
Graph Lab -- Due at 5pm on Monday, 26 September (Week 9) -- Instructions and files available here.

Section 4: String algorithms (Matthew Egbert)

A description of this section can be found here: Section 4: String algorithms

Lectures

• W8 L23: Algorithms and complexity
• W8 L24: Motif finding
• W9 L25: Repeat finding and k-mer counting
• W9 L26: Pattern matching
• W9 L27: BLAST
• W10 L28: An alternative approach: artificial life

Labs

• W9: 27 September: Dynamics on graphs
• W10: 4 October: Session for working on string lab

Assessements

Assessment 4
String Lab -- Due at 5pm on Friday, 7 October (Week 10)

Section 5: Applied Systems Biology (Cristin Print)

A description of this section can be found here: Section 5: Applied systems biology 

Lectures

• W10 L29: Introduction to genomic systems biology
• W10 L30: Bioinformaticians applying systems biology to better understand cancer 
• W11 L31: Industrial-scale bioinformatics applications 
• W11 L32: Using gene Networks to find new drug targets and biomarkers

Labs

• TBC

Assessements

Assessment 5
Systems biology lab exercise [TBC]

Slots for revision / make-up lectures as necessary

• W11 L33: NO LECTURE SCHEDULED
• W12 L34: NO LECTURE SCHEDULED
• W12 L35: NO LECTURE SCHEDULED
• W12 L36: NO LECTURE SCHEDULED