CSC8331 : Bio-design Automation
- Offered for Year: 2022/23
- Module Leader(s): Professor Anil Wipat
- Lecturer: Dr Jichun Li, Dr Tim Rudge
- Owning School: Computing
- Teaching Location: Newcastle City Campus
Semesters
| Semester 2 Credit Value: | 10 |
| ECTS Credits: | 5.0 |
Aims
• Synthetic biology is the application of engineering principles to the design and implementation of biological systems
• Synthetic biology is paradigm shift in biology allowing biological systems to be built at a genome scale from parts derived from a diverse range of organisms or even completely synthetic devices
• The ability to apply engineering principles to biology opens up the possibility of applying automated strategies to the design, build and testing of synthetic biological systems
• The latest research in synthetic biology has resulted in the development of automated software systems for the design of biological systems, and downstream robotic systems for building and testing biological systems
• These approaches have led to a step-change in the rate at which synthetic systems can be built and tested for many applications
• This research focussed module will explore the latest approached to automating the synthetic biology life cycle
Outline Of Syllabus
Automating the Engineering biological system – overview
Joining up the DBTL
Parts assembly strategies
Automating design using standards and modelling
Combinatorial planning and assembly
Process build automation: including robotics, liquid handling, microfluidics,
Software workflows
Equipment interfacing
Synthetic Biology foundries
Standard approaches to data representation and provenance
Appropriate aspects of machine intelligence
Statistical learning and reasoning over test data
Advanced use case and literature reviews
Teaching Methods
Teaching Activities
| Category | Activity | Number | Length | Student Hours | Comment |
|---|---|---|---|---|---|
| Structured Guided Learning | Lecture materials | 10 | 1:00 | 10:00 | PiP Lectures |
| Scheduled Learning And Teaching Activities | Practical | 3 | 3:00 | 9:00 | Asynchronous online practicals |
| Guided Independent Study | Directed research and reading | 14 | 2:00 | 28:00 | Lecture follow up |
| Guided Independent Study | Project work | 12 | 1:00 | 12:00 | Coursework carried out in the computer and wet laboratory. |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 1 | 3:00 | 3:00 | Tutorial feedback session to support formative and summative assessment- C/W 1 PiP |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 3 | 1:00 | 3:00 | To support queries about lecture material or practicals, PiP. |
| Guided Independent Study | Independent study | 35 | 1:00 | 35:00 | Background reading |
| Total | 100:00 |
Teaching Rationale And Relationship
Lectures will be used to introduce the learning material and for demonstrating the key concepts by example. Students are expected to follow-up lectures within a few days by re-reading and annotating lecture notes to aid deep learning.
Discussions, both using canvas and in drop-in surgeries will be used to emphasise the learning material and its application to the solution of problems and exercises set as coursework.
This is a very practical subject, and it is important that the learning materials are supported by hands-on opportunities provided by practical classes.
Students aiming for 1st class marks are expected to widen their knowledge beyond the content of lecture notes through background reading
Assessment Methods
The format of resits will be determined by the Board of Examiners
Other Assessment
| Description | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|
| Practical/lab report | 2 | M | 100 | Group Practical Exercise -A practical report on the design and automation of synthetic biology exercise. Max 2,000 words |
Formative Assessments
| Description | Semester | When Set | Comment |
|---|---|---|---|
| Report | 2 | M | Formative assessment: Initial design report for student feedback |
Assessment Rationale And Relationship
Students will analyse problems as individuals and in teams. This group practical exercise gives a group mark.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- CSC8331's Timetable