COMP3212 Computational Biology

Module Overview

Modern biology poses many challenging problems for the computer scientists. Rapid growth in instrumentation, and our ability to archive and distribute vast amounts of data, has significantly changed the way we attempt to understand cellular function, and the way we seek to treat complex diseases. Data from biology comes in various forms: nucleotide and amino-acid sequences, macromolecular structures, measurements from high-throughput experiments and curated literature in the form of publications and functional annotations. It is nowadays widely acknowledged that computational modelling will play a key role in extracting useful information from vast amounts of such diverse types of data. The computational challenges faced by the human genome project and Alan Turing’s contribution to morphogenesis are classic examples of such roles.

The aim of this module is to develop an understanding of some of the computational challenges that form the basis of research in modern biology, skills associated with which are seen as important in biomedical informatics and pharmaceutical industries. You will get hands-on experience in formulating computational problems and analysing large and complex datasets to make model-based predictions about the underlying biological problems.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

Have a clear understanding of how advanced data analysis and computational models are applied to analysing biological data.

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Fundamental assumptions that drive the use of computational techniques to understand biological data.

Transferable and Generic

Having successfully completed this module, you will be able to:

Data analysis, Pattern recognition

Syllabus

Introduction
Concepts in molecular biology
Computational challenges and tools in biology
Biological Sequence Analysis
Dynamic programming and sequence alignment
Probabilistic models of alignment, hidden Markov models
Stochastic context free grammars and RNA structure modelling
Analysis of high throughput data
Transcriptomic, Proteomic and Metabolomic data
Modelling by clustering and classification; inferring regulation
Systems Biology
Autoregulation
Morphogen diffusion

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	main delivery of taught material	20
Computer Lab	The module includes substantial hands-on work under supervision in a computer lab environment. Hence the optimum group size is 25.	20
Tutorial	Small group tutorials, which shall be optional and aimed at students who find the material difficult and need help in mathematics / programming etc.	3

Assessment

Assessment methods

best two of in-class tests will be used (2x15%=30%)

Method	Hours	Percentage contribution
short assignments (maximum two weeks turn around)	-	30%
major assignment (to be done over a four-week period)	-	40%
Three in-class quizzes, of which your best two will be used	-	30%

Referral Method: By set coursework assignment(s)

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ELEC6205 Bionanotechnology

Module Overview

This module will provide an introduction to the theory and practice of bio-nanotechnology, and introduce students to working in a cleanroom and a wet laboratory.

ELEC6205 includes a bionanotechnology experiment involving state-of-the-art equipment that is normally only used by researchers. The experiment starts with fabrication and characterisation of a microstructured master mold, and continues with casting of an elastomeric stamp and printing microscale patterns of biological molecules. This will take place partly in the Mountbatten clean room and partly in the bio-ECS lab (Centre for Hybrid Biodevices) in the Life Sciences building.

This module is a prerequisite for ELEC6210 Biosensors, except for students that already took ELEC3223 in Part 3. ELEC6205 cannot be taken by students who took ELEC3223 in Part 3.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

Biomolecules and biomolecular interactions
The basic physics of the behaviour of molecules and molecular interactions

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Explain biophysical mechanisms relevant in the context of bionanotechnology
Evaluate the experimental techniques used to characterise bio-nano systems

Transferable and Generic

Having successfully completed this module, you will be able to:

Critically evaluate experimental procedures and experimental data
Write concise engineering reports

Subject Specific Practical

Having successfully completed this module, you will be able to:

Perform some basic wet laboratory procedures
Perform soft lithography procedures involving biomolecules

Syllabus

Fundamentals:

Molecules, proteins, DNA and cells
DNA for coding and information storage
Behaviour of molecules in solution
Kinetics and reaction rates
Dielectrics and optics
Electrokinetics and particle/molecular interaction forces

Applications:

Scanning probe microscopy – measuring molecular interactions and forces
Single molecule detection techniques
Interfacing bio-systems with electronics
Biomimetics and biosensing
Molecular motors
Patterning single molecules
Nano-structured surfaces – applications in cell engineering
DNA machines; computing with molecules and DNA

Practical work:

Fabrication of patterned wafer ('master') in clean room
Surface modification procedures and evaluations
Culture cells on patterned surfaces.

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	Lectures on general background material.	22
Tutorial	Two tutorial sessions to support the laboratory work plus exam revision tutorials.	6
Specialist Lab	BioNanotechnology lab - three 4 hour experimental sessions on micro contact printing.	12

Assessment

Assessment methods

The lab report (coursework 1) will not be marked if the student has not attended the laboratory sessions.

Method	Hours	Percentage contribution
Lab report	-	30%
Exam	2 hours	70%

Referral Method: By examination

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ELEC6204 Microfluidics and Lab-on-a-Chip

Module Overview

This module teaches the basics of the behaviour of fluids in microsystems, specifically focussing on the interaction of fundamental physical mechanisms and the design of microfluidic devices. It also reviews and analyses the state of the art in applied microfluidics such as Laboratory-on-a-Chip technology

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

The theory and physical principles of fluid mechanics on the microscale
Operating principles and physical mechanisms unique to microfluidics
fabrication methods used in the production of lab-on-a-chip systems
the use of lab on a chip systems for different analytical purposes

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Propose design strategies for microfluidics systems based on fluid mechanical principles
Demonstrate an understanding of scaling of electrical, thermal, and fundamental dynamics in microsystems and the effects on system design

Subject Specific Practical

Having successfully completed this module, you will be able to:

Mathematically model microfluidic devices and systems

Syllabus

Principles of miniaturisation, scaling laws
Theory of Microfluidics and nanofluidics
The diffusion of molecules and microscale mixing
Technological production of components: mixers and pumps
Fundamentals of electrical/electrochemical effects in microfluidics
DC fields in microsystems: electroosmosis and electrophoresis
AC fields in microsystems: spectroscopy and dielectrophoresis
Soft lithography, novel methods and fabrication of Lab on a Chip devices.
Detection methods – electrical, optical, thermal
Bio-analytical applications
Magnetic particle biotechnology
Surfaces, forces, electrowetting: Digital Microfluidics
Diagnostic systems – medical systems
Separation, purification, concentration technologies
Simulation and design of mixing devices for chemical reactors

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	2-hour lectures focussing on fundamentals and translation to application	22
Tutorial	Tutorial discussion of problems, solutions and exam revision	4
Specialist Lab	Simulation labs	9
Tutorial	Feedback and discussion sessions on coursework activity	2

Assessment

Assessment methods

Method	Hours	Percentage contribution
Report on simulation laboratory and technology review	-	30%
Exam	2 hours	70%

Referral Method: By examination, with the original coursework mark being carried forward

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ELEC6203 Introduction to MEMS

Module Overview

The student will gain a basic understanding of current MicroElectroMechanical Systems (MEMS) technology and industrial instrumentation systems, with particular emphasis on smart sensors and actuators. The course introduces the fundamental of measurement systems and focuses in particular on MEMS fabrication, MEMS transducer types and applications. This is a core module for the MSc MEMS course and is optional for MSc Bionanotechnology, MSc Nanoelectronics and Nanotechnology, and Pt 4 MEng Electronics and Electromechanical courses.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

The basic principles of measurement systems
The principles of some common transducer types, their strengths and weaknesses and their use in MEMS
The benefits of MEMS technology in relation to applications

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Appreciate the scaling effects arising from miniaturising systems
Design a MEMS pressure sensor

Transferable and Generic

Having successfully completed this module, you will be able to:

Structure and write a technical report

Subject Specific Practical

Having successfully completed this module, you will be able to:

Simulate MEMS structures using finite element analysis

Syllabus

Introduction Lecture
Microfabrication
Magnetic Sensors
Piezoresistive MEMS
Pressure Sensors
Thick-film and PiezoMEMS
MEMS Actuators
Resonant sensors
MEMS resonant sensors
Measurement systems
Physical sensors
Modelling the dynamics of sensor systems
Intelligent sensors
Thermal sensors
Charge amplifiers

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture		36
Tutorial		12
Computer Lab	COMSOL	12

Assessment

Assessment methods

Laboratory sessions are scheduled in the labs on level 2 of the Zepler building
Length of each session: 3 hours
Number of sessions completed by each student: 3
Max number of students per session: unlimited
Demonstrator:student ratio: 1:12
Preferred teaching weeks: 6 to 11

Method	Hours	Percentage contribution
laboratory report	-	30%
Exam	2 hours	70%

Referral Method: By examination

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ELEC6202 Advanced Memory and Storage

Module Overview

The aim of this module to provide an overview of advancement of memory and storage devices in line with the development of nanoelectronics and nanotechnology. Students will gain knowledge of how silicon device scaling has moved semiconductor memory into the nanoelectronics area. Then they will become familiar with state-of-the-art non-volatile memory technologies which are intended to replace or complement semiconductor memory. Longer term data storage in the form of high density portable devices such as hard disks and Blu Rays will be discussed as well.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

device scaling of semiconductor memory
the underlying operating principles of state-of-the-art nanodevices for memory and storage applications
practical characterisation of materials used for nanodevices

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

demonstrate specialised practical and theoretical knowledge of particular nanodevices for memory applications

Transferable and Generic

Having successfully completed this module, you will be able to:

ability to write a short essay on a given subbject using knowledge from hournal articles and lectures
understand the inter-relation between different technologies in the design of integrated devices

Syllabus

Semiconductor Memory

Static Random Access Memory
Dynamic Random Access Memory
Flash (3D integration)

Advanced Nonvolatile Memory

Ferro-electric RAM
Phase Change RAM
Resistive RAM
Magnetic RAM
Emerging memory technology

Data storage

Hard Disk Drives
DVD and Blu Ray

Laboratory

Raman characterisation of device materials

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	Lectures on the module topics	20
Tutorial	Coursework feedback and exam revision	3
Specialist Lab	Raman characterisation laboratory, tutorials and laboratory sessions	6

Assessment

Assessment methods

The lab report will not be marked if the student has not attended the Raman characterisation lab sessions

Method	Hours	Percentage contribution
Advanced memory device review (20%) and laboratory report (30%)	-	50%
Exam	2 hours	50%

Referral Method: By examination

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ELEC6201 Microfabrication

Module Overview

This module provides an overview of modern microfabrication technologies, and is as such structured around the state-of-the-art facilities in the new Southampton Nanofabrication Centre. The various fabrication techniques that are relevant for microdevices in the field of electronics, optoelectronics and micro-electro-mechanical-systems (MEMS) will be addressed in the lectures, with an emphasis on their physical and chemical principles. The integration of these techniques will be explained with an example of a complete process flow for the fabrication of a specific microdevice. The organization of a fabrication facility, including risk assessment aspects, will be addressed with a cleanroom tour and laboratory-based coursework. This laboratory will take place in the clean room.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

The microfabrication technology for the microsystem devices that are used in modern electronic, optoelectronic and lab-on-a-chip applications
Fabrication process flow in a cleanroom environment

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Appreciate how fabrication process limitations influence device design
Design a process flow for electronic/optoelectronic/MEMS microsystem devices

Transferable and Generic

Having successfully completed this module, you will be able to:

Write concise technical/laboratory reports in the format of a journal paper

Subject Specific Practical

Having successfully completed this module, you will be able to:

Perform some basic microfabrication pattern transfer processes in a cleanroom environment
Perform some device characterization procedures

Syllabus

Microfabrication introduction and overview

Material for fabrication
Fabrication equipment
Growth technology
Silicon-based process

Fabrication technology

Pattern transfer technology

Lithography – photolithography
Resist technology
Micromachining – wet etch and dry etch

Materials processing technology

Material deposition methods
Basic ion implantation and diffusion doping process
Low and high temperature process
Device packaging methods

Characterisation technology for microfabrication process
Design criteria and fabrication method for micro device applications
Microfabrication process integration

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	24 lecture hours	24
Specialist Lab	Microfabrication cleanroom laboratory	6
Tutorial	Tutorial session	6

Assessment

Assessment methods

The coursework will not be marked if the student has not attended the laboratory sessions.

Method	Hours	Percentage contribution
Fabrication report	-	30%
Exam	2 hours	70%

Referral Method: By examination

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ELEC3210 Design Studies

Module Overview

The design of an artefact is a complex sociotechnical problem. The module is designed to extend the students’ knowledge of the design process beyond normally expected of a graduate engineer (as defined by the accreditation process). The module in part will take a Design Thinking approach, which considers the cognitive processes involved in design.

While the technical problems are widely understood, a holistic view of the design process includes considerations of problems of how does the design team capture the design rationale, what are the risks associated with the design relative to the costs of mitigation, how is the IPR in the additive manufacturing process.

In taking the module student will gain an in depth understanding of design processes and how the sociotechnical issues will impact on the pure technical challenges.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

understand the design process from the perceptive of various stakeholders
formulate and articulate a design problem correctly.
be capable of making informed design desisions based on known parameters

Transferable and Generic

Having successfully completed this module, you will be able to:

communicate the design solution effecitively.
work as part of a small group or team in a professional manner

Subject Specific Practical

Having successfully completed this module, you will be able to:

use tools to both capture the design rationale and undertake its analysis

Syllabus

What is design. Iconic Designs.
What is design thinking and how does it influence the designer and the design process. The wicked problem
Why does a design fail - materials and processes.
The design process - assessment, problem formulation, abstraction, analysis, implementation.
Design for X and n^thgeneration design.
Design Knowledge. Capture and Reuse; Representation and codification; web based systems. How does a design team operate
Risk, how to measure and avoid. ALARP
Quality- what is quality, how can it be measured. TQM, six sigma, Deming Wheel, Quality Functional Deployment
Additive manufcaturing - the IPR and legal challanges

Learning & Teaching

Learning & teaching methods

The module will be seminar based, with a high level of student participation through the study and presentation of industrial and research case studies.

Activity	Description	Hours
Lecture	The lectures are design to be interactive seminars where student participation in encouraged	24

Assessment

Assessment methods

The design exercise is a group activity in which design rational capture and assessment tools are to be used. Assessment requires the production of a group report, presentation and individual refection documents.

Method	Hours	Percentage contribution
Design Thinking Exercise	-	50%
Design Study: preparing a design to resolve a specific issue	-	50%

Referral Method: By set coursework assignment(s)

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ELEC3208 Analogue and Mixed Signal Electronics

Module Overview

To cover in some depth those areas of circuitry likely to be used between an analogue signal source and a digital signal processing system, making maximum use of available integrated circuits.

This fits in with our overall programme of providing a broad based electronics engineering course, with this module covering the main aspects of measuring outputs from a variety of sensors, designing interface circuits and amplifiers, filtering, and data conversion.

The course will also cover important topics such as clock generation, noise management, power supply design, as well as practical issues such as packaging, EMC and PCB design.

It is assumed that the students at least understand the basics of opamp circuits, and basic analogue to digital conversion principles as for example covered in part 1 ELEC1207 and part 2 ELEC2216 Advanced Electronic Systems.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

Understand the various techniques which can be used for signal conditioning, including filter design
Understand the sources of noise in electronic circuits, and the limitations they impose
Understand the various techniques used for analogue to digital conversion and their relative merits

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

design Interface and Amplifier circuits

Syllabus

Signal conditioning using op amps and discrete devices

Review of available op amp specifications
Interface requirements for various signal sources (voltage, current, charge)

Analogue filters

Filter types, filter implementation – passive, active, IIR FIR
Filter approximations, max flat amplitude, ripple, transmission zeros, group delay; Butterworth, Chebyshev, Bessel, Elliptic
Filter transformations, normalised filter design methods
Passive filter implementation, terminated filters
Active filter types; gyrator, single op-amp S-K, Rausch
State-variable Tow-Thomas Biquad circuit, derivation
Biquad tuning, LP/BP/BS/AP/Equaliser variants
Biquad Q tuning and use as a sine wave oscillator
Practical implementation issues; dynamic range, component sensitivity; adaptive tuning

Introduction to phase locked loops

Basic operation of PLL, linear phase domain model
Oscillators and basic phase detectors
Tracking filter and FM demodulator
Advanced phase detectors;
Clock and data recovery

Analogue to digital conversion

ADC specs, linearity, resolution, linearity, bandwidth (revision)

Fundamentals of noise in digital and analogue systems
Sample and Hold Circuits, track and hold
Quantising noise, anti-aliasing
More ADC types ; flash, dual slope

Transmission lines for HF signals

Basic theory; coax, parallel wire, stripline
Characteristic impedance, termination
Pulse behavior with mismatch
Frequency dependent characteristics
Applications issues in data comms and RF; losses; intersymbol interference; SWR

Digital to Analogue Conversion

R-2R Digital to Analogue Converters
PWM Signal Generation
Applications of digital to analogue converters

Low noise amplifiers

Fundamentals
Physical noise models, passive and active devices
Input referred noise model
Noise in simple amplifiers and opamps
Discrete and op-amp specs
Practical low noise input circuitry

Power Supplies and Power Amplifiers

Linear Regulators
Buck Converters
Boost Converters
Power Supply Stability
Power Amplifiers

Class A/AB/B/D Amplifiers
Applications (Audio and Power)

Driver Circuits

Power Conversion

AC/DC Rectification
Inverter Design

Practical Aspects

EMC
PCB Design
Screening
Thermal Design Aspects

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture		36
Tutorial		12

Assessment

Assessment methods

Method	Hours	Percentage contribution
Analogue Circuit Design	-	10%
Exam	2 hours	90%

Referral Method: By examination

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COMP3211 Advanced Databases

Module Overview

This module builds on the first year Data Management module by examining the construction of database management systems, and the data structures and algorithmic techniques used to represent and manipulate data effectively.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

The internals of a database management system
The issues involved in developing database management software
The variety of available DBMS types and the circumstances in which they're appropriate

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Choose appropriate approaches for data storage and access
Demonstrate how a DBMS processes, optimises and executes a query
Identify issues arising from concurrent or distributed processing and select appropriate approaches to mitigate those isues

Subject Specific Practical

Having successfully completed this module, you will be able to:

Select an appropriate DBMS for an application
Implement components of a DBMS

Syllabus

DBMS Internals
Relational Algebra
Data

Types of data, including spatial and temporal

Data Storage

The memory hierarchy
Fields, records and blocks
The Five Minute Rule
Row stores vs. column stores

Access Structures

Indexes
B-Trees
Hash tables
Multidimensional Access Structures: grid file, partitioned hash, kd-tree, quad-tree, R-tree, UB-tree, bitmap indexes

Query Processing

Physical plan operators: one-pass algorithms, nested-loop joins, two-pass algorithms
Query optimisation: algebraic laws, cost estimation, cost-based plan selection

Transaction Processing: chained transactions, nested transactions, savepoints, compensating transactions
Concurrency
Parallel Databases

Partitioning techniques
Types of parallelism: intraquery, interquery, intraoperation, interoperation

Distributed Databases
Message Queues
Stream Processing
Information Retrieval
Data Warehouses and OLAP
Non-Relational Databases: hierarchical, network, object-oriented, object-relational, XML
NoSQL

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture		36

Assessment

Assessment methods

Method	Hours	Percentage contribution
Database Programming Exercise	-	25%
Exam	2 hours	75%

Referral Method: By examination

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COMP3210 Advanced Computer Networks

Module Overview

This module is designed to be a follow-up module to the Computer Science or ITO second year introductory networking module.

The module is split fairly evenly between two areas, each principlally delivered by a separate lecturer. The wireless part reviews wireless technologies and their application in areas such as sensor networking. The coursework gives students the opportunity to get hands-on experience with wireless networking for small, embedded devices. The other part of the module reviews emerging networking technologies, which might include topics such as future routing protocols, IPv6 transition, and software-defined networking.

Students should consider taking this module if they are interested in learning about networking systems and their architectures in more detail than covered in the introductory module, and exploring emerging topics which are delivered as part of ECS' research-led teaching philosophy.

Aims & Objectives

Aims

Knowledge and Understanding

Having successfully completed this module, you will be able to demonstrate knowledge and understanding of:

Operation of wireless networks
Emerging topics in computer networks
A range of network architectures and protocols

Subject Specific Intellectual

Having successfully completed this module, you will be able to:

Design and critically analyse networking protocols for a range of technologies and scenarios

Subject Specific Practical

Having successfully completed this module, you will be able to:

Build a wireless networking demonstrator for an embedded system

Syllabus

Wireless networking:

Bluetooth, 802.11 standards
Information theory, bandwidth, multiple access
Wireless sensor networks
Wireless roaming; eduroam
Mobile IPv6; host and network mobility

Emerging networking technologies:

Host configuration and service discovery principles
Future routing architectures
IPv6 deployment scenarios and challenges, IPv6 transition/integration
Advanced IP multicast, including IPv6 multicast and SSM
Software-defined networking
Delay-tolerant networking
Future home network architectures
IP network management and monitoring
Network security; intrusion detection and prevention

Learning & Teaching

Learning & teaching methods

Activity	Description	Hours
Lecture	Regular lecture slots.	21
Tutorial	Tutorial support on the coursework and specific lecture topics	8
Seminar	Guest lectures from industry experts	4
Tutorial	Revision (last teaching week)	3

Assessment

Assessment methods

Method	Hours	Percentage contribution
Wireless networking for embedded systems	-	30%
Exam	2 hours	70%

Referral Method: By examination

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