Faculty of Natural Sciences
Department of Life Sciences
MSc Bioinformatics and
Theoretical Systems Biology
Student Handbook
2022-23
Contents
Welcome to the College .......................................................................................................... 1
Our Principles .......................................................................................................................... 2
Welcome from the Graduate School ..................................................................................... 3
The Graduate School............................................................................................................... 4
1.
Introduction to the Department ....................................................................................... 5
Welcome from Programme Director .............................................................................. 5
Academic and Administrative staff ................................................................................ 5
English language requirement ....................................................................................... 7
Attendance and absence ............................................................................................... 7
Key dates 2022–23 ........................................................................................................ 7
2.
Programme Information ................................................................................................... 8
2.1 Course Outline and Key Information .................................................................. 8
2.2 Taught Component .................................................................................................................10
2.2.1 Bioinformatics and Systems Biology I ................................................................................10
2.2.3 Computing ...........................................................................................................................13
2.2.4 Bioinformatics and Systems Biology II ...............................................................................14
2.3 Projects ............................................................................................................................. 15
2.3.1 Computing Project ........................................................................................... 16
2.3.2 Data Analysis Project ...................................................................................... 17
2.3.3 Research Project - Bioinformatics and Theoretical Systems Biology ...... 17
Imperial Mobile app ...................................................................................................... 18
Welcome to Imperial app ............................................................................................. 18
Imperial Success Guide ............................................................................................... 19
3.
Assessment ..................................................................................................................... 20
3.1: Criteria for Assessment of Written work – exam questions and exercises ............ 24
3.2 : Criteria for Assessment of Mathematical Questions ........................................... 27
There are three components in grading a question that is primarily or exclusively
mathematical. The relative grades award will depend on the particular question set.
But as a guide the criteria with relative weightings are: ................................................ 27
3.3 : Criteria for Assessment of Multiple Choice (MCQ) Questions ............................ 27
3.4: Criteria for Assessment of Laboratory Work ........................................................ 28
3.5: Criteria for Assessment of Work Presented Orally .............................................. 29
3.6: Criteria for Assessment of Work Presented in Reports ....................................... 30
3.7 Criteria for Assessment of Web Page Reports ..................................................... 31
3.8: Structure of Examination Questions ..................................................................... 31
3.9 Guidelines for Exercises ........................................................................................ 31
3.10: Guidelines for Reports ........................................................................................ 31
General guidelines for all reports ............................................................................ 31
Additional Requirements for Computing Project reports ......................................................33
Additional guidelines for web-based report of data analysis ................................................36
Additional guidelines for Project 3 report ................................................................................35
Writing Resources ........................................................................................................ 35
Plagiarism..................................................................................................................... 36
Collusion....................................................................................................................... 36
Exam offences ............................................................................................................. 37
Dishonest practice........................................................................................................ 37
Research Integrity ........................................................................................................ 37
4.
Board of Examiners ....................................................................................................... 40
5.
Location and Facilities ................................................................................................... 40
6.
Working While Studying ................................................................................................ 42
7.
Health and Safety............................................................................................................ 43
8.
College Policies and Procedures.................................................................................. 45
Regulations for Students.............................................................................................. 45
Provisional Marks Guidance ........................................................................................ 45
Late Submission Policy ................................................................................................ 45
Mitigating Circumstances ............................................................................................. 45
Academic Misconduct Policy and Procedures ............................................................ 46
Unsatisfactory Progress ............................................................................................... 49
Academic Appeals Procedure ..................................................................................... 46
Arithmetic Marks Check ............................................................................................... 46
Student Complaints ...................................................................................................... 47
Student Disciplinary Procedure ................................................................................... 47
Intellectual Property Rights Policy ............................................................................... 47
Use of IT Facilities........................................................................................................ 47
General Data Protection Regulation (GDPR) .............................................................. 48
9.
Wellbeing, Support and Advice .................................................................................... 49
In your department ....................................................................................................... 49
Your Union ................................................................................................................... 49
Student Hub ................................................................................................................. 50
Student Support Zone .................................................................................................. 52
Useful support contacts ............................................................................................... 50
10. Student Administration .................................................................................................. 53
13. Work-life Balance ............................................................................................................ 54
Graduate Students’ Union............................................................................................ 54
Move Imperial ............................................................................................................... 54
14. Student feedback and representation .......................................................................... 54
Feedback from students .............................................................................................. 55
Student representation................................................................................................. 55
Staff-Student Committee.............................................................................................. 55
15. Student Surveys.............................................................................................................. 56
16. And finally ........................................................................................................................ 57
Alumni Services ........................................................................................................... 57
Opportunities for Further Study ................................................................................... 57
1. College Introduction
Welcome to the College
Congratulations on joining Imperial
College London, the only university in the
UK to focus exclusively on science,
medicine, engineering and business.
From Fleming’s discovery of Penicillin to
Gabor’s invention of holography, Imperial
has been changing the world for well over
100 years. You’re now part of this
prestigious community of discovery and
we hope you will take this opportunity to
make your own unique contribution.
You’re now very much a part of this
community of discovery and we hope you
will take this opportunity to make your
own unique contribution. At Imperial, we
expect all members of our community,
whether students or staff, to share and
demonstrate our values of respect,
integrity, collaboration, innovation and
excellence in all we do and strive to
achieve.
We understand that this is a challenging time for our student community due to the impact of
coronavirus and we are committed to providing you with the very best academic resources to
enrich your experience. Information on teaching and learning, services and facilities to support
the wider student experience during the Covid-19 pandemic can be found on the College’s
webpages, alongside local information provided by your Department. We also provide a
dedicated support network and a range of specialist support services to make sure you have
access to the appropriate help, whether that’s further training in an academic skill like note
taking or simply having someone to talk to.
You’ll have access to an innovative range of professional development courses within our
Graduate School throughout your time here, as well as opportunities to meet students from
across the College at academic and social events – see page 6 for more information.
We actively encourage you to seek out help when you need it and try to maintain a healthy
work-life balance. Our choice of over 360 clubs, societies and projects is one of the largest of
any UK university, making it easy to do something different with your downtime. Access to the
gym and other sporting facilities will be dependent on government guidance. We are working
to ensure that you have access to a variety of resources online to support your health and
wellbeing if there are restrictions.
As one of the best universities in the world, we are committed to inspiring the next generation
of scientists, engineers, clinicians and business leaders by continuing to share the wonder of
what we do through public engagement events. Postgraduate students, alongside our
academics and undergraduate students, make a significant contribution to events such as our
annual Imperial Festival and our term-time Imperial Fringe events – if you’re interested in
getting involved then there will be opportunities for you to do so.
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Our Principles
In 2012 the College and Imperial College Union agreed ‘Our Principles’ a series of
commitments made between students and the College. The Principles are reviewed annually
by the Quality Assurance and Enhancement Committee and changes recommended for
Senate approval.
Imperial will provide through its staff:
• A world class education embedded in a research environment
• Advice, guidance and support
• The opportunity for students to contribute to the evaluation and development of
programmes and services
Imperial will provide students with:
• Clear programme information and assessment criteria
• Clear and fair academic regulations, policies and procedures
• Details of full programme costs and financial support
• An appropriate and inclusive framework for study, learning and research
Imperial students should:
• Take responsibility for managing their own learning
• Engage with the College to review and enhance provision
• Respect, and contribute to, the Imperial community
The Imperial College Students' Union will:
• Support all students through the provision of independent academic and welfare
assistance
• Encourage student participation in all aspects of the College
• Provide a range of clubs, societies, student-led projects and social activities
throughout the year
• Represent the interests of students at local, national and international level
www.imperial.ac.uk/students/our-principles
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Welcome from the Graduate School
Welcome to Imperial College London and the Graduate School!
The Graduate School is responsible for the postgraduate experience at the College and we
work closely with the Union and the Graduate Students’ Union to ensure that when decisions
are being made, which affect your time at Imperial, your voice is heard.
Another important aspect of our role is to offer you a free and exciting range of professional
development opportunities which you can access wherever you are in the world.
Our team of tutors have a variety of research and other career experiences. We understand
the importance of developing professional skills and our programmes will help you to progress
in your academic studies and research and will prepare you for your future career. Whether
you wish to pursue a career in academia, industry or something else, professional
development training will improve your personal impact. You will also get to meet students
from other Departments when attending our courses.
The Graduate School runs exciting competitions throughout the year which are an opportunity
to broaden your knowledge as well as to meet other students and have fun. Our primary way
to communicate to you will be through our monthly newsletter. However, do check our
website, blog and social media platforms to keep up to date with all the latest activities
available to you.
Finally, Imperial College is an extremely exciting, stimulating and diverse environment in which
to work, to study and to research. Do make the most of all that the College and your
programme has to offer.
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The Graduate School
You automatically become a member of the Graduate School when you register as a
postgraduate student at Imperial.
The Graduate School has been set up to support all postgraduate students at the College
through:
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Training and development courses and
retreats
Networking activities, social and
academic events to encourage crossdisciplinary interactions
Forums to represent the views of
postgraduate students throughout the
College
Coaching
Research Degree Mediation
Professional skills courses
You can see the full range of free professional
skills courses for postgraduate students on the
Graduate School website:
www.imperial.ac.uk/study/pg/graduate-school/students/doctoral/professionaldevelopment/
All courses can be booked online.
Contact us
Level 3, Sherfield Building, South Kensington Campus
020 7594 1383
graduate.school@imperial.ac.uk
www.imperial.ac.uk/graduate-school
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1.
Introduction to the Department
Welcome from Programme Director
As Director of the MSc in Bioinformatics and Theoretical
Systems Biology, I would like to warmly welcome you to our
course. We look forward to sharing our excitement of working at
the interfaces between Biosciences, Biomedicine, Computing
and Mathematics. After formal training in the first term, you will
engage in research-level projects across Imperial.
Best wishes –Michael Sternberg
Academic and Administrative staff
Professor Michael
Sternberg
Sir Ernst Chain Building
020 7594 5212
Course Director
m.sternberg@imperial.ac.uk
Dr Derek Huntley
Chair of Examiners
239, Sir Ernst Chain Building
020 7594 5149
& Computing Coordinator
d.huntley@imperial.ac.uk
Ms Sally Dennison
Postgraduate Administrator
Room 202, Sir Ernst Chain
Building
020 7594 2170
•
s.dennison@imperial.ac.uk
Dr David Mann
Director of Postgraduate
Studies
Sir Ernst Chain Building
020 7594 5209
5
d.mann@imperial.ac.uk
Dr Tony Southall
Postgraduate
Tutor/Disability Liaison
Officer
220 off lab 216, 2nd Floor,
Sir Ernst Chain Building,
South Kensington Campus
020 7594 5338
t.southall@imperial.ac.uk
Dr Suhail Islam
Senior Research Officer
301, Sir Ernst Chain Building
020 7594 5333
suhail.islam@imperial.ac.uk
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English language requirement
If you are not a native English speaker you must meet the College’s English language
requirements.
See the Admissions website for details:
www.imperial.ac.uk/study/pg/apply/requirements/english
For information on English language support available while you’re here, see
English language support | Imperial students | Imperial College London.
Attendance and absence
You must inform your Senior Postgraduate Tutor if you are absent from the College for more
than three days during term. If the absence is due to illness you must produce a medical
certificate after seven days. If you are ill and miss an assessment deadline (this could be an
examination, presentation or a coursework submission) you will need to make a claim for
mitigating circumstances within 10 working days of the deadline. Please see the section on
mitigation below.
The Registry will be informed of all student non-attendances as the College is obliged to
report the non-attendance of students on Tier 4/Student Route visas to the Home Office.
Key dates 2022–23
Please note that this course runs beyond the term dates but acknowledges all closure
term dates
Term dates
Autumn term:
Spring term:
Summer term:
Closure dates
Christmas/New year:
1 October 2022 - 16 December 2022
7 January 2023- 24 March 2023
29 April 2023 - 30 June 2023
24 December 2022 - 2 January 2023
(College reopens on 3 January 2023)
Easter Holiday:
6 April 2023 – 12 April 2023
(College reopens on 13 April 2023)
Early May Bank Holiday:
Spring Bank Holiday:
Summer Bank Holiday:
1 May 2023
29 May 2023
28 August 2023
Key events
Great Exhibition Road Festival:
17 June 2023 – 18 June 2023
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2.
Programme Information
2.1 Course Outline and Key Information
Taught courses in the first term - The first term of the year will be spent on taught courses.
These courses reflect the background of the students as much as the requirements of the
working research bioinformatician and theoretical systems biologist. We will provide an
introduction to computing, mathematics/statistics and biology as well as a survey over recent
developments in bioinformatics and systems biology. All computer languages will be taught
without assuming any previous knowledge of that specific language. However, students are
expected previously to have had some experience of developing computer code and so they
are familiar with the basic concepts of algorithm development. Depending on your background
you may find parts of the course familiar while other parts will introduce novel material and
concepts. Students with a background in biology will have to become familiar with a range of
mathematical and numerical techniques, while those from the mathematical and physical
sciences will have to learn genetics and genomics, typically at the level of final year
undergraduate biologists. The amount of time spent on learning the material covered in the
different courses will necessarily have to reflect this. Time for revision is built into the timetable.
Please note the exact topics covered in the lectures may be modified slightly from the details
provided in this handbook in order that we can provide some flexibility into the depth and time
spent on topics based on student feedback during the lecture course.
Lectures. All lectures will be recorded and available on-line. Lectures will mainly be delivered
on campus but circumstances may require some to be remote. You are expected to follow all
the lectures except if some introductory topics were clearly covered in your previous training
(e.g. introduction to statistics or mathematics).
Class tutorials, computing and bioinformatics workshop. These will be mainly delivered
on campus but circumstances may require some to be remote.
January Examinations. These will be timed and in person.
Projects in the subsequent terms - The remainder of the course consists of two research
projects. The first (Project 1) is the Computational Project and will last about 11 weeks. This
is normally undertaken as a group project. The second (Project 2) is the Bioinformatics and
Theoretical Systems Biology Project and will last about 22 weeks. The Computational Project
is normally supervised by academics from the Department of Life Sciences whose main
research interest is in bioinformatics and/or theoretical systems biology. Students undertaking
the second project can be part of groups located across many of the Imperial Campuses
including South Kensington, St Mary’s Hospital Campus, Hammersmith Hospital Campus, the
White City Campus and the Silwood Park Campus. The research projects cannot be
undertaken at non-Imperial locations. Each project is assessed.
Assessment – Assessments are outlined in this section with full details of the assessment
and grades given in Section 3 of the Handbook. Please refer to Section 6 for details of the
report format including word count.
Outcomes - At the end of the MSc degree students should have gained an overview of
bioinformatics and theoretical systems biology, as well as a proper foundation to develop these
fields further. Bioinformatics and theoretical systems biology are highly active and quickly
changing research areas and there is no substitute for a sound understanding of basic
concepts of biology, mathematics/statistics and computing. Students should also have
developed their abilities in software design and statistical analysis, including the critical
discussion of scientific results. Finally they should have improved their skills in presenting
scientific work verbally and in written form.
Health and safety
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Alarm and escape – If you are on campus, it is essential that in any area you are
working you know the warning mechanism for alarm calls and the routes to escape if
there is an emergency. In particular, when you start a new project, you may well be in
a new area so please ensure you are aware of the alarm and escape procedure.
Lone working – Staff and students may lone work during office activities. In these cases staff
and students should follow the basic guidance below (from the College code of practice):
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If staff/students disclose any medical conditions and vulnerability that might put them
especially at risk they are required to apply for lone working consent from their
manager.
Ensure you know the nearest fire exit and where to assemble
Ensure the emergency number for security is known (Ext 4444 or 020 7589 1000)
Ensure you have a mobile or access to a landline phone
If you are working late ensure someone knows your expected time of finishing and
return home
Consider personal safety if travelling home late at night from the College and Dept.
Do not carry out high risk prohibited activities while lone working in a benign
environment
Work within the core work hours as much as possible: 08.00 – 18.00
Normal building access hours: 07.00 – 00.00
Building closed: 00.00 – 07.00
Dangerous items in lifts – On no account enter a lift where there is notice advising you
against this or there are unaccompanied goods. Dangerous items include, but are not
limited to, a compressed air cylinder or a large box of dry ice.
Health and other problems - Should personal and/or health problems require the
student to take some time off, then this should be immediately brought to the attention
of the Course Director. Similarly if there are major technical problems in projects or exercises
the student should promptly advise the Course Director or Deputy Director. Failure to notify
promptly may make the student ineligible for subsequent mitigation including a delayed hand
in.
Absences - During the first three months of the course students are expected to follow the
lectures and all other classes either on campus or remotely. Persistent failure to follow lectures
and join classes (either in person or remotely) may result in a student being asked to leave
the course. The research projects aim to introduce students to an active research
environment. Performance during the project is part of the formal assessment and students
should arrange working hours together with their supervisor. The students must agree leave
of absence both with their project supervisor and the Course Director. Failure to do so may be
reflected in the mark for lab performance. This is a full-time degree and we are unlikely to
approve total absences of more than one week except for major health reasons. Some
students require leave to attend interviews and this is included in the allowance of one week.
Travel - All students must include an appropriate time for a delay to their travel arrangement
to meet an examination, viva or hand-in deadline. This applies to both any assessment oncampus or remotely. Failure reasonably to meet this requirement will result in no allowance
for missing the exam, viva or late hand in penalty. For any flight, sea crossing or rail journey
more than 100kms, the scheduled arrival must be before midnight three days before the exam
– for example if the exam is on Friday, the scheduled arrival must be by midnight of the
proceeding Tuesday. For land travel 100 kms or less, arrival should be before midnight two
days before the exam. In addition, students taking an assessment must take into account any
quarantine restrictions in place that might affect them.
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Modification to handbook - Course contents may vary slightly during the year in order to
reflect the students’ needs as well as the fast pace at which these fields are progressing. Thus
there may be minor changes to the topics to be presented from those identified in this
handbook. In addition, the mode of delivery may have to alter if the health situation or
government guidelines change.
Panopto and Blackboard – All lectures and other recordings will be available on the student
VLE Blackboard. All teaching rooms at ICL are Panopto enabled. Links to recordings will be
available on Blackboard as necessary. Blackboard will also feature past exam papers for
2021/22.
2.2 Taught Modules (First Term)
2.2.1 Bioinformatics and Theoretical Systems Biology
Learning
outcomes
Module content
Learning and
Teaching
Approach
•
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Understand the principles of the modern life- and biomedical sciences
Ability to undertake the analysis of DNA, protein, biological diversity and
molecular interaction data
• Knowledge and understanding of algorithms in bioinformatics and theoretical
systems biology
• Ability to decide appropriate scientific methods and techniques for analysing
raw data and solving phylogenetic problems
• Ability to develop and implement strategies for modelling biological systems
Part A
Basic concepts including biochemistry, structure and function of biological
macromolecules, and cell biology.
Part B
• The most important bioinformatics tools in core areas and experience of
systems biology analysis.
• Key computational methods that impinge directly on contemporary
bioinformatics and systems biology.
Lectures, backed up by external reading, Q&A feedback sessions and practical
classes.
Assessment
Strategy
There will be two practical exercises on i) protein annotation and iii) genome
annotation and an exam.
Feedback
Feedback will be provided via group meetings with the course convenors and
assessment of the course work components.
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Reading list
Part A
• Molecular & Cell Biology for Dummies by Rene Fester Kratz pub Wiley (an
introduction that is suitable for non biologists prior to joining the course)
• Essential Cell Biology Albert et al pub Garland Science
Part B
• Introduction to Bioinformatics by A Lesk, 5th ed Oxford University Press
• Introduction to Genomics by A Lesk, 3rd ed Oxford University Press
• Bioinformatics: Sequence and Genome Analysis, Second Edition by D Mount
pub Cold Spring Harbor Laboratory Press (sections go beyond what is
required)
• Understanding Bioinformatics by Zvelebil and Baum pub Garland Science
• An Introduction to Systems Biology, Uri Alon, Chapman & Hall/CRC 2006
Details of module content
Part A) Introduction to molecular, cellular and systems biology
The introduction will briefly introduce basic concepts including biochemistry, structure and
function of biological macromolecules, and cell biology. Students from a non-biological
background will acquire an introduction to key concepts in biochemistry and molecular cell
biology. All students will acquire knowledge of contemporary genetics, genomics and
proteomics that will be required as a foundation for studies in bioinformatics and systems
biology.
Typically, the following topics are covered:
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Genes and Genomes
Proteins
Gene Expression
Cell Biology
Cellular Biochemistry and Metabolism
Functional and Structural Genomics
Integrative Systems Biology
Part B) Bioinformatics and Theoretical Systems Biology
This is a major aspect of the taught component and aims:
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To provide students with a state-of-the-art understanding of the principles, algorithms and
programs in bioinformatics and systems biology methodologies across a broad range of
application areas.
To introduce the most important bioinformatics tools in core areas and experience of
systems biology analysis.
To introduce key computational methods that impinge directly on contemporary
bioinformatics and systems biology.
To provide an understanding of the limitations of contemporary bioinformatics and systems
biology.
Typically, the following topics are covered:
•
Protein bioinformatics: Principles of protein structure and function. Annotation and
prediction of protein structure, function and interactions.
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Genomic bioinformatics: DNA sequence analysis; genome assembly and annotation;
expression analysis.
Statistical and population genetics
Systems biology: networks and mathematical modelling.
Introduction to machine learning (could be covered in the Maths component depending on
class progress)
Delivery of Module – There will mainly be by lectures which will be recorded and available
on-line. There will be two practical classes covering the protein and genomics bioinformatics.
There wil be feedback for the two exercises.
Assessment of Module- There will be two practical exercises which will each occupy the
student for 10 -15 hours and will be phased throughout the first term. The exercises will be i)
protein annotation and iii) genome annotation (order subject to timetabling). In total the two
exercises contribute 25% of the mark for this module (each being equal). There will be an
exam in January (75% of mark) covering all topics in this module. The exam will consist of
multiple choice questions (MCQs) and three long questions. The material covered in Part A
will be assessed via the MCQs. The material covered in Part B will be assessed via the MCQs
and the three long questions. Although the questions focus on the material taught in this
module, there can be aspects of the question testing material taught in the other module.
2.2.2 Mathematics and Computing
Learning
outcomes
Module content
Learning and
Teaching
Approach
• Ability to develop program in Python
• Ability to use Linux operating system
• Understanding of relational databases and SQL
• Understanding of statistical probabilities, variables and distributions
• Understanding of Bayesian methods and inference
• Ability to apply statistical analysis to biological data
• Ability to undertake analysis of differential and ordinary differential equations
Part A
• Introduction to the Linux operating system
• Introduction to Python.
• Relational database and SQL
Part B
• Probability and discrete random variables
• Independence, joint and conditional probabilities
• Continuous random variables and distributions
• Population vs sample statistics and descriptive statistics
• Likelihood
• Bayesian methods and inference
• Statistical tests
• Markov processes
• Analysis of differential equations
• Dynamical systems and ordinary differential equations
Lectures, backed up by external reading, Q&A feedback sessions and practical
classes.
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Assessment
Strategy
Maths and Python coursework.
Python timed assessment.
Maths exam.
Feedback
Feedback will be provided via group meetings with the course convenors and
assessment of the course work components.
Reading list
Introductory texts
• Mathematics for biological scientists by Mike Aitken, Bill Broadhurst, and
Steve Hladky, Garland Science
• Practical Statistics for Medical Research by Douglas Altman Chapman & Hall
Advanced texts
• An Introduction to Systems Biology, Uri Alon, Chapman & Hall/CRC 2006
• Nonlinear dynamics and Chaos, Steven Strogatz, Westview Press, 2000
• MATLAB Deep Learning, Phil Kim, Apress, 2017
• Elementary probability by Stirzaker,
• Probability and random variables: a beginner’s guide by Stirzaker,
• Statistical methods in bioinformatics by Ewens and Grant,
• Mathematical Statistics and Data Analysis by Rice
• Probability and Statistics, The Science of Uncertainty by Evans and
Rosenthal,
• Biological Sequence Analysis: Probabilistic models of proteins and nucleic
acids by Durbin, Eddy, Krogh and Mitchison,
• Mathematical and statistical methods for genetic analysis by Lange
Details of module content
The module will consist of two parts. Part A will teach the Python programming language with
a focus on applications to bioinformatics and theoretical systems biology. There will also be
an introduction to Linux.
Part B will cover the mathematics underpinning bioinformatics and theoretical systems biology
with an emphasis on state-of-the-art modelling systems using differential equations. In
addition, the module will describe statistical concepts arising in bioinformatics and systems
biology applications, such as hypothesis testing, the problem of multiple comparisons and
Bayesian statistics. To facilitate discipline hopping for less mathematically skilled students,
the module will also introduce key mathematical methodologies.
Part A) Computing
Details of module content
This module introduces the key programming language (Python in 2022/2023 but reviewed
annually) in bioinformatics and theoretical systems biology together with skills in database
design. The module aims to provide highly transferable skills and will cover:
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•
Introduction to computing: this will be a general overview of computing techniques,
including relational databases and SQL, computer architectures, features of a major
programming language (currently Python);
Python - Students who have taken this module should be able to develop Python code
to undertake many typical tasks in bioinformatics and theoretical biology. They will have
developed a conceptual framework so they able to learn new methods and languages
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•
•
independently if the need arises. Students who have taken this Python course should be
able to learn new methods and languages independently if the need arises.
Introduction to Databases - The course is a general introduction to relational
databases. Topics covered include database design and an overview of normalisation.
This will be followed by a presentation of MySQL and how to create, populate and
access information in a database.
Linux and web development. – An introduction to the Linux operating system and a
general introduction to website development.
Delivery of Part A– Delivery will be mixed mode with teaching and hands-on computing. We
envisage teaching databases, Linux, and web design early in the second term, but this can
change based on student progress and feedback.
Assessment of Part A - There will be one marked assignment in Python (contributing 40%
of the marks for Part B and one timed open-book assessment (contributing 60% of Part B).
There will be sufficient time in this test to allow students who have limited previous computing
experience and are competent to finish the questions. The timed exam style test will be held
in April 2023. The skills in databases and web development may be assessed as part of the
research projects if relevant to the project. The timed exam style test may be replaced by an
additional exercise if all students are unable to be on campus.
Part B – Mathematics
Details of module content
Part B will introduce basic mathematical methodologies such as ordinary differential equations
for systems biology modelling. In addition, the theory of probability and statistics will be taught.
The module will describe issues arising in bioinformatics and systems biology applications,
such as hypothesis testing and the problem of multiple comparisons. Examples of the
application in bioinformatics and systems biology will be given. The precise content will reflect
the pace of the class and some topic may be covered in Bioinformatics and Theoretical
Systems Biology
Lectures typically include:
Part B.1 - Statistics
• Probability and discrete random variables
• Independence, joint and conditional probabilities
• Continuous random variables and distributions
• Population vs sample statistics and descriptive statistics
• Likelihood
• Bayesian methods and inference
• Statistical tests
Part B.2 – Mathematics and modelling
• Key concepts in algebra and calculus.
• Analysis of differential equations.
• Dynamical systems and ordinary differential equations
• Guided by the pace of the class advanced topics such as stochastic approaches
including the chemical master equation and Gillespie simulations.
Delivery of Part B
14
Teaching will mainly be via lectures which will be recorded and available on-line There will
be on-line Q&A sessions/tutorials following several of the lectures.
Assessment of Part B – There will be a graded exercise in the first term (25% of marks)
and examination in January (75% of marks).
2.3 Projects
The following are general points which apply to both projects. All projects must be
supervised by Imperial staff and external placements are not permitted.
Project and supervisor choice
A list of potential supervisors and projects is compiled and circulated in advance before each
project. Students can indicate their top four preferences. Normally, we can accommodate
students’ top four but can make no guarantee about allocations. For project 2, students may
also approach supervisors to explore areas of interest assuming they meet the requirements
of the course and are authorised by the Course Directors. The supervisor must be a member
of the Imperial staff and the project takes place on an Imperial campus.
Attendance in laboratory.
If possible, students are expected to work at Imperial and cannot expect their supervisor or
work colleagues (while they are on campus) to provide scientific guidance by email rather than
face to face meetings. If working is remote you should interact via Teams or similar and not
extensively by e-mail. During the projects, you are expected to be proactive in raising issues
with your supervisor and work colleagues. In particular, during the group project it is expected
that you will be working as a team.
Remote project supervision
If required due to a change in circumstances, both research projects will be supported by
remote supervision. We will ensure that the student has adequate access to the required
software and data.
Group project
The first project (January – March/April) is a group project when normally 2 to 4 students jointly
tackle a project. If due to distancing requirement and/or remote working and/or other factors,
some or all of the students may be offered a comparable individual project.
Data security.
Please note that it is your responsibility to ensure all files for both research and reports are
securely backed up. You must discuss file back up with your supervisor and not assume
it is secure. In particular if you are just working on a desktop, you need to ensure it is
backed up regularly on a central secure file system. You must consider that all data on
a laptop can be unrecoverable and you must back it up regularly. If you fail to implement
a sensible file back up policy, then you will be penalised for limited results and late hand in.
Computational and mathematical requirements of projects.
15
To pass each project, the work reported must demonstrate a level of mathematical, statistical
or computational skill that extends beyond just the use of existing programs. If you have any
concerns whether your project meets this requirement, you must discuss it with the Course
Director or Deputy Director.
Submission format
Please refer to section 6 for details of the report format including word count.
2.3.1 Project 1 - Computing Project
Learning
outcomes
Module content
•
Ability to apply research techniques, including information and data retrieval,
study design, program development and implementation and data analysis
• Development of management and communication skills, including problem
definition, project design, decision processes, teamwork, written and oral
reports, scientific publications.
• Understand and evaluate current research through reading published papers
in recommended journals
• Ability to collaborate effectively in a group project
• Ability to plan, undertake and write up a group research project.
• Ability to prepare technical reports
This is a group project, where typically 2-4 students will implement a large
software or research project under the supervision of a member of the Centre for
Integrative Systems Biology and Bioinformatics (CISBIO).
Learning and
Teaching
Approach
Supervision by academic staff member and regular group meetings.
Assessment
Strategy
The project is assessed by individual performance during the project, a group
project report and an individual presentation and viva.
Feedback
Ongoing feedback during project and supervisor/examiner feedback on
completion.
Module content
The aim of this project is to further develop students’ computational expertise in a
bioinformatics and/or systems biology setting and to apply the newly acquired skills in the
development of a substantial piece of software. The development of a functional genomics
database with a web-based user-interface is an example of a previous project. Depending on
the nature of the project students may have to learn new computational techniques.
This is a group project, where typically 2-4 students will implement a large software or research
project under the supervision of a member of the Centre for Integrative Systems Biology and
Bioinformatics (CISBIO). The supervisor will, however, only give limited guidance and leave
planning, development, implementation and tuning of the research or software to the students.
16
Each group has approximately 11 weeks to complete the project. Further detail of the report
including the length are given
The group report should provide an account of the project which may be an overview of the
software product and information on how to use it. In the group report you must clearly
indicate in each section by use of initials who wrote that section and who undertook
the work. Joint authorship is allowed in some, but not all, sections. The one-page
personal reflection details any challenges you faced during the project to provide context for
our assessment. This one-page report by itself is not assessed.
Module assessment
•
•
•
Performance during the project. (20% of total mark)
The report. (40% of total mark)
Performance in a presentation and a viva. (40% of total mark)
The presentation and viva are held after report submission and will be graded by two
examiners and not the supervisor.
2.3.3 Project 2 - Bioinformatics and Theoretical Systems Biology Project
Learning outcomes
Module content
•
Ability to apply research techniques, including information and data retrieval,
study design, program development and implementation and data analysis
• Development of management and communication skills, including problem
definition, project design, decision processes, written and oral reports, scientific
publications.
• Understand and evaluate current research through reading published papers in
recommended journals
• Ability to plan, undertake and write up an individual research project.
• Ability to prepare technical reports
The project can be across a range of topics in bioinformatics and theoretical
systems biology. It must include bioinformatics and/or systems biology research
and cannot be purely computational, mathematical or statistical.
Learning and
Teaching Approach
Supervision by academic staff member
Assessment Strategy
The project is assessed by individual performance during the project, a project
report and an individual viva.
Feedback
Ongoing feedback during project and supervisor/examiner feedback on completion.
17
Module content
The project is research across a range of topics in bioinformatics and theoretical systems
biology ranging from applied bioinformatics all the way through to mathematical biology.
However it must not be purely computational, mathematical or statistical but must serve to
engage the student with a high quality bioinformatics and theoretical systems biology research
environment. The project must not include any experimental work.
The second project can be hosted by any suitably qualified bioinformatics and systems biology
group within Imperial College London, including all associated hospitals and Silwood Park
campuses. Students cannot perform their bioinformatics project outside of Imperial College.
Typically, during the project each student will become part of their host laboratory and work
alongside PhD students and postdocs on a topic agreed with the supervisor.
Module assessment
•
•
•
Performance during the project. (20% of total mark)
The report. (40% of total mark)
Performance in a viva. (40% of total mark)
The viva, which will typically last about 30-45 minutes, is held after report submission and
will be by two examiners and will not include the supervisor.
Imperial Mobile app
Don’t forget to download the free Imperial Mobile app for access to
College information and services anytime, anywhere, including your
programme timetable, College emails and a library catalogue search
tool.
www.imperial.ac.uk/imperialmobile
Welcome to Imperial app
The College has a Welcome to Imperial app which contains important
information about campus operations, aspects of student life, a
schedule of welcome activities and information about life in halls. All
new students should download this guide to ensure they have the
most up to date information and event schedule for the start of term.
You can download the App from the Apple or Google App Stores.
18
Imperial Success Guide
The Imperial Success Guide is an online resource with advice
and tips on the transition to Master’s level study. More than just
a study guide, it is packed with advice created especially for
Imperial Master’s students, including information on support,
health and well-being and ideas to help you make the most of
London.
www.imperial.ac.uk/success-guide
19
3.
Assessment
Any assessments or project reports that are handed in late will be downgraded. Every
day (or part of day) late will result in a 10% reduction from the original mark for the
assessment or the report.
We may need to deliver examinations by timed remote assessments where these are deemed
the most appropriate method of assessment under the circumstances
Overview
The course is divided into four modules
Credits
Percentage of final mark
Bioinformatics and Theoretical Systems Biology
15
15/90 = ~ 16.7%
Mathematics and Computing
10
10/90 = ~ 11.1%
Computing Project (Project 1)
25
25/90 = ~27. 8%
Bioinformatics and Theoretical Systems Biology
Project (Project 2)
40
TOTAL
90
Module Title
40/90 = ~ 44.4%
90/90 = 100%
There are four outcomes from your MSc course: distinction, merit, pass and fail.
Class of Degree
There are two conditions both of which must be met to establish the class of degree (i) the
Programme Overall Weighted Average and (ii) the mark in the Bioinformatics and
Theoretical Systems Biology Project (Project 2).
The College sets the class of Degree that may be awarded as follows:
(i)
Programme Overall Weighted Average
1. Distinction:
The student has achieved a Programme Overall Weighted Average of
70.00% or above across the programme.
2. Merit:
The student has achieved a Programme Overall Weighted Average of
above 60.00% but less than 70.00%.
3. Pass:
The student has achieved a Programme Overall Weighted Average of
50.00% but less than 60.00%.
and (ii) mark in Project 2.
20
a. Students must normally achieve a distinction (70.00%) mark in the Bioinformatics and
Theoretical Systems Biology Project (Project 2) in order to be awarded a distinction.
b. Students must normally achieve a merit (60.00%) mark in the Bioinformatics and
Theoretical Systems Biology Project (Project 2) in order to be awarded a merit.
Borderline students
There will be procedures established to consider upgrades for borderline students and you
will be advised of these.
Ratification of marks
All marks, results and indicative grades, both at assessment component level and element
level, are provisional until considered and ratified by the appropriate Examination Board.
Assignment of course credit
Where a student passes a module/element, the student will be awarded the volume of credit
assigned to that module/element. The award of partial credit for a module/element is not
permitted.
Resits
A student is allowed to resit once any module where the student failed. A module that has
been passed, and for which credit has been awarded, may not be repeated in order to improve
a mark or gain additional credit. We reserve the right to (and typically do) hold resits at the
same time as the corresponding examination in subsequent years.
External Examiners’ meeting
The External Examiners review the marks obtained from all four modules from the course.
The External Examiners will viva some students from the course. Examiners normally will
also see representative students from each classification; students who represent a balance
of disciplines; students who have failed and candidates for the student prize. Please note that
no student can be downgraded as a result of the External Examiners’ meeting.
In addition, all students are invited to meet the External Examiners without any staff present
to give feedback about the course. This will be conveyed anonymously to the staff and may
be included in the report of the External Examiners to the College.
Assessment of Module 1 – Bioinformatics and Theoretical Systems Biology
There will be two practical exercises which will each occupy the student for 10-15 hours and
will be phased throughout the first term. The exercises will be i) protein annotation and ii)
genome annotation, the order of which will depend on the timetabling. In total the two
exercises contribute 25% of the mark for this module (each being equal). There will be an
exam in January (75% of mark) covering all topics in this module. The exam will consist of
multiple choice questions (MCQs) and three long questions. The material covered in Part A
will be assessed via the MCQs. The material covered in Part B will be assessed via the MCQs
and the three long questions.
The examination will be split into two parts. For the first part (Part I), which lasts one hour,
students have to answer multiple choice questions (MCQs) covering Parts A and B of the
module. After a short break, the second part (Part 2), lasting two hours, will require the
students to answer three questions from five. The first three of set questions will be primarily
21
focussed on bioinformatics (Part 2.1) and the remaining two of systems biology (Part 2.2).
The student must answer one question from Part 2.1, one from Part 2.2, and one from either
Part 2.1 or 2.2. The MCQs provide 25% of the exam mark, while the three long questions
provide 75% in total. Each long question carries the same weight. Although the questions
focus on the material taught in this module, there can be aspects of the question testing
material taught in the other module.
Assessment
Assessment
The practical
exercises
The two practical
exercises
Contribution to total mark for module
25%
(25% of mark)
Examination
(75% of mark)
Examination
(MCQs)
25% of 75% = ~18.8%
Examination
75% of 75% = ~ 56.2%
(3 questions)
TOTAL
100%
Assessment of Module 2 – Mathematics and Computing
Part A Mathematics contributes 60% and Part B Computing contributes 40% to the grade for
this module
Part A - Mathematics
Part A is assessed through a two-hour written exam, where students have to answer three out
of six short questions and two out of four long questions. Each short question contributes 10%
to the final examination mark and each long question 35%. The assignments contribute 25%
to the final mark of Part A.
Part B - Computing
There will be one marked assignment in Python (contributing 40% of the marks for Part B and
one timed open-book assessment (contributing 60% of Part B). There will be sufficient time
in this test to allow students who have limited previous computing experience and are
competent to finish the questions. The timed exam style test will be held in April 2023. The
skills in databases and web development will be assessed as part of the research projects.
Module Part
Assessment
Contribution to total mark for
module
Part A – Computing
Computing exercise
40% of 40%
= 16%
(40% of total mark)
(40% of total for Part A)
60% of 40%
= 24%
Computing timed
assessment
22
(60% of total for Part A)
Part B– Mathematics
Mathematics exercise
(60% of total mark)
(25% of total for Part B))
Mathematics examination
25% of 60%
= 15%
30% of 75% of 60% = 13.5 %
(3 short questions
Jointly 30 % of
examination mark)
Mathematics examination
70% of 75% of 60% = 31.5 %
(2 long questions
Jointly 70 % of
examination mark))
TOTAL
100%
Projects – general principles of assessment
For all projects marks are awarded by the supervisor and by two other examiners who normally
will be bioinformatician/ theoretical systems biologist. Board of Examiners may moderate
grades to ensure consistency with the marking criteria.
Project 1
After the report is submitted, the examiners will hold a viva with student probing the ability of
the student to explain the report and engage in a productive scientific discussion. The
assessment is:
Supervisor’s
mark
Agreed joint mark of
examiners
Total contribution
Lab performance
20% of total
None
20%
Group report
10% of total
30% of total
40%
Oral presentation
None
40% of total
40%
Topic assessed
Project 2
23
Project is the final research project. After the report is submitted, the examiners will hold a viva
with student probing the ability of the student to explain the report and engage in a productive
scientific discussion. The assessment is:
Topic assessed
Supervisor’s
mark
Agreed joint mark of
examiners
Total contribution
Lab performance
20% of total
None
20%
Group report
10% of total
30% of total
40%
Oral presentation
None
40% of total
40%
Timetable
These dates are provisional and may change.
Assignment
Module
Start/Deadline
Feedback date and
provisional marks no
later than
Python 1
LIFE97011
21 October 2022 - 31
October 2022
14 December 2022
(NOT MARKED FOR
BIONFORMATICS)
Python 2
LIFE97011
4 November 2022 – 14
November 2022
16 December 2022
Genomes
LIFE97006
11 November 2022 – 21
November 2022
5 December 2022
Mathematics
LIFE97030
18 November 2022 – 29
November 2022
12 December 2022
Protein
LIFE97006
25 November 2022 –
19 December 2022
5 Dec 2022
Bioinformatics
exam
LIFE97006
January 2023
42 working days
Maths exam
LIFE97030
January 2023
42 working days
Project 1
Computing
LIFE97012
16 January 2023 – 3 April
2023
30 working days after
vivas
Python
LIFE97011
TBC - Week of 17th April
2023
30 working days
3 April 2023 – 29 August
2023
30 working days
Timed
Assignment 3hr
Project 2
Bioinformatics
LIFE70008
24
and Theoretical
Systems Biology
Internal Viva
External Viva
LIFE97009
30 August 2023 – 14
September 2023 –
Precise Date TBC
Last 2 weeks in
September 2023 – Data
TBC
Provisional results
provided after external
viva subject to
ratification by Registry
25
3.1: Criteria for Assessment of Written work – exam questions and exercises
These criteria are used to assess exam answers and exercises. Note that account is taken of the
teaching of the subject, the instructions provided for the work and the type of question set. For
examination answers, allowance is made for what is reasonably achievable under examination
conditions. See 3.2 for criteria for mathematical questions
Literal
Grade
Percentage
Grade
Criteria
A*
85-100
Distinction+. Answer is an exceptionally well presented exposition of the
subject showing: (i) complete command of the relevant concepts and facts,
(ii) a high critical or analytical ability in exposition including figures when
appropriate** or outside reading, and (iii) not marred by clearly irrelevant
information or any non-trivial errors.
A+
A
AB+
B
B-
C+
C
C-
D+
D
D-
80
76
72
Distinction. Answer is a very well presented exposition of the subject,
showing the above features, but not fully achieving one of them.
68
65
62
Merit. Answer has the following features, but without fully achieving one of
them: (i) shows a clear grasp of the relevant concepts and facts, (ii) gives
an accurate account of the relevant taught material, (iii) shows evidence of
some outside reading, or of critical or analytical ability** and (iv) not marred
by significant errors or clearly irrelevant material
58
55
52
Pass. Answer: (i) shows a grasp of the basic concepts and facts, (ii) gives
a mainly accurate account of at least half of the relevant taught material,
but (iii) does not go beyond that, or goes beyond that but is then marred by
significant errors.
50
PASS MARK
48
45
42
Fail. Answer: (i) shows only a basic grasp of the fundamental concepts and
facts and is marred by major errors or omissions and (ii) presents
accurately at least a third of the material expected.
40
Answer: (i) shows a confused understanding of the question, and (ii)
presents less than a third of a material expected.
30
Answer: (i) is too inaccurate, too irrelevant, or too brief to indicate more
than a vague understanding of the question, and (ii) presents only about a
quarter of a material expected.
20
Answer: : (i) is too inaccurate, too irrelevant, or too brief to indicate more
than a vague understanding of the question, and (ii) presents only about a
sixth of a material expected.
10
Answer presents only two or three sentences or facts that are correct and
relevant.
5
Answer includes at most one sentence or fact that is correct and relevant to
the question.
0
Answer contains nothing correct that is relevant to question. Mark to be
given where the work is discovered not to be that of the candidate
(plagiarised). Further disciplinary action is usually taken in cases of
plagiarism
F
** Analytical = assessing a hypothesis or statement by breaking it down into its elements and
examining their inter-relationships and contribution to the whole; cf. Critical = judging a hypothesis
or conclusion by examining the validity of the evidence adduced for it.
26
3.2 : Criteria for Assessment of Mathematical Questions
There are three components in grading a question that is primarily or exclusively
mathematical. The relative grades award will depend on the particular question set. But as
a guide the criteria with relative weightings are:
1) The correct final answer. (30%)
2) Detailed presentation of the step undertaken (60%)
3) Textural explanation of the science/ mathematical principles underpining the steps
undertaken including, where appropriate, an interpretation of the meaning of the
result (10%).
3.3 : Criteria for Assessment of Multiple Choice (MCQ) Questions
For Bioinformatics and Theoretical Systems Biology II there will be multiple choice
questions. Details of the type of questions and the scoring scheme will be provided in the
autumn term.
27
3.4: Criteria for Assessment of Laboratory Work
Criteria used to assess laboratory work. Due allowance is made for what is reasonably achievable under
laboratory conditions and in the time available. There is no requirement for positive results.
Literal
% Grade
Criteria
Grade
85-100
Distinction+/ Exceptional. Quality and quantity of results achieved comparable
A*
to that in leading-journal research article. Research demonstrates (i) complete
command of the background and context of the work, (ii) a high critical and
analytical ability** including an appreciation of the limits of the experimental
procedures, possible sources of errors and significance of results, (iii) a
proactive approach throughout including, where relevant, evidence of
substantial outside reading in discussion and (iv) a productive interaction with
supervisor/group.
A+
A
AB+
B
B-
C+
C
C-
D+
D
D-
F
80
76
72
68
65
62
58
55
52
Distinction. Quality and quantity of results achieved approaching that of
leading-journal research article. Work successfully completed, showing the
above features, but not fully achieving one of them. No significant deficiencies.
Merit. A substantial body of quality research. Research demonstrates the
following, without fully achieving one of them: (I) a clear grasp of background
and context of the work, (ii) a complete and fully accurate account of the
experimental procedures and results, and (iii) evidence of some outside
reading or of critical or analytical ability** including an understanding of the
limits of the experimental procedures. Student was committed to the research.
Pass. A respectable body of research. Research demonstrates (i) a grasp of
the background and context of the work, (ii) an accurate account of most of the
experimental procedures and results, but (iii) did not go beyond that, or went
beyond that but has significant errors of interpretation. Student showed only
limited commitment to the project.
50
PASS MARK. Students failing to show commitment to the project will be
awarded a grade below this.
48
45
42
Fail. A limited body of research. Research demonstrates (i) a limited grasp of
the background and context of the work, (ii) an accurate account of about half
of the expected experimental procedures and results, but (iii) did not go
beyond that, or went beyond that but has significant errors of interpretation.
40
Fail. A very limited body of research. Research demonstrates (i) a very limited
grasp of the background and context of the work, (ii) an accurate account of
about 1/3 of the expected experimental procedures and results, but (iii) did not
go beyond that, or went beyond that but has significant errors of interpretation
30
Fail. Work (i) shows a confused understanding of the experiment, and (ii) was
able to give an accurate account of about 1/4 of the experimental procedures
and results, but (iii) did not go beyond that, or went beyond that but had
significant errors of interpretation.
20
Work (I) is too inaccurate, too irrelevant, or too brief to indicate more than a
vague understanding of the experiment and results
Only a few trivial experiments performed or results obtained.
10
0
Experiment not attempted, or no results of relevance obtained. Mark given
where the work presented is discovered not to be that of the candidate
(plagiarised). Further disciplinary action is usually taken in cases of plagiarism.
28
3.5: Criteria for Assessment of Work Presented Orally
These criteria are used to assess all oral presentations during your MSc course. Allowance is made for
what is reasonably achievable under the conditions of the presentation and viva. . There is no
requirement for positive results.
Literal
Percentage Criteria
Grade
Grade
A*
A+
A
AB+
B
B-
85-100
80
76
72
68
65
62
58
55
52
C+
C
C-
Distinction+/Exceptional. Presentation and discussion demonstrates: (I)
complete understanding of the material to be presented showing high
critical or analytical ability** as relevant, (ii) clear and logical organisation
of the material, (iii) excellent use of appropriate resources and teaching
aids, (iv) preparatory work including substantial background reading, and
(v) ability to instruct with clarity of exposition and productive engagement
with the audience resulting in a very positive learning experience.
Distinction. A very well presented exposition of the subject, showing all the
above features, but not fully achieving one of them.
Merit. Presentation and discussion has the following features, but without
fully achieving one of them: (i) shows a clear understanding of the material
with an accurate account that demonstrates good critical or analytical
ability**, (ii) good use of resources, (iii) evidence of appropriate background
reading, and (iv) succeeds in delivering all the relevant material clearly to
the audience so that they appreciate its significance.
Pass. Presentation and discussion: (i) shows a solid grasp of the material,
(ii) gives a mainly accurate account of most of the relevant material, (iii)
shows evidence of some background reading ,and (iv) successfully delivers
most of the material to the audience in a way that they can understand it,
but does not go beyond that.
50
PASS MARK
48
45
42
D+
D
D-
Fail. Presentation and discussion: (i) shows only a basic grasp of the
material (ii) shows evidence of little background reading or preparation, (iii)
delivers most of the material accurately but makes errors or omissions
resulting in a poor learning experience for the audience.
40
Presentation and discussion: (i) shows that little of the material has been
understood, (ii) shows little evidence for background reading or
preparation, and (iii) presents the material largely inaccurately and does not
increase the audience’s understanding.
F
30
Presentation and discussion: (i) shows that the material has not been
understood, (ii) shows no evidence for background reading or preparation,
and (iii) presents the material inaccurately and does not increase the
audience’s understanding.
20
Presentation and discussion: (i) is too inaccurate, too irrelevant, or too
brief to indicate more than a vague understanding of the material, and (ii)
only succeeds in misinforming and confusing the audience.
10
Presentation and discussion: includes almost nothing that is correct and
relevant.
0
Failure to make a presentation at all or presentation involves plagiarism.
** Analytical = assessing a hypothesis or statement by breaking it down into its elements and
examining their inter-relationships and contribution to the whole; cf. Critical = judging a hypothesis
or conclusion by examining the validity of the evidence adduced for it.
29
3.6: Criteria for Assessment of Work Presented in Reports
These criteria are used to assess all reports during your MSc course. Allowance is made for what is
reasonably achievable under the conditions of the research project report (resources available, time
and space allowed, etc.). . There is no requirement for positive results.
Literal
Percentage Criteria
Grade
Grade
Distinction+/Exceptional. Report presents: (i) a substantial body of
A*
85-100
challenging work, (ii) complete understanding and focused presentation of
the material to be presented showing high critical or analytical ability**
including making work accessible to a broad audience within the discipline,
(iii) clear and logical organisation of the material, (iv) substantial
background reading and (v) is devoid of technical faults (e.g. legends &
references)
A+
80
A
76
Distinction. A very well presented report of a substantial body of
A72
challenging work, showing all the above features, but not fully achieving
one of them. A report with substantial technical faults cannot be awarded a
B+
68
distinction.
B
65
B62
Merit. Report has the following features, but without fully achieving one of
them: (i) shows a clear understanding of the material with an accurate
account that demonstrates good critical or analytical ability**, (ii) good use
of resources, (iii) evidence of appropriate background reading, and (iv)
succeeds in delivering all the relevant material clearly to the audience so
C+
58
that they appreciate its significance.
C
55
C52
Pass. Report (i) shows a solid grasp of the material, (ii) gives a mainly
accurate account of most of the relevant material, (iii) shows evidence of
some background reading ,and (iv) successfully delivers most of the
material to the audience in a way that they can understand it, but does not
go beyond that.
D+
D
D-
50
PASS MARK
48
45
42
Fail. Report (i) shows only a basic grasp of the material (ii) shows
evidence of little background reading or preparation, (iii) delivers most of
the material accurately but makes errors or omissions resulting in a poor
learning experience for the audience.
40
Report: (i) shows that the material has not been understood, (ii) shows no
evidence for background reading or preparation, and (iii) presents the
material inaccurately and does not increase the audience’s understanding.
30
Report (i) is too inaccurate, too irrelevant, or too brief to indicate more than
a vague understanding of the material, and (ii) only succeeds in
misinforming and confusing the audience.
20
Report includes very little that is correct and relevant.
10
Report includes almost nothing that is correct and relevant.
0
Failure to submit a report or report is plagerised
F
** Analytical = assessing a hypothesis or statement by breaking it down into its elements and
examining their inter-relationships and contribution to the whole; cf. Critical = judging a hypothesis
or conclusion by examining the validity of the evidence adduced for it.
30
3.8: Structure of Examination Questions
Where a question provides a breakdown of the weighting attached to parts of a question, the
final grade is based on the evaluation of the question as a whole against the above criteria.
The breakdown only provides guidance as to the suggested emphasis in your answer for each
part of the question.
You will be able to view past exam papers on the VLE, Blackboard.
3.9 Guidelines for Exercises
There are marked exercises in the Bioinformatics and Theoretical Systems Biology module.
The format of the answer will be specified. For Tables, Figures and References you must
follow the guidelines for the report in 6.8 below. The word and display items limits for exercises
are strict.
These exercises are graded. If the instructions are unclear, then you can of course ask the
appropriate staff member. But note that the aim of these exercises is for you to make your
decisions as you would in an exam.
3.10: Guidelines for Reports
The following are draft guidelines for the project reports. These may be modified to reflect the
developments of the project and staff/student discussions. Word limits are guidelines but
answers that substantially exceed these guidelines, particularly if as a result they are
unfocussed, will be marked down.
General guidelines for all reports
FAILURE TO FOLLOW THESE GUIDELINES CAN RESULT IN A PENALTY
1. Students are expected to discuss their reports with their supervisors before starting to write
up. At least two weeks before submission students should concentrate on completing the
report. It is more important to produce a quality report than obtain all the results. You are
permitted to show your supervisor or one other person your report for general feedback
before submission, but please allow sufficient time for your supervisor to provide feedback.
Detailed feedback can only be provided by one person once for any section.
2. The report should be in the style of a paper in a bioinformatics or systems biology journal..
Your report must be aimed at readers who work in these areas but who are not a
specialist in the precise area of your project. In contrast to a scientific paper, your
report should clearly and extensively identify in the text what was your contribution to the
project. You can use “I” to show your work. Reports that fail overall to be accessible to
a broad bioinformatics/systems biology readership will be penalised and are
unlikely to be awarded a distinction.
3. Students are advised to make frequent back-up copies of their work. Disk failure can occur,
must be planned for, and is not a valid excuse for late submission. Projects must be
submitted by the deadline. The penalty for late submission is 10% of the mark for the
31
report per day or part of day.
4. With the exception of the data analysis web-based report: the font size must be no
smaller than 11 point and the report can be 1.5 or double spaced. Reports using LaTeX
must be in at least 12 point font. The report can be on one or both sides of the paper. Each
major new section (e.g. Methods) should start on a new page. Pages must be numbered.
Please use a single column for the text.
5. It is important to ensure that the report is concise, well laid-out and in scientific style
English. Avoid slang and abbreviations such as “won’t”. Remember that “it’s” is an
abbreviation for “it is” and “its” is used for the possessive.
6. The project report must include the word count on the title page (the number of words will
be checked and failure to comply with the word limit will incur penalties).
7. As this is an MSc project undertaken in a limited time period, we appreciate that positive
results (such as an improvement in an algorithm or a statistically significant observation)
might not be obtained. Negative results are not penalised. In your report you need to
show that you have undertaken a rigorous scientific study and critically evaluated your
results.
8. The format should follow that of a scientific paper and must include the following sections:
Title page, Abstract, Contents page, Abbreviations, Introduction, Conclusion, References,
and if required an Appendix. The main part of the report can either follow the standard
three sections of Methods, Results and Discussion or can be modified to best present the
information. You are advised to discuss such a modification with your supervisor. For
example, if there is a series of studies, you are free to report each study in turn as a main
section and then under subsections detail the Methods, Results and Discussions.
9. The Abstract should be structured (i.e. aims, methods, results, conclusion), be no more
than one side of paper (in written reports). Ideally the Abstract should cite some key
numerical results rather than just generalities. Making a point in an abstract does not
remove the requirement for it to be made elsewhere in the report. The report must be
comprehensible even if the abstract is removed. References in an abstract should be
avoided and if given should be given in full and not refer to the bibliography.
10. The Introduction should provide the necessary background to understand the relevance
and topicality of the aims and objectives and your contribution of the research. In particular,
how has this project advanced the field.
11. The Methods should be sufficiently (but not excessively) detailed, such that the reader
can fully understand how the study was performed. It is important to provide an overview
of the methodology, for example by a flow chart.
12. The Results should provide the necessary data, including negative results, to justify the
conclusions drawn. It is important to summarise the results (for example in tables and/or
graphs) and not just put in the output of the program. The results should describe testing
where appropriate and an assessment of possible errors. Results should also discuss the
conclusions drawn from the specific results.
13. The Discussion section should place the results into the context of published knowledge
and understanding and provide details of future work and more general applications of the
knowledge gained from the project. Avoid simply repeating the Results section.
14. The Conclusion can provide a brief summary of the key results and provide a brief
statement of the impact of the work. Do not repeat previous sections. It is best to have a
separate discussion and conclusion.
15. An ethical statement is required in EVERY project report. This must be a clearly
identified as a separate heading. If there are no ethical issues, you simply state this
and explain why. If there is any human data, you need to report any ethical issues
guided by discussion with your supervisor. Some information on ethical
considerations can be found at
https://www.imperial.ac.uk/research-ethicscommittee/ethics-approval-overview/
32
16. All mathematical expressions must have all the symbols defined and used consistently
throughout the report.
17. All Figures must be clearly labelled with a full explanation of the different information
(e.g. colours) presented. Graphs must have the axes labels and the lines in an easy to
read presentation without tiny fonts and faint lines. Units are required on the axes.
Figures must be referred to in the text i.e. see Figure X.
18. All Tables should be clearly explained with units and numbers given to the appropriate
degree of accuracy. Use a sensible number of significant figures. Tables must be referred
to in the text i.e. see Table X.
19. Full reference citations must be given: authors, year of publication, journal title, volume
and page numbers are all needed. Two reference styles are acceptable. The first is author
and date in the text with the references arranged alphabetically by first author’s surname.
The second is numbering in the text and in the reference list in order of citation of the
reference in the text. Authors’ first names must consistently be by initial only, even if you
know the first name. The reference style must be consistent throughout.
20. Abbreviations and glossary. You should list on a separate page all the abbreviations
that you have used in your thesis. Many of these are standard, such as DNA, and do not
need to be defined. Try not to invent too many abbreviations of your own, as it can make
it hard work for your examiner to read. In addition, the first time that you use an
abbreviation in the main text, you must define it, e.g: We analysed the number of nonsynonymous single nucleotide polymorphisms (nsSNPs). The next time you can simply
use the abbreviation, e.g. Table 3 details the number of nsSNPs. You must be consistent.
Once you have defined an abbreviation, always use the same abbreviation and do not
revert to the original. For some reports, it can be helpful to go beyond a list of abbreviations
and provide a glossary explaining technical terms
21. It is vital that any information including a mathematical derivation taken from another
source is duly acknowledged otherwise you are plagiarising. Note many figures in books
and papers are subject to copyright and cannot be reduced without copyright permission.
The Library can advise but it is probable simplest not to use any published figure directly.
You can of course redraw a figure and acknowledge the source upon which it is based.
22. The project report must be written in your own words. Imperial has software that will detect
plagiarism – automatic zero mark if plagiarism is detected, with the burden of proof is on
the student.
23. Occasionally a paper describing your project work will have been produced for submission
to a conference or a journal prior to you writing your report. You cannot use the text from
this paper – you must rewrite this for your report - even if you wrote the original paper. If
this occurs, you must discuss this with the Course Director or Deputy Director at the writing
up stage. Failure to follow this is likely to result in a penalty and can raise a query
over plagiarism.
24. If your report follows on a from any previous project, not just from this MSc, you must make
it explicit in the text (and not just by a reference) what was previous work and what was
the further work undertaken during the project. For example, if you run a pipeline
established developed in a previous project this must be made explicit in the text. One
approach would be to place all previous work in the introduction. Failure to follow this is
likely to result in a penalty and can raise a query over plagiarism.
25. Details of the submission mechanism of your report will be provided later.
Additional Requirements for Computing Project reports
1. The project consists of an integrated student report, submitted by the group and an
individual statement.
33
Group report:
.
2. The group report should not exceed 60 pages excluding the title page, acknowledgements
and the reference list. You can use an Appendix to provide supporting data (e.g. list of
proteins) but not to extend the report.
3. In the group report you must use two sets of initials at the start of each section to
indicate (i) which student undertook the work and (ii) who wrote the section. This
applies even if the same person undertook the work and wrote the section. We understand
some sections are joint work and this should be indicated. Failure to clearly indicate who
contributed to each section may well result in deduction of marks.
Individual report:
4. The individual report is a page-long reflective statement of the individual’s contribution to
the project and the report. This is not graded but provides context to assess the group
report and laboratory performance.
34
Additional guidelines for Project2 report
1. The reports should be about 7,000 words plus abstract (no more than 250 words) title,
diagrams, graphs, tables, legends to figures and tables, references, acknowledgements
and Appendix. There is a maximum of 12 display items (Figures or Tables). Figure and
table legends should be used solely to define the data presented and not to extend the
report. You can use an Appendix to provide supporting data (e.g. list of proteins) but not
to extend the report. Please indicate on the front the number of words.
2. As this is the report on your final project, we are looking for a demonstration of critical and
analytical ability. The best projects would be in a suitable for submission to a journal or a
conference with only the most minor of modification (excluding any consideration of
whether the report presents positive or negative results).
3. As this is your major report, technical faults (references, figure legends etc) will be
penalised more heavily than in the earlier report. Irrespective of the quality and quantity of
the research, a reported substantially marred by technical faults will not be awarded a
distinction.
4. The overall aim, methods and results of the study must be accessible to a general
bioinformatician/ theoretical systems biologist.
Writing Resources
There are many guides on the internet about writing styles. Here are a few
suggestions. It is worth reading these guides
•
Penn State Writing Guidelines for Engineering and Science Students (general
guidelines about a paper or report)
o http://www.writing.engr.psu.edu/
•
Writing a better scientific paper (note some comments about a chatty style are not
appropriate for Biology, but good hints especially about mistakes non-native English
scientists often make)
• http://rmp.aps.org/files/rmpguapa.pdf
•
The Internet Grammar of English from UCL (useful to check a detail))
o http://www.ucl.ac.uk/internet-grammar/
Instruction to Candidates for Examinations
Students who are candidates for examinations are asked to note that all examinations are
conducted in accordance with the College Regulations. The relevant set of regulations will
depend on your programme and year of entry, please see our Regulations webpage to
determine which apply to you:
www.imperial.ac.uk/about/governance/academic-governance/regulations/
35
Instructions for exam candidates can be found here:
www.imperial.ac.uk/media/imperial-college/administration-and-supportservices/registry/academic-governance/public/academic-policy/exam-arrangementsand-re-sits/Instructions-to-candidates-for-examinations.pdf
Academic Integrity and Academic Misconduct
As your programme of study continues, you will be taught the concept of academic integrity
and how you can ensure that any work that you complete now, or in the future, conforms to
these principles. This means that your work acknowledges the ideas and results of others,
that it is conducted in an ethical way and that it is free from plagiarism.
Academic misconduct is the attempt to gain an academic advantage, whether intentionally or
unintentionally, in any piece of assessment submitted to the College. This includes plagiarism,
self-plagiarism, collusion, exam offences or dishonest practice. Full details of the policy can
be found at:
www.imperial.ac.uk/student-records-and-data/for-current-students/undergraduateand-taught-postgraduate/exams-assessments-and-regulations/plagiarism-academicintegrity--exam-offences/
Definitions of the main forms of academic misconduct can be found below:
Plagiarism
Plagiarism is the presentation of another person’s thoughts, words, images or diagrams as
though they were your own. Another form of plagiarism is self-plagiarism, which involves using
your own prior work without acknowledging its reuse. Plagiarism may be intentional, by
deliberately trying to use another person’s work by disguising it or not citing the source, or
unintentional where citation and/or referencing is incorrect.
Plagiarism must be avoided, with particular care on coursework, essays, reports and projects
written in your own time but also in open and closed book written examinations. You can
support your understanding of proper referencing and citation by using the resources available
from the College such as the Library learning support webpages at:
www.imperial.ac.uk/admin-services/library/learning-support/plagiarism-awareness/
www.imperial.ac.uk/students/success-guide/pgr/progression-and-feedback/writingreports-and-presentations/being-original-and-plagiarism/
Where plagiarism is detected in group work, members of that group may be deemed to have
collective responsibility for the integrity of work submitted by that group and may be liable for
any penalty imposed, proportionate to their contribution.
TurnitinUK is an online text matching service which assists staff in detecting possible
plagiarism. The system enables institutions and staff to compare students' work with a vast
database of electronic sources. You will be expected to run your early stage assessment
through the Turnitin software – your department will be able to give you further information
about this process.
www.imperial.ac.uk/admin-services/ict/self-service/teaching-learning/turnitin/
Collusion
This is the term used for work that has been conducted by more than one individual, in
contravention of the assessment brief. Where it is alleged that there has been collusion, all
parties will be investigated under the Academic Misconduct procedure.
36
You should note that whilst the College encourages students to support each other in their
studies you should be careful to ensure that you do not exceed any assessment brief with
regards to individual work, acknowledge the contributions of others in your work, and do not
leave yourself open to allegations that you have supplied answers to enable another student
to commit academic misconduct.
Exam offences
Exam offences fall into two categories. These are offences that may be disruptive in the exam
venue or are considered an attempt to cheat. This can include behaviour such as bringing
unauthorised material into an exam, attempting to communicate with others apart from the
invigilator, trying to remove examination material without permission, taking an exam for
someone else or getting someone else to take an exam for you. It would also include having
an electronic device that has not been fully turned off or failing to follow a reasonable
instruction of the invigilators.
Dishonest practice
This is the most serious category under the procedure. Examples of dishonest practice include
bribery, contact cheating (buying work from an essay mill (which is illegal in the UK) or other
individual to submit as your own), attempting to access exam papers before the exam, making
a false claim for mitigating circumstances or providing fraudulent evidence, falsifying
documentation or signatures in relation to assessment or a claim for mitigating circumstances.
Research Integrity
Research integrity is about your research practices, how you present the findings of your
research and how your research impacts on society and the wider world. At Imperial College
London, you will work with internationally renowned academic staff who will guide you to
design rigorous, robust, and reproducible research methods. This will ensure that your
research is lawful and that any adverse impact your research may have on society, natural
environment, or animals is justified and minimised. Research integrity is also about
presenting the findings of your research in a responsible manner.
The College has adopted the Council for Science and Technology's Universal Ethical Code
for Scientists and upholds its three principles, which are:
•
•
•
Rigour, Honesty and Integrity
Respect for Life, the Law and the Public Good
Responsible Communications: Listening and Informing
The primary way to ensure research integrity is to promote and maintain a culture of
honesty, openness and responsibility. To this end, the Graduate School has the following
professional development opportunities available to postgraduate students:
•
Plagiarism Awareness, mandatory for both Master’s and Doctoral students
This online course was developed by the Graduate School, in conjunction with the
Library. It aims to equip you with a working knowledge of the concept of plagiarism
and how to avoid it. It also aims to provide you with information to enable you to use
and share information ethically, with academic integrity and in accordance
with Imperial College's Examination & Assessment: Academic Integrity Policy.
•
Copyright for Researchers (Doctoral)
37
This course aims to equip you with a working knowledge of copyright
and licencing so that in your career you can use and share information in a copyright
safe way. The course has activities and discussions to give you the opportunity to
practice the knowledge and skills acquired through context-based scenarios and
examples. You are recommended to share your reflections on the digital canvases
throughout the course. This will give you a chance to elaborate what you have learnt
in the readings, share examples and challenge your understanding by interacting
with your peers.
•
Intellectual Property (Doctoral)
This course aims to equip you with a working knowledge of the concept of Intellectual
Property (IP), and an awareness and understanding of the basic principles
surrounding IP rights, such as patents, copyright, design rights and other forms of IP.
An understanding of IP and its application is important for all students; for those
intending to continue in academia as well as those intending to enter the commercial
world after graduation.
•
Introduction to Making your Thesis Open Access (Doctoral)
This workshop will provide a general introduction to open access, with specific
reference to the PhD thesis, and related research outputs that may arise from PhD
study. You will be introduced to: open access repositories, open access publishing
and online support tools such as the Directory of Open Access Journals and Open
access button. You will also be provided with the opportunity to discuss Creative
Commons licences, the re-use of third-party copyright materials in your thesis and
why your thesis is made open access.
•
Data Management (Doctoral)
Data is a key research asset, underpinning almost all published research
conclusions. In recent years, new technology has enabled us to:
1. Generate and record far more data than ever before; and
2. Share, reuse and combine that data in new ways to generate new insights.
Research data is increasingly a first-class research output, and a little bit of planning
will enable you to take advantage of this shift. This course will highlight key
considerations and help you to assess when it is appropriate to share your data and
how to write a data management plan.
This workshop is supported by a webinar on Research Data Management Plans
which covers some of the more practical elements of research data management and
will help students to create their own data management plans.
•
Science, Research and Integrity (Doctoral)
This workshop is designed to give you a chance to explore and critically analyse the
ethics of scientific research in a constructive way. We will critically discuss the
structure and implications of specific cases of scientific fraud and will also look at
different moral theories and how they might apply not only to specific moral
dilemmas, but also to science in general. The session will aim to forearm you by
providing a safe environment within which to formulate and articulate your own views
on how you might deal with the sorts of dilemmas you are likely to face during your
career.
38
The San Francisco Declaration on Research Assessment (DORA)
The College has signed the San Francisco Declaration on Research Assessment (DORA).
The ethos behind DORA is to improve the ways in which the output of scientific research is
evaluated by funding agencies, academic institutions, and other parties. The outputs from
scientific research are many and varied, including: research articles reporting new
knowledge, data, reagents, and software; intellectual property; and highly trained young
scientists. Funding agencies, institutions that employ scientists, and scientists themselves,
all have a desire, and need, to assess the quality and impact of scientific outputs. It is thus
imperative that scientific output is measured accurately and evaluated wisely.
As such the College has signalled that it will assess research based on quality rather than
where it is published, for example journal impact factor. The Graduate School promotes the
ethos behind DORA at the following professional development workshops:
•
•
•
•
•
•
Writing for publication
How to be an effective researcher
Global Research Impact and Influence retreat
Finish Up Move On
Impact in academia webinars
Understanding the reviewer
References:
The San Francisco Declaration on Research Assessment DORA [accessed 26.06.20]
The UK Concordat to Support Research Integrity – Universities UK [accessed 26.06.20]
The Universal Ethical Code for Scientists [accessed 26.06.20]
The European Code of Conduct for Research Integrity – ALLEA (All European Academies)
[accessed 20.06.20]
39
4.
Board of Examiners
Board of Examiners
Board of Examiners
Dr Derek Huntley (Chair)
Professor Michael Sternberg
For external examiners
Dr Irilenia (Irene) Nobeli, Birkbeck University
Dr Andrea Rocca, University of Surrey
External examining acts as an essential part of the College’s quality assurance and
enhancement process, serving to ensure that academic standards are maintained. The
knowledgeable and independent views of external examiners are invaluable in certifying that
the College’s awards are appropriate and comparable as well as highlighting good practice
and potential areas of enhancement.
During your programme you may be invited to meet your external examiners to discuss how
you have found the. It is not appropriate however, for you to seek to submit complaints or
representations directly to external examiners or to seek to influence them other than by giving
feedback in a meeting. Inappropriate communication towards an examiner would make you
liable for disciplinary action.
A summary of External examiners reports from the previous academic year can be found here:
www.imperial.ac.uk/about/governance/academic-governance/academic-policy/externalexamining/
5.
Location and Facilities
Imperial has a number of campuses in London and the South East. All have excellent travel
links and are easily accessible via public transport.
Your main location of study will be:
South Kensington campus
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London SW7 2AZ
Research projects can be at any Imperial Campus including hositals and Silwood Park.
Facilities
40
Computer access and printing is available at 310/311, Floor 3, Sir Ernst Chain Building. The
Department’s postgraduate office is located at Room 202, Sir Ernst Chain Building and open
Monday to Friday, 09.00 – 17.00.During Autumn 2020 this will be on an appointment basis –
please contact s.dennison@imperial.ac.uk
The PG common Room is on Floor 7 of Sir Ernst Chain Building.
Facilities for when you are your project rotation is confirmed nearer the time.
Library Services
The Central Library at South Kensington is open around the clock for study space pretty much
all year. Make sure you find out who your departmental librarian is as they’ll be able to help
you find resources for your subject area. Also, don’t forget to check out the Library’s range of
training workshops and our other campus libraries for access to specialist medicine and life
sciences resources. Alongside these physical spaces and resources, the Library provides over
300,000 electronic books, journals and databases available both on and off campus and a
free document delivery service to help you source books and articles from around the UK and
the rest of the world. In order to keep you safe many of our services are operating remotely
and we will be controlling the numbers who can visit our libraries. Services may be slightly
reduced but you can keep up to date with the latest developments on our website and on
Twitter @imperiallibrary.
www.imperial.ac.uk/library
Maps
Campus maps and travel directions are available at:
www.imperial.ac.uk/visit/campuses
Accessibility
Information about the accessibility of our South Kensington Campus is available online
through the AccessAble access guides:
www.accessable.co.uk/organisations/imperial-college-london
Smoke-Free Policy
All Imperial campuses and properties are smoke-free. This means that smoking by staff,
students or visitors is not permitted on or within 20 metres of College land. The policy covers
all College properties, including student accommodation and sports grounds.
www.imperial.ac.uk/smoke-free
SafeZone
41
SafeZone is a College app through which you can quickly and
directly contact the Security team whenever you need them.
Whether you're in an emergency situation, in need of First Aid or
want to report an incident on campus, SafeZone allows you to be
immediately put in touch with a member of our Security team
and, at the touch of a button, can share your location and
personal profile so that they can respond quickly and effectively
to your specific needs. It also allows the entire College
community to stay informed in the event of a major incident in
London or wherever you may be in the world. Safezone also
provides information on other services, such as real-time updates
on the College shuttle bus.
SafeZone is optional to register for and is now available to download on the Apple and
Android App stores. Visit www.imperial.ac.uk/campus-security for more details about
SafeZone.
All existing phone numbers for the Security team are still operational. In the event of an
emergency, you can still call 4444 from any internal College phone. In the event of a wider
incident in London, you can now also call 0300 131 4444, Imperial’s Emergency Recorded
Message Line, which will point you in the direction of up-to-date information and advice.
6.
Working While Studying
If you are studying full time, the College recommends that you do not work part-time during
term time. If this is unavoidable we advise you to work no more than 10–15 hours per week,
which should be principally at weekends and not within normal College working hours.
Working in excess of these hours could impact adversely on your studies or health.
If you are here on a Tier 4/Student Route visa you can work no more than 20 hours a week
during term time. Some sponsors may not permit you to take up work outside your studies and
others may specify a limit.
If you are considering part-time work during term time you are strongly advised to discuss this
issue with your supervisor or Senior Tutor (PGR). If you are on a Tier 4/Student Route visa
you should also seek advice from the International Student Support team regarding visa
limitations on employment.
Please note that these rules also apply to your work as a GTA:
www.imperial.ac.uk/media/imperial-college/study/graduate-school/public/gtawebsite/GTA-Framework_Updated-May-2021.pdf
The College’s examination boards will not normally consider as mitigating circumstances any
negative impact that part-time work during term-time may have had on your performance in
examinations or in other assessed work. Examinations or vivas cannot be rescheduled to
accommodate your part-time working arrangements.
42
7.
Health and Safety
Keeping you safe is a top priority for us. Since 1 April 2022, the UK Government removed all
restrictions on public areas, including Universities and education settings. Imperial College still
encourages students to wear face coverings in crowded areas, to stay at home if you have
symptoms of respiratory disease, to get fully vaccinated, to cover your coughs and sneezes,
and to respect others’ personal space.
The latest Imperial College guidance to students can be seen at:
www.imperial.ac.uk/about/covid-19/students/
The College’s Health and Safety Statement can be found at:
www.imperial.ac.uk/safety/safety-by-topic/safety-management/health-and-safetypolicy-statement/
Your Departmental safety contact is:
Stefan Hoyle
518, 5th Floor, Sir Alexander Fleming Building, South Kensington Campus
07872 850 018
s.hoyle@imperial.ac.uk
All new members of the Department must acquaint themselves with the Dept safety web
page;
https://imperiallondon.sharepoint.com/sites/fons/faculty/safety/LS/SitePages/Newhome.a
spx
You MUST also take the following courses:
Mandatory courses
•
All staff and PG students - Risk Assessment Foundation Training: No enrolment
necessary, just start the e-Learning course by clicking on this link and then at end of the
course
take
the
multiple
choice
test:
http://www.imperial.ac.uk/safety/raft/frameset/frameset.htm
•
All staff and PG students - Month One Safety Training: No enrolment necessary, just start
the e-Learning course by clicking on this link and then at the end of the course take the
multiple-choice test: http://www.imperial.ac.uk/safety/most/
For fire safety training:
• All PGs do the online Fire Safety and Awareness Training e-Learning course: No
enrolment necessary, just start the e-Learning course by clicking on this link and at the
end of the course complete the online test: http://www.imperial.ac.uk/safety/firesafety/
43
The College Safety Department
The Safety Department offers a range of specialist advice on all aspects of safety. This
includes anything which you feel might affect you directly, or which may be associated with
teaching, research or support service activities.
The College’s activities range from the use of hazardous materials (biological, chemical and
radiological substances) to field work, heavy or awkward lifting, driving, and working alone or
late.
All College activities are covered by general health and safety regulations, but higher risk
activities will have additional requirements.
The Safety Department helps departments and individuals ensure effective safety
management systems are in place throughout the College to comply with specific legal
requirements.
Sometimes the management systems fail, and an accident or a near-miss incident arises; it is
important that we learn lessons from such situations to prevent recurrence and the Safety
Department can support such investigations. All accidents and incidents should be reported
online at:
www.imperial.ac.uk/safety
To report concerns or to ask for advice you should contact your programme director, academic
supervisor or departmental safety officer in the first instance. You may also contact the Safety
Department directly.
Occupational Health requirements
The College Occupational Health Service provides services to:
•
•
•
protect health at work
assess and advise on fitness for work
ensure that health issues are effectively managed
The Service promotes and supports a culture where the physical and psychological health of
staff, students and others involved in the College is respected, protected and improved whilst
at work.
www.imperial.ac.uk/occupational-health
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8.
College Policies and Procedures
Regulations for Students
All registered students of the College are subject to the College Regulations. The relevant set
of regulations will depend on your programme and year of entry, please see our Regulations
webpage to determine which apply to you:
www.imperial.ac.uk/about/governance/academic-governance/regulations
www.imperial.ac.uk/students/terms-and-conditions
Provisional Marks Guidance
Provisional marks are agreed marks that have yet to be ratified by the Board of Examiners.
These results are provisional and are subject to change by the Board of Examiners. The
release of provisional marks is permitted except in certain circumstances. Further information
can be found in the Guidelines for Issuing Provisional Marks to Students on Taught
Programmes:
www.imperial.ac.uk/media/imperial-college/administration-and-supportservices/registry/academic-governance/public/academic-policy/marking-andmoderation/Guidelines-for-issuing-provisional-marks-to-students-on-taughtprogrammes.pdf
Late Submission Policy
You are responsible for ensuring that you submit your coursework assessments in the correct
format and by the published deadline (date and time). Any piece of assessed work which is
submitted beyond the published deadline (date and time) would be classed as a late
submission and will incur a penalty (a cap at the pass mark, or it is classed as a fail). Further
guidance on Late Submission of Assessments can be found on the Academic Governance
website:
www.imperial.ac.uk/media/imperial-college/administration-and-supportservices/registry/academic-governance/public/academic-policy/marking-andmoderation/Late-submission-Policy.pdf
If you submit late due to mitigating circumstances, you may be able to make a claim that
means that the cap on your mark is lifted. Please see below and the policy document.
Mitigating Circumstances
During your studies you may be affected by sudden or unforeseen circumstances. You should
always contact your personal tutor for advice and support. If this happens at the time of, or
immediately preceding your assessments you may be able to make a claim for mitigating
circumstances. If successful this claim enables the Board of Examiners when reviewing your
marks at the end of the year to have greater discretion with regards to offering repeat attempts
(either capped or uncapped), a repeat year, or with your progression or final classification.
Please note, the Board are not permitted to amend the marks that you were awarded, only to
take your claim into account making decisions.
All claims must be supported by independent evidence and submitted within 10 working days
of the assessment deadline. Any claim made after this deadline is likely to be rejected unless
there is a good reason (such as you were still unwell) until the point of submitting the claim.
Details of the College’s Mitigating Circumstances procedure can be found under the Mitigating
Circumstances tab on the page below:
www.imperial.ac.uk/about/governance/academic-governance/academic-policy/examsand-assessment/
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Through the procedure you may also be able to request an extension deadline to some forms
of assessment. Wherever possible it is expected that this is used as it will enable to you
complete your studies within the same College year (rather than over the summer holiday or
in the next year).
Your department will have specific instructions for making a claim for mitigation or for
requesting an extension. Details can be found at Examination and assessments | About |
Imperial College London and you can email a completed claim to your Programme
Administrator.
Support for ongoing or long-term conditions, or for registered disabilities would not normally
fall under the remit of mitigating circumstances and students should be supported through
their studies with Additional Examination Arrangements. More details can be found at:
www.imperial.ac.uk/disability-advisory-service/support/exams/
Academic Misconduct Policy and Procedures
As has been highlighted under the Academic Integrity section, it is important that you learn
how to properly attribute and acknowledge the work, data and ideas of others. Any proven
form of academic misconduct is subject to penalties as outlined in the College’s Misconduct
Policy and Procedures.
www.imperial.ac.uk/about/governance/academic-governance/academic-policy/examsand-assessment/
Unsatisfactory Engagement
Unfortunately, sometimes students struggle to make satisfactory progress in their study or
their engagement with their studies falls below our expectations. The College has a process
to identify and support students by reaffirming these expectations with an action plan. If a
student does not engage satisfactorily engage with these supportive measures, they can be
withdrawn from their studies. The full details of this process, and the appeals procedure
relating to it can be found at:
www.imperial.ac.uk/about/governance/academic-governance/regulations
www.imperial.ac.uk/about/governance/academic-governance/academicpolicy/complaints-appeals-and-discipline
Academic Appeals Procedure
We have rigorous regulations in place to ensure assessments are conducted with fairness and
consistency, claims for mitigating circumstances have been considered reasonably and in line
with the regulations of the College, and that the decisions of the Boards of Examiners maintain
the integrity of our academic awards. In the event that you believe that you have grounds to
appeal these decisions, we have laid out clear and consistent procedures through which
appeals can be investigated and considered:
www.imperial.ac.uk/about/governance/academic-governance/academicpolicy/complaints-appeals-and-discipline
Arithmetic Marks Check
If you consider that there may have been an error in the adding up of your marks, you may
request an arithmetic mark check. Please note that this must be requested within 10 working
days of the official notification of your results from the Results team in Registry. You may not
request a marks check for a previous year of study.
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Student Complaints
The College strives to ensure that all students are well supported in their studies and receive
a good experience of their programme and the wider College activities. If you feel that your
experience has not lived up to these expectations the College has an agreed Students
Complaints process through which your concern can be investigated and considered.
If you have any concerns about your experience at the College and have been unable to
address these informally, you should contact Student Complaints who can provide advice
about what is the appropriate way to seek to resolve this at:
student.complaints@imperial.ac.uk
www.imperial.ac.uk/about/governance/academic-governance/academicpolicy/complaints-appeals-and-discipline
Student Disciplinary Procedure
The College has the right to investigate any allegation of misconduct against a student and
may take disciplinary action where it decides, on the balance of probabilities, that a breach of
discipline has been committed. This Procedure is currently under review and will be updated
during the 2022-23 academic year. The general principles of the Student Disciplinary
Procedure are available on the College website:
www.imperial.ac.uk/about/governance/academic-governance/academicpolicy/complaints-appeals-and-discipline/
Copyright
Copyright is an automatic right given to creators that allows them to control who copies,
adapts, translates and makes public their work. Unless you have the copyright holder’s
permission, you cannot do these things unless permitted by law or licence.
www.imperial.ac.uk/admin-services/library/learning-support/copyright-guidance/
Intellectual Property Rights Policy
For further guidance on the College’s Intellectual Property Rights Policy is available on the
College website:
www.imperial.ac.uk/research-and-innovation/research-office/ip/ip-policy/
Further information about the Imperial Enterprise Lab can be found at:
www.imperial.ac.uk/students/enterprising-students
www.imperialenterpriselab.com/support/experts-in-residence
Use of IT Facilities
View the Conditions of Use of IT Facilities:
www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/staffcomputers/conditions-of-use-for-it-facilities/
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General Data Protection Regulation (GDPR)
All staff and students who work with personal data are responsible for complying with GDPR.
The College will provide support and guidance but you do have a personal responsibility to
comply.
In line with the above please see the College’s privacy notice for students which form part of
the terms and conditions of registration with the College.
https://www.imperial.ac.uk/media/imperial-college/administration-and-supportservices/registry/academic-governance/public/academic-policy/admissions/ICL--Privacy--Notice-for-Students-and-prospective-students.pdf
48
9.
Wellbeing, Support and Advice
In your department
Your department has a system of academic and pastoral care in place to make sure you have
access to the appropriate support throughout your time at Imperial.
Senior Tutor (PGR)
The Department’s Senior Tutor (PGR) can offer pastoral support and advice. You can arrange
to have a meeting with them at any time during your studies – what you discuss will be
completely confidential.
If necessary, they will direct you to an appropriate source of support.
Departmental Disability Officers
Departmental Disability Officers are the first point of contact in your department for issues
around disability. They can apply for additional exam arrangements on your behalf and will
facilitate support within your department.
Your Departmental Disability Officer is: Dr Tony Southall
Email: t.southall@imperial.ac.uk
More information on Departmental Disability Officers is available at:
www.imperial.ac.uk/disability-advisory-service/support/ddos
More information about how to request additional arrangements for exams if you have a
disability is available at:
www.imperial.ac.uk/student-records-and-data/for-current-students/undergraduate-andtaught-postgraduate/exams-assessments-and-regulations/additional-examarrangements-in-respect-of-disability
Your Union
All Imperial students automatically become members of Imperial College Union when they
register at the College. The Union provides a range of independent support.
Imperial College Union Advice Centre
The Union’s advisers are on hand to provide free, confidential, independent advice on a wide
range of welfare issues including housing, money and debt, employment and consumer rights,
and personal safety.
www.imperialcollegeunion.org/advice
Student representatives
Imperial College Union operates two Representation Networks of over 600 elected student
representatives – the Academic Representation Network and the Wellbeing Representation
Network. Reps represent the voice of students and can direct you to internal and external
support services. The Union’s Liberation Officers also work to make sure that the views of
under-represented and interest groups are heard at the College.
If you have any feedback about issues in your department relating to academic or wellbeing
issues, you can speak to one of your student representatives.
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www.imperialcollegeunion.org/your-union/your-representatives/a-to-z
Student Hub
The Student Hub represents a single point of contact for all key administrative information and
support. The Student Hub team can help you with enquiries about:
▪
▪
▪
▪
▪
▪
▪
Accommodation (including checking contracts for private accommodation)
Admissions
International student enquiries
Research degrees
Student financial support
Student records
Tuition fees
Level 3, Sherfield Building, South Kensington Campus
020 7594 9444
student.hub@imperial.ac.uk
www.imperial.ac.uk/student-hub
Student Support Zone
Student Support Zone has lots of information about the resources available at Imperial and
beyond to help you to stay healthy and happy. It’s a great place to start when you’re looking
for some support – it covers advice about housing and money, health, wellbeing and
maintaining a good work-life balance, and provides the details of who you can contact if you
need some extra support.
www.imperial.ac.uk/student-support-zone
Imperial College Union Advice Centre
Imperial College Union runs the Advice Centre independently of the College with advisers on
hand to provide free, confidential, independent advice on a wide range of welfare issues
including housing, money and debt, employment and consumer rights, and personal safety.
www.imperialcollegeunion.org/advice Useful support contacts
Careers Service
The Careers Service has strong links to your Department and you will have a named Careers
Consultant and Placement and Internship Adviser who will run both group sessions and
individual meetings within your Department. You can arrange to meet with your linked Careers
Consultant or Placement and Internship Adviser either in your Department or centrally at the
South Kensington Campus on Level 5, Sherfield Building where the Careers Service is based.
Visit the Career Service’s website to:
•
•
Book a careers appointment
Find resources and advice on successful career planning
www.imperial.ac.uk/careers
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Student Counselling and Mental Health
The Student Counselling and Mental Health Advice Service offers short-term counselling to
all registered students. The service is free and confidential. Counsellors are available at the
South Kensington, Hammersmith and Silwood Park Campuses.
www.imperial.ac.uk/counselling
Financial support and tuition fees
If you’ve got any questions about student financial support (loans, scholarships and research
council studentships, US and Canadian loans) then contact the Student Financial Support
team:
020 7594 9014
student.funding@imperial.ac.uk
If you suddenly find yourself in financial difficulties or experience an unexpected change in
circumstances, you may be eligible to apply for emergency financial help through the Student
Support Fund. The Fund offers a one-off payment of up to £2,000 to cover such emergencies
as last-minute accommodation and travel necessities, equipment and childcare. It does not
have to be repaid.
www.imperial.ac.uk/students/fees-and-funding/financial-assistance/student-supportfund/
For tuition fees queries, contact the Tuition Fees team:
020 7594 8011
tuition.fees@imperial.ac.uk
Health and wellbeing
Imperial College Health Centre
40 Prince’s Gardens, South Kensington Campus
020 7584 6301
imperialcollege.hc@nhs.net
www.imperialcollegehealthcentre.co.uk
Imperial College Dental Centre
Prince’s Gardens, South Kensington Campus
020 7589 6623
www.imperialcollegedental.co.uk
Student Counselling and Mental Health Advice Service
020 7594 9637
counselling@imperial.ac.uk
www.imperial.ac.uk/counselling
Multi-Faith Chaplaincy Service
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Chemistry Building, South Kensington Campus
chaplaincy@imperial.ac.uk
www.imperial.ac.uk/chaplaincy
Disability Advisory Service
Room 566, Level 5, Sherfield Building, South Kensington Campus
020 7594 9755
disabilities@imperial.ac.uk
www.imperial.ac.uk/disability-advisory-service
International students’ support
Centre for Academic English
Level 3, Sherfield Building, South Kensington Campus
english@imperial.ac.uk
www.imperial.ac.uk/academic-english
International Student Support team
020 7594 8040
www.imperial.ac.uk/study/international-students
ICT and software
ICT Service Desk
Central Library, South Kensington Campus
020 7594 9000
www.imperial.ac.uk/ict/service-desk
Software shop
www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/devices-andsoftware/
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10.
Student Administration
11. The Student Administration Team are responsible for the administration and maintenance of
the student records for all students studying at the College. This includes enrolments,
programme transfers, interruption of studies, withdrawals and processing of examination entry
for research degree students. The team also use this information to fulfil reporting duties to
the Student Loans Company, Transport for London and the UKVI, as well as other external
bodies.
12. The Team is responsible for the processing of student results and awards on the student
record system as well as the production and distribution of academic transcripts and
certificates of award.
13. The Student Administration Team produce a variety of standard document requests for both
current and previous students including council tax letters, standard statements of attendance
and confirmation of degree letters.
14.
15. Student Records
+44 (0)20 7594 7268
student.records@imperial.ac.uk
16.Degree certificates
+44 (0)20 7594 7267
certificates@imperial.ac.uk
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13.
Work-life Balance
The pace and intensity of study at Imperial can be demanding so it’s important to find time for
outside interests.
Graduate Students’ Union
The Graduate Students’ Union is the postgraduate arm of Imperial College Union. The GSU
works alongside the Imperial College Union President to ensure that the requirements of
postgraduate students are catered for. It also organises a number of academic and social
events during the year.
Move Imperial
Imperial College has a wide range of sports and activities on offer that cater for all
experience levels and abilities. We have a recreational activity offer, competitive sports
teams and an elite sport programme. We are dedicated to ensuring we have a diverse,
inclusive and exciting offer for all.
More information about Imperial student memberships and updates to our services can be
found at:
www.imperial.ac.uk/ethos/memberships/students
With an annual fee of £35 you will get use of the gym and swimming facilities on our
campuses.
www.imperial.ac.uk/sport
We have a huge collection of online resources, home workout videos, healthy recipes and
playlists available to all as part of our MoveMore campaign, more information can be found at:
www.imperial.ac.uk/sport/move-more/
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14.
Student feedback and representation
Feedback from students
The College and Union is committed to continually improving your education and wider
experience and a key part of this is your feedback. Feedback is thoroughly discussed by your
student representatives and staff.
Student representation
Student Representatives are recruited from every department to gather feedback from students
to discuss with staff. More information about the role, and instructions on how to become an
academic representative, are available on the Imperial College Union website.
www.imperialcollegeunion.org/your-union/your-representatives/academicrepresentatives/overview
Staff-Student Committee
Staff-Student Committees are designed to strengthen understanding and improve the flow of
communication between staff and students and, through open dialogue, promote high standards
of education and training, in a co-operative and constructive atmosphere. College good practice
guidelines for staff-student committees are available here:
www.imperial.ac.uk/about/governance/academic-governance/academic-policy/studentfeedback
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15.
Student Surveys
Your feedback is important to your department, the College and Imperial College Union.
Whilst there are a variety of ways to give your feedback on your Imperial experience, the
following College-wide surveys give you regular opportunities to make your voice heard:
•
•
PG Student Online Evaluation (SOLE) module survey or departmental equivalent
Student Experience Survey (SES)
The PG SOLE module survey (or equivalent for your department) runs at the end of the autumn
and spring terms. This survey is your chance to tell us about the modules you have attended.
The Student Experience Survey (SES) is an opportunity to give your views on your experience
beyond the lecture theatres or labs. This survey will cover a range of College services and on
the Imperial College Union.
All these surveys are confidential and the more students that take part the more representative
the results so please take a few minutes to give your views.
The Union’s “You Said, We Did” campaign shows you some of the changes made as a result of
survey feedback:
www.imperialcollegeunion.org/you-said-we-did
The Union’s response to surveys can be found here:
www.imperialcollegeunion.org/your-union/your-representatives/responses
If you would like to know more about any of these surveys or see the results from previous
surveys, please visit:
www.imperial.ac.uk/students/academic-support/student-surveys/pg-student-surveys
For further information on surveys, please contact the Registry’s Surveys Team at:
surveys.registrysupport@imperial.ac.uk
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16.
And finally
Alumni Services
When you graduate you will be part of a lifelong community of over 190,000 alumni, with access
to a range of alumni benefits including:
•
•
•
•
•
•
discounts on further study at the College and at Imperial College Business School
alumni email service
networking events
access to the Library and online resources
access to the full range of careers support offered to current students for up to three
years after you graduate
access to our Alumni Visitor Centre at the South Kensington Campus, with free Wi-Fi,
complimentary drinks, newspapers and magazines, and daytime left luggage facility
Visit the Alumni website to find out more about your new community, including case studies of
other alumni and a directory of local alumni groups in countries across the world.
www.imperial.ac.uk/alumni
Opportunities for Further Study
After you have completed MSc Bioinformatics and Theoretical Systems Biology, you may
choose to complete a PhD. Many previous graduates have gone on to complete PhDs in the
UK, overseas and at ICL.
57