MD1A1-15 Foundational Laboratory Skills & Computing Skills
Introductory description
MD1A1-15 - Foundational Laboratory Skills & Computing Skills. The module aims to equip students with essential core skills in molecular biology and scientific computing. This will function to bring students up to speed with the course philosophy and prepare them for the main modules that will follow.
Module aims
The purpose of this module is for the students to learn basic coding theory, understand data structure and handling and the associated mathematics principles behind these. This will be contrasted with data flow in biological systems, and the principles of molecular biology. Principle techniques learnt in the classroom will be reinforced in the laboratory session, which will see the students introduced to a modern, working molecular biology lab.
Outline syllabus
This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.
Block 1: Foundational Computing Skills
Lecture 1 & 2: Variables in Python.
Lecture 3 & 4: NumPy Arrays.
Lecture 5 & 6: Loops and Control Structures.
Lecture 7 & 8: Script Debugging; Data Input, Data Output.
Lecture 9 & 10: Plotting and Elementary Fitting.
Lecture 11 & 12: Writing Function. Random Processes.
Lecture 13 & 14: Image Processing.
Block 2: Introduction to Molecular Biology
Lecture 1: Structure and coding capacity of DNA.
Lecture 2: How DNA replicates.
Lecture 3: Techniques for analysing & manipulating DNA.
Lecture 4: Transcribing DNA. The flow if information in molecular biology.
Lecture 5: Translating mRNA. Ribosomes, transfer RNAs.
Lecture 6: Techniques for analysing and detecting proteins.
Lab 1: Isolating DNA.
Lab 2: Purifying protein I.
Lab 3: Purifying protein II.
Lab 4: TEV cleavage assay.
Lab 5: Analysis of cleavage restrictions.
Lab 6: Measuring gel densitometry.
Learning outcomes
By the end of the module, students should be able to:
- Use coding techniques to process data from experiments in molecular cell biology and relevant physical sciences.
- Demonstrate experimental skills in basic molecular cell biology and relevant physical sciences.
- Explain the principles of information flow in molecular biology from DNA to RNA to protein.
- Explain how DNA can be manipulated to produce recombinant organisms.
- Operate safely within a laboratory environment.
- Demonstrate relevant writing / reporting / collaborative working skills including the ability to succinctly summarise scientific information.
- Accurately record experimental data in a laboratory setting.
Indicative reading list
J. M. Kinder and P. Nelson, “A Student’s Guide to Python for Physical Modeling”, Princeton University Press (September 22, 2015).
Molecular Biology of the Cell (6th ed.). Bruce Alberts et al. 2014
Molecular Cell Biology (8th ed.). Harvey Lodish et al. 2016
Cold Spring Harbour Protocols Molecular Biology - http://cshprotocols.cshlp.org/site/Taxonomy/molecular_biology_l1.xhtml
Interdisciplinary
Students will learn to solve scientific problems in molecular biology by integrating concepts from computing and contrasting them with the information flow in biological systems.
Subject specific skills
Demonstrate the ability to accurately summarise a scientific experiment. Estimate quantitative solutions to scientific problems. Outline the principles of the major techniques of modern molecular biology.
Transferable skills
Demonstrate relevant writing / reporting / collaborative working skills including the ability to succinctly summarise scientific information. Demonstrate competency in writing python scripts to solve basic computing problems.
Study time
| Type | Required |
|---|---|
| Lectures | 12 sessions of 1 hour (8%) |
| Tutorials | 12 sessions of 1 hour (8%) |
| Practical classes | 12 sessions of 3 hours (24%) |
| Private study | 41 hours (27%) |
| Assessment | 49 hours (33%) |
| Total | 150 hours |
Private study description
31 hours of self-directed study
Costs
No further costs have been identified for this module.
You do not need to pass all assessment components to pass the module.
Assessment group D1
| Weighting | Study time | |
|---|---|---|
| Assessment of laboratory skills | 20% | 36 hours |
|
Assessing the proficiency in laboratory techniques, observing good laboratory practice, engagement and contribution to group experiments. |
||
| Written examination | 80% | 13 hours |
|
A written examination consisting of short answer questions encompassing topics covered in the lecture and practical sessions. |
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Feedback on assessment
Laboratory reports - submission annotated and returned, general comments/'what was good'/'what could be improved' alongside marking rubric.
Assessment of laboratory skills - at the end of each two-week laboratory session, block leads will provide comments on proficiency, Good Laboratory Practice (GLP) and engagement/group contribution that arise. Due to the volume of feedback, stock phrases will be provided to the block leads, which may be amended or expanded at the lead's discretion. Further verbal feedback will be given to students on request.
In terms of practicalities, following GLP, executing the laboratory protocol, attaining proficiency in techniques taught and engaging/contributing to group activities (where required) will be based at 62 on the 20-point University scale. Exceptional attainment/contributions will grade higher, whereas disengagement, not observing GLP, and an unwillingness to acquire lab proficiency will score lower. Marks will not take into account whether a student achieved a desired experimental result or not. The block lead will work with the laboratory technician in observing and recording these across the cohort. Feedback will be provided biweekly at the end of each block.
Courses
This module is Core for:
- Year 1 of UMDA-CF10 Undergraduate Integrated Natural Sciences (MSci)