CSC8335 : Computing Environment for Digital Biology
- Offered for Year: 2025/26
- Module Leader(s): Dr Pawel Widera
- Lecturer: Dr Katherine James
- Owning School: Computing
- Teaching Location: Newcastle City Campus
Semesters
Your programme is made up of credits, the total differs on programme to programme.
| Semester 1 Credit Value: | 20 |
| ECTS Credits: | 10.0 |
| European Credit Transfer System | |
Aims
The module provides an elementary introduction to important topics in computing science and data handling that are relevant for biological data analysis and software development, including:
• Computer Architecture.
• Data Representation and Storage.
• Operating Systems and Virtual Machines.
• Command Line and REPL Environment for biological data analysis with Python and R.
Outline Of Syllabus
• Relationship between biology and computing.
• Introduction to computer architecture and CPU/memory/disk/network bounds on computation.
• Structured and unstructured data storage formats and databases.
• GNU/Linux operating system.
• Bash shell and scripting.
• Virtual machines and containers.
• Scientific writing with LaTeX.
• Basic statistical analysis and visualisation with R.
Teaching Methods
Teaching Activities
| Category | Activity | Number | Length | Student Hours | Comment |
|---|---|---|---|---|---|
| Structured Guided Learning | Lecture materials | 10 | 1:30 | 15:00 | Asynchronous online materials. |
| Scheduled Learning And Teaching Activities | Lecture | 16 | 1:00 | 16:00 | Lectures (in person). |
| Guided Independent Study | Assessment preparation and completion | 65 | 1:00 | 65:00 | Coursework preparation and practical exercises. |
| Scheduled Learning And Teaching Activities | Practical | 8 | 2:00 | 16:00 | Practicals (in person). |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 8 | 1:00 | 8:00 | Bookable office hours. |
| Guided Independent Study | Independent study | 16 | 3:00 | 48:00 | Background reading. |
| Guided Independent Study | Independent study | 16 | 2:00 | 32:00 | Lecture follow-up. |
| Total | 200:00 |
Teaching Rationale And Relationship
Lectures will be used to introduce the learning material and for demonstrating the key concepts by example. They will be followed by hands-on computer lab sessions where students will apply the thought concepts in practice. Students will be expected to watch asynchronous online materials following each in-person teaching session to strengthen their understanding and enable deep learning.
Students will be expected to spend time on coursework outside the timetabled classes.
Students aiming for merit/distinction mark will be expected to widen their knowledge beyond the content of lecture notes through background reading.
Assessment Methods
The format of resits will be determined by the Board of Examiners
Other Assessment
| Description | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|
| Practical/lab report | 1 | M | 85 | Main assignment testing the theoretical and practical understanding of the computational technologies used to organise biological data. |
| Prob solv exercises | 1 | M | 15 | Low stakes programming assignment testing the understanding of biological data handling in R. |
Formative Assessments
Formative Assessment is an assessment which develops your skills in being assessed, allows for you to receive feedback, and prepares you for being assessed. However, it does not count to your final mark.
| Description | Semester | When Set | Comment |
|---|---|---|---|
| Prob solv exercises | 1 | M | A series of small computational exercises testing ability to apply taught concepts in a new context. |
Assessment Rationale And Relationship
The practical/lab report assesses the understanding of the theory, the ability to use computational thinking, and competence in application of taught technologies to solve selected problems common in digital biology.
The low stake programming assignment allows students to explore practical applications of R to biological data handling.
The formative problem solving exercises help students to test their skills against teaching expectations.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- CSC8335's Timetable