Postgraduate Course: Introduction to scientific programming for MSc in Drug Discovery & Translational Biology (PGBI11039)
Course Outline
| School | School of Biological Sciences |
College | College of Science and Engineering |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Availability | Not available to visiting students |
| SCQF Credits | 10 |
ECTS Credits | 5 |
| Summary | This course will expose the student to the computer programming methods need to write simple software for the types of data handling expected in structure-based drug design. The student will carry out a series of computer-based practical exercises. Supervision will be provided on an introductory basis as well as ad hoc. |
| Course description |
The lectures will try and cover the following areas; however topics covered will be coupled with progress in the practical exercises.
- How programming is done
- Introduction to general concepts
- Input and Output
- Using data structures
- A typical program for the analysis of a protein data bank file
- Exercises will be in Python/Java
|
Entry Requirements (not applicable to Visiting Students)
| Pre-requisites |
|
Co-requisites | |
| Prohibited Combinations | |
Other requirements | This course is an introductory programming course and therefore NOT recommended for any students with a programming background. |
| Additional Costs | Recommended course book(s). |
Course Delivery Information
|
| Academic year 2019/20, Not available to visiting students (SS1)
|
Quota: 66 |
| Course Start |
Semester 1 |
| Course Start Date |
16/09/2019 |
Timetable |
Timetable |
| Learning and Teaching activities (Further Info) |
Total Hours:
100
(
Lecture Hours 20,
Programme Level Learning and Teaching Hours 2,
Directed Learning and Independent Learning Hours
78 )
|
| Assessment (Further Info) |
Written Exam
0 %,
Coursework
100 %,
Practical Exam
0 %
|
| Additional Information (Assessment) |
100% in-course assessment. There will be 6 assessed practical exercises.
Practical Exercises
1. Modification of simple programs (15%)
2. A program to perform a simple mathematical calculation (12%)
3. Develop and test extensively a program to reformat text input files (13%)
4. Write a program to read and interpret a common chemoinformatics format using an external library (12%)
5. Develop a class to read protein databank format files and use it in a simple file reading program (12%)
6. A multi session practical to develop and test a program to compute molecular similarity (36%) |
| Feedback |
Feedback is in the form of marks given for each section (Functionality of Code, readability, comments in code and documentation) and some comments about which sections need improvement. |
| No Exam Information |
Learning Outcomes
On completion of this course, the student will be able to:
- Describe how computer programmes can be used to carry out simple data selection, data processing and data comparison work.
- Understand basic python programming
- Interpret and summarise the function of Python/JAVA code
- Compose simple command line programs in the Python/JAVA language
- Diagnose compilation and runtime faults in JAVA code.
|
Reading List
Recommended Reading
The JAVA language websites:
http://docs.oracle.com/javase/tutorial/java/index.html
http://www.oracle.com/technetwork/java/javase/documentation/index.html
Python 2.7 tutorial
https://docs.python.org/2/tutorial/ |
Additional Information
| Graduate Attributes and Skills |
Not entered |
| Keywords | IntroSciProg |
Contacts
| Course organiser | Dr Paul Taylor
Tel: (0131 6)50 7058
Email: p.taylor@ed.ac.uk |
Course secretary | Mrs Claire Black
Tel: (0131 6)50 8637
Email: Claire.Black@ed.ac.uk |
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