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DRPS : Course Catalogue : School of Biological Sciences : Postgraduate

Postgraduate Course: Introduction to scientific programming for MSc in Drug Discovery & Translational Biology (PGBI11039)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) AvailabilityNot available to visiting students
SCQF Credits10 ECTS Credits5
SummaryThis 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 2018/19, Not available to visiting students (SS1) Quota:  66
Course Start Semester 1
Course Start Date 17/09/2018
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:
  1. Describe how computer programmes can be used to carry out simple data selection, data processing and data comparison work.
  2. Understand basic python programming
  3. Interpret and summarise the function of Python/JAVA code
  4. Compose simple command line programs in the Python/JAVA language
  5. Diagnose compilation and runtime faults in JAVA code.
Reading List
Recommended Reading

The JAVA language websites:

Python 2.7 tutorial
Additional Information
Graduate Attributes and Skills Not entered
Course organiserDr Paul Taylor
Tel: (0131 6)50 7058
Course secretaryMs Louise Robertson
Tel: (0131 6)50 5988
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