Gwybodaeth Modiwlau
Module Identifier
CSM0120
Module Title
Programming for Computational Biology
Academic Year
2013/2014
Co-ordinator
Semester
Semester 1
Pre-Requisite
Only available to students registered on MSc Statistics for Computational Biology
Other Staff
Course Delivery
| Delivery Type | Delivery length / details |
|---|---|
| Lecture | 10 x 2hour lectures |
| Practical | 5 x 2hour practicals |
Assessment
| Assessment Type | Assessment length / details | Proportion |
|---|---|---|
| Semester Assessment | Practical programming assignment 1 | 40% |
| Semester Assessment | Practical programming assignment 2 | 60% |
| Supplementary Assessment | Resubmission of failed/non-submitted coursework components or ones of equivalent value | 100% |
Learning Outcomes
On successful completion of this module students should be able to:
write code to perform common bioinformatics tasks
query/modify a data file or a database
make use of data in XML format
retrieve information from popular bioinformatics APIs such as ENSEMBL and BLAST
Aims
This module aims to equip the students with programming skills for information retrieval, data manipulation, data/model/knowledge storing and sharing, and high performance computing.
Brief description
This module will emphasise use of the scripting language, Python to carry out tasks in Bioinformatics and to manage data using specialist Bioinformatics tools as well as conventional files and database.
Content
1. Basics of Python: types, variables, if, for, while, functions. Understanding how to use the interpreter, how to read error messages, how to write and run code.
2. Reading and writing files. Examples of bioinformatics file formats e.g. CSV, FASTA, FASTQ, SAM, etc. Example programming tasks collecting basic information from these files, reformatting files. General familiarity and experience using Python.
3. Databases: Examining database structure (tables, keys, relations). Interfacing to databases using SQL and Python. Basic design of databases.
4. XML: structure, parsing, correctness and schema. SBML and other examples.
5. Using remote APIs (e.g. ENSEMBL or BLAST) to query online bioinformatics resources
2. Reading and writing files. Examples of bioinformatics file formats e.g. CSV, FASTA, FASTQ, SAM, etc. Example programming tasks collecting basic information from these files, reformatting files. General familiarity and experience using Python.
3. Databases: Examining database structure (tables, keys, relations). Interfacing to databases using SQL and Python. Basic design of databases.
4. XML: structure, parsing, correctness and schema. SBML and other examples.
5. Using remote APIs (e.g. ENSEMBL or BLAST) to query online bioinformatics resources
Module Skills
| Skills Type | Skills details |
|---|---|
| Application of Number | Inherent in the study of programming for bioinformatics |
| Communication | |
| Improving own Learning and Performance | Inherent in the module. |
| Information Technology | Programming, interfacing with online data systems |
| Personal Development and Career planning | Gives students practical skills for a career in this field |
| Problem solving | Identifying and using programming techniques to solve problems in Computational Biology |
| Research skills | Problem analysis, data resource discovery, experimental design, data analysis |
| Subject Specific Skills | |
| Team work |
Notes
This module is at CQFW Level 7