Computational Biology (BIO 315)

Christoforos Nikolaou

Room A, Monday 14.00-16.00

The course covers a broad spectrum of computational approaches to biological problems. Classes are oriented towards problem solving, each having a plausible biological question as startpoint and then proceeding with suitable computational methods to solve it. The subjects with which we will be dealing include: "word" occurence in DNA sequences and nucleotide composition, motif discovery, analysis of genomes and gene annotation, alignments of biological sequences, genetic variation in populations, molecular evolution and phylogenetics, comparative genomics, analysis of gene expression, proteomics and analysis of biological networks.

Structure of the course:
1. Lectures 
Lecture cover a wide range of topics, focusing on biological sequence analysis and genomics. There will be 12 lectures in total that are not compulsory but students are advised to follow.
2. Practicals
Practical problem sets are taught at the Computer Room (Biology Department) on selected Mondays and in two groups 16.00-17.30, 17.30-19.00. There will be 8 practicals in total which will be focused on the use of available resources (online web-services, databases and open-source software) aimed at the solution of simple (and not so simple) biological questions. Attendance is not compulsory but handing in of the Practical Report Exercise in paper is a compulsory prerequisite for the completion of the course. Handing in of the Papers has to be done before the next practical exercise (hard deadline). 
3. Evaluation
Completion of the course will be evaluated on the basis of: a) At least 7/8 completed practicals, handed in on time and with an average grade>5. This will be given a weight of 30%. b) Final Exams will be open-book, and will be given a weight of 70%. Only grades >5 will be taken into account for the Final Grade. 

In brief: FinalGrade= 0.3*(Practicals)+0.7(Exams) # assuming both Practicals and Exams are >5. In case Exams<5 this will be the Final Grade but student will be allowed to "keep" their Practical Grade and will not be asked to repeat the Lab work.

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