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University of Helsinki Department of Computer Science
 

Department of Computer Science

399671 Practical Bioinformatics Module III –Biodatabases, 2 cp and 582604 Practical Course in Biodatabases, 4 cp

Contents

Course Description

Techniques for accessing and integrating data in biological databases are studied. The course contains project work.

Prerequisites

Introduction to Bioinformatics course. If you want to complete practical course in biodatabases, you should have some basic familiarity with programming and databases. For example, attending the course, Programming for Biologists, would give you a suitable background knowledge. Taking some other introductory programming course or being self-taught is also acceptable.

Course Structure and Completition

This course will consist of three parts.

  1. part introduces some of the biological databases, and their www interfaces.
  2. part will cover programmatic access to biological databases. Concepts of relational databases and SQL language will be introduced. In addition, Perl language will be used for programming on the course.
  3. part is an exercise, completed on student's own time.

The first two parts make up the course Practical Bioinformatics –biodatabases (2 cp). If you want to complete the Practical course in biodatabases (4 cp), that is compulsory for master's degree in bioinformatics, you should additionally do the exercise (3. part).

We are hoping to highlight the tasks programming is really required for, and to contrast these needs with what can be accomplished by using the point-and-click interfaces to databases.

This is a practical course, consisting of lectures and workshops. In addition, home exercises are distributed during the lectures. Completing home exercises will give some points towards the grade.

Lectures

Lectures will be hold on Mondays and on Tuesdays in Kumpula campus Exactum D122 at 14.00-16.00.

Handouts:

Workshops

Workshop like exercises will be hold on Tuesdays in Exactum B221 at 16.00-18.00 (exception: week 1 on Monday in B221 at 16.-18).

Credits and Exam

Passing the course is worth 2/4 cp, and the course is graded from 0 to 5.

You need to attend the lectures and workshops, pass the examination, do the exercise (for 4 cp), and return the course feedback form in order to pass the course.

The exam is on Tuesday 24.2 at 16.00-19.00 in Kumpula Exactum B221.

Examination will be done using a computer. Examination contains five questions. Every question scores a maximum of 5 points. Home assignments give you 5 points (every home exercise you have completed, you can receive a maximum of 1 point). Thus, a maximum score for the first part of the course (without practical work) is 30 points. To pass the first part of the course with grade 1, you need to score at least 15 points, so submitting your home exercises in the first part does get you a long way towards a passed score. To get a grade 5 you need 5/6 of the maximum points which is 25 points.

The maximum score for the second part of the course (practical work) is 30 points. So the maximum score for the whole course is 60 points (exam=25, exercises=5, practical work=30). To pass the course and get a grade 1 you need at least 15 points from the first and 15 points from the second part of the course. To get the maximum grade 5 you need at least 50 points.

Practical Work

Practical work contains two tasks: Part 1 and Part 2

Practical work assistance starts on 18.3. and ends on 10.4. and are held on Wednesdays at 16.20-18.00 (A218) and on Thursdays at 10.00-12.00 (A319).

Once a week 20 minutes personal space. Book the slot day before (by 6 pm) by email and it is recommended that you attach the code and problem description to this email. You will get reply which tells you which time slot is available.

Guidelines for writing the documentation

Documentation should include documentation of the two given tasks (part 1 and part 2) and manual for running the program (part 1).

  • In the documentations
    • PART1: Write down the program description. What does the program do, what does it take as input and what does it give as output. Tell which kind of data structures you have used and how does the program solve different problems that arise from the original description.
    • PART2: Describe the steps you had made to accomplish the given task. Give results.
  • Manual for the program: Give instructions how to run the program. Make sure that the program is possible to run just by following the manual instructions. The program should work on cs department machines and alkokrunni (db.cs.helsinki.fi) server.

Guidelines for writing the code

Try to minimize complexity and maximize the readability and efficiency (less time consume, less space). Use descriptive variable names. Use comments to make the code more readable. For the methods write down a method description and what does the method take as input and give as return. Use data structures wisely. If you have to install any additional modules for the program to run, inform these in the manual.

Test the code and check that it handles possible exceptions. Make sure the program displays something informative in case of any exception. You can use display to give instructions for the user to how to run the program and what does the program take as input and where does it save output files if there is any.

Instructions for returning the practical work

Practical work deadline is on 17.4. at 18.00. Create directory (yourFirstnameLastname) and under that create directories part1 and part2 which contains answers (code, manuals, documents) of the two practical works. Return your work (preceding directory hierarchy) in one .tar or/and .gz archive. Send the archive as attachment to astikain(at)cs(dot)helsinki(dot)fi. Write "PCBD PW yourfirstname lastname" as subject and your student number into the mail body.

Materials and Methods

The course will not follow any book. Course materials will basically consist of lectures and their notes, exercises and their solutions. Links to possible web materials and recommendable tutorials are listed in here.

Registration

Registration at ilmo.cs.helsinki.fi. A maximum of 30 student can be admitted on the course.

Note that you need to apply for a CS user account (right to use servers at the department of computer science).

Contact Information

Lecturers are Adjunct professor Siru Varvio , PhD Jarno Tuimala and BSc Ilari Scheinin.

Practical work assistant will be MSc Katja Astikainen


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