Laboratory of Computer and Information Science / Neural Networks Research Centre CIS Lab Helsinki University of Technology

T-61.6070 Special course in bioinformatics I:
Computational modeling methods in bioinformatics V P, (7 cr)

Lecturers Prof. Sami Kaski, Laboratory of Computer and Information Science, Helsinki University of Technology
In Collaboration withDoc. Christophe Roos and Jukka Matilainen, Medicel Oy
Assistant M.Sc. Merja Oja, Department of Computer Science, University of Helsinki
Credits (ECTS) 7
Sessions On Thursdays at 14-16 in lecture hall T4
Registration TKK students: WebTopi, others: send mail to


o Link to feedback form added. Filling the feedback form is a requirement for passing the course.
o More information about the final report, draft final report and project presentation added.
o The schedule has been updated.
o Added references to the articles presented at each session.
o Remember to submit your project plan to your supervisor one week after your seminar presentation. (Guidelines given in Slides.)
o Please send a copy of your written project plan also to the course assistant Merja (merja.oja (at)

Link to course description

Signing up for the course

HUT students: In Webtopi
Other universities: Send email to the organizers or sign up at the introduction lecture.

The project work

The project work includes the following parts:
  1. Each group selects (with the help of the lecturers) one state-of-the-art article as the basis of the project work.
  2. Brief seminar presentation of the details of the model/algorithm and plans for implementing and testing it. (Guidelines given in Slides.)
  3. Submit a written plan of the project to your supervisor, who will give you feedback.
  4. Carry out the plan and meet with the supervisor a few times during the project.
  5. Submit a first version of the results of your project to your supervisor (at least slides) a week before the mini-conference.
  6. Oral presentation of the results in a mini-conference.
  7. Submit a brief written report and documentation of the codes.
The timetable of the project work is described below in the course schedule.

Medicel Integrator [back to top]

You can use the Medicel Integrator platform in your project work. The Integrator is available over the Internet (e-mail Jukka Matilainen for access information).

Final report [back to top]

The draft version of the final report

The draft version of the final report should include an outline of your project presentation, i.e. a basis on which you can build your slides. The draft should be about 2-3 pages long and contain the following sections:

  1. Introduction of the reseach problem,
  2. methods used to study the problem,
  3. overview of the implementation,
  4. overview of the expriments you have conducted (what?, why?)
  5. the results that validate that your implementation works
  6. other results from your experiments (based on your project plan)
  7. conclusion
  8. references

Project presentation

The presentation should be 20-25 minutes long (30 minutes with questions), 30-35 minutes for the two person group (40 minutes with questions). The contents of the presentation the same as for the draft final report.

The final report

The final report of the project should be written like a scientific article. The length should be 6-12 pages, depending on how many figures you have included. Please use the Word or Latex templates for the journal "Bioinformatics" to format your report.

Hand in also the code you have implemented and return it in addition to the final report (you can license your code with GPL if you want). Please consider also making the code available through the Medicel Integrator (more info about itegrating your code to Medicel Integrator is coming a bit later).

Please return the report and code to Merja by e-mail by 31rd May.

Feedback [back to top]

All students must fill in the feedback form in order to pass the course. Please fill the English version of the feedback form: Feedback form.

Schedule [back to top]

Time Lecturer Subject and material
19.1. Sami Kaski, Christopher Roos, Jukka Matilainen
  • Administrative issues
  • Introduction
  • Demo of Medicel Integrator platform
26.1. Merja Oja, Jukka Matilainen
  • Practical issues. We will agree on timetable of the presentations and fix the topics, articles and supervisors for each group, Slides.
  • Demo and possibility to try out Medicel Integrator
2.2 Medicel
  • Medicel Integrator, hands on opportunity for participants: demo and trials using the Medicel integrator starting from the users' own questions. We also prepare some specific examples that can be used.
  • The demo will be held at A346.
9.2. Abhishek Tripathi, Antti Ajanki
16.2. Danai Laksameethanasan, Hanna Heikkinen
23.2. Protein-protein interaction group, Tommi Ripatti
28.2. onwards
  • Possibility to use Medicel Integrator at HUT
9.3. Abhishek Paliwal
  • Abhishek Paliwal: Plaid Models for gene expression data, Laura Lazzeroni and Art Owen, Statistica Sinica 12(2002), 61-86.
at week 11
  • Possibility to use Medicel Integrator over the web
  • Groups meet with their supervisor a few times.
18.5, 12:00-16:00 all groups
  • Project presentations by each group (A half day seminar about the results of group projects)
  • Location: Seminar room A328 (Computer science building, 3rd floor, in the middle of the corridor that is on the side of the road)
  • Preliminary schedule:
    • 12:00-12:40 Maruti Gangumolu and Lei Dong
    • 12:40-13:10 Abhishek Tripathi
    • 13:10-13:40 Hanna Heikkinen
    • break
    • 13:50-14:20 Antti Ajanki
    • 14:20-14:50 Danai Laksameethanasan
    • 15:00-15:30 Abhishek Paliwal

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