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 with	Doc. 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 t616070@cis.hut.fi
E-mail	t616070@cis.hut.fi

News

18.5. o Link to feedback form added. Filling the feedback form is a requirement for passing the course. 4.5. o More information about the final report, draft final report and project presentation added. 27.2. o The schedule has been updated. 15.2. o Added references to the articles presented at each session. 10.2. 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) hut.fi).

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	Abhiskek Tripathi: Exploratory Modeling of Yeast Stress Response and its Regulation with gCCA and Associative Clustering. Janne Nikkilä, Christophe Roos, Eerika Savia, and Samuel Kaski. International Journal of Neural Systems, Special Issue on Bioinformatics, vol. 15, no. 4, pages 237-246, 2005. Antti Ajanki: Learning Module Networks Eran Segal, Dana Pe'er, Aviv Regev, Daphne Koller, Nir Friedman Journal of Machine Learning Research, 6(Apr):557--588, 2005.
16.2.	Danai Laksameethanasan, Hanna Heikkinen	Danai Laksameethanasan: Expectation-maximization restoration of band-limited truncated point-process intersities with application in microscopy, T.J. Holmes, J. Opt. Soc. Am., 6(7):1006-14, 1989. Hanna Heikkinen: Discriminative clustering. Samuel Kaski, Janne Sinkkonen, and Arto Klami. Neurocomputing, 69:18-41, 2005.
23.2.	Protein-protein interaction group, Tommi Ripatti	Group: o A bayesian networks approach for predicting protein-protein interactions from genomic data. R Jansen, H Yu, D Greenbaum, Y Kluger, N J Krogan, S Chung, A Emili, M Snyder, J F Greenblatt, and M Gerstein. Science, 302(5644):449-453, Oct 2003. o Kernel methods for predicting proteinprotein interactions Asa Ben-Hur and William Stafford Noble, Bioinformatics, Volume 21, Suppl 1, Pp. i38-i46, 2005. Tommi Ripatti: Predicting transcription factor binding sites from sequence
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
March-April		Groups meet with their supervisor a few times.
11.5.		Deadline for returning a draft version of the final report.
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
31.5.		Deadline for submitting the final version of the report and the documentation.