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@ Comenius University

Computational Biology
Study CS (undergrad)
Study CS (doctoral)

Teaching

Methods in Bioinformatics
Machine Learning
Graphical Models
Bioinformatics Seminar

Thesis topics

Bioinformatics
Other projects (bachelor)

Other sites

Computational genomics at Cornell
Bioinformatics at Waterloo
Slovak Olympiad in Informatics
Internet Problem Solving Contest

Tomas Vinar's homepage

Name: Tomas Vinar (Tom\'a\v{s} Vina\v{r})
Assistant Professor and Independent Researcher
Associate Dean for Information Technologies
Dept. of Applied Informatics,
Faculty of Mathematics, Physics, and Informatics
Comenius University
Address: Mlynska Dolina, 84248 Bratislava, Slovakia
Office: M163 Phone: +421(2)60295207
Professional interests: bioinformatics, algorithms, probabilistic modeling
E-mail:
Important: Brona

schedule and plans:

Office hours: Mon 12:20-13:50 (TBA, for faculty); Thu 13:00-14:00 (M-163, for students)

Weekly (Fall 2011):

Mon: 14:00 Faculty council or AI seminar

Tue: 9:00 Meetings | 17:20 Bioinf. seminar (I-9) | 19:00 Apollo

Thu: 14:00-19:00 Methods in Bioinformatics (F1-328/M218)

Fri: 11:00 CS seminar (M-213)

Long term (tentative):

28.9.-3.10.: Italy

15.10.-22.10.: SPIRE 2011 (Italy)

28.10.-5.11.: Shanghai

teaching:

Spring 2011: Bioinformatics Seminar

Fall 2010: 2-INF-150: Machine Learning

Fall 2010: 2-AIN-501: Methods in Bioinformatics

Fall 2010: Bioinformatics Seminar

Spring 2010: 2-INF-238: Graphical Models in Machine Learning

Fall 2009: 2-INF-150: Machine Learning

Fall 2009: 2-AIN-501: Methods in Bioinformatics

Summer 2009: Summer Bioinformatics School, Modra, Slovakia

Spring 2009: 2-INF-150: Machine Learning

Spring 2009: 2-AIN-504: Bioinformatics Seminar (2)

Summer 2007: Summer Bioinformatics School, Bratislava, Slovakia

Fall 2005: UW CS240: Data Structure and Data Management (instructor)

Winter 2003: UW CS341: Algorithms (instructor)

Fall 2002: UW CS466: Advanced Algorithms (TA)

Spring 2002: UW CS466: Advanced Algorithms (TA)

Winter 2002: UNIX consultant

Fall 2001: UNIX consultant

Spring 2001: UNIX consultant

Winter 2001: UW CS341: Algorithms (TA)

Fall 2000: UW CS341: Algorithms (TA)

Spring 2000: UW CS360: Theory of Computation

Winter 2000: UW CS341: Algorithms (TA)

Fall 1999: UW CS134: Principles of Computer Science (TA)

Summer 1999: Comenius University: Introduction to programming theory (tutorial instructor)

Winter 1998: Comenius University: Design of efficient algorithms (tutorial instructor)

Winter 1998: Comenius University: Introduction to distributed algorithms (tutorial instructor)

software:

ExonHunter: A comprehensive gene finding program that allows incorporation of ESTs, proteins matches, genome-genome similarities, and more. You can download a version compiled for Linux, or you can contact me if you need a version for other platforms, or parameters for organisms other than ones available there.

Mikroskop: A simple, yet feature-rich viewer of gene finding and sequence annotation results. It is written in Perl, and you can download it here.

TreeArrange and Treeps: A post-processing tool for analysis of expression arrays. Enhances output of hierarchical clustering programs such as Cluster or XCluster. Increases visibility of clusters by reordering the data and creates (potentially labeled) output in encapsulated postscript. Available for download.

med2bib.pl: Downloads PubMed records and turns them into BibTeX for easy inclusion in LaTeX articles. Available as a web server and for download.

Mendel: A simulation/educational program for instruction of mendelian genetics, written ages ago. You can still download MS-DOS executable. It was actually used in instruction for both high-school and university students.

former activities:

1994-1999 co-organizer Correspondence Seminar in Programming (CSP), Slovak Olympiad in Informatics and other activities around in the CSP group.

2002, 2003, 2004: TAM (Tyzden Absolventov Matfyzu) - annual alumni miniconference at Comenius University, Faculty of Mathematics, Physics, and Informatics, Bratislava, Slovakia. [TAM www page]

1997-1999 singing in Mixed choir Apollo, Bratislava

1999(F)-2000(F),2001(S) University of Waterloo choir [music ensembles]

2001(W,F),2002(F),2003(W,F),2004(W) University of Waterloo chamber choir [music ensembles]

1999-2001 board member of the TROJSTEN foundation (funds for correspondence seminars organized at Comenius University Bratislava) [foundation www page]