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TUCS Newsletter 13.9.2012

Content of the newsletter


TUCS Distinguished Lecture Series

TUCS launches a new TUCS Distinguished Lecture Series from fall 2012. The series is a forum for public lectures by outstanding national and international researchers in all aspects of computing, coming both from academia and industry. All lectures are free and open to the public.

Forthcoming lectures:

1.10.2012 Yuri Matiyasevich (Steklov Institute of Mathematics, Saint Petersburg, Russia) at 13.15, "Turing Machines vs. Diophantine Machines". Lecture room Lambda (ICT-Building)

3.12.2012 Masakachu Ohashi Chuo (Chuo University, Japan) at 13.15, "Business and IT Operations Continuance in Japan After the 2011 Earthquake". Lecture room Lambda (ICT-Building)


TUCS Research Programme activities


TUCS website layout change

The LOCAL-link from the main navigation is now moved to the footer of the page, where it can be found reading "Log in". The ABOUT US -link has been moved from the left end of the main navigation menu to second from the right.


TUCS GP information meeting for new students

TUCS Graduate Programme invites all new TUCS GP students to attend an information meeting on Thursday 4.10.2012 at 14.00 in the TUCS conference room, ICT-building, Joukahaisenkatu 3–5B, 6th floor.

There will be a short presentation of TUCS and the TUCS staff and some of the practical issues concerning the PhD studies, benefits and duties related to the Graduate Programme, traveling instructions, TUCS Publication Series and so on will be discussed.


Defense of Doctoral Thesis

On Wednesday, September 12th, TUCS GP student Thomas Canhao Xy presented his Ph.D. thesis "Hardware/Software Co-Design for Multicore Architectures" for public criticism. The opponent of M.Sc. Xu is Professor Per Gunnar Kjeldsberg from Norwegian University of Science and Technology, Norway. Adjunct Professor Pasi Liljeberg will act as the custos at this public defense.


Time: 12 noon
Place: Auditorium Beta, The ICT Building


Award for TUCS PhD student Adnan Ashraf

PhD student Adnan Ashraf got the Best Doctoral Research Proposal Award at 38th Euromicro Conference on Software Engineering and Advanced Application (SEAA), Cesme, Turkey, September 5–8, 2012.

Title: Cost-efficient resource allocation for multi-tier web applications in a cloud environment.


Fudan–Turku Cooperation

A delegation from the Fudan University, Shanghai, PRC was visiting the University of Turku from Sunday to Tuesday August 26th to Aug 28th. The visit was very fruitful, and concentrated on engineering education and especially interdisciplinary ICT education issues.



Autumn courses listed

We have now listed the TUCS courses for Autumn 2012 on our courses-page. The courses are also available on the TUCS Courses Google Calendar, for the convenience of especially those who use Google Calendar otherwise too.



TUCS short course: Bio-Operations and Combinatorial Algorithms

Course name: Bio-Operations and Combinatorial Algorithms (2 cr)
Lecturer: Prof. Victor Mitrana, Department of Computer Science, University of Bucharest
Time: One week in the period 15.10-15.11 (details to be announced later)
Place: ICT Building

Course description: A basic problem in the area of combinatorial algorithms for genome evolution is to determine the minimum number of large scale evolutionary events (genome rearrangements) that transform a genome into another. We focus in this course on the algorithmic study of genome evolution by crossovers (translocations).

We present results related to the combinatorial analysis of genome evolution focused on evolution distance in terms of crossovers for chromosomes formed from different markers which correspond to unique segments of DNA. From the formal point of view this means that all symbols of the strings representing the chromosomes are different. Two new types of crossover distance between two sets of strings (genomes) are introduced; we examine the complexity of computing these distances in the case of uniform crossover, that is at each step the strings exchange prefixes of the same length, as well as arbitrary crossover. We present exact polynomial algorithms based on the “greedy” strategy, approximation algorithms and prove that some problems are NP-complete.

Other algorithms computing distances based on another bio-operation, namely hairpin (partial) lengthening are to be discussed. We consider a language-theoretic approach to three variants of the hairpin lengthening viewed as formal operations on strings and languages.

We first consider a few decidability problems regarding the hairpin lengthening operation and present algorithmic solutions for some of them and partial solutions and open questions for the others. Then, some combinatorial problems, mainly hairpin distances, and algorithms for solving them are presented. We discuss the time complexity of these algorithms and some possibilities to improve them. Several open problems that naturally arise are also to be discussed.


Upcoming INFORTE.fi events

Helsinki 13.–14.9.2012
Speaker: Prof. Molly Wasko (University of Alabama at Birmingham, USA)
Organizer: Prof. Virpi Tuunanen, Aalto-University
Registrations and more information:

Helsinki 19.9.2012
Speakers: Prof. Youngjin Yoo (Fox School of Business, Temple University, Philadelphia, Director, Urban Apps & Maps Studios, USA), Associate Prof, George Kuk (Nottingham University Business School, UK), Assistant Prof. Juho Lindman (Hanken School of Economics, Finland)
Organizer: Prof. Virpi Tuunainen, Aalto-University
Registrations and more information:

Turku 4.–5.12.2012 (Please, notice new dates!)
Speakers: Mayumi Hori (Hakuoh University), Masakazu Ohashi (Chuo University)
Organizer: Prof. Reima Suomi, University of Turku
Registrations and more information:


EIT ICT Labs Doctoral School: Raising I&E awareness

Whether setting up your own start-up or just interested in improving your business skills this Innovation & Entrepreneurship course is for You!

RAISING I&E AWARENESS event for PhD students
DATE: 10–11 October 2012
VENUE: 1st floor Seminar Hall at Open Innovation House, Otaniementie 19 B, Espoo, Finland
ORGANISER: EIT ICT Labs Doctoral Program in ICT Innovation, Helsinki.

REGISTRATION, DEADLINE Friday 5 October 2012:
Registration is binding. Participation includes lectures, social program and serving described in the program.

PROGRAM, please visit: http://www.eitictlabs.eu/education/education-catalyst-and-co-funding-model/innovation-entreprenuership-education-for-doctoral-programs/doctoral-ie-education-in-helsinki/raising-ie-awareness/

WHO CAN ATTEND: The event is available for DOCTORAL STUDENTS from Aalto University, University of Helsinki, University of Turku, Åbo Akademi, University of Oulu, University of Tampere and Tampere University of Technology. Also doctoral students from other EIT ICT Labs nodes and their partner universities can attend.


ACCOMMODATION (not included): please visit: http://www.eitictlabs.eu/ict-labs/nodes-co-location-centres/helsinki/hotel-and-directions/.


Join the Academic Track at Open Knowledge Festival in Helsinki 17.–22.9!

From 17th – 22nd September 2012 in Helsinki, the world's first international Open Knowledge Festival will take place! Join us for a week of participatory sessions, keynote lectures, workshops, hackathons and satellite events. The event will include 170 sessions structured around 13 key Topic Streams, which range from Government Transparency to Open Hardware and beyond. Find out more: http://okfestival.org/

Get your ticket here: http://okfestival.org/early-bird-okfest-tickets/

The Open Research and Education stream will offer presentations, panel discussions, workshops and hackathons geared particularly towards the academic community. Some of the highlights include:

In addition, the stream will feature book sprints, peer review sessions, a social and much more! See the program for details http://okfestival.org/open-research-and-education/. Buy your ticket now to join hundreds of change-makers and experts from private, public and community sectors and help build an international open knowledge ecosystem with us in Helsinki.

On behalf of the Open Science and Education team, Leo Lahti and Laura Newman


Latest issue of Academy of Finland’s Apropos newsletter (in Finnish):



Courses on transferable skills at University of Turku

Continuous seminars & courses

First Article Language Checking Service
Time: 1.3.-31.12.2012- nb! summer break 15.6.-15.8.2012
Target group: PhD students at the University of Turku working on their first article for publication (in English)
Organizers: The University of Turku Language Centre and UTUGS

Life after PhD - Seminars in the Fall 2012
Time & Place:

Target group: PhD students, supervisors, other researchers and those interested in the topic
Further information: eeva.sievi(at)utu.fi
Organizer: UTUGS

Tieteen popularisointi – näin kerron tutkimuksestani (1 op)
Tohtorikoulutettava kirjoittaa väitöskirjatutkimuksestaan lyhyen (max. 4500 merkkiä) ja yleistajuisen jutun, luetuttaa tekstin ensin ohjaajallaan ja jatkaa tekstin työstämistä Suomen Akatemian tiedottajan Risto Alatarvaan kanssa. Valmis juttu julkaistaan Suomen Akatemian Tietysti.fi-sivustolla.
Järjestäjä: UTUGS ja Suomen Akatemia
Lisätietoja: Eeva Sievi (eeva.sievi-at-utu.fi, 040-1612970) ja Risto Alatarvas (risto.alatarvas-at-aka.fi, 040-828 0648)

"Suomen kielen klinikka" for international students and staff
Target group: all non-Finnish speakers at the university who already are at the level of being able to express themselves in written and oral Finnish (=B to C-level)
Further information: Markku Nikulin (marnik-at-utu.fi)
Organizer: suomen kielen oppiaine


Työoikeutta tutkimuksen ammattilaisille (3 op)
Aika ja paikka:
Ke 19.9. klo 13-17 (Cal 3, Vänrikinkatu 2)
To 20.9. klo 13-17 (Cal 3, Vänrikinkatu 2)
Ti 25.9. klo 14-17 (Cal 3, Vänrikinkatu 2)
Ke 26.9. klo 14-17 (Cal 3, Vänrikinkatu 2)
Vastuuopettajat: työoikeuden professori Martti Kairinen ja professori Kevät Nousiainen
Ilmoittautuminen: 6.9.2012 mennessä www-ilmoittautumislomakkeella
Järjestäjä: UTUGS

Working Life Outside Academia Time: starting September 28 at 11:00 in Auditorium Externum, Kiinanmyllynkatu 10 (for further details, see the programme) Registration: by 19.9.2012 via eRegistration Organizer: Turku BioNet Doctoral Programmes http://www.utu.fi/tutkimus/tutkijakoulu/WorkingLifeSkills2012.pdf


Educating adults & teaching at university (2 ECTS) Time: starting 1.10. at 13-16 (see the course description for details) Place: University of Turku Responsible teacher: Mari Murtonen Registration: by 17.9.2012 via eRegistration (max. 20 course participants) Organizer: UTUGS http://www.utu.fi/tutkimus/tutkijakoulu/UniversityTeaching2012.pdf

Ethics of Academic Research (2 ECTS) Time: Monday 29.10.2012 at 10.15-11.45 & Mondays from 5.11. to 10.12. at 9.15-11.45 Place: Pub 2 (Publicum, Assistentinkatu 7) Responsible teacher: Dr. Helena Siipi Registration: by 17.10.2012 via eRegistration Organizer: UTUGS http://www.utu.fi/tutkimus/tutkijakoulu/ResearchEthics2012.html


Courses on transferable skills at Åbo Akademi University

EFFECTIVE PRESENTATIONS IN ENGLISH in Turku & Vasa During the course you will get the opportunity to make different kinds of presentations and you will get constructive feedback from teacher and colleagues. Clips from the content:

Time and place: October 5th & 19th; Åbo and October 12th & 26th; Vasa
Facilitator: Patrick Gallagher, BA, Cert. TEFLA

För dig som har eller kommer att ha rösten som arbetsredskap. Under kursen lär du dig använda din röst på bästa sätt, sköta om sin röst, undvika sådant som kan vara illa för rösten. Tid och plats: november-december, både Åbo och Vasa

SÖK I NELLI - portalen för databaser, e-tidskrifter och e-resurser, 2h
Tidpunkt: Alt 1. 25.9.2012 kl. 10.15-12
Alt 2. 23.10.2012 kl. 13.00-15 (In English)
Alt 3. 20.11.2012 kl. 10.15-12

Introduktion till referenshanteringsprogrammet RefWorks och hur man använder Write-N-Cite då man skriver texter i Microsoft Word. Vi lär oss att importera referenser till vår egen referensdatabas, skapar mappar och editerar referenser. Vi övar oss i att göra en referenslista och hur man kan jobba offline (utan Internet) med programmet.
Tidpunkt: Alt 1. 2.10.2012 kl. 10.15-12
Alt 2. 30.10.2012 kl. 10.15-12 (In English)
Alt 3. 27.11.2012 kl. 10.15-12

Följande kurser i Åbo är öppna och gratis för alla FORSKARSTUDERANDE vid ÅA:

För närmare information, se kurskatalogen: http://www.abo.fi/personal/kurskatalog
Anmälningar: http://www.abo.fi/personal/anmalan




(* Adobe Connect betyder att du kan delta i kursen från din egen dator)

The following courses are open and free for all doctoral students at Åbo Akademi University:

Course information: http://www.abo.fi/personal/kurskatalog
Registration: http://www.abo.fi/personal/en/anmalan


Open jobs at University of Turku and Åbo Akademi University


TUCS GP travel reports

TUCS GP Muhammad Nazrul Islam's Travel Report from APCHI 2012

Muhammad Nazrul Islam

TUCS GP Henri Korvela's Travel Report from AMCIS 2012

Henri Korvela

TUCS GP Hongyan Liu's Travel Report from ICDM 2012

Hongyan Liu

TUCS GP Hongyan Liu's Travel Report from AMCIS 2012

Hongyan Liu

TUCS GP Student Diana-Elena Gratie's Report from the Oxford Summer School in Computational Biology

The Oxford Summer School in Computational Biology is a yearly event organized by the Genome Analysis Group at the Department of Statistics, University of Oxford. This year, it took place between July 9th and August 17th. The event gathered 36 students (out of 350 applicants) with background in mathematics, computer science, biology, physics and chemistry. The aim of the summer school was to provide hands-on experience of research on real problems at the cutting edge of the field.

Students were grouped into teams of three, based on competencies and interests, and assigned a project. There were 12 projects, ranging from Arabidopsis thaliana annotation to human genome annotation, MCMC parallelization, protein co-evolution, path sampling in CTMC and RNA structure prediction. Each day started with a 60-minute lecture, followed by work on the project and meetings with the supervisors. In the Friday of the first week all teams presented their project and what they planned to do. In the last day each team presented their results.

Together with my team mates Maria Astefanoaei and Cyrus Rich we worked on the project “Alignment Postprocessing for Secondary RNA Structure Prediction using Stochastic Context Free Grammars and Alignment Graphs”. We extended the CYK algorithm to alignment graphs (a DAG structure having as vertices the unique columns from multiple alignments), and included in our prediction the Knudsen-Hein grammar. We ran our prediction on 50 samples with known structure, and got an average sensitivity of 0.587.

During the summer school we had many social events, some organized by the staff, and some organized by students: welcoming lunch, theater evening (The merchant of Venice), trips to London, Stonehenge, Windsor castle and Hastings, goodbye dinner.

The summer school was very well organized. The daily lectures and meetings were extremely useful for our project work and enriched our knowledge. There was a perfect balance between work and social activities. It was a wonderful experience, and we made contacts all over the world.

TUCS GP Student Peter Sarlin's Travel Report from a research visit at the European Central Bank

TUCS provided partial funding for a research visit from March to June 2012 at the European Central Bank (ECB), Financial Stability Surveillance Division in Frankfurt, Germany. I spent main parts of the stay working on a project in which we are modeling bank-specific vulnerabilities as well as interdependence in the European banking sector. The developed model enables signaling risks and vulnerabilities in European banks and assessing the possible spread of distress through estimated interdependence networks. Based upon the research results during my visit, we wrote a paper entitled “Predicting bank distress and identifying interdependencies among European banks”, co-authored by Frank Betz, Silviu Oprica, Tuomas Peltonen and Peter Sarlin, which is currently under review for the ECB Working Paper series and an international journal. The model is not only of academic interest, but also policy relevant. It is being implemented for active use to be part of a larger macroprudential toolbox of decision support tools at the ECB and was also referred to by the vice-president of the ECB in his recent speech as a promising approach to assessing bank distress (http://www.ecb.int/press/key/date/2012/html/sp120614_1.en.html). The research visit seemed to be an enough mutually beneficial experience for us to proceed with a follow-up project in which we are developing a similar model for assessing entity-level vulnerabilities and the spread of distress, but this time with a focus on the European insurance sector.

Peter Sarlin

TUCS GP Shahrokh Nikou's Travel Report from ICMB 2012

Shahrokh Nikou

TUCS GP Adnan Ashraf's Travel Report from SEAA 2012

Adnan Ashraf


Latest publications at TUCS

Edited special issues of journals (1):

Articles in journals (3):

Articles in proceedings (7):

Chapters in edited books (3):

Technical reports (6):