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TUCS Newsletter 8.11.2012

Content of the newsletter


TUCS activities


TUCS Distinguished Lecture Series

The TUCS Distinguished Lecture 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.

Friday, November 9, 2012 at 13.15
ICT Building, Auditorium Lambda
Coffee served from 12.45

Prof, Esko Ukkonen, Department of Computer Science, University of Helsinki
“Turing machines vs Diophantine machines”

Host: Ralph-Johan Back, Åbo Akademi.

Since the invention of DNA sequencing in the 1970’s, the analysis of molecular biological sequences has been an inspiring source of computational problems. Unlike most data in natural sciences, the biological sequence data such as DNA and amino acid sequences is discrete rather than continuous by nature. Hence biological sequence analysis is, in addition to fields like text processing and information retrieval, another natural application area of combinatorial algorithms for strings (stringology). A new discipline, called bioinformatics or computational biology has emerged. With the advent of high-throughput sequencing the amount of sequence data has exploded, making molecular biology research totally dependent on efficient computation. The talk will discuss some computational problems, algorithmic techniques and future goals of bioinformatics, ranging from the genome reconstruction and sequence indexing to the analysis of gene regulation.

Esko Ukkonen is a professor of Computer Science at University of Helsinki and a former Academy Professor of the Academy of Finland. He has been the director of the Academy of Finland’s Centers of Excellence in Research “Algorithmic Data Analysis” (2008-2013) and the “From Data to Knowledge” (2002-2007), as well as the leader of several other national and European research projects. He has played a major role in the development and the advancement of computer science in Finland, especially in the development of the school of algorithmic research. His research covers very diverse areas, including algorithmics, numerical methods, complexity theory, theoretical aspects of compiler construction, and logic programming. In particular, Ukkonen is a world leading expert in combinatorial pattern matching. Esko Ukkonen’s work has found applications in several areas: computational methods for the analysis of DNA sequences, information search on the Internet, information retrieval from image and music databases, and computational modeling in biology. He has published about 200 articles, including more than 150 papers in refereed international journals and conference proceedings, and several articles in Finnish media popularizing computer science.



TUCS research programme activities

BioHealth guest lecture: Dr. Vladimir Rogojin, University of Helsinki on “Cancer Related Studies in Cellular Signalling Networks: Identifying Essential Nodes Via Feedback Loops” on October 12, 2012

Link: http://tucs.fi/research/research-programmes/biohealth/


TUCS highlighted stories

Early-warning model for European banks

Peter Sarlin, a TUCS Graduate Programme student, visited the Financial Stability Surveillance Division at the European Central Bank, working on a project entitled “Predicting bank distress and identifying interdependencies among European banks”.

Read the full article: http://tucs.fi/news/article/ecb.php

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.

Read the full article: http://tucs.fi/news/article/fudan.php


TUCS GP doctoral defenses

On Thursday, November 8th, TUCS GP student Alessandro Buoni presents his Doctoral thesis "Fraud Detection in the Banking Sector: A Multi-Agent Approach" for public criticism. The opponent of M.Sc. Buoni is Professor Colin Eden from University of Strathclyde, United Kingdom. Professor Christer Carlsson will act as the custos at this public defense.
Time: 12 noon
Place: Auditorium Gamma, The ICT Building

On Friday, November 2nd, TUCS GP student Tuomas Mäkilä presented his Doctoral thesis "Software Development Process Modeling – Developers Perspective to Contemporary Modeling Techniques" for public criticism. The opponent of M.Sc. Mäkilä was Professor Hannu Jaakkola from Tampere University of Technology. Adjunct Professor Timo Knuutila acted as the custos at this public defense.
Time: 12 noon
Place: Auditorium Lambda, The ICT Building

On Friday, November 2nd, TUCS GP student Shahrokh Nikou presented his Doctoral thesis "Opening the Black-Box of IT Artifacts: Looking into Mobile Service Characteristics and Individual Perception" for public criticism. The opponent of M.Sc. Nikou was Professor Dr. Lieven De Marez from University of Ghent, Belgia. Professor Christer Carlsson acted as the custos at this public defense.
Time: 12 noon
Place: Auditorium Gamma, The ICT Building


TUCS conference list on the TUCS website

The list of all conferences that TUCS has supported in the last few years is now posted at http://tucs.fi/news/conferences/


New courses


Upcoming INFORTE.fi events

Turku 4.-5.12.2012
Speakers: Mayumi Hori (Hakuoh University), Masakazu Ohashi (Chuo University)
Organizer: Prof. Reima Suomi, University of Turku
Registrations and more information:


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:
05.11.2012 at 14:00 - 16:00, Researchers` mobility, Lecture Hall II, University Main Building
11.12.2012 at 14:00 - 16:00, Akateeminen kulttuuri (in Finnish), Tauno Nurmela lecture hall, University Main Building
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


Tiedeviestintä (2 op)
Aika: 1.11.-4.12.2012 (ks. kurssiohjelma)
Paikka: Turun yliopisto
Vastuuopettajat: prof. Marianne Liljeström ja prof. Marjut Johansson
Ilmoittautuminen: 22.10.2012 mennessä www-ilmoittautumislomakkeella (max. 20 osallistujaa)
Järjestäjät: Humanistisen tiedekunnan tohtoriohjelmat Juno ja Utuling

Aika & paikka:
*1. tapaaminen: pe 2.11.2012 klo 9.15-12.00, Porthan-sali/Maaherran makasiini)
*2. tapaaminen: pe 9.11.2012 klo 9.15-12.00, Porthan-sali/Maaherran makasiini)
*3. tapaaminen: to 22.11.2012 klo 9.15-12.00, Rekryn auditorio
*4. tapaaminen: to 29.11.2012 klo 9.15-12.00, Rekryn auditorio
Kohderyhmä: tohtorintutkintonsa loppuvaiheessa olevat Turun yliopiston tohtorikoulutettavat
Ilmoittautuminen: 18.10.2012 mennessä www-hakulomakkeella - huom! max. 6 osallistujaa (www-hakulomakkeeseen kirjatut perustelut osallistumismotivaatiosta keskeisessä roolissa osallistujia valittaessa)
Järjestäjät: Rekry & UTUGS

Philosophical, Methodological and Pragmatic Approaches to Scientific Futures Research (3 ECTS)
Time: Nov 28 – 30, 2012
Place: seminar room E323 in Minerva-building of Sirkkala campus (3. floor, Kaivokatu 12), University of Turku
Registration: before Oct 30 2012 via eRegistration
Further information: Sari Söderlund (sari.soderlund-at-utu.fi)
Organizer: Finland Futures Academy (FFA)


Courses on transferable skills at Åbo Akademi University

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:
Anmälningar: http://www.abo.fi/personal/anmalan

* Informationssökning i Nelli-portalen, 20.11 kl. 10-12, Åbo
* Webbinarium: Doktoranduppföljning, 26.11, 12.30-13, Adobe Connect*
* Hantera citat och referenser med RefWorks, 27.11 kl. 10-12, Åbo

* Handledningsgruppen och –processen, 2.11 kl. 10.00-12, Åbo
* Handledarutbildning: Slutseminarium, 26.11 kl. 13-17, Åbo-Vasa

* Rösten som arbetsredskap, 12.11 kl. 15-17, Åbo
* Genomströmningsseminarium: Smidig studiegång och snabb utexaminering – genomströmningsideal? 13.11 kl. 9.30-12, Åbo + Adobe Connect
* Adobe Connect för möten och handledning på distans 15.11 kl. 13.00-15, Adobe Connect
* Informationssökning i Nelli-portalen, 20.11 kl. 10-12, Åbo
* Hantera citat och referenser med RefWorks, 27.11 kl. 10-12, Åbo
* Rösten som arbetsredskap, 27.11 kl. 13-15, Åbo
* Bytestorg för Moodle-idéer, 30.11 kl. 9.00-12, Åbo + Adobe Connect
* MinPlan-nyheter: Skapa och revidera kurser enklare än förr! 3.12 kl. 13-15, videokonferens Åbo-Vasa
(* Adobe Connect betyder att du kan delta i kursen från din egen dator)




European Commission ICT: Consultations on directions for Future and Emerging Technologies research

As part of our ongoing effort to chart and shape the evolving landscape of future and emerging technologies, the European Commission is launching a public consultation to identify promising and potentially game-changing directions for future technological research. They are inviting, among others, scientists, researchers, engineers, innovators, artists, entrepreneurs and citizens to submit their ideas on such directions of research for future technologies before November 30th 2012.

Link: http://cordis.europa.eu/fp7/ict/fet-proactive/fetconsult2012_en.html


Open jobs at University of Turku and Åbo Akademi University

University of Turku: http://www.utu.fi/ajankohtaista/avoimet/
Åbo Akademi University: https://www.abo.fi/personal/rekrytering


TUCS GP travel reports

TUCS GP travel report: COLLA 2012 by Kashif Javed

Full name of the event: The Second International Conference on Advanced Collaborative Networks, Systems and Applications (COLLAS 2012)
Place and date: Venice, Italy, June 24th–29th 2012
Type of event: Conference

My article:

The scientific profile of the event: The Second International Conference on Advanced Collaborative Networks, Systems and Applications (COLLA 2012) conference brings researchers together from academia and industry and provides an excellent opportunity to exchange ideas and information on Cooperation and collaboration mechanisms, architectures and mechanisms, applications, inftrastructure, services, users, and tool & benchmarking.

Opinion on the best paper and its topic: In my opinion, one of the most interesting talks was given by a keynote speaker “John Terzakis”. He shared his 13 years of Intel experience in developing, writing and testing of software. He also explained how to enhance product requirements in order to decrease planning & development times, to reduce defects and to improve overall product quality with respect to collaboration.

Number of participants: Round about 300

Social events: Yes, one day trip in Venice was arranged and bus picked from novotel venezia mestre castellana hotel. In evening there was a Gala Dinner where traditional dance and music was presented.

Touristic impressions: Venice is among the most beautiful and enchanting places on earth, and any verbal description of it will probably not do any justice. There are numerous attractions in Venice, such as St Mark's Basilica, the Grand Canal, and the Piazza San Marco. The Lido di Venezia is also a popular international luxury destination, attracting thousands of actors, critics, celebrities, and mainly people in the cinematic industry. The city also relies heavily on the cruise business

TUCS GP travel report: IISSOSS by Jose Teixeira

Full name of the event: International Summer School on Open Source Software (IISSOSS)
Place and date: Como, Italy, June 22nd 2012
Type of event: Summer school

The scientific profile of the event: First summer school on open-source software as a research topic. Event provided an opportunity for students, academics, and professionals with an opportunity to learn on the latest findings in the field of Open Source Software.

Opinion on the best paper and its topic: The best presentation, was from Martin Michlmayr on open-source licensing. An topic that I usually considered boring. He introduced the tool FOSSology that automatically detects GPL intellectual property-rights violations from binary code.

Number of participants: 18 students + 10 lecturers (all male)

Social events: There was a evening social event. A dinner in a local restaurant with expertise in mushrooms.

Touristic impressions: Como is a great place, its lake (Laco di Como) where the Alps start are excellent for trekking adventures

Learning diary:
18 June: Sandro Morasca on Quality and trustworthiness assessment of Open Source Software products and Marin Michlmayr on Licensing, compliance and governance of open source.
19 June: Davide Talbi on Open Source Marketing: how to make your product attractive for the community and end users and Luigi Lavazza on Open Source support of process and product evaluation: the GQM method and the GQM tool.
20 June: Tony Wasserman on The Business of OSS and the social event.
21 June: Alberto Sillitti on Evaluation of Open Source Software Development and Stefano Zacchiroli on Grassroots Free Software.
22 June: Alberto Venturini on ERP, SCM and CRM Open Source and Davide Tosi on Open Source Testing

Presentations capturing most interest (marked to read):
Martin Michlmayr on open-source licensing.
Alberto Venturini on Adempiere – The open-source way.

Possible academic research topics (inputed on the event):
Open-source: EU tool to counter-strike USA dominance on the software industry?
Organization of OSS vs CS teams .. Planing? Deadlines? Agile? Choice? Forcing?
How to automatically map cloth pieces on videos. When people see a video and click on cloths … by time and mouse coordinates, how can we see the descriptions?
Why so few test suits on OSS communities ?
Possible entrepreneurship ventures (inspired on the event):
Exploration of the FOSSology tool, helping companies to not violate GPL code.
Implementation of the Adempiere tool for SME's.

TUCS GP travel report: IADIS ICT 2012 by Jose Teixeira

Full name of the event: IADIS International Conference ICT, Society and Human Beings 2012
Place and date: Lisbon, Portugal, July 21st–23rd 2012
Type of event: Conference (double binded peer-reviewed)

My article:

The scientific profile of the event: This is the conference where many ICT tools promoting sustainability (environmental, economic, and social sustainability) are presented and discussed. Research focus more on the human side of ICT artifact over the traditional engineering/business dominating point-of-views. Research on this effects of ICT on human beings get together people from distinct disciplines contrasting from most computer science or information-systems usual conferences.

Opinion on the best paper and its topic: Perhaps not the best presentation, but the one that directly addresses my research interests on open-source software. From Christos Bouras, Anestis Filopoulos, Vasileios Kokkinos, Sotiris Michalopoulos, Dimitris Papadopoulos and Georgia Tseliou they produce research with high implications for police-makers entitiled: “Policy recommendations for free & open-source software usage by public administrations”

Number of participants: No exact number but, we were circa 50 participants. Participation on the conference decreased a bit day after day (perhaps due to Lisboa good tourism offer).

Social events: There was a late-afternoon social event. First we went to see the town of Óbidos from where we followed to a restaurant serving tasty Portuguese food.

Touristic impressions: As Portuguese I might be biased, but Portugal in general and Lisboa in particular have an excellent tourism offer. Tourism often takes very little part in journeys to academic conference but Lisboa it's a attractive destination for academic conferences on that regard. Public transportation and food were of high quality at modest prices.

Learning diary:
21 June: Conference sessions
22 June: Conference sessions + social event
23 June: Conference sessions

Presentations capturing most interest (marked to read):
“Blind ICT student challenges at higher education: An empirical study” by Ali AlSoufi.
“Supporting young people's life management with a mobile solution” by Tiina Siitonen, Tuula Nousiainen and Marja Kankaanranta.

TUCS GP travel report: CSR 2012 by Ville Salo

I attended the conference CSR 2012 (Computer Science in Russia) in Nizhny Novgorod, Russia from July 3rd to July 7th. CSR 2012 was one of the Alan Turing Year events, celebrating the important work of Turing on his 100th birthday. Accordingly, the main invited talk by Yuri Matiyasevich was about his work, an interesting exposition of some of his less known work in number theory on the Riemann Hypothesis, which I was not aware of. The focus of the conference was on automata and algorithmics, and as the conference was relatively small (37 talks), there was only one lecture track, and it was thus possible to attend every talk.

To me, the most interesting talks were probably Mikołaj Bojańczyk's "Infinite Sets That Are Finite Up to Permutations", Prateek Karandikar and Philippe Schnoebelen's "Cutting Through Regular Post Embedding Problems" and Timo Jolivet and Jarkko Kari's "Consistency of Multidimensional Combinatorial Substitutions". It was interesting to hear a talk by Mikołaj Bojańczyk for the simple reason that he has solved many problems on tree-walking automata which I tried - and failed - to solve for my master's thesis. Not surprisingly, the talk was great (although on a very different topic), and perhaps finally opened my eyes to the great capability of logic to capture the gist of, and immensely generalize known results. The talk by Karandikar and Schnoebelen was interesting to me since the post correspondence problem has been studied a lot in University of Turku and I have given some thought to it myself. Yet, Karandikar and Schnoebelen were able to ask a seemingly very simple new question about this object, and it turned out the solution was far from simple. Jolivet and Kari's talk was perhaps the closest to my own talk in topic (although still very different), and it surprised me to hear how little is still known about two-dimensional substitutions.

The topic of my own talk was "A Characterization of Cellular Automata Generated by Idempotents on the Full Shift", and it was the only talk on cellular automata in CSR 2012. This was my first peer-reviewed paper, and one of my few papers studying cellular automata without additional structure. The characterization was one of my first results on cellular automata, and at the time of publication, it was already a year old. It was nice to finally find a publication venue for it. Inspired by the talks, I also took some time in the evenings to prepare a paper for the Russian Finnish Symposium on Discrete Mathematics 2012, which I presented in September in Turku.

Of course, in addition to the scientific program, I had time to explore the city of Nizhny Novgorod with other conference participants. None of us spoke any Russian, so there were some problems with language, but we always managed to find a way to communicate eventually. As there is quite a bit of collaboration between Finnish and Russian universities, I decided to take a basic course in Russian as a preparation for future trips. There was also an organized sight-seeing tour around the city, and I was particularly impressed by the elaborate yet serene decorations of the churches.


Latest publications at TUCS

Articles in journals (5):

Articles in proceedings (9):

Technical reports (2):