Welcome to the international (English-speaking) blog of the Department of Computer Science at the University of Helsinki. Our blog invites views on research, education, student life, and other societal themes connected to our computer science fields. The intention is to build a forum as an open window for readers from inside and outside computer science. If you have any good ideas or articles to share on this blog, please feel free to contact us: cs-blog [ät] cs.helsinki.fi.

Assembling the Genomic Puzzle of a Butterfly

by Leena Salmela

Since 2009 when I came to work at the department I have been involved with the Glanville fritillary genome project. In this blog post I will tell about my experiences in the project.

The genome of an organism consists of chromosomes, long molecules of DNA, which can be represented as strings of A, C, G, and T. For current technology the reading of a whole genome in a single lump is not possible. Instead the DNA molecule is broken into small pieces which can then be read by the sequencing machines. Typically in a whole genome project, billions of pieces are generated and the genome is then reconstructed from these pieces similar to putting together a giant jigsaw puzzle. If the genome was a random string, this would be a rather straightforward process as the sequenced pieces are long enough to uniquely characterize a position in a random string. However, genomes consist largely of repetitions making it impossible to say for many of the pieces from which part of the genome they come from. This is like a jigsaw puzzle consisting largely of grass or clear blue sky.

In 2003 when the human genome was published, DNA sequencing was still too expensive for a single biological group to investigate the genome of a higher organism. But the technology has evolved rapidly and by the end of the last decade the new, cheap high-throughput technology was accessible to many biological researchers. However the characteristics of this data were quite different from the data used in the early genome projects like the human. The pieces were much shorter and contained more errors, rendering the old methods for reconstructing a genome impractical. It was at this time that Prof. Ilkka Hanski's group in the Faculty of Biosciences in Viikki decided to sequence the genome of the Glanville fritillary butterfly which you can see in the jigsaw puzzle below (at least if you assemble it first).

Link to the Jigsaw Puzzle

In a sense this was a pioneering project as no big genomes had been sequenced in Finland before. It was also known that insect genomes are especially repetitive and the plan was to use a mix of different technologies which was a new strategy at the time. Therefore some trouble was anticipated and we as computer scientists of the Algodan CoE were asked to join in. However, probably none of us understood exactly how challenging the project would be.

In a couple of months the first pieces of the puzzle, or reads as they are called, arrived at my desktop and the journey into the fascinating world of genome assembly began in earnest. The field turned out to be rich in both computational and molecular biology challenges. The raw data coming from the sequencing machines first needs to be filtered and then the sequencing errors are corrected to make further processing easier. The pieces are then joined into larger contiguous chunks called contigs. After this, special reads, called paired ends or mate pairs, are utilized. These reads come in pairs such that the approximate distance in the genome between the two reads in a pair is known which allows to organize the contigs into longer linear sequences containing gaps. Finally the gaps are filled by reusing the reads and utilizing the knowledge of which contigs are consecutive.

While we were struggling with the errors in the reads and the repeats of the genome, the molecular biologists had a different problem. The DNA of the butterfly tended to fragment on its own into small pieces which caused problems in producing paired reads which are crucial in handling the repeats while reconstructing a genome. All these issues were discussed in regular project meetings along with more exotic topics for a computer scientist like gathering the butterflies in the Åland islands and rearing and breeding them in Lammi.

Finally after successful production of the data and overcoming the last computational problems in early 2012, the first draft of the genome was freezed. In the end the draft genome contained over 8,000 pieces whose combined length totalled almost 390 million base pairs. Then the analysis of the sequence began to understand the biological meaning of the sequence of A's, C's, G's and T's. For me it was exciting to see what kind of biological research and new findings could be done based on our reconstruction of the genome. For example it turned out that the genes of the butterfly had stayed in the same place in the genome for a very long time. This is very different from for example mammalian genomes like the human and the mouse where blocks of genes have moved from one chromosome to another over the course of evolution. After the analysis was complete, the genome was released in 2014 to be publicly available as a resource for biological research.

Additional information:

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The CS Blog Task Force

Paba is a PhD student in Ubiquitous Interaction Group (UIx group) at
HIIT, CS Department of UH. Her research focus is on developing
interaction models to predict user interests and information-needs in
exploratory search.

http://www.kumaripaba.com/

Aaron is doing his PhD in the NODES group at the CS department. His research focuses on mobile computing and energy efficient design for multi-interfaced mobile devices.

http://www.cs.helsinki.fi/u/yding

Ella is a PhD student in the Nodes group. She is interested in e.g. distributed algorithms, real-life data mining, clouds and ubiquitous computing.

http://www.cs.helsinki.fi/en/people/peltoel/

Giulio is a Professor at the CS department. His area is Human-Computer Interaction. For more information, please find his homepage here

http://www.hiit.fi/giulio.jacucci

Tomi is a Professor at the CS department. His area is Software Engineering. For more information, please check

http://www.cs.helsinki.fi/u/tomimann/

31.08.2015 - 14:10

The Department of Computer Science at the University of Helsinki has a tradition of annual summer trip for all the staff members. This year, the TKTL staff members are invited to take a boat trip on J. L. Runeberg and spent a beautiful day in Porvoo.

For the memory, we share a set of photos contributed by Arto Wikla and Frans Ojala:

10.08.2015 - 11:00

by Kumaripaba Athukorala

Recently I got my first, first authored journal article accepted to the Journal of Association for Information Science and Technology (JASIST for short). I thought of sharing what I learnt from the journal article writing process while my experience is still fresh.

Some of the lessons might be specific to the JASIST journal. However, I generalized the details so that this article is useful to anyone.

30.12.2014 - 12:34

By Teemu Roos

After conferring with senior professors P. Myllymäki and J. Paakki, we get some perspectives into the main issues at (or with) the department over the years. The discussions are based on the CS department Strategy Seminar of 2014.

02.12.2014 - 16:13

by Leena Salmela

Since 2009 when I came to work at the department I have been involved with the Glanville fritillary genome project. In this blog post I will tell about my experiences in the project.

04.11.2014 - 23:56

Lauri Suomalainen

On October 27th, Juhani, Lirim, Ashwin and I set forth to 3rd OpenStackFin User Group meetup. The event is a get-together for Openstack enthusiasts and experts in Finland. Its main goal is to gather like-minded people to share insights and experiences about OpenStack. The event was held in the evening at the restaurant Kaarle XII. Ashwin and I were first time aboard, while both Juhani and Lirim have attended the previous two meetups. So far the meetups have been organized once every six months. We arrived to the scene around four o’clock and there were already a few dozen people gathered to enjoy food, snacks and beverages.

21.10.2014 - 12:50

Interaction Lab is initiated and founded by Ubiquitous Interaction research group in 2014 for providing a space where novel interaction in between human, computer, and the physical environment can be developed and experimented.

28.09.2014 - 16:51

by Anna Kantosalo

Computational creativity is a new and hot topic in computer science. This year I had a wonderful opportunity to participate in the International Conference for Computational Creativity (ICCC) at the Jozef Stefan Institute in Ljubljana and present my first academic paper for the Discovery Research Group. The great community and fascinating topics of the conference made me want to share the highlights of my first conference experience with all of you!

07.09.2014 - 21:22

by Juhani Toivonen and Lirim Osmani

The European Grid Infrastructure (EGI) is a federation of research organisations that provide computational resources and services to European researchers and their partners around the world. It consists of National Grid Initiatives, one of which is in Finland (http://fgi.csc.fi) and is managed by an organisation called EGI.eu.

09.04.2014 - 11:53

by Sini, local member of the international branch in the department well-being group

24.01.2014 - 21:05

By Carolina Lindqvist

20.12.2013 - 12:51

On Monday the 16th of December 2013, NODES research group organized the traditional NODES/KOPS-glögi before the Christmas holiday. (Glögi translates to 'mulled wine', and is a popular red spicy drink enjoyed around Christmas time.)

10.12.2013 - 13:35
By: Ella Peltonen and Tiina Niklander
 
07.11.2013 - 17:59

by Antti-Pekka Tuovinen

16.10.2013 - 21:04

by Kalle Viiri

 

12.09.2013 - 00:41

by Aino Sipari

Our Kumpula club buddy program is recruiting new buddies!

29.08.2013 - 14:34

Have you ever been worried about you mobile phone's or tablet's energy consumption? Do you need to charge your device every night, perhaps even in the middle of the day? It is generally known that large screens and continuous network connections eat our phones' battery faster than we really want. Our goal in the Carat project is to survey and analyze what else could be going bad in our phones' matters.

01.07.2013 - 11:39

The national yearly Computer Science event (Tietojenkäsittelytieteen päivät) is the main event of the Finnish Society for Computer Science (TKTS). The society hands out two awards every year, the best MSc thesis of the year, and the best PhD thesis, which is awarded by The Finnish Information Processing Association, FIPA (TTL in Finnish). This year the PhD thesis award was granted to Jouni Siren from our department, for his thesis "Compressed Full-Text Indexes for Highly Repetitive Collections". Congratulations, Jouni!

04.06.2013 - 14:03

Interview with Tiina Niklander

Question 1: What's your role in the union? Please introduce yourself and if possible, the current status at department.

I am a university instructor at the department. In addition to giving courses and guiding thesis a lot of my work at the department is related to guiding study planning of Networking and Services students. I also coordinate the international master's studies at the whole department.

I have been one of the shop stewards at the university for several years.  

08.05.2013 - 22:32

In early March, the Department of Computer Science and Innofactor organized a week-long Windows Azure CodeCamp for students. The course was held 1-11.3.2013, during which the students were asked to produce small-scale applications utilizing the Windows Azure platform - Microsoft's cloud computing platform for building, deploying and managing applications and services, like Amazon's AWS or the Google App Engine.

05.04.2013 - 13:15

Dear readers, this is the second interview of our TKTL group leader series. The goal is to provide an open forum for group leaders to present their latest research development, activities in teaching, project work opportunities, and general comments about our department. This time, we interviewed Prof. Giulio Jaccuci, who is leading the Ubiquitous Interaction (UiX) group.

31.01.2013 - 14:04

Prof. Jussi Kangasharju started a blog to chronicle his sabbatical year - first 5 months in Korea, then 5 months in the Bay Area in the US. He comments, "It is partly intended to show people in our department that going abroad is not a scary thing." We repost here his latest blog entry about the winter experience in Korea. For further interesting stories, check out his blog.

18.12.2012 - 13:56

Sasu Tarkoma

This has been a busy year for the networking and services specialization line and the NODES research community at the Department.  We have made the headlines from rooftop greenhouses to energy-optimising mobile apps and squeeze-based smartphones.  We should not forget the best paper awards and other mentions either. We did well in the university research assessment exercise as well. We have also strengthened the industry connections and the recent Internet of Things (IoT) research program is one example of this.

18.12.2012 - 13:42

At the end of November 2012, the department of computer science threw its Christmas party in "Berghyddan", an old building in the area where Helsinki was originally founded.

24.10.2012 - 15:13

In this month's NODES Pizza Seminar, postdoctoral researcher Suzan Bayhan from HIIT gave a presentation about "Energy Efficiency in Cognitive Radio Networks". In brief, a cognitive radio node is capable of changing its communication frequency in order to better take advantage of underutilized parts of the radio spectrum.

24.09.2012 - 17:04

On September 17th, the well-being group and the department invited our international staff for a casual coffee break for the start of the new semester.

20.06.2012 - 10:03

On a beautiful summer day, our department invited staff members to the idyllic located villages of Billnäs and Fiskars, which is about 80 km west of Helsinki, famous for their long tradition of iron works.

14.03.2012 - 19:13

by Jussi Kangasharju

(Instead of a literal translation, I've chosen to translate the meaning of the title. As the most astute of you may have already noticed, the title is not in English, but in fact in Italian and recapitulates the words of Italian Coast Guard Captain De Falco when "encouraging" Captain Schettino, the captain of the sinking cruise ship Costa Concordia, to go back on board the ship to coordinate the rescue. The intended meaning is: "Stop whining and start doing your job!")

This article is mainly me venting my frustration, since over the past year or so, I've noticed that the laziness and general lack of effort have reached completely unexplored peaks. Although this article is only my personal opinion, in the discussions with many other teachers in the department, I've heard very similar experiences on their part as well.

08.03.2012 - 11:28

by Ella Peltonen

This year the Department's Strategy seminar was organized from 1st to 2nd March 2012 in Hotel Haikko Manor near the city of Porvoo. Beautiful Haikko is known for a place of fabulous summer weddings, but it seems to be also a practical conference centre and a nice small spa. And so our two strategy days contained both working and relaxation.

08.03.2012 - 11:25

by Jussi Kangasharju

For two years, my group has conducted research on data center cooling optimizations, and as part of that work, we have had computers out on the roof terrace of Exactum for over 2 years, in all sorts of enclosures. For a full recap of our research, please see Mikko's excellent blog (which also discusses washing of keyboards in a dishwasher).

14.02.2012 - 14:13

Dear readers, the interview series of TKTL group leaders is making its debut today! The goal of the series is to provide an open forum for research group leaders to present their latest research developments, activities in teaching, project work opportunities, and general comments about our department.

02.01.2012 - 16:34

by Esther Galbrun

13.12.2011 - 16:52

by Oskar Gross

Autumn school on Computational Creativity was held in Porvoo from 7th till 11th of November. It is interesting to note that it was a landmark in the field of computational creativity, as it was apparently the first "school" dedicated on this topic. Moreover, the lectures were given by the leading researchers in the respective field.

09.11.2011 - 14:54

In autumn 2010 a Finnish course was organized in Kumpula for the staff of the Computer Science Department. After one year, we are interested in how the attendees feel about the course and if there is a demand for organizing such a course again.

Here are the comments from some of last years attendees:

"Overall I found the Finnish course very useful. Unfortunately I am spending just one year here in Finland, so I did not have a lot of time to study and practice what I learnt :)

17.10.2011 - 10:20

by Stefan Schönauer

Throughout my career the question of how to improve the internal communication and collaboration has been a topic at every institution I worked for. Here I present some of my thoughts on the topic, which are based on personal experience and discussions with several people.

26.09.2011 - 11:14

The new university year has just begun. It is an exciting time for our fresh Master's students as well as senior ones, both aiming at obtaining their MSc degree from the CS department. To provide an insight into the international part of the Master's students, we start from the recruitment statistics of new students, and then share with you five fascinating stories.

05.09.2011 - 13:36

by Laura Langohr

Last October I headed to Ljubljana, Slovenia, for half a year's research visit. Sitting in the airplane I remembered colleagues and friends back in Helsinki wondering about my plan to take a Slovene course. Even though I would stay only six months I wanted to learn some Slovene, a language only 2 million people speak.

15.08.2011 - 10:23

By Liang Wang

In the early morning on April 26, Prof. Kangasharju, Tiina and I started our journey from Helsinki to Petrozavodsk. The whole journey was quite pleasant thanks to the sunny weather. After 12 hours, we reached our destination – Petrozavodsk, a quiet and lovely small town in western Russia. Even though it was not our first visit there, it was the first time we visited Petrozovadsk in spring. Everything looked so fresh and full of vigor compared with my memory of last winter.

27.07.2011 - 11:14

We consulted a few staff members and students what they expect from this blog.

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