Spring term finished

The spring term has finished. Courses were pretty time-consuming this semester so I could not focus o n our research as I did last semester. Grades are not available yet but I expect them to be satisfying. I've taken Data Mining, Analysis and Design of Algorithms, Software Engineering courses.

In the data mining project, I worked on Yeast localization of proteins database and did classification&clustering analysis.

In the Software Engineering project, as I told before, I've developed a bus-timetable program JIstanbul which has both mobile and desktop versions with J2SE+Swing and J2ME. My project was selected as the best in the class. Currently, in the mobile version, the program can detect the day and fetch the timetable for that day. In the future, I'm planning to add storing time information, closest bus time, frequently used buses features.

Now I have 1 course and masters-thesis left for the next year. I'll be focusing on Robinviz in these summer days.

RobinViz Paper and School Projects

After releasing RobinViz, I focused on my school projects. I've written a Turkish Flag drawer, Conway's Game of Life and Julia Set Fractals drawer in Java and presented the latter one in the Software Engineering class.

Currently I'm developing an Optimal Binary Search Tree implementation in Python as part of my Algorithms class. I've registered for a github account and I put all my codes there.
On the other hand, I'm working on some edge bundling stuff nowadays as part of my academic work. It's really nice but complicated. I hope I can come by a good solution to our problems in our mind.

I think I'll be fixing some problems of Robinviz in the following months. Our published paper (An integrated model for visualizing biclusters from gene expression data and PPI networks) can be found here.

As part of my Software Engineering project, I'm planning to develop a J2ME application to fetch bus timetables from the Internet and display the closest bus times for you to find the best route without waiting your bus.

RobinViz Beta released

Things are going well and I've finished my first semester of my Masters. All of my grades are great and I'm just starting the second semester. On the other hand, I'm working on our project. When I joined the project in September 2009, one last step was missing. That was the Horizontal Coordinate Assignment Problem in Layered Graph Drawings. I've implemented Fast and Simple Horizontal Coordinate Assignment paper of Brandes et. al and we submitted our paper to International Symposium in Biocomputing (ISB 2010) in Calicut, India. Our paper was accepted and after that we decided to improve the GUI of our implementation. We developed a brand new GUI with PyQt4 and used the C++ code behind the scene to do the most of the scientific calculations. We published this novel software, RobinViz Beta version on http://code.google.com/p/robinviz.

With RobinViz, you can visualize PPI Networks and Gene Ontology as biclustered graphs. In these graphs, reliability of interactions are expressed with the thickness of the edges, h-value of the biclusters are expressed as node width etc. So the most important part of the data comes in front. I hope it shall be useful for all the scientists working on this subject.

This semester I'll be taking Algorithms, Data Mining and Advanced Java courses. I hope I'll learn a lot from them. By the way, while our professor presented our paper at the conference, I gave Introduction to Java tutorial lectures in his classes. That was also a nice experience.

Avatar 3D

After a long time, I went to cinema, to the film Avatar. I was not sure wheter to see this film but I wanted to taste a 3D movie so this could be a good candidate for my first 3D film.

The film was more than I expected, but not the 3D effects. It had both sorrow and thrill. For the ones who was not seen it, I won't spoil it but here's a summary.

It's the year 2154 and humans want to mine a valueable mineral on the Planet Pandora. But this mineral lies under a great tree, in which all the Pandora folk lives. So humans want Pandorians to leave their homes but of course, Pandorians won't do it. So a war begins and one human, who controls a mind-controlled avatar (Pandorian body) for diplomatic purposes, sees the fact that this is not fair and lines up on the Pandorians side. Going further, he becomes the commander of them by achieving the rank "Toruk Macto".

I felt so ashamed of being a human while watching this film. How cruel these humans are!

Research Assistantship

Again, it's been a long time since I wrote last time. Things went unexpectedly and I've found myself in a position nowhere near I imagined.

I said that I applied Boğaziçi University for masters but although all of my qualifications were well above most of the applicants, I got rejected because that I did not bring a reference letter from my thesis advisor. Well, I went to him and he was off the office so I took the letters from my other professors. I thought these letters would be enough as they even admit students with 2,77 / 4.00 GPA! So reference letter should not have been a major issue. But it seems like it was.

Meanwhile, I had some job interviews but could not find an appropriate position according to my taste :)

Then my ex-professor who transferred to Kadir Has University from Işık University (where my BSc is from) offered me a position in his funded project. I was going to do my masters in Kadir Has University and get paid for working on the project. I accepted and started working. We are working on Graph Drawing and Visualization of Bioinformatics Networks. I'm using Pardus Linux and Python for my implementation works and I'm really happy about that. Thanks to my advisor who lets me be free on choosing my tools.

Our team consists of 3 members: me, my professor Cesim Erten and my ex-school-mate Melih Sözdinler. After I joined the team, I've done the unfinished part of their work and we submitted it to a conference and it got accepted. I'm really happy about that. I'll write about the paper when it's officially published (in February 2010).

My new university is pretty infant compared to my ex but I like it. At least everybody seems to be much more friendly. The biggest problem for me is that it takes 2-3 hours to get there and that much to come back home via public transport although we are in the same city. So I'm going to school on limited days.

Fall term is about to finish. I've taken Parallel Programming from Computer Engineering (my) department and Operating Systems, System Programming courses from IT department. They are mostly homework and presentation based. I've done my presentation on Parallel Sorting algorithms last Friday and it was good.

So, I'm a unofficial research assistant from now on. Great!

Back from Carleton, graduated!

Again, it's been a long time since I wrote last time. I've been struggling with writing my extensive Canada diaries in Turkish. So I couldn't write even a word here. I talked about my exchange plans and my final project. Our final project was a late success. It was late because at the first sight, we thought it was unsuccessful. But then I found out that it is indeed successful. We managed to get an error rate of 2.25% after we applied PCA on the channels.

Before finishing the project, I went to Carleton University, Ottawa, ON, Canada. It was the 1st of January and -13*C when I got there. The weather was terrible going down to felt like -32*C. I stayed in the dorms of the university and I liked Carleton except for its dorms with cartoon-seperated walls. The system in university was both similar to and different from Işık University. In the first days, I found it difficult to talk and understand what I hear but after 3 weeks, I got used to it. Lecturers were great and they did their best to make us understand the material. They were welcoming to any kind of problem we faced preventing our studies (I would especially thank Julie Thorpe. She was the greatest instructor I've ever seen in my university life.). They were relax and I saw a nice learning / research environment.

University also provides great facilities to the students. There are over 120 student clubs and they are very active. I should admit that only Computer Society was a bit passive. They organized “Eclipse plug-in development seminar”, a faculty-student meeting, and some movie nights. That might be normal for 4 months but I get this result when I compare it with our club in Turkey.

Of course, I have to talk about Canadian People. They are very kind, respectful, trustworthy and helpful. But they won't talk first unless you start a chat. They are mostly busy people and rush all the day. But the foreigner people are more warm and welcoming. Because of that, most of my friends were non-Canadians.

Ottawa is a really pleasant city. I returned back to Turkey at the end of the April, when the best times of Ottawa had just been starting. It has a wonderful nature. Parks, green fields, waterfalls, bike paths of total 110 km... It is also very safe compared to Toronto. People, even women are not afraid to walk in the late hours of the night. Transportation is very easy. I also visited Toronto (and of course Niagara Falls) but I didn't like Toronto that much. It seems a bit dangerous.

I've been in Canada for 4 months and it was a great experience for me. Living on your own, without anybody you know to help, being obliged to speak only in English, seeing different cultures (Canada is a real mixture of cultures), meeting people from all over the world and of course examining the academic life there. I wanted to apply for Master of Computer Science in Carleton but the envelope carrying my reference letter had been opened by DHL on the way! A note was posted on the package: “This package has been inspected under the supervision of the shipper.”. Shipper seems to be the local carrier company, not my professor! So I could not apply for the masters program. Maybe I might try it later.

Among the other applications I've made, I've been admitted to Master of Artificial Intelligence program in Katholieke Universiteit Leuven, Belgium. I've been put in waitlist of Purdue University, USA but then rejected because of the limited quota. And finally Sweden central placement system has lost my documents so I was rejected as they said “you haven't finished university, you haven't taken Algebra and Programming courses...”!

Returning back to Turkey, I graduated and I applied for Master of Computer Engineering in Boğaziçi University, Istanbul. Now I'm between KUL and Boğaziçi. KUL will be more costly for me and recently we're facing liquidity problems. So it seems my next university will be Boğaziçi.

Exchange plans

I haven't written for a long time, among the reasons I can say is that blogspot is unreachable from Turkey and whenever it is reachable, it has a long response time. That's not the only reason of course. I've been very busy. I've completed my Pardus Internship and received my TOEFL scores. I've scored 105 (R:27, L:27, S:22, W:29) in iBt. That's a great score for me, I needed 92 to apply for exchange to Carleton University in Ottawa,ON,Canada. Then I applied and I was the only student nominated for this exchange agreement. I sent a course list that I'd like to take and after some iterations, they registered me to Computer Vision and Applied Cryptography with 3 additional social courses. But I will consider dropping some of them when I arrive there, figuring out their course loads and the study time requirements. I need 2 courses to take and I'll graduate when I return back to Turkey if I don't face any problems.

After the registration, they sent me the letter of acceptance and I applied for Canadian Visa with Student Permit. I've sent the application documents wednesday afternoon and my visa had come back the next tuesday! It is wonderful that they are that fast! The next step was to look for a plane ticket. I've spent my 2 days in searching for the cheapest and the best alternative and finally I've found one on http://www.ekobilet.com. The plane will take off on 1st of January and fly to Frankfurt and then Ottowa waiting me 6 hours in Frankfurt airport. My return flight is on 28th of April.

Meanwhile, I had made some research on the accomodation and decided to stay in the residences with the suggestion of some friends there. Hasan, Serhat and other people I've found through facebook has helped me a lot in deciding what to do in the preparation process. I want to thank all of them, especially Hasan. I've applied for the residences on the Carleton Central web site and specified my preferences (quiet, wake up and sleep early etc.) and they offered me a single suite Leeds residence room. Rooms are great as far I see on the net. There are 4 single rooms around a common kitchen and there are 2 bathrooms which are shared by 2 people each. The residences get open on 3rd of January and I'm flying there 2 days before so I will need to stay somewhere. We'll look at it when the time comes. But the only thing I know for now is that Ottawa is freezing cold around -19*C.

Nowadays I'm looking for the payment options for the residence fees and the health insurance. And I have started to pack up slowly. I won't bring my laptop there as I need a new one so I have to organize my files and take the important ones with me. I also started to-know, to-bring, to-do lists to avoid any surprizes on the way. Hope I haven't forgotten much to tell :)

We're now on holiday and we have already passed half of it :( Now I have to do the master application organization and study the courses I'm currently taking: Bioinformatics, Software Engineering, Computer Networks, Cultural Anthropology and the Final Thesis. I and my friend Remzi are working on the Driver Recognition project of Assist. Prof. M. Taner Eskil. I'm planning to focus on that issue in another post but as far as I can sum, the project aims to recognize the car driver by analyzing the driving features (acceleration, velocity, engine RPM, brake, steering). We're trying to do PCA on the features to find the most dominant features to reduce the processing time.

Hope to write soon! :)