Visiting Kenya

26. February 2012, Sunday, Nairobi, Kenya

After a day of travels I am arriving to the Nairobi International Airport for my second visit of Africa, first in Kenya and as I saw on the map, first on the southern hemisphere.  I came for meetings and future-project discussions with people from the International Livestock Research Institute (ILRI). Similarly as in Ethiopia, also here I would like to note down my feelings and experiences. As in case of Ethiopia, take it as a random sample and do not make general conclusions out of it, this is what happened to me described from my viewpoint.
As I said I came for discussions, but the travel is actually bounded with the program of people coming from Swedish Agricultural University (SLU). The have already a project running in Kenya, and their goal is to visit the project sites, among others. They kindly agreed to take me along, which is a great opportunity for me to see the actual countryside of Africa. One of the SLU people is a “giant” of development research, so I hope to listen and learn as much as I can during the trip. My very first stay in Addis was mostly within the ILRI campus, so now I am going to see more diverse environments. Today we take as the arrival day with only some leisure program, the work begins tomorrow.

We arrived for a nice sunny day with daytime temperatures around 30. A pleasant day indeed, although I am quite tired after the long flight. We drive through the city on Narobi when coming to hotel and I must say that I like it more than Addis. It is much greener with more parks and nicer buildings. The signs of the British Empire are clear in the country with the driving on the left, cars with steering on the right. Our way was very fluent the whole time, but according to insiders this was due the Sunday morning drive with almost no cars. Otherwise traffic jams are quite common here as well, or so I heard. We will do quite a bit of car driving during the week, so I can tell more about this at a later stage.
 The hotel we are in is a nice one, on a good spot. Upon arrival everybody got a keycard except me. I got a normal key with an attached plastic holder with the most famous Barrack and a YES WE CAN on it. The receptionist said that it is the “best key”. Not sure what he meant, but it might be a reference to the picture. Other fun fact: When I came to the room and browsed through the tv channels, I found the opening scenes of “Out of Africa” with Meryl Streep and Robert Redford. Old, slow paced, a bit-too-long, but a reasonably good movie with most of the cast done in Kenya.


27. February 2012, Monday

Today was the first working day of the stay, spent mostly at the ILRI campus. Right at the breakfast I was asked if I brought malaria pills along. I guess this was a standard question, but I had to answer with a ‘’no”.  Then I realized that we are going to a region where there is more than a theoretical chance to get infected. It was not an issue in Addis, but in wet lowlands of Kenya it is possible indeed. Naturally I freaked out. Fortunately the Swedish “big boss” got a spare box of pills which he gave to me. As I understood you could get malaria also with the pills, but the outcome should be much less serious. I hope I can skip the experience anyway.
After arrival to ILRI we were discussing the details of the ongoing SLU sheep project already running in the country. I realized (again) that it is a huge undertaking to get information about the animals in a “developing” country. Traits and data which you expect to be there are collected, transferred and translated into digital form with a great effort. Additionally one has to think about keeping the good relationships with the farmers, hire trustworthy enumerators or deal with their eventual imprecisions.  One of the issues was that on a certain remote site the sole computer got a virus and was unusable for some time, stopping the data flow. The other issue was that one of the regions is inhabited by two tribes, and they were not accepting enumerators from the neighboring tribe. And there were lots of other issues that you would not think about in a “European” setting.  After the whole day meeting and the quick tour of the (huge!) BecA lab facilities we returned to the hotel.
Naturally we thought about dinner. The suggestion was to go outside. After a discussion of the dubious security of Nairobi after dark I felt quite uneasy., but finally we settled on a place nearby. After my dinner-burger and fries we went back to the hotel on foot. Almost immediately we got tailed by a woman offering something to sell. She appeared to be harmless except of the constant chatter, but I felt re-assured that walking outside is not the best choice.  Eventually the woman gave up, and we arrived to the hotel avoiding the many small claques on the pavement (btw. another good reason why to avoid unlit areas, especially after rains).

Other fun fact from today: After the malaria discussion at the breakfast I kept thinking about it. During the meeting before noon I was feeling very hot, and assumed to be the first signs of an illness from the mosquito from yesterday. This was until I realized that I am sitting in a light sweater in a room near the equator (about 25-30 C) and I am drinking the second big cup of coffee in 2 hours… Happens… Removing the sweater and stopping with the coffee made the trick, of course.  

28. February 2012, Tuesday

I just returned from the full day field trip, visiting sites of the sheep project. We started early in order to bypass the traffic jams and be at given times at given places. We went with 2 all-terrain vehicles, which turned to be out the only possible solution. Details later. The first part of the trip were on a newly built very good quality tarmac road. I have to mention that this road led to Mombasa, one of the major cities of Kenya. Despite of its importance there were no signs pointing out directions, at least at its newest parts. The driver knew of course where to go, but if I would be on my own I would have a 50% chance to take a wrong turn on each junktion. Crossing of major roads by pedestrians at any place is quite prevalent in Nairobi as well, similarly to Addis. But is you think the pedestrians are not the only ones causing dangerous situations. During a traffic jam I seen cars, matatus and even buses extending the road and using a proper pedestrian walkway! Just unimaginable back at home.

Also the overtaking on the Mombasa road is quite an experience. Imagine a truck going uphill with 20km/h. A second truck overtaking it, going 30km/h. A third truck overtaking the other two at the same time and just after it our jeep hoping to squeeze in… I can tell you, at some point I was rather not looking what is going on.
Finally, at one point we turned to a dirt side road, and from there on the things were getting bumpy. It rained again during the evening, so the road was full of mud, which would have caused great problems if we had any other type of car. Of course the signs were missing here as well, which is more understandable in the middle of the savannah. Although I would appreciate a “Next settlement 50 km” sign for the unaware travelers. The outcome is that you have to do your homework before trying to go somewhere around here on your own. You have landmark points though. To get to the farm of Moses, where we were heading, one has to turn right on a crossing with 3 trees. Not joking here… Literally there were 3 trees in a crossing. After that you have a bunch of unmarked crossings leading in all directions, where you just have to know where you are going. At some point I was not even sure if we are on road any more, as you could not see the car trails on the rocky ground. As I was told the layout of the roads keep changing all the time from various reasons, they might be completely erased by the combination of sand and wind and on the top of that they are completely unusable during the rainy season. If you are somewhat familiar with development issues you often hear the term “market access”. I can tell you, after today’s ride I realized the meaning and the importance behind the “access” part.

The farm of Moses consisted of a simple house and several fenced off areas where he keeps quite large flocks of sheep, goats and cattle. I knew that he was the bigger farmers, but seeing 100+ animals was interesting. The natural companion of such amounts of livestock are the flies, which were all over the place. First they bothered me quite a lot, especially when I was thinking about all the places they might have visited just minutes ago. But after some time I accepted them as such, occasionally hushing them away. We proceeded with the grading and the interview of the farmer, mainly focusing on questions such: Which are the best, average and worst animals per breed?, Why?, their advantages and disadvantages? Later on the team also proceeded with body measurements. From the works done by other guys at BOKU I was aware about certain difficulties, one might face douring the field work, but this was the first time I took part. Moses appeared to be a knowledgeable person who knew his flock very well. He is a bright example of a farmer keeping records, which is not that usual in many places even in “more developed” countries. Despite of this the answers he gave were like “I liked the dam of this animal.” “This one had two offspring in 2 years, one died.” “This one takes care of the lambs very well.” “This one has problems all the time and it is kept alive only via vaccinations.” Depending on the aim of the study these are valuable information, but it is far away from the databases I used to handle. It is very difficult to put statistics on his answers, but I think the statistics should not be the main driver of the study anyway. Animal breeding in these countries requires a very different mindset, even if the underlying goal of genetic gain is the same as everywhere else. One has to re-phrase the questions and ask what are the farmer’s needs? How can we help them with, given environment and the available resources? Tackling these questions one can give phrases such “poverty alleviation” and “food security” a real meaning.

29. February – 3.March 2012

The program of the stay continued with discussions of the results/experiences from the previous day and gearing up for the next field visit. This time it should be an area requiring about half a day travel time. I left my laptop and main suitcase in the hotel and started the two day trip with only a backpack, some food and a bottle of water.
The ride to the Amboseli area offered a snapshot of the life in Kenyan small cities and rural areas. At the beginning we took the Mombasa road again, but this time a longer part. At places where it was crossing with other roads it created its own small cities consisting from small shops selling food, car spare parts, mobile phones and all other things that people, in this case mainly truck drivers, might need. Hotels were there as well starting from the ones looking reasonably good (at least from the outside), but there where also some shacks from tin plates, apparently advertising free room capacities.
In the evening we arrived into a small place called Sultan Hamud which was very similar to other Kenyan small cities. Low profile buildings, quite clean but dusty roads. This had a mosque and several houses with satellite dishes on them in addition to the other “regular” ones. Sultan Hamud was the place where I saw the biggest contrast so far. From inside it was a beautiful hotel belonging to an Italian guy, outside the present reality of Kenya. In between a high fence with barbed wire.  It was an odd feeling walking inside the garden, looking at the hotel pool, knowing that just a few meters away there are people living in completely different conditions.

Inside of the hotel facilities...

...and the outside world.

The next day we went to visit another farm with Red Massai sheep. This area was quite different from the previous one, with traditional Massai huts loosely grouped together with a fairly large area holding the livestock in the middle. Most of the animals were sheep and goats with a few heads of cattle and a small donkey herd. I was told that the reason of such low number of cattle around in that most of the cows died during the serious draughts in the previous years. People started to re-stock just recently, which was visible from the apparent low age of cows. The draughts are also the reason why the people started to look at the milk production of sheep. The ILRI people told that the focus on milk in sheep became stronger in the recent years in an increasing absence of cattle. Also there was quite a big number of goats around, I guess also mostly for milk.
The farmer we were visiting was new in the project, so we did not know what to expect. At the end both the questions part and the measurement of the animals went quite smoothly, although it took a little longer than expected. The farmer turned out to be the elder small “village” and he asked if the other surrounding flocks could join the program. This was a very good sign that he is interested in the program. I am not sure if he was aware of the benefits that a recording and selection program could give, but in any case in the mid-long term it would definitely help them to increase production and income from their flock.

Our next destination was the place of a young Massai who understood our intentions very well. Leonard spoke perfect English, working with ILRI for some time in the past, now a leader of a small organization dealing with various issues. They provide work for a number of local people as well as supporting children with scholarships, so they can study.  He is a farmer in the sheep project, but also has a camp for tourists which we visited for lunch and discussions concluding our efforts during the week. There were several interesting moments during this visit. One of the most memorable ones was the picture of the 4 PhDs and two university professors listening to the explanations of the young Massai in the traditional clothing. It is a pity that I did not took a video during the event, so you could hear his words. If I will be around I will definitely do so.

After leaving Leonard’s place we said farewell to half of the team returning to Nairobi. The SLU group and myself went for a short tour of the Amboseli National Park, which was nearby. Well… It supposed to be nearby… Our contacts told us that it is 1 – 1,5 hours drive, which turned out to be more like 3 - 4 hours in the car. We started quite late on the usual dirt road of rural Kenya. In addition there was a light rain just before, so our progress was somewhat hindered. We, or more precisely our Kenyan recording person, had some idea about the directions, but we put him out close to his home place. He left behind some verbal instructions and a hand drawn map which should lead us to Amboseli. It was a long way, I can tell you… We were in middle of Kenya, in the dark, on a dirt road and all we could see was an occasional wildebeest. Fortunately we hit the a more strudy road before it started to rain again. Frankly, I was starting to prepare for a night in the car.
Finally we arrived to some lodges where we could as for directions and after additional 20-30 kilometers we arrived to the gate of Amboseli park. The funny thing was that we were already in the park. We probably entered it when turning to the main road, but there were zero signs denoting the border area. Of course the first question of the guard was about our non existing tickets. She was not in a good mood, and finding out that we crossed the park border illegally did not added to the friendliness either. Quite the opposite. Our driver went out for some negotiations, and returned with a very friendly person dealing with the tickets. We wanted to come to the park anyway, so the 24 hour valid tickets were a good deal for everybody. The next day we returned to see the touristic part of Kenya, the way we see it on National Geographic or other documentary channels. We could see a number of species, only “simba” was elusive on that day. It was really a great experience to see these animals in their natural habitat.

After a few hours in the park we went for a lunch and afterwards back to Nairobi. It was my last day returning to Vienna the next day.

I was leaving Kenya with a bunch of experiences and thoughts which would undoubtedly shape my thinking about “developing country” issues. After the my previous visit in Addis somebody mailed me:  “ I hope you will get to see through what is sometimes presented on the streets of the big cities--and get to see the country side--it is another life--and the heartbeat of the continent.  Come again and hopefully we will take you round further.”

That happened indeed. I went one step further with a hope that I can continue my journey.

Bland - Altman plot in R

Not so long time ago I did a comparison study of two software packages, more precisely their ability to estimate random effects. The plain approach was to do correlations among the outcomes, and if they were high I assumed that both programs are OK. I presented this to my more experienced colleagues who suggested to use Bland-Altman plots to confirm the results. This is a reasonably simple technique to measure the agreement of the two outcomes. As they say in their paper Statistical methods for assessing agreement between two methods of clinical measurement (pdf linked, worthwile to read):

In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old. Such investigations are often analysed inappropriately, notably by using correlation coefficients.The use of correlation is misleading. An alternative approach, based on graphical techniques and simple calculations, is described, together with the relation between this analysis and the assessment of repeatability.

 Simple, yet beautifull technique.

Naturally I was searching for implementartion in R. I quickly found and installed a package called ResearchMethods, but personally I thought it has very few soft tuning possibilities (e.g. scaling or color change). I went deeper and found a quite well documented page with a custom/modified R function. 

I used this one, as I could scale the y axis, so the final plot was nicer. On the other hand I also found that this particular function was written for demonstration purposes, but it had difficulties to run on other data.

For example the limits of the y axis were hard coded to -60, 60, which is quite problematic if you are interested in much higher or smaller differences (In my case on the 0.01 level...). Also the data set names were hard coded into the funtion.

So I modified the code to a more generic function like this:

BAplot <- function(x,y,yAxisLim=c(-1,1),xlab="Average", ylab="Difference") {
   d <- ((x + y)/2)
   diff <- x - y        
   plot(diff ~ d,pch=16,ylim=yAxisLim,xlab=xlab,ylab=ylab)
   abline(h=mean(diff)-c(-2,0,2)*sd(diff),lty=2)
}

 You call it as:

BAplot(testSet1,testSet2,yAxisLim=c(-0.1,0.1))

The "testSet"s are the datasets to compare, the yAxisLim modifies the scaling of the axis according to your needs. You might modify the labels of x and y axis if you wish with xlab and ylab.

R crash course

This is a follow up post for my R course held in Addis Ababa last week. You can find the description of the stay in the Inside Ethiopia (part 1) and Inside Ethiopia (part 2) blogposts, if interested. 

This post is a shorter and more practical one. I promised to multiple people to put the presentations online, so I thought I will make them available through my blog in combination with my Dropbox account. Here they are:

1. Introduction to R
2. Basic commands of R
3. Statistics and programming in R

The other links I am referring to in the presentations are An Introduction to R, the R reference card and the other variations of cheat sheets.

You are free to re use and replicate the presenations, provided that the initial work is acknowledged.

Have fun with R! :)

Inside Ethiopia (part 2)

 This is a continuation of a previous story describing my experiences in Addis Ababa, Ethiopia.

Day2 (21.11.2011): Setting the scene

I just returned from the workshop, which was going on for the whole day. As I found out this workshop is sort of a feedback to the previous activities done by people from SLU and ILRI. The participants are from all around Africa, sharing their experiences, challenges they face as well as proposals for improvement for the current situation. Most of the day was taken by these presentations from representatives of 15+ countries, some additional ones from the FAO representative and ILRI people.

Two main take home messages, at least for me, was the need for improved collaboration between countries and the need of implementation of national recording schemes, or even better: the combination of these two. I will explain more in the next few lines.

One of the major challenges that every country mentioned was the lack of funding. This is an unhappy situation that it might well appear in other parts of the World as well. In addition there is the lack of trained personal and facilities for research (e.g. molecular labs).  To come out of this the need of intensified cross country collaboration was suggested, as the countries have often common issues to deal with. The lack of finances also forces the people to select priorities they should work on. 

One of the burning issues raised by multiple countries as both challenges and suggestions for improvements was the implementation of national performance and pedigree recording schemes. A short simplified description for those who don’t know: Performance recording is to measure the production of each individual animal (e.g. kg of milk), so when the farmers could select those with high production and eventually get better animals. The performance recording is the backbone of animal breeding virtually non-existent in most of the countries presenting today. The establishment of such a recording scheme is a huge task, so this is where the across country collaboration comes in. Additionally the same breed is often present in multiple countries eventually exchanging breeding stock, so there is a huge benefit of a compatible recording system for a certain breed or species at multiple places. The other key issue is that the recording is done on the farm level, so one has to convince the farmers to participate.  So the purpose of the recording is not only to have a nice database which is eventually used for selection, but also the farmers need to have benefit from their participation in the recording, which can be either getting information on the performance level of their animals so they can compare themselves to others or a proof of a high performance which increases the market value of their animals.

From the description above I left out many details, but I hope you got a feeling about the complexity of the issues. Frankly, this is one of the most challenging goal I can imagine. 

Day 3-4 (22.-23.11.2011): Two days later

I am coming back to write this report after two days of workshop. The participants were discussing various around conservation strategies of animal genetic resources and the needs of their respective countries. The open aim of this workshop is that the participants take over the initiative and move the things forward in the region. In order to achieve this goal they were divided to small groups of 4-5 people from 2-3 countries, so they can discuss future collaborations. Although one can not guarantee that they will eventually work together, the selection of the groups and their common sub-regional interests are good reason for optimism regarding their joint work.

I have to mention that yesterday I put forward some of my thoughts on data recording, basically proposing that one should try it with a single huge push. Right after during the coffee break I was confronted by a much wiser person than myself, telling me that the procedure as I outlined would lead to failure in African context. He was even pointing out a similar case from the past. I have to admit that it was not one of my brightest moments… But at least I learnt something new.

Half of today’s discussions were devoted to computer based applications such as the Animal genetics training resource and the Mistro database. It was a pleasant surprise that our ABG Hub (my blogpost) is linked from the main page of the Animal genetics training resource.

Tomorrow is THE day for me, where I will present the R to the workshop participants. Quite a few people were already asking questions or said that they are looking forward to my part of the workshop. The presentations are prepared, so let’s see what happens…

Day 5 (24. 11. 2011): The course and beyond

Today I held my course, teaching about 20 people about the basics of R. (attach photo of the room, upload presentations in a separate blogpost). It went reasonably well with lots of questions from the “students”. Clearly they were very interested in the program as it gives a zero cost alternative to SAS. I started on with the installation and the very basic features slowly going towards statistics and data visualization. I constructed the presentations in a way that I could drop the programming part if necessary. And was necessary indeed, as I run out of time in the mid of the “statistics and visualization” part. But I have to say that we explored some of the features of R in more detail. The people were particularly interested in data loading from text files and Excel which were not covered very deeply in the initial plan. Also they asked various questions about genetic analysis, with focus on animal breeding data. I answered what I could or pointed out resources where they could find more. I guess it would make sense to make a course in R with a special focus on animal breeding and genetic analysis related issues, it was clear for me that there would be a clear interest for something like that.

Just after the lunch we hoped on a bus and went out to the town to do some shopping. Frankly, it was one of the most devastating experiences I ever had. (ref to a blog post, or some pictures to the end of this post). We visited two places in Addis. One of them was near the main post office with a bunch of small shops selling traditional clothing, small statues and such things, but clearly oriented on tourists. The other place (as far as I could guess) was a more central one with huge concentrations of jewelry shops, mostly gold and silver.  I saw a similar environment as few days ago, so I knew what to expect. There were people trying to sell various stuff which I kind of expected, but there were also small children all around, asking people for money. One can find this in any major city in any country, but the sheer numbers were shocking for me. I saw children even younger than my son alone on the streets, mothers with children on their backs, people sleeping on the streets. Just a shocking experience. I am not sure if I want to go back there again. 

What I also know is that my denial does not change anything. Why is that some people bath in money, others don’t have anything? 

Day 6 (25.11.2011): Homecoming

Yesterday ended with an unexpected twist and I saw yet another side of Ethiopia. All workshop participants were invited to a restaurant with traditional music and dances. As I steped through the door I found myself in a huge hall with low tables and plenty of people inside. Majority of them were tourists I guess. Of course there were two guards and a security check at the entrance. After the previous experiences in town I was not in a high mood to go for such a place, but since this was the last evening of the workshop I went on. At some point I was pulled up to the stage and served as an entertainment show for the rest of the guests. Apparently they liked it, as I received many congratulations from friends and strangers alike.

 Today is the packing and leaving day. Already packed most of the things, but I will fly only during the night. I will go around the campus once more and then close the chapter of my first ever visit of Ethiopia. Most likely the work will go on, as many of the course participants will re-connect via email, but for now I am happy to go home.

Inside Ethiopia (part 1)

Yesterday I arrived to Ethiopia, first time ever. So I thought it would be good to note down the experiences while they are fresh, catching the current feelings and ideas. I want to do this day by day and finally put it on my blog. 

Inside of the ILRI campus

 Day 0 (19.11.2011): Arrival

I started from my place in Vienna around 6 to catch the plane going to Frankfurt and from there to Addis Ababa. Everything went well. Surprisingly on the plane to Frankfurt I got the emergency exit place, so plenty of space to stretch the legs. The luck was not doubled on the six hour flight of economy class, but it was still ok. When we landed in Addis I had the sequence of events in my mind: I need visa for entrance to the country, collect my bag, change money and find the driver who will take me to accommodation place. But of course it turned out to be a bit more complicated.

I found the “Visa on arrival” place immediately, but I was not sure if I should collect my bag first. Frankly this was the preferred option for me, but I realized quite quickly that this is just not possible. The 2 minutes I spent with asking around caused that the queue for the visa doubled. So I went to this one and waited there. At the same time I was thinking that there is no way I can catch my bag on the belt in the next hall. But had simply no other option… After a short time I found out that I was quite lucky with the waiting time for the visa, as the number of people in the row doubled again (e.g. 4-5 times of the original queue size). I rushed through the visa procedure paying the 17 Euro fee, went to the bank nearby to change in some Euros to Birrs and then to the passport checking place, which they called “immigration office” or something like that. When queuing there for the third time from my arrival two things caught my attention (except from the huge mass of people waiting in the hall). 

The first one was a young man around 20 who was telling the people at our side of the hall where to go. The strange thing was that he didn’t wear any kind of uniform or a sign of an employee. As for me he could be any random person form the street. But obviously it was his job, as he was in front of the properly dressed officers the whole time even speaking with them. 

The other one was a sad story. I don’t know any details, just describing what I saw. There was this young lady around her 30 brought by a guard to sit down nearby. Not that she would like to flee, but she barely stood on her legs any cried all the time. Something terrible should have happened, but no idea what it was. Hopefully some manageable problem as loss of passport, or maybe she was denied to enter the country. I don’t know… But I hope they managed to solve the problems shortly after.

Back to me. When I went through the immigrations I found the belt for the Frankfurt plane with lots of suitcases on it. Obviously most of the people were like me spending long time in the queues. So I waited some time there but my bag was not appearing anywhere. Just about the time I started to get worried I found my bag on the floor in the middle with about 10-12 other bags. Just laying around. Somebody put them down and just left them. Very strange. After that point it was a clear way of finding the driver who took me to the ILRI campus where I got my room.

Day 1 (20.11.2011): First errands

This is the day I started to write this post. It is noon local time, and about 10 a.m. at home.

I went for breakfast where I met couple of other guys from the workshop. As it turned out they hadn’t changed money yet and were looking for a bank. The one on the ILRI campus is closed on Sundays so the only solution was the city, more precisely the Hilton hotel. At first I was considering if I should go with them, but then I thought I will use the free time and the company of people to see the city as well. We wanted to take a taxi, but the guy who took me the evening before appeared (bringing somebody else to the campus) so we asked him if he can give us a ride. 

At the Hilton area it is hard not to notice the bunch of guards, some just with “normal” accessories, but I saw at least one with a Kalashnikov . Then I thought, “OK, these guys are serious around here!” Of course a security check at the entrance with metal detectors. 

As almost none of the shops were opened, we went back to the campus, where is a supermarket for food and a shopping mall with various things. And yet the next surprise here: Security checks again! This time without detectors, but 2 guards at entrance and several other ones inside for a not-so-big mall seemed to be a bit too much for me. Anyway, not all the shops were opened, so this would be a place to revisit some day.

The other thing I have to mention is the general impression from the place. There is a HUGE difference between the campus where I stay and the outside world in the city. Here everything is very nice, good roads, palm trees, cafeteria and dinner place, swimming pool, tennis and squash courts. So you get the idea. 

The city outside is totally different. Judging from this car trip, it seems that the entire city is being built just now. You see huge concrete skeletons of buildings in different stage of construction. But as for me it seemed that there is much more work to be done before the first inhabitants arrive. It would not be a bad thing, but if you see really many of them along the road you start to wonder if they will be finished in a reasonable time. Maybe it is just my impression, but it seems that they started quite some time ago and struggling to finish them. 

The other major thing is the road infrastructure in the city and the driving habits. Let’s start with the driving. Imagine a highway 2 lanes in each direction separated in the middle by small raised pavement.  Our driver took the one on the right side, but he consistently drive on its left side. Then the discussion came up if the driving habits are the same as in England, to which he responded yes, that’s why he is taking the left side of the road. But this did not explain why we are taking the right side of the highway. After a few turns and small streets full of people and small shops we arrived to a major road of the size similar to the highway, but not separated in the middle. In here the driver went for the left-most lane, with a short explanation that he knows that this is strange, but this is how it goes around here. Confused? So was I.  (Note: The drives in the city in other occasions were not this chaotic, pretty much European style.  Although the drivers had no problem to stop in the middle of the street for some time creating minor traffic jams all around.)

The other difficulty a driver will face in Addis that the infrastructure for pedestrians is not well developed, non existent or the pedestrians tend to ignore it. I saw plenty of people crossing the 4 lane highway at any point. Sometimes we encountered a person in our way in every 50 meters, sometimes a person walking on the inside (!!!) lane, although there was a fair enough and much safer zone for the pedestrians on the outer side. Sometimes this was missing as well, so we had people walking near the road, or the best: a “custom” market on the side of the road, effectively blocking one lane from the 2 lane highway! No more comments… Just amazing. I really don’t understand this. At all.

The poverty (for my European standards) was noticeable on almost every step. One could see this on the clothes of some (but definitely not all!) people and on most of the small houses. I have to say that I also saw quite many middle class apartments in huge houses, so to say that poverty is everywhere would not be a fair statement. I have seen too little so far to judge this. It is a different country, different continent, so I have to see more. 

Evening update:

Just returned from the local pub/dinner place, which supposed to serve as a meeting place for people and it is also used for dinners on Sundays. I met a guy from Sudan and we ended up near the bar discussing some more-or-less serious issues. The nice addition to the evening was the Chelsea vs. Liverpool football match broadcasted live. I knew from before that people in Africa are quite big fans of football, which seemed to be proven during this evening as well. Quite a few of us watched Liverpool defeating Chelsea, which was good news for some, not so good for others. As for me I enjoyed the match and the Ethiopian beer, and rolled back to the accommodation place with the final whistle. 

Tomorrow the workshop is starting. I am quite curious about it…

The story continues in the next blog post.

Out for Africa

When I was starting to write this blog wanted to focus on more "work type" topics, mostly dealing with agriculture or animal breeding. This was the initial plan, which has slightly adapted in the meantime. One thing I was clear about from the beginning that I would like to deal with my two main interests, the advancments in technology related issues and my passion for agriculture with special interest in developing countries.

While writing this post I am thinking about the reasons behind this. Although I had little formal education in "development studies" so far, I met a bunch of people from these regions. I have in mind my former and current colleagues and friends from the BOKU office or from the EMABG. Although I have never been in those countries, they became one of my main interests, through the people I met.

So you can imagine how excited I was when I got the opportunity to participate on the ILRI - SLU - FAO workshop called "Capacity building for sustainable use of animal genetic resources"  in Addis Ababa, Ethiopia end of November this year. I was even happier that I could be one of the presenters. According to the plan I will have half a day to present the R data analysis and programming environment to the participants. I had similar (although shorter) presentations few times before, mostly for EMABG students, so I have bit of an experience with it. Although this will be a different setting and a different audience, so I am going to adapt the contents accordingly.

I was traveling quite a lot inside Europe, but this will be my first jouney outside the continent. First one goes to Africa. 

Survival Analysis - Theory and Application

Last week I experienced a summer school from the other end. Together with Hans Soelkner we gave a two day course on survival analysis focusing on its application. This was a  satelite workshop of the 19th Animal Science Days in Primosten, Croatia. The attendance was surprisingly good! :) We had 30 participants from 6-8 countries!

The view from the course venue...

As always the theory behind is important, so Hans spent the mornings with explaining the stuff right from the beginning. Afterwards it was my responsibility to turn it into practice, using the Survival Kit v6, a program package capable to analyze large databases. For those who know me the software choice is not such a surprise :)
(For those who wonder: I a involved in its development, so it is kind of an obvious choice.)

What can I tell... The course went ok, at least according to the written (and of course anonymous) feedback after the course. One thing I would do differently is that originally I planned much more for day 1, but ended up skipping half of the stuff. I could provide the basics of usage, one or two examles but nothing more. Hans warned me before but I thought it will be ok. Well... It was on the edge, to be honest.

On day 2 we started with an example repeating the approach from the previous day. This was done by the participants themselves, so I was very happy that most of them did it without any assistence, and those who required some advice got the results soon after the "early birds". So the first day was reasonably ok, I guess... After this one we continued the day with examples on including random effects and relationship matrices, eventually ending at breeding value estimations.

In overall the conference which followed aftervards was a very nice event. A number of presentations mostly from the Central/Eastern European region, providing a good overview about the work being done on participating universities.

Last but not least I would like to express my great thanks to Ino Curik and all organizers for the invitation and the very nice time in Croatia! Hope to return one day!? ;-)

Post publication note:
Attaching my Delicious bookmarks on survival analysis. More on Google...

One week, five countries

Most of the time I try to post some stuff here that might be interesting to some of you (or at least I hope). But as you might have noticed I write some “personal” notes as well from time to time, about things that I want to keep in mind or not want to forget. This post is one of the personal ones as well.

Last week I had the opportunity to visit 5 European countries in 7 daysIt was a nice experience worth to remember, so I am posting it here with some accompanying photos.

Monday: Munich, Germany – actually I was the whole previous week there on the Synbreed Summer School The lake was not integral part of the  course, but I like the photo :) My work... One of the best so far I guess...

Monday evening: Wageningen, The Netherlands – The EMABG Welcome event was running, and I had 2 presentations there. Good time! (p.s. This is the main building of the animal breeding people there, but they will move to new locarion soon dubbed as the "New Zodiac", so likely it was my last visit in this building.)

 

Thursday: Vienna, Austria – I spent the shortest time here from the 5, basically landing by plane going through the city to the train station, but it counts ;)

Thursday evening: Slovakia – home sweet home

Friday: Budapest, Hungary – finally some leisure trip with my family to the Tropicarium (said to be the biggest in central Europe) 

Sunday: Slovakia, a "ranch" neaby Galanta. Family time again :)

Next Generation Sequencing: Departure to New Frontiers

Last week I have competed the Synbreed Summer School called “Next Generation SequenceAnalysis: Practice and Departure to New Frontiers”. It was organized in Herrsching am Ammersee, Germany which is a place just near Munchen. The main organizers were animal breeding people from Technical University Munchen and researchers from the Helmholz Zentrum. 

I have to say: It was an exceptionally good summer school!

There were several thing in the course that were “out of the ordinary”, yet contributed for the course success (at least for my viewpoint).

1.       Focus on practical data handling: I liked this part very much. We went through everything, starting for the installation of the software up to imputation. It is not easy, but manageable.

2.       Usage of free software: I mean all software, including the operating system. Actually I had to install the Ubuntu Linux because of this. But now I am glad I did. The main interface is far from the command line feeling, which often keeps people from installing Linux. At least with this new Ubuntu graphical interface I had the feeling I am browsing a smartphone… Of course the things can become pretty complicated, depending on the actual aims of the user, but the basic navigation is without problems.

3.       Course given by PhD students: I was realizing this just by the end of the summer school. Not that PhD students are not good enough (in fact they were excellent), but I would expect somebody older “by default”. But I guess this was the strategy of the course to bring in people who are working with these things on daily basis,as they are the most qualified ones to introduce the techniques to us.

4.       Evening sessions: After the daily workload we often went for a beer-or-two, often ending in the billiard room. Good time! 

Except from the practical sessions there were also presenteres, who contributed to afternoon sessions. They were specialist in their fields highlighting various possibilities of sequence data. The list is as follows: Mario Caccamo and Jared Simpson on De novo assembly, Paul Kersey on Genome browsers and databases, Ben Hayes on Genomic selection, Agricultural genome projects and Perspectives of using sequence data, and last but not least Karl Schmid on  Next generation population genomics.

The list of software and other useful links:

• Burrows Wheeler Aligner - for alligning short sequence reads
• SAMtools - various utilities to manipulate allignments
• SEQanswers - all-around forum for sequencing issues. They have a wiki too with the list of most popular software. If you are into sequencing, this is the place to dive deeper. 

Be sure to check out the "World map of sequencing" too. Well... I think it displays the number of sequencers by region, consequently the amount of effort put into sequencing everything what comes around. As of August 2011 it seems that the most powerfull players are the US and China as individual states. Europe comes third if we look at total sums.