11 Temmuz 2015 Cumartesi

9th to 11th of July 2015

Greetings world! I am Mehmed Canatan and i will be the second person to give you weekly blogs in English. I am responsible for the last three days (Thursday, Friday, saturday) out of our six working days at the Bioinformatics Summer Camp at Genkok located in Kayseri, Turkey. The first three days shall be blogged none other than my elder brother Mustafa Canatan. I am currently a student at Gaziantep University and will attend my second year there next year in the Faculty of Medicine. I am the second by-product of the marriage between a Turkish male; my father Halit, and a Turkish Cypriot female; my mother Ayse alongside the first and third by-products, my elder brother Mustafa whom i mention before and my younger brother Ahmed respectively. We as three brother were all conceived and produced in the United States of America, in Columbus, Ohio. The aim of this blog is to inform readers of the ups and downs on this Bioinformatics course-wave we are riding, so buckle down, here we go!


09/07/2015


Today we started the day off with presenting our reports, in a brief manner. Ahmet went first, and his topic was Entrez. It was early in the morning, and hence, it was a calm session. Canan (My partner) was next and she presented on Gene ontology. I was next and i was responsible for GEO (Gene Expression Omnibus). Seyt was next and he had ensemble. He connected to the site (http://www.ensembl.org/index.html) and he showed us a few features. Osman hoca also added that we could check http://plants.ensembl.org/index.html for plants. You can download full genomes from these ensemble sites. Next was Mustafa, my big brother. He presented KEGG. He visited http://www.genome.jp/kegg/ and showed us a pathway on folate metabolism. Neslihan took to the floor next and she lectured us on Pdb (Protein Database). At http://www.rcsb.org/pdb/home/home.do she demonstrated how you could download full 3D shape of proteins and even combine and interact them with each other. She also included that we required one of three specific programs to run the 3D display and manipulations. Cansu had Drugbank as her assignment, and she presented and demonstrated using the site; http://www.drugbank.ca/ on how you could even draw shapes to search for dugs on the site interface. Fatma concluded the presentations with her presentation about Uniport analysis. She showed us the features of the analysis at  http://www.uniprot.org/. Up next we took a ten minute break, and when we returned we had more coding, related and similar to what we did yesterday.



My partner Canan was responsible for presenting chapter 3 of Data Science from Scratch today. She presented up until bar graphs, and i took the rest of the job and finished off the chapter with line graphs and scatter graphs. Canan explained about how bar graphs can be used to display histograms, and compare two  variables with each other. She went into detail, explaining almost all the code functions. I did a overview of the features of line graphs, and how they focus on trends using plt.plot(). I also covered scatterplots, and how they allow the visualization of the relationship between two paired sets of data. Moreover, scattering comparable variables using scatterplots, you might get a misleading picture if you let matplotlib (http://matplotlib.org/)  choose the scale,


Later on, we took on coding which was straight forward at first. we had a number; abcd, another number; dcba, where abcd = 4(dcba), and where abcd <10000. The answer our code gave was 2178, and hence multiplied by for gives 8712. This was not initially the question however, we were originally assigned to code for when abcd =10000. we all spent some time on the wrong equation before we swapped over to the reassigned, correct version (abcd <10000). The coding takes long, at least a good forty-five minutes. and it is usually followed by a series of other assignments that we have to code. The feeling you get when your code finally works is exhilarating, but until that point it is easy to get ticked off after your rewritten code attempts do not work for 15 times in a row. These days, we always code, we don’t even have a schedule for it anymore, when ever we have time after an activity such as presentations or Minecraft, we jump to Python to stretch our finger.


We did a good bit on Minecraft today. We finished the structures of the president's building and the library, and we furnished the inside, and it really is something to marvel at. The library is made of blue building blocks, and a blue roof glass while the president’s building has a green theme to it, with a green glass roof, and green building blocks. Besides that we created a Park directly past and on the road from when you enter the University. I took the liberty to build a big pool of water. I removed the debris for the water with TNT. and filled it with water from the bucket of water item. I found out that due to miscommunication, i was tasked to the same task others were carrying out close to the library and president’s building. so basically i dug a big hole in the ground and filled it with water, and now we will probably have to cover it up. It was fun blowing up the TNT, so i guess it was worth it. Around the park, we laid down red colored building blocks and created a walking pitch, and going across the park, we created a Double helix DNA strand by digging the mold into the ground and later applying water over it. i found out about snowballs today. All i will share about them is that they truly are a great way to piss off people and get your team mates mad at you for no good reason, so i caution alert.


As a crew we had dinner outside on the lawn. It was nice and breezy, and the sun was setting. After that we surprised Mustafa with a cake, as it was hs 21th birthday! The cake had chocolate, and this really in all you need to know. After the chocolate cake, the crew packed and cleaned up and went inside for a movie, because Thursdays are our movie days. I recommended the “Inside Man”, which is about a bank heist. It has a smashing 7.6 score on IMDB! (http://www.imdb.com/title/tt0454848/)
10/07/2015


We started the day with coding. We were given the original DNA sequence of human_CDKN2A, and we were told to  replace “T”; Thymine, with “U”; Uracil. The second assignment asked us to code for the Fibonacci Sequence. It is, simply put, a series of numbers: 0, 1, 1, 2, 3, 5, 8, 13, 21, 34, ... where the next number is found by adding up the two numbers before it. For example; the 3 = 1+2, 34 = 13+21 and so on and so forth. For the third assignment, we had to find the most frequently used word from a .txt file which we had saved to the .txt file from the link; https://tr.wikipedia.org/wiki/Dolmabah%C3%A7e_Saray%C4%B1.


We got back to the pixelated world of Minecraft after lunch break. We have created a very well built campus so far, but there is still much more to build, many more tons of dirt to punch into evanesce, and that much more blocks of quartz to place down, but it looks promising. So far today we built the structure of two new faculties, went as far as fully furnishing one, the hospital and Medical faculty combination complex. For our next faculty, we are thinking of building to separate structures with a bridge in the middle. We also have a few ideas about creating a fitness center next to the lake, which will include platforms for water activities such as jet skis. If not, we might just cover the lake up, and use the space for another building.


Up next we head over to the presentations. Ahmet went first, like he usually is asked to go. “Kendi satislainizin yamyamiolun!” was his topic. All of our topic subjects are actually a page each from the book: 101 Things I Learned in Business School.He explained that we should focus on our on sales as salesperson, and he provided the example of the company Apple, and how they sell older products for cheaper, e.g. iphone 3, he only presented two minutes and twentyfive seconds, out of the minimum of four minutes, but he did improve from last time overall with slide structure and design. Fatma went next and talked to us about “her seyi cok bilen bence uzman degil”, i really liked her presentation, it was mind-opening. It was about how someone who knows everything about a certain topic isn’t actually a professional in the area. This is because knowledge is static, and without experience and wisdom to shape your actions, you really are just a bookworm. Up next was Canan, she went above her 5 minute limit, and her text on the slides were small and their colors got distorted due to the projector, but besides that she was on point. She presented on the topic of “hiring your own boss”. Seyt took to the floor next, and talked about Debt. He also had very well made slides, and his presentation was ‘A OK’, if you ask me that is. He talked about selling and buying debt, drastic increase of debt over the last few years, types of debt and how to overcome them respectively. It was eye opening, and showed me one situation i don’t want to be in later in life. I went next and presented my topic and, ...well… things got a bit tricky, since apparently i misunderstood the whole point of the assignment. We were supposed to research our topic and present about our findings. Instead of that, i extracted a fairly specific aspect of my topic, and elicited examples of it, which unfortunately led to me giving a somewhat off topic presentation, which was to my detest, misleading for my crew. Hold up, it gets worse. I also went overboard with with half a minute, and kind of made a fool of my self *Happy Face*. At the end of the day, i learned to focus more on what the topic is before i dive into researching, and i also learned to cope with presentation stress a bit more due to sensitization, so i take this failure as a success overall: it was just another lesson i need to learn, and now i have learned it...hopefully. Cansu presented next on a topic with a interesting point of view. “Malzeme bedavadir, geri hersey icin para odersin” meaning supplies (goods) are free, and everything else, you have to pay for. My big ‘bro’ Mustafa fought the tides next as he explained about the 80:20 rule, he ran out of time before he could finish his presentation, but was given a bit more to add one last example which sealed the deal (=we understood the topic, and he did successfully present it.) His slides were good, but he took too long trying to explain what all the 80:20 graph pictures ment. Not but not least, Neslihan was left to close the presentations session. Her topic’s moral was that things that take the most time are redundant; competition, jealousy, gossip, mobbing;psychological pressure, etc, which waste a lot of time in the life of most people are actually unnecessary but unfortunately unavoidable. This requires a solutions; Ethics: rules endorsed by law to create pressure free and healthy environment for daily functioning. Moreover, we also have “Ahlak”: (manners respective to the situation) which is also a code of ethics which is unofficial and not supported by law. It is however regardlessly something still expected of coworkers to a point of symbiosis between them. Afterwards, the crew jumped back onto the Minecraft server to grind some more success, because we just can’t get enough of building a dream realm.


11/07/2015


Today we started off with…, you guessed it; Coding! I  can honestly say today  we got assigned the hardest code we have faced so far. We spent a good four and a half hours pouring over this single situation. It was frustrating and nerve wrecking. Personally, i couldn’t figure it out, nor could any of our crew at first, but hard work does pay off. Furthermore, we got assigned a second part of the same situation to complete at home, that’s if you can pass the first part. In its essence, both tasks are fairly simple. We were given a sequence;


>VIT_00s0120g00270.t01|1008724|1008724|1009729|1
(ATG...ACG)


We were assigned to initially identify and present the exons between 1008724-1009729 bases, a length of 1005 bases in string form. Simple right? Secondly, after displaying the exons via Python, we had to do the same thing for the introns. This task also sounds simple. My partner Canan was absent today, so i was solo, and two heads are better than one; Hence being left with only my own head lead to my progress being hindered and minimal because Canan is the alpha coder when regarding me and her combined partnership. About the three hour mark, people started making some progress. At the end of a good five hours (yes >5< hours) a few of our crew did reach success, at least with respect to the first assignment. We invested too much time into coding, that we had to move on, hence the second part was left for homework.


Up next came the presentations by Ahmet and Fatma on chapter 5 of Data Science from Scratch. Ahmet went first, totally violating the ‘Ladies first’ chivalry act. He presented on how to describe  a single set of data. He touched on central tendencies, dispersion, median, mean and variance. He defined mean as the sum of a set of number divided by the numeric quantity of those respective numbers. Moreover, he defined variance as a measure of how far a set of numbers is spread out. A variance of zero indicates that all the values are identical. Variance is always non-negative and that a small variance indicates that the data points tend to be very close to the mean and hence to each other, while a high variance indicates that the data points are very spread out around the mean and from each other. He is getting better at presenting, showing a much better execution compared to his presentation on day one. Fatma took to presenting next. She talked about correlations. Besides the variance that Ahmet had touched on, she explained that there was also covariance. Covariance can be negative or positive. A positive covariance indicates that both functions are either decreasing or increasing in value, whereas on the other hand a negative value indicates that the functions are inverse-proportionally either decreasing or increasing. Also, She explained that correlation is measured on a scale of (-)1 to (+)1. She touched on outliers. Furthermore, she explained and example of Simpson’s Paradox; a study that was conducted and which concluded with data that people of the West coast had more friends and hence were friendlier than people of the East coast. She concluded with an explanation on correlation and causation and their relationship.


Afterwards, we took to the realm of Minecraft. Today was awesome, besides when we had to cover up the lake i made using TNT because it got in the way of our future constructions from a geographic and strategic standpoint. We finally decided on what we wanted to build next, and well, we were a little unimaginative when choosing what to build, because we built the very same building we were currently in, and simultaneously the same building our Bioinformatics summer camp would hopefully take place until the end of this one and a half month journey; Genkok. A few crew members went outside and took pictures of all four sides of the building so we could replicate it exactly in our block-made fantasy world. I used Google Maps to snap an image of the roof of the building. And then we chose the colors of the building blocks in Minecraft to represent the actual building in real life. After that we got to building! I have to say the result is almost identical to its reality copy, and left the whole crew with grins upon completion. We were super stoked,  we gathered like we usually due after a hard effort of engineering and block-placing to take a quick selfie for memory sakes, finishing the day of with joy. Compare for yourself;






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