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How To - Determinants of Matrices

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The determinant of a matrix is very useful and commonly asked for in exams. With it, you can determine if a matrix is invertible (thus find the inverse for sure, without wasting tons of precious time in an exam) and it's a sure way to get points even if you are pretty hopeless and just want to pass

There are three basic cases for matrices, dimensions 2x2, 3x3 and dimensions 3<.
Results for the three exercises will be posted at the end.

Tipp: a matrix can only be inverted if the determinant does not equal 0 !



In the case of matrix A (2x2) the main- minus minor-diagonal formula applies; with upper left times lower right, minus upper right times lower left.


For example B (3x3) it becomes more complicated. We can apply the rule of Sarrus (Wikipedia). For that, we replicate the first two columns to the right side. Now we create the main and minor diagonals, as seen in the picture below:


After this, we subtract the sum of the minors from the sum of the main diagonals and receive the determ…

How To - Citric Acid Cycle

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The citric acid cycle is one of the central logistical hub in our metabolism. It provides oxidative breakdown for organic substances, energy by releasing CO2 and H2O from Acetyl-CoA and so on.


There are 10 basic steps to the cycle and its goal is to catalyze the condensation of Oxalacetate to Citrate.
I will list the intermediates of this reaction and their respective enzymes, as well as their components:
Citrate + Aconitase -> cis-Aconitate  (H20)
cis-Aconitate + Aconitase -> Isocitrate(H20)
Isocitrate + Isocitrate-dehydrogenase -> Oxalsuccinate (NAD+, NADH)
Oxalsuccinate + Isocitrate-dehydrogenase -> Alpha-ketoglutaric-acid  (CO2)
Alpha-ketoglutaric-acid + alpha-ketoglutarate-dehydrogenase-complex -> Succinyl-CoA  (CoA, NAD+, CO2, NADH/H+)
Succinyl-CoA + Succinyl-CoA-Synthase -> Succinate (GDP, ADP, GTP, ATP)
Succinate + Succinate-dehydrogenase -> Fumarate  (FAD, FADH2)
Fumarate + Fumarase -> Malate  (H2O)
Malate + Malate-dehydrogenase -> Oxalacetate  (NAD+, NADH)
Oxa…

Heartbeat

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Still here, still studying, still working.
I've been gone for more than a year I think, but I'm picking up at where I left off. There might be a new segment coming additionally to the Science and Travel aspect - I have lots of photos ^-^



How to - Java Interfaces and Abstrac Classes

Today's topic - what is an interface? And what the hell does that have to do with abstract classes?

As you can see, we introduce this program not as a class, but an interface. Inside the interface there are methods, which can or can not contain any kind of parameters but the bodies of these methods are empty. 
But why would you want that .__.

Look at the interface as a kind of blueprint. When you are a contractor and you are supposed to build a whole neighbourhood with 14 houses that look the same (kitchen, 2 bedrooms, 3 baths and a porch) you might not want to sit down at your desk 14 times and draw plans for every single house if they are going to look the same fucking way in the end ._.

Sure, you might want to paint one green and the other red - but that can be added later on.

So our interface is a blueprint for a type of class that should in the future be used over and over again, with the same kinds of methods in them.
Note here: once you implement an interface int a class like suc…

How To - Java Methods

Let's begin with the basics. 
In the first post we took a look at the small Program HelloWorld which printed the message Hello World out into our command line.

This was a very simple program and with a basic command, but when we write scripts or programs that calculate values, or help sorting stuff we will need methods.

We will write a program that calculates the middle value of two fixed values we give the method.


Try to read the code and understand what part stands for what:
- class name, main method, what is being called in the main method

So here again in line 1 we have a public class with the class name MiddleVal for Middle Value, then open brackets to open the class body,
line 2 contains the main method (which makes this class autonomous in itself) which also calls out method in the 3. line with 2 parameters that we give to the method.

Now we can take a closer look into line 6 - what does the method in line 3 actually do?
It's called public static int middleValue and to use this …

The New Semester - 6.

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The first week of the new semester is over.
I totally forgot that I wanted to do a post each time a new semester starts, so sorry, her it is ._.

The next 5 months will consist of me struggling against programming in Algorithmic Bioinformatics, which has a 50% homework hurdle to be entitled to take the exam at the end of the term, 
Formal Language & Complexity for which I already have a tutorial on one of the topics,
Algorithms and Datastructures, Logic & Diskrete Structures and last but not least Statistics.

Some people might wonder, thinking "hey, she was supposed to pass all those exams in the past semesters already - what a looser"
Well fuck you too :)
I am well aware that the 6. semester is (on paper) the term in which you write your bachelor thesis and start applying for the Master courses already, unfortunately not all of us make the cut in exact 6 terms.
I am where I am, like many other students too. Sure, there are those that pass every course in flying colors and th…

The ROSALIND Platform

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Hey guys, I was introduced to this fantastic platform a couple of days ago (probably would have been useful 2 years ago already).
It's called the ROSALIND Platform and is a mainly bioinformatics exercise website, where you are challenged to engage real bioinformatics problems and brainbugs.

I have started 2 days ago, and am very happy to say, I may not have made my Asian ancestors proud - but less ashamed^^


As you can see, the problems are organised in a Tree or List, from easy to tough and there is the possibility to add more problems if you come up with one yourself.


You are not bound by the system to finish off the easy exercises before the hard ones, but I would advise you to start simple. I stumbled over a couple of silly mistakes in the beginning -_- so yeah. Go for it.

The problems listed here, are form the section Bioinformatics Stronghold, but there are also others like Python Village (with an introduction on how to install and work it) and a more theoretical maths section cal…