Picture of Birat

Hi there! My name is Birat Koirala and I like to solve problems. 

## You sound boring, is that it?
Okay, okay let me tell you more about myself. I like video editing. And playing games. And occasionally play guitar and singing badly. I like playing football and breaking ankles (figuratively, you boomers). I like chilling with my friends. I also like getting deep with it. You want to talk about why I think that life forms scale infinitely? Let's do it. You wanna talk about what makes J Cole the 🐐? Let's do it. You wanna talk about how beautiful the sunset hue on the clouds are? Let's get it.

I have a passion for learning and am constantly seeking out new challenges and opportunities to grow. Not just as a developer, but as a person. In order to do this as a software engineer however, I felt that any experience I could get with software in the real world would definitely come in handy.

So that's what I did. I applied to internships and more internships and... you guessed it, more internships. After a long year of applications, the wonderful people at [Fundapps](https://fundapps.co) reached out to me, asking if I was free for an interview. I immediately said yes and two interviews later, I had a internship offer lined up. I was on top of the world.

## So, how was Fundapps?

At Fundapps, I learned a lot of things. First and foremost was production level code. I'd barely even gotten introduced to the difference between "prod" and "dev" in my own time, so I had no idea what to expect. But, I persevered. I tried to learn as much as I could, whilst not knowing the impact this internship would have in my life.

![Pikachu Meme](https://images.ctfassets.net/jazmsg2p4oit/3DzHhU8BAghpqMBZrF5plg/5ea791750dd501538f13d552f7810ad6/image.png)

To my team at Fundapps, if you're reading this, absolute big shoutout to every single one of you. My manager, my manager's manager, and especially my buddy who believed in me, pushed me and encouraged me to keep going, no matter the challenges I faced. I had an ABSOLUTE blast. I learned a lot, which is what I wanted to do all along. I created friends and it barely even felt like work. 

I knew that my time there was potentially limited so I wanted to learn as much as I could. But also... I wanted to fail. I'm a big believer in iterating to become a better person and falling a lot lot lot of times before learning a lesson. So I got to work and went to town on..... the backlog tickets 😈. I was pushing tickets from the backlog left, right and centre. Sometimes, the tickets from backlog became bigger, and sometimes the tickets had already been fixed. But that didn't matter. 

What mattered was I got to enjoy the best of what engineers do day to do - talk to each other about how to solve a problem, and again, and again. I felt like I was a part of the company. I started off as an intern, but by the end of it I felt like an actual engineer at FundApps. That's how I know it was a success. (and also because I knew if I came back here in the future, I would be happy)

## Okay, you got an internship, big deal... tell us what happened next!
Then came second year of university, where I made many more lifelong friends than I did first year. Only in hindsight do I recollect the impact that COVID-19 had on all of our lives. It was an insane time. I also applied to more internships, I had the return offer from Fundapps under my belt and it was a place I would love to return to. But I wanted to keep learning and see what it was like at a different company. A company with a different scale of audience. Luckily enough, on a random day on March 14th I received an offer from Amazon to go to Dublin. I was ecstatic, overjoyed, filled with purpose. No words could describe how I felt at that moment because it felt like all the work I had done so far had been rewarded.

Skipping to the internship though, while the initial feeling itself was a reward the experience of moving to Dublin (for the first time) was not an experience I want to experience again (and hence, I'm moving to Dublin for the second time not the first😅 this summer). It was difficult to say the least - the housing crisis in Dublin was worse than I thought. Finding an accommodation seemed an absolute impossibility. And it was really nearly impossible.
(To be continued)

The world is a beautiful and all consuming place. So my plan is to take it slow, not get caught up in the intricacies of it all. And hopefully, have an okay-ishly renovated shed by the end of summer :)

This is an introduction to me and the type of person I am. I've tried to put as much character and "myself" into this post, so that anyone reading can virtually get to know me.

Who am I, really?

This is just going to be one of the places where I start to take down notes on what I have been doing in my individual project. It's been a tough ride up to now and I'm sure it will get more tough from here. First and foremost, the initial title I went with was as follows:

> Simulating cancer immunotherapy using an eventually consistent distributed system.

I was super happy with this title because it covered a lot of what I wanted to do. Distributed systems is something I find interesting to this day. The topic of "cancer" intrigued me because I'd always thought about it as a disease that has some cause and we can find and cure it. If this project would help me even a tiny bit then I would absolutely love that. I've always had a curiosity in biology and the medical sciences too.

![helpingWithCode](https://www.explainxkcd.com/wiki/images/0/01/here_to_help.png)

This all sounds great but I needed to make a start. I needed to find resources that would help me solve this issue. I wanted to do this step by step, in steps which I thought were calculated. I wanted to focus on the viability and the methodology of how I could **simulate** cancer immunotherapy. For this I started to read some papers online, I tried to find different ways in which I could address this problem. In doing this I came to two realisations:

1. This could turn out to be more of a Machine Learning paper rather than a distributed systems paper. I say this because the simulation requires handling multivariate data. 
2. This was a bigger project than I had initially thought. Finding papers for it were difficult and there were different branches of knowledge I had to cover before attempting to understand some relevant papers. With this in mind, I needed to boil down the question to something I can do within my viable 6-7 month period. 
![image](https://imgs.xkcd.com/comics/dubious_study.png)

Both of these realisations pointed to the same thing that I had to do. *Remove distributed systems from the question* (for now). With this my new title became: 
> Exploring different methods to simulate cancer immunotherapy

So that's where I went with it. I explored. I saw what was out there and thought about that. After a lot of research the **first** method became apparent - Ordinary Differential Equations (ODEs). 

# ODEs to simulate cancer immunotherapy
A paper I found, with title [Modeling immunotherapy of the tumor – immune
interaction](https://deepblue.lib.umich.edu/bitstream/handle/2027.42/42105/285-37-3-235_80370235.pdf?sequence=1), resembled somewhat the general "thing" that I wanted to do. Page 237 of this Journal had the following ordinary differential equations:
$$
   \frac{dE}{dt} = cT - \mu_2 E + \frac{p_1 E I_L}{g_1 + I_L} + s1
$$
$$
   \frac{dT}{dt} = r_2 (T) T - \frac{aET}{g_2 + T}
$$
$$
   \frac{dI_L}{dt} = \frac{p_2ET}{g_3 + T} - u_3 I_L + s_2
$$

where $E$ is the number of effector cells i.e. the cells in your immune system that fend your body from any harmful pathogens, $T$ is the number of tumour cells and $I_L$ is the level of cytokines. The equation, initially is quite hard to understand and it contains a lot of different variables and constants so we're going to take equation in it's simple differential form. Each equation represent the growth or decline of Effector Cell, Tumour Cell and Cytokine levels. 

> "...the cells that orchestrate the immune response use cytokines as signaling mechanisms for immune-response stimulation as well as lymphocyte stimulation, growth and differentiation." 

## So, how do effector cells and cytokine work together?
Let's break down the answer. Into diagrams.

### Step 1: Identifying Pathogens/Tumours

![Cytokine Process - 1](https://images.ctfassets.net/jazmsg2p4oit/3iJpD8oY8TWS9TObOFdRO0/9b903a363a5d50667aa172d075f28cbf/image.png)

First, the cytokine (or $I_L$) is injected into the area with tumours. The presence of $I_L$ tells the Effector Cells that there is something wrong in that area and therefore, they must deal with it.

### Step 2: Dealing with it

![Cytokine Process - 2](https://images.ctfassets.net/jazmsg2p4oit/d4HsZz8iD7RBHf2sAfy6t/82dc0a526b7eba3123fe754dda4010ec/image.png)
As you can see in the left section of picture above, the effector cells divide and grow rapidly to combat this pathogen wherever the Cytokine is located (in this case Location 2). The location of the cytokines tell the effector cells the general area of which the pathogen is located. The effector cells then attack and destroy the pathogens (and potentially, some healthy cells in the process too, eek). After they're done, that location has no more unhealthy cells (as seen in the right section of picture above).

# Okay, but now what do we do with the equation?

We use the equation, plug in some values, and see which one leads to the eradication of the tumour and which one leads to something else. Simple. Right? Not really. At the time of doing this, the first thought I had was -  *What are "some" values?* The differential equation had a number of distinct variables that needed a specific value in order to calculate the growth rate. In no particular order, these were: $E_0$, $T_0$, $I_{L_0}$, $c$, $\mu_2$, $p_1$, $g_1$, $g_2$, $r_2$,  $a$, $\mu_3$, $p_2$, $g_3$, $s_1$, $s_2$.

Fortunately enough, the same paper had some information as to what values should be fed into some of the variables.

![paperImage](https://images.ctfassets.net/jazmsg2p4oit/5qJWLpPZ6QXTVpJ0VgNEZf/565f5d6162e84e3aea74a5ff183eaacc/image.png)

However, this isn't enough. There is no indication for the values of $s_1$ and $s_2$ in this table. Upon further reading of the same paper, (on page 243) we find that:
1. The model (or the set of differential equations) considers **either** or **both** $s_1$ and $s_2$ to be non-zero.
2. $s_1$ represents the addition of **LAK** or **TIL** cells to the tumour site.
3. $s_2$ represents the addition of interleukin-2 (IL-2) to the tumour site.

> (According to Wikipedia) **Lymphokine-activated killer cell (LAK)** is a white blood cell that has been stimulated to kill tumor cells. **Tumor-infiltrating lymphocytes (TIL)** are white blood cells that have left the bloodstream and migrated towards a tumor.

![image](https://imgs.xkcd.com/comics/data_trap.png)


This is a blog about what my thought processes were, alongside links, equations and images to explain the my dissertation paper and/or processes.

My dissertation process - Individual Project

So this is my first ever post. This is extremely cool. This will be going on my website for which I will have a link that says blog post. That website will be entirely about me. For now that is all I'm gonna say. Just below this, I'm gonna test out a few things to see how they render a page. This is a test for rendering, pretty much. See you guys on the other side.
__Bold Entry__
*Italic Entry*

```java
    public static void (String[] args){
      System.out.println("This is the code entry");
    }
```

[Link Entry](https://google.com)
- First item in List
- Second Item in list

| Table     | Heading 2 |
| ---------- | --- |
| First       | First right |
| Second       | Second right |

I also wanted to test out equations:

$$
\begin{equation}
1 + 2 = 3
\end{equation}
$$

$a^2 + b^2 = c^2$

Thank you,
Birat


Birat Koirala

Who am I, really?

My dissertation process - Individual Project

My very first blog post