INTO THE UNKNOWN: BioInformatics

 Step in the right direction

For as long as I can remember, I used to enjoy maths. 

Also for as long as I can remember, I used to think ''golly-I'm bad at maths''

Perhaps the paradox was because of the 'maths' I referred to. I loved the process of reasoning, of logic, of following patterns and applying rules. 

I loved mathematical puzzles and thought experiments, and digging into highly abstract mathematical concepts.

And yet I was bad at maths. Well, by typical people standards maybe I was okay at maths, but in my mind (I am working on this) I thought I was horrible. By about Y5, I was doing the UKMT final, and I knew in my mind I wouldn't have been selected or won the previous rounds without some aptitude, and yet all I could think was 'I'm the imposter, the other people deserve to be here and I'm here out of pity'. 

My maths ability was quite strong relatively up until Y9, and that's when I started really being knocked by my anxiety and it started actually affecting my work. Coupled with the lockdown during my GCSE years, I had actually started slipping in grades (still relatively high, but for me, back then, and maybe to some aspect still today, anything less than 100% and A*s was a failure). I did manage to recover for my GCSE and despite not being proud in the moment, I am proud looking back after immense challenges that I did achieve an 8 in the GCSE, even if my mind still whispered 'but it wasn't a 9!'.

PS: for readers, England has a 1-9 system for GCSE exams, taken at around age 16 before the final exams pre university. 8 is an A

But the reason I am talking about maths, and the feelings alongside it, is because I have always put off bioinformatics and computational biology out of fear.

I LOVE all aspects of learning biology, but with my love for patterns, and my need for some remote opportunities, you would think some kind of data analysis would be the obvious choice. When I was younger, excel spreadsheet manipulation and learning new coding languages and making clumsy websites excited me- now I almost don't try because I'm worried they won't  be 'good enough'.

But I love this quote:

''Any first draft that is ever made is perfect, because a first draft need only to exist to be the best ever made''

Perhaps  if more of us took on that mindset, especially in projects that scared us, we would all learn so many new skills and create so many more fantastic innovations in the world- but alas, self doubt and imposter syndrome can befall us all.

I know of the importance of practice in nearly any domain, but especially maths and computing. It is less 'memorise these facts' and more 'learn which websites will have the facts' (hint: stack overflow, social media computing forums, lab manuals for programs, etc are always good). It's almost a stereotype in programming that everyone just copies each others' code and mixes and matches to get what they need (and it's useful and celebrated if credit is given). And yet, my idea of 'I don't know but let's look it up' can be useful for when I learn about biological concepts, or psychology, history, pretty much anything else.. and yet in maths I think 'I don't know so I will never know so I am a failure'.

This may be getting too personal and yet I think it's an important message, not just everyone, but especially researchers, scientists and academics are more prone to that negative self talk and black and white thinking. I always found it helpful when my role models discussed their own experiences of failure, rejection or imposter syndrome- so I commit to trying to do that for those who may benefit from my (select) openness.

So today, I decided to 'eat the frog' (a process of doing tasks you put off first/early in the day to reduce anxious anticipation and make everything else seem easier- on the idea that you have to eat a frog and some ice cream... it's weird but it kind of stuck in productivity vocab spaces). 

I (credit once again to the amazing list by Sofya https://necessary-eggplant-cd9.notion.site/Bioinformatics-Fundamentals-101-6cd2f726cdb442e6932d1d868f5d3e10) started today. And failed. At about the first step (installing the right software). And tried again. And failed again (who knew there were so many T&Cs for python??), and tried again, and succeeded (yay!), then failed (turns out check you added admin commands before you install everything), then tried and something worked (kind of), then something didn't (uhhhhh why). But eventually, I did get the first part up and running (downloading some R and Python, the Bash and Git programs, opening up the Unix lesson 1 instructions and completing 'Introduction to Shell Commands').

Let me tell you... it is not easy failing, but it is even harder to try again when you are beating yourself up. If I focused only on the failures (crashes, errors, 'invalid commands', more errors, 'file not found', invalid command... did I mention 'invalid command'), I would not now know the (very very very) basics of using a command line interface to navigate directories!!

And in simple terms it means instead of graphics (like clicking on your computer), you use text (Writing commands) to move around your files and documents.

Anyway, this blog post is to show that you can go from 'what is a command line' to 'i think i vaguely know what it is but now what do i do with it and how?' (and maybe one day to 'pssh, command lines, easy!' or 'I have invented a new command line' -- which I don't even know if that's possible but we shall find out!!)

So join me next time (whenever that is.. may be today, maybe in 3 months) for adventures into the unknown world of bioinformatics. And please be prepared to fail when you start, because the best projects are the ones that you just jump into.

Be kind and stay curious,

Sofiia

Below is more content bioinformatics stuff so only read if you're interested

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Now, for someone brand new, this may be wrong so cross reference or learn yourself via the linked resources... but I thought posting some new things I've learnt would build some accountability plus a way to look back and see how far I've come (who is betting that I can successfully make a data graph via CLI by 2025.... we shall see)

These commands may be different, wrong or just absolutely incorrect- so read at your own peril (and please comment/email to let me know as I'd love to learn)

cd : current directory

cd (name): go to that directory (whether an absolute path like /root/Users, an absolute path on W11 C:/root/users or relative Desktop

cd.. : go back to the parent (where the current directory or file is located in)

cd - : go back (sometimes this means up, but just means return to prev so if you did it twice you'd go in a loop)

cd / : cd root

sudo : super user do, means use admin privilidge

whoami: some info on your account

pwd: print working directory, tells you where you are in your files

ls : list

$ is usually in the Bash interface before your input text, and / is a separator if in your text and / means root if in the command unit

Paramaters and Switches (or options?? I don't know) are next on my list to learn (told you I was on the basics!)

Tomorrow I will be looking up these and will post (eventually, I've learnt not to overpromise)

-F (I think show details), -rt (show in non alphabetical but chronological update order in reverse), -h (make human readable), -a (show hidden files??), --help (I've used this one a LOT)