Scripts Toolbox for Protein Art

Look at me, all grown up using git and creating websites with sphinx. Why I started all this? Well to finish a course project. And also I had to obtain better programming practices. If you want to read a fancier, longer answer including why I needed better programming practices here is your answer:

Coding is an activity feared by quite a few biologists yet it is a necessary skill to have at least on beginners level within many fields of biology. Computational biology is on the far end of those fields, as it requires more knowledge on programming than biology.

Why is programming more important than the biology in this field? Well to answer this question I will summarize my own experiences as a biologist in computational biology field before I made the decision to tame my computational skills.

I have used a computer for the very first time in 2004. I have met with terminal in 2009. I have tried to learn programming by myself. However, let’s face it, no purpose means no progress. So I it wasn’t until my master thesis that I wrote a functional script. I learned Python and wrote lines of codes in the worst possible way, perhaps and those lines gave me what I needed. All was well at that point.

I started my PhD, subject is structure & function of ligand-gated ion channels. The name doesn’t strike as something extraterrestrial. It is a protein and I’m a biologist. Besides the title, everything was and is extraterrestrial. I have learned that quite many of the data on articles were generated by in house scripts or programs. Even if there was a tool, the output was not in the format you desired. Porting 5000 data points to excel and manual clicking 100 times to get a simple bar graph was meant suicide and no thesis would be finished within my life time. I had to rely on my scripting knowledge increasingly.

I am a person who learns things on the fly and gets the job done in any possible way. Then finds a way to improve it if needed. Although this motto provided me with three articles and a few more about to be published, it also damaged my sustainability. Spending the same long hours for similar analysis was just ridiculous. And that’s why I needed to obtain better practices: version control and documentation especially.

Enjoy the Scripts Toolbox for Protein Art and watch my baby grow up (sounds creepy). Just enjoy the website.

Yay! I have got the response. I was expecting a score well below the threshold but seems like I have got a good, ambitious idea. I bet many do make it to the the threshold point. Anyways, I just need a CV boost to provide background for it for they have no excuse in giving me a 100 over 100 🙂

That pretty much decides the question for the future. Keyboard or pipette? While I have a good connection with keyboard, I need to obtain a pipette to get funding for the project.

But first things first, I need to write that thesis!!!!

Making a Change

That wasn’t so bad… I actually survived the infectious attack with the minimal possible damage, meaning in about 3 years I’ll be deaf in my right year. If I’m lucky I’ll still have a healthy left ear by that time.

I found myself wondering what I really want to do with my life after PhD. I’m seriously considering something more public. Say go help build a school or shelter… Go be a volunteer in an education park… Just go play with the kids… Take care of elderly… I don’t know if I’ll ever do any of these but it’s nice to know there are people who actually does try to make a change.

Living on One , Born Into Brothels

Just two examples came to my mind, watched recently. I guess I’ll start by not having that PhD party after all. I have these days when I get skeptical about the long chains the donations passes through. How much of that donation actually goes to the very reason of the donation in the first place? I don’t know. I never searched for the answer. Some other days it feels like you make a donation just to feel better about yourself. Well whatever days are left, in those days I think you make a change with the donations. So I’m thinking now… skip that PhD party. Host a small cocktail at SciLifeLab. Ask people to voluntarily make a donation for clean water, education, food or clothes instead of contributing to the party.

I should actually finish writing my thesis for all this to happen, of course. I’m writing just not as fast and not as nice. I hate organising my thoughts. Everything is a big network of neurons for me. Finding a path within that complex interconnected thoughts is just… sad. Not difficult, not impossible no. It’s upsetting. Is it because writing marks a change, marks an ending I wonder. Contrary to the wish of making a change for a better world, I don’t like to make a change for myself for better or worse.


Day 8 or 9

I forgot the count already. Yesterday was a lie, it is all back! The headache, the blocked ears, everything… In case of a real apocalypse, I want to be the first one dead! Surviving viral infections in 21th century with food, clean water and sewage systems is not something I can accomplish. I can’t possibly imagine myself raising from ashes to save the humanity.

Or maybe I could survive… as a zombie tough not human, or vampire. I’m eating the wrong food, maybe I need zombie or vampire food to get better 😛 (as in a joke!)

What’s Happening?

Day 7

I actually feel fine. I spent the day sleeping with high-fever. Oddly enough I didn’t have fever till today. I woke up to eat food only and drink some water. At 5pm today, I woke up again for dinner (only to realise that I have slept too much and my brain forgot how to function) with no ear pain, no blockage. Sure I still have my sinuses full and my usual tinnitus level but my ears…

The long standing problem I had with them… Could this be the end of it?

As I was told, I have bilateral hearing loss, cookie bite shaped. It’s hereditary and I should not worry about it at all. I kept it checking with this awesome program:  Hearing Test . I was convinced that after a year of no change in the level that it was something I always had, even tough it was discovered after a long lasting respiratory infection. Today for the first time my hearing did increase. I only have a dip at 2 kHz. The rest is pretty close or above 20dB.

Have I finally grown up and fighting back with those bacteria? I wonder whether that 2 kHz dip is related to a damage by infection. Let’s see if I can preserve this level.

I have the urge to write to all the doctors I have seen so far and say politely that they were wrong!


Dairy of a Survivor

Day 5, still keeping my hopes up. I’m not a zombie yet. Not a vampire either, I still don’t shine under the sunlight. I might turn into a werewolf tough, I am getting allergic to my silver jewellery. Perhaps it’s against all the jewellery not particular to silver. I’m getting a bit sick of people fighting over so called treasure.

I have come to realise that my immune system didn’t actually kick in much. I did get some IgM perhaps but IgG is not going to be produced anytime soon. Today, my right ear is fine without any medication. But my left ear is as bad as yesterday. So I will go back to pseudoephedrine and paracetamol.

I said hello to bronchitis symptoms today. How lucky I am, my larynx was spared this time. From today on I will determine a category for my respiratory infections. It is such a big part of my life, it truly deserves its own channel.

I have finished the Black Mirror series on Netflix. It’s mesmerising! It is dark, twisted and futuristic. Do not be fooled, it is today’s life with a fancier touch.

Happy Back to the Future Day! We haven’t got everything they predicted but at least some of it.

Love microbes

On the bright side of being ill, I have a chance to do Korean Drama Marathon. This time it was “Secret” and “Producers”. No I don’t recommend you to watch “Secret” unless you are sick and you just need noise to be around. “Producer” was bearable but it ended so abruptly. Watch “It’s OK, It’s Love” or “Master’s Sun” instead they are much better. Being ill also gave me the chance to level up in Diablo 3. Now that my immune system kicked in, I get headaches and feel tired.

Day 4, this time my immune system reacted on Day 4. I’m of course not counting the days where I only had a sore-throat and did everything in my power to prevent it. I tell you nothing works. If it’s gonna take over your ears, nose and throat, it will take over your ears, nose and throat. I envy people who takes one aspirin on Day 1 and they are ok the next day. This virus is quite different than the rest tough. Past couple of years, I got used to starting with laryngitis and then having all the other -itis on the side. This one decided it will just mess my sinuses and ears.

It left me in pain with completely blocked ears for days. Not exaggerating the blocked ears. My hearing was impaired. Right ear was hearing 20dB less then usual, which would place me on the age of mid hearing loss. Left ear was still on the mild range as its used to be. I usually take pseudoephedrine and I feel better after. This time nothing helped. Not to mention the pain and the tinnitus.

Now that my immune system kicked in and it’s fighting, they are a bit better. But I have a headache that is not helped by paracetamol. I have never ever had a headache not cured by 500mg of paracetamol.

Talking this long about a simple respiratory infection, as you can guess I am quite bored. I gave blood samples for genetic screening last Friday. They are going to sequence my STIM1 gene. Hurray!!! Since I got the diagnosis as TAM, my doctor looked up some articles and decided that I should get this gene screened for mutations. Well I, of course, knew about this gene all along. But I try not be a know-it-all at the doctors office. Not always helps, like during my last visit to ENT. She spent 30 seconds on my diagnosis. She has an underbite. Her tinnitus and pain must be caused by the jaw. I hate to say it but it was bullshit. My jaw had nothing to do with it. Sure I might have predisposition due to the anatomy which would include my jaw shape but tinnitus and all that problems started after long lasting infection. It’s most likely eustachian tube dysfunction. Diagnosing yourself doesn’t go beyond guess since I can’t take a CT or MRI to rule out anything else.

I should get rich and invest to the labs for the analysis of my upper respiratory infections. Or just wait for the STIM1 sequence. If there are mutations to it, it would explain my problems with them. I hate being sick. It hurts and nothing helps. I cannot even use onions for cooking when I’m sick. They burn like hell when I chop them.

Waiting room is this way!

This is one hell of a waiting time… They even placed a counter (not saying for what but you can guess). In the meantime I need to write my thesis. CounterI also have a very exciting structure to look at. The GlyR structure is out! Not the best resolution but it is in multiple states. And I’m no expert (well compared to researches studied these channels for more than a decade) but it will (not might) shake our view on LGICs. Just when I think the picture was complete, it just got more exciting!

Survival Guide to TEVC in Oocytes

Lessons learned this path month:

  • If you are working with a new compound have one control that you know the response to.
  • If you are working with mRNA, get one good stock and abuse that as much as possible.
  • If you obtained a fancy perfusion system, get a simple one in which you can just dip into the vials and prepare solutions on the fly.
  • If you ever get a response from one oocyte just record the whole damn thing… modulation, dose response curve… whatever you can think of… you may never find that response again!
  • Don’t out smart the bioanalyzer … If it says equilibrate it at room temperature for half an hour, let it wait for half an hour not less.
  • Learn not to weep over a 96 well plate full with oocytes thrown into the graveyard… actually cross that do cry over them, because you have just spent an entire week waiting for nothing.
  • If you ever let them outside, record max in 2 days.
  • Plan ahead when to inject, when to record!

Even better just stick with your simulations, don’t bother with experiments 🙂 It was so much fun last week, I manage to get concentration curve from 2 oocytes. I was ready for alcohol modulation… But no response. I tried like 20 oocytes… nothing nothing! Why o why you do this to me oocytes. I am sorry I had to abandon you and do shit loads of writing. I have deadlines, you know!