Category Archives: Life as a PhD

Dear PIs

Disclaimer: The term principal investigator is used synonymously for head of the lab/mentor/manager/… you fill in the blanks!

I wanted to start with “No need to state the obvious…” yet it seems no matter how many times the obvious is stated in academia, things doesn’t seem to change. Perhaps it is my expectations that is too high. But how can I not expect the most from a profession that is supposed to learn from the past experiences? If repeating and learning is in the core of science, and science is in the core of academia then the logic dictates that it is also in the core of academia.  It is not though, isn’t it?

Continue reading Dear PIs

OMG It is real!!!

It is truly happening! I am defending my thesis. June 1st, I will give my presentation a test run. June 13th, I will defend for real.

I am trying not to freak out about it despite me having hearing loss, essential tremors, anxiety, IBS, GERD, tinnitus, ear pain, muscle pain and all that jazz to top up my nervousness. Focusing on my beautiful thesis cover is my only option to calm down. It did work for today, but let’s see what will happen tomorrow. Continue reading OMG It is real!!!

Panic mode: ON

Everything is fixed for the dissertation and I will be in panic mode for the next six weeks.

Luckily I know how to fight the chaos. With chaos! I bought kinect and dance central.  I don’t think I will rock the dance floor anytime soon but the pain on my muscles after playing the game will certainly create a distraction.

Oh and I still don’t know if I have a mutation in causing this long and painful cramps and sore muscles, because the last blood sample was not for the genetic test it turned out. She just ordered a test for liver function or something like that. I actually don’t know the results of that test either.  I hate the medical systems, not just here but everywhere. You have to talk to many strangers. There are days I can’t talk to people I know over the phone, but I have to call and talk to strangers. Brrr… I will just wait until I get another appointment from the doctor, she would get in touch with me if the results were not good. For the genetic test I have to wait a little longer.

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.

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.

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!

Lots of ‘Oh no! I didn’t finish the project!’s and ‘Why?’s …

Starting to feel like my brain is the crazy one here and there is actually nothing wrong with my body. Now I’m suffering from knee pain… I have been standing a bit more than usual, but so what! You don’t have to punish me for several days for that. I got the message already.

I came home early because of the pain with little motivation to finalise the analysis on GluCl, I decided to finish the project for the course ‘Software development toolbox‘. The course was very useful. I actually think I would do two PhDs within 5 years, if I had learned and applied all that. I probably should fail the course for delivering the project awfully late though.

Regardless for now I should focus on finishing the project, otherwise I’ll never start using github and I’ll never create proper documentation.

Here is the link to the project’s website: stb.proteinart.net .