I present you Protein Art…

It is funny how I have searched for the name protein art for this website with a concept in mind and never actually work on it. Inspiration struck before, had lots of ideas and I have managed to create a masterpiece for my thesis cover but no action after that…

I finally picked up this project again. As usual a painting is done within a short time and never touched again *facepalm* But I am getting there, at least working on them longer. Maybe that’s just who I am, I have to make many different paintings to improve not work on the same painting for a long time.

As long as I do what makes me happy, there is no need to dwell on things. I have always been ok with creations that are not perfect. Things need to be just and honest. The rest is a preference and taste.

I will update the gallery as I make new ones, and maybe write stories about them later… Full versions will be on my deviantart page. Trimmed versions are in the Protein Art page.

Controlling the happiness

I do not know when one draws a line and says ‘No, the happiness you are feeling right now, is not right? Just as your sadness the other day.’ I, once, asked a psychiatrist why he/she mentioned that treating bipolar disorder is the hardest. Her/His response: How can you convince someone that they shouldn’t be this excited, and happy? How can you even identify that their happiness would be self- harming? Continue reading Controlling the happiness

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

The Pitfalls

It is ironic how easy yet difficult it is to start learning computational methods or tools. I am looking back at the first ever code I wrote in python (available at the end of my master thesis). It’s not bad at all, considering the fact that I used to, literally, hate computers in the years prior to 2009. I have used “try, except”, created classes, defined functions.

8 years have passed since I wrote that code. Although it was easy to start, how much I have progressed since then? The answer is ‘quite a lot’. Have I truly become an expert? ‘Probably not!’

Continue reading The Pitfalls

Getting Ready for BPS? Insider Tips for Food & Alcohol

You are probably making your plans, and booking your hotels for the BPS Annual Meeting in Baltimore. First things first, there isn’t a safe street in Baltimore.  I cannot name a street I have felt absolutely safe. But no, you won’t get shot every other day either. Be alert, probably take uber or bus late at night. You will be fine.

Except, if you are a woman and for some reason attract all the idiots around. People might ask to exchange clothes with you (in a very serious manner), call you a liar or bitch when you say you don’t have a lighter, men might grab your arm when you are waiting to cross the street, again men might want to lick/bite/eat your pussy, again men might yell ‘Jesus loves you’… “But you know it is not that bad.” I don’t have the best impression of this city as you have guessed and anyone who tells me this is a beautiful city should simply frak off.  No city is beautiful if I feel scared, and I am intimidated.

That said, despite the annoying experiences and my tight budget, I have been exploring Baltimore as much as I can. I have shared some of the restaurants I have visited myself in the map below. There are a few, I haven’t been to yet have a pin. Those I just had to add, you will know when you read the comments. I have a sensitive stomach, had some bad experiences. As a result Baltimore turned me into a picky eater and the bar for being a great place has increased a lot.

So many places will get a ‘Good’ mark from me at best, but check them out yourself and decide. Two places have red flags(they serve alcohol of course), you will love them, they are great. If you don’t, just drink more.

Feel free to share the map, I will keep it up-to-date till the meeting.  Wishing you all happy holidays.

A tutorial for MD simulations in Turkish

 

http://mdrehberi.proteinart.net/

It was fun, and frustrating at the same time to work with a jupyter notebook. Running it on your computer is so much fun. Thanks to NGLViewer  I was able to show the structures in a more interactive way. Writing everything in Jupyter notebook and uploading it to Github is a nice combination. The source of the frustration was trying to keep the html interactive. But found a workaround for that by rendering each cell output in a separate html window within ipython.

The resources in Turkish are very limited. I wrote this tutorial for EpiSTEM Turkiye . It is an initiative by Gozde Eskici. Our aim is to provide reliable scientific information in Turkish. We do our best to explain the scientific jargon in our posts so that anyone can understand.

The me within me that loves to sabotage

The remove command I use in the terminal… No proper backups… Working on several projects at the same day, simultaneously… Several terminal windows, several desktops… I can almost hear you screaming ‘Nooooo! This is a recipe for disaster! ‘ .

It was.

After all that struggle with many stupid things and the rush to get data (not to mention the idiotic mistakes that was made way before and during the rush) in March-April, I have spent the entire May to clean up the mess that was left from previous months. I have thought finally in June things would go back to how they were. I would just work on getting healthy data and finalize the atomization (no no not making an atom bomb here, just trying to type automation) of the parameterization for Drude force field… I did it again.

The me within me decided to sabotage me again. One thing led to another and long story short I have removed the scripts folder that was at my home directory. This folder held all the changes that I have made to the pre-existing scripts in the lab, and all the scripts&inputs I have prepared for everything that I have done/will be doing for the past 1.5 year and the remaining time in these projects.

I cannot even say that “I still have the brain that created those scripts, I’ll work day and night and to rewrite them”. Because I am not even sure if my brain is mine truly. It was after all with that brain I have removed that folder and didn’t take regular backups.

Make the time to create backups! I wouldn’t be crying now if I had a proper backup routine. I wish my body also had some backups. I would love to restore myself back to June last year. Absolutely everything is just going downhill ever since.  Restoring that month would be a good fix.

Why do science?

I haven’t felt this much before. Perhaps I was inexperienced or didn’t know how to relate to others. This year’s Biophysical Society Meeting while browsing the posters, I have sensed this fear of those few presenters. I know the topic they are working on, which I shall not disclose here, is quite hot because more roles were identified for that particular complex. It is one hell of a drug target. I understand the need for secrecy, yet I cannot help but to question why do we do this?

Why do we do science? Is it for the sake of saving lives? Is it simply the need to satisfy the thirst for knowledge? What is your reason to become a scientist?

Continue reading Why do science?

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