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!’

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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?

Testing the speed of sun-acquired redness under the sun of San Francisco

It’s fast ladies and gentlemen. I can no longer tolerate sun! Why? When? How exactly this change happened but I can no more brag about not getting red from too much sun.
Is it 7 years living in Sweden that altered my skin? Or because I was bragging too much that my body wanted to teach me a lesson? No matter the reason I have to become best friends with the sunscreen. Now I’m off to the conference venue.

Baltimore Communities and Bridges

This is a question I have been asking to myself. What is there to like in this city? When I say I’m giving it time but probably Baltimore is not the city for me, my dislike is directed towards not-so-good public transportation, not feeling safe, the invasive interactions (if someone’s t-shirt has a brand label sneaked out and displayed itself publicly, it is absolutely nobody’s business to touch me and turn that label back inside), and the culture of peeing on the street (not the homeless). When I find more and more things to dislike in the city, how some people could find more and more love here?
The answer was simple as I have learned yesterday. Community, support, friends like family. My airbnb host when I came to Baltimore is an amazing woman who has a great taste in furniture and a big heart. She has lived in several cities, but chose Baltimore as her home. Her reason to like Baltimore as I understood from her examples was the community she has formed here. One might say as a counter argument if you want you can form that community anywhere in the world. But that argument doesn’t work. Why?
She has a big heart; empathy and healing powers, the best I can describe without invading her privacy much. The conversation that took place at last night’s Friendsgiving dinner was not meant for public, so I have to do my best to convey the message without specifics. So to give an example, I see the bad in any situation and get frustrated, blame myself or others and leave at that. But she tries to understand, she listens without judging. She builds bridges as she put it. That is her role in this life. She also accepts that everyone has a different role to play, and if you have a more aggressive approach to solve a problem that approach is not to be destroyed but to put in use for the situations that calls for it.
Taking into account the fact that she is a person that builds bridges, she should be able to form that community anywhere in the world, shouldn’t she? But she chose Baltimore for this, or rather Baltimore allowed for that community to be built. Not any other city. Baltimore. Perhaps there are some truth in her words. Perhaps Baltimore is a city full with people that supports each other, one just has to give the chance.
The question is now this: Am I ready for it? Am I ready to allow people to my world? Am I ready to invite people to my house, my temple and watch it to be filled with different opinions? Am I ready to be healed?
Some things are difficult to be rid of. For example my philosophy is any women who has/had access to knowledge should stop following/believing religion. This is a very aggressive argument. It is an all-out attack. I strongly believe that women are better off without religious craps. Can I find a way to phrase this not in an offensive way? I formed this argument after many years with the idea that it would make them question what they believe. It is not something I can give up easily. I came to like its offensive nature (yes I am evil sometimes). Am I ready to trade this argument to create space for those bridges?
No, not yet anyways, not this argument. But there is something to learn about building bridges. Hear, listen and understand before judging. Now that, that is something I can work on. Perhaps while I learn to do that I will find myself a community to love, support and be supported. Who knows maybe I will end up making Baltimore a home to myself.

Still Alive

It is hard not to keep laughing at the recent events in both Turkey and USA. Not because it is funny, but simply because there is nothing left to do besides laughing hysterically. I hope that there will be some countries left on the face of the earth in the upcoming years. Sure as hell, Turkey as in my imagination will not be there. It is already gone.

Trying to cheer up but geez it is tough. I still don’t like this city but I’ll be around for a little more for sure (being another year or two). I have come back from shopping and wondered once again why I am just not paying over 120$/week to Blue Apron & Hello Fresh to avoid it completely. Even ignoring doesn’t help in this city. I really don’t understand how things got this bad in this city. It is not the poverty I am talking about. To give an example, there is a culture of peeing in the streets. No! Not only the homeless does that. It is difficult to see what this city has to offer when I just feel fear walking down the street. Sure, Istanbul wasn’t superb, but I am not living there am I?

At least research is progressing. It is a slow progress, but I have completed the parametrization of my first molecule. Confession; I am close to be finished Getting used to analysis in charmm, learning to work with SAXS data, … and many more things. Some analyses are just too slow in CHARMM, like counting waters. But other things are nice. Being able to select the residues on the fly and not dealing with an index file for example is heaven. Parametrization is easier… I repeat easier.

I should find the time to update the toolbox and put up proper references to the scripts. Quite a few of them are based on Samuel Murail’s scripts I have inherited. Now I am inheriting quite many scripts from Justin Lemkul. Aa, I don’t think I have mentioned that I had work with him for a short while before he moved on to Virginia Tech. If you have used GROMACS, then you have definitely heard of him. It is safe to say he is one of the celebrities in the field 🙂 Rumor has it he is looking for postdocs if you are interested.

October… It is that time of the year again. Nobel Prize announcements, BPS abstract deadlines and my birthday. Unfortunately, this year too I won’t get to celebrate it. However, this year’s gift to me is the trip to San Francisco, and the BPS conference. I will submit my thesis cover painting to the image contest. When I dream too much about something, it doesn’t come true. Nevertheless, I shall see if I at least make it to the finals.

Entertainment Parks

Found one other cause for the long-lasting muscle cramps. Entertainment parks… Being afraid of the roller coasters, and long waiting times of course two of the reasons. It was fun at least, but the cause is noted so next time I’m prepared.

Hershey Park is a fun place to be in summers for sure. The scaredy cat I am, I tried only two-three rides. The boat shaped slide is the best! It is way better than those roller coasters. There are maybe two not so bad roller coasters you can take. The rest is crazy!

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