Category Archives: Life as a PostDoc

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.

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

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?

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.

Haha

I cannot find any other words to describe the current political situations. Haha! One good thing that came out of Trump’s election as president… We are not alone anymore! I can’t stop giggling at what he said; can you believe it? Sweden!  The situation is no different from you-know-who saying one thing and the crowd cheering for the total opposite. I hope those crazy beings will leave us a world worth saving.

Life in Baltimore is getting better. Making progress in using Charmm, though I am not learning as fast as I would like it to be. But dealing with three countries is just too much. Taking care of taxes in Sweden, changing my address in Turkey so I can vote, filling in papers in USA… still filling in papers…

Some things just don’t make sense in this country. I know I have prejudice against the “system” here. Instead of seeing things as different, I see them as wrong. Paper sizes, how the apartment doors opens or not opens (you have to hold them), how they can deduct almost everything from my salary yet they ask me to write a check for the healthcare… I just don’t understand…

Oh I should mention that Baltimore is as expensive as Stockholm I would say. Give it a few more years and I bet it will be more expensive. There are definitely cheaper ways to live here, which is something almost didn’t exist in Stockholm. But I found those ways scary. Maybe because I think I cannot protect myself or maybe it is again the prejudice and looking down on people. I am seeing a new side of me. I just have to understand the roots of it so I can change it for the better.

Ah it could also be due to an empty house. While I get more and more things, I should, no, I will become happier. Lack of stuff certainly increases creativity; like I know now how to open a beer with a tiny screwdriver (it just takes time since I don’t have strength) or how to open a can with a knife and hammer…

Time… I just need to give myself and this city more time…

The journey to J-1

I have decided to start from the beginning. Obtaining J-1.

I am not sure if it is generally like that, but obtaining a J-1 visa was pretty easy.  That said, getting residence permit in Sweden was much easier, on application level only. In Sweden, you fill in one form, you pay one application fee, then you wait… you wait… and you wait… Where as for getting a J-1, you fill in several forms, pay fees to several places and then you get it, that’s it.

The first step is waiting for documents from the university.  They have to get this DS-2019 form. To get that form from them, you need to fill in a form. Once you have the DS-2019 form, you can go ahead and pay the SEVIS fee which is also called I-901 form. Print the proof of SEVIS fee payment and keep it safe. Then, start your visa application by filling in the DS-160 form. Keep in mind: You need to have a digital copy of a biometric photo of yours. Some photographers do offer that. If you are in Stockholm, Fuji Foto Center at Ostermalm has an excellent service.

This form is tricky. You fill out many pages of information, type in your previous travel information to US, the names of two people in your home country (not quite sure about the reason behind this request), yada yada… You pass all those stages, and you think I’m all done. Well not yet, you have to upload that photo of yours. Here comes the annoying part. Not every browser works with this website. I have tried Chrome, Safari, Opera and Firefox. I’m not sure if it was Opera or Firefox that worked. But one of these surely does. If you get a problem with the photo, save the application and try in at another browser. When you complete the application, book an appointment with the embassy. Of course you have to pay a fee for this too. At the embassy, you will provide many many more documents than DS-2019, SEVIS Fee, DS-160 and your offer letter from your new boss but won’t care 🙂 They will take only these and then decide whether or not to give you the visa at that moment. It is still good to have those documents with you though. You’ll never know what they will ask.

The embassy will send the passport via mail. In my case, it was just placed inside the mailbox. I would have preferred a more secure way but hey I have got the visa within 2 months. The whole process, including the waiting times for DS-2019 etc. By the way, the fees adds up to 300-360$.

The whole process of getting J-1 actually is a sign of how your first week will be spent. But more on that next week.