Moms being moms, sons being sons.
Pictured: My graduation from UC Berkeley.
First win on Rosalind
Rosalind is a great learning resource. Its coding challenges cover a variety of bioinformatics applications, and each problem includes a concise wiki for the interested reader. The following script is my solution to the first challenge: determining the nucleic acid profile of a single-stranded DNA sample (.txt input), returned as raw counts of each nucleotide.
#!/usr/bin/env python
”’Counting DNA Nucleotides”’
filePath = #provide input file path as string
#open source file, read data, close source file
sourceFile = open(filePath, ‘r’, 0)
dnaSample = sourceFile.readline()
sourceFile.close()
#prints a numeric count of each nucleotide in sample
print dnaSample.count(‘A’), dnaSample.count(‘C’), dnaSample.count(‘G’), dnaSample.count(‘T’)
Excellent! Thank you for sharing your response to the first challenge and for drawing my attention to Rosalind. I once wrote a script that is relevant to the second and third challenges (that you’ve also coded at your blog) but with some stricter guidelines that you can check out here. Click on the Read More link below to look at my filthy code that I’m sharing because I have nothing better to do at the moment.
Yesterday, the Nobel Prize for Medicine was awarded to Sir John Gurdon and Professor Yamanaka. I was surprised at how incredibly emotional this made me, I have believed for a while that these two have done some of the most groundbreaking and interesting research in my lifetime. John Gurdon proved a while ago that all cells contain the same genetic information and that these cells can be reprogrammed to act like specific cell types. Yamanaka proved a few years ago that mature adult cells from a mouse could also be reprogrammed into stem cells and reproduced this with human cells. This has led to breakthrough technology that bypasses the ethical dilemmas of using embryonic stem cells. Scientists can now take “diseased cells” and turn the clock back to watch their development.
The reason perhaps that this has made me feel all warm and fuzzy inside is that I have always felt Gurdon was a scientist to look up to and aspire to. His experiments are applauded as being highly sophisticated and elegant by his colleagues and anyone in research knows that academia is not a profession filled with back patting and honest compliments. He is an honorary fellow at my college and I have always heard him spoken of with nothing but fondness and admiration. Many academics have said that he is approachable and willing to help all students and colleagues with even the simplest of queries. Perhaps what I admire most of all has to do with a story one of his students told us in our first year. Gurdon wanted to go to university to study science but at school he was actively discouraged from doing so. He was told it was a waste of his time and everyone elses, that his scientific knowledge was poor and he would never achieve anything as a scientist.
I don’t know if he lacked confidence or if he simply didn’t enjoy learning facts. But what I do admire is that Gurdon looks back on this school report when things in the lab don’t go according to plan and he still wonders if that school teacher was right. I admire that someone who has achieved so much, who has an entire institute in Cambridge named after himself, is still able to take a step back and doubt himself. As a person who regularly feels that I don’t deserve to be at the university which I’m at, Gurdon has been one of the few scientists that have inspired me to think that self-doubt can be used in a positive way.
I once had tea with a brilliant geneticist whose name I won’t reveal here and he said “I’ve never wanted to be special, I just want to be good at what I do”. That’s the impression I get from Gurdon and that’s exactly what I hope for myself too.
A couple of the drosophila flies that I modified to express eye cells instead of wings. Sexy.
Remember when I did this for fun?
I also modified other drosophila melanogaster to carry different mutations, you can view some of their phenotypes at this link. Note: I’m not a fan of the names for some of the mutations (links to NPR) but as far as I can tell, the website I linked does not include those in the NPR link.
Anyway back to real point of this post, my mom called me recently to make me promise that I wouldn’t send her photos of things like this that I do in lab. She was adamant and I could sense the seriousness and chills that accompanied the thought of seeing tanother photo akin to the one above was having on her via her voice. Hah. love my mom, she’s far and away my best friend.
My other sister would text me a few a days later to ask me to send her these and other photos so that she could show them to her high school biology teacher. I felt a little cool.
Hey #obama (Taken with Instagram)
![I’ve been in class since the morning so I’ve been out of loop with the news today and then the first story I read is about how four U.S. soldiers “plotted to overthrow the government and assassinate President Obama” by purchasing $87,000 worth of “guns and bomb-making materials.” [Yahoo News]
Then it goes on to talk about how some soldiers who want to overthrow the Zionist Occupational Government enlist to “get trained and get out to brace for the coming race war.”
Hahaha Hahaha Hahaha Hahaha, I think I’m done with the news for the day.](http://25.media.tumblr.com/tumblr_m9fp7bAVH41qzs6yjo1_1280.jpg)
I’ve been in class since the morning so I’ve been out of loop with the news today and then the first story I read is about how four U.S. soldiers “plotted to overthrow the government and assassinate President Obama” by purchasing $87,000 worth of “guns and bomb-making materials.” [Yahoo News]
Then it goes on to talk about how some soldiers who want to overthrow the Zionist Occupational Government enlist to “get trained and get out to brace for the coming race war.”
Hahaha Hahaha Hahaha Hahaha, I think I’m done with the news for the day.
50% Salvi, 50% Mexi, 100% terrible at photos.
The Take-Home Final is the scourge of the testing world.
It’s true that you have all of the resources in the world available to you for the exam but if you’re anything like me, you’re going to obsess over every detail until you have to physically hand it in to the professor. These 4 sheets of paper are now my world until next Tuesday.
Finished. Although tomorrow my other professor will handout their take-home final. I also have two presentations and an exam in the next few days. This week is just awful.
Good night.
