My First Rotation

     I'm giving my first poster talk of my graduate school career tomorrow, along with approximately half of my cohort (the other half had their posters today). We are supposed to present what we accomplished over the past 10 weeks, during our first rotation. Though I understand that the real purpose of this poster session is to practice our communication skills and have the to opportunity to see what our peers have been doing, it's still mildly frustrating to feel like you don't have enough material to work with. Let's be honest, it's basically impossible to do enough novel research, in a field you're new to, in 10 weeks, to adequately fill an entire poster.

     I wanted to upload the entire poster here, but there are probably some issues with that. On going research and all... But, I've gotten a couple of compliments on my poster design, so I'm thinking that I may use it as a template in the future. I've removed most of the text and details from the poster, so you can give me feedback on the visual aspects. A couple of things to take into consideration: there's a difference between an empty and filled poster, and some of the specifics of the current layout are a bit "bloated" to make up for the fact that there wasn't a ton of content (a bit more could be squeezed in, I'm sure).

Also, check out that QR code. It can take attendees straight to some of my microscopy videos, to help them visualize what I'm talking about. It wasn't my idea, but it's still pretty exciting. Here's the link it takes you to :

https://www.youtube.com/user/jessime100

You can watch one of the videos here too, if you prefer.




But back to the actual poster, I'd gladly take any comments or suggestion about layout, style, design, etc.

What is Genomics?

I just began my second of three rotations this week, so it's been a busy transition time. But I thought I would share this short genomics video. It's really basic, which may or may not be appealing to you.

This video came from the "Education" tab from the website of my new lab. Feel free to check it out (or the rest of the site, for that matter) to get a better idea of what I'm working on at the moment.

http://www.med.unc.edu/pharm/calabreselab/education

The Desktop

With my Birthday, Black Friday, and Christmas all right around the corner, I haven't been able to keep myself from thinking about the possibility of purchasing my first desktop upgrade. It's not that my computer needs work per se, I just built it in July, but I did stay under budget with the idea of upgrading in mind.

The relevancy of my desktop is complicated by two matters.

Generally, in the computational biology world, desktops can be a bit of an awkward middleman. For most everyday computing (reading papers, browsing the web, note taking, PowerPoint creation, light scripting, etc.), I am going to be on my laptop. I have to be in lab and class, so portability is necessary. On the other hand, if any real analysis is going to be needed, the lab should have workstations built for their pipeline or access to a cluster. I suppose that between those two things, it's easy to think that a home desktop isn't worth it.

Specifically, because I'm still rotating, I don't know what my long term computing needs are going to be. The bottlenecks are obviously going to be dependent on the nature of the analysis. Or the data may absolutely require that it be run on a cluster, so as long as I have a functioning terminal, everything is fine.

In this past rotation, however, having a desktop has been fantastic. I've been generating about 6 GB of image data per experiment-- and already filled 142 GB of my storage drive. Analyzing videos in ImageJ on a laptop with 4 GB of RAM isn't pleasant, and the lab didn't have an open workstation for me at the moment. One particular analysis quickly maxes out the 16 GB I currently have on my desktop. Homework also gets finished a lot faster with the extra screen space. I like the ability to have RStudio, Chrome, and the problem set all open side by side.

I don't have a particular point I'm trying to make here, I'm just considering the pros and cons of sinking money into what I primarily use as a work machine. Of course, I have made a bit of a hobby out of computer building and component researching, so there's a large amount of enjoyment simply from the process. And I would be lying to myself if I didn't admit a bit of pride in having a (fairly) fancy desktop I built sitting in the living room.

Anyway, now that the background and situation have been established, I'll leave brief updates as I continue to add and refresh components in the coming months and years. Having a complete history might be quite interesting by graduation if Moore's law keeps up. Here's a link to my current build:

http://pcpartpicker.com/user/jessime/saved/kg9nTW

I'd love to see what everyone else is working with (or dreaming about), so share your build below. Or, if you have suggestions for my first upgrade, post that.

What Did You Accomplish This Week?

A few weeks ago I was jokingly asked by a friend (who has never set foot in a lab) if I had made any great discoveries that week. I had just finished confirming a genetic transformation, so I laughed and replied, "Well, I did make a new type of yeast." You may or may not consider that a bit of a stretch, but I thought it was a clever answer to an unexpected question. Apparently my exaggeration was enough to impress my friend, since I found out later that he went on to tell others about my "accomplishment." This brief interaction made me think about a couple things...

My first thoughts were about how annoying difficult it can seem to have enough things go right in a given week to really feel accomplished. You know those terrible Fridays when you look back on your week and think, "Where did it go, and why haven't I done anything?" Sure you do, we've all had them. But the question I was asking myself at that moment was "Is it unreasonable to consistently expect significant progress on a thesis project each week"? The answer obviously depends on the connotation of 'significant'. You probably won't add a line to your CV every week, and it's easy to default to a, "Well, science is hard and things go wrong," sort of attitude. The best answer I've found is a middle-of-the-road viewpoint is appropriate; I think it would be beneficial to note at least one achievement at the end of the week. This deed isn't to brag about, but to be self motivational.

I realized later that my friend was actually correct to be impressed with my statement. Not because I had done anything noteworthy, per se, but because the technique and the science behind it IS impressive. After a certain amount of time in the lab it becomes easy to lose sight of how awesome what we get to do is. You get into all of the little gritty details of thinking about the struggle of perfecting your sterile technique and ensuring that your epitubes are all properly labeled in your neatest tiny handwriting. You don't stop to consider that what you're doing. Taking traits from one organism and bestowing them on another could only be called magic a few generations ago. And there are people alive today who were born before this "mundane" task was ever done:

http://www.ncbi.nlm.nih.gov/pubmed/8150273.

For a slightly more humorous perspective, watch this Jimmy Kimmel clip:
https://www.youtube.com/watch?v=EzEr23XJwFY.

The point is, even the little things scientists do on a daily basis are awesome. My advice for this week, to myself as much as anyone, is to appreciate the opportunity you have to work in the field you do, and be sure to make the most out it.

Leave a comment below showcasing the most impressive thing you have accomplished in a week. Exaggerate at your own discretion.

Cheers  

Topic Results

For anyone who's curious how the survey is going, below is the current average with error bars showing one standard deviation.

I didn't bother with any t-tests, but I'm pretty sure that these aren't significantly different...

The survey was still a success, however. I received a large amount of advice that I should write whatever I want and focus on what interests me. So, that's exactly what I'm going to do. A big thanks to everyone who took the time to take the survey.

Be sure to stay tuned!

A Prelude (Part II)

This second "housekeeping" post is the last I have planned for establishing the essence of this blog, I promise. In the coming weeks I'll get into some deeper topics and actually have something for you guys to look into and think about. But I do think that it's important to take some time to determine what I want this blog to be and what my goals are for it. I hope to at least keep this active through the entirety of graduate school, and I believe spelling out both the motivations and the purposes of the blog will contribute to ensuring that I make enough time for it each week. The first Prelude post covered the motivations, so now I want to not only tell you my ideas, but also get feedback from all of you on what you feel would be useful and interesting to read.

The suggested topics I have listed below are from what I would consider least to most technical:

(1) Personal journey through graduate school and related career advice.
     I'd like to chronicle my journey through graduate school and the interactions I have with others in the scientific community. Even though I'm just starting out, in a sense, I still have a story to tell and maybe even some advice to give about how to succeed in school and science... or at least fail gracefully. For those of you who want to keep up with me personally, this option might be the most interesting.

(2) Philosophical, cultural, and ethical issues in biological sciences.
     The social/cultural/ethical issues in biological sciences are something that every good scientist has a responsibility to consider. The earlier we recognize a problem the sooner we can begin to address it. For all of the wonders of science, it does seem to have a way of creating ever more difficulties. The spread of antibiotic bacteria, politics of health data privacy, and the potentials of genetic therapies are just a few of the issues that come to mind that need to continue to be discussed. These aren't theoretical hurdles for scientists to talk about over a late night beer, they are problems that society is going to have to solve whether they want to or not.

(3) Current and future applications of bioinformatics.
      I LOVE thinking about current and future bioinformatics based technologies. Their potential for enhancing people's lives are part of what "gets me out of bed in the morning" and pushes me to deal with all of the failures and difficulties that characterize research. Personalized healthcare, regenerative medicine, synthetic biology, and biologically inspired nanotechnology are mostly science fiction buzzwords for now. But science fiction seems to have a way of being closer than it seems. I'd enjoy sharing my take on where these applications are heading.

(4) Bioinformatics techniques and tutorials.
     As a computer-centric community, there are a large number of bioinformatics blogs focused on tutorials and techniques for others in the field to learn from. It's great, and I'd love to contribute my tiny drop of knowledge. Obviously this would be the most technical type post. While I greatly value the open source nature of the field, I don't want overwhelming technicalities or jargon to be a deterrent to others outside of the field.

Note that I WILL talk about all of these to some degree or another. So it's really a matter of how much emphasis I'll put on any give subject that's being considered here. Thank you very much for taking the time to read through this and vote.

Logistic Map

Been playing around with some of the math functions in Python. I think it's really cool how such a simple formula can create something so complicated. If you're interested, I've documented the code I used to make the video (apologies for the lack of syntax highlighting at the moment):


import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation

# Set up the figure, the axis, and the plot element
fig = plt.figure()
ax = plt.axes(xlim=(0, 60), ylim=(0, 1))
line, = ax.plot([], [], lw=1)

# initialization function: plot the background of each frame
def init():
    line.set_data([], [])
    return line,

# animation function. This is called sequentially
def animate(r):
    n = np.arange(0,60,1)
    x_n = .5 #initial value for x
    x_list = [] #initiate list

    for i in n:
        if i == 0:
            x_list.append(x_n) #initial value for x
        else:
            x_n1 = r*x_n*(1-x_n) #logisitic equation (the magic)
            x_list.append(x_n1) #add to x
            x_n = x_n1 #new x becomes old x
    x = np.array(x_list) #turn list into numpy array
    line.set_data(n, x)
    return line,

# specify array of parameter values
r = np.arange(2,4.5,.01)

# animate, save, show plot
anim = animation.FuncAnimation(fig, animate, init_func=init,
                               frames=r, interval=60, blit=True)
#anim.save('log_map2.mp4') #use default ffmpeg
plt.show()