Final Presentation for REU

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Yesterday afternoon I gave my final presentation for the NSF REU. I’ve posted it on Slideshare for you all to see. It wasn’t real obvious, until I started working on the presentation, how much Anthony and I have done over the last several months. We’ve gotten a lot accomplished!

I have had such a great experience this year that I volunteered to continue coming to the lab this summer. Thankfully Anthony and Dr. Koch aren’t tired of me and agreed to let me stay involved this summer. I hope to be able to work in Koch Lab at least 4 hours a week. I’m interested to see how the e.coli in D2O progresses.

Also, Anthony is really moving and shaking in the Open Notebook Science community. This is really exciting to me.  I’ll be taking my ONS experience with me to my next opportunity…

I’ve been given another NSF internship opportunity, the STEM Talent Expansion Program (STEP), for the summer. [I think that is the right link… the NSF site is down for maintenance until tomorrow night. Let me know if the link isn’t correct]. I’ll be working part-time with Dr. Ramiro Jordan, who seemed open to me keeping an online notebook. Stay tuned for some information about VHDL and circuits.

I am indebted and full of gratitude for all the support and guidance that both Anthony and Dr. Koch gave me this past year. Thank you seems like not enough. Thank you both.


Open Notebook Science — Taking what I’m Learning Outside


Some Background: I”ve got a full++ course load this semester, so I haven’t been in the Lab much this week to work on research related stuff. I’m a Computer Engineering major, hoping to get accepted into UNM’s 3+2 program and end up with a BS in Computer Engineering and an MBA in May 2015. My main motivation for working with Dr. Koch and Anthony was the Open Notebook Science portion of their work (and I just love the atmosphere of our lab — we’re the cool kids in our building).

So while I find all the stuff we do with D2O and protein studies really fascinating,my first love is with ONS. I truly believe that this is the way of future science and I’m so very grateful to get to be a part of it.

When I’m busy with all the engineering studies, in the back of my mind is a constant buzz … How can I take what I’m learning in school, the goals that I have, and marry all that with this exciting ONS movement — that I really want to continue to be a part of, even after my REU is over? :End Background

Here it comes… wait for it… wait for it… wait for it:

I had a really interesting experience today and I think that the marriage I want is going to arise.

In between classes this morning I ran into my Logic Design Prof (Marios Pattichis), and we started talking about the Lab portion of the class. He asked me what I thought, and I told him (truthfully) that VHDL is cool, but the supporting documentation for the lab really sucks. We then got into this discussion about my past experience (15 years as a technical writer, documentation manager, and trainer) and how I could maybe contribute to make the lab better.

I have been thinking about talking to him about this very thing, but was afraid that as an undergrad I wouldn’t qualify, I would be turned down, or whatever else the fear wanted to tell me for that day.

I said I would love to start a dialog with him about this over the rest of the semester. He then says, “Do everything (i.e., my lab work) open source.” I’m hoping that what I heard was what he really meant. Anyway, then I start to get really excited, and tell him about what I’m doing in the KochLab with Open Notebook Science.

 “OMG, this is really exciting,” I’m thinking. This is just the opportunity that I’ve been looking for. So that is my story.

I’m going to set up another blog for my Logic Lab Notebook in the next week (in my spare time LOL). Dr. Pattichis seemed to like that idea, and mentioned something about making it available to the class. So I need to get on it soon. I’m also hoping to start reworking the lab tutorials so that maybe I can be a TA or something next fall.

I’ll have to get really dedicated about blogging every day.  That is my weakness. My strength is my excitement about ONS.

REU January Presentation

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Today was presentation day at CHTM. All the REU students (me included) gave a 20 minute presentation about what we have been doing for our research. I don’t know why, but I get extremely nervous for these presentations. The strange thing is I have a lot of experience speaking to crowds of people. I used to teach continuing education classes, and was never even a little bit nervous. I wonder what is going on?

Anyway, all this week Dr. Koch, Anthony and I have been working on my Mind Map presentation. I wanted to do something different from the standard PowerPoint presentation. Don’t get me wrong, PowerPoint is a good tool, I just wanted to do something different. We decided a Mind Map would be a good way to show case one of the many tools/applications that we use here in Kochlab.

In addition, I handed out little cards with a qr code and a short link to a google docs spreadsheet with links to many of the tools we use for our ONS. My Mind Map also had links to most of the information that I used for my research and presentation.

After it was all over I realized that I had forgotten to show the really cool, time lapse growth images that Anthony had put together for the D2O experiments.

Next presentation I will take Dr. Koch’s suggestion and practice, out loud, the entire presentation. If I do this several times I might not get stage fright quite so bad.

I’m really grateful for the opportunities that have come my way  since I’ve been working here at CHTM and KochLab. Dr. Koch and Anthony have been absolutely great to work with. Linda Bugge has been a good friend and really helpful with all the administrative “stoof.” It is an honor to have been selected to be a part of the NSF grant. I’m meeting some really awesome and brilliant people here. I’m super lucky.

What is R?

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Last month Dr. Koch decided we would use R as our graphing/statistics tool for our figures. I had never heard of it before the email (and was wondering what happened to the letters between D and Q). So I did a quick search right before the holidays for a little introduction to R. I found a webinar by David Smith with Revolution.

Note: I watched the entire webinar before I realized that this was a third party presentation. Although the webinar has some good information the best place to start is at the R project’s home page.

Today I spent my first day back in the lab downloading, installing, and learning the basics of R. It looks like an interesting tool. I don’t think it qualifies as a full-on language like C/C++, but it looks like it may be just as powerful as say MATLAB. I’m not sure yet, and will spend tomorrow going through some online lessons. I also did some searching for a good R book… I’m hoping to get the ‘Introduction to R’ book.

I also spent part of the day reviewing my notes from before break, prioritizing my to-do list, and looking at a few of the other tools that Kochlab uses for open notebooks. I tried my hand at the Basic offering of Mind Meister, opened up Slide Share, and I’ve got Google+ operating with video.

Finally I started to jot down some notes for a presentation I have in two weeks. What I would like to do is take all of Anthony’s data from the DDW and Repeating Crumley experiments, analyze them, and create some really kick-a** graphs for the presentation using R.

Fixing posting errors


I had a small ethical dilemma this morning. I say small because it doesn’t seem like a big deal on the surface. Here is what happened:

Yesterday I posted What I’ve learned about Open Notebook Science, and I gave myself some tasks associated with some of what I’ve learned. One of the tasks was in reference to my Open Notebook Science blog; I need to post consistently. I mentioned that both Anthony and Dr. Koch are consistent bloggers. I see posts from Dr. Koch all the time, in several arenas, mainly on Twitter and Friend Feed, about his work and Open Science. When I was posting yesterday I made an assumption that because he is always (electronically) around, that he must update his blog every day too, and that is what I wrote.

So this morning while I’m getting ready to come into the lab and all of a sudden, in my mind I see Dr. Koch’s blog page from the day before, and I realize that his last post was in August. Uh oh I think. What should I do? I don’t want to be “that” undergrad. I don’t want to be the kind of scientist that “assumes.” Wait… I can just access WordPress and change that one sentence. My mind is racing for about 60 seconds – how do I fix this (I might be having a finals stress hangover)? Then I calm down and realize it’s not a big deal, or is it?

I decide to wait until I get to the lab and talk to Anthony. Turns out that no, this particular situation isn’t really a big deal, but it does touch on an interesting ethical Open Notebook Science question. Would editing an Open Notebook Science blog post defeat one of the main underlying purposes of Open Notebook Science… freely sharing all information, right, wrong, imperfect? I wonder?

With Open Notebook Science, we post everything, even our mistakes. The first Open Notebooks were kept with wikis. Wikis have revision tracking. That means that every revision is accessible by anyone that wants to look. I keep my Notebook in this blog. A lot of scientists are doing the same thing. If I inadvertently make a mistake (i.e. post misinformation), I can simply edit my previous blog post and no one gets to see my mistake. Is that honest or am I helping to keep to a minimum the amount of misinformation that is available online?

We decided I should add an update to yesterday’s post. Thoughts?

What I’ve learned about ONS thus far


During the last month, I have been able to do some reading, and I’ve gotten even more excited about Open Notebook Science (ONS) than I was when I started. Michael Nielsen has a great TED talk about ONS. While I was at TED, I watched anther talk by Clay Shirky about what he calls ‘cognitive surplus.’ Basically, when we all work together things get done quicker, bigger, and so much better than when we work alone. Go figure.

Here’s what I’ve learned so far about starting and keeping up with an open notebook:

  • Wow! There is a plethora of tools out here that everyone is using to stay connected: social networks, blogs, wikis, etc., and each type of tool has several applications available to choose from. I had a Facebook page when I started working here. Now I have Google+, FriendFeed, Twitter, and this Blog. Although I’ve never felt technically challenged in my life, there have been a few moments where I felt seriously behind the crowd. For a second I even wondered if I picked the wrong major (computer engineering). I’m okay now, but gosh that is a lot to keep up with and learn, in addition to being a full-time student.
  • I now appreciate how a full-time scientist, who is already working long and hard on the next big thing, could easily be dissuaded from ONS. There are a lot of technical obstacles, in addition to the current perceived drawbacks. It’s similar to the late ‘80s, early ‘90s when none of the PC software was entirely compatible (Anthony says I’m dating myself, but this is a great analogy). Anyone remember using WordPerfect, Lotus, and Dbase III+, and trying to get them to all work well together? That is kind of how ONS looks to me now.
  • There are some valid concerns/challenges about ONS, patents, information deluge, and intellectual property seem to be the top three. I’ll post some information about that later.
  • Right now everyone seems to be using a little bit of everything for their open notebooks. What would be helpful for me is to get one daily feed, that pulls all the sites I’m watching (Google+, FriendFeed, individual blogs), into my main inbox.
    • Task:

    • Find a tool that can pull from all the places I’m watching into one daily email feed. Does anyone know of such a tool?
  • I don’t like, nor do I have the time to post the same information to more than one site (Google+, FriendFeed, blog, etc.). I wonder if there is also a tool that will allow me to post concurrently to my blog and my walls?
    • Task:

    • Research tools that can post concurrently to multiple social networking walls and a blog.
  • Blogging seems the most user friendly way to keep a notebook. There are several online, free applications available (we use WordPress), and they are fairly easy to learn. There is a slight learning curve, but it isn’t too daunting.
    • Tasks:

    • Become more adept with blogging. Read up on what makes a successful blog; what drives people to a blog, and what encourages them to participate.
    • Update my notebook on a regular basis… Daily! This is a hard habit to get into, but it is essential for success. Anthony and Dr. Koch are awesome at doing this. I aspire to their level of greatness.

    UPDATE 12/14: I realized this morning that I made an incorrect assumption with this last task. Dr. Koch is very active, posting multiple times a day in several Open Science arenas. Based on this knowledge, when I was reading his blog, I didn’t really pay attention to the dates of the postings. So although he posts regularly in multiple conversations he doesn’t update his blog as often as Anthony updates his ONS.

  • Wikis are not as user friendly as blogs. If I had the time, it wouldn’t have been a big deal for me to learn how to create and use a wiki, but I’m time challenged. If I was a typical scientist (outside of engineering), learning how to use a wiki could possibly be a nightmare.

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