Saturday, January 31, 2009

Our (open) contributions to science the past week

I want to make a short post to point out the contributions to science members of my lab made last week. Our activities have really been ramping up, so I don't think we can keep up these kinds of updates, which is good! Here are the things I wanted to note:

  • Anthony started doing open notebook science. His notebook is on openwetware. Actually he started this a couple weeks ago, but I was so used to using our private wiki that I didn't notice until this week. I think Anthony has the perfect demeanor for open notebook science, so I'm thinking this is going to work out really well. There are still problems ahead, though, especially since he's going to be working in a collaborator's lab, on totally new science to him. So there will be technical (it's tough to do wet lab and wiki at same time) as well as procedural issues (some people may not be comfortable with openness).
  • Andy began posting much of the work he's done w/ Google Sketchup in his "3D warehouse." He's very talented with this application, and he's built a whole bunch of models of optical components (mostly from Thor Labs). I think these modules will be useful to others around the globe who are using Sketchup for designing optical systems. You can see one of his full designs on this youtube video. A very interesting point about that video is that he found a Sketchup model of an Olympus IX-81 microscope that another user had generously shared. Since it's pretty much the same as the IX-71 we have, it saved Andy a bunch of time--and is a perfect example of how sharing these kinds of things can speed research progress.
  • Caleb also began open notebook research. His notebook is on OpenWetWare. He's only been using the notebook for the past couple days, and he's been adding notebook features daily. For example, today he implemented a feature so he can link to differences in the code he's writing. I thought that was pretty cool. Caleb has many amazing talents with computers, networking, and that kind of stuff (I don't know the correct terminology). He set up our incredibly useful and stable lab network, which includes a windows server, exchange server, VPN, MediaWiki server, ... and I don't know how many other things that I don't even know about, but which make our research so much easier. This semester, he's leveraging those talents for the purpose of creating new tools to make open science easier for us and others who use MediaWiki. For example, he's currently working on an extension to make it easy and transparent to recover any notebook data lost due to wiki problems. Another thing we're thinking about is implementing an "email to wiki" feature, which I think would be very helpful for lab workers.

Tuesday, January 27, 2009

My First Grant Application

This is for a small student grant. The award is $3500 or so and I wrote on some cancer related research in the field of telomeres. You can find my application (written back in October) on Scribd:

Open Science

I guess I'm officially the guinea pig of the KochLab (I don't know why Koch puts a space there... it's not like it's his lab or anything). Well Koch is the real pioneer because he is the one who initiated the whole open science thing 2 years ago. If I have to guess, I would say I am the most open person to the idea. This could stem from the fact that I really have no clue how most scientists behave when it comes to research. I always envisioned a world where everyone shares what they study. In a sense that is true, but I never imagined that there would be underhandedness like scooping. Wikipedia and other internet media have fueled my ideas, but then Koch showed me the real world.

Anyways, as Koch mentioned in another post (on another blog) we've been a part of OpenWetWare (KochLab)for two years now. While a part of them for so long, we have not performed much open research. We have had our own little community on a private wiki they supplied us. That experience has been amazing. On there I have the freedom to do anything. I mean anything. I keep a lot of personal information there (which can be viewed on my personal blog). The private wiki allows me to enjoy science a little more and the fun things I do there have really helped me learn wiki-ing a lot. Some of those things I don't feel I could/should do in the public eye because it isn't of the utmost professionalism. Maybe in time I will loosen on that stance.

I started on the public wiki around the time I first joined the lab (same time I started using the private wiki). Koch warned us of some dangers of going open, and since I've kept my exposure at a minimum. I'm not saying Koch is holding me back, that's far from the truth. I just felt that since there are more reputations than my own at stake, I should be a team player and do what I think is best for us all.

My initial work involved some minor changes to the OWW logo and some random other things. I stole the userbox template from Wikipedia and added that to OWW. The Wiki-ing and the OWW logo allowed me to rediscover a passion in a new media - graphic design. After messing with the OWW logo I embarked on a mission to create the ultimate KochLab logo (hopefully soon to be added to this page). I do other graphic design too (also on my blog), but that has been put aside so that I can focus on developing my own projects. I will post descriptions of these in more detail eventually on the public site.

Koch realized that I have some talents in the biological aspects of our course of study (we all have been physics trained), and now I am joining (part time) a biology lab in the cancer research section of campus. I will publish everything I do in my notebook on OWW, and hope to bring a little open science to our friends over at UNM Cancer Research (sorry, I'm just tired of adding links). You can follow everything I do (almost daily) research wise in my notebook and I encourage you to follow our lab on OWW as well. Also check out other things that I do on my user page.

Times are changing and I'm proud I get to be one of the pioneers of it all.

Saturday, January 24, 2009

Build your own laser diode control system

Andy hasn't started blogging yet, so I wanted to put up a quick note. Andy designed and built a laser diode system using OEM parts from Thor Labs and elsewhere. Anthony and Larry helped him assemble it, and I think Linh helped with some of the latter parts too. We're going to use it with a 1 watt 690 nm laser diode for our optical tweezers (OT). The idea for doing this came from both Andy and Mark Williams, who visited us and told us that they really like using laser diodes for OT, because when the diode is shot, it's only $500 or less to replace it. The reason I'm posting now is because Andy has posted on OpenWetWare his detailed instructions for how to do build the setup. I've been encouraging him to do so, because I think his instructions could really help out a bunch of people around the globe who would like to assemble the same system. My over / under is six months before someone emails Andy to say, "Thank you / one more question:". If you take a look at the page, I think you will agree with my conclusion that two things kick ass:
  • The laser diode system that he built
  • Andy for writing up and illustrating such amazing instructions

Thank you, Andy!

Monday, January 19, 2009

Draft of our first paper: Shotgun DNA Mapping!

Today, Larry, Anthony, Linh, and I hunkered down and created a draft of our first paper that will come out of our lab. We had been really struggling to write this paper collaboratively in bits and pieces on the wiki, and so we decided to just block off a bunch of time and try to write it together using Word, an overhead projector, and a whiteboard. This took us about 9 hours and worked fantastically. Pats on the back for all of us.

You can find a draft of our paper on Scribd. We welcome any comments or criticisms on this draft!

The work we are describing was done by Larry at the end of last year (2008, August and on) and we believe it presents really promising evidence that shotgun DNA mapping (SMD) by unzipping single DNA molecules will work in a variety of applications. We've been discussing the idea for over a year, particularly during Diego Ramallo Pardo's work towards single-molecule chromatin mapping in collaboration with the Osley laboratory. We had been thinking that SDM would enable single-molecule mapping of native chromatin molecules (we'll call that "shotgun chromatin mapping"), but we now envision other areas of high impact. One area would be in structural genome mapping. We cite the paper by Kidd et al. (2008) which described the amount of structural genome variation between 8 human individuals. Due to the nature of this kind of variation, it would be very well suited for detection by single-molecule DNA unzipping. Furthermore, we envision in the future shotgun DNA mapping of DNA from tumor cells, which (if someone made the method suitably high-throughput) could be a way of typing tumors based on structural genome variety. Another possibility is a genome could be scanned for protein binding sites by shotgun DNA mapping in the presence of purified protein (e.g. finding new binding sites for a newly purified protein of interest).

We're currently planning on submitting our paper to Biophysical Journal. This is a very good journal that we often read. However, we're still wondering whether we may be able to publish in a higher impact journal and reach more biologists if we can better explain the potential applications of our work. We're hoping our biologist friends will have some suggestions about this after reading our draft. And please do let us know your opinion!

(You can read more of Steve's comments about the writing process on his research blog.)

Tuesday, January 13, 2009

Early Days of Grad School

I have been in the lab for about 1.5 years and a graduate student for 2.5 years. Seems like a long time for me (maybe not so much for some grad students), and even though I am where I am now... it hasn't always been the easiest path. In fact it has been quite the opposite.

There were moments where I thought I was going to fail out of grad school. Classes were so hard. In undergrad I was used to putting in a total of 5 hours (max) a week for all my classes. Coming to UNM, Larry (the other grad student) and I realized we needed to do far more. For our first couple of semesters (Fall 06 - Spring 07) we needed to work at least 20-30 hours a week on homework. We were taking half as many classes and putting in 5 times the effort.

We even saw a decrease in our GPA. We went from being 4.0 students to getting B-'s (2.66 roughly) in ALL of our classes. Passing at UNM is a 3.0 for graduate students. Needless to say, I felt very defeated and I didn't believe that I belonged at UNM. I was recruited by Koch with the aid of Larry to join his new startup lab. This was the first turning point of my career.

That summer (2007) Larry and I did a lot of work in the lab, and had a really good time doing it all. My confidence was returned. Thanks to our awesome PI. He had so much faith and confidence in our abilities that I believed that I could survive grad school and attain my Ph. D.

The end of my first summer in the lab came the prelim exams. I had just returned from a trip to Hawaii, and Larry and I began studying at least 10 hours a day for a week for these tests. After all that work I had failed both exams I took (there are a total of four with each being in a different branch of Physics) and Larry had passed both (we studied for two). I was again feeling down. The upcoming semester brought more hardships through classes which we did slightly better in (now achieving B's and B+'s). But I still wasn't getting above the level required for staying at UNM.

Winter 08 brought my next try at the prelims. I had to pass 2 exams in order to stay here. Larry and I took the tests we hadn't taken over the summer. Larry passed them both and I felt like I did horrible. I even took a third test to improve my chances. That test I didn't study for though. Surprisingly I managed to pass one of the exams I studied for and the one I didn't. I was here to stay for at least another semester and the summer.

Spring 08 helped me by a mile. This time we did well in our classes and met the requirements (although barely). The summer came and research continued. It was full of productivity and ingenuity and all those other appropriate words that describe a lab kicking ass (sorry for the vulgarity). I had to derail myself though because I had to pass two more prelim exams.

Koch and I set up a competition to help me study. He would run 1 mile for every hour I studied. I managed to rack up a lot of hours (each week was on the order of 30 hours) and he managed to get in good shape. The prelims came. Those tests can really knock the wind out of your sails. I went in feeling really confident and left thinking that I was on the verge of a dropout. When all was said and done though, I had passed both exams and I was set to stay in grad school. My stresses (for the time being) were over!

Now I am here contributing to several places (this blog and to name a few) and more importantly a firm member of the KochLab.

If I can offer one piece of advice to any aspiring Grad Student it will be: Do what you can in undergrad to make sure you understand everything. Grad School will be a pain in the ass and very difficult, but once you are past the obstacles you are free to embark on the career path of your choosing. Enjoy it while it lasts because not everything is fun and games!

Monday, January 12, 2009

Hi from New Mexico!

My name is Anthony and I am one of the first grad student members of the KochLab. I will come with news of all sorts for everyone to read. I will describe what it is like to be a graduate student and what it is that I do here. I will also be telling you some funny stories from the lab.

I come from the internet age I suppose. What does this mean? Well in science right now there seems to be 2 groups. Science 1.0 and Open Science. Science 1.0 is the old way of doing things. 1.0ists will discuss science with others, but they certainly wouldn't broadcast it out there for the world. I would fit more in with the open science crowd.

What is open science? Just think of Wikipedia. Everything known, and hypothesized is published there and anyone can come and read it and others still can contribute to the general knowledge. The KochLab are members of OpenWetWare which is a community of open scientists that want to share their research with the world. We joined because the PI (Steve Koch) wanted to be able to join the "open" world while still being able to protect himself from unseen harms as a new PI with a new lab.

We call our research interface the Wiki because we can post and edit each other's work (on OpenWetWare) just like you could on Wikipedia. We have two aspects, one is a private wiki and the other is public. As of now most of the students (and Koch himself) make great use of the private, but not so much on the public site. This is all going to change real soon...

I am going to take the leap into open science by broadcasting all my work in the public light. You can follow our lab work on our page as well as follow along here. Other lab stuff include facebook groups, citeulike, a youtube channel, and soon to be many more. You can also follow my personal life (non science stuff) on my own blog.
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