I updated the FigShare figures and slightly modified the excel files. Check it out.
I didn’t do too much science in Florida, but I did do some. I spent a day at the Kennedy Space Center, took lots of pictures of birds, and spent a day at a marsh on Amelia Island. I thought that I would share some of these science photos with you. I’m also going to adapt them at some point and update the pictures that cycle in the header of this notebook. Anyways….
Click to see the full glory of all the pictures. Some notes:
- the wildlife in florida seemed extra vivid compared to New Mexico. It provided quite the photo experience.
- the picture of the bald eagle is real! I stood there for about 30 minutes taking pictures waiting for it to fly away. I got one decent picture, but it is a bit blurry. I’m going to try to fix that. It was rather lucky that I came across it in the first place. I was walking with my mom and I told her I wanted to head back. We saw a bench about a tenth of a mile ahead and we decided to go there before turning around. The path turned a corner before approaching the bench and right about the corner in the tree was the bald eagle. Had I just turned around, I would have never seen this magnificent creature.
- Also the Saturn V rocket is real as well, and so is the space shuttle. Obviously the shuttle was reused many times for many missions, but I think the rocket was a test rocket that was never used in a real mission. The bridge though, I think was used on the launchpad.
- The crawler, launchpads, rockets, towers, and vehicle assembly buildings are insanely large objects. It’s almost unfathomable that humans have built such ridiculously large objects. The vehicle assembly building is the world’s largest enclosed space. Apparently the volume inside is large enough to fit 4 Empire State Buildings (but only as tall as half)! Ironically when inside, you almost get that dizzy feeling from looking down, but you are looking up!
- I spent one cloudless night taking pictures of the stars. Most of the pictures came out blurry because I don’t have a remote shutter, except the one of Jupiter. Looking through the viewfinder of my camera, it looked like a smudge. It wasn’t until looking at the picture after did I realize the smudge was actually the Galilean Moons of Jupiter! I took that picture with my 55-250mm zoom lens. Stef has a 10in Dobsonian telescope that I’m going to adapt for my camera. Hopefully I’ll get some kickass pictures.
- I’ll attribute a Creative Commons License to these pictures so anyone can use these pictures however they like. Just say that You heart Anthony’s pictures, and I’ll be happy.
So my trip to Florida was amazing, but I didn’t get a whole lot done in terms of science while I was there. The resort I stayed out had no internet (surprising isn’t it), and I only managed to read one paper while I was there, which only made me ask questions instead of answering them. I did manage to read halfway through Michael Nielson’s book: Reinventing Discovery (which I keep thinking is actually titled Rediscovering Science).
The book is pretty good and it is fun to hear the stories of groups who have succeeded in implementing an open network approach in their fields. It has given me a few ideas that I think can greatly impact open notebook science and my PhD quest.
I’ve also decided to write up summaries of papers I’ve read here. Mostly it will be for my use, but perhaps someone someday will be able to use the summaries. I won’t republish anything in the papers (like figures or quotes) for copyright reasons, but I will reference them and of course properly cite the article I’m summarizing.
On top of that I’ll be starting up some new experiments this week. I’m going to do a large scale DDW experiment and another run of the Repeating Crumley experiment. I’m also looking to start doing DDW tests with other organisms, but need to refresh my molecular bio techniques.
It’s good to be back and I can’t wait to get going again.
I will be celebrating Thanksgiving in FL this year so I will be out all of next week. I’m packing a bunch of papers to read for my travels and down time and they are all about FT-IR spectroscopy of water and D2O. Hopefully I have some revealing information when I get back.
When I get back I’ll be starting up some new exciting experiments. Aside from the FT-IR stuff, I’ll be growing e.coli in DDW and D2O (sort of a Repeating Crumley branch) and trying to adapt the organisms to grow in high amounts of D2O and then switching them to DDW to see if anything happens. Also I’ll be beginning a new trial of the RC experiments and trying again with the plant DDW experiment.
In the meantime though feel free to surf through the notebook and look back on all the cool things I’ve done in the past few months. Take the time to share them on Facebook, Twitter, and now LinkedIn and Google+ (see the new buttons?). I’ll also still be posting Analytics Monday and hopefully there will be something cool to show.
See ya when I get back!
The purpose of this post is to test whether I can add picture to a slideshow over time and the slideshow updates itself. Hard to explain why that would be a problem, but the way this script works is that it only incorporates images added via this post and you can’t select old pictures from the media library in wordpress.
The reason I want to do this is so that I can have like posts for each type of seal in the water evaporation experiment. For this it doesn’t make sense to update by day, but rather by type. This experiment is the equivalent of watching paint dry so I thought it would be more intuitive to compare a bubble growth to itself rather then against other bubbles. If that doesn’t make sense it will in about 1.5 weeks.
Yesterday, Tito Jankowski sent me an email requesting to see the log files from the OpenPCR machine. Part of the software function is to record the programs used and possibly error reports (I didn’t ask too much in this regard). Immediately I noticed something interesting. According to Windows XP, the log files did not exist on the computer!
OpenPCR calls saved programs from a directory hidden in the logged in user’s application directory. If there are no files in this directory then you should have no saved programs. Interestingly enough there were saved programs, but the files were no where to be found. I tried a Windows search on the whole computer and nothing could be turned up. Somehow the machine was calling files that either didn’t exist or were extra hidden.
I ran some tests to try and repeat the glitches from my last report. I was able to repeat the hold screen glitch (shown in the featured image at the top of the page), I was able to repeat the crash and restart on completion (which interestingly only happened in the saved program), and I was able to repeat the error that wouldn’t allow OpenPCR to run immediately after a completed program.
Then I remembered that I had initially installed the OpenPCR software on the lab’s laptop (that I mostly monopolize for my computing pleasures). I actually found the log files from the initial setup on that computer and Tito suggested I run the same tests on the laptop to generate the errors (he was convinced that the glitches were a hardware malfunction).
Turns out, NONE of those errors were repeatable on the laptop! In fact every error I had from my previous tests with OpenPCR did not occur, and every trial I ran went swimmingly. I did not receive the glitch shown above, I was able to start a reaction immediately after a completed reaction, and the restart crash did not happen. As of now it appears that all the problems were caused by the other computer to which OpenPCR was tethered.
So I want to thank Tito for his support throughout the afternoon yesterday and his suggestions on how to possibly fix the errors. When all looked bleak, a simple last minute trial ended up being the solution. Chalk this up as a win for open science, and open notebook science!
Update: I thought it would be fun to show you my actual notes of the experiments which are usually short enough so that I can recall what I did in more detail for posting here as soon as possible.
It should be noted that this isn’t all the notes from my experiment, but just the ones that I definitely wanted to remember in detail. The remainder are just upwards of the frame edge but the earlier tests were an identical repeat of the tests shown under the page separation that I drew.
My name is Anthony Salvagno and I would like to welcome you to the new open notebook of my research. My goal is to make the information here as accessible to everyone on the planet as physically possible. Over the next few weeks this site will be going through some major changes, but since science is 24/7 the research will be pouring in.
If you follow my personal blog, the Randomly Grad Life, then this marks the official split of my research from everything else. If you are new to me, my blogging style, and my research, then you are in for a treat. With that said, I’d like to tell you a little about myself for all the newcomers (and maybe those that know me will learn something new).
I am a 5th year Physics grad student in the KochLab at the University of New Mexico. My research was primarily focused on manipulating DNA with optical tweezers, don’t worry if you don’t understand that because in the next few days I’m going to tell you all about it. I’ve recently hit a road block in that department and because of funding issues I am switching focus to a new project. I’m beginning to examine how different organisms live and grow under differing water environments. At some point I’ll be playing with kinesin motor proteins (which are the bread and butter of the lab) and testing their stability under similar conditions.
While in grad school I stumbled upon graphic design, which has become quite the hobby for me and one day soon will become my next profession. I created IheartAnthony about a year and a half ago as my personal brand. I wanted it to be a place where everything me could be stored in one location. With the addition of this notebook, that dream is nearly complete.
With the introductions out of the way let’s take a magically journey into the world of the KochLab where science sizzles.