Biochemistry Boot Camp

Students Attend 2021 Biochemistry Boot Camp

Dr. Chris Johnson presents a lecture on DNA properties.

Last week students from Mississippi, Alabama, Louisiana, and Tennessee congregated in Starkville to attend Biochemistry Boot Camp, a program sponsored by the National Science Foundation and organized by Dr. Nick Fitzkee to teach young researchers how to more effectively use computers in their biochemistry research.

“Undergraduate biochemistry is a great course, but we simply don’t have the time to teach all of the skills that students need when they first walk into a research lab,” Fitzkee said. “Biochemistry Boot Camp is designed to show new researchers that they can save a lot of time at the bench by familiarizing themselves with some simple computer software.”

Biochemistry Boot Camp 2021 Students

The program lasted three days, June 7-10, and over 60 students attended, including 12 students from the University of Alabama’s summer REU program. Other faculty participants included Dr. Christopher Johnson from MSU and Dr. Matt Thompson from UA’s Department of Chemistry and Biochemistry.

“It’s exciting to see the growth of biochemistry and biophysics in the southeast. This program not only trains students to be better scientists, it also allows those students to form relationships with other student researchers in the region,” Johnson said. “There’s a lot of value to that.”

The students agreed. Madison Hejny is an undergraduate researcher in Fitzkee’s lab who is participating in summer research. “The program was intense, but it really helped me to understand how I could use computers to streamline my research,” Hejny said.

The slides and handouts used for the Boot Camp program are available the Boot Camp 2021 Web Page, and videos of all sessions have been posted to Dr. Fitzkee’s YouTube Channel.


Boot Camp Videos are Now Available!

Dr. Fitzkee works with Dan and Radha on video edits with Davinci Resolve.

If you weren't able to join us this year, or if you want to review one of the sessions, videos for all of this year's Boot Camp Sessions are now available on the Fitzkee Lab YouTube Channel. All of those who helped organize the camp this year truly hope that these sessions help accellerate your research and benefit your understanding of how computers can inform biochemistry.

If you enjoyed the camp, please consider liking and subscribing to our YouTube channel, and follow us on Twitter @FitzkeeLab!


Practice for Linux - Virtual Machines

One of this year's participants asked about more practice using Unix. Your accounts will be disabled after a week or so, but you will be able to continue using Linux if you want by using a "virtual" machine. Virtualization allows your computer to emultate an entire computer as a software application, and you can run Linux on your own Windows or Mac system without installing another operating system - something that can be difficult.

The easiest way to do this is to download Virtualbox, a free program that runs on either Mac or Windows. Virtualbox is simply the software that handles the virtualization; you will still need to download a "virtual hard drive," which is a file that stores data for the virtual computer.

There are several sites that provide a virtual hard drive that contains a working linux installtion. You can find some instructions for installing these files into virtualbox here. I've included some links to virtual drives below:

  • NMRPipe Virtual Machine (CentOS) - This link is provided by Frank Delaglio, the author of NMRPipe, a popular NMR processing software. You can download the virtual machine at this site (File 9), and it runs CentOS. The administrator (root) password and default username are both given on the site.
  • Scientific Linux (Ubuntu) - This image is provided by Fermilab. It is based on Ubuntu and should have many of the features you would want for python programming and graphics. It may not have all of the biochemistry tools (e.g. Python), but since it is running Ubuntu, installation of Pymol is easy ("sudo apt install pymol").



Boot Camp 2021 Group Photo

Biochemistry Boot Camp Participants 2021

We're grateful for this year's 62 Biochemistry Boot Camp participants! To download a high-resolution version of the photo, follow this link.


A Note About Excel Downloads Using Chrome

Some of the links for the sessions are not working on Chrome. They work on Firefox and Edge, but Chrome has a security feature that is preventing the downloads from working.

This feature is designed to prevent a secure site (like from serving files from an insecure site (like The "folding" site has a lot more space than my university-provided "fitzkee" site, but it's not encrypted. Chrome (rightly) thinks that's a red flag.

The simplest way to work around this is to view this site through Firefox or Edge. At some point, when I have more time, I'll convert "folding" over to a more modern, encrypted site. But for now, that's the best work around.

You can read a little more about this feature at the following sites. Note that they are using an older version of Chrome, so the options listed are slightly different. Note that I don't recommend disabling safe browsing (at all - seriously, please don't do this).


Boot Camp 2021, Day 2 Materials

The materials for the second day of boot camp are available below. Please download non-PDF files using Firefox or Edge. Chrome will not work.


Boot Camp 2021, Day 1 Materials

The handouts for the first day are given below. Please download non-PDF files using Firefox or Edge. Chrome will not work.


Boot Camp Registration Now Closed

We've had an incredible turnout for Boot Camp this year, with over 60 students currently signed up. Because of COVID restrictions, we are reaching the capacity of our room and administrative load, and registration is now closed. All students who are registered should have received an email confirmation; if you believe you registered on time, please contact Nick Fitzkee.

If you were not able to get in this year, please check this site for video sessions, and please consider signing up next year!


Final Boot Camp Program

Boot Camp Flier

Just over one week until Biochemistry Boot Camp 2021! We have a great program lined up, with new content and two new sessions! We also have recruited a talented group of instructors and guest speakers to lead the sessions this year.

The program this year is the largest its ever been, and we will meet in the Mitchell Memorial Library Auditorium (room 1000, lowest floor). You can find a map and a final program PDF below.

Looking forward to June 7!



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