BioRender

Imagine for me, if you would, this scenario: you are trying to make a diagram for a lab report (or assessment or poster or whatever) but you can’t find the right figure. So you draw something that resembles what you want, or you use an image you found online that is similar to what you want, but then you spend almost as much time identifying and discussing the weaknesses of the model as you do working with the model itself.

Diffusion Diagram

[ESPN Documentary Narrator Voice] What if I told you there was a free way to make high-quality, detailed models with your students?

My wife’s uncle shared BioRender with me this week, and I knew I needed to share this ASAP.  Watch this intro video you’ll see when you sign up for a free account, and try to act cool… I’ll wait.

DID YOU FREAK OUT A LITTLE BIT?! I did. (OK, maybe more than a little bit.) There is a lot to explore with this, but here are some highlights for me. Not only are there 1000s of icons you can add to your figure, but you can control the color scheme for many of them and add labels to make your models even more robust.
It has some built-in support to pull models from the Protein Databank. When you have the EXACT protein you want to use, you can control how your protein is visualized and rotate the protein so you show the exact part of interest. After Andrew Taylor’s Fall Conference presentation on 3D-printed models, I went looking for the proteins associated with the pharmaceutical product Gleevec.  

I encourage you to go check this out. Visit https://biorender.io/ and create an account. Once you start creating, share your best figures with us here or on social media. I may be speaking for myself here, but I can’t wait to start using and making these models with my students!

KABT: Facebook Group  or   Twitter
BioRender: Twitter

edited to fix a capitalization mistake 8/13

DIY Circulation Chamber

In my recent 3D printing exploits I have realized that I need a clean way to circulate fluids around and through samples. My need is to pass D-limonene over HIPS prints to dissolve in-fill and support structures. I then realized others may have similar needs for circulation.

So I found a way to build a simple circulation system with a few relatively cheap components. It was also a pretty quick build once I had all the parts.

Part list:

IMG_20150720_152355 IMG_20150720_152407

I hope most of the build is apparent from the pictures above. I would mention that I use the output line to dump the liquid on top of my part, so the hook holds the short line in place. Use the nut to secure the pump to the coffee can so it doesn’t rattle itself loose over time. I like using the lid as a drying platform to minimize my mess. I’m also using the top half of a pop bottle to hold my printed part up out of the the reservoir and still within the flow.

So that’s what I did today. What kind of summer projects are occupying everyone else?

 

 

 

 

Electrophoresis is Hard

I know many upper-level biology classes perform some version of the classic (are they old enough to be classic yet?) biotechnology procedures at some point in the year. Bacterial transformation, PCR, and DNA electrophoresis are all experiments that occur in many labs at high schools and universities. I say occur but what I mean is attempt. At least in my classroom the success rate for these procedures is… let’s say <100%.

Par for the course...
Par for the course…

Practice makes improvement but in this setting practice is also really expensive. To solve this problem my predecessor (the venerable Paula Donham to cite her properly) allowed students to practice some procedures on dummy supplies first before using actual reagents and equipment. This is particularly useful in electrophoresis procedures. Micropipetting is difficult to novices and errors can ‘break’ the experiment with discouraging frequency. This is a particular problem in experiments that are culminating in the electrophoresis step after substantial investment, such as the arabidopsis epigenetics lab that I’ve raved about before.

A practice gel can be cast in a Petri dish with the much cheaper agar (as opposed to agarose) and water. Mix a 1% agar solution with tap water and boil to dissolve. Pour molten agar into Petri dishes to a depth of about 5mm. While it is still molten add a comb that creates several rows of wells similar to those in an electrophoresis gel. After the agar solidifies fill the dish with water. Use glycerol with food coloring to practice filling the wells with no harm from gel punctures, spills or other experimenter errors.

In the current model, the comb teeth are slightly more widely spaced.
In the current model, the comb teeth are slightly more widely spaced.
3D printed in red, store bought in white
3D printed in red, store bought in white

Usually you could buy equipment or kits (like here) but there is a DIY option. You can mix your own reagents as I’ve described above and you can 3D print your own comb. Download the STL file here and get your nearest 3D printer to create you an army of combs. Now every student can practice melting, pouring, comb-removing, and loading. This time your students can make much more interesting mistakes than simply misloading their wells.

Capture Capture 1

 

VOTE (Dancing, not politics)

[Note: At this time, voting is no longer active. The videos are available in a playlist below, and you can read more about the assignment in the original blog post.]

Exercise your right to vote! Your unique skill set as science teachers makes you the perfect voters. You can help decide which group does the best job of dancing their energy reaction. Is it photosynthesis? Aerobic cellular respiration? Maybe fermentation? Help out my AP Biology students and vote for your favorite dances.

Vote here (Google Acct needed): https://docs.google.com/forms/d/1yn7HTw_hRr7mcoPs-UXEflYUAJ8fZAZSmE0GwzQ-P7A/viewform?usp=send_form

Thank you for your time and help!    [VOTING IS NO LONGER ACTIVE AT THIS TIME.]

Want to know more about this assignment? Check out the blog post here:

Statistics in the Biology Classroom

Saturday at KU Edwards Campus I attended the “Statistics in the Biology Classroom” workshop, the 2nd part of April’s PD opportunities provided the KU Center for STEM Learning (under who the UKanTeach program can be found). You can find my notes, ideas, and instructions for incorporating statistics in the biology classroom using Excel spreadsheets here.

Like last time I won’t rehash everything from my notes and I think continuing a discussion of statistics in biology here on KABT as well as within the document would serve a greater purpose. Brad started the class telling a now classic story of a British woman claiming to tell whether milk was added before or after her tea and then the conversation led to how we could model this using spreadsheets. The conversation weaved its way around the AP curriculum (including which labs different stats can be used in), the sometimes over-reliance on Chi-Square as a statistical test, and how to build students conceptual understanding of stats, distributions, and p-values, without really having to “learn” complicated formulas.

So with that, what does everyone else think? How should statistics be used on biology? How does it look different vertically between grade levels? When and how should students first begin working with modeling statistics?