DIY Biology

It's been quite awhile since my last post and my interests have taken a radical shift into the world of biology. I am currently attending Quest University and a whole new universe of labs and all their related shit that has opened up to me. I haven't lost interests in DIY electronics and have been working on combining the two skills. So here's a brief overview of what I've been working on:

Bio-Indicator Plasmid based on Green Flourescent Protein

An annotated view of my new plasmid using a program
called SnapGene

First to demystify a "plasmid": a plasmid is a circular piece of DNA that encodes a series of genes. This plasmid can be shoved inside of a bacterial cell, usually E. coli and made to induce those genes. Imagine a DIY electronics analogy: Imagine that the bacterial host cell is a microcontroller and the plasmid as the code that you upload into the microcontroller, or in the case of cells, you transform the host cell with the plasmid. So essentially I set out to create a brand new plasmid based off of a previous bioluminescent plasmid called pGFP. My new plasmid has an added tail to the bioluminescent protein that makes it attracted to 2+ metal ions. This tail is called a 6his tag, because it adds a tail of six histidine amino acids. My goal in this project is to be able to detect metal ions that are harmful to the environment, specifically copper and nickel ions.  I have successfully created my new plasmid using PCR, restriction enzymes, and a couple other lab techniques. My next goal is to isolate the GFP protein with the 6his tail and see if I can quantify the concentration of metal ions in water.

Glowing colonies of E. coli transformed with my new plasmid, you can see the
green fluorescence on a UV lightbox 

PCR: DIY Thermal Cycler
PCR is a lab technique that allows you to amplify a specific piece of DNA from a small amount of template DNA. PCR has huge potential in diverse areas of biology: it can be used to screen for specific genes in humans, it can be used to mutate and create new plasmids and much more. PCR uses a piece of lab equipment called a thermal cycler to carry out a PCR reaction. A thermal cycler simply cycles a small tube through a series of temperature cycles that allow an enzyme called DNA Polymerase to make copies of DNA. An alumni from Quest built a proof of concept thermal cycler from simple electronic components. He successfully performed PCR, but the speed of his thermal cycler was really slow. A commercial PCR machine might take an hour and a half for a reaction, that same reaction in his DIY thermal cycler would take 5 hours. I have taken over his project and aim to build a DIY thermal cycler that has comparable speed to a commercial machine but at 1/10 of the price.

RepRap In School: A Short Film

Here's a short video that was filmed by my school documenting my RepRap build.


Grade 12 Students' 3D Printer Project from Toronto Waldorf School on Vimeo.

RepRap and High School integration

Jeeze, I've really fallen behind with my blogging as my life has transitioned away from the RepRap scene towards the future of University life and a new start on the west coast of Canada in Squamish BC.

When I originally built my RepRap I really wanted to include my school, the Toronto Waldorf School in the project so that both the community and myself could benefit from the future of 3D printing. I originally built my RepRap for a senior project in my high school, I worked with the science department to find a way to integrate the project into the actual fabric of the school. Our solution was that the school would pay for the printer through the science department budget and in return I donated the printer to the school when I was done building and playing with it. I was given the opportunity to present and demonstrate the printer to both the middle school (grades 5-8) and the high school. The students were enthralled with the potential of 3D printing, I ended up answering questions non stop for over an hour until the teachers finally had to pull the students away so they could go back to their regular classes.

Now that the printer is safely stowed away in one of the demonstration classrooms in my old school I face the challenge of creating a clear guide that students can follow to be able to confidently operate a Prusa Mendel and take advantage of 3D printing... This task has been much harder than it seems, as anyone who has tried to get started in reprap will know. For example, when your printer stops homing on the x axis, or does not extrude evenly, you dive into the sketchy search engine on the reprap forum and look for some kind of answer, more often than not you end up finding a post that directs you to some obscure blog that has a nice tutorial on trouble shooting your specific problem. So how do I go about compiling some form of guide that will be able to answer the majority of questions and problems a highschool student might face?

Another perspective on this challenge is getting more than just the technically inclined interested in printingt Thingiverse has something to offer to everyone, whether that be a bracket for a mountain biker or a lens hood for a photographer. How do I attract those students that would never think of themselves as the technical type to 3D printing? In more succinct words: How do I bridge the gap from the technically inclined to the mainstream?

My answer to this two fold challenge is still being developed. I plan on visiting the school sometime next school year to give a workshop to get students comfortable using it, to complement the workshop, I intend to put together some form of guide or list of resources that students can refer to in my absence.

I would love to hear feedback from the community about how I should go about integrating my RepRap into my school community in a way that is inclusive of the whole student body, and furthermore, how to go about structuring a workshop and creating a guide that would give any student the confidence necessary to begin 3D printing.

RepRap Toolchain Guide

One of the most tedious challenges that I had to face on my RepRap journey was understanding how each of the different software options worked and what was best for me. Reading through the forum, I find that this is one of the most common questions asked by newcomers to RepRap "what do I install and whats best for my RepRap?"

I decided to create a comprehensive map, or overview briefly describing each of the options for each step of the toolchain. This is not meant as an indepth look at every option there is, instead I tried to keep the descriptions brief and only included options that are widely supported by the community. There are a couple of spelling errors that I couldn't fix as my computer was stolen and with it my original Photoshop file. Luckily, I had uploaded a copy of the picture online that will have to suffice.

Prusa Tips & Tricks: Why Layer Height Matters

After getting my printer fully calibrated and so forth, I began to experiment with the different settings available inside of slic3r to determine how different parameters affect the quality output of my printer. I found that what affected quality the most was layer height, not only would lowering the layer height make the ribbing on a print less prominent, it also created more precise angles within the model.

I decided to create a comparison of a model using layer height as the variable for determining quality. As you can see, I achieved pretty good results using a 0.5mm nozzle. When printing at 0.1mm layer height or lower, any slight errors in calibration are greatly exaggerated, any slight miscalculations in the amount of plastic being extruded can wreak havoc on quality.

Another issue with layer height is the time it takes to print an object. Printing something at 0.1mm takes 4 times longer than at 0.4mm. When printing large objects this has to be taken into consideration when selecting an appropriate layer height.

In conclusion of my makeshift experiment, I found that my Prusa prints optimal quality at 0.2mm layer height, good to know. 

Prusa Tips & Tricks: Y-Axis Bed Mod

While building my Prusa, I found certain areas of the build process to be seriously lacking on the documentation front, specifically the Y-axis and the hot end. From my humble experimentation, I came up with a simple Y-axis carriage that allows unimpeded movement, is light weight and simple to make.

The first step was to cut a 9.5in x 9.5in square of plywood and then cut it into three pieces to form a middle section and two extensions as shown in the picture. I screwed it together with some screws I found laying around and voila:

The first time I tried to mount the square piece I found to my dismay that I only had about 70% mobility on the Y axis form the plywood hitting the frame, significantly lowering my maximum print area. Hence, the reason for the "H" shape of the Y axis bed, giving the extension pieces just enough height  so that it clears the front of the frame. You can see how the wooden extensions clear the frame in the picture.



After some initial printing directly onto the PCB heated bed with Kapton tape, I quickly found that the PCB was not perfectly flat, so I began looking for some flat material that I could print onto. I asked around on the RepRap forum about whether people using glass were using heat treated glass or just normal glass. I found that the majority had found that any type of glass would serve the purpose. I quickly found a glass pane from an old picture frame that fit perfectly across the X axis of the bed. I was initially worried about the extra two inches that stuck off the Y axis (the clear part in the picture), but I soon realized that it was a great way to remove the pane right after printing as it wouldn't heat up as much as the rest of the glass surface. As an added bonus, I could move the glass around without getting oil from my fingers on the actual printing surface. I covered the glass with Kapton tape, clipped it on to the PCB heated bed with butterfly clips and it printed beautifully.

My one problem after getting the pane of glass all rigged up, was that I could barely get the heated bed above 90C with the element constantly on. The underside of the PCB was heating the air and losing precious heat meant for the printing surface.  I had read on a blog about someone using a piece of cardboard as insulation. I decided to try it out as an alternative to the spray on insulation that seems to be the most popular solution. It ended up working extremely well, it took half the time for the bed to get up to 100C than it had before, now it heated up in approximately 5 minutes. In the last picture you can see my most current setup. It has been working great, I can print at 95C for relatively large pieces and have absolutely no warping. I pull the pane of glass off after printing, let it cool on the table for a couple minutes, and the piece breaks off with a little bit of force no problem.

Overall, I am really happy with my Y axis bed design. I hope that for newcomers to RepRap, this post will help to demystify one of the build processes that I found had the least documentation. Good luck!

The Prusa Build: COMPLETE!

It has been a solid six months since I first embarked on building a Prusa RepRap printer, and last week I finally printed my first print! (yes I have been printing non-stop for a week, hence the week delay for this post) The final build stages before my first print were to assemble the hot end from MakerGear, mount the PCB heated bed, and attempt to wire everything up in some sort of cohesive form. The hotend ended up being a very finicky and almost ended in complete disaster; the connection inside the cured heatcore broke, so I ended up making my own MakeDue hot end from salvaged MakerGear parts which has been working very well so far. After I got the hotend working, I mounted the PCB heated bed and went through a series of slightly dodgy upgrades which I will cover in more detail in a following post. The wiring is still a work in progress, I plan on cleaning the wiring up some time in the future.


My first print was the symbolic RepRap shot glass. The print turned out much better than I expected, I was dreading the big blob of goo that most reprap bloggers write about, but was pleasantly surprised when the print actually resembled the desired object. I used Sprinter firmware with Slic3r for gcode and controlled the printer using Pronterface.






I  put kapton tape directly on the PCB heated bed as a quick fix for a piece of glass. There were some uneven areas on the PCB surface, but overall it did not severely effect print quality.

After my surprising success with the shot glass I went about fine tuning slic3r settings. I followed an excellent blog post tutorial for slic3r calibration that can be found on RichRap's blog,
I would highly recommend reading through the post as it clearly outlines how to properly calibrate Slic3r settings. After my calibration was complete, I set about testing the capabilities of my new Prusa. I started with some gears and pulley parts, and then went on to experiment with lower layer height with a Yoda head. I also began to experiment with the effects of extruder retraction while printing a bracelet from thingiverse. I found that changing the amount of retraction even 0.5mm and adding a little bit of Z lift between moves significantly changed the amount of stringing on a print.

I'm really blown away with how straightforward printing has been and the significant leaps and bounds in quality that I have experienced over the last week. Over the next few days I am hoping to post some of the simple improvements I have made as well as a few observational posts regarding the effects of layer height and other slic3r settings on print quality.