LabCraft is a community-driven mod for the popular video game Minecraft (published by Mojang). LabCraft is meant to be used as a teaching tool and to expose children to various biology-related disciplines. Feel free to contact any listed author if you’re interested in helping develop or deploy LabCraft.
We will be using 64-bit Java version 8u25, so make sure you get the jdk for that version from Oracle’s site.
After some digging, I found a new version of Minecraft Forge for Minecraft 1.8. It is already in the GitHub, and a tutorial is shown below. I do not think that we each need to do all the setup steps since it is in the shared folder.
If you are using Eclipse, you should use the import projects wizard to import all projects in the entire GitHub repository. You should find 3:
Include all of them in your workspace.
Other related project links:
Backbone vector synthesis
Bacteria (E. coli)
centrifuge to collect protein
dye === medium if applicable
run gels (to teach size separation principals); gel acts like map in game.
Use extractor to get proper protein from gel? Or maybe just something like HPLC
Protein and Membrane Biophysics
General Lab Equipment, Setup, Protocols (keep it easy, but make it somewhat realistic - ie collecting samples, centrifugation, adding and measuring appropriate fluorescent markers. All data should be clean too, not “raw” data but something that is immediately useful. Perhaps a later development could export raw data to ComputerCraft for them to mess with, but that’s a completely different story.)
It may be beneficial to make our stuff work with these common mods. ComputerCraft lets you program in Minecraft, someone even made a version that lets you do Python. Thus it is a cool system to teach programming. Our system would teach whatever we want to do with biochemistry / biophysics.
MineChem / Advanced Chemistry
A couple other related mods are BioCraft and Advanced Genetics, but neither teach stuff in a useful way.
A question we need to consider is what is really needed and what people will actually use. People probably don’t want to do “experiments” but they will want to use our stuff in things they craft or just will make stuff cause it’s cool. If we target middle/high school students then there must be some sort of fun goal or something for them to do.
I think developing a really thorough protein purification module would be the best first move. Users would be able to take some organic(ish) object they find in the game, use a protein sequencer object to obtain the AA sequence, then use that to design a plasmid for expression in e. coli. It’s a relatively simple process that we can make as coarse as we’d like (we can go straight from AA sequencing to simply “creating” the plasmid, avoiding intermediate steps if we’d like), and it provides something that is of immediate value to them in the game. I imagine them having labs that are like factories, making useful resources for them with little maintenance required.
–> So I think to start, we make bacteria kind of the basic ’unit’ of the mod. Eukaryotes can be added later, most importantly yeast (make your own minecraft beer!). Bacteria will be a slimy looking thing that you can put on surfaces, but will decay and die over time if not placed on proper growth medium, such as LB agar plates. Bacteria grow up plasmids, which code for proteins as you described. I don’t want this to be like the Advanced Genetics mod, so I think it would be cool to work in some model pathways where they can produce things. For example, we could make things like glycolysis and the TCA cycle available to “engineer”. So the idea would be that they will produce X product in cell culture 1, which is then converted to Y in cell culture 2. This could be manually done by “harvesting” the bacterial products somehow (centrifuge?) or with automated machines that are expensive to make and run. Perhaps these machines would be run with IndustrialCraft power sources. That would be easy to implement I think and IC is a very common mod.
–> Also cloning would be a sweet module. Cloning plasmids in general should be a step. So you get your AA sequence, and then convert that to a DNA sequence, use a synthesizer to make the sequence for you, then clone that sequence into a generic expression vector plasmid. So say you wanted to clone a cow. You sequence the cow’s proteins/DNA, clone the genome, then put it into some mammalian cells somehow, then maybe inject into a cow that exists and it will spit out a calf like normal when mating. This way you can double the rate of population growth with your animals, because usually two have to come together to mate, making one new calf, then have to wait for like an 8 minute cool down. Now, two calfs are produced with the same cool down.
–> To encourage people to wear proper personal protective equipment (PPE), we should make it so if there is like a spill or you get too close to a bacterial sludge or something like that, you get briefly sick. This would be like when coming into contact with sludge and other toxic liquids in the game already. But with PPE on (gloves, coat at least), then you will be ok. They’re put on like armor in the game.
DNA extraction kit - salt, water, ethanol, detergent
salt - saltpeter (railcraft) or salt from some saltOre we make
ethanol - sugarcane + water + incubator
detergent - make fat a drop from cows or press vegetables to make oil
PCR Tubes - for DNA amplification
1.5 mL tubes - for DNA / protein samples
50 mL tubes - for larger samples?
Cell culture plates (10 cm) - for growing cells/bacteria
96 well plates - for doing experiments
Erlin-Meyer Flask (1L) - for growing bacteria
Bacterial Culture Medium (“LB”?)
Cell Culture medium (“DMEM”?)
Agar (can be crafted w/ LB to make LB agar –> crafted w/ cell culture plate to make bacterial culture plate)
Agarose? (for DNA / protein gels) - would anyone even want to use these?
Cell lysis solution
Cell DNA extract
protein (+ antibodies?)
Machines will be built around plastic chassis and circuits which will be the standard units to build things by. Some will be more or less expensive and may span multiple blocks (see coke oven, steamer for multi-block examples in mods)
liquid nitrogen tank (cells)
freezer (cell components)
fridge? (some solutions)
centrifuge (+ ultra-centrifuge?)
protein sequencer (sequence things found in the wild so they can design plasmids to express the thing they found (i.e. make silk in a culture after sequencing it)) –> Thought - We have to define things that they can “make” with the bacteria. So for example, say they want to make string, then they would sequence string or perhaps get a sample from a spider and sequence it’s proteins. They they would find out there are, say, 4 important proteins. We can even draw from the literature to get legit stuff. Then they have to produce each in a bacterial culture as I said before above to get them to produce products along the path to silk/string. Some immediately useful things I can think of are making beer from yeast and hops/barley, biofuel from bacteria expressing energy converting enzymes (Perhaps they would get energy from feed or from the sun? Photosynthesis needs to be in there somewhere. Making modules for important metabolic networks seems like a good biochem learning point in general), and other general materials that players will find useful.
DNA sequence generator (manually create sequences for use as PCR primers and such)
microscope (add fluorescent filters to make fluorescent)
flow cytometer? (crafted with fluorescent microscope + expensive stuff)