Virtual laboratory

Welcome to the Virtual Lab, a dedicated learning platform for students who want to work in molecular labs. In the virtual lab, you will have the opportunity to learn the basics of molecular biology and gain practical skills in liquid handling and operating essential equipment such as pipettes, electrophoresis, centrifuges, and more.

The Virtual Lab is not just about theory, it is about practical training. You will have the opportunity to practice these techniques in a controlled and safe environment. Your specific task will be to prepare and amplify vectors for plant CRISPR/Cas9 mutagenesis. You will follow a detailed protocol that closely resembles actual laboratory procedures.
The lab was established in 2021 for the CRISPRes teaching programme, funded by the University of Milan, Charles University, and the University of Copenhagen within the 4EU+ project.
The Virtual Lab was created by:
  • Jiří Kubík - creation of virtual environment, graphics
  • Adéla Přibylová - creation of protocols, procedures
  • Aleš Soukup - debugging, administration

Try pipetting too!

The Virtual Lab is an educational program that can be freely used for personal or educational purposes. It can run on Windows 10 and does not need to be installed. Just download the zipped file, unzip it and run the lab-game.exe file. The virtual lab is graphics demanding, so we recommend running it on machines with at least 8 GB of RAM and, ideally, a dedicated graphics card.

You may download the Virtual Lab HERE. A protocol to follow is included in the lab, as well as instructions on how to navigate the lab. You can download a PDF version of the protocol HERE.

What can you learn?

In the Virtual Lab, you can try to create a vector for CRISPR/Cas9 mutagenesis.
We tried to simulate a real lab, including unpleasant things like changing pipette tips and balancing the centrifuge rotor. This makes the "game" quite complex, and we hope you will find it a useful and interesting experience. However, we must point out that we had limited time and resources to create it, and so some things may not work 100%. For that, we apologize. We have had two CRISPR courses, and students have gone through the lab and have gotten by without much trouble.

In the Virtual Lab, you will have oligonucleotides representing the target region sequence for Cas9. You will create oligo-dimers from these, then phosphorylate them and check their size on electrophoresis gel. Next, you will cleave the target vector with a restriction endonuclease, which will linearize the vector and create sticky overhangs, allowing the phosphorylated oligo-dimer to be ligated into the vector. However, you will need to purify the restriction mixture on electrophoresis beforehand to separate the linearized/cleaved vectors from the non-linearized/non-cleaved vectors. You will then cut and isolate them from the electrophoretic gel. Into the purified linearized vector with sticky ends, you ligate phosphorylated oligo-dimers representing the target region for Cas9. You transform the ligation mixture by heat shock into E. coli bacteria, which you seed onto culture plates. After the bacteria have grown into larger colonies, you test the individual colonies by PCR to verify that they indeed contain the inserted sequence from the oligo-dimers.