20.109(F12): Online cloning lab and defense

We're excited to partner with LateNite Labs to offer a virtual environment to run the 20.109 DNA engineering experiment we are performing in Module 1. Why do the lab within a virtual environment when we're running through the lab in the physical space as well? Well, for one thing, it may help you to see the connections of the day to day work we do. When the experimental steps are days apart, as they have to be in the physical lab, it's awfully easy to lose track of why we're doing one step or another. Here you can run a few days of lab in just a few hours! Another reason we like this virtual environment is that it allows you to simulate many different runs of the work--and actually see the results you'd get in the physical lab! In other words, you can make "virtual" mistakes and see how they'd come out in the lab. Finally, this virtual environment will show you parts of the lab that we don't have time or capacity for everyone to do in the physical lab. Here you can pour the gel or make the solution you need, rather than have them done for you by the teaching faculty...and so in that sense this is a more "real" view to the work you'll do when you leave our 20.109 class!

So, if you're willing to pilot this effort with us, we're excited to hear what you like and what you don't.

Introduction to the Platform

Getting started

• URL: latenightlabs.com
• ID: nkuldell@gmail.com
• Pswd:labsnitelate

Sign in (upper right blue button), the "Launch your labs"

• Your laboratory work area is the green counter top called the workbench.
• All of your lab supplies are available to you on the glass shelf above the workbench. It is actually three shelves in one, switchable by clicking on one of the three shelf-tabs that appear just below the shelf:
  • • Containers (test tubes, beakers, etc.)
    • Materials (chemicals, plants, etc.)
    • Instruments (thermometers, balances, etc.)

To get what you need, just click on the relevant shelf-tab, then click on the item on the shelf, drag it down to the workbench, and drop it in the middle part of the benchtop.

• A few notes about this virtual bench:
  • It's 2 dimensional so you're restricted in some of the actions you can perform.
  • There is an unlimited supply of everything, as many test tubes as you need, even multiple thermometers and pH meters, so don't worry about running out of equipment or materials, or about breaking anything.
  • Once you’ve taken an object off the shelf it can’t go back. Discard anything you no longer need in the Recycling Bin below the workbench.

The golden rule of this lab space

Everything revolves around containers! This means, simply, that materials go into containers, and instruments measure and manipulate what is inside of those containers.

Practice

Try this 1. Take an Erlenmeyer Flask from the shelf (click on the Containers shelf-tab to make the containers appear) and place it on the workbench (click, drag, drop). You need to make sure to place any Containers or Instruments in the middle of the workbench. If you place a container so that part of it is not resting on the workbench or part of it is suspended above the workbench an error message will pop up. Discard that container; otherwise materials will not react properly when added to the container.

2. Add 200 ml of Water from the shelf (click on the Materials shelf-tab to make the materials appear). Click on the Water bottle, drag it down on top of the flask and let go. Enter 200 into the amount box and click Enter.

Note: Whenever you drop an object onto another object, like the Water bottle onto the Beaker, the cursor has to be over the target object, which in this case is the Flask, if the object you drop is over the second object and not the cursor it won’t add.

3. Take a Constant Temperature Bath from the shelf (Instruments shelf-tab, this time). Take the Flask and place it in the Bath. That is, click the Flask, drag it onto the Bath and let go. Watch it snap into place in top of the Bath.

4. Raise the temperature of the Bath to 100°C and watch as the water in the flask starts to boil.

5. When you're finished with one or two objects, you can clean up your area by dragging everything to the yellow Recycle Bin underneath the workbench. Don't worry, everything you’ll need later on the lab will be available on the shelves for you to use. To clear the whole bench press the trash button on the lower left.

6. If you want to take a closer look at what you're working on, use the navigation tools in the lower right corner of the lab:

The "+" and "-" buttons zoom in and out. The red rectangle pans around the lab. The reset button will bring you back to the original zoom. You can use these navigation tools anytime. Go ahead and try, if you like.

In the lower-left corner of the screen in front of the workbench is a set of icons. One of those looks like a clock. In some experiments, you will be asked to use the “Timer”. In order to set a new timer, you’ll click on the clock icon and move the timer anywhere convenient.

Details for the 20.109 Assignment