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Virtual Lab

Open the notes page for the user interface (these are the same notes that appear further down on this page, but having them in a separate window may be convenient). Be aware that links in the notes window will open in this window, and close your lab session!


Notes to Users

Guest Login

If you access the Virtual Laboratory through this page, it will ask you to log in. If you have signed up for a free account through the Simzymes online catalog, you should use that user name and password to login here. Any items you have 'ordered' from the catalog will appear in the lab when you log in. You will only be able to save your lab configuration in our database if you have your own account.

If you log in as a guest, you will be presented with a standard read-only configuration; currently, it is set up for RFLP analysis of sickle cell anemia. For more details on a suggested experiment to perform with this configuration, see the RFLP and Electrophoresis demo.

If you want to try the lab without registering, read the Guest Access pages.

Using the Interface

Below are brief notes on how to use the Virtual Lab. For more details, see the User Interface section of the FAQ, or look up particular reagents and items of equipment in the Simzymes catalog. For more examples of lab configurations and experimental protocols, see 'Demos' on the Guest Access pages.

  • To log in to the lab, either use the default e-mail and password to log in as a guest, or enter the ones from your Simzymes account to open your own personal configuration, then click the OK button.
  • To move the pipette to a tube, click the tube. The top should pop open, and the pipette will fly over if it has a tip. The pipette will not go to the selected tube if it does not have a tip. You have to click a tube without dragging to select/deselect it. If you drag a tube, it will not be selected. The selected tube (with its top open) can not be dragged; if you want to move it, deselect it first.
  • Click the pipette plunger to toggle it up and down. Select the pipette volume by dragging across it with the mouse, and type in a new volume. Only volumes between 0 and 100 µl are valid. Alternatively, you can click on the left and right sides of the volume dial wheel to change the volume.
  • Click the tip box to put a tip on the pipette if it doesn't already have one. You cannot use the pipette witout a tip.
  • To throw a tip away, click on the opening to the waste can. Alternatively, click the tip ejector on the pipette.
  • Use Ctl-click (Mac) or right click (Windows) to bring up the Flash menu. This will let you zoom in (and back out again). It is much easier to read the tube labels and see the gel wells if you zoom in, but you can't mix inredients in tube easily if you are zoomed in too far.
  • To see approximately how much solution is in a tube, zoom in. Drag the tube a tad so it pops in front of the tube rack (drag by the cap hinge, so the hand doesn't block the label). It will snap back in place when you let go. To see how much solution is in the pipette tip, you can move the pipette to the pipette stand, either by deselecting the tube, or by clicking on the pipette stand. This will let you zoom in to inspect the tip contents.
  • To measure exactly how much solution is in a tube, try to remove more than you have with the pipette. The pipette volume will only take up what is available, and the pipette volume be set to the amount drawn up.
  • Only one tube can be selected at a time. Choosing a different tube will open its top, and close the top of the previously selected tube.
  • Drag tubes around to move them. You can only place tubes in the holes of tube racks and the PCR machine. If you try to drop a tube anywhere else, it snaps back to its former position.
  • To throw a tube away, drag it to the waste can.
  • To get a new tube, drag it from the tube jar. (NOTE: tubes fresh from the tube jar act differently from normal tubes, because they have not been assigned a rack position yet. You can drop them in mid-air, for example. They are also frozen (below 0°C). Once you drop a tube from the tube jar onto a valid tube position, it behaves normally (i.e., won't hang in mid-air any more.) Tubes take their temperatures from their positions. The water bath is adjustable, the ice bucket is 0°C, and room temperature is 20°C.
  • The water bath takes time to equilibrate to a new temperature. When the water temperature matches the set temperature, the readout turns green.
  • Solutions in tubes are always incubating. Nothing happens if the tube is at zero degrees or below. The lengths of the incubations are measured by the digital clock on the wall.
  • Enzyme activity is temperature dependent; most cut best at 37°C, but will also cut slowly at room temperature. Enzymes also degrade in a temperature dependent fashion.
  • You can look in the Simzymes catalog to find details about particular enzymes, such as recognition sites and buffer requirements.
  • To speed up virtual time for incubations, gels, PCR runs, and so forth, hit fast forward on the clock. You can also cheat and stop the clock to set up reactions if you like.
  • To load the gel, suck up a solution into the pipette, then click on the target well. The pipette will fly over. Click the plunger to dispense the solution into the well. Wells can hold up to 100µl.

Please contact us if you have any questions, comments, or suggestions about the interface.

Simzymes

The Simzymes Virtual Reagent Company online catalog is where you go to 'order' reagents to use in the Virtual Lab. Registering with Simzymes is also how you set up a user name and password to use in the Virtual Lab. Please note that if you are using the lab within a course on the CMS, registration should be automatic.

Course Management System (CMS)

Login to the Course Management System or create a new account if you don't have one yet. Courses in the CMS will be much more detailed than the free demos, and take advantage of the extra capabilities you get when you register.