Frequently Asked Questions


Who is this site for?

Our long-term goal is to make the technology of molecular biology more accessible to a wide audience of users, including workers in fields as diverse as laboratory science, criminal justice, medicine, and agriculture. Because many of the virtual laboratory exercises will probably require guidance and oversight from an instructor with actual laboratory experience, our focus at this stage is on undergraduate college and university level curricula.

Are you serious?

Yes! Don't let the funny looking people fool you. The Cybertory Virtual Molecular Biology Lab includes some pretty hard-core technology, but we try to keep the presentation light, and maybe even a bit whimsical, because learning should be fun.

Is the Virtual Lab available in other languages?

The Virtual Lab is designed with minimal labeling and built-in messages, most of which can be specified in the configuration script, so that they can be easily modified to other languages. Translating the protocols and documentation for an exercise does not require modification of the software.

Some translations have been undertaken by volunteers. The prototype system was updated and translated into Spanish by Dr. Angel Herráez, and is hosted at the Universidad de Alcalá. This FAQ page has a Belorussian translation provided by 1-800-Flowers.

What can I do without signing up?

You can explore the lab in various 'read-only' configurations, including one for pH experiments, and one for PCR of bacterial templates. You can register with Simzymes for a temporary account (without entering any information into the CMS) which will allow you to customize your own laboratory configuration. You can also look through many of the CMS courses as a guest, though many resources, such as tutorials which track your progress through the material, are only available to users who are registered and logged in. If you are dead-set against signing up for a free CMS account, you may want to check out our open-source companion site at, which does not use registration.

Why don't my reactions work?

That is a good question, and it is one you nead to learn to answer for yourself. You need to be able to tell the difference between an experiment that gives a negative result and a failed experiment.

The Virtual Lab models a lot of things that can go wrong. Enzymes can go bad, either through age, or by the action of contaminating proteases; keeping them on ice should keep them safe, but if you leave them out on the benchtop too long they may lose activity. Enzymes are sensitive to buffer conditions, including pH, salt concentration, and the presence of co-factors and substrates. DNA can be degraded by nucleases. PCR is particularly tricky, since the polymerase needs a certain amount of magnesium, and certain concentrations of each dNTP, but dNTPs chelate magnesium ions, so the ratio between these ingredients matters. Too high dNTP concentration lowers the available magnesium ions, and inhibits the polymerase. PCR can also be poisoned by the presence of ddNTPs. Melting and annealing efficiencies depend on temperature and the sequences of the templates and primers.

Often, you will need to run both positive and negative controls to ensure that each step of you experiment works, and distinguish negative results from non-results. Proper controls will let you troubleshoot your procedures and figure out where problems arise. Figuring out appropriate positive and negative controls is a major part of good experimental design.

The configuration of the laboratory can control to a great extent how difficult it is to sucessfully complete reactions. A very focused configuration might come with pre-assembled positive controls or master mixes, while a very general one might make you mix your own buffers from scratch. It all depends on what students are expected to learn from a given exercise, and how much technical detail the instructor wants them to handle. As in life, more freedom generally gives you more opportunity to screw up.

Do you really expect me to take notes?

Yes! You need to take notes for the same reasons you need to take notes in a real lab. These experiments can be complicated, and you need to know exactly what you have done. This is especially important if something in your experiment does not work, and you need to troubleshoot to figure out what has gone wrong. Generally, you should use the same type of notebook you would use in a real lab. If you have a lab partner in the Virtual Lab, it may be more convenient to use a paper notebook than an electronic one, since one partner can run the computer, and the other can keep notes.

User Interface

Is there an overview of how to use the Virtual Lab interface?

Read the section on 'Using the Interface' in the Notes to Users on the Virtual Lab Login Page.

How do I move the Pipette?

Just click on where you want the pipette to go. When you click on a tube, its pop should snap open, and the pipette should fly to it. You can also click on a well in the gel to move the pipette to the well. Note that there must be a tip on the pipette for it to fly to tubes or gel wells when you click on them. You can put the pipette away by clicking on the pipette stand. It also goes to the stand if you close the lid of the selected tube.

How do I move liquid into and out of the Pipette?

When the tip of the pipette is in a tube or gel well, click on the plunger to move it up or down. It will try to take up the volume shown on the dial, which can be adjusted from 1 to 100 microliters. If there is not elough solution in the tube, the pipette will take what is there, and the dial will automatically adjust to show how much volume was taken up. To change the volume, you can either highlight the volume with the mouse and type in a new number, or click on the left and right sides of the volume dial to increment or decrement by one microliter at a time.

Can tips really be contaminated?

Yes! The lab can be configured to model contamination of pipette tips. The amount of carryover on the pipette tip, if any, can be set in different configurations. Cross-contamination is generally only something to worry about with PCR, though the lab could be configured so that you could contaminate your enzymes with protease, and degrade them if you are not careful. Changing tips will avoid this major avenue of contamination.

Is there pipetting error?

While we don't use a random Gaussian error model, the lab can be configured to model volume loss from wetting containers. In other words, if you put ten microliters into a clean, dry tube and then try to pull it back out, you will actually get back less than you put in, since some of the solution sticks to the container. The pipette display will show the volume rounded to the nearest whole microliter. The amount of solution needed to wet the containers can be customized for different configurations. It can be set to zero if the exercise author doesn't want students to deal with volume loss.

How do I move a tube?

You can click and drag tubes to move them around, but you can only drop them in empty slots of things that can hold tubes. Tube holders include tube racks, including those in the water bath and ice bucket, the spectrophotometer, and the PCR machine. If you drop a tube on the waste can it will disappear into oblivion, never to be seen again. If you drop one anywhere else, it will snap back to its "home", that is, the last tube slot it was in. The exception to this is new tubes fresh from the tube jar; they don't have a home yet, so they will just hover in the air wherever you leave them. Once you sucessfully put a new tube in a tube holder slot, it can only go in slots from then on.

How do I move a tube rack?

Grab the front edge of the tube rack to move it around. Be careful not to just grab a tube from the rack, lest you just drag one tube around. The lab may be configured to only allow tube racks in particular locations. If so, the shadow of the rack will appear in allowable locations as you drag the rack over them. If you drop the rack anywhere except an allowable location, it will snap back to its last position.

Moving racks to conveniet locations can make it much easier to load gels, transfer tubes to and from the PCR machine, and assemble the various components of reactions.

Where do I get new tubes?

Click on the tube jar, and a new tube will appear underneath your mouse pointer. Drag the new tube to a rack. Note that the tube appears when you press down on the mouse key. This means you can click, hold and drag tubes from the tube jar in one mouse click.

How do I change pipette tips?

There are two ways to eject the pipette tip. You can click either on the waste can, or on the tip ejector bar of the pipette. In either case, the pipette will fly to the waste can and eject its tip. Likewiase, there are two ways to get a new tip: click either on the tip box, or click the ejector bar again. This will cause the pipette to fly to the tip box and get a new tip.

Why is the writing on the tubes so small?

The writing is small because the tubes are small. In real life, several sizes of tubes are commonly used, with capacities from 1.5 ml to 0.2 ml. The smallest ones, used for PCR, only hold a few drops. In general, you can only write a few letters or numbers on them.

We recommend two approaches to keeping your tubes straight. First, you can write a code on the tube (up to three numbers or letters). You cannot write as much information on the tube as the printed labels contain, but your writing will be much larger, and you can see it without having to zoom in as closely. You can write on both blank tubes, and tubes that already have printed labels. You can also change the writing on tubes. You should write the key to your code in your notebook.

Second, you should keep track of your tubes by their positions in the tube racks. You may need to zoom in very close to read the labels, but then zoom out a bit to do the pipetting. Arrange your tubes so you know which is which by where they are in the racks.

How can I read the fine print on the tube labels?

You can either zoom in to read the labels, or hover the mouse over a tube to bring up a magnifying glass view. The magnifying glass will disappear when you move the mouse. If you both zoom in and use the magnifying glass, it is even bigger.

How do I zoom in and out?

Right-click (control-click on a Macintosh) to bring up a menu which will let you zoom in or out. You may need to experiment to find the best zoom level for performing protcols such as setting up reactions and loading gels.

How do I move around the lab?

You may need to move around in the lab if you are zoomed in. Just click on anything that is not draggable, and you will drag the whole lab around.

How can I speed up incubations and running gels?

Note that the clock on the wall has a fast-forward button. This will make virtual time pass more quickly, so that gels, PCR cycling, and enzymatic incubations can be finished in less real time.

There are three fast-forward settings on the clock; click multiple times on the double forward arrows to go to the fast, faster, and fastest speeds. If you click once more, the speed cycles back to normal time. There is also a stop button, which may be useful for setting up reactions so incubation doesn't start until you are ready; this is sort of like putting the whole laboratory on ice.

How do I change the temperature on the water bath?

Use the up and down arrows under the digital display to change the temperature setting. The water bath takes a while to equilibrate temperature; the digital display will turn green when the actual temperature matches the setting. Fast forward the clock to speed up this equilibration.


Why do you use a Course Management System?

The Cybertory simulators provide a platform for doing virtual experiments, but the experiments themselves are not built into the software. Integrating the Cybertory platform with a Course Management System gives us an optimal environment to provide background materials, scenarios, protocols, and other curricular materials to accompany exercises in the Virtual Lab. This also makes it possible to offer other services, including grading of multiple choice quizzes, monitoring of tutorial completion, and so forth.

Why Moodle?

Moodle is a popular, open-source Course Management System with a large and active community of users and developers. Its clean, modular, and extensible design, as well as access to the underlying code, allows us to integrate the Cybertory resources so we can use a single login for the whole system.

Why should I sign up for an account?

There are two main advantages to signing up for an account. First, it gives you access to the full program, where the Cybertory interface, simulations, and resources are integrated with curricular materials to make a more complete and immersive learning exercise. Second, it gives you the chance to participate in a community of users, providing feedback to the developers, and helping us to make this website a more useful and valuable resource. This will help us to keep this resource available in the future, as well as to improve it.

What courses are available?

Browse the list of courses to see what is available. The exercises at show some additional technologies and applications suitable for use with these simulators.


Can I use this site for a course I am teaching?

You are welcome to use this site. Please be advised that we intend to make some of these courses available on a subscription basis in the future. If you are planning to use a free (non subscription) course in a class, please let us know. Many of these courses are in the process of being developed, and may change dramatically; if we know your plans, we will be better able to work around your requirements.

Can I write an exercise myself?

Absolutely! Please contact us if you are interested in developing exercises for use in the Virtual Lab.

Can I dry-lab my experiment in the virtual lab?

If your experiment uses technologies supported by our system, and genomes already in our database, you may find that you can configure a dry-lab simply by ordering the appropriate materials from Simzymes. In any case, please contact us if you are interested in developing exercises for the Cybertory lab. We are very interested in collaborating with instructors and scientists on exercise development.

Can you add the genome for my favorite organism to the PCR simulator?

The PCR simulator is loaded with a variety of genomes from the RefSeq database at NIH. If you have another complete genome you would like to use, please let us know.

Can you add my PCR primers?

Actually, you can use any primer sequences you like in the Virtual Lab; simply register for an account with Simzymes, then 'order' your custom oligonucleotide primers from the on-line catalog. All prices are virtual, so don't worry about your budget!

Molecular Biology

Why molecular biology?

Molecular biology focuses on techniques to elucidate the information contained in nucleic acids (DNA and RNA), the substances that comprise the genetic materials of living things. This gives it almost unimaginably broad applicability in fields as diverse as medicine, forensic identification, bioterrorism detection, food science, biofuel production, and family law. This broad applicability makes these technologies important to people in a large number of professions, and even to citizens and jurors.

Why virtual molecular biology?

The technologies behind molecular biology focus on nucleic acids, and in particular on DNA. The behavior of DNA molecules in reactions such as hybridization, primer extension, and electrophoresis is very predictable, and can be easily modeled. This gives us a system that is both widely applicable (since all living things have genes) and amenable to simulation, so it can form the basis of a large number of different types of problem-based exercises, in an exceptionally broad array of scenarios.

One can easily imagine other technologies, such as protein separations, immunoblotting, and so forth, that might form the basis of interesting exercises, but would be much more difficult to simulate in a generally applicable manner.


What software did you use to make the Virtual Lab?

The Virtual Lab interface is programmed in Flash. Some of the simulation code is included in the Flash module, while other aspects of simulation are run as web services. We use the PCR and DNA Sequencing simulators from, for example.

What software did you use to make these documentation pages?

These pages are maintained as a Freemind "Mind Map", and the website is generated from it using an XSLT stylesheet.

Most of the content of the website is from assorted CGI scripts and Moodle content. The Freemind file is just used to hold the meta-information, that is, information about the site, not the main content of the site itself. This is a small enough amount of information to contain in a mind map.

We use a pull-down navigation bar menu for all of this meta-information, with separate pages for each of the top-level items. We use the "suckerfish" Javascript/CSS drop-down menus because they are open-source, and thus both free and customizable. They also have the benefit of storing the menu information as nested HTML lists, so the menu is usable though not very pretty) even on browsers that do not use Javascript or Cascading Style Sheets.

Freemind has the built-in capability to export maps as nice HTML outlines, where you click on topics to expand them. We were not able to use these, since we wanted a menu bar across the top of each page. Freemind also has the built-in ability to apply external XSLT stylesheets, using a built-in XSLT engine. We were not able to use this either, since it does not seem to support writing multiple output files. However, since Freemind so wisely stores its files natively in XML format, we can apply an XSLT stylesheet to the Freemind file directly.

The root node is labelled with the URL of the web site. This information is not used by the stylesheet, but you need to put something in that node, and the URL documents where you will put the resulting web site.

Immediate children of the root will appear in the menu bar across the top of each page. You need to be sure all these items will fit on a menu bar. Each of these first-level nodes will be made into a separate web page. At this level, titles can have abbreviations (in parentheses) that will be used on the menu as as the name of the associated file, while the full name will be used in the page title. For example, a node called "Frequently Asked Questions (FAQ)" will have a full title of "Frequently Asked Questions", and an abbreviation of "FAQ"; the menu will show "FAQ", the file name will be "FAQ.html", and the title of the page will be "Frequently Asked Questions".

The abbreviation "Home" is special because its file will be named "index.html", rather than "Home.html", but the word "Home" will be used in the menu bar instead of "index".

Title Nodes

Any node that has children will be used as a section title. Terminal nodes ("leaf nodes") are of several types:

Terminal Nodes

1) Normal nodes become paragraphs in the web page. These must contain plain text, not HTML. This limits what you kinds of markup you can apply. There is currently no way to add italics or bold, for example. I do not find this a serious limitation, since you generally want a hyperlink for important terms anyway, but see node type 4 below.

2) Image nodes ("Insert"Image (File Chooser or Link)") become image tags.

3) Nodes with a LINK attribute (added in Freemind using "Insert:Hyperlink ...") must repeat a term or phrase from one of the paragraph nodes. When the page is generated, all occurrances of this phrase or term will be hyperlinked to the target.

4) Nodes named "include_body" must point to an HTML file ("Insert: Hyperlink"). The contents of the 'body' section of this HTML file will be copied into the output. This lets you do fancier editing on some pages that you maintain either by hand-editing the HTML, or using an HTML editor. This way you can, for example, have tables, italics, bold text, and so forth. There are some limitations is that your external HTML file must be valid XML (XHTML), and you cannot use entities other than the very basic ones (< > &) unless you provide the appropriate DTD.


Freemind does not have a spell-checker, so you need to run the XML file through one before you process it (I use TextWrangler on OS X). This is a minor inconvenience, but in some ways it can be helpful to separate the editorial spell checking from the creative writing aspect.

How do you make pictures of fake people?

The pictures of people are made with the commercial 3D modeling program "Poser". This program breaks down appearance into a set of parameters (nose length, mouth width, and so on) that can be adjusted using dials. That makes a pretty decent approximate foundation for simulating the genetics of human appearance. Where particular traits affecting human appearance are known, especially those documented in the OMIM database, we try to use those; for example, we have added traits for "widow's peak" and "earlobe attachment".


I found an error; will you fix it?

We are always interested in bug reports, usability issues, and in any suggestions you may have. Please contact us by email, or using the moodle forums.


What is Simzymes?

The 'Simzymes Virtual Reagent Company' is an on-line catalog that lets users 'order' enzymes, DNA samples, and other materials for use in the Virtual Lab. It also provides documentation in the form of information about the various reagents, equipment, and supplies you will use in the virtual lab. The prices in the catalog are virtual as well, though we can track your students' spending, if you want to monitor that.

How do I check out from Simzymes?

Read the instructions! The online catalog requires you to confirm that you understand the terms and conditions, for example. You have not successfully completed the checkout process until you have made it through several screens and clicked the 'Confirm Order' button.