StarGenetics User Manual

Learn how to set up and analyze experiments in StarGenetics.

Contents

1. Welcome to StarGenetics
2. Opening StarGenetics
3. StarGenetics at a glance
4. Fly exercises
   • Mating experiment
5. Punnett Square tool
6. Yeast exercises
   • Non-tetrad experiments
   • Tetrad experiments
7. Renaming experiments & organisms
8. Matings involving progeny
9. Discarding experiments & removing organisms
10. Saving experiments
11. Exporting data
12. Reporting bugs or asking questions

Welcome to StarGenetics

StarGenetics provides a set of tools for analyzing genetic traits. This software simulates mating experiments between organisms that are genetically different across a range of traits and allows students to analyze the nature of the traits in question. StarGenetics runs on standard Linux, Windows and Mac computers.

Opening StarGenetics

To get started with StarGenetics:

1. Navigate to http://web.mit.edu/star/genetics.
2. Click on the Start button to launch the StarGenetics application.
3. Click Trust when a prompt appears asking if you trust the certificate.
4. Click on File -> New in the drop-down menu.
5. On the Welcome page choose an exercise and click on it. To open an exercise that is not bundled with StarGenetics, click on File -> Open and then click on the desired file.

StarGenetics at a glance

This is the view you will see when you open an exercise in StarGenetics.

Fly Exercises

Mating Experiment

To perform a mating between two organisms:

1. To mate two organisms you can use one of the following 2 methods:
   
   • drag each organism to the Mating site using the mouse.
     

   -OR-

   • click on the organism and then click on the Set as a Parent icon at the bottom of the Strainsbox.
     
2. Next, click on the Mate button.
3. Mating results can be viewed individually under the Individual tab, in sorted form under the Sorted tab, or in summary form under the Summary tab.
   
   Individual results: progeny listed individually
   
   
   Sorted results: progeny sorted by sex and phenotype
   
   
   Summary results: progeny listed by phenotype
   
4. To start a new experiment click on the Save experiment button.
   

   

   Old experiments will move to the Saved experiments area. Each tab within the Saved experiments area represents a prior experiment. Any action that can be performed within the Active experiment box can also be performed for a past experiment with the exception of adding more matings to the experiment (see bellow in “Tip – carrying out multiple matings from the same cross”).

   

Matings involving progeny

To reserve a progeny for a future mating:
Reserve an organism from a mating result for a future experiment by doing one of the following:

• Fly exercises: with the Individual tab selected, drag the organism to the Strains box.
• Yeast exercises: drag one of the individual tetrads to the Strainsbox.

-OR-

• click on the organism/tetrad and then click on the Add to strains icon at the bottom of the Strains box.
  

To directly use a progeny for a new experiment:
You can also use a progeny from a past experiment for a future experiment without reserving it and adding it to the Strains box. Click on the progeny and drag it to the Mating site or set is as parent as previously described in section “Mating organisms.”

Punnett Square tool

You can use the Punnett Square tool to help decipher the genotype of a particular organism after performing a genetic cross. The Punnett Square tool allows you to determine the expected genotypic distribution of the progeny given the genotypes of the parents.

To use the Punnett Square tool:

1. Click on the Punnett Square button in the Tools box.
   
2. Select a genotype for each parent:
   
   • AA: homozygous dominant
   • Aa: heterozygous
   • aa: homozygous recessive
3. The genotypic frequencies for the cross are summarized at the bottom of the tool.
4. You can view a monohybrid cross or a dihybrid cross:
   
   
   

Yeast Exercises

When you open a yeast exercise, you have two choices for experimental set up:

• Non-tetrad experiment
• Tetrad experiment

Non-tetrad experiment

This type of experimental set up allows you to:

1. Test individual or multiple strains in selective media.
2. Perform a complementation test with one or more strains at a time.

Tetrad experiment

This type of experimental set up allows you to:

1. Mate two strains at a time and perform a simple complementation test.
2. Mate two strains and sporulate to generate tetrads for tetrad analysis.
3. Mate tetrads to other strains, including MATa or MATalpha tester strains to deduce tetrads' mating type.

Experiments using the Non-tetrad experimental setup

1. Drag a strain to the Drop strain here box. The Drop strain here box moves down to allow the addition of other strains to the same test.
2. Select
   
   • a lawn within the Select lawn box containing one of the available strains + the appropriate media within the Select media box to perform a complementation test
     
   OR
   
   • the appropriate media within the Select media box in which you would like to replica plate your strain(s) to test the strain(s) phenotypes. More than one media can be selected at a time by clicking on Crontrol + Command (PC) or Control + Apple (Mac).
     
3. Click on the Add button at the bottom of the Select media box.
4. Additional experiments can be performed by selecting the appropriate lawn and/or media and then clicking on the Add button.

Experiments using the Tetrad experimental setup

To perform a mating between two strains

1. To mate two strains you can use one of the following 2 methods:
   - drag each strain to the Drop here to mate box
   OR
   - click on the strain and then click on the Set as a Parent icon at the bottom of the Strains box.
2. The two strains will automatically mate to produce a diploid.
3. You can either
   - replicate plate the newly created diploid to do a simple complementation test by selecting the appropriate media within the Select media box. Click on the Add button at the bottom of the Select media box. More than one media can be selected at a time by clicking on Crontrol + Command (PC) or Control + Apple (Mac).
   
   OR
   - sporulate the diploid to perform tetrad analysis by clicking on the Sporulate button.

To conduct tetrad analysis

1. Once tetrads are generated (see "To perform a mating between two strains" section), you can perform tetrad analysis by selecting the appropriate media within the Select media box in which you would like to replica plate your tetrads. More than one media can be selected at a time by clicking on Crontrol + Command (PC) or Control + Apple (Mac).
2. Click on the Add button at the bottom of the Select media box.
   
3. To mate the generated tetrads to one of the available strains, select the appropriate strain within the Select lawn box + the appropriate media within the Select media box and click on the Add button at the bottom of the Select media box.

Renaming experiments & organisms

To rename an experiment:

1. To rename an active experiment, click on the text field containing the experiment's name
   -OR-
   To rename a saved experiment, click on the Rename button
2. Enter the new name into the prompt and click OK.

To rename an organism/strain:

1. To rename an individual organism/strain first click on the organism/strain. The organism's/strain's properties will appear in theProperties box on the left hand corner.
   
2. Click the "Name" text field.
3. Enter the new name into the prompt and click OK.
   

Discarding experiments & removing organisms

To discard an experiment:

1. Click on the Discard button next to the Mating button (Fly exercise) orSave experiment button (Yeast exercise).
2. A prompt will appear asking if you are sure you want to discard the experiment.
3. Click OK.

To remove an organism:

To remove an organism/strain from the Strains box, click on the organism/strain and then click on the Remove icon at the bottom of the Strains box.

• You can remove an organism/strain from the Strains box.
• You can't remove an organism/strain from the Mating site, but you can replace it with another organism/strain.
• You can't remove an organism/strain from the resulting progeny of a mating experiment.

Saving experiments

To save your work so that it can be accessed at a later time:

1. Click on File -> Save.
2. In the “Save As” field box, enter your desired name for the file.
3. To access the experiment at a later time, open StarGenetics. Click on File -> Open and click on the previously saved file.

Exporting data

To export the data generated in your StarGenetics experiments:

1. Click on File -> Export to Excel.
2. In the “Save As” field box, enter your desired name for the file.
3. Open the Excel file. The first tab within the Excel file corresponds to a summary of all your "Saved experiments". A summary of the "Discarded experiments" is available in a second tab.

Note: exporting data is currently only available for "Fly exercises".

Reporting bugs or asking questions

To report a bug, request a feature, make a comment,or ask a question on StarGenetics:

1. Click on the Send suggestionsbutton in the Tools box (Fly exercises) orSendSuggestion box (Yeast exercises).
   
2. Fill out the feedback form and click on Send Report.