Introduction to Biology
Workbench
Go to Biology Workbench from the class web site
and set up your account, if you don't already have one. I
suggest running the tutorial in one window, and Workbench in
a second window. That way you can toggle between them.
Although you will be saving sequences on your account,
you'll still want to keep a log for making notes, recording
ideas, results, and most importantly- questions which you
want to follow up in discussions.
Topics of focus 2/7:
- General considerations & tips
- Session Tools
- Protein & Nucleic Tools- search & management
tools
General considerations & tips:
1. Click on the top banner to select the
navigation format you prefer. I find that depending on what
I'm doing, I sometimes want to switch. Toggling is
accomplished on any page with a Title banner. Until you are
familiar with the available tools, you'll probably prefer
one of the two types of menu lists.
2. Avoid using the back button on the web browser.
Instead, use "return" and "abort" buttons in
Workbench to go back.
3. You need to save the sequences you import to
the Workbench. Alignments are saved as part of
running them. Analysis results are not saved. You'll need to
download and/or print them for future use.
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Session Tools:
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Tools
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Descriptions
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Resume Session
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Selects the marked session in the list, allowing
access to the sequences in that session.
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Start New Session
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Creates a new session.
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Copy Session
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Creates a new session containing the stored
information of the selected session.
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Rename Session
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Changes the name of a session.
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Delete Session
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Removes a session permanently- be careful!
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Download Session
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Saves a copy of the session to your computer
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Upload Session
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Restores a session from your computer
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1. To actually begin a session, select Start
New Session, then click the "Run" button.
2. To name your session, enter the information in
the text box. To change the name later, use Rename
Session.
3. The sessions you create or rename will be
automatically saved.
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Protein Tools & Nucleic
Tools:
Listed below are the file management tools available as
part of the listed protein sequence tools and nucleic
sequence tools. More information regarding these and the
other tools is provided in Biology Workbench. For
help and expanded information, click the "Help" button on
the active page.
The tools listed here might seem "dull", but a little
time spent with them will make navigation and use of the
Workbench more comfortable and productive. [The nucleic
list is similar.]
- Select All Sequences
- Deselect All Sequences
- Ndjinn - Multiple Database Search (pronounced
"engine")
- Retrieve BATCH Output
- Add New Protein Sequence
- Edit Protein Sequence(s)
- Delete Protein Sequence(s)
- Copy Protein Sequence(s)
- View Protein Sequence(s)
- Download Protein Sequence(s)
- View Database Records of Imported Sequences
- View Available Scoring Matrices
1. After starting a session, select Ndjinn
to search for and retrieve some sequences. Select one or a
few databases to search. Be aware that you may retrieve
identical sequences from different databases, due to shared
files.
2. You can select all, or some, sequences to
retrieve. To be selective for several sequences at once, use
Ctrl-click to highlight what you want.
3. You can enter sequences from your files or logs
by using Add New Protein Sequence. Copy/paste the
sequence into the text box. I strongly recommend that you
enter sequences as FASTA, or check to see that your file
format is supported.
4. Using Edit Protein Sequence(s), you can
name them so they are recognizable in results pages. For
example, you may want to use the names of the source
organisms or the name of the gene product. The default
display in results is the accession number. You can also
modify the sequences themselves. [See 5 below.]
5. To modify a retrieved sequence, such as
limiting it to a given motif or domain, use Copy Protein
Sequence(s), then edit away. It is a good idea to make a
notation in the label as well. By copying first, you have
the option of returning to the original sequence to try
other things.
6. If you want to use tools which are not part of
Workbench, it isn't a problem. Just download them to
your computer, then you can easily upload them to
applications of your choice.
Play with your sequences to become familiar with these
tools. Check out some of the "interesting tools". Let me
know which ones you want included in focused discussions in
future.
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For next week, I've already selected for you based
on interest and inquiries I received last semester. ClustalW
[MSA], Boxshade, and tree-building will be the focal
points. [It would really help if you do some MSA runs
before next week, since sometimes these can take a while to
do.]
1. Browse/Read in Bioinformatics: Ch 8
& 9
2. Set up one or two working sessions on
Biology Workbench. a. Select sequences of
interest. Run BLAST on one sequence. Compare results
between gapped and ungapped, +/- filtering. Printing these
will help in making comparisons. b. Try running
MSA [ClustalW] on 3-4 closely related
sequences plus 3-4 sequences which are somewhat related, all
as a single group. We'll use these next week for some
alignment applications, such as "Boxshade" and
tree-building.
3. Continue with the Workbench tutorials
and the game. Make note of difficulties you encounter for
discussion in lab next week.
4. Bring your laptops for Dina's interactive
PowerPoint presentation. I have Apple laptops for anyone who
needs one. Please let me know.
5. You'll want to bring some paper for printing
computer lab results as well, such as alignments and
trees.
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