Biology WorkBench (v 3.0)

• Serves as a resource used by students, professors and researchers to keep track of the latest happenings in the     exploration of molecules.  The Workbench views sequences as objects on which it can perform Protein, Nucleic     and Alignment tasks.

• Overview of a Introductory Session.

• Necessary resources for utilizing Biology Workbench:
• The preferred browser is Netscape 3.0 but 4.0 is also OK.  See downloads.  Microsoft Explorer 4 will not work satisfactorily and is currently being worked on..
• Access the  Biology Worksheet website to begin.
• To view molecular structures from within your web browser, you will need CHIME for Netscape or RasMol for other browsers.  See downloads.

After accessing the Biology Workbench webpage biology.ncsa.uiuc.edu the first thing that you should do is register.  Access the User Registration page in order to start your session and provide your name and email address.  Enter a User ID and Password that you will have to remember for access for Biology Workbench sessions.
 
Note: Biology Workbench 2.0 has been discontinued since May 17th, 1998 but the entry page still welcomes you with this version. Just access version 3.0 which is in a smaller font below it after you have registered.

After being prompted for a User ID/password you are ready to begin your first session:

• The demo is just a look at what the interface looks like and does not seem to provide any more then that,so below is just a quick introduction on using the Protein Tools.
• The user may pick Session tools which is a way to keep track of previous sessions to be retrieved at a later time or you can simply do a one time session.
• Don't forget to have something highlighted when you press either the "submit" or "Perform Selected Operation" buttons

1. Select Protein Tools.  The WorkBench views sequences as objects on which it can perform tasks.

• The Protein Tools take protein sequences as inputs.
• The Nucleic Tools take nucleic sequences as inputs.
• The Alignment Tools take aligned sequences as inputs.
• The sequences created using the Protein or Nucleic Tools will send you to the Alignment tools.
 
1. Select SRS - Multiple Database Search

• Unless you are Adding sequences to the DataBase then you are limited to Searching Databases.  The search tool is the SRS which allows users to access multiple databases.  See database description for a description of how each database organizes it data.
• You are now in the SRS - Database Query Form.  Enter only word per field but you may use wildcard characters.  '*' searches for a particular pattern.
 
1. Type in "2mcg" in the field (this is an immunoglobulin sequence) and select the "PDBFINDER" database in which to query you submittal.

• The results should state which records match the field that was submitted.  If there was a match then select that sequence and choose either View Objects, View Sequences or Import to Workbench.
• View Objects displays the original database annotation that was indexed for that record along with the sequence from that record.
• View Sequence will display the sequence associated with that database record.
• Import to Workbench brings sequence information from ALL selected records, to the WorkBench for comparison and alignment. to other sequences.

1. Highlight the Sequence and Select View Objects.  You may select view the structure of that sequence. See below.

• You need to have the appropriate molecular viewer installed in order to view the structure.  See downloads and get CHIME.
• See tutorials for instructions on how to use CHIME.

1. After viewing the sequence select Import to Workbench which enables you to save it for future sessions.

• There will be another introduction to Biology WorkBench 3.0 in the near future which will cover the Nucleic and Alignment Tools.
• A very good tutorial in the meantime is one developed by Dr. Eric Jakobsson at  www.ncsa.uiuc.edu/edu/rse/bw/bw_demo.html as an introduction to molecular evolution.