- What does the Teacher's Kit contain?
- A short series of prepackaged lectures designed to introduce a group of students to sequence analysis and bioinformatics. These lectures can be modified in any way to better suit the needs of your particular group. Powerpoint slides are included.
- A practical class exploring BioNavigator, and including a set of exercises to set your students.
- A teachers' pamphlet including general guidelines and answers to the set questions.
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- What is the BioNavigator Tour?
BioNavigator is intuitive to use, and takes only a short time to get to know. Take the tour for a quick overview to get you started. For a more in-depth introduction to BioNavigator, try the tutorial which leads you through the various sections of BioNavigator and demonstrates how to run a program and access the sequence databases.
- What are Protocols and who should use them?
Protocols are step-by step guides to complex bioinformatics analyses which allow you to answer "high level" biological questions or perform routine analyses. Protocols remove the need to spend hours puzzling over which programs or files to use with your data, and are an excellent way to learn about many bioinformatics tools.
Protocols are most suitable for novice bioinformaticians, or for biologists who don't have a lot of time to spend at the computer. Protocols are a convenient and simple way to discover the secrets of many useful bioinformatics analyses, letting you analyze data easily and efficiently so that you can return to the laboratory sooner. Protocols cater for busy scientists, who may need to interrupt an analysis unexpectedly, but want to return later to complete it, without having to repeat the steps they have already done.
Protocols also let you perform analyses that are unfamiliar or you do infrequently, in an efficient way. With their guided and highly visible approach to bioinformatics analysis protocols are also an invaluable teaching tool.
- What is the BioNavigator Tutorial?
The BioNavigator tutorial is a 2-volume series of workbooks in PDF format which provide a detailed introduction to BioNavigator’s user-friendly and accessible interface, using step-by-step instructions that take you through worked examples.
These workbooks have been developed to be used in conjunction with a BioNavigator account.
- What are the future plans for BioNavigator's Educational Resources?
Entigen is involved in setting up an internet-based community education program open to high school students and other interested parties. The aim of this program will be to ensure that teachers of young people, students of all ages and experience, and the wider population have a good understanding of the issues at the heart of the `biotech revolution'. In the slightly longer term, a text book to accompany BioNavigator will also be available.
How do I get HELP?
- How do I get HELP?
Look for  at the top right hand corner of the BioNavigator screen if you require help or more information at any point while using BioNavigator. Type in your keywords and click the Help button. BioNavigator will search all relevant documents and display your results in a pop-up window.
Alternatively, if you click the Help button a context-specific help window will appear e.g. if you are viewing Text Search when you click Help, the help window will contain information on using Text Search.
If you cannot find help on what you are looking for email support at your institution.
- Help Topics
"Help Topics" contains 6 sections:
- Contents: This contains General Help topics, such as ambiguity codes and scoring matrices, help on Sections of BioNavigator such as File Manager and Work Bench, help on all Programs e.g. blastn and Macros and help on Databases such as about the different databases and understanding database entries.
- A-Z Index: This contains an alphabetical list of all the help topics available in BioNavigator.
- Programs: This contains a list of all the programs available within BioNavigator. Click on a program name to view the help for that program.
- Databases: This contains a list of all the databases available on BioNavigator. Click on a database name for a brief description of that database. There is also help on understanding the different database records.
- Protocols: This contains information on how to use Protocols in BioNavigtor as well as a list of all the Protocols available in BioNavigator. Click on a Protocol name to read the overview for that Protocol.
- Search: This is a search function which allows you to search all of the BioNavigator help documents by typing in keywords to search for. You can use this if you cannot find the information you require using the other headings.
- How do I get Help on using Help?
When you view a Help window, click the  button for a complete description of the online help system.
- How do I get Help on a particular subject?
Type in your keywords in the box at the top right hand corner of your screen and click the Help button. BioNavigator will search for relevant help documents and display your results in a pop-up window. Note: You can also search help from Help Topics and Using Help.
- How do I get Help on the page I'm currently viewing?
BioNavigator's Help is context-sensitive. This means that when you click the Help button at the top right hand corner of your BioNavigator screen a help window will appear which is specific to that screen e.g. if you are viewing Text Search when you click Help the help window will contain help on using Text Search. If you are viewing a page such as a multiple sequence alignment file or a nucleotide sequence file the context-specific help will explain the features of these files.
- How do I get Help about a particular program I want to run in BioNavigator?
Detailed Help is available on each program available in BioNavigator including help on options used by the program, references for the program including how to cite it and information on the algorithm used by the program. This can be accessed in BioNavigator by:
- When you view the list of available programs in Program Index you will see a short description of each program. This description is followed by the words "(more...)". If you click this then help on that particular program will appear in a pop-up help window. OR
- When you are viewing the program options page to run a program click the program name (in the top left of the page) to access the Program Help. You can click an option name to find a description of that particular option within the Program Help. OR
- Click
 within a Help window. The contents of the Help Topics page includes a link to an alphabetical list of programs. From this list, clicking on the program name will find the Program Help for that program.
- How do I get Help on Macros?
All Macros, including ones that you generate, have individual help pages. This provides the author, description, functional category, a graph displaying all the analytical pathways involved (including program options used that you can access and change by clicking on the program name), all input file types required, all output file types produced and instructions for citing the results of the Macro in a publication.
Help is available by clicking on the (more...) link next to a Macro description in Program Index and Protocols or by clicking the Macro name in the top left corner of Work Bench or the main Macro page. The same help is also available from within the BioNavigator help system. Click the Help Topics button at the top of this page, then the A-Z list of program and Macro help link.
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bioinformatics workspace
