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Questions about the Project

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What is the Molecular ScienceStudent Workbench?
The Molecular Science Student Workbench (this web site), known as Biology Student Workbench, consists of curricular materials centered around molecular biological investigations, links to educational, scientific, computational, and informational resources, and communication tools to bind together a contributing community of educators. It is designed to give a transparent introduction to the use of the Biology Workbench for learning and teaching biology at all levels.

What is the Biology Workbench?
The Biology Workbench is a web-based tool for biologists. It is an open access computational interface and environment that permits anybody with a web browser to readily perform bioinformatics investigations, for research, teaching, or learning. The Workbench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.

This diagram of the workflow architecture of the Biology Workbench may help explain the functionalities of the BW.

What is the student interface to the Biology Workbench?
The Student Interface to the Biology Workbench (SIB) is an educational orientated interface to the Biology Workbench interface developed as part of the Molecular Science Student Workbench. We have developed SIB for people who have little experience with bioinformatics and associated tools. In particular, the development of SIB has been orientated towards high school and undergraduate education. For more information, see the home page for the SIB project.

How can I participate in the MSSW?
If you are a teacher or student at any educational level and are interested in bioinformatics, we welcome your participation. If you have designed or are interested in designing educational materials for investigating bioinformatics topics, and would like to share these materials with others, please contact Kevin Messner or Brent Palmer for suggestions on how to post your materials.

The MSSW project team also presents workshops to teachers and researchers interested in bioinformatics education.

We welcome your ideas, large and small! Please feel free to contact us for more information on participating or if you have other ideas for possible contributions and collaborations.

What is the "Inquiry Page?" What does it have to do with biology?
The Inquiry Page is a dynamic virtual community where inquiry-based education can be discussed, resources and experiences shared, and innovative approaches explored in a collaborative environment. At its core, the Inquiry Page provides an easy way for users to generate web pages with little to no experience in HTML, on any subject of interest to them, which are viewable across the Internet.

Many of the Molecular Science Student Workbench resources are available on the Inquiry Page. This arrangement allows open access and a wide audience of educators for MSSW units. Biology teachers may also be interested in other biology subject content on the Inquiry Page site. Additionally, because users can easily comment on and "spin off" ideas they see on the Inquiry Page to make their own units, the site is becoming a forum for discussions, collaborations, and idea growing.

Please also see the Inquiry Page section of our Curricular Materials page for more information on how the Inquiry Page can be used for posting MSSW materials.

Who can I contact for more information on the MSSW project?
For questions about the MSSW program and how you can get involved, contact Umesh Thakkar. For questions about bioinformatics and its part in biology curricula, contact Eric Jakobsson. For information on the Inquiry Page and inquiry-based learning, contact Chip Bruce. For technical questions about the student interface to the Biology Workbench, contact Bruce Southey. For questions, problems, and suggestions for this website, please contact Deanna Palmer.

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Questions about Bioinformatics

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What is bioinformatics? Why is it important?
A National Institutes of Health committee defined "bioinformatics" broadly as "Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data." When most biology researchers talk about bioinformatics, they are talking about using computers to compare and analyze DNA/RNA sequences and protein structures.

To understand the basic idea of bioinformatics, one might think of a written language. The text you are reading consists of a series of letters, words, sentences, and paragraphs. If you did not know the meanings of the words and the rules of the language, this page would just be a collection of meaningless symbols. Similarly, the first time scientists saw gene and protein sequences, they saw a string of symbols with no clear meaning in terms of biological function. But now, bioinformatics is showing us many things about what sequences mean. Using bioinformatics, sequences are being used to reveal relationships among different life forms that we could not find out any other way. Bioinformatics is revealing the rules and meaning of a language that is new to human beings but in fact is billions of years old -- the "Language of Life."

Bioinformatics is an important part of modern biology because it allows scientists useful, powerful ways to look at their data. It's one thing to have several DNA sequences from different organisms written down on a piece of paper, but it's quite another to have those sequences available in computer databases and to be able to use computers to compare how similar those sequences are, investigate what functions the DNA sequences might have, etc. Another important point is that the number of available DNA sequences is growing exponentially, so bioinformatics work is becoming more productive because larger datasets on more organisms and genes are available for exploration.

Where can I learn more about bioinformatics?
Please see our Resources and Links page for many other sources of information on bioinformatics.

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Technology Questions

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What browser requirements are there for using the Biology Workbench and the various tools?
Suggested Web Browser: we suggest that people use Netscape Communicator or Navigator, preferably the latest version that can be obtained (any 4.x version should work well). Microsoft Internet Explorer (especially older versions) can be unpredictable when loading the Biology Workbench. In addition, because we are unable to force Internet Explorer to open seconary windows with our software, showing database records and reading help pages can be a bit clumsy. Nonetheless, most Biology Workbench operations *should* work within Internet Explorer.

Structure Viewing: PDB structures can be viewed for PDBFinder records that are returned from a database search. One way to do this is to use the Rasmol program. The Chime plugin is another option for viewing structures on Windows and Macintosh machines, and we may eventually provide a Java-based structure viewer. For molecules with Protein Data Bank structures, we also provide links to the PDB Structure Explorer page for that particule molecule, and to the Protein Explorer display for that particule molecule.


Why is my Biology Workbench session sometimes very slow?
We have long been aware that the connections with the Biology Workbench can be rather slow. I've had suspicions over the cause of these problems, but until now have been unable to determine the cause(s) for certain. Information provided to be by Mary Ball helped me determine the likely culprit. Mary noted that connections to Mihye Won's student interface for the Biology Workbench were quite a bit faster and more reliable. Since Mihye's program acts as a front end for the Biology Workbench, this places the blame on the Internet connection between the site of the user(s) and UC-San Diego / San Diego Supercomputer Center (SDSC). The connection between the University of Illinois / National Center for Supercomputing Applications (NCSA) and SDSC is on the Internet 2 -- a much faster network with much less traffic. Illinois must have sufficient capacity to handle incoming traffic from the public/commercial network that the users are on, but SDSC at times doesn't. After conferring with a network expert at SDSC, I have learned that this is indeed the cause of the slowdown. We will try to get capacity at our site increased; we now have good cause to show it is not sufficient. I don't think this will happen in a reasonable time, however, so there are two solutions:

1. Use Mihye's student interface for now, if that is sufficient for your needs.
2. In the near future (by the end of the year, I would hope), we should have a mirror of the Biology Workbench up and running at NCSA. We will suggest that most workshops and activities use that site.

I'm having trouble understanding how to use the Biology Workbench. Is there someone I can contact with my questions?
As a first step, if you have not tried one of our tool usage tutorials, this is a logical place to start to learn to use the Workbench. We also suggest you take a look at the Biology Workbench's FAQ page to see if your question is answered there. If you encounter software problems or find any bugs in the Biology Workbench, and are unable to send a bug report from within the software, please send a report to Biology Workbench Help at the San Diego Supercomputing Center. You may also contact Eric Jakobsson or Deanna Palmer with questions about using the Biology Workbench. Questions on the Student Interface to the Biology Workbench should be referred to Bruce Southey.

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