Graduate Education in the Chemical Sciences Issues for the 21st Century: Report of a Workshop (2000) / Chapter Skim
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5 Portals to Knowledge: Information Technology, Research, and Training
5 Portals to Knowledge: Information Technology, Research, and Training
Pages 56-72
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From page 56... ...
What I mean is that you ought to be able to fire up your Web browser and have, at your fingertips, all the important information sources, plus the tools to analyze that information, calculational tools to correlate and make sense out of the raw data, visualization tools when that is appropriate, simulation tools, and molecular dynamics and quantum chemistry tools. It all ought to be available, point and click, on your Web browser.
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From page 57... ...
The key is that we now have the ability to take, for example, a whole series of databases in varying formats, such as various molecular biology databases, and a whole series of application programs, such as programs to visualize molecules, align molecular sequences, and construct phylogenetic trees of relationships based on those sequences, and so forth, and make them all look like one program. You interface through them and point and click as though you were on a Macintosh.
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From page 58... ...
, the Workbench searches through multiple databases simultaneously, with thousands of sequences. The results returned by the search include the number of database entries found relating to "human," the number relating to "myoglobin," and the number that related to both (Figure 5.5~.
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From page 59... ...
The Workbench then allows you to take that sequence and use a program called BLAST to find closely related sequences. For human myoglobin, BLAST returned several "hits" of myoglobin sequences from a chimpanzee, another kind of ape, a gibbon, a gorilla, and an orangutan (Figure 5.10~.
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From page 60... ...
But students and teachers need some introductory training in the use of the tool. Instead of trying, ourselves, to introduce the Biology Workbench to all of the faculty in the country, we started a process this past summer, in collaboration with the BioQUEST Curriculum Consortium at Beloit College, of building a community of biology instructors nationwide, working with them, and having them work with each other, to build curricular materials around the Biology Workbench and, in this fashion, to build a community of people who are building curricular materials.
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From page 61... ...
We are currently extending the Biology Workbench capabilities to a variety of computational chemistry functionalities. We are building Web interfaces for molecular dynamics, stochastic dynamics, and electrostatic programs.
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From page 62... ...
friendly computing and information environments are poised to have a profound impact on chemistry and all scientific education. DISCUSSION Robert L
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From page 63... ...
In fact, there is a growing amount of literature about people finding mistakes in the sequence databases. My colleague Shankar Subramaniam has developed a very powerful algorithm called PDS, Potential Density Functions.
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From page 64... ...
They talk about two tendencies: on the one hand, we should use the Internet to democratize information; on the other hand, there is a big difference in how people use this information and it depends on economic class, which cuts across the same fault lines as everything else in our society. I think the technology is getting so cheap that the real fault line is not going to be between people who physically have access to it or not; it will be between people who have access to the right guidance in using it or not.
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From page 65... ...
I also see a lot of research proposals that require an educational component, such as for the Research Corporation or for a NSF CAREER award, for which the educational innovation boils down to putting something else onto the Web. In my teaching of both freshman chemistry and advanced inorganic chemistry at the graduate level, I have two experiences that I think are important to relate.
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From page 66... ...
Then I asked myself what it was in my training that gave me this ability to connect 2D to 3D, which we do, whether it is on a computer screen or in a textbook. What suddenly dawned on me was that my wood shop classes in the seventh, eighth, ninth, and tenth grades were probably the greatest asset to my education in terms of my being able to connect two dimensions to three dimensions, a skill that is absolutely important to chemistry.
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From page 67... ...
This operation involves sliding the given sequence across all the thousands of sequences in the database of Protein Information Resource, and finding the ones that are most closely related. This figure shows the "hits" the most closely related sequences.
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From page 68... ...
to implement them in my classroom, without being personally involved in the creative process, I will do a mediocre job. If I have an intimate role in the creative process, then I will do a great job.
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From page 69... ...
The bottom line is that, in terms of how many bytes of information you can transmit per dollar, including dollars for infrastructure, this is a much more powerful technology than, for example, the printed word, in addition to the various things that it can do. It is like a fire hose.
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From page 70... ...
FIGURE 5.13 Executive summary of the National Computational Science Alliance Common Portal Architecture Project, taken from the Web site of Dennis Gannon of Indiana University, the "roadmaster" of the Alliance effort in this area. is a question of diverting the "stream" to a useful problem it is an engineering problem analogous to how you are going to get hydroelectric power from a waterfall.
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From page 71... ...
We talked about the need to speed things up and the need to be multidisciplinary in graduate education. It is the kinds of tools made available by information technology that can allow us to maintain a shorter time frame and let the students take their physical or chemical backgrounds and address the biological problem.
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From page 72... ...
involved with these types of issues is not a way to work John Schwab, National Institute of General Medical Sciences: I have heard people here comparing the Internet-driven information glut to a fire hose. This is a valid metaphor in terms of quantity, but not in terms of quality.
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