Updated: 4 March 2003
There are no written examinations in C472. Student grades will be based
on class participation (20 percent), a final paper or project (20 percent),
and assigned exercises, which account for the remaining 60 percent.
1/29 Exercise 1 SciFinder Scholar
2/12 Exercise 2
3/12 Exercise 3
3/26 Exercise 4
4/23 Exercise 5
4/30 Exercise 6
5/7, 5:30 PM Paper (Choice of topics; in lieu of final exam)
5/7, 5:30 PM Project (in lieu of final exam)
Your paper should be no less than ten pages long (double-spaced, type-written),
exclusive of the bibliography and title page.
References must conform to the second edition of
The ACS Style Guide (QD8.5.A25 1997 Chemistry Library Reserves).
Your final authority for journal abbreviations is CASSI (available via any
Web OPAC in any library on the IUB campus at the
libfind page: http://www.indiana.edu/~libfind or
in print form at the IUPUI University Library).
I am not looking for an original contribution from you, but rather, a
review-type article that tells what's available in the various areas.
You should demonstrate to me that you have read about and investigated the
appropriate databases/software/publications/etc. and describe them in some
You could look for secondary information sources in the various reading lists
for the chemical informatics courses. See the Web pages at:
In the C571 list, you'll see a lot of references to the Encyclopedia of
Computational Chemistry. That's a very good source that is in the IUB
Chemistry Library Reference Area: QD39.3.E46 E53 1998. Its coverage is much
broader than the title implies.
Note that you are not limited to the topics suggested below.
However, topics that are not yet on this list must be approved in advance by
- CrossFire Commander: software and databases searchable through it
- Front-end and Web Software for Searching Chemical Databases: A comparison
of SciFinder Scholar, STN Express and others
- Access Routes to the Chemical Abstracts database: What are they and
why should you use one over the other
- Physical Property Databases and Publications
- Spectral Databases and Publications
- Crystallographic Databases and Publications
- Biosequence and Biostructure Databases and Publications
- Proteomics Databases and Publications
If you choose to write on any of the database topics, a good source of
information is the STN Database Summary Sheets found at:
Use the Journal Citation Reports (found at the
http://www.indiana.edu/~libfind page) to identify the top three primary journals
in each of the database fields and write a brief paragraph about each journal.
Write a brief introduction to the bioinformatics and proteomics databases and
programs, concentrating on those available at NCBI,
the National Center for Biotechnology Information,
(You may want to create a Web page that links to some of the
- Identify commonly-used molecular biology information resources
- Describe the components of a GenBank record, including the similarities and
differences with a bibliographic record
- Explain how to retrieve nucleotide and protein sequence records by text
term searches in the Entrez system
- Include information on commercial systems for sequence searching,
such as STN
- Explain how to conduct a basic sequence similarity search using the BLAST
search system with a nucleotide or protein sequence as the search key
- Explain how to retrieve 3-D structure records by text term searches and
display them with a structure viewing program
- Identify genome and mapping resources on the NCBI Web site for humans and
- Explain how to retrieve genome records by text term searches and display
the graphic view of the genome map(s)
Your grade in this class is based on the following:
||Value of Each
six exercises, etc.
- above 980: A+
- 951-980: A
- 901-950: A-
- 851-900: B+
- 801-850: B
- 751-800: B-
- 701-750: C+
- 651-700: C
- 601-650: C-
- 551-600: D+
- 501-550: D
- 451-500: D-
- 401-450: F+
- 351-400: F
- 301-350: F-
The final paper or project is due no later than Wednesday, May 6, 5:30 p.m. The
exercises, etc. are due no later than
the beginning of the class period on the the day on
which they are listed in the class schedule. Unless you have a very
valid excuse, four
points are deducted for each day the assignment is late. Four points are
also deducted if you fail to put your name on a hand-in assignment.
If handed in after the day/time indicated, you lose:
- W after 5:45 PM 4 points
- Th after 5:45 PM 8 points
- F after 5:45 PM 12 points
- M after 5:45 PM etc.
- Not accepted if more than one week late.
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