Educational materials

Guest Lectures

NMPDR - Connecting Bioinformatics to the Bench
McNeil LK

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Presented to:
MCB 426 Bacterial Pathogenesis
Chem 574 Genomics, Proteomics and Bioinformatics
MCB 432 Computing in Molecular Biology
Subsystems Annotation
Reich CI

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Presented to:
MCB 432 Computing in Molecular Biology
CPSC 569 Applied Bioinformatics

Assignments

Exploring selenocysteine biosynthesis across all three Domains using the National Microbial Pathogen Data Resouce

Prerequisite reading:
iconNMPDR training workshop handout (new window)
On the road to selenocysteine   iconfull text

Assignment worksheet   icon writable document

Used by:
MCB 432 Computing in Molecular Biology
CPSC 569 Applied Bioinformatics
Using NMPDR to investigate pathogenesis

Prerequisite reading:
icon NMPDR training workshop handout (new window)
Mechanisms of Bacterial Pathogenesis   icon full text

Inquiry Unit (a loosely structured, gently guided search of the Web)   icon writable document
On-line versions focused on Campylobacter, Listeria, Staphylococci, Streptococci, or Vibrio are writable after registration at the iLab site that hosts our user forums.

Used by:
MCB 426 Bacterial Pathogenesis

Other Resources

Using NMPDR and GBrowse
NMPDR training workshop handout, illustrated
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Annotating Proteins and Adding Proteins to Subsystems—A Worked Example
NMPDR-SEED training workshop handout, illustrated
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Introduction to NMPDR
Training course via webCT at NCSA


Suggested References

The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation.
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53; [Epub 2006 Dec 1]    icon PMID: 17145713

This paper is the primary description of the data and tools available at NMPDR.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702.    icon PMID: 16214803

In this paper, subsystems are defined, and the SEED annotation environment that supports the creation, curation, population and exchange of subsystems is described. The SEED is used by the NMPDR curation staff, and a public version is available for community annotation.

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