John David N. Dionisio, PhD

John David N. Dionisio, PhD

Assistant Professor, Computer Science

http://myweb.lmu.edu/dondi

dondi@lmu.edu

Doolan 106, (310) 338-5782

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Fall 2009
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- Fall 2006
- Summer 2006, Session I
- Spring 2006
  - BIOL 498/CMSI 698
  - CMSI 252
  - CMSI 365
  - CMSI 499
  - CMSI 587
- Fall 2005
- Summer 2005, Session I
- Spring 2005
- Fall 2004

Curriculum Vitae

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`BIOL 498/CMSI 698` Special Studies: Bioinformatics Spring 2006

Kam D. Dahlquist (kdahlquist@lmu.edu) and John David N. Dionisio, Co-Instructors

Note: This page is maintained as an archival record of the course shown above, and as such, some links on this page may no longer be valid nor accessible. They are kept here as a record of the resources that were available at the time of the course offering.

All materials are in PDF. Sorry, you won’t find source code or solutions here; contact us directly for those.

Syllabus
Assignments
Handouts
- 0112: What is Bioinformatics?
- 0112: The Relational Data Model: Structure
- 0126: PostgreSQL Quick Start
- 0126: XML, Objects, Relational Databases, Oh My!
- 0209: UML Specification by Example 1: Use Cases
- 0209: UML Specification by Example 2: Data Models
- 0427: Final Report and Evaluation
Our XMLPipeDB SourceForge project — be there or be square :-)

Related External Links

These links take you to Web sites beyond this server.

Biological Databases

Nucleic Acids Research Annual Database Issue (January 2006)
NCBI: National Center for Biotechnology Information
- GenBank (nucleotide); RefSeq; UniGene
- Gene
- PubMed
- OMIM/OMIA
- Taxonomy
UniProt (formerly known as SwissPort)
Ensembl
Gene Ontology
PDB: Protein Data Bank
Pfam
KEGG: Kyoto Encyclopedia of Genes and Genomes
BioCyc (including EcoCyc, MetaCyc, HumanCyc)

Model Organism Databases

Saccharomyces cerevisiae	yeast	SGD: Saccharomyces Genome Database
Caenorhabditis elegans	nematode/roundworm	WormBase
Drosophila melanogaster	fruit fly	FlyBase
Mus musculus	mouse	MGI: Mouse Genome Informatics
Rattus rattus	rat	RGD: Rat Genome Database
Arabidopsis thaliana	Thale cress (mustard plant)	TAIR: The Arabidopsis Information Resource

UCSC Human Genome Browser
TIGR Comprehensive Microbial Resource

Biological Dictionaries Online

Biology-Online.org
Dictionary of Cell and Molecular Biology
BioTech’s Life Science Dictionary
Cancer Dictionary
Biomedical Abbreviation Server
Wikipedia is a good starting point for virtually any lookup, biology or otherwise
- Wikipedia search for bioinformatics

Journals in Bioinformatics and Related Areas

High-impact, general journals that publish the occasional paper
Specialty journals
- PLoS Computational Biology
  - Many useful links in this article on the bioinformatics “resourceome”
- Nucleic Acids Research
- Bioinformatics
- Genome Biology
- Genome Research
- Journal of Computational Biology
- Molecular and Cellular Proteomics
- Briefings in Bioinformatics
Industry news: Genome Technology

Societies

International Society for Computational Biology

Software and Programming Resources

BLAST: Basic Local Alignment Search Tool
The GenMAPP home page
Open Bioinformatics Foundation
Pick a language or technology: BioPerl, BioJava, BioPython, BioRuby, BioPipe, BioSQL/OBDA, BioMOBY, BioDAS, BioLisp
The SourceForge home page
The PostgreSQL home page: an industrial-strength, open source database management system
- Go to http://jdbc.postgresql.org to access PostgreSQL’s JDBC Driver
Hibernate home page
Xdoclet home page
XML resources:
- Tutorial and reference on XML Schema (xsd)
- JAXB home page
- HyperJAXB home page
The LaTeX home page
The MikTeX home page: a highly popular LaTeX implementation
The Perl Documentation Web site
Perl Monks: Ask for Perl advice here, and ye shall receive

Useful and Amusing, by Jeff Shrager