Classes

Research

Publications

Personal

Links





Links to Useful and Interesting Websites

 









List of Topics
Regional Scientific Meetings
Gene and Gene Product Databases

Gene and Gene Product Analysis
DNA Array and Microarray Technology
Viruses
Scientific Journals
Biotechnology Sites
Biotechnology Corporate Websites
Environment and Sustainability
Chemistry Websites

Utility Programs
Miscellaneous

Regional Scientific Meetings
Argonne Symposium for Undergraduates
Butler Undergraduate Research Conference
IRC Undergraduate Research Symposium
Poster Presentation Advice (Colin Purrington's website)
Giving Science Talks (Colin Purrington's website)

Gene and Gene Product Databases

NCBI (National Center for Biotechnology Information, a branch of NIH)
Entrez
(Genbank, the main repository for genetic information; this is a part of the NCBI)
TIGR Database (The Institute for Genomic Research, a genome sequencing company)
Uniprot (EMBL database of protein sequences)
The Human Genome Project (The organization coordinating the sequencing of the human genome)
Genome Web (List of gene databases)
BLAST server (Sequence alignment and search server at NCBI)
Center for Genome Research (Whitehead Institute at MIT)
JGI Genome Portal (Database of sequenced genomes with analysis tools)
RNA Modification Database (database of modifications to RNA bases)
GMoS (G-protein coupled receptor Motif Searcher, a web-based program for finding sequence motifs in GPCRs)

The Complete Human Genome

Science
Special issue on the human genome
Nature
Special issue on the human genome
Human Genome Project
(U.S. Department of Energy website covering the genome sequencing effort; note that the actual sequence information is deposited in Genbank)
Cracking the code (PBS NOVA program on the genome project)

Gene and Gene Product Analysis
Protein Databank (Repository of protein 3D structural information)
NCBI (National Center for Biotechnology Information)
ORF finder (NCBI server for finding open reading frames)
Guide to Molecular Sequence Analysis (Guide to bioinformatics nomenclature and techniques)
BLAST server (sequence alignment and search)
EMBL (European Molecular Biology Laboratory)
ExPASy Molecular Biology Server (Server that contains a variety of molecular biology tools, including translation of nucleic acids, similarity searches and alignments, and secondary and tertiary structure prediction)
Uniprot (Curated database at EMBL-EBI containing protein sequence and functional information)
IntAct (Molecular interactions database at EMBL-EBI)

Serial Cloner (Macintosh/Windows program for performing restriction and other types of analysis on DNA sequences)
tacg  This is a website that performs restriction analysis of DNA sequences. It is less convenient than programs like DNA Strider, but it runs on both PCs and Macs.

Webcutter (Server that performs DNA restriction enzyme analysis)
NEBcutter (Server that performs DNA restriction enzyme and ORF analysis)
Swiss-Model (Automated homology modeling server)
K2D3 (Server for predicting secondary structure content from CD data; instructions are here)
DNA Learning Center (Cold Spring Harbor Laboratory analysis tools and resources)
SAGE (Serial Analysis of Gene Expression, run by NCBI)
Cytochrome P450 Homepage (David Nelson's page on cytochrome P450 properties and nomenclature)
GEO (Proposal for database of gene expression data)*
ArrayExpress (Pilot database of microarray gene expression data)
WIT "What Is There", a site devoted to analysis of genome information and development of metabolic models (note: registration required)
RNA Secondary Structure Prediction Server (RNA structure prediction and information page)
Online Mendelian Inheritance in Man (NCBI Database of genes and genetic diseases)
Genomics Glossary (Compendium of terms used in biotechnology and pharmacology)
Comparative Toxicogenomics Database (database of environmental chemicals and disease)
DNA Array and Microarray Technology
Gene Chips (DNA microarray summary site)
Affymetrix (GeneChip manufacturer)
SuperArray, Inc. (Arrays using small numbers of probes)
ArrayExpress (Pilot database of microarray gene expression data)
Microarray (website containing discussion and links related to microarray technology)

Viruses
CDC (Centers for Disease Control and Prevention)
NIAID (National Institute of Allergy and Infectious Diseases, the NIH organization coordinating and funding research related to viruses and bacteria)
Emerging Infectious Diseases Journal Homepage (a CDC journal)
All the Virology on the WWW (compendium of virus related websites)
World Health Organization Avian Influenza Page
PandemicFlu (US government website with information about current influenza issues)
Influenza Virus Resources (NCBI website with tools for influenza genetic analysis)
Virology (website at University of Leicester)
Retroviruses (On-line textbook at NCBI)
Virology Journal (Open access journal devoted to virus research)

Scientific Journals (Note: some of these sites restrict information available to non-subscribers)
PubMed (Web-based free Medline search)
Science Virtual Library (Compendium of science oriented websites)
Science

Nature

Cell
Journal of Biological Chemistry

Proceedings of the National Academy of Sciences

Chemical & Engineering News
Endocrine Society Journals
New England Journal of Medicine

The Lancet


Biotechnology Sites
NBIF (National Biotechnology Information Facility)
Council for Biotechology Information (A biotechology news and information website)
PhRMA (A news and information website run by a pharmaceutical lobbying group)
Genetic Trail (Howard Hughes Research Institute site discussing genetic disorders)
Human Genetics Education Resource (A compendium of links to different university genetics websites)
Food Biotechnology (International Food Information Council)
OBA (Office of Biotechnology Activities at the NIH)
Biospace ("The Global Hubsite for Life Sciences")
ISB (Information Systems for Biotechnology)
Molecular Biology Resources Online (a compendium of history and techniques links related to molecular biology)
NCBE (Guide on genetically modified foods run by a site in the United Kingdom)
Global Issues in Biotechnology (US Government site for addressing biotechnology issues)
Genome Channel (Annotated genome information; Note: requires recent version of Java)
BIO (Biotechnology Industry Organization)
REBASE (Database of available restriction endonucleases)
BioProcess (Amersham website containing information and techniques related to protein purification)
Protocol Online (A compendium of protocols for biochemistry laboratory techniques)

Biotechnology Corporate Websites
Amgen
Bio-Rad
Clontech
Eli Lilly and Company
Genentech
Life Technologies (Invitrogen)
New England Biolabs
Perkin-Elmer Applied Biosystems
Promega
Stratagene

Environment and Sustainability Related Sites
Green Chemistry (Green Chemistry site at the Environmental Protection Agency website)
GEMs Database (Greener Education Materials for Chemists)
Toxnet (Portal to NIH databases on toxicology, hazardous materials, environmental health and related topics)
Haz-Map (NIH Database of hazardous agents)
Comparative Toxicogenomics Database (database of environmental chemicals and disease)
State of the Climate (reports from the National Oceanic and Atmospheric Administration)
IPCC (Intergovernmental Panel on Climate Change, see especially the 2007 and 2013 Physical Science Basis reports)
Greenhouse Effect (American Institute of Physics coverage of the science underlying the effects of carbon dioxide on climate)

Chemistry Websites
SDBS Database (Integrated Spectral Data Base System for organic compounds)
NIST Chemistry Webbook (National Institute of Standards and Technology spectral and physical property database for chemical compounds)
Handbook of Chemistry and Physics Online (An extensive compendium of tables for chemical and physical properties)
ChemExper (ChemExper Chemical Directory, a database of chemical compounds)
ChemBioFinder (Chemical compound database; registration required)
ChemIndustry (Chemical industry search engine)
PhysProp (Physical properties database at Syracuse Research Corporation; requires CAS number of compound)
Sigma-Aldrich (Catalog and database of molecular properties)
Cheminformatics (Databases and web-based software for predicting properties and NMR spectra)
Comparative Toxicogenomics Database (database of environmental chemicals and disease)
SpectroscopyNow (News and database site for IR, NMR, and other types of spectroscopy).
Organic Chemistry Help (Tutorials on organic chemistry)
The Delights of Chemistry (Demonstrations of chemical experiments)
NIST Fundamental Constant Database (National Institute of Standards and Technology database for physical constants)
Protocol Online (A compendium of protocols for biochemistry laboratory techniques)
GE Healthcare Life Sciences Handbooks (protein purification and chromatography information)
Accelrys Draw (Formerly Symyx Draw; Free chemistry drawing program from Accelrys)
ChemSketch (Free chemistry drawing program from Advanced Chemistry Development)
ChemDraw (Commercial chemistry drawing program from Perkin-Elmer Informatics, formerly CambridgeSoft)
Wavefunction, Inc. (authors of the commercial Spartan software)
WindNMR (NMR Simulation program)
ChemAxon (chemical and bioinformatics software)

EPA (Environmental Protection Agency)
FDA (Food and Drug Administration)
Haz-Map (Toxicological information database at the National Library of Medicine at NIH)
ATSDR (Toxicological profies from the Agency for Toxic Substances & Disease Registry at CDC)

The Screaming Gummy Bear video
Explosions

Utilities
Acrobat Reader Download site
Rasmol (3D molecular visualization software)
Swiss-PDB viewer (3D Protein graphics viewer and manipulation software)
VMD (3D molecular visualization and manipulation software)
Accelrys Draw (Formerly Symyx Draw; Free chemistry drawing program from Accelrys)
ChemSketch (Free chemistry drawing program from Advanced Chemistry Development)
Webmol (Java-based 3D molecular visualization software)
Gepasi (Metabolic Control Analysis biochemical pathway simulation software)
Copasi (Complex Pathway Simulator software)
Serial Cloner (Program for performing restriction and other types of analysis on DNA sequences)
Molecular Biology Software (a variety of downloadable programs)
Statpages (John Pezzullo's statistical software compendium)

Miscellaneous
Visual Models of Morphogenesis (Algorithmic Botany at University of Calgary)
Ethics Workshop (AAAS Program of Scientific Freedom, Responsibility and Law and NIH Office for Protection from Research Risks)
Online Ethics Center for Engineering and Science
OTP (United States Office of Technology Policy)
USPTO (United States Patent and Trademark Office)
Office of Biotechnology Activities (NIH)
NIH Stem Cell Information (news site for research concerning human pluripotent stem cells)
National Hormone & Pituitary Program (an NIH organization that purifies and distributes peptide hormones)
Physical Constants (NIST Fundamental Physical Constants Page)
The Biophysics Textbook Online
CDC (The Centers for Disease Control and Prevention)
Science Songs (a variety of mp3 format songs by Greg Crowther)
Scitable (A collaborative learning space for science, organized by Nature Publishing)

Computer Related
Installing the full version of Spartan on Rose-Hulman computers
Installing Spartan on Macintosh computers (running Spartan requires being logged onto the Rose-Hulman network)
Installing the nomenclature module for ISIS/Draw
Printing via tibia from Macintosh OS X
Configuring RHIT-1X for Macintosh OS X





  Copyright 2002-2013 Mark Brandt, Ph.D.