We provide here an annotated index of favorite web sites with information, downloadable software, databases, and other web-based technologies for scientists.
If you know of something that could be useful, please contact us.
Genes and Genomes
Images and Articles
and Laboratory Tools
Clinical Research Support
Genes and Genomes
From The Beginning
An animated primer on the basics of DNA, genes, and heredity,
organized by key concepts. A resource provided by the DNA
Learning Center at the Cold Spring Harbor Laboratory.
Expression Nervous System Atlas (GENSAT)
The GENSAT database contains a gene expression atlas of the
central nervous system of the mouse based on bacterial artificial
chromosomes (BACs). A resource provided by the Rockefeller
University and is supported by an NINDS grant.
Genome Variation Database (HGVbase)
HGVbase is an attempt to summarize all known sequence variations
in the human genome, to facilitate research into how genotypes
affect common diseases, drug responses, and other complex
phenotypes. HGVbase is the product of a European consortium
involving the Karolinska Institute (Sweden), the European
Bioinformatics Institute (UK), and the European Molecular
Biology Laboratory (Germany).
Proteome BioKnowledge® Library
This site, made available by Incyte Genomics, Inc., provides
extensive, searchable, highly annotated information on yeast
and worm genome information. Site is subscription-based. Access
is free for Disease Spotlight of the month.
The International HapMap Project is a multi-country effort
to identify and catalog genetic similarities and differences
in human beings. Using the information in the HapMap, researchers
will be able to find genes that affect health, disease, and
individual responses to medications and environmental factors.
Jackson Laboratory Mouse Genome Informatics Page
Provides access to data on the genetics, genomics and biology
of the laboratory mouse.
Encylopedia of Genes and Genomes (KEGG)
From Kyoto University, an incredible web site, one of the
most comprehensive biological information resources on line.
The site provides detailed metabolic, regulatory and functional
pathways of a huge number of genes/gene products, and a powerful
search engine pulls up a compendium of interesting information
about specific genes.
A site hosted by the Neurobiology of Disease Program, Baylor
College of Medicine, with the goal of promoting discovery
of gene function in the nervous system and the development
of novel mouse models of neurological disease. List your mutant,
join a bulletin board, find out about new models and learn
about where to get your mouse phenotyped.
Mendelian Inheritance in Man
This database is a catalog of human genes and genetic disorders
authored and edited by Dr. Victor A. McKusick and his colleagues
at Johns Hopkins and elsewhere. The database contains textual
information, pictures, and reference information.
Human Genome Research Institute
Heads the Human Genome Project for NIH. Site contains link
to the Human Genome Project, grant information, and an extensive
list of genomic and genetic resources.
Entrez Genomes Page
Entrez Genome provide access to the whole genomes of over
1000 viruses and over 100 microbes. The genomes represent
both completely sequenced organisms and those for which sequencing
is in progress. All three main domains of life - bacteria,
archaea, and eukaryota - are represented, as well as many
viruses and organelles.
Human Genome Resources
The NCBI Human Genome Resources sit serves as an integrated,
one-stop, genomic information infrastructure for the Human
Genome Project and other related projects.
Analysis of Gene Expression (SAGE Genie)
SAGE Genie was produced as part of the Cancer Genome Antamony
Project (CGAP) SAGE project by collaborators from Johns Hopkins
University, Duke University, the Ludwig Institute for Cancer
Research (Sao Paulo Branch), and the National Cancer Institute.
SAGE is a method to efficiently count large numbers of mRNA
transcripts by sequencing short tags, usually 10 or 17 bp
in length. SAGE Genie uses a new analytical method of reliably
matching SAGE tags to known genes. Based on this novel tag
to gene mapping, the website visualizes human and mouse gene
expression analysis in tissues or individual libraries using
displays that are highly intuitive.
Nucleotide Polymorphisms Database (dbSNP)
Launched in September of 1998, dbSNP accepts submissions from
all laboratories and is especially interested in mutations
in genes and/or where additional biological information is
known. The database has been designed to accept several classes
of genetic variation: SNPs, microsatellite repeats, and small
SNP Annotations for Genomewide Association Studies (downloads tab)
This site, from Patrick Sullivan's lab at UNC-Chapel Hill, contains annotation files for all of the major genotyping platforms. These annotations are meant to aid investigators in prioritizing the follow-up of GWAS findings. Annotations are available for Affymetrix 100K, 5.0, and 6.0; Illumina 550K and 650K; and Perlegen 600K. For each SNP on each of the platforms, there are over 40 annotations with basic information about the SNP, potentially problematic issues with a SNP, genomic structural features of the SNP, and predicted function of the SNP.
Sullivan Lab Evidence Project (SLEP)
SLEP, created by Patrick Sullivan's lab at UNC-Chapel Hill, allows users to search the accumulated data to find the evidence in support of the involvement of a particular genomic region with a set of the disorders of central importance in psychiatry—autism, bipolar disorder, major depressive disorder, and schizophrenia. Study types include genomewide linkage and genomewide association, and microarray studies are being added.
Technology And Money Are Limited (TAMAL)
TAMAL provides semi-automated SNP selection for association studies, and was created by Pat Sullivan's lab at UNC-Chapel Hill. Its purpose is to help the user select single nucleotide polymorphisms (SNPs) in a specified set of candidate genes for genotyping. The user can specify the ancestral populations to study and a set of SNP selection criteria (e.g., haplotype tag and predicted function). The results can be output as an Excel file or in XML (for exchange or processing with other applications). SNPs selected by TAMAL can be displayed in the UCSC genome browser.
Peptides and Proteins
ExPASy Proteomics Server
Expert Protein Analysis System of the Swiss Institute of Bioinformatics.
The site dedicate to the analysis of protein sequences and
structures as well as two-dimensional polyacrylamide gel electrophoresis.
This site, created and maintained by Chris Carter, contains lists of genes and environmental risk factors positively associated with Alzheimer's disease, bipolar disorder, or schizophrenia. It describes the interactions between the protein products of these genes, which together etch out specific signaling networks. These networks may underpin the pathology of each disease and are also relevant to the pathways triggered by the environmental risk factors implicated in the disease. Links to Entrez gene, Pubmed, Kegg pathways, Biocarta, and Genecards are provided.
A web accessible compendium of information on the protein
kinase family of enzymes. This resource includes tools for
structural and computational analyses as well as links to
related information maintained by others. The PKR is a collaborative
project of protein kinase researchers and computational biologists
working to create a database integrating molecular and cellular
A database with over 24,000 3-D macromolecular protein structure
data determined by X-ray crystallography and NMR. Maintained
by the Research Collaboratory for Structural Bioinformatics.
Images and Articles
Provides a video library of cells related to microbiology,
cell biology, infectious diseases and others. Also provides
basic educational materials related to cells.
Internet Pathology Lab for Medical Education
Includes over 1900 images that demonstrate gross and microscopic
pathologic findings associated with human disease conditions, as well as a section on images in normal neuroanatomy and neurohistology.
Atlas Project (MAP)
The Laboratory of Neuroimaging at UCLA develops MAP which
aims to develop a dynamic, probabilistic atlas of the adult
and developing C57BL/6J mouse. MAP serves as an imaging framework
to house and correlate gene expression with anatomic and molecular
information drawn from traditional and novel imaging technologies.
Created by a researcher at Harvard Medical School, this excellent,
image-based resource includes MRI, functional imaging, clinical
descriptions and tours of normal and diseased brain images.
Provides links to antibodies suppliers, including contract
and custom preparations of antibodies and immunological services.
Research Contracts and Reagents Program
Genentech supports investigators in academic institutions
throughout the world by supplying key reagents for their research.
To initiate work with Genentech, you can complete the Material
Request Form available on their web site to request proteins,
antibodies, and cDNAs from Genentech. These requests are granted
on the basis of scientific merit and availability of material.
This program is not for human protocol or for clinical use.
The Jackson Laboratory, a non-profit institution, is the world's
largest mammalian genetic research facility. The Laboratory
supplies approximately 2 million JAX® Mice to the global research
community from more than 2,700 varieties.
Institutes of Health (NIH) Stem Cell Information
The NIH Stem Cell Information web site includes the NIH
Human Embryonic Stem Cell Registry listing stem cell lines
that meet the eligibility criteria for Federally funded research
that are currently available for shipping. Also available
through the website are resources such stem cell material
transfer agreements; reports and general information such
Cell Basics; administration statements and recent congressional
Directory of regional research centers, academic facilities, commercial sources and other information on aged non-human primates.
Whole Mouse Catalog
A compendium of web sites with useful information for scientists
using mice in research.
and Laboratory Tools
Developed by Developed by University of Illinois at Chicago researchers Neil Smalheiser
and Don Swanson, this novel information retrieval system searches
the biomedical literature for implicit connections, for example
between one biological process and a seemingly unrelated one.
This demonstration site is free for anyone to use. The creators
welcome feedback from users.
Organization, Inc. (Bioinformatics.org)
Founded in 1998 by J.W. Bizzaro, Bioinformatics.Org aims
to facilitate world-wide communications and collaborations
between practicing and neophyte bioinformatic scientists and
technicians. The Organization provides these individuals,
as well as the public at large, free and open access to methods
and materials for and from scientific research, software development,
The Computational Neuroscience/Neuroinformatics website
aims to unravel the complex structure-function relationships
of the brain at all levels from molecule to behavior in an
integrative effort of many scientific disciplines and intends
to foster the development of the field and the growth of an
active community with a focus on Europe.
Cytoscape is an open-source bioinformatics software platform
for visualizing molecular interaction networks and integrating
these interactions with gene expression profiles and other
state data. Cytoscape is under continuous development by scientists
at Institute of Systems Biology, UC San Diego, Whitehead Institute
and The Memorial Sloan-Kettering Cancer Center. Other scientists
and software developers can download the source code at no
A basic how-to site on gene chip technology, run by computational
chemist Leming Shi. Includes extensive directories of links
to other sites with microarray information.
Free, public-domain software for image capturing, processing
The SenseLab Project at the Yale University School of Medicine
is a long term effort to build integrated, multidisciplinary
models of neurons and neural systems. Databases from this
project includes three neuronal databases: Cellular Properties
Database (CellPropDB); NeuronDB; and ModelDB, and three olfactory
Developed at the University of Washington, the goal of the
Telemakus System is to enhance the knowledge discovery process
by developing retrieval, visual and interaction tools to mine
and map research findings from the research literature. The
Caloric Restriction & Nutritional Aspects in Aging database
covers the majority of original research articles in English
with data tables in that field since 1935. The Biomarkers in Alzheimer's Disease (bioAD KB) database covers studies on the biomarkers apolipoprotein E, amyloidβ, tau and isoprostanes, among others, in Alzheimer’s disease.
Clinical Research Support
Innovative Clinical Research Solutions
ICRS is a not-for-profit clinical research services group located at the Nathan S. Kline institute for Psychiatric Research, specializing in support for mental health research, particularly schizophrenia research. The group develops Web-based applications to support their data management and study monitoring services.
Schizophrenia Trials Network
The structural components of the CATIE study—a centralized coordinating center at the University of North Carolina, Chapel Hill, and a network of clinical sites around the United States—were retained as the Schizophrenia Trials Network, which can design and carry out studies of schizophrenia treatment effectiveness in a community setting (with "real world"
populations), or research with a significant translational component.
Molecular Biology Database Collection: 2005 Updates
The Nucleic Acids Research Molecular Biology Database
Collection is a public online resource that lists publicly
accessible databases that are of values to biologists. The
2005 updates contain 719 databases from around the world.
on the Internet
A searchable and browsable index of neuroscience resources
on the Internet.
The Wisconsin Schizotypy Scales (aka Chapman Scales of Psychosis Proneness)
These seven scales of psychosis proneness are available for download and may be used free of charge as long as they are appropriately cited in published work. The packet of scales includes norms developed at four different sites, as well as instructions for administering the questionnaires.