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Research Tools

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
Peptides and Proteins
Images and Articles
Laboratory Resources
Bioinformatics and Laboratory Tools
Clinical Research Support

More Resources

Genes and Genomes

DNA 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.

Gene 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.

Human 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).

Incyte 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.

International HapMap Project
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.

The Jackson Laboratory Mouse Genome Informatics Page
Provides access to data on the genetics, genomics and biology of the laboratory mouse.

Kyoto 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.

MyMouse.org
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.

Online 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.

The National 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.

NCBI 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.

NCBI 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.

Serial 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.

Single 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 insertion/deletion polymorphisms

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.

Polygenic Pathways
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.

Protein Kinase Resource
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 information.

RCSB Protein Databank
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

CELLS Alive!
Provides a video library of cells related to microbiology, cell biology, infectious diseases and others. Also provides basic educational materials related to cells.

The 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.

Mouse 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.

Whole Brain Atlas
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.

Laboratory Resources

Antibody Resources Page
Provides links to antibodies suppliers, including contract and custom preparations of antibodies and immunological services.

Genentech 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
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.

National 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 as Stem Cell Basics; administration statements and recent congressional testimony.

Primate Resources
Directory of regional research centers, academic facilities, commercial sources and other information on aged non-human primates.

The Whole Mouse Catalog
A compendium of web sites with useful information for scientists using mice in research.

Bioinformatics and Laboratory Tools

Arrowsmith
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.

Bioinformatics 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, and education.

Computational Neuroscience/Neuroinformatics
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
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 cost.

Gene Chips (DNA Microarrays)
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.

NIH Image
Free, public-domain software for image capturing, processing and analysis.

SenseLab
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 databases.

Telemakus System
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.

More Resources

The 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.

Neurosciences 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.



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