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Medical Resources – News, Data, Libraries

A
Alzheimer’s Database

B
Bioinformatics Resource for Oral Pathogens
BioMart: developed jointly by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI).
Bioinformatic Harvester: 4DXpAceViewBLASTBiocompareCDARTCDDensEMBLEntrezFishMapGalaxyUCSC GenomeBrowsergfp-cDNAGoogle-ScholargopubmedHarvester42H-InvHomoloGeneiHOPIPIMapViewMGIMINTMitocheckOMIMPolyMetaPSORT IIRGDSMARTSOSUI SOURCESTRINGTAIRUnigeneUniprotKBWikipediaWikiProtein Harvester Sequence Search device – YaCy-Sciencenet p2p search engine

British Medical Journal   http://www.bmj.com
C

Cancer Clinical Trials Database: National Cancer Institute Cancer Genome Atlas Data Portal Cancer Molecular Analysis Portal: Cancer Biomedical Informatics Grid Cancer: PDQ Natinal Cancer Institute Comprehensive Cancer Database Carcinogenic Potency Database Cell Signalling Information ChemSpider Comprehensive Microbial Resource Collaborative Bio Curation CRISP (Computer Retrieval of Information on Scientific Projects) is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions Cytokines & Cells Online Pathfinder Citeline- Worldwide drug development activity Clinical Trials.gov CureResearch.com
D Diabetes Association Researcher Database Diseases Database Diseases and Disorders Database: Karolinkska Institutet – Sweden
E
Entrez: Life Sciences Search Engine ennfsa Environmental Health and Toxicology EU Health.net
F
http://freebooks4doctors.com:  Find free reference books of great use and written by excellent field specialists in different languages, such as The Orange Book.
G
Genetic Association Database General Practice Notebook: Database of clinical medicine (United Kingdom) Genomic Variants (Database)
Human IDCM Gene Expression
H
Health on the Net Database HIV Molecular Immunology HubMed.org Human Gene Database Database Download
I
Indian Bioresource Information Network International Classification of Diseases Database International Protein Index Intute: Health and Life Sciences
J
Japan Biological Information Research Center Journal Watch
Johns Hopkins Institute of Computational Medicine:

Human IDCM Gene Expression
DTMRI Data Sets
2-D DIGE Data Sets

M Medical Images: Karolinkska Institutet, Sweden Medical Journal Library Databases: Washington University in St. Louis School of Medicine Medline Plus Medical Subject Headings Browser Mediscan Image Data Search Merck Disease Modules Multilingual Glossary of Medical Terms in 9 European Languages
N National Cancer Institute 3D Structure Database National Center for Biotechnology Information National Library of Medicine Catalog National Library of Medicine Databases and Resources National Library of Medicine Locator Plus National Library of Medicine Gateway NCBI Resource Guide NCI Screening Data Miner: A tool for interactive analysis and visualization of the National Cancer Institute anti-tumor datasets. Contains 41,000 chemical compounds versus 155 cancer cell lines. Neuromuscular Disease Center New Medicine Oncology Database National Institute of Diabetes and Digestive and Kidney Diseases Resources
New England Journal of Medicine: http://www.nejm.org/medical-articles/research
P Panther: Classification of Genes and Proteins Parasites:  American Society of Tropical Medicine and Hygene Proteome Commons
R Rare Disease Database
S Science Links Japan Signaling Gateway, powered by the San Diego Supercomputer Center Stanford Online Universal Resource for Clones and ESTs
T tRNA Database
U
UCSC Gene Sorter USDA Plants Database
V Visualizing Splices of Genes from EST Data

Adult Acute Liver Failure Study Group (ALFSG) http://www8.utsouthwestern.edu/utsw/cda/dept25203/files/89624.html

The Acute Liver Failure Study Group is collecting biosamples and information on the natural history, causes and outcomes of Acute Liver Failure in the United States. In addition to the database, a clinical trial conducted to test whether the drug N-acetylcysteine (NAC) improves outcome (survival) for patients with Acute Liver Failure not caused by acetaminophen overdose has recently been completed. Results should be available in the near future. For more information, contact Dr. Patricia Robuck, DDN, Program Director for Clinical Trials in Digestive Diseases and Nutrition Program

Beta Cell Biology Consortium (BCBC) http://www.betacell.org/

The mission of the BCBC is to facilitate interdisciplinary approaches that will advance our understanding of pancreatic islet cell development, regenerative capacity and function. The long-term goal is to develop a cell-based therapy, or treatments leading to controlled beta-cell renewal, in order to restore normal insulin production to diabetic patients. For more information, contact Dr. Olivier Blondel, DEM, Director, Endocrine Systems Biology Program or Dr. Sheryl Sato , DEM, Director, Neurobiology of Obesity and Developmental Biology Programs

Bioinformatics Information Support Contract (BISC) http://www.niddk.nih.gov/fund/diabetesspecialfunds/consortia/BISC.pdf

The goal of the Bioinformatics Integration Support Contract (BISC) is to advance the discovery and testing of new therapies for immune-mediated diseases and to further the understanding of the basis of innate and adaptive immunity by providing advanced computer support for scientific data handling and disseminating best practices in scientific data analysis. For more information, contact Dr. Lisa Spain, DEM, Director, Immunobiology of Type 1 Diabetes Program and Autoimmune Endocrine Diseases Program

Central NIDDK Repository for Biosamples and Data http://www.niddkrepository.org

On July 1, 2003, The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health (NIH) established Central NIDDK Repositories for biosamples and data collected in clinical studies. The purpose of the Central Repositories is to expand the usefulness of these studies by providing access to the biosamples and data to a wider research community beyond the end of the study. For more information, contact Dr. Rebekah Rasooly, Deputy Director of the Division of Kidney, Urologic, and Hematologic Diseases

Clinical Outcomes Research Inititative (CORI) http://www.cori.org/

The Clinical Outcomes Research Initiative, CORI, provides gastrointestinal physicians, nurses and researchers with software, research data and tailor-made services aimed to advance the overall practice of endoscopy. For more information, contact Dr. Jay Everhart, DDN, Director, Epidemiology and Data Systems Branch

Collaborative Islet Transplant Registry (CITR) http://www.citregistry.org

The mission of CITR is to expedite progress and promote safety in islet/beta cell transplantation through the collection, analysis, and communication of comprehensive and current data on all islet/beta cell transplants performed in North America and soon some transplants in Europe and Australia. An Annual Report that is available on the public web site. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. For more information, contact Dr. Michael Appel, DEM, Director, Islet Biology and Transplantation Research Program

Diabetes Genome Anatomy Project (DGAP) http://www.diabetesgenome.org/

The Diabetes Genome Anatomy Project (DGAP) represents a unique, multidimensional initiative whose goal is to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes. The overall goal of the project is to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. For more information, contact Dr. Olivier Blondel, DEM, Director, Endocrine Systems Biology Program

Diabetes in America http://diabetes.niddk.nih.gov/dm/pubs/america/

A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States. For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program

Diabetes Prevention Trial–Type 1 (DPT-1) dataset https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp#DPT-1

The Diabetes Prevention Type 1 (DPT-1) trial is a NIDDK-funded multi-center clinical trial to determine if treatment with beta-cell antigens can delay the onset of Type 1 Diabetes Mellitus (Type 1 DM) in non-diabetic relatives of persons with Type 1 DM. Insulin is a well characterized antigen specifically produced by beta-cells, and it was used for this purpose in the initial DPT-1 studies. The protocol for high risk subjects uses daily subcutaneous insulin injections and an annual course of intravenous insulin treatment, while the protocol for intermediate risk subjects uses daily doses of insulin administered orally. For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program

Digestive Diseases in the United States: Epidemiology and Impact http://digestive.niddk.nih.gov/statistics/statistics.htm

A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost.

Epidemiology of Diabetes Interventions and Complications (EDIC) http://www.niddk.nih.gov/patient/edic/edic-public.htm

or http://www.bsc.gwu.edu/bsc/studies/edic.htmlAn observational study examining the risk factors associated with the long-term complications of type 1 diabetes. The study began in 1994 and follows the 1441 participants previously enrolled in the Diabetes Control and Complications Trial (DCCT). For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program

Federal Databases for Biomedical and Nutrition Related Research http://dnrc.nih.gov/highlights/database-page.htm

The Division of Nutrition Research Coordination at NIH provides the HNRIM database (Human Nutrition Research and Information Management), one of a collection of databases of interest to nutrition researchers, including CARDS (Computer Access to Research on Dietary Supplements), CDMRP (Congressionally Directed Medical Research Programs), CRIS (U.S. Department of Agriculture Current Research Information System).

Globin Gene Server http://globin.cse.psu.edu/

This database provides data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences. For more information, contact Dr. Terry Rodgers Bishop, KUH, Director, Hematology Research Programs

Healthy People 2010 http://www.healthypeople.gov/

A statement of national objectives for health promotion and disease prevention for the first decade of the 21st century, the book has two overarching goals: increase quality and years of healthy life and eliminate health disparities. Specific parts of Healthy People 2010 relate to prostate and urinary bladder cancer, chronic kidney disease, and diabetes complications. For more information, contact Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination or Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs

Hembase http://hembase.niddk.nih.gov/

Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. To date, Hembase contains 15,752 entries from erythroblast Expressed Sequenced Tags (ESTs) and 380 referenced genes relevant for erythropoiesis. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. For more information, contact Dr. Terry Rodgers Bishop, KUH, Director, Hematology Research Programs

Human Biological Data Interchange http://www.ndriresource.org/Biospecimens_Programs/HBDI/36/

HBDI maintains a repository of DNA and immortalized cell lines collected from 540 families of subjects with type 1 diabetes. It also houses a database that includes more than 6700 families with diabetes, related complications and other genetic diseases.

Human Nutrition Research Information Management (HNRIM) http://hnrim.nih.gov/

HNRIM is a searchable database of nutrition research and research training activities supported by the federal government.

Inflammatory Bowel Disease Genetic Consortium (IBDGC)

The NIDDK Inflammatory Bowel Disease Genetics Consortium (IBDGC) consists of investigators from seven sites in the U.S. and Canada, who have recruited a large sample of inflammatory bowel disease patients, their relatives, and control subjects. All of the individuals in this sample have been evaluated according to a standardized protocol for clinical traits related to IBD, and have donated blood samples as a source of DNA. The IBDGC investigators are conducting genetic linkage and association studies to identify genes influencing predisposition to IBD. Phenotype, genotype and pedigree data and DNA samples will be available through the NIDDK Repositories in 2008. For more information, contact Dr. Robert Karp, DDN, Director, Genetics and Genomics Programs in Digestive Diseases and Obesity Programs

Major Histocompatibility Complex Database (dbMHC) http://www.ncbi.nlm.nih.gov/projects/mhc/MHC.fcgi?cmd=init

The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC). For more information, contact Dr. Beena Akolkar, DEM, Director, Immunopathogenesis and Genetics of Type 1 Diabetes Program

Mammalian Gene Collection (MGC) http://mgc.nci.nih.gov/

Mammalian Gene Collection (MGC) and Zebrafish Gene Collection (ZGC) The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes ( http://mgc.nci.nih.gov/). The companion Zebrafish Gene Collection (ZGC) project is providing FL-ORF clones for zebrafish genes (http://zgc.nci.nih.gov). For more information, contact Dr. Rebekah Rasooly, Deputy Director of the Division of Kidney, Urologic, and Hematologic Diseases

Mouse Metabolic Phenotyping Centers (MMPC) http://www.mmpc.org

The Centers are housed at outstanding academic institutions, staffed by experts in state-of-the-art technology. Researchers can ship mice to one of the four Centers and obtain on a fee-for-service basis a range of complex exams used to characterize mouse metabolism, blood composition including hormones, energy balance, eating and exercise, organ function and morphology, physiology and histology. Many tests are done in living animals and are designed to elucidate subtle to complex traits that would define models of metabolic disease. For more information, contact Dr. Maren Laughlin, DEM, Senior Advisor for Integrative Metabolism

Murine Atlas of Genitourinary Development (GUDMAP) http://www.gudmap.org/

The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are:

  • a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract
  • a high resolution molecular anatomy that highlights development of the GU system
  • mouse strains to facilitate developmental and functional studies within the GU system
  • tutorials describing GU organogenesis
  • rapid access to primary data via the GUDMAP database

For more information, contact Dr. Elizabeth Wilder, KUH, Director, Developmental Biology of the Kidney and Urogenital Tract Program

National Diabetes Education Program (NDEP) http://www.ndep.nih.gov/

The NDEP is the leading federal government public education program that promotes diabetes prevention and control. The mission of the NDEP is to reduce the morbidity and mortality associated with diabetes and its complications. The NDEP is jointly sponsored by the National Institutes of Health and the Centers for Disease Control and Prevention and over 200 partner organizations. Target audiences include people with diabetes and those at risk, including the racial and ethnic populations disproportionately affected by the disease, health care providers and payers and purchasers of health care. For more information, contact Ms. Joanne Gallivan, Director, National Diabetes Education Program (NDEP)

National Diabetes Information Clearinghouse (NDIC) http://www.diabetes.niddk.nih.gov

The diabetes clearinghouse provides comprehensive information about diabetes for the public: online, in booklets and fact sheets, by email, and over the phone. For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses

National Digestive Diseases Information Clearinghouse (NDDIC) http://www.digestive.niddk.nih.gov

The digestive diseases clearinghouse provides comprehensive information about digestive health and disease for the public: online, in booklets and fact sheets, by email, and over the phone. For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses

National Gene Vector Laboratories (NGVL) http://www.ngvl.org/

The National Gene Vector Laboratories (NGVL) are composed of an interactive group of academic production and pharm/tox laboratories whose primary goal is to provide eligible investigators with clinical grade vectors for phase I/II gene therapy clinical trials and to provide support for relevant pharmacology/toxicology studies leading up to clinical gene transfer protocols. If the application is approved, clinical grade material will be produced at no cost to the investigator. For more information, contact Dr. Catherine McKeon, DEM, Senior Advisor for Genetic Research in Diabetes, Endocrinology and Metabolic Diseases

National Kidney and Urologic Diseases Information Clearinghouse (NKUDIC) http://kidney.niddk.nih.gov

or http://www.urologic.niddk.nih.gov The kidney and urologic diseases clearinghouse provides comprehensive information about bladder and renal health and disease for the public: online, in booklets and fact sheets, by email, and over the phone. For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses

National Kidney Diseases Education Program (NKDEP) http://www.nkdep.nih.gov/

The National Kidney Disease Education Program (NKDEP) aims to increase awareness of kidney disease and its risk factors, the importance of testing those at risk, and the availability of treatment to prevent or slow the progression to kidney failure. NKDEP’s target audiences include individuals at risk, particularly those with diabetes, high blood pressure, and a family history of kidney disease, and primary care providers. For more information, contact Dr. Andrew Narva, Director, National Kidney Disease Education Program; Senior Scientific Advisor or Ms. Eileen Newman, Associate Director, National Kidney Diseases Education Program

NIDDK Endocrine and Metabolic Diseases Information Service http://www.endocrine.niddk.nih.gov

This public service provides information about endocrine and metabolic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone. For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses

NIDDK Hematologic Diseases Information Service http://www.hematologic.niddk.nih.gov

This service provides information about certain hematologic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone. Additional hematologic information for the public is available at http://www.nhlbi.nih.gov. For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses

Nuclear Receptor Resource Project (NRR) http://nrr.georgetown.edu/NRR/nrrhome.htm

The Nuclear Receptor Resource (NRR) Project is a collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. For more information, contact Dr. Ronald Margolis, DEM, Senior Advisor, Molecular Endocrinology

Nuclear Receptor Signaling Atlas (NURSA) http://www.nursa.org/

Commensurate with this directive, NURSA’s goals can be distilled into two broad aims: (i) to execute research strategies designed to rapidly and efficiently elucidate those facets of orphan nuclear receptor biology we deem most critical to its understanding; and (ii) to facilitate the generation of hypotheses, design of experiments and communication of results by scientists active in this field. We anticipate that this initiative will provide a valuable service to the nuclear receptor community by developing a web-accessible bioinformatics resource, in which current and emerging data will be organized into more accessible and “user-mineable” forms. For more information, contact Dr. Ronald Margolis, DEM, Senior Advisor, Molecular Endocrinology

Organ Procurement and Transplantation Network (OPTN) http://www.optn.org/

The U.S. Organ Procurement and Transplantation Network (OPTN) maintains a registry of human tissues in order to ensure the success and efficiency of the U.S. organ transplant system. For more information, contact Dr. Thomas Eggerman, DEM, Director, Islet Transplantation Clinical Trials Program

Pediatric Acute Liver Failure Study Group (PALF) http://www.palfstudy.org

This multi-center, multi-national collaborative group of pediatric clinical liver centers is aimed at identifying, characterizing, and developing management strategies for infants, children, and adolescents who present with acute liver failure (ALF). In addition to a database of pediatric patients with ALF, a clinical trial is being conducted to test whether the drug N-acetylcysteine (NAC) improves outcome (survival) for patients with ALF not caused by acetaminophen overdose. For more information, contact Dr. Patricia Robuck, DDN, Program Director for Clinical Trials in Digestive Diseases and Nutrition Program

United States Renal Data System (USRDS) http://www.usrds.org/

The United States Renal Data System (USRDS) is a national data system that collects, analyzes, and distributes information about chronic kidney disease and end-stage renal disease (ESRD) in the United States. The USRDS publishes and Annual data report which can be downloaded at http://www.usrds.org/adr.htm. The missions of the USRDS are: (1) To characterize the total renal patient population and describe the distribution of patients by socio-demographic variables across treatment modalities; (2) To report on the incidence, prevalence, mortality rates, and trends over time of renal disease by primary diagnosis, treatment modality and other variables; (3) To develop and analyze data on the effect of various modalities of treatment by disease and patient group categories; (4) To identify problems and opportunities for more focused special studies of renal research issues; (5) To conduct cost effectiveness studies and other economic studies of ESRD; and (6) To make the data available to investigators, and by supporting investigator-initiated projects, to conduct biomedical and economic analyses of ESRD patients. For more information, contact Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs, or Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination. For more information, contact Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination or Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs

Urologic Diseases in America Compendium (UDA) http://kidney.niddk.nih.gov/statistics/uda/

Urologic diseases cover a wide range of conditions, symptoms, and problems that include such diverse diagnoses as cancer, pelvic pain, sexual dysfunction, urinary incontinence, kidney stones, and benign prostatic hyperplasia (BPH). To remedy this lack of information, NIDDK initiated the Urologic Disease in America (UDA) project. The UDA compendium delineates the changes in the epidemiology, health economic impact, and practice patterns for the diseases currently included within the scope of practice of the specialty of urology, analyzed retrospectively over a ten-year period. The UDA compendium consists of data tables annotated in chapters that amplify the data analyses. The objectives of the UDA project include secondary data analyses of the following topics: (1) changes in the overall health care burden for individual urologic diseases; (2) changes in physician practice patterns for each urologic disease; (3) changes in demographics of persons with urologic disease; (4) the impact of specific urologic diseases, especially diseases of the prostate, on the minority populations of the U.S.; (5) documentation of new and evolving therapies for urologic disease and their potential impact on treatment outcomes and health care costs. The resultant compendium can be found at the above web address. In addition to updating the original compendium, the second phase of the UDA is to focus less on descriptive analyses and more on analytical outcomes analyses, and it will also attempt to increase involvement of the urologic community in analytical activities. For more information, contact Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs or Dr. Leroy Nyberg, KUH, Director, Urology Programs

PubMed.gov PubMed Central: A free archive of Life Sciences Journals. PubMed Tutorials
RX Centric
ToxNet
Unified Medical Language System Visible Human Project

Max Planck Institute for Infection Biology, Berlin, Germany – DE

Access databases:

 

US Dept of Health and Human Services: Practitioner Databanks Practitioner’s Guide to the Databanks – PDF

National Institutes of Health

Tools & Resources

General Scientific Support

Partnerships

Collaborative Research

Computational SIGs

Research Studies

Publications

Projects

Supercomputing

  • The Biowulf supercomputer provides NIH researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations and PET brain scan processing to identify plaques associated with Alzheimer’s disease. The Biowulf cluster requires a Helix System account and a justification describing the research project and why the cluster is necessary to perform the computations.
  • Helix Managed Storage is provided for NIH Helix user login directory and includes seamless access to files among Helix Systems computational platforms, convenient access from users desktop computers, regular snapshots of files for online access and backup to offline tapes, and high performance using highly redundant network file servers.
  • The NIH Helix System is a high-performance computer running Linux that provides a comprehensive set of scientific applications and biomedical databases tailored to the needs of NIH researchers.
  • Imaris services allow researchers and scientists to visualize and analyze microscopic image data. Imaris services also provides licenses to use Imaris and associated modules including MeasurementPro, Coloc, Track, FilamentTracer, and XT.
  • MASCOT Server and Support. The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. The CIT-managed Mascot server provides a centralized, shared resource with updated databases, and allows NIH researchers to run Mascot searches directly on the NIH Mascot website or by using the Mascot daemon on a desktop PC.

NIH Computational Molecular Biology Database Catalogs

Helix Systems Scientific Databaseslocally available databases (NIH only) WHALESWeb Homology Alert Service (NIH only)

Genomic

UCSC Genome Browserthe gold standard of genome browsers National Center for Biotechnology Information (NCBI)clearinghouse for all genomic information Ensembljoint project between EBI and Sanger Institute GADThe Genetic Association Database, at NIA COMPAREmulti organism information system, at the Developmental Biology Institute of Marseille The Cancer Genome Atlas Data Portalclinical information associated with cancer tumors and human subjects, genomic characterization, and high-throughput sequencing analysis of the tumor genomes.

Nucleic Acids

EntrezThe Life Sciences Search Engine, at NCBI SRSSequence Retrieval System, at EBI dbESTsequence and mapping data on partial, “single-pass” cDNA sequences or ESTs NDBNucleic Acids Database, at Rutgers Tumor Gene Databaseinformation about targets for cancer-causing mutations Riboapt DBRibozymes & Aptamer Database, at Univ. of Southern Mississippi SILVAQuality checked and aligned rRNA sequence data, at Max Planck Institute ASPicDBAlternative Splicing Prediction Data Base, at Univ. of Bari

Proteins

SwissProtat ExPASy.org EntrezThe Life Sciences Search Engine, at NCBI SRSSequence Retrieval System, at EBI Molecules To Gotext-based interface to the PDB on Helix Systems MEROPSThe Peptidase Database, at the Wellcome Trust Sanger Institute Human Mitochondria l Protein Databasemultiple query types available, at NIST HIV Protease Databaseat NCI-Frederick Human Protein Reference Databaseat Johns Hopkins University and the Institute of Bioinformatics SCOPStructural Classifications of Proteins CATHHierarchical classification of protein structural relationships FSSPFamilies of structurally similar proteins PFAMDatabase of multiple sequence alignments GPCRDBDatabase of G-protein coupled proteins ModBaseDatabase of 3D protein models HOMSTRADHomologous Structure Alignment Database Database of Macromolecular Movementswith online analysis tools, at Yale Univ. gpDBDatabase of G-proteins and their interactions with GPCRs, at Univ. of Athens ProteopediaThe Collaborative, 3D Encyclopedia of proteins and other molecules Microbial Protein Interaction Databaseat the J. Craig Venter Institute OPMOrientations of Proteins in Membranes Database, at Univ. of Michigan

Factors and Motifs

Transfac Professionaltranscription activation factor database (NIH only) BIOBASEfree registration required

Pathways

Reactomea curated knowledgebase of biological pathways KEGGKyoto Encyclopedia of Genes and Genomes PIDPathway Interaction Database, at NCI BioCycLarge collection of pathway/genome databases

Enzymes

REBASEgood old New England Biolabs ENZYME Databaseat ExPASy.org IntEnzat EBI Biology-oriented newsgroupsat Indiana University CATRESDatabase of catalytic residues, at EBI CSACatalytic Site Atlas, at EBI

Plasmids

Genome Database of Naturally Occurring Plasmids

Organism-Specific Databases

Mammalian

Mouse Genome Databasesynoptic descriptions with bibliographic citations Portable Dictionary of the Mouse Genomecompact, downloadable database

Worm

Worm Basebiology and genome of C. elegans Caenorhabditis elegans WWW Serverone-stop shopping for C. elegans

Insect

FlyBasecomprehensive database for genetics and molecular biology of Drosophila

Yeast

Saccharomyces Genome Databaseat Stanford

Protozoan

PlasmoGFPlasmodium gene families, at Wenzhou Medical College

Fungi/Mycobacteria

MycoperonDBPredicted operon and transcriptional units of Mycobacteria

Prokaryote

IECA Database Portalcollection of E. coli servers around the world SubtiList WWW Serverall about B. subtilis, Pasteur Institute Entrez Microbial Genomes348 completed genomes and counting… BAGETvery nice tool for getting sequence & info from prokaryotic genomes, from Université Paris

Plants

Arabidopsis Information Resourcevery nice gateway to our favorite mustard weed Grain genesdatabase for triticaea and avena The Korea Rice Genome Databaseat Myongii University ChromDBthe plant chromatin database, at University of Arizona

Other

Ribosomal Database Projectat Michigan State University National Human Genome Research Instituteongoing research into genomics