BARcodes

BioAnalytical Research - Links to Life Science News, Resources & Databases


This web page is focused on links to predominantly free data and information sources in the field of life sciences and bioanalytics.
It contains several hundred individually selected links and is currently under reconstruction.
We are not responsible for the contents or reliability of any other websites to which we provide a link and do not necessarily endorse the views expressed within them.

Copyright © 1997 - 2024, 2025 by Gerhard M. Kresbach

--- Last update: 2025-02-17 ---

Editor: Dr. Gerhard M. Kresbach, D-79219 Staufen, Germany   ORCID logo https://orcid.org/0000-0002-1688-4520

Comments and suggestions for enhancements and new links are very much appreciated --- email: kresbach@kresbach.de


Index

Life-Science News & Information
Scientific Literature
Scientific Resources
Patents & Trademarks
Bioanalytics
Bioinformatics
Genomics, Proteomics & Transcriptomics
Rules and Regulations

Life-Science News & Information

News & Alert Services
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News & Alert Services

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Scientific Literature

Literature Search
On-Line Journal Aggregators and Open Access Publishers
E-Libraries & E-Archives
Publications - Varia
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Literature Search

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On-Line Journal Aggregators and Open Access Publishers

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E-Libraries & E-Archives

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Publications - Varia

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Scientific Resources

General
Scientific & Linguistic Dictionaries
Protocols
Scientific Images & Illustrations
Spectroscopy Databases
Biology, Biotechnology & Molecular Biology
Chemistry & Analytics
Medicine
Pharma
Physics, Maths & Engineering
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General

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Scientific & Linguistic Dictionaries

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Protocols

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Scientific Images & Illustrations

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Spectroscopy Databases

  • BMRB - Biological Magnetic Resonance Data Bank Repository of spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites
  • EPA Spectral Database Repository of spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites
  • NIST Chemistry WebBook Contains IR, mass, electronic/vibrational, and UV/VIS spectra as well as constants of diatomic molecules (spectroscopic data) and ion energetics data, etc.
  • SpectraBase Limited free on-line access to NMR, IR, Raman, UV-Vis, and Mass Spectra.
  • Spectral Database for Organic Compounds SDBS Integrated spectral database system for organic compounds: electron impact mass spectra (EI-MS), Fourier transform infrared spectra (FT-IR), 1H nuclear magnetic resonance (NMR) spectra, 13C NMR spectra, laser Raman spectra, and electron spin resonance (ESR) spectra.
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Biology, Biotechnology & Molecular Biology

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Chemistry & Analytics

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Medicine

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Pharma

  • ChemBank Collection of data about small molecules and resources for studying their properties, especially their effects on biology
  • Drug Discovery Online Site devoted exclusively to drug discovery and early-stage drug development - buyer's guide, feature stories, case studies, industry news, and newswire feeds related to the science and business of discovering new drugs
  • etc. The Enzyme Technology Consultancy - Reports for the diagnostics industry
  • Global Pharmaceutical Industry - Statistics & Facts
  • HTScreening.net High throughput screening (HTS) web portal
  • Medtrial.com Information source for clinical trials
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Physics, Maths & Engineering

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Patents & Trademarks

Patent-Retrieval Databases
Additional Patent Information
Trademarks
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Patent-Retrieval Databases

  • DEPATISnet On-line search of patents world-wide - Deutsches Patent- und Markenamt
  • Espacenet Database of the European Patent Office
  • FPO Free Paternts Online search system
  • FreshPatents Listing of recent US patent applications with keyword monitoring
  • Google Patents Google patent search system
  • Lens.org Global patent and scholarly knowledge search system
  • Patent Center USPTO's patent application information retrieval system
  • Patentscope World International Property Organization searchable database
  • Swissreg Trademark, patent and designs register data as well as protected topographies of the Swiss Federal Institute for Intellectual Property
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Additional Patent Information

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Trademarks

  • DMPAregister Marken Database of German trademarks - german
  • Markengesetz Full text of German trademark law - german
  • Swissreg Marken Database of Swiss trademarks - german
  • TMview Database of trademarks in Europe
  • TESS USPTO's database of registered trademarks and prior pending applications
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Bioanalytics

Microarrays
Field Flow Fractionation
Mass Spectrometry
Nanotechnology
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Microarrays

  • ArrayExpress Public EBI sponsored repository for microarray based gene expression data. Currently the EBI is establishing a pilot database containing microarray gene expression data that are available publicly
  • ABRF Microarray Research Group Microarray Research Group in the framework of the Association ob Biomolecular Resource Facilities
  • BASE project page Open source web-based comprehensive database server to manage the massive amounts of data generated by microarray analysis
  • BioChipNet NMI / BMI website on biochip technologies
  • Diagnostic Microbial Microarrays Microbial microarray projects carried out at the Department of Biotechnology of the Austrian Research Centers, Seibersdorf, Austria
  • DNA Microarray Methodology - Flash Animation Animation that demonstrates how DNA microarrays are performed
  • EMBL-EBI The microarray informatics group at the EBI addresses the problem(s) of managing, storing and analysing microarray data
  • Gene-Chips Leming Shi's Array Page
  • GermOnline Cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well as gametogenesis
  • Genome Consortium for Active Teaching (GCAT) Initiative to allow college students to work with DNA microarrays
  • Lab-on-a-Chip News server for microarray and microfluidics activities
  • Longhorn Array Database - LAD The LAD is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases.
  • Microarrays Research Today Free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software
  • microarrays.com Vanderbilt microarray core facility
  • MicroArray Quality Control (MAQC) Project The project involves six FDA Centers, major providers of microarray platforms and RNA samples, EPA, NIST, academic laboratories, and other stakeholders. It aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods
  • MUSC DNA Microarray Database Repository for DNA microarray data generated by MUSC investigators. At the discretion of the contributors, DNA microarray data is placed into the public domain and can be viewed and downloaded via the web interface - Medical University of South Carolina
  • ProteomicsSURF - Microarrays Comprehensive list of links to DNA and protein microarray activities and literature
  • University of Geneva Hospitals - Genomic Research Laboratory Microarrays in prokariotic research
  • Y.F. Leung's Functional Genomics - Microarray List of links to microarray related activities

    Microarray Publications Compilations

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Field Flow Fractionation

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Mass Spectrometry

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Nanotechnology

  • CC NanoChem Center of competence nanotechnology - german interdisciplinary network of nanotechnology activities
  • Exploring the Nanoworld Educational website to investigate the frontiers of the nanoworld
  • Nanomat Superregional NETWORK for Nanotechnology Materials - sponsored by the german Ministry of Research
  • Nanonet Information on aspects of the nanoworld - sponsored by the bmb+f (german federal research department) and the VDI (german engineering association)
  • NAS Computational Molecular Nanotechnology Survey of NASA Ames molecular nanotechnology activities - publications, images, links
  • Nanotechnology Database Up-to-date sources of information on nanotechnology in the following areas: major research centers, funding agencies, major reports and books
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Bioinformatics

Global
Microarrays
Oligonucleotide Primer Synthesis / Positioning
Nucleic Acid Structures & Sequences
Proteins
Prediction of Biological Function
Varia
File Formats
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Global

  • 2Can Support Portal Bioinformatics Introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators
  • BIOINFORMATICS.PHRMA.ORG Page of the Pharmaceutical Research and Manufacturers of America
  • bioinformatik.de Webdirectory for bioinformatics
  • CMS Molecular Biology Resource Compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Modeling. Among others: PCR primer selection, primer databases, PCR reaction setup, and PCR protools - Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids
  • HSLS Online Bioinformatics Resources Collection Annotated information and guided links to more than 1500 open sources bioinformatics databases and software tools
  • The Elements of Bioinformatics Summarizing a large range of bioinformatics tools via a periodic table like structure
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Microarrays

  • A 'module map' showing conditional activity of expression modules in cancer Integrated analysis of a compendium of 1975 published microarrays spanning 22 tumor types. Expression profiles in different tumors are described in terms of the behavior of modules, sets of genes that act in concert to perform a specific function.
  • BRB ArrayTools Integrated package for the visualization and statistical analysis of DNA microarray gene expression data - NCI
  • Cyber-T Statistics program with a web interface that can be conveniently used on high-dimensional array data for the identification of statistically significant differentially expressed genes. It employs statistical analyses based on simple t-tests that use the observed variance of replicate gene measurements across replicate experiments, or regularized t-tests that use a Bayesian estimate of the variance among gene measurements within an experiment - University of California, Irvine, Functional Genomics Center
  • CMS Molecular Biology Resource Compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Modeling. Among others: PCR primer selection, primer databases, PCR reaction setup, and PCR protools - Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids
  • DNA-Chip Analyzer (dChip) Software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures - Harvard School of Public Health
  • GEDA Gene Expression Data Analysis Tool Users can perform a number of simple transformations, finds differentially expressed genes using a variety of simple tests and performs agglomerative clustering on the samples using the retained genes as features with a user-selected clustering algorithms - University of Pittsburgh Cancer Institute
  • GEDS Gene Expression Data Simulator - University of Pittsburgh Cancer institute
  • GenMAPP Gene MicroArray Pathway Profiler - Computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes
  • GeneXPress GeneXPress is a visualization and analysis tool for gene expression data, integrating clustering, gene annotation, and sequence information. It allows to load clustering results and automatically analyze them for significance of functional groups through correlation with functional annotations (e.g. Gene Ontology) and for enrichment of motif binding sites (e.g. TRANSFAC motifs).
  • Genomics and Bioinformatics Group (GBG) web site Bioinformatic program packages, microarray data analysis information, and molecular databases for genomic and proteomic research: MatchMiner, GoMiner, MedMiner, CIMminer, MIMminer
  • GSCope Suite of bioinformatics software packages: SOM clustering and gene-ontology analysis of microarray data, integrated viewer for biomolecular network graphs, viewing and analyzing expression data on biological pathways
  • High-density Array Pattern Interpreter (HAPI) Method for interpreting the conceptual similarities of a cluster or group of genes that have been identified by a statistical methods such hierarchical clustering, Self-Organizing Maps, "gene shaving", k-means clustering, etc.
  • L2L Microarray Analysis Tool Tool for discovering hidden biological significance in microarray expression data
  • Module Map Tool to parse microarray data to identify groups of genes that work in concert during normal activities or in cancerogeneous cells
  • OligoArray 2.0 Software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
  • ONCOMINE Camcer Microarray Database Bioinformatics infrastructure for cancer genomics research that provides tools to query and visualize cancer microarray data for a gene or cancer type of interest
  • ProMAT - Protein Microarray Analysis Tool Software module for data analysis of protein microarrays
  • PubGene Web Tools On-line packages for up-to-date gene data, protein and mutation data, import and export options, clustering methods, disease, process, and function associations and advanced graphics
  • TM4 Online Suite of tools that consist of Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer(MeV), as well as a Minimal Information About a Microarray Experiment(MIAME)-compliant MySQL database - TIGR
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Oligonucleotide Primer Synthesis / Positioning

  • ALIGN Query ALIGN query using sequence data at the GENESTREAM network server IGH Montpellier, F
  • ExonPrimer Perl script that helps to design intronic primers for the PCR amplification of exons - Tim Strom, Institute for Human Genetics, Technical University of Munic
  • GeneFisher Interactive PCR primer design - University of Bielefeld, D
  • IDT SciTools Oligonucleotide sequence designer tools - for primers, RNAi and microarray probes
  • LALIGN Query LALIGN query using sequence data at the GENESTREAM network server IGH Montpellier, F
  • NetPrimer Free web-based interface using the latest primer design algorithms - Premier Biosoft
  • OligoAnalyzer Oligonucleotide parameter calculator from IDT BioTools
  • Oligo Calculation Oligonucleotide parameter calculator from Genset
  • Oligonucleotide Properties Calculator Comprehensive calculator with open algorithms
  • OligoCalc Oligonucleotide melting point calculator
  • PRIDE Primer Design for large-scale projects in sequencing, PCR, and DNA array design
  • The Primer Generator Automated generator of primers for site-directed mutagenesis
  • Primer3web Pick primers from a DNA sequence - Whitehead Institute for Biomedical Research
  • Primer Design Java applet by Luca Ida Giovanni TOLDO
  • Primer Selection Interface to a PCR primer selection program based on xprimer - University of Minnesota
  • POLAND Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids
  • Primer Selection Interface to a primer selection program based on Xprimer
  • QPPD The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays. All data has been gathered from published articles, cited in PubMed.
  • Tinoco Plots Simple tool to investigate possible secondary structure elements in RNA or DNA single strands
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Nucleic Acid Structures & Sequences

  • Beacon Designer Free Edition Free on-line qPCR design software that can be used to screen SYBR® Green primers and TaqMan® probes for possible secondary structures such as dimers or hairpins
  • Bioinformatics Software Packages Mayo Clinic's software packages to analyze, visualize and interpret genomic data
  • GeneDesign Web-based program for the design of synthetic genes. It consists of several modules that automate the tasks associated with the manipulation of synthetic sequences
  • GQuery (Global Cross-database NCBI search) Integrates information from databases at NCBI which include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE
  • InstaSeq Tool to search the World-Wide-Web for any fragment of DNA, RNA or Protein Sequence
  • RNA mfold RNA folding server of Michael Zuker, Washington University in St. Louis - calculation of secondary RNA structures
  • SEQUEROME Web-based sequence profiling tool of BLAST results allowing to extract the maximum out sequence alignment reports
  • Sfold Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids
  • SMS Collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences
  • UNAFold Unified Nucleic Acid Folding and hybridization package - access to mfold & DINAMelt RNA & DNA folding calculation software
  • VISTA Comprehensive suite of programs and databases for comparative analysis of genomic sequences
  • WatCut On-line tool for restriction analysis, silent mutation analysis, and SNP analysis
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Proteins

  • AbMiner Relational database of information on antibodies that we have screened specificity against the NCI-60 cancer cell lines. The database includes results of screenings by western blot, practical information for purchase, identifiers such as UniGene cluster and gene name for each antibody, and out-links to major public bioinformatics resources
  • BIND Biomolecular Interaction Network Database - a database designed to store full descriptions of interactions, molecular complexes and pathways
  • DeepView Visualization, comparison, analysis, and modeling of proteins - former SwissPDB Viewer
  • Molecular Docking Web Software for automated docking and scoring of flexible ligands to receptors
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Prediction of Biological Function

  • AmiGO HTML-based browser for Gene Ontology - established by the Gene Ontology Consortium
  • BioModels Database The BioModels Database is a new effort to develop a data resource that will allow biologists to store, search and retrieve published mathematical models of biological interests. The models in the BioModels Database are annotated and linked to relevant data resources, such as publications, databases of coumpounds and pathways, controlled vocabularies, etc.
  • eGOn eGOn (explore Gene Ontology) is a tool that facilitates use of biological background knowledge in analysis of genes selected from high throughput analysis like e.g microarray analysis. Lists of identifiers containing i.e. differentially expressed genes, are submitted to our annotation database, and eGOn automatically extends the list with Gene Ontology (GO) terms annotated to these genes.
  • E-Cell The E-Cell Project is an international research project aiming at developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
  • Gepasi Software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
  • GRAM - Genetic RegulAtory Modules Algorithm that identifies modules, collections of genes that share common regulators as well as expression profiles. The algorithm combines direct information from DNA binding experiments with indirect functional information from expression experiments.
  • LocusLink Single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.
  • Onto-Express Tool to automatically translate lists of genes found to be differentially regulated in the condition under studyl into functional profiles characterizing the impact of the condition studied
  • Pandora Protein ANnotation Diagram ORiented Analysis - protein-clustering tool to help to identify their mode-of-action
  • PubGene Web tools for the analysis of expression data in the context of literature or sequence associations
  • The ConSurf server Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
  • Virtual Cell Modeling cell biological processes. The approach associates biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular locations. A transparent mathematics framework develops numerical simulations, and results can be analyzed as images. Developed by the National Resource for Cell Analysis and Modeling (NRCAM)
  • 3d Mind Tools Tools for modeling pharmacological activity using neuronal networks
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Varia

  • Argo Java Tool for visualizing and manually annotating whole genomes
  • BioLinux Free bioinformatics software tools
  • Chemical Structure Searching Servers Access to National Library of Medicine's information databases on drugs, pesticides, environmental pollutants, and other potential toxins
  • ELECTRAS Web-based electronic data analysis service for the mathematical analysis of numerical data sets
  • Interactive Statistical Pages Powerful, conveniently-accessible, and free multi-platform statistical software package. Links to online statistics books, tutorials, downloadable software, and related resources
  • IUBio Archive for Biology Data and Software Indiana University archive of biology data and software, established in 1989 to promote public access to freely available information, primarily in the field of molecular biology
  • NCBI Structure The Structure Group at NCBI has created an up-to-date database of 3-dimensional macromolecular structures along with a rich set of tools for comparing and visualizing structures and sequences, searching for similarities, and associating these data with other information sources such as taxonomy and literature databases
  • Visual Molecular Dynamics Free downloadable software package for modeling proteins, lipid bilayers, and nucleic acids
  • Webcutter Determination of the restriction maps - automatic sequence search-and-entry from NCBI's GenBank
  • 2D and 3D Structural Information from DTP About half a million structures of the Developmental Therapeutics Program of the NCI
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File Formats

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Genomics, Proteomics & Transcriptomics

Global Access to Databases
Genomics
Proteomics
Glycomics
Lipids
Pathways
Pharmacology
Pharmacogenetics
Physiome
Toxicology & Drug Metabolism
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Global Access to Databases

  • Blast Search BLAST Search using sequence data at the GENESTREAM network server IGH Montpellier, France
  • Databases on Medicine and Molecular Biology Comprehensive annotated link list to genomics, pharmacology, toxicology and related databases
  • Entrez, The Life Science Search Engine Cross-database search page for all NCBI Web and FTP sites - NCBI
  • Entrez Nucleotide Access to Genbank - NCBI
  • FASTA Search FASTA Search using sequence data at the GENESTREAM network server IGH Montpellier, France
  • GenBank Database Query Text and Similarity Searching - National Center for Biotechnology Information
  • GeneStream2 Nucleic acid sequences from Genbank, EMBL, Genbank-new, EMBL new and GB-expressed sequence tag databases are concatenated and duplicate entries removed to produce a single dataset. The current size of the non-redundant database is over 3.0 million sequences. Its size requires that access to search this data base by some search programs is resticted to a mail only service.
  • OLCODIBS - On Line Colection of Databases in the Biological Sciences Broad structured collection of links to life science databases
  • Sequence Retrieval System EMBL service for a combined search of SWISS-PROT, EMBL, TrEMBL, GenBank, etc.
  • SSEARCH Search SSEARCH Search using sequence data at the GENESTREAM network server IGH Montpellier, France - email service only
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Genomics

  • addgene Non-profit plasmid repository operating a plasmid repository for the research community
  • ARS Genome Database Resource Set of agricultural genome databases. They include plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varieties
  • Atlas of Nucleic Acid Containing Structures Extremely comprehensive database of the Nucleic Acid Database Project covering DNA structures, RNA structures, unusual structures, protein/DNA complexes, and protein/RNA complexes
  • Bacteriophage Home Page Bacteriophage T4 and other phages home page - Evergreen State College
  • BGMUT - Blood Group Antigen Gene Mutation Database Database of variations in the genes that encode antigens of blood group systems
  • Cancer Genome Anatomy Project Survey of commonly used approaches to high throughput, comprehensive analysis of relative transcript expression levels
  • Caenorhabditis elegans WWW Server Webserver for Caenorhabditis elegans research
  • Cancer Cell Line Project Characterization of 600 tumor cell lines with respect to in vitro acquired additional genetic abnormalities
  • CGEMS - Cancer Genetic Markers of Susceptibility Genome-Wide Association Study (GWAS) on over 500,000 genetic variants to determine their role in cancer susceptibility
  • Consensus CoDing Sequence (CCDS) project Annotated high quality core set of human protein-coding regions
  • Cyanosite Webserver for cyanobacterial research
  • Comparative RNA Web Site Information on structure and evolution of especially ribosomal and transfer RNAs
  • DG CST - Disease Genes Conserved Sequence Tags Database collection of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts
  • DHGP - Deutsches Humangenomprojekt German Human Genome Project - Resource Center
  • DHGP - Deutsches Humangenomprojekt German Human Genome Project - Resource Center
  • DNASU Central repository for plasmid clones and collections. Currently over 200,000 plasmids including 75,000 human and mouse plasmids are stored and distributed
  • DISC DNA Information and Stock Center, National Institute of Agrobiological Resources, Tsukuba, Japan
  • EGAD - The Expressed Gene Anatomy Database Non-redundant set of human transcript (HT) sequences and non-human transcript (ET) sequences
  • EST Clone Resources American Type Culture Collection (ATTC) cDNA collection including clones deposited by TASC/I.M.A.G.E.
  • E.coli Index Comprehensive guide to information relating to Escherichia coli
  • FVII Mutation Database Searchable database covering mutations of Factor VII
  • genepaint.org Digital atlas of gene expression patterns in the mouse
  • Gene Expression Database Query Database of human and mouse gene activities in various cells and tissues - Novartis Research Foundation
  • Genlink Multimedia database resource for human genetics - Washington University St. Louis
  • GeneSeeker Search engine to interrogate different databases simultaneously, given a known human genetic location and expression/phenotypic pattern
  • genome gateway Comprehensive genomics web resource established by Nature and Nature Genetics
  • Genome Reviews Standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes - EMBL-EBI
  • Genetic Association Database Archive of human genetic association studies of complex diseases and disorders
  • geo - Gene Expression Omnibus Public gene expression data collection - launched by NCBI. Gene expression data repository and online resource for the retrieval of gene expression data from any organism or artificial source. Gene expression data from multiple platforms, including spotted microarray, high-density oligonucleotide array , hybridization filter and serial analysis of gene expression (SAGE) data, will be accepted, accessioned, and archived as a public data set.
  • GOLD - Genomes OnLine Database Information covering complete and ongoing genome projects around the world
  • Gottschling Lab Homepage Collection of core yeast protocols
  • GeneCards Concise information about the functions of all human genes that have an approved symbol (gene listing)
  • Gramene Curated, open-source, Web-accessible data resource for comparative genome analysis in the grasses
  • HapMap Multi-country effort to identify and catalog genetic similarities and differences in human beings. The haplotype map of the human genome, the HapMap, will describe the common patterns of human DNA sequence variation.
  • Harvard Medical School - George M. Church Laboratory & Lipper Center for Computational Genetics Computational & comparative functional genomics
  • Hembase Information about genes transcribed in blood cells
  • HemoPDP The Hematopoiesis Promoter Database (HemoPDB) is as a publicly available, web-based information resource focused on transcriptional regulation in hematopoiesis
  • Human Genome Project Information Information about the U.S. and worldwide Human Genome Project, research in progress site
  • Human Genome Resources Links to key genomic databases, maps, and markers for all 23 pairs of human chromosomes. LocusLink - starting place for a quick summary of all top-level information about a gene. Launched by the National Center for Biotechnology Information (NCBI)
  • hum-molgen Communication forum in human molecular genetics
  • IDbases - databases for immunodeficiency-causing mutations Large collection of databases for immunodeficiency-causing mutations
  • International Sequencing Consortium Large-scale Sequencing Project Database Web site to provide a single, central site for the scientific community and the public to have access to up-to-date information about animal, plant and other eukaryotic genomic sequencing projects
  • Mapping the Icelandic Genome An ANTHROPOLOGY of the scientific, political, economic, religious, and ethical issues surrounding the deCode project and its global implications
  • Mouse Encyclopedia Index About 20000 end sequenced cDNA clones compiled by the Genome Exploration Research Group of RIKEN (Japan)
  • National Center for Biotechnology Information - Genes and Disease Map Physical maps with identified disease-causing genes
  • NCBI Reference Sequence Project Non-redundant collection of naturally-occurring biological molecules
  • NDB - Nucleic Acid Database Project Atlas of nucleic acid containing structures, archives, searching options
  • NIA/NIH Mouse Genomics Home Page NIA Mouse cDNA Project / NIA Mouse t-complex Genome Sequencing Project
  • Oncogenomics Normal Tissue Database High-density gene expression database derived from 42,000 clone cDNA microarrays containing 18,927 unique genes for 158 normal human samples from 19 different organs of 30 different individuals
  • PheLiGe Web-service that provides access to publicly available results from human genetic association studies and among others allows for exploration of genome-wide and regional associations, finding phenotypes associated to a genetic variant, and comparison of associations patterns between different traits
  • PhosPhAt Arabidopsis Protein Phosphorylation Site Database
  • PicSNP Catalog of non-synonymous SNP (Single Nucleotide Polymorphism)
  • Probe Database The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities
  • PubMatrix Tool to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything: gene names, diseases, gene functions, authors etc.
  • RDP - Robosomal Database Project Provision of ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
  • repairGenes Site containing information about DNA repair genes from a set of selected species. The information is organised by organism and by biological process term as defined by the Gene Ontology (GO) project
  • RestrictionMapper On-line restriction mapping
  • RiboWEB The RiboWEB is a knowledge base containing templates (or structured representations) for the most common experiments used to study the structure of RNA/Protein complexes. It is currently populated with information (almost 5800 individual observations) from 150 articles about the 30S ribosomal subunit in procaryotes
  • RNA Interference siRNA Database and Resources for RNA Interference Studies
  • rrnDB Searchable database documenting variation in ribosomal RNA operons (rrn) in Bacteria and Archaea
  • SAGEmap Information on SAGE libraries and access to the data produced from these libraries
  • SAGE Genie SAGE Genie uses a new analytical method of reliably matching SAGE tags to known genes. Based on this tag to gene mapping, the website visualizes human gene expression analysis in tissues or individual libraries using displays that are highly intuitive
  • SAGE - Serial Analysis of Gene Expression Genzyme molecular oncology (GMO) homepage for academic SAGE applications
  • SEGE - Single Exonic Genes in Eukaryotes Database Collection of gene sequences that are annotated to have single exon structure in Genbank feature table
  • SNPs.com A site dedicated to the creation, collection and dissemination of information pertaining to single nucleotide polymorphisms (SNPs), sponsored by Orchid Biocomputer, Inc
  • The Genome Channel Atlas for finding genes - links to sequencing centers for 24 organisms
  • The tmRNA Website Links to tmRNA sequences of about 250 bacteria
  • TubercuList Collection and integration of various aspects of the genomic information from M. africanum, M. bovis, M. bovis BCG, M. canetti, M. microti, and above all, M. tuberculosis. TubercuList provides a complete dataset of DNA and protein sequences derived from the paradigm strain M. tuberculosis H37Rv, linked to the relevant annotations and functional assignments.
  • UKNCC United Kingdom National Culture Collection
  • The Whole Mouse Catalog The Web site serves as a central place to find numerous Internet resources of particular interest to scientific researchers using mice or rats in their work
  • Virtual Genome Center Access to tools and databases for molecular biologists

    Sequence Databases

  • BacMap Interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes
  • Botanical Databases
  • coliBASE Online database for E. coli, Salmonella and Shigella comparative genomics
  • CUTG Codon usage tabulated from gene bank
  • dbSNP NIH database of human genetic variation
  • DDBJ - DNA Data Bank of Japan All known nucleotide and protein sequences
  • EBI Databases European Bioinformatics Institute
  • EMBL Nucleotide Sequence Database All known nucleotide and protein sequences
  • Ensembl Annotated information on eucariotic genomes
  • GDB - The Genome Database International collaboration in support of the Human Genome Project
  • GenBank All known nucleotide and protein sequences
  • Genewindow DNA browser that allows to scroll through a particular gene nucleotide by nucleotide, identifying SNPs and other landmarks like protein-coding segments
  • GOBASE GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to organelles with a focus on the mitochondrial and chloroplast subset of data
  • HGMG - Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff Database of known (published) gene lesions responsible for human inherited disease
  • HGVbase HGVbase (Human Genome Variation database)is a database of intra-genic (promoter to end of transcription) single nucleotide polymorphisms - hosted by the Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden
  • HIV Sequence Database Access to databases, alignments, and tools and interfaces produced at Los Alamos National Laboratories
  • HuGEIndex Database The Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues
  • Integrated Microbial Genomes (IMG) Access to nearly 300 draft or completed genome sequences from archae and bacteria
  • IMAGE consortium database Query The world's largest public collection of genes
  • Jackson Laboratory Mouse Genome Database Collection of mouse genetic and phenotypic data
  • KSD - Kinase Sequence Database Collection of protein kinase sequences grouped into families by homology of their catalytic domains. The aligned sequences are available in MS Excel format, as well as in HTML
  • Mammalian Gene Collection (MGC) New effort by the NIH to generate publicly accessible full-length complementary DNA (cDNA)resources. The project entails the production of cDNA libraries and sequences, database and repository development, as well as the support of research forimproved library construction, sequencing, and analytic technologies
  • Mitomap v. 3.1 Human mitochondrial genome database; structure - function correlation
  • Mobile group II introns Resource to identify and catalog group II introns
  • NONCODE Database of noncoding RNAs
  • OMIM Online Mendelian inheritance in man - catalog of human genes and genetic disorders
  • PeptideAtlas Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments
  • RTPrimerDB - Real Time PCR Primer and Probe Database Public database holding real time PCR primers and probes for popular chemistries (Intercalating Dyes, Hydrolysis Probes, Hybridisation Probes, Molecular Beacons) to prevent time-consuming primer design and experimental optimisation
  • snoRNA-LBME-db Database of human C/D box and H/ACA modification guide RNAs
  • Stanford University - Saccharomyces Genome Database Scientific database of the molecular biology and genetics of the baker's (or budding) yeast
  • STACKdb Database of virtual human transcripts, based on GenBank Data
  • Subviral RNA Database About 1300 nucleotide sequences for viroids and related solo RNA molecules
  • The Gene Expression Database (GXD) The Gene Expression Database is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development
  • TIGR databases Databases of The Institute for Genomic Research: The TIGR Microbial Database, The TIGR Parasites Database, TIGR Gene Indices, The TIGR Arabidopsis thaliana Database, The Expressed Gene Anatomy Database, Sequences, Sources, Taxa
  • The Genetics of Cancer Information resource to help to understand the genetic basis of cancer and to interpret new discoveries in the field of cancer genetics
  • UniGene Non-redundant, gene-oriented clusters

Alternative Splicing Databases

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Proteomics

  • Bioinformatic Harvester Harvester caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information
  • CCSB Interactome Database Information about efforts to map the human interactome
  • DBSubLoc - Database of Protein Subcellular Localization Database of protein subcellular localization that contains proteins from SWISS-PROT and PIR, is annotated with respect to subcellular localization and is classified and categorized by cross reference to taxonomies and gene ontology
  • DSDBASE - disulphide database Database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein
  • EMBL Protein and Peptide Group Protein and peptide group WWW server of the European Molecular Biology Laboratory
  • Enzyme Enzyme nomenclature database
  • Enzyme Structures Database Contains close to 4000 known enzyme structures that have been deposited in the Brookhaven Protein Data Bank
  • ExactAntigen Comprehensive gene-specific and species-specific information resource for reagents (antibodies, ELISA, siRNA, recombinant proteins, chemicals, and tissue arrays), researchers, and patents
  • G2P - Genomics 2 Proteins Portal Broad Institute's Portal to Link Genetic Screening Outputs to Protein Sequence and Structure
  • HPMR Site dedicated to studies on plasma membrane receptors in the human genome, combining text-based and sequence-based search tools. The web site categorizes major groups of human plasma membrane receptors based on protein sequences, evolutionary relationships, and published literature
  • IntAct Open source database system and analysis tools for molecular interaction data
  • InterPro Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences
  • IMGT Server ImMunoGeneTics database, an integrated database specialising in Immunoglobulins (Ig), T cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species
  • LPFC - A Library of Protein Family Cores Database of proteins classified into families of structures
  • LOCATE subcellular location database Curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM3 mouse protein sequence set
  • MEROPS Peptidase database of the Babraham Institute in Cambridge / UK - catalog of more than 900 proteases among others with structural data and occurrance in organisms
  • Meta-MEME Motiv-based hidden Markov modeling of biological sequences - software toolkit for building and using motiv-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences.
  • MIA - Molecular Information Agent The Molecular Information Agent (MIA) is a web server that searches biological databases to find the existing information about a macromolecule. At the present time, the MIA supports search by molecule identification number, gene symbol, sequence, and key word.
  • MSRS Website Searchable database of antibodies and probes including antibody, host, antigen species, label,...
  • MOWSE Search Form Rapid identification of proteins by peptide-mass fingerprinting
  • MPDB Membrane Protein Database On-line, searchable, relational database with select structural and functional information on membrane proteins and peptides
  • National Center for Biotechnology Information Gateway to protein and DNA databases
  • Natural System of Gene Families from Complete Genomes Clusters of orthologous groups (COGs) were delineated by comparing protein sequences encoded in 8 complete genomes, representing 6 major phylogenetic lineages
  • Nuclear Protein Database (NPD) Searchable database of information on proteins that are localised to the nucleus of vertebrate cells
  • NURSA - Nuclear Receptor Signaling Atlas Resource for information relating to key aspects of orphan nuclear receptor biology
  • PDB WWW Home Page USA Archive of experimentally determined three-dimensional structures of biological macromolecules
  • PEPTIDE MASS SEARCH Searches the protein database for multiple peptides of individual proteins
  • Pfam - Protein families database of alignments and HMMs Large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
  • PhosphoSite Curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites
  • PRIDE - PRoteomics IDEntifications database Public repository for protein and peptide identifications together with the evidence supporting these identifications
  • PrionDB Molecular specific information system for prion proteins
  • PROLYSIS Protease and protease inhibitor Web server at the University of Tours, France - Introduction to proteases and their inhibitors, including assays and enzyme kinetics
  • ProteinDBS Real-time database search and similarity rankings of 3D protein structures
  • Protein Prospector Tools for mining sequence databases in conjunction with mass proteometry experiments
  • Proteome Alliance Page of the Project of the German Research Ministry "Proteom-Analyse des Menschen". This project focusses on the development of research tools and their clinical application in human proteome analysis
  • proteomicsSURF Covers bioanalytical approaches in the field of proteomics covering microarrays, spectroscopy, spectrometry, and bioinformatics
  • PROTONET Global classification of the proteins into hierarchical clusters
  • PROW - Protein Reviews on the Web International WWW Resource/Journal on Human Proteins - NCBI
  • PROWL Protein information retrieval on-line world wide web lab
  • The Human Serum Proteome Comprehensive human serum proteomic database
  • UniProt UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
  • WEB P.A.G.E Phoretix´ World-Wide Collaboration in 2D Gel Electrophoresis: On-Line Databases
  • 2D Gel Databases World-Wide Phoretix´ links to 2D gel databases on the internet

    Sequence Databases

  • Brookhaven Protein Database Originated by the Brookhaven National Laboratory, now hosted at the Research Collaboratory for Structural Bioinformatics
  • ExPASy University and Hospital of Geneva WWW server, database entry point for SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ExPASy Tools
  • Cogent - Complete Genome Tracking Database Single resource containing predicted peptides from all publicly available fully sequenced genomes
  • Human Mitochondrial Protein Database The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases
  • HPRD - Humane Protein Reference Database Platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All OMIM genes have been annotated
  • MEROPS - the Peptidase Database Information resource for peptidases and their protein inhibitors
  • STACKdb Database of virtual human transcripts, based on GenBank Data
  • SWISS-PROT Annotated protein sequence database - EBI site
  • SWISS-PROT and TrEMBL Annotated protein sequence database - ExPASy site
  • UAB Proteomics Database Repository for the storage and linkage of two-dimensional gel images and the associated information obtained through mass spectrometry analysis
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Glycomics

  • Carbhyd Links to information on carbohydrate structures, biochemistry, and related graphics tools for modeling sugar molecules
  • Complex Carbohydrate Magnetic Resonance Database - CCMRD Solid-state NMR database for complex carbohydrates
  • Complex Carbohydrate Research Center - CCRC On-line neural net recognition system for GC profiles and NMR spectra
  • Glycominds Database Glycomics database that compiles information about glycoconjugated molecules - including their structures, functions, and interactions with other molecules
  • GlyCosmos Web portal aiming to integrate the glycosciences with the life sciences; providing information about genes, proteins, lipids, pathways and diseases
  • GLYCOsciences.de (SweetDB) Databases and bioinformatics tools for glycobiology and glycomics
  • GlycoSuiteDB Annotated and curated relational database of glycan structures containing most published O-linked glycans, and N-linked glycans in the literature from years 1990-2000. Information is available concerning the glycan type, linkage and anomeric configuration, mass and composition.
  • NetOGlyc The web server returns probable O-glycosylation sites of mammalian mucin glycoproteins based on the predictions of a neuronal network
  • Sugabase Links to various glyco-related directories and databases
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Lipids

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Pathways

  • BBID-Biological Biochemical Image Database Searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships
  • Biocarta Pathways On-line maps depicting dynamic graphical models of gene interactions
  • Biocatalysis/Biodegradation Database Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic chemical compounds
  • BioCyc Database Collection Collection of Pathway/Genome Databases. Prediction of metabolic pathways of completely sequenced organisms, prediction of which genes code for missing enzymes in metabolic pathways, and prediction of operons
  • Biozon Unified biological resource on DNA sequences, proteins, complexes and cellular pathways
  • BRENDA Comprehensive enzyme information system
  • CST Pathways Pathway diagrams assembled by CST scientists and outside experts to provide succinct and current overviews of selected signaling pathways
  • Database of Cell Signaling Information on the components of cellular signaling pathways and their relations to one another, organized into pathways called Connections Maps, Free registration required
  • GenePath Web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks
  • iHOP - information hyperlinked over proteins Network accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
  • Interactive Pathways & Processes R&D System's collection of pathway visualizations that can be explored interactively
  • KEGG - Kyoto Encyclopedia of Genes and Genomes Database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information
  • Reactome Open-source, curated and peer reviewed pathway database
  • Roche Chemical Pathways Searchable charts covering metabolic pathways and cellular and molecular processes
  • The Signaling Gateway UCSD Signaling Gateway Molecule Pages providing essential information on over thousands of proteins involved in cellular signaling
  • WikiPathways Curated platform covering biological pathways

    P450 Isoenzymes

    PDE Family - Phosphodiesterase

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Pharmacology

  • BindingDB Database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds
  • ChemMine Compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens
  • Clinical Pharmacology Comprehensive information on all FDA-approved drugs and OTC pharmaceuticals - indications, effects, and side effects
  • PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge Base Central repository for genetic and clinical information about people who have participated in research studies at various medical centers in the PGRN. In addition, genomic data, molecular and cellular phenotype data, and clinical phenotype data are accepted from the scientific community at large.
  • RXList Information about the top 200 US prescriptions Dispensed
  • Self-Organizing Map of NCI Antiviral Screen Compounds Searchable database about antiviral compounds
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Pharmacogenetics - Cancer

  • COSMIC - Catalog of Somatic Mutations in Cancer Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types
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Physiome

  • PhenomicDB Multi-species genotype/phenotype database
  • Physiome Project The Physiome Project is a worldwide effort to define the physiome through the development of databases and models which will facilitate the understanding of the integrative function of cells, organs, and organisms
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Systems Biology

  • Protein Lounge Interactive web-based databases and software to cope with the complexity of systems biology
  • The BioGRID Comprehensive database of protein and genetic interactions
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Toxicology & Drug Metabolism

  • DSSTox The Distributed Structure-Searchable Toxicity (DSSTox) Database Network provides a community forum for publishing standard format, structure-annotated chemical toxicity data files for open public access
  • Eurotox Homepage of the International Union of Toxicology
  • Genetic Association Database Archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature
  • OSIRIS Property Explorer The OSIRIS Property Explorer allows to draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid
  • IUTOX Homepage of Eurotox, the Association of European Toxicologists and European Societies of Toxicology
  • TOXNET Access to different toxicology related databases
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Rules & Regulations

Regulatory Affairs
GMP and ISO 9001
Material Safety Data Sheets
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Regulatory Affairs

  • ORA - Office of Regulatory Affairs FDA site featurung among others compliance policy guides, regulatory procedures manual and other FDA compliance documents and information like 21 CFR Part 11
  • 21CFRPart11.com The web site provides access to information on the 21 CFR Part 11 rule and also maintains an email list that actively discusses issues and concerns with industry peers and government regulators. The site features the latest conference, meeting and seminar information as well as links to vendors and consultants.

GMP and ISO 9001

  • GMP Navigator GMP related news and information - hosted by Concept Heidelberg
  • ISO Online The source of ISO 9000 and more than 13 700 International Standards for business, government and society

Material Safety Data Sheets

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