Medical research targets are based on Biotechnologie knowledge for academic sources and Universities

New tools for Biotech Research

Heraeus is consulting these ressources to improve our insturmentation. Most ar Biology and lab German databases.

1. Analytik News Edited portal for analytical life science related information – german
2. Bionity.com Search engine and database for products and news in the field of life sciences
3. Bioportfolio Information portal related to bio/pharma/life science industries
4. BioSpace Biotech and pharmaceutical news & jobs
5. BioWorld Biotechnology daily news and information
6. BIO-IT World Information Technology for the Life Sciences
7. BIO – Biotechnology Industry Organization Biotechnology related news
8. Drug Discovery from Technology Networks News, products,and resources related to drug discovery
9. EurekAlert Online, global news service operated by AAAS
10. Forschungsportal Search engine to scan german research activities and to locate BMBF funded reports and publications – german
11. idw – Informationsdienst Wissenschaft News platform covering activities of several hundred universities and research institutions in Germany, Austria and Switzerland – german
12. Life-Sciences-Germany.com Life sciences web portal for german-speaking Europe – german
13. MedBioWorld Online resource portal for professional medical and biotechnology information
14. PubCrawler Alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases
15. Research Explorer Information about over 25,000 institutes at German universities and non-university research institutions
16. Royal Society of Chemistry News updates, on-line magazine, job and conference notices, and product infos
17. theLabRat.com Information center for scientists and researchers – job listings, company profiles, suppliers, and protocols

Blasting gene sequences and align

Scientific databses and ressources

1. GQuery NCBI Global Cross-database Search
2. Laverne Virtual research assistant to locate and browse bioinformatics data related to gene, pathway or disease of interest and explore relationship and context
3. ScienceResearch.com Deep web science and technology search engine
4. Scirus Comprehensive science-specific search engine
5. WorldWideScience.org Global science gateway comprising national and international scientific databases and portals

Quiries with fuzzy logic and elastic search relational databases of biologic and medical aggregation.

Medical suppliers

1. ABC der deutschen Wirtschaft Comprehensive database of German B2B suppliers – german
2. Biocrawler Database of companies involved in biotechnology
3. HUM-MOLGEN Biomedical Companies Database of US biomedical companies
4. mediLexicon Database of pharmaceutical companies worldwide

Distributors and suppliers of Life Science reagents

1. AuthorMapper Online tool for visualizing scientific research, enables document discovery based on author locations and geographic maps. Integrating content and mapping technology,
2. BASE – Bielefeld Academic Search Engine Highly configurable search engine for scientific publications
3. Crossref Metadata-based broad search of scientific published information and authors of scientific publications
4. DIMDI – Deutsches Institut für Medizinische Dokumentation und Information Search of publications with focus on medicine and pharmacology
5. DART-Europe E-theses Portal European portal for electronic theses and dissertations
6. Google Scholar Access to a broad range of scientific publications
7. LIVIVO Database to search scientific publications and authors
8. PubFacts Search portal for medicine, health, nutrition, environmental and agricultural sciences literature
9. PubMed Search of biomedical publications in MEDLINE, life science journals, and online books – NCBI / NHI
10. ScienceResearch.com Real-time deep web search engine for scientific publications
11. Science.gov Search for publications in over 60 databases and over 2200 selected websites from 15 federal agencies – Science.gov Alliance
12. SCOPUS Abstract and citation database of peer-reviewed research literature
13. Subito Access to publications in academic libraries in Germany, Austria, Liechtenstein, and Switzerland
14. BioMed Central Publisher of open access peer-reviewed biomedical research journals
15. ChemWeb Access to selected full-text articles from chemistry publishers
16. DOAJ – Directory of Open Access Journals Aims to be the one stop shop for users of open access journals
17. HighWire Press ePublishing platform to facilitate the digital dissemination of journals, reference works, books, and proceedings – Stanford University Libraries
18. PLoS – Public Library of Science Publisher of scientific open access journals

Medical Libraries

1. ANNO Archive of the Austrian National Library – Access to scanned historical newspapers and journals with focus on Austria
2. BnF Access to the digital library of the Bibliotheque Nationale de France
3. botanicus Freely accessible portal to historic botanical literature from the Missouri Botanical Garden Library
4. Digitale Bibliothek Braunschweig – Access to scanned historical books and journals with focus on pharmacy
5. Internet Archive Archival storage of internet publications
6. OPACplus Archive of the Bayerische StaatsBibliothek – Access to scanned historical books and journals
7. lanl.arXiv.org Open access to e-prints in physics, mathematics, computer science, quantitative biology, quantitative finance and statistics – Cornell University Library
8. Library of Congress Searches for printed and digital inventory
9. MDZ – Münchener Digitalisierungszentrum Digital Collections of the Bavarian State Library
10. NDLTD – Networked Digital Library of Theses and Dissertation e-Archive for digital theses and dissertations
11. Rare Book Room Rare books, manuscripts, and antiquarian printed material in digital formatInfomine Scholarly internet resource collections – University of California
12. MIT OpenCourseWare Web-based publication of virtually all MIT course content
13. Scientist Solutions Moderated internet discussion site to provide scientists a resource for the exchange of ideas and information
14. The Why Files Science behind the news – addresses scientific, technical, as well as mathematical backgrounds of everyday issues
15. The WWW Virtual Library: Natural Sciences and Mathematics Directory of science related web sites compiled by subject areas
16. Dictionary of Cell Biology Dictionary of cell biology terms
17. Glossary of Genetic Terms Dictionary of cell biology terms
18. Organic Chemistry Glossary Dictionary of organic chemistry terms
19. alphaDictionary.com Search engine for an extensive number of dictionaries from and into english
20. ARGH: Biomedical Acronym Resolver Heuristically constructed approach to identify acronyms/abbreviations and their definitions within MEDLINE records
21. Acronyms Acronyms and abbreviations including chemical terms
22. BEOLINGUSEnglish, Spanish, and Portuguese to German and reverse dictionary
23. IATE Inter-Active Terminology for Europe – inter-institutional terminology database of EU-specific terminology, technical terms, acronyms, and abbreviations of European institutions
24. LEO – On-line dictionaries English, French, Spanish, Portuguese, Italian, Russian, Polish, and Chinese to German and reverse dictionary
25. Merriam Webster On-line version of thesaurus and dictionary
26. Word2Word Online Dictionaries and Translators Extensive link list to free online resources
27. Brown Lab Protocols Protocols covering the full range from microarray preparation to data processing
28. bio-protocol Comprehensive collection of experimental protocols in life sciences
29. Buffers for pH control Calculation of thermodynamically correct recipes for the control of pH in aqueous biological systems
30. Cold Spring Harbor Protocols Selected free of charge protocols
31. IPMB DNA Microarray Core Laboratory Protocols Protocols adapted from the “DNA microarray protocols” of the Arabidopsis Functional Genomics Consortium
32. Molecular Biology Protocols Selection of molecular biology protocols, techniques, methods and books
33. NIA Protocols Protocols cover especially nylon membrane microarrays – National Institute of Aging
34. Protocol Online Comprehensive collection of protocols and methods in molecular and cell biology
35. Protocols List of recipes of salt solutions, laboratory buffers, media, antibiotics etc. and a collection of protocols of H.Lehrach laboratory at MPI Mol Gen
36. Zbio.net Protocols On-line calculation of composition of buffer and media solutions

Maxanim Animations

1. BIODIC – The Ultrastructure Website Collection of high resolution electron micrographs of cells, bacteria, fungi, pollen, biological structures, etc.
2. BrainInfo Maps of brains of primates
3. Cells Alive Drawings, micrographs, and movies of cells and microorganisms
4. Database of Macromolecular Movements Animations and movies of motions that occur in proteins and other macromolecules
5. Jena Library of Biological Macromolecules Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis
6. Nanoworld Scanning electron, transmission electron, and optical microscopy images of microorganisms and biological structures
7. PDBsum Pictorial database of 3D structures in the Protein Data Bank
8. Protein Imager Tool to visualize protein structures directly in the browser
9. Structural View of Biology Images of biomolecules utilizing Protein Data Bank data, focusing on the biological function of the molecules
10. The Visible Human Project Complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies
11. Virtual Cell Animation Collection Visualization of cellular functions
12. Anatomia 1522 – 1867 – Anatomical Plates from the Thomas Fisher Rare Book Library Approximately 4500 full page plates and other significant illustrations of human anatomy selected from the Jason A. Hannah and Academy of Medicine collections in the history of medicine
13. EPACT – Scientific Instruments of Medieval and Renaissance Europe Electronic catalogue of medieval and renaissance scientific instruments from the Museum of the History of Science, Oxford, the Istituto e Museo di Storia della Scienza, Florence, the British Museum, London, and the Museum Boerhaave, Leiden.
14. Images from the History of Medicine Collection including portraits, pictures of institutions, caricatures, genre scenes, and graphic art in a variety of media, illustrating the social and historical aspects of medicine
15. Medicine and Madison Avenue Images and database information for various health-related advertisements printed in newspapers and magazines from the 1910s through the 1950s
16. MEMS Image Gallery Electron micrographs of micromachined devices
17. Pictures of Famous Physicists Photos, drawings, stamps and other portraits of scientists
18. The Edgar Fahs Smith Memorial Collection Prints, engravings,and photographic images of scientists, laboratories, and scientific apparatus
19. The Periodic Table of Comic Books Chemical elements in comic books
20. Virtual Polyhedra Collection of thousands of virtual reality polyhedra

Chemical substances databses, Beilstein

1. BioMagResBank Repository for NMR data of proteins, peptides, and nucleic acids
2. Infrared Spectra Downloadable free infrared spectra library
3. IR-Spektrensammlung der ANSYCO GmbH IR spectra of gaseous state compounds – german
4. MassBank Public repository of mass spectral data
5. NIST Chemistry WebBook National Institute of Standards Reference databases, covers MS, IR and UV/VIS spectra
6. NMRShiftDB Open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data
7. SDBS Integrated Spectral Data Base System for Organic Compounds – MS, NMR, IR, Raman, and ESR spectra
8. SPECARB – Raman Spectra of Carbohydrates Experimental database that contains Raman spectra of carbohydrates
9. TeleSpec Simulation of infrared spectra, especially for compounds whose spectra are not available in any database

PCR, qPCR

1. Bacteria and Viruses: How Are They Different? Basic as well as advanced information about bacteria and viruses
2. Biochemistry of Metabolism Instructional materials for a studio-format course
3. BioChemWeb Virtual library of biochemistry, moleculer biology and cell biology
4. biolinks.de Selected and commented links to fields of biology equally relevant for science and society – german
5. BiosciEdNet Digital library portal for teaching and learning the biological sciences
6. BioED Online Science teachers resources from Baylor College of Medicine
7. Digital Learning Center for Microbial Ecology Information on microbial ecology for students and teachers
8. DNA from the beginning Animated experiments illustrating modern genetics
9. Fishbase Global information database about fishes
10. GBIF – Global Biodiversity Information Facility Open access database on biodiversity
11. GSLC – Genetic Science Learning Center Science education program of the University of Utah
12. Giftpflanzen Poisonous plants – covering different aspects of poisons in plants and herbs, their chemistry, toxicity, antidots, as well as biological function – german
13. MendelWeb Educational resource for teachers and students interested in the origins of classical genetics, introductory data analysis, elementary plant science, and the history and literature of sciencee
14. MicrobeWorld Educational website providing information about basic microbiology and issues involving microbiology
15. Molecular Station Science and discussion forum for molecular biology methods and protocols
16. NCBI Bookshelf Free access to books and documents in life science and healthcare
17. Protist Information Server Images and movie clips of protists and other microorganisms
18. The Biology Project On-line interactive resources for learning biology
19. Tree of Life web project Vast collection of information about biodiversity compiled in a phylogenetic tree
20. TreeBASE Database of phylogenetic knowledge
21. Understanding Genetics Introduction to basic principles of genetics for a general audience
22. Vascular Plant Types Catalog Database and images of approximately 92,000 vascular plant type specimens of the New York Botanical Garden
23. Virtual Genetics Lab Simulation of transmission genetics that approximates, as closely as possible, the hypothesis-testing environment of genetics research
24. Zbio.net Methods, information and programs for molecular biologists – international russian – german collaboration
25. Analytical Chemistry Springboard Comprehensive list of analytical chemistry resources on the Internet
26. Chemexper Search engine to locate chemicals and suppliers
27. Chemical Information Sources Wikibook covering a wide range of chemistry information resources on the internet
28. ChemIDplus Advanced Database allowing users to search the NLM ChemIDplus database of over 400,000 chemicals for among others physical, chemical, and toxicological properties
29. Chem1 Virtual Textbook Comprehensive virtual textbook for General Chemistry
30. Chemie.de German chemistry information service – german
31. Chemistry animations and movies on the World Wide Web Link list for chemistry related animations
32. Chemistry Webercises Directory Extensive collection of links to various areas of chemistry
33. Enhanced NCI Database Browser 2.2 Data base with structures, data, tools, programs and other useful information to the public
34. Experimentalchemie.de Chemical experiments for teaching, educational and show purposes – german
35. Global Instructional Chemistry Chemistry tutorials, course materials, reviews, and reports
36. Molecular Modeling for Organic Chemistry Lecture course aimed to introduce in a simple way into the hierarchy of computational modelling methods
37. Namensreaktionen Chemical mane reactions – german
38. Nobel Prize for Chemistry Information about Nobel price winners in the field of chhemistry
39. Organic Chemistry Resources Worldwide WWW resource guide for synthetic organic chemists covering literature, bench work, structural analysis, and communication
40. Organic Chemistry Portal Overview of recent topics, interesting reactions, and information on important chemicals for organic chemists
41. Panopticon Lavoisier Virtual museum of the collections of the French chemist Antoine Laurent Lavoisier
42. Periodic Table Resource: Tungsten, Palladium and Other Transition Metals Detailed information about transition metals
43. Prof. Blumes Bildungsserver für Chemie Large collection of chemistry related texts and experiments especially suited for educational purposes – german
44. Selected Classic Papers from the History of Chemistry Papers from the history of chemistry as html files
45. Virtual Chemistry 3-D simulated laboratory for the teaching of chemistry
46. Virtual Mass Spectrometry Laboratory Interactive, educational tool to teach mass spectromtery
47. Yeah Science Entertaining introduction to chemistry

Biomedical interactions

1. A Nurse’s Guide to the Human Body Comprehensive link list covering a multitude of functional and regulatory systems of the human body
2. Anatomy of the Human Heart ACLS link list to educational resources related to the heart
3. Digital Anatomist Information System The long term goal of the Digital Anatomist project is an anatomy information system that is available from any desktop computer on the network
4. Genetics Home Reference National Library of Medicine’s web site for consumer information about genetic conditions and the genes or chromosomes responsible for those conditions
5. MedNets Medical database designed for use by physicians, administrators, patients and the general public as a health research and information resource
6. Introduction to Cardiothoracic Imaging Illustrated tutorial to heart and lung anatomy
7. Medscape Online resource for medical information – Medline, Toxline, Aidsline access
8. MedBioWorld Resource portal for professional medical and biotechnology information
9. Merck Manual of Medical Information–Home Edition Based on The Merck Manual of Diagnosis and Therapy, commonly referred to as The Merck Manual, transformed into commonly used English while retaining the vital information about diseases, diagnosis, prevention, and treatment
10. RN to BSN Online Programs Listing of RN to BSN Programs in America
11. The Internet Pathology Laboratory for Medical Education Web resource that includes over 1900 images along with text, tutorials, laboratory exercises, and examination items for self-assessment that demonstrate gross and microscopic pathologic findings associated with human disease conditions
12. The Ultimate List of Anatomy and Physiology Resources Comprehensive link list covering medical, biological as well as chemical areas
13. Virtual Autopsy Mini-tutorials on aspects of anatomy
14. Who Named It? Comprehensive dictionary of medical eponyms – including bibliographic information
15. ChemBank Collection of data about small molecules and resources for studying their properties, especially their effects on biology
16. 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
17. etc. The Enzyme Technology Consultancy – Reports for the diagnostics industry
18. Global Pharmaceutical Industry – Statistics & Facts
19. HTScreening.net High throughput screening (HTS) web portal
20. Medtrial.com Information source for clinical trials

Heraeus Statistics ressources

1. Einstein Archives Online Online access to Albert Einstein’s scientific and non-scientific manuscripts held by the Albert Einstein Archives at the Hebrew University of Jerusalem and to an extensive Archival Database
2. Engineering Statistics Handbook On-line handbook to help scientists and engineers to incorporate statistical methods in their work as efficiently as possible
3. Galileo Galilei´s Notes on Motion Manuscript of Galileo Galilei published by the Max-Planck Society for the History of Physics
4. Geomuseum TU Clausthal Comprehensive classified collection of mineralogy related images – german
5. The Museum of Unworkable Devices Collection of fascinating devices that don’t work

Scientific Biotech patents information

1. DEPATISnet On-line search of patents world-wide – Deutsches Patent- und Markenamt
2. Espacenet Database of the European Patent Office
3. FPO Free Paternts Online search system
4. FreshPatents Listing of recent US patent applications with keyword monitoring
5. Google Patents Google patent search system
6. Lens.org Global patent and scholarly knowledge search system
7. Patentscope World International Property Organization searchable database
8. Public PAIR USPTO’s patent application information retrieval system
9. Swissreg Trademark, patent and designs register data as well as protected topographies of the Swiss Federal Institute for Intellectual Property
10. Copyright US Copyright Office’s informations on US copyright
11. DMPAregister Official publications and register database of the German Patent and Trademark Office
12. Index to Manual of Classification of Patents Determination of patent classes via searching keywords
13. Patentrecherchen im Internet Online training course for patent search – german
14. DMPAregister Marken Database of German trademarks – german
15. Markengesetz Full text of German trademark law – german
16. Swissreg Marken Database of Swiss trademarks – german
17. TMview Database of trademarks in Europe
18. TESS USPTO’s database of registered trademarks and prior pending applications

Anygen Arrays targets

1. 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
2. ABRF Microarray Research Group Microarray Research Group in the framework of the Association ob Biomolecular Resource Facilities
3. BASE project page Open source web-based comprehensive database server to manage the massive amounts of data generated by microarray analysis
4. BioChipNet NMI / BMI website on biochip technologies
5. Diagnostic Microbial Microarrays Microbial microarray projects carried out at the Department of Biotechnology of the Austrian Research Centers, Seibersdorf, Austria
6. DNA Microarray Methodology – Flash Animation Animation that demonstrates how DNA microarrays are performed
7. EMBL-EBI The microarray informatics group at the EBI addresses the problem(s) of managing, storing and analysing microarray data
8. Gene-Chips Leming Shi’s Array Page
9. GermOnline Cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well as gametogenesis
10. Genome Consortium for Active Teaching (GCAT) Initiative to allow college students to work with DNA microarrays
11. Lab-on-a-Chip News server for microarray and microfluidics activities
12. 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.
13. Microarrays Research Today Free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software
14. microarrays.com Vanderbilt microarray core facility
15. 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
16. 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
17. ProteomicsSURF – Microarrays Comprehensive list of links to DNA and protein microarray activities and literature
18. University of Geneva Hospitals – Genomic Research Laboratory Microarrays in prokariotic research
19. Y.F. Leung’s Functional Genomics – Microarray List of links to microarray related activities
20. EMBL-EBI Microarray Publications Listing of EMBL-EBI publications in chronological order
21. Microarray & Data Analysis Collection of papers with emphasis on analysis of microarray data
22. NCI Technical Talks and Reports TeleChem//arrayit.com hosted Microarray Resource Center
23. TIGR Microarray Publications List of microarray-related publications from the TIGR faculty and staff
24. Field Flow Fractionation (FFF) & Nanoparticle Separations Survey of FFF variants and applications
25. Field-Flow Fractionation References Web Site FFF web site maintained by Marc R. Schure

Mass Spectrometry

• American Society for Mass Spectrometry
• Australian and New Zealand Society for Mass Spectrometry
• Belgian Society for Mass Spectrometry
• European Molecular Biology Laboratory Bioanalytical Research Group
• IonSource Comprehensive resource for mass spectrometry especially in life sciences
• LC/MS Homepage Extensive information resource for LC/MS equipment
• i-mass.com Comprehensive web site and reference source on mass spectrometry
• University of Arizona MS tutorials
• University of Alberta Homepage Prof. Liang Li

Nanotechnology

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

Protocols

1. 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
2. BIOINFORMATICS.PHRMA.ORG Page of the Pharmaceutical Research and Manufacturers of America
3. bioinformatik.de Webdirectory for bioinformatics
4. 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
5. HSLS Online Bioinformatics Resources Collection Annotated information and guided links to more than 1500 open sources bioinformatics databases and software tools
6. The Elements of Bioinformatics Summarizing a large range of bioinformatics tools via a periodic table like structure

Microarrays

1. 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.
2. BRB ArrayTools Integrated package for the visualization and statistical analysis of DNA microarray gene expression data – NCI
3. 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
4. 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
5. 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
6. 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
7. GEDS Gene Expression Data Simulator – University of Pittsburgh Cancer institute
8. GenMAPP Gene MicroArray Pathway Profiler – Computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes
9. 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).
10. 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
11. 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
12. 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.
13. L2L Microarray Analysis Tool Tool for discovering hidden biological significance in microarray expression data
14. Module Map Tool to parse microarray data to identify groups of genes that work in concert during normal activities or in cancerogeneous cells
15. OligoArray 2.0 Software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
16. 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
17. ProMAT – Protein Microarray Analysis Tool Software module for data analysis of protein microarrays
18. 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
19. 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

Primes synthesis

1. ALIGN Query ALIGN query using sequence data at the GENESTREAM network server IGH Montpellier, F
2. 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
3. GeneFisher Interactive PCR primer design – University of Bielefeld, D
4. IDT SciTools Oligonucleotide sequence designer tools – for primers, RNAi and microarray probes
5. LALIGN Query LALIGN query using sequence data at the GENESTREAM network server IGH Montpellier, F
6. NetPrimer Free web-based interface using the latest primer design algorithms – Premier Biosoft
7. OligoAnalyzer Oligonucleotide parameter calculator from IDT BioTools
8. Oligo Calculation Oligonucleotide parameter calculator from Genset
9. Oligonucleotide Properties Calculator Comprehensive calculator with open algorithms
10. OligoCalc Oligonucleotide melting point calculator
11. PRIDE Primer Design for large-scale projects in sequencing, PCR, and DNA array design
12. The Primer Generator Automated generator of primers for site-directed mutagenesis
13. Primer3web Pick primers from a DNA sequence – Whitehead Institute for Biomedical Research
14. Primer Design Java applet by Luca Ida Giovanni TOLDO
15. Primer Selection Interface to a PCR primer selection program based on xprimer – University of Minnesota
16. POLAND Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids
17. Primer Selection Interface to a primer selection program based on Xprimer
18. 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.
19. Tinoco Plots Simple tool to investigate possible secondary structure elements in RNA or DNA single strands
20. 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
21. Bioinformatics Software Packages Mayo Clinic’s software packages to analyze, visualize and interpret genomic data
22. 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
23. InstaSeq Tool to search the World-Wide-Web for any fragment of DNA, RNA or Protein Sequence
24. RNA mfold RNA folding server of Michael Zuker, Washington University in St. Louis – calculation of secondary RNA structures
25. SEQUEROME Web-based sequence profiling tool of BLAST results allowing to extract the maximum out sequence alignment reports
26. Sfold Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids
27. SMS Collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences
28. UNAFold Unified Nucleic Acid Folding and hybridization package – access to mfold & DINAMelt RNA & DNA folding calculation software
29. VISTA Comprehensive suite of programs and databases for comparative analysis of genomic sequences
30. WatCut On-line tool for restriction analysis, silent mutation analysis, and SNP analysis

Proteomics

1. 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
2. BIND Biomolecular Interaction Network Database – a database designed to store full descriptions of interactions, molecular complexes and pathways
3. DeepView Visualization, comparison, analysis, and modeling of proteins – former SwissPDB Viewer
4. Molecular Docking Web Software for automated docking and scoring of flexible ligands to receptors
5. AmiGO HTML-based browser for Gene Ontology – established by the Gene Ontology Consortium
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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
13. Pandora Protein ANnotation Diagram ORiented Analysis – protein-clustering tool to help to identify their mode-of-action
14. PubGene Web tools for the analysis of expression data in the context of literature or sequence associations
15. The ConSurf server Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
16. 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)
17. 3d Mind Tools Tools for modeling pharmacological activity using neuronal networks
18. Argo Java Tool for visualizing and manually annotating whole genomes
19. BioLinux Free bioinformatics software tools
20. Chemical Structure Searching Servers Access to National Library of Medicine’s information databases on drugs, pesticides, environmental pollutants, and other potential toxins
21. ELECTRAS Web-based electronic data analysis service for the mathematical analysis of numerical data sets
22. Interactive Statistical Pages Powerful, conveniently-accessible, and free multi-platform statistical software package. Links to online statistics books, tutorials, downloadable software, and related resources
23. 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
24. 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
25. Visual Molecular Dynamics Free downloadable software package for modeling proteins, lipid bilayers, and nucleic acids
26. Webcutter Determination of the restriction maps – automatic sequence search-and-entry from NCBI’s GenBank
27. 2D and 3D Structural Information from DTP About half a million structures of the Developmental Therapeutics Program of the NCI
28. File FormatsBABEL Conversion software for chemical file formats
29. Converter’s Paradise 60 downloadable file converter tools
30. Data Formats in Science
31. Every File Format in the World List of file name extension or suffixes that indicate the format or usage of a file and a brief description of that format – part of whatis.com
32. File Formats by Extensions Compiled by Beeline Publications
33. VEGA Conversion software for chemical file formats and 3D visualization tool for molecules
34. Wotsit The programmers file formats collection
35. Blast Search BLAST Search using sequence data at the GENESTREAM network server IGH Montpellier, France
36. Databases on Medicine and Molecular Biology Comprehensive annotated link list to genomics, pharmacology, toxicology and related databases
37. Entrez, The Life Science Search Engine Cross-database search page for all NCBI Web and FTP sites – NCBI
38. Entrez Nucleotide Access to Genbank – NCBI
39. FASTA Search FASTA Search using sequence data at the GENESTREAM network server IGH Montpellier, France
40. GenBank Database Query Text and Similarity Searching – National Center for Biotechnology Information
41. 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.
42. OLCODIBS – On Line Colection of Databases in the Biological Sciences Broad structured collection of links to life science databases
43. Sequence Retrieval System EMBL service for a combined search of SWISS-PROT, EMBL, TrEMBL, GenBank, etc.
44. SSEARCH Search SSEARCH Search using sequence data at the GENESTREAM network server IGH Montpellier, France – email service only
45. addgene Non-profit plasmid repository operating a plasmid repository for the research community
46. ARS Genome Database Resource Set of agricultural genome databases. They include plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varieties
47. 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
48. Bacteriophage Home Page Bacteriophage T4 and other phages home page – Evergreen State College
49. BGMUT – Blood Group Antigen Gene Mutation Database Database of variations in the genes that encode antigens of blood group systems
50. Cancer Genome Anatomy Project Survey of commonly used approaches to high throughput, comprehensive analysis of relative transcript expression levels
51. Caenorhabditis elegans WWW Server Webserver for Caenorhabditis elegans research
52. Cancer Cell Line Project Characterization of 600 tumor cell lines with respect to in vitro acquired additional genetic abnormalities
53. CGEMS – Cancer Genetic Markers of Susceptibility Genome-Wide Association Study (GWAS) on over 500,000 genetic variants to determine their role in cancer susceptibility
54. Consensus CoDing Sequence (CCDS) project Annotated high quality core set of human protein-coding regions
55. Cyanosite Webserver for cyanobacterial research
56. Comparative RNA Web Site Information on structure and evolution of especially ribosomal and transfer RNAs
57. 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
58. DHGP – Deutsches Humangenomprojekt German Human Genome Project – Resource Center
59. DHGP – Deutsches Humangenomprojekt German Human Genome Project – Resource Center
60. DNASU Central repository for plasmid clones and collections. Currently over 200,000 plasmids including 75,000 human and mouse plasmids are stored and distributed
61. DISC DNA Information and Stock Center, National Institute of Agrobiological Resources, Tsukuba, Japan
62. EGAD – The Expressed Gene Anatomy Database Non-redundant set of human transcript (HT) sequences and non-human transcript (ET) sequences
63. EST Clone Resources American Type Culture Collection (ATTC) cDNA collection including clones deposited by TASC/I.M.A.G.E.
64. E.coli Index Comprehensive guide to information relating to Escherichia coli
65. FVII Mutation Database Searchable database covering mutations of Factor VII
66. genepaint.org Digital atlas of gene expression patterns in the mouse
67. Gene Expression Database Query Database of human and mouse gene activities in various cells and tissues – Novartis Research Foundation
68. Genlink Multimedia database resource for human genetics – Washington University St. Louis
69. GeneSeeker Search engine to interrogate different databases simultaneously, given a known human genetic location and expression/phenotypic pattern
70. genome gateway Comprehensive genomics web resource established by Nature and Nature Genetics
71. Genome Reviews Standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes – EMBL-EBI
72. Genetic Association Database Archive of human genetic association studies of complex diseases and disorders
73. 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.
74. GOLD – Genomes OnLine Database Information covering complete and ongoing genome projects around the world
75. Gottschling Lab Homepage Collection of core yeast protocols
76. GeneCards Concise information about the functions of all human genes that have an approved symbol (gene listing)
77. Gramene Curated, open-source, Web-accessible data resource for comparative genome analysis in the grasses
78. 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.
79. Harvard Medical School – George M. Church Laboratory & Lipper Center for Computational Genetics Computational & comparative functional genomics
80. Hembase Information about genes transcribed in blood cells
81. HemoPDP The Hematopoiesis Promoter Database (HemoPDB) is as a publicly available, web-based information resource focused on transcriptional regulation in hematopoiesis
82. Human Genome Project Information Information about the U.S. and worldwide Human Genome Project, research in progress site
83. 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)
84. hum-molgen Communication forum in human molecular genetics
85. IDbases – databases for immunodeficiency-causing mutations Large collection of databases for immunodeficiency-causing mutations
86. 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
87. Mapping the Icelandic Genome An ANTHROPOLOGY of the scientific, political, economic, religious, and ethical issues surrounding the deCode project and its global implications
88. Mouse Encyclopedia Index About 20000 end sequenced cDNA clones compiled by the Genome Exploration Research Group of RIKEN (Japan)
89. National Center for Biotechnology Information – Genes and Disease Map Physical maps with identified disease-causing genes
90. NCBI Reference Sequence Project Non-redundant collection of naturally-occurring biological molecules
91. NDB – Nucleic Acid Database Project Atlas of nucleic acid containing structures, archives, searching options
92. NIA/NIH Mouse Genomics Home Page NIA Mouse cDNA Project / NIA Mouse t-complex Genome Sequencing Project
93. 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
94. 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
95. PhosPhAt Arabidopsis Protein Phosphorylation Site Database
96. PicSNP Catalog of non-synonymous SNP (Single Nucleotide Polymorphism)
97. 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
98. 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.
99. 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
100. 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
101. RestrictionMapper On-line restriction mapping
102. 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
103. RNA Interference siRNA Database and Resources for RNA Interference Studies
104. rrnDB Searchable database documenting variation in ribosomal RNA operons (rrn) in Bacteria and Archaea
105. SAGEmap Information on SAGE libraries and access to the data produced from these libraries
106. 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
107. SAGE – Serial Analysis of Gene Expression Genzyme molecular oncology (GMO) homepage for academic SAGE applications
108. SEGE – Single Exonic Genes in Eukaryotes Database Collection of gene sequences that are annotated to have single exon structure in Genbank feature table
109. SNPs.com A site dedicated to the creation, collection and dissemination of information pertaining to single nucleotide polymorphisms (SNPs), sponsored by Orchid Biocomputer, Inc
110. The Genome Channel Atlas for finding genes – links to sequencing centers for 24 organisms
111. The tmRNA Website Links to tmRNA sequences of about 250 bacteria
112. 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.
113. UKNCC United Kingdom National Culture Collection
114. 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
115. Virtual Genome Center Access to tools and databases for molecular biologists
116. BacMap Interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes
117. Botanical Databases
118. coliBASE Online database for E. coli, Salmonella and Shigella comparative genomics
119. CUTG Codon usage tabulated from gene bank
120. dbSNP NIH database of human genetic variation
121. DDBJ – DNA Data Bank of Japan All known nucleotide and protein sequences
122. EBI Databases European Bioinformatics Institute
123. EMBL Nucleotide Sequence Database All known nucleotide and protein sequences
124. Ensembl Annotated information on eucariotic genomes
125. GDB – The Genome Database International collaboration in support of the Human Genome Project
126. GenBank All known nucleotide and protein sequences
127. Genewindow DNA browser that allows to scroll through a particular gene nucleotide by nucleotide, identifying SNPs and other landmarks like protein-coding segments
128. 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
129. HGMG – Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff Database of known (published) gene lesions responsible for human inherited disease
130. 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
131. HIV Sequence Database Access to databases, alignments, and tools and interfaces produced at Los Alamos National Laboratories
132. 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
133. Integrated Microbial Genomes (IMG) Access to nearly 300 draft or completed genome sequences from archae and bacteria
134. IMAGE consortium database Query The world’s largest public collection of genes
135. Jackson Laboratory Mouse Genome Database Collection of mouse genetic and phenotypic data
136. 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
137. 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
138. Mitomap v. 3.1 Human mitochondrial genome database; structure – function correlation
139. Mobile group II introns Resource to identify and catalog group II introns
140. NONCODE Database of noncoding RNAs
141. OMIM Online Mendelian inheritance in man – catalog of human genes and genetic disorders
142. 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
143. snoRNA-LBME-db Database of human C/D box and H/ACA modification guide RNAs
144. Stanford University – Saccharomyces Genome Database Scientific database of the molecular biology and genetics of the baker’s (or budding) yeast
145. STACKdb Database of virtual human transcripts, based on GenBank Data
146. Subviral RNA Database About 1300 nucleotide sequences for viroids and related solo RNA molecules
147. 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
148. 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
149. 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
150. UniGene Non-redundant, gene-oriented clusters
151. Alternative Splicing Database Alternative splicing evidence collected
152. Human Alternative Splicing Database (HASDB) Over 6200 human alternative splice variants predicted from EST data
153. Bioinformatic Harvester Harvester caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information
154. CCSB Interactome Database Information about efforts to map the human interactome
155. 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
156. 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
157. EMBL Protein and Peptide Group Protein and peptide group WWW server of the European Molecular Biology Laboratory
158. Enzyme Enzyme nomenclature database
159. Enzyme Structures Database Contains close to 4000 known enzyme structures that have been deposited in the Brookhaven Protein Data Bank
160. ExactAntigen Comprehensive gene-specific and species-specific information resource for reagents (antibodies, ELISA, siRNA, recombinant proteins, chemicals, and tissue arrays), researchers, and patents
161. 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
162. IntAct Open source database system and analysis tools for molecular interaction data
163. InterPro Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences
164. 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
165. LPFC – A Library of Protein Family Cores Database of proteins classified into families of structures
166. 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
167. 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
168. 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.
169. 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.
170. MSRS Website Searchable database of antibodies and probes including antibody, host, antigen species, label,…
171. MOWSE Search Form Rapid identification of proteins by peptide-mass fingerprinting
172. MPDB Membrane Protein Database On-line, searchable, relational database with select structural and functional information on membrane proteins and peptides
173. National Center for Biotechnology Information Gateway to protein and DNA databases
174. 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
175. Nuclear Protein Database (NPD) Searchable database of information on proteins that are localised to the nucleus of vertebrate cells
176. NURSA – Nuclear Receptor Signaling Atlas Resource for information relating to key aspects of orphan nuclear receptor biology
177. PDB WWW Home Page USA Archive of experimentally determined three-dimensional structures of biological macromolecules
178. PEPTIDE MASS SEARCH Searches the protein database for multiple peptides of individual proteins
179. 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
180. PhosphoSite Curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites
181. PRIDE – PRoteomics IDEntifications database Public repository for protein and peptide identifications together with the evidence supporting these identifications
182. PrionDB Molecular specific information system for prion proteins
183. PROLYSIS Protease and protease inhibitor Web server at the University of Tours, France – Introduction to proteases and their inhibitors, including assays and enzyme kinetics
184. ProteinDBS Real-time database search and similarity rankings of 3D protein structures
185. Protein Prospector Tools for mining sequence databases in conjunction with mass proteometry experiments
186. 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
187. proteomicsSURF Covers bioanalytical approaches in the field of proteomics covering microarrays, spectroscopy, spectrometry, and bioinformatics
188. PROTONET Global classification of the proteins into hierarchical clusters
189. PROW – Protein Reviews on the Web International WWW Resource/Journal on Human Proteins – NCBI
190. PROWL Protein information retrieval on-line world wide web lab
191. The Human Serum Proteome Comprehensive human serum proteomic database
192. 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.
193. WEB P.A.G.E Phoretix´ World-Wide Collaboration in 2D Gel Electrophoresis: On-Line Databases
194. 2D Gel Databases World-Wide Phoretix´ links to 2D gel databases on the internet
195. Brookhaven Protein Database Originated by the Brookhaven National Laboratory, now hosted at the Research Collaboratory for Structural Bioinformatics
196. ExPASy University and Hospital of Geneva WWW server, database entry point for SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ExPASy Tools
197. Cogent – Complete Genome Tracking Database Single resource containing predicted peptides from all publicly available fully sequenced genomes
198. 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
199. 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
200. MEROPS – the Peptidase Database Information resource for peptidases and their protein inhibitors
201. STACKdb Database of virtual human transcripts, based on GenBank Data
202. SWISS-PROT Annotated protein sequence database – EBI site
203. SWISS-PROT and TrEMBL Annotated protein sequence database – ExPASy site
204. UAB Proteomics Database Repository for the storage and linkage of two-dimensional gel images and the associated information obtained through mass spectrometry analysis
205. Carbhyd Links to information on carbohydrate structures, biochemistry, and related graphics tools for modeling sugar molecules
206. Complex Carbohydrate Magnetic Resonance Database – CCMRD Solid-state NMR database for complex carbohydrates
207. Complex Carbohydrate Research Center – CCRC On-line neural net recognition system for GC profiles and NMR spectra
208. Glycominds Database Glycomics database that compiles information about glycoconjugated molecules – including their structures, functions, and interactions with other molecules
209. GlyCosmos Web portal aiming to integrate the glycosciences with the life sciences; providing information about genes, proteins, lipids, pathways and diseases
210. GLYCOsciences.de (SweetDB) Databases and bioinformatics tools for glycobiology and glycomics
211. 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.
212. NetOGlyc The web server returns probable O-glycosylation sites of mammalian mucin glycoproteins based on the predictions of a neuronal network
213. Sugabase Links to various glyco-related directories and databases

1. LIPIDAT Relational database of physical and chemical properties of lipids
2. LIPID MAPS – LIPID Metabolites And Pathways Strategy Integrated approach to the study of lipidomics

1. BBID-Biological Biochemical Image Database Searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships
2. Biocarta Pathways On-line maps depicting dynamic graphical models of gene interactions
3. Biocatalysis/Biodegradation Database Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic chemical compounds
4. 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
5. Biozon Unified biological resource on DNA sequences, proteins, complexes and cellular pathways
6. BRENDA Comprehensive enzyme information system
7. CST Pathways Pathway diagrams assembled by CST scientists and outside experts to provide succinct and current overviews of selected signaling pathways
8. 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
9. GenePath Web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks
10. 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.
11. Interactive Pathways & Processes R&D System’s collection of pathway visualizations that can be explored interactively
12. 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
13. Reactome Open-source, curated and peer reviewed pathway database
14. Roche Chemical Pathways Searchable charts covering metabolic pathways and cellular and molecular processes
15. The Signaling Gateway UCSD Signaling Gateway Molecule Pages providing essential information on over thousands of proteins involved in cellular signaling
16. WikiPathways Curated platform covering biological pathways

1. Dave Flockhart’s Cytochrome P450 Drug Interaction Table Cytochrome P450 drug interaction table listing drug interactions that are the result of competition for, or effects on the human cytochrome P450 system
2. Cytochrome P450 Homepage Cytochrome P450 database, general informations on the P450 family
3. P450 Drug Interaction Table: Abbreviated “Clinically Relevant” Table Compilation of clinically relevant substrates
4. The Human Cytochrome P450 (CYP) Allele Nomenclature Database Allele nomenclature for Cytochrome P450 enzymes
5. The P450 Site of the University of Arizona Arabidopsis P450 knockouts and microarrays
6. Phosphodiesterase Nomenclature, contact info, meetings

1. BindingDB Database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds
2. ChemMine Compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens
3. Clinical Pharmacology Comprehensive information on all FDA-approved drugs and OTC pharmaceuticals – indications, effects, and side effects
4. 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.
5. RXList Information about the top 200 US prescriptions Dispensed
6. Self-Organizing Map of NCI Antiviral Screen Compounds Searchable database about antiviral compounds

1. 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

1. PhenomicDB Multi-species genotype/phenotype database
2. 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

1. Protein Lounge Interactive web-based databases and software to cope with the complexity of systems biology
2. The BioGRID Comprehensive database of protein and genetic interactions

1. 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
2. Eurotox Homepage of the International Union of Toxicology
3. 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
4. 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
5. IUTOX Homepage of Eurotox, the Association of European Toxicologists and European Societies of Toxicology
6. TOXNET Access to different toxicology related databases

Regulations

• 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 13485

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

protocols and data sheets

1. IPCS INCHEM Access to internationally peer reviewed information on chemicals commonly used throughout the world, which may also occur as contaminants in the environment and food
2. IRIS Database for Risk Assessment The Integrated Risk Information System (IRIS), prepared and maintained by the U.S. Environmental Protection Agency (U.S. EPA), is an electronic database containing information on human health effects that may result from exposure to various chemicals in the environment
3. ISI – Informationsstelle für Sicherheitsdatenblätter Comprehensive MSDS collection in german
4. Material Safety Data Sheets
5. MSDS Public Service Library Electronic material safety data sheets
6. Vermont SIRI MSDS Archive Material safety data sheets collection of the University of Vermont, USA