“RESEARCH and the INTERNET”^©

Course Bookmarks

( list from 2005 - still updated when suggestions are made [Jan.2011] )

JdD's Bookmarks
vanSluis b ookmarks ACGE Course 1997
Svan Sluis Bookmarks

JdD's Bookmarks

PubMed
Journals (Walaeus)
Google
Lexibot

Grants _ Organizations EU CORDIS - EU CORDIS - UK EG-Liaison Homepage EU BioTech R&D (Biovista) NEST (Dutch EG Liaison) Rijk Ministerie van Economische Zaken Mandela Studie Fonds IOP LUMC Intranet Alzheimer Nederland ASHG - American Society of Human Genetics Born-Bunge Foundation CBG - Centre for Biomedical Genetics ECA - European Cytogenetics Association EMBO ENMC - European Neuro Muscular Centre ESF - European Science Foundation FEBS HFS - Human Frontier Science HUGO - HUman Genome Organization HDF - Hereditary Disease Foundation ISAO - Internationale Stichting Alzheimer Onderzoek KNCV - Koninklijke Nederlandse Chemische Vereniging KWF - Koningin Wilhelmina Fonds (Dutch Cancer Society) Merck Genome Research Institute MGC - Medisch Genetisch Centrum Zuid-West Nederland MIBITON NEST - Netherlands house for Science and Technology NVE (Netherlands Society for Endocrinology) NWO LUMC - Leids Universitair Medisch Centrum LUMC - PKL-Home Senter (overheid_ondernemer) STW Subsidies _ fondsen Subsidies, etc. (Nijmegen) gopher___HEARN.nic.SURF....nic.SURFnet.NL_SUBSI-L<_A > SURFnet Wellcome Trust NAV - VKGN homepage ESF - Functional Genomics HUGO BBSRC (UK)
Literature _ Journals Publication searches PubMed (Medline) Entrez MedHunt OCLC - Reference Services WebMedLit BioMedNet - journals Journal Impact Factors PubMed Central Home Manuscript Review Form for Nucleic Acids Research IDEAL homepage The American Physiological Society Homepage AG journals Biochemistry and Molecular Biology Journals Institute for Scientific Information (ISI)_ Science Citation Index Journal Contents_ IDEAL(R) Alert Walaeus Bibliotheek - University Leiden Walaeus Library (OVID) PubMed - Cubby (retrieve notification) PubMed - PubCrawler (Email) notification Bioinformatics -- Table of Contents (16 [11]) Medline _ ERL (Silverplatter) Bioinformatics (OUP) EHG home Genomics Journals - SCI (Walaeus) Nucleic Acids Research Journals - Leiden University Mary Ann Liebert, Inc. The Leading Publishers of Biotechnology Books, Journals, Trade Publicati
Genome data GDB GDB browser (US) GDB browser (NL) GDB browser (UK) Large genome centers Sanger Centre (Cambridge) Baylor College of Medicine Human Genome Sequencing Center Washington University CEPH - Genethon DKFZ - Heidelberg HGMP-RC NHGRI - National Human Genome Research Institute RZPD - Resource Center_Primary Database TIGR Whitehead Institute Genome maps Human Genome Web Resource (NCBI) WWW ACeDB (Webace - Sanger Center) UDB, The Unified Database HuGeMap - human genome maps Human_Mouse homology maps RHdb (Radiation Hybrid Database) STRP's from Marshfield All chr. (CEPH-Généthon) All chr. (MIT) Expression Human Transcript Map (Science) The Expressed Gene Anatomy Database (EGAD) Diffs - Find differentially expressed Genes 2D proteome database (human) GXD - Gene Expression Database (mouse) mouse atlas (expression) Genome sequencing Comparative Sequencing Man_Mouse Genome Sequencing - human (NCBI) Genome Sequencing - Celera Sequencing index (human) Sequenced genomes (Magpie) Sequenced microbial genomes (TIGR) How much of man is sequenced _ Non-human E.coli EcoCyc (Encyclopedia of E. coli Genes and Metabolism) E.coli strains, mutations, etc. mouse Mouse genome (MIT) mouse Genome Project mouse X-map (MGC Harwell) mutagenesis project (EU - mutabase) OmniBank (Lexicon Genetics, Inc. _ MERCK) yeast GeneCrunch - Yeast genome XREFdb (S.cerevisiae homology; NCBI) MIPS (Munich Information center for Protein Sequences) SGD (Saccharomyces Genome Database) YPD (Yeast Proteome Database) Drosophila (FlyBase) Drosophila Encyclopaedia Fugu rubripes Rat (MIT) RATMAP SNP databases HGBase Human SNP Database (MIT) Transgenics OmniBank random KO's (Lexicon) Lexicon Genetics Mining the Genome TBASE (targeted alleles database) Nature Genome Information Centre Lexicon Genetics Mining the Genome Human Genome Web Resource (NCBI) The Genome Web (HGMP-RC) Virgil - links database (Human Genome Project) Human Genome Project Multi-dimensional Human Embryo CPL - querying diverse DB's Genome sizes (DOGS) Human Transcriptome Map Linkage analysis Human Genome Project Information (HGMIS) The Human Genome (NCBI) Human Genome (draft) - Tour (NCBI) HumGen - for policy makers
Disease (genetic) _ Mutations Disease THE MERCK MANUAL HotMolecBase - database promising targets medical applications Mutations (databases _ analysis tools) Locus Specific Databases ImMunoGeneTics database Leiden Muscular Dystrophy pages PAH DB XLRS1 mutations X-linked agammaglobulinemia (BTKbase) EMD mutation database Software MuStaR(TM) Sequence Variant Database Software MutationView databases (KMeyeDB) Universal Mutation Database EBI - amino acid > codon (reverse translator) EBI - mutation checker EBI - mutations ALLELE VARIANT ENTRY FORM Association of Mutation Databases List of mutation databases Mutation database guidelines Nomenclature Human Gene Mutation Database CARMEN - Concerted Action for Research into Myopathies due to ENzyme deficiencies Neuromuscular Disorders Muscular dystrophy research Dr. Kevin Campbell's Lab homepage DMD Research Center - Pittsburgh Giovanni Naso's Muscular Dystrophy page Neuromuscular Disease Center - St.Louis MuscleNET (Italy) AFM Congenital Muscular Dystrophy Group MDA - Muscular Dystrophy Association (USA) Duchenne Parent Project - NL MDA - (Australia) MDG - Muscular Dystrophy Group Parent Project (muscular dystrophy) VSN WMS - World Muscle Society Submission of mutations (journals) Human Genetics Human Mutation Understanding Gene Testing Human Cytogentics Forum GENEDIS - human gentic disease database MuscleNET (Italy) MDI Initiative European Neuromuscular Centre DMD Das Testlaboratorium Breitnau - Muskeldystrophie, DMD-Forschung, CK-Suchtest EDDNAL (DNA diagnostic labs) GeneTests (formerly HELIX) Genetics and Public Issues (GPI at NCGR) MCNdb - Mendelian Cytogenetics Network Database Mutation Research Genomics Initiative Mutational Spectrum Analysis OMIM (human genetic disease) Protein Mutant database Somatic Mutation Testing - index Leiden Muscular Dystrophy pages CentralMutations.Org MutaProt (Weizmann) Care4Cure
Disease - Cytogenetics - Gene (positional cloning _ candidate gene) Target region identification Genome sequence (BLAST search - nr_htgs_EST databases) Literature (PubMed) GeneMap (NCBI) Physical map __ Clones _ Contigs GeneMap (NCBI) Genomes Guide - Map View (NCBI) UDB - Unified DataBase (Weizmann Institute) WICGR (Whitehead Institute) Clone resources - FISH probes BAC _ PAC probes BAC _ EST project (CIT) BACs _ PACs (CHORI) CCAP - Cancer Chromosome Aberration Project (NCI) YAC probes CEPH WICGR (Whitehead Institute) Sequenced clones (BLAST search - nr_htgs_EST databases) Literature (PubMed) genome wide molecular cytogenetics (Berlin) mapped genomic clones (CMSC - Korenberg) mapped YACs (+subtel) (Italy)
Companies clones _ genome resources BIOS (PAC screening) BACPACs P. de Jong CSMC YAC_BAC_PAC Leiden Genome Technology Center (LGTC) Genome Systems Inc. HGMP-RC (Cambridge).. Research Genetics SeeDNA--Price (FISH) Product searches (SciQuest.com) Agilent Technologies Antibodies BaseClear Biotechnology Companies BioRobotics Boehringer Mannheim Celera Cambridge BioScience 1999 Companies in Biology_Biochemistry Eurogentec Nature buyers'guide Novocastra Laboratories Ltd. Promega Roche Rosetta Inpharmatics, Inc. Sigma Nanogen Febit® gmbh ArrayPro - Leiden Glaucus Proteomics B.V.
Biology searches Pedro's BioMolecular Research Tools - All (No Pictures) Molecular Biology databases (NAR, follow link to database issue) Search BioMedLink ATCC Biolinks BioMedNet - HMS Beagle BioNetbook - links into Biology Bio-Research Sources on the Internet BIOSCI_bionet network BioTechniques database Chemicals_ Fisher Scientific DBcat - a catalog of biological databases From product to supplier HyperCLDB (cell lines database) Kimball's Biology Pages LabSEARCH Materials & Culture Collections mutant human cell cultures Trends Guide to the Internet Biotechnology Industry Organization -- Trade Association for Biotechnology Material Safety Data Sheets (Sigma-Aldrich)
BioInformatics Penn State - Bioinformatics Group www.doubletwist.com BioComputing Hypertext Coursebook Bioinformation Systems e.V. CBIL (Computational Biology and Informatics Lab) CMBI Home Page (KUN) DKFZ - Theoretical Bioinformatics (TBI) Heidelberg EBI -- Industry Support Programme IMDS Seminar Series KNCV - Bioinformatica Object Management Group _ CORBA PCBI_ Center for Bioinformatics University Pennsylvania VSMS - Virtual School of Molecular Sciences Weizmann Institute of Sciences - Bioinformatics and Biological Computing 39.709 BIOINFORMATICS - Lectures BETA WWWtacg Ver 2.38 Form Bioinformatic education in NL EMBO Practical Course on the Analysis and Informatics of DNA-Array Gene Expression Data 29 Oct GENLAB - BioInf - Delft MIPS - BioInf PEDANT Werkgroep Bioinformatica Bio-Informatica (Saxion - Enschede) ISCB - International Society for Computational Biology
Meetings Cold Spring Harbor Laboratory FASEB Office of Scientific Meetings Genome meetings Keystone Symposia Beyond the Identification of Transcribed Sequences ECB9 - EUROPEAN CONGRESS ON BIOTECHNOLOGY IUBMB_FEBS 2000 - Sunday July 16 - Thursday July 20, 2000 SAGE99 Agenda IOP Genomics Keystone Symposia Homepage
Sequence analysis - DNA _ protein _ genes (ESTs) Start sites ABIM Online analysis tools (aBi) Pedro's BioMolecular Research Tools - All (No Pictures) NCBI BCM - Search Launcher CMBI Home Page (KUN) DDBJ (Japan) EBI - European BioInformatics Institute DKFZ - Biocomputing Erasmus University Rotterdam EMBL - European Molecular Biology Laboratory GENIUSnet (Heidelberg) DNA Analysis large sequences Large-scale sequence analysis - Genotator Large-scale sequence analysis - NIX session (HGMP-RC) Sequence Analysis Server (a.o. CAP3) Manual_ analyzing 'pre-finished' genomic sequence data Genome Annotation Consortium GeneMachine - automic annotation Repetitive DNA RepBase Repeat mask (TIGEM) Primer calculation Primer3 (MIT) NetPrimer (Weizmann Institute) PRIDE (Heidelberg) MEDUSA (primer calculation) Promoter scan (yeast) AlignACE Oligo analysis YEBIS Restriction enzymes ATCC REBASE Roberts_Macelis) Sequence Utilities (BCM) Retrieve sequences (Entrez - NCBI) Sequence assembly - CAP Blast tools (NCBI) BLAST output reformat - MSPcrunch FastA (EBI) Ensembl Genome Server Fugu search (Blast) TIGR search EST Extractor (TIGEM) - Blast, EST retrieval, EST consensus (multiple alignment) Gene_exon prediction links (Banbury) Gene Prediction (overview) Sequence Utilities (BCM) ORF Finder (NCBI) MAR Finder Melting profile calculation UTRdb transcription factors (AG BIODV) Muscle_ transcription regulation DNA folding prediciton Reputer Genes _ ESTs UniGene (NCBI) UniBlast server (TIGEM) EST Clustering Projects at TBI IMAGE Consortium Geneindex EST Extractor (Tigem) EST_STS Guided identification of Genes in Human Genomic DNA GeneCards_ genes, proteins and diseases Gene Name search Gene Nomenclature GDB Gene nomenclature (Nat.Genet.) Human Transcript Map (Science) DRES Homepage EST machine (TIGEM) Muscle genes (EstPD database) Stack_ Sequence Tag Alignment Consensus Konowledgebase Human Transcriptome Map (Amsterdam) Protein Protein domains _ sites Pfam (protein domains) ProDom (protein domain database) PROSITE (ExPASy) BLOCK Maker (protein homology blocks) MEME (detects motifs) PRINTS ProClass SMART - Simple Modular Architecture Research Tool Blocks DART (Domain Architecture Retrieval Tool) - NCBI Structure CATH - classification LPFC - Library of Protein Family Cores SCOP - Structural Classification Of Proteins Scan Leu-zippers Protein Links (R. Munro) Blast tools (NCBI) FastA (EBI) Beauty (BCM) ExPASy Predict signalpeptide Protein families Rasmol 3DB browser SYSTERS Cluster Set BRENDA The comprehensive Enzyme Information System Biological Data Representation and Query at SDSC Hits Home Protein structure prediction - BioInfo.PL Meta Server Protein sturcture prediction - Threading, metaserver Protein Subcellular location prediction (SubLoc) Metabolic function _ Biochemical pathways Biological Biochemical Image Database (pathways) Kyoto Encyclopedia (KEGG database) ExPASy - Biochemical Pathways WIT WIT (metabolic reconstruction) Sequence Alignment Align two sequences - TwoBlast (NCBI) PROCRUSTES (align protein with DNA_ evolutionary distant) ClustalW - align multiple sequences (EBI) CINEMA Match-Box Multalin Pretty print alignments (BOXSHADE) CHROMA - multiple alignment (colour) Sequence submission Feature Table Definitions Sequin (NCBI) Submit (EBI) Software + descriptions Directory of _molbio AceDB _ Jade Advanced Chemistry Development, Inc. Core Page Husar (WWW demo) Software descriptions Staden Manual VISTA - align two genomic sequences (2 species) Ensembl Genome Server EST Clustering Projects at TBI Geneindex CAP _ assemblage de sequences The NEW EST Extractor at TigemNet - Swiss EMBnet Gene Connection SMART - Simple Modular Architecture Research Tool The Expressed Gene Anatomy Database (EGAD) Gene_exon prediction links (Banbury) WebBallast Introduction to NIX BIC - Bioaccelerator (EMBL) Coffee Break Archives (NCBI) Sequence Gazing (Nat.Genet.) Swiss-Flash (news) Protein alignment Local Alignment Tool BLAST WWW System PhyloBLAST Gene2EST ParAlign SeWeR - Sequence Analysis using Web Resources BioiMolQuest - www.bioinformatics.danforthcenter.org yury public home.html E A S Y Query submission 405 Method Not Allowed
Starting points Erasmus Remote Network Access (ERNA) HUM-MOLGEN (news group) MGC - Dept. Human Genetics (Leiden) MGC - EUR Nederland
Teaching DEAMBULUM _ Online courses of biology (0) Virtuele Studie Omgeving Boerhaave Commissie LUMC - Virtuele studie omgeving (VSO) Start Geneeskunde DNA Files HGP+sequencing in the classroom Molecular Biology Quiz Natural History of Genes PAON Teaching_ Access Excellence T.I.G. - Teaching resources TMB TMB - WWW cursus (algemeen) VSMS - Virtual School of Molecular Sciences NIHES HGP - education kit European Genetic Foundation (Sestri courses) Hogeschool Leiden Twisted Ladder Media Human Genome - Educationkit (NHGRI) Inheritance patterns of mongenic disorders Onderwijs - LUMC VSO Syllabus - Biology 572 Array_presentations Genomics Course - DNA Microarrays (Chips) Biology 4 1999 Winter Term Movies micro-arrays Human Genetics Education Resource (contributed by Lauren Jackson)
Search Nederland ILSE Vindex Vinden.NL NL-URL V2.0 Zoek Meta searches WebCrawler Mamma search.com Profusion Metacrawler All-in-One diverse Gericht_Zoeken LookSmart Open Text General information - Search Engine Watch AltaVista AltaVista (NL) Excite Google Go _ Infoseek HotBot Lycos Lycos (NL) Northern Light Yahoo! Biology servers BioTechniques Database Dictionary of Cell Biology Searching help Searching tutorials Search WWW - Scirus (Scientific Information Only)
Techniques DNA chips _ grids filters Atlas Arrays (Clontech) Gene Discovery Array (Genome Systems) Human GeneFilters (Research Genetics) ABRF Microarray Research Group MicroArray Explorer- MAExplorer Expr. Regulation - UvA ABRF2000 meeting arrays Affymetrix Bio Dot Oligonucleotide chips Brown lab (Stanford) Display Systems Biotech Genetic Microsystems Inc. Genexpress - brain transcriptome Incyte Pharmaceuticals, Inc. LBL - BioImaging & Microscopy Micro array links (NHGRI) Micro array links (NCBI) microarrays.org MicroArray Explorer (MGAP) Molecular Diagnostics Lab (Tapei) General Scanning (ScanArray) SuperArray Inc._science and biotechnology leaders for the new millennium papers on microarray data analysis Array products (Rockefeller) Micro-array sub-selections ViroGen (embryo RNAs) FISH PCR PCR - incl. software tools (Alkami Biosystems) PCR troubleshooting_ Promega's Amplification Assistant PCR PCR - multiplex SAGE SAGE (Serial Analysis of Gene Expression) SAGEnet (John Hopkins) NCBI _ CGAP Sequencing Informatics (Washington University) Kaleidaseq (CSHL) Protocols (Washington University) Centre for Protein Engineering_ Home Page MALDI-TOF (GeneTrace) PNA technology Phage display (FAQ) Technical Tips Online Mass Spectrometry Microarray Center Toronto Prof. Andreas Pluckthun Homepage -- Protein Engineering and Directed Evolution LYNX Home Illumina Equipment (used)
To look at Services at MBCR and throughout the world CMGS-MRCPath Self-Help Course GCB00 - Paper submissions Redirecting to GSLC Infobiogen's R&D projects EDGP Home Page Multi-dimensional Human Embryo, Home Page page inserm RECOMB 2001 INSERM Quiz LabOnWeb GenePix Pro 3.0 Software Web Events
Patents World-wide patent offices Biotechnology Patents Bureau IE (Min. EZ) DNA Patent database IBM Intellectual Property Network European Patent Office IPR-Helpdesk (CORDIS - EC) Patents and Patent Searching Patent Search Service US Patents Patent Offices world-wide
IPI - International Protein Index
Pise - ....
ERGITO - Lewin
BioLayout - interaction viewer
The Digital Optical Chemistry System
LUMC - Intranet
GenMAPP
Genome Biology protein family review Dystrophins and dystrobrevins
PubGene .org

“RESEARCH and the INTERNET”©

Course Bookmarks

JdD's Bookmarks

DNA/genome (used most)

Grants _ Organizations

EU

Rijk

Literature _ Journals

Publication searches

Genome data

GDB

Large genome centers

Genome maps

Expression

Genome sequencing

Non-human

E.coli

mouse

yeast

SNP databases

Transgenics

Disease (genetic) _ Mutations

Disease

Mutations (databases _ analysis tools)

Locus Specific Databases

Software

Neuromuscular Disorders

Muscular dystrophy research

Submission of mutations (journals)

Disease - Cytogenetics - Gene (positional cloning _ candidate gene)

Target region identification

Physical map __ Clones _ Contigs

Clone resources - FISH probes

BAC _ PAC probes

YAC probes

Companies

clones _ genome resources

Biology searches

BioInformatics

Meetings

Sequence analysis - DNA _ protein _ genes (ESTs)

Start sites

DNA

Analysis large sequences

Repetitive DNA

Primer calculation

Promoter scan (yeast)

Restriction enzymes

Genes _ ESTs

Protein

Protein domains _ sites

Structure

Metabolic function _ Biochemical pathways

Sequence Alignment

Sequence submission

Software + descriptions

Starting points

Teaching

Search

Nederland

Meta searches

diverse

Techniques

DNA chips _ grids

filters

FISH

PCR

SAGE

Sequencing

To look at

Patents

Bookmarks Advances Course GE, October 1997

Structural Protein Analysis

Transcription Factors

Miscellaneous

Databases

General

Genomics

Mol. Biology/WWW

Bio-Companies

“RESEARCH and the INTERNET”^©