Linkliste

A collection of german bioinformatics institutions

Hannover - Universität Hannover, Fachbereich Gartenbau, Lehrgebiet Bioinformatik
http://www.bioinf.uni-hannover.de/

Universität Bielefeld, Center for Biotechnology (CeBiTec), Institute of Bioinformatics (IfB)
http://www.cebitec.uni-bielefeld.de/

Uni Bielefeld Software: http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_Alignments.html
Uni Bielefeld Practical Computer Science:http://www.techfak.uni-bielefeld.de/ags/pi/

UHH > Zentrum für Bioinformatik > Forschung > Abteilung für Genominformatik
http://www.zbh.uni-hamburg.de/research.php

Institut für Pharmazie und Molekulare Biotechnologie (IPMB)
Abteilung Bioinformatik & Funktionelle Genomik
http://www.dkfz.de/tbi/uni/

Center of Informatics,Statistics and Epidemiology UKG, University of Göttingen
Department of Bioinformatics
http://www.bioinf.med.uni-goettingen.de/

Bielefeld University Bioinformatics Service
Cologne University Bioinformatics Center http://www.uni-koeln.de/math-nat-fak/biochemie/ds/dsak_d.htm
DKFZ Heidelberg, Department of Molecular Biophysics
Freie Universität Berlin, Algorithmic Bioinformatics Group

GBF Braunschweig, Department of Genome Analysis
Bioinformatik-Kompetenzzentrum Braunschweig

Georg-August University Göttingen, Department of Bioinformatics^

GSF Munich, MIPS, Institute for Bioinformatics
NGFN SMP Bioinformatics data management group

Ludwig-Maximilians-Universität Munich, Teaching and Research Unit Bioinformatics
MDC/EMBL Heidelberg, Comparative Sequence Analysis
MDC Berlin, Bioinformatics Department
University of Würzburg, Institute of Bioinformatics

Zentrum für BioinformatikTübingen
Nachwuchsgruppe "Proteomics Algorithmen und Simulation"
Computer Architecture

Bioinformatics web

Microarrys allgemein - Übersichten

Y.F.LEUNG: Havard University: Homepage Super Zusammenstellung
North Shore LIJ Research Institute: Microarray & Data Analysis super aktuelle Literatur / Bibliographie

Stanford Microarray Database Software & Links
Berkeley: Terry Speed's Microarray Data Analysis Group Page
Microarrays.org: A public source for microarray protocols and software (AMAD, ArrayMaker etc.)
The Sanger Institute: The Microarray Facility - Links Page kurze Übersicht
TIGR The Institute for Genomic Research - Microarray-Software
National Human Genome Research Institute Bethesda, Maryland: http://research.nhgri.nih.gov/microarray: MicroArrayProject
Gene Expression Data Analysis Department of Biostatistics & Medical Informatics University of Wisconsin - Madison

Microarray Database Systems von Jing-Ying Chen

Institute und andere Einrichtungen

Center for Molecular Biology of RNA University of California, Santa Cruz
DKFZ Heidelberg, DKFZ Theoretische Bioinformatik
EMBL European Molecular Biology Laboratory, Heidelberg
EBI European Bioinformatics Institute Teil des EMBL, Hinxton Cambridge
I.M.A.G.E. Collection of public genes (cDNA) bei: Lawrence Livermore National Laboratory University of California
MPI Molekulare Genetik Berlin
NCBI national resource for molecular biology information, Bethesda
NCGR: National Center for Genome Resources Santa Fe, New Mexico (GeneEx)
NGFN Nationales Genomforschungsnetz
NIH: National Institute of Health NIH headquarters are located in Bethesda, Maryland
North Shore LIJ Research Institute: Center for Genomics and Human Genetics
RIKEN für cDNA Sets
Stanford Genomic Resources
San Diego Supercomputer Center
The Wellcome Trust Sanger Institute
TIGR - The Institute for Genomic Research

Öffentliche Arraydatenbanken

ArrayExpress von EMBL EBI ArrayExpress is a public database of gene expression experiments.
GEO: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Literaturlink

http://www.ncbi.nlm.nih.gov/SAGE/

Microarray Services

DNA Microarray Facility
DNA Microarray Facility. University of Göttingen Faculty of Medicine
Humboldtallee 23 37073 Göttingen. Services; Guidelines; Microarrays; ...

DKFZ Intelligent Bioinformatics Systems: iChip

DKFZ Microarray Data Warehouse and Analysis Tools: MCHiPS can be used as a LIMS for DNA chip experiments
M-CHIPS database: Statistical access to experimental conditions

DKFZ Theoretische Bioinformatik

MIPS Munich Information Center for Protein Sequences am GSF-Forschungszentrum für Umwelt und Gesundheit:
MIPS Expression Data Repository
http://mips.gsf.de/cgi-bin/proj/mouseExpress/start.cgi

Auswertung / deutsche Seiten

Oliver Hartmann
Institute of Medical Biometry and Epidemiology, Marburg

Projektgruppe Bioinformatik Göttingen

Anja von Heydebreck's Home Page
Max Planck Institute for Molecular Genetics: Computational Molecular Biology Berlin

Homepage Wolfgang Huber dkfz
Variance stabilization and robust normalization for microarray ...
www.dkfz-heidelberg.de/mga/whuber/ talks/goettingen-100103.ppt

DKFZ Benedikt Brors

Institut für Medizinische Biometrie und Statistik Uni Lübeck

Stanford Software Site Super Übersichtsseite
Y.F.LEUNG: Havard University: Microarray Software Comparison Super Zusammenstellung
TIGR The Institute for Genomic Research - Microarray-Software
SMD The Stanford Microarray Database - microarray data storage, retrieval, analysis, visualization, and database software

Arrayplot

BASE - BioArray Software Environment
BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. It is released under the GNU General Public License. Further details about BASE can be found by following the links to the left or by reading the BASE manuscript (see below).

Cyber-T für Affymetrix Chips von Institute for Genomics and Bioinformatics, Univ. California

GenEx National Center for Genome Resources GeneEx Open Source Projekt
GenMAPP Gene Micorarray Pathway Profiler

MADAM, implemented in Java, facilitates the entry of data into a relational database. MADAM guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyzes. Canned reports provide information on RNA samples, studies, slide maps, and other pertinent data, and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials. Although not yet supported, MADAM is being adapted to read and write MAGE-ML, the XML data exchange format being developed by an international consortium of leading public databases and microarray research centers. A MAGE-ML version of MADAM should be available by the end of this year and will facilitate submission of microarray data to public repositories such as Array Express and GEO.

PAM: Prediction Analysis for Microarrays.
Performs sample classification from gene expression data via "nearest shrunken centroid method" of Tibshirani, Hastie, Narashiman and Chu (2002).
ScanAlyze Microarray Image Analysis: Eisensoft: ScanAlyze

Biostatistics Harvard School of Public Health: MA Software DCHIP http://www.biostat.harvard.edu/complab/dchip/

Holloway OptionsAvailable II Web Table L erweitert

Package	Author	URL	License	DE	DB	Norm	DA
BASE	Lund University	http://base.thep.lu.se/	free		j	j	j
Cluster	Eisen Lab	http://rana.lbl.gov/EisenSoftware.htm	free				j
GeneCluster	Whitehead Institute	www-genome.wi.mit.edu/cancer/software/software.html	free				j
GenEx		http://www.ncgr.org/genex/
GenePix	Axon	www.axon.com/GN_GenePixSoftware.html	not free
GeneSight	Biodiscovery	www.biodiscovery.com/genesight.asp	not free				j
Genespring	Silicon Genetics	www.silicongenetics.com	not free				j
GeNet	Silicon Genetics	www.silicongenetics.com	not free
GeneTraffic	Iobion Informatics	www.iobion.com	not free				j
Matlab	Mathworks	www.mathworks.com	not free				j
Minitab	Minitab Inc.	www.minitab.com	not free				j
MSBNx	Microsoft Research	www.research.microsoft.com/adapt/MSBNx/	free / not free				j
Quantarray	Packard Bioscience	http://lifesciences.perkinelmer.com/producttemplates/ProductList.asp?levelId=19165	not free
R	The R Rroject for Statistical Computing	http://www.r-project.org/ http://www.bioconductor.org/ Mailinglist R Help	free				j
SNOMAD	PevsnerLab	http://pevsnerlab.kennedykrieger.org/snomad.htm	free
S-plus	Insightful	www.insightful.com	not free				j
Spot	CSIRO Mathematical & Information Sciences	http://experimental.act.cmis.csiro.au/Spot/index.php	not free
TIGR Microarray	The Institute for Genomic Research TIGR	www.tigr.org/software/	free
Treeview	EisenLab	http://rana.lbl.gov/EisenSoftware.htm	free
WEKA	The University of Waikato	www.cs.waikato.ac.nz/~ml/	free

SMD Microarray Links : Software & Tools:

http://genome-www5.stanford.edu/MicroArray/SMD/restech.html

Stanford Software
Program	Description	Author	Platform
Cluster	Perform hierarchical clustering, self-organizing maps	Michael Eisen	Windows
SAM	Significance Analysis of Microarrays : Supervised learning software for genomic expression data mining	Rob Tibshirani	Excel Add-in
ScanAlyze	Processes fluorescent images of microarrays	Michael Eisen	Windows
SLCView	Creates images in many different formats from cdt and gtr files, from the unix command-line	Swaine Lin Chen	UNIX/Linux
SMD Package	Full source code for the Stanford Microarray Database	SMD Staff	UNIX + Oracle
TreeView	Graphically browse results of clustering and other analyzes from Cluster	Michael Eisen	Windows
XCluster	Perform hierarchical clustering, self-organizing maps	Gavin Sherlock	UNIX Linux MacOS Windows
KNNimpute	Estimation of missing microarray values	Olga Troyanskaya	UNIX Linux
PAM	Prediction Analysis for Microarrays	Hastie/Naras/Tibshirani	Excel /R under Windows/Unix

Software from other sources
Program	Description	Provider	Platform
Array Designer	Tool assisting in primer design for microarray construction	Premier Biosoft International	JAVA
ArrayViewer	Identification of statistically significant hybridization signals	National Human Genome Research Institute	JAVA
ArrayVision	Automated analysis of macro & microarrays	Imaging Research Inc.	Windows
BASE	Microarray database and analysis platform	Lund University	Web
Cluster 3.0	An enhanced version of Mike Eisen's Cluster	University of Tokyo, Japan	UNIX Linux MacOS Windows
DNA arrays analysis tools	Hierarchical clustering, Self Organizing Maps and more	Spanish National Cancer Center, Bioinformatics Unit	Web
Expression Profiler	Analysis & clustering of gene expression data	European Bioinformatics Institute (EBI)	Web
ExpressionSieve	Microarray data analysis package, strong in linking biological significance to expression patterns, data and analysis process management, signature gene discovery and class discovery & prediction.	BioSieve	Java
GeneCluster	Self-organizing maps	Whitehead Institute/MIT Center for Genome Research	JAVA Windows NT
GenMAPP	Tools for visualizing data from gene expression experiments in the context of biological pathways.	Conklin lab; Gladstone Institute & the UCSF	Windows
GeneX	Gene Expression Database : integrated toolset for data analysis and comparison	National Center for Genome Resources	Windows Linux SunOS/Solaris
GenMaths	Analysis of high density microarrays and gene chipshttp://www.icp.ucl.ac.be/bioinfo_links.htm	Applied Maths	Windows
Genowiz™	A Gene Expression Data Analysis and Management Tool.	Ocimum Biosolutions	Windows Macintosh Unix Linux Solaris
MicroArray Suite	Extracting and visualizing DNA microarray data	Scanalytics Inc.	MacOS
Partek Pattern Recognition	Extracting and visualizing patterns in large multivariate data	Partek Incorporated	Linux, Unix, Windows
TIGR MultiExperiment Viewer	Analysis and Visualization of Microarray Data	TIGR	JAVA
TreeArrange and Treeps	Software for displaying and manipulating hierarchical clustered data	University of Waterloo, Canada	Linux Unix Windows

WEKA	The University of Waikato	www.cs.waikato.ac.nz/~ml/	free

Protokolle

Holloway OptionsAvailable II Webtable H: Sources of Protocols for Microarray Analysis

Web Site Name	Details	URL for Protocols
Pat Brown’s Laboratory, Stanford University	Protocols for preparing array material, labeling nucleic acids and hybridization	http://cmgm.stanford.edu/pbrown/protocols/index.html
Microarrays.org	Compilation of public access protocols, mainly derived from Cold Spring Harbor Laboratory manuals	http://www.microarrays.org/protocols.html
The Institute for Genomic Research (TIGR)	Protocols for preparing array material and labeling	http://pga.tigr.org/protocols.shtml
National Human Genome Research Institute (NHGRI)	Protocols for RNA extraction, labeling and hybridization	http://www.nhgri.nih.gov/DIR/Microarray/protocols.html
Ontario Cancer Institute (OCI)	Comprehensive list of protocols for RNA extraction, labeling and hybridization	http://www.oci.utoronto.ca/services/microarray/protocols/
Penn State DNA Microarray Facility	Protocols for RNA extraction, labeling and hybridization.	http://sgio2.biotec.psu.edu/protocols.html
Stress Genomics	Protocols for preparation of array material and extraction of RNA from plants	http://www.stress-genomics.org/stress.fls/expression/array_tech/tech_aspects_index.htm#_Protocols
Zea mays DataBase Microarray Project	Protocols for preparation of array material, extraction of RNA from plants and microarray hybridization	http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html
Institute of Ecology – Plant Biology and Physiology, University of Lausanne, Switzerland	Protocols for preparation of DNA, slide printing, RNA isolation from Arabidopsis leaves, RNA labeling and hybridization	http://www.unil.ch/ibpv/microarrays/WWWPR/Docs/protocols.htm

Genetische Datenbanken

Open Source Projekt National Center for Genome Resources:
NCGR: Databases and other software tools for Gene Expression
UCSC Genome Bioinformatics Site
GeneCards Homepage Weizmann Institute
GeneCards Search Weizmann Institute
If you are a Web developer and you want to make links to particular GeneCards, just use "http://bioinformatics.weizmann.ac.il/cards-bin/carddisp?XXX" (with XXX being the official gene symbol approved by the UCL/HGNC human gene nomenclature database.
HUGO Gene Nomenclature Committee
GenePix National Cancer Institute Eingang zu Arrayauswertung
Resource Center/Primary Database: Project DESPRAD
The European Molecular Biology Linked Original Resources TEMBLOR

http://bioinfo.hku.hk/ucsc/goldenPath/gbdDescriptions.html

Compugen's GenBank GO annotation: GO annotation list (GeneOntology at Stanford)

gsf: Munich Information Center for Protein Sequence http://mips.gsf.de/services/drs

http://www3.oup.co.uk/nar/database/paper.html

Weblinks aus: Bioinformatik - Ein Leitfaden für Naturwissenschaftler

Andrea Hansen, Birkhäuser Verlag , 2001 - ca. 120 S.
Aktualisierungen unter: http://www.bioinformatik.de/mybooks ISBN 3-7643-6512-9 Erscheinungsdatum: Juni 2001 Bestellung: direkt beim Birkhäuser-Verlag oder bei Amazon