In the past decade, researchers have witnessed an
explosive growth in the amount of information available
to them at internet-based sites. In this day and
age, researchers requiring supplementary information
to a particular aspect of a research technique can do so
by using a search engine or browsing through the
internet, but this is more often than not a timeconsuming
and frustrating endeavour where one ends
up having to deal with thousands of hits that are not
relevant to the initial query.
This section lists outstanding resources for cell
and molecular biology research that complement and
extend the usefulness of the research protocols
described in the previous sections. We have found the
sites listed here to be comprehensible, useful, and generally
well run and consequently we recommend them
as good starting points for any researcher rummaging
around for information. Nonetheless, this compilation
is intended solely as a valuable aid to the research techniques
described throughout this book rather than a
stand-alone guide of laboratory procedures or an
exhaustive listing of Web resources.
II. INTERNET RESOURCES FOR
A. Cells and Tissue Culture
1. The World Federation for Culture Collections
The WFCC is a federation concerned with the collection,
authentication, maintenance, and distribution
of cultures of microorganisms and cultured cells. The
WFCC, through the World Data Center for Microorganisms
(WDCM), developed an international database
on culture resources worldwide. This data
resource is now maintained at the National Institute
of Genetics (NIG, Japan) and has records of nearly
469 culture collections from 62 countries (http://
wdcm.nig.ac.jp/hpcc.html). The records contain data
on the organisation, management, services, and scientific
interests of the collections. Each of these records
is linked to a second record containing the list of
2. European Collection of Cell Cultures (ECACC)
In addition to being a bank of cell lines and
hybridomas, ECACC also provides an EBV immortalisation
service to establish lymphoblastoid cell lines
from patients and their families with genetic and chromosomal
abnormalities. This site boasts a full 25,000
cell lines and approximately 420 hybridomas.
3. RIKEN Cell Bank
The RIKEN cell bank has been organized as a
unique, nonprofit public collection for deposit, isolation,
preservation, and distribution of cultured animal
cell lines produced by the life science research community.
It houses a large number of cell lines as well
as hybridomas established by its staff.
4. American Type Culture Collection (ATCC)
The ATCC Cell Biology Collection (http://www.
atcc.org/SearchCatalogs/CellBiology.cfm) includes a
very comprehensive and diverse cell bank, consisting
of 4000 cell lines from more than 150 different species. It holds 950 cancer cell lines (including 700 human
cancer cell lines) and over 1200 hybridomas for the
production of monoclonal antibodies, as well as a
variety of special collections.
5. The Mammalian Genetics Unit at Harwell (MGU)
Home page of an integrated campus for mouse
genetics research with facilities for molecular genetics,
genomics, mutagenesis, transgenesis, and bioinformatics.
The MGU has a large collection of mouse
stocks containing over 200 mutant, chromosome
abnormality, and inbred lines. The stocks are maintained
for experimental and breeding purposes and
are available to investigators on request.
6. Stem Cell Information at NIH
A Web site provided by the National Institutes of
Health (NIH) hosting information and links on stem
7. The Stem Cell Database (SCD)
A joint project of the laboratories of Ihor R.
Lemischka (Princeton University) and G. Christian
Overton (University of Pennsylvania), the SCD contains
data on the molecular phenotype of hematopoietic
1. All the Virology on the WWW
A site that collects many virology-related Web sites
of interest for virologists and others interested in learning
more about viruses.
2. The Universal Virus Database (ICTVdB)
The directory of ICTVdB is an index of viruses, a
list of approved virus names linked to virus descriptions
coded from information in "Virus Taxonomy: The
Seventh Report of the International Committee on
Taxonomy of Viruses" by van Regenmortel et al. (eds.),
Academic Press (2000), and includes updates subsequently
approved by ICTV. It also incorporates the
plant virus database VIDEdB and is illustrated with
EM pictures, diagrams, and images of symptoms contributed
by virologists around the world.
1. The Antibody Resource Page
A site that provides a broad collection of links to
companies that sell antibodies or antibody-related
products on the internet. Furthermore, it also presents
sections containing links to online educational
resources about antibodies and databases and software
with immunological relevance.
AbCam features an extensive compilation of antibody
information and advice for locating specific antibodies
with a large selection of antibodies available
online and a search engine to other antibody companies.
In addition, AbCam provides a conference
calendar, a database of conferences that have been
submitted by research scientists.
A site that provides information on antibody structure
and sequence as well as other useful links.
4. Information Resources for Adjuvants and
A very useful Web page for any researcher interested
in antibody production. A rather comprehensive
set of references is an added value.
5. Developmental Studies Hybridoma Bank (DSHB),
at the University of Iowa
The DSHB supplies investigators with low-cost
monoclonal antibodies useful for studies in developmental
and cell biology. They may be ordered as tissue
culture supernatants, ascites, or partially purified
immunoglobulins. Certain selected hybridomas are
also available as frozen or growing cells.
6. IMGT, the International ImMunoGeneTics
An integrated information system specializing in
immunoglobulins, T-cell receptors, major histocompatibility
complex, and related proteins of the immune
system of human and other vertebrate species. This site contains standardized and annotated data on proteins
of the immune system, which include databases
of nucleotide and protein sequences, gene maps,
genetic polymorphisms, specificities, 2D and 3D structures,
and a collection of interactive tools.
D. Flow Cytometry
1. Flow Cytometry Core Laboratory at
the University of Florida
One of the core laboratories that compose the Interdisciplinary
Center for Biotechnology Research at the
University of Florida in Gainesville, Florida. This Web
page provides a wealth of information and links
related to flow cytometry. Included is the database
for antibody cross-reactivity (htt-p://www.keithbahjat
.com/abcxr/), a repository for flow cytometry software,
and protocols for FACS-based analysis.
2. Flow Cytometry on the Web
A collection of links for those interested in flow
cytometry. A good starting point if one is looking for
software, protocols, instrumentation, protocols, or any
flow cytometry-related subject.
An immunohistochemistry database query system
to help determine the best panel of immune stains that
will aid in the differential diagnosis of tumors. It lists
antibodies that can differentiate between tumors
entered by the user (e.g., lung adenocarcinoma vs
breast carcinoma), ranks the antibodies in terms of
their ability to differentiate between tumors, and provides
instant references to journal articles describing
the reactivity of these antibodies.
2. IHC World
A Web site dedicated to everything related to
immunohistochemistry. Provides comprehensive and
updated information regarding tissue processing,
antigen retrieval, antibody selections, antibody protocol
database, image analysis, protocol links, books, and
3. DAKOCytomation's Immunochemical Staining
Methods Online Handbook (3rd Ed.)
This site features a pdf-based online version of
DAKO's IHC handbook. A very useful book, with
detailed information on basic immunohistochemistry
techniques including protocols and reviews of alternative
4. PathBase: The European Mutant Mouse Pathology Database
Pathbase is a database of histopathology photomicrographs
and macroscopic images derived from
mutant or genetically manipulated mice. This site
containes a searchable database of histopathological
images mainly from transgenic and knockout mice
with effects on cell proliferation and cancer, and the
response of adult and fetal animals to environmental
insults such as radiation at high and low doses relevant
to accidental, environmental, and medical irradiation
A site comprising a histology search engine for
searches over 20,000 Web pages from histology-related
sites on the internet, hyperlinks to other histology
sites, and to relevant newsgroups and archives.
F. Transgenes and Gene Knockout and -down
1. C. elegans Gene Knockout Consortium
This consortium aims at facilitating genetic research
of this important model system through the production
of deletion alleles at specified gene targets. Targets
are chosen based on investigator requests. Strains produced
by the consortium are freely available with no
restrictions to any investigator.
2. BioMedNet's Mouse Knockout and Mutation
A comprehensive database of phenotypic and genotypic
information on mouse knockouts and classical
mutations with more than 8000 database entries covering
over 3000 unique genes.
3. The Nagy Laboratory Cre Transgenic Database
This Web site contains a database of published as
well as unpublished and in the making Cre transgenic
lines. Also some mouse genetics protocols and links.
All in all, a good site for those researchers with an
interest in ES cell-mediated rodent genome alterations.
4. Database of Gene Knockout
A mouse gene knockout database with strains classified
alphabetically or according to the viability of the
knockout: viable mice, or resulting in prenatal, postnatal,
or perinatal mortality.
5. Gene Targeting Protocols
A set of 23 gene targeting protocols from Practical
Approach Online (in pdf format).
6. Antisense Gene Targeting
GeneTools produces antisense morpholino oligosnucleotides
to shut down selected RNA sequences.
Provides a very good alternative to phosphorothioates.
Microinjection or electroporation of Morpholino
oligosnucleotides into the embryos of frogs, zebrafish,
chicks, and sea urchins has been shown to successfully
and specifically shuts down the expression of desired
mRNAs. Another alternative is locked nucleic acid
oligosnucleotides that can be obtained through
7. RNA Interference Resources
A resource containing a wealth of information on
siRNA-mediated gene silencing, with many useful
reviews, rererences, and link to other sites of interest.
An additional site of interest is McManus home
html), a very good Web site for researchers interested
in the process of RNA interference.
G. Organelle Systems
1. Cell Biology Topics: Organelles
A collection of links to Web pages providing basic
information on organelle systems. Most of the topics
focus on structure/function correlations.
2. The Virtual Cell Web Page
A nice presentation on cell organization and function/
structure relations. A similar resource can be
found at http://www.life.uiuc.edu/plantbio/cell.
1. DNA Microarray Web Site
A Web page boasting a collection of links to academic
and industrial sites of interest for researchers
with an interest in microarrays (DNA as well as protein
2. Grid It
A useful resource for researchers interested in
microarray technology. Includes an introduction to
microarray technology and links to sources of equipment,
analysis software, and other microarray sites.
3. LGM Microarray Links
A collection of links to microarray resources.
4. Genomics: A Global Resource
A gateway to a plethora of genomic resources.
1. Meta-Database Catalog of Two-Dimensional Gel
Images Found in Web Databases (2DWG)
A catalog of some of the 2D gel images that can be
found in 2D gel databases on the Web.
2. Two-Dimensional Gel Electrophoresis Tutorial
A tutorial written by Dr James R. Jefferies. Sections
covering this topic include 2D gel electrophoresis,
immobilized pH gradients, 2D procedure, sample
preparation, sample solubilisation, chaotrophe, reductants,
detergents-surfactants, ampholytes, interfering
substances, protein estimation, gel electrophoresis, IEF run, strip equilibration, SDS-PAGE run, staining,
general considerations, and references.
3. The Danish Centre for Human Genome Research's
2D PAGE Databases
A site containing proteomic databases developed
for the study of global cell regulation in health and
disease, focusing on skin biology and bladder cancer.
Procedures are illustrated with still images and videos.
The site also features a gallery of 2D gels of cells,
tissues, and fluids, as well as 2D gel immunoblots.
4. EXPASy World 2DPAGE Index
A site containing references to known 2D PAGE
database servers, as well as to 2D PAGE-related
servers and services.
1. Spectroscopy Now
A gateway to various spectroscopy resources,
including mass spectrometry, RAMAN, and NMR.
2. Protein Prospector
A collection of proteomics tools for mining sequence
databases in conjunction with mass spectrometry
K. Cell Signaling
1. The Alliance for Cell Signaling
The AfCS-Nature Signaling Gateway is a comprehensive
and up-to-the-minute resource for anyone
interested in cell signaling. The AfCS is an initiative
with the aim of performing comprehensive experimental
analyses of selected signaling systems, providing
these data freely to the research community.
Several tools of interest to investigators within the signalling
community are also available here.
A database of phosphorylation sites, including two
implementations of algorithms for prediction of potential
3. List of Apoptosis Regulators
A Web site providing general and specific information
of apoptosis regulators and signalling pathways,
as well as quick access to relevant papers and
4. Science's Signal Transduction Knowledge
A global resource useful to scientists who specialize
in signal transduction, as well as the many scientists
who need to follow and apply the current findings of
this field even though their primary interest may not
be in signal transduction mechanisms themselves.
A Web-based resource for inositols, phosphoinositides,
phosphatidylinositols, and other essential cellsignaling
6. BioCarta's Pathways
A Web site containing interactive graphic models of
molecular and cellular pathways.
L. Databases of Molecular Interactions and
1. Biomolecular Interaction Network
This site consists of a search engine, PreBIND, that
allows the user to mine the biomedical literature for
protein-protein interactions and a database, BIND,
that stores descriptions of interactions, molecular complexes,
and pathway records.
2. General Repository of Interaction
A database of genetic and physical interactions containing
interaction data from many different sources.
This site is also home to the Osprey Network Visualization
servlet/Index), a powerful application for graphically
representing physical and genetic biological interactions
that is coupled to the GRID database.
3. Database of Interacting Proteins (DIP)
A database of experimentally determined interactions
between proteins. It combines information from
a variety of sources to create a single, consistent set of
4. Molecular Interactions Database (MINT)
A database of functional interactions between biological
molecules (proteins, RNA, DNA). Beyond cataloguing
the formation of binary complexes, MINT
also stores other type of functional interactions,
namely enzymatic modifications of one of the partners.
5. Curagen's PathCalling Yeast Interaction Database
PathCalling is a proteomic technology designed to
identify protein-protein interactions on a genomewide
6. Biomolecular Relations in Information
Transmission and Expression (BRITE)
BRITE is a database of binary relations for computation
and comparison of graphs involving genes and
proteins. It contains diverse sets of binary relations,
including the generalized protein interactions that
underlie the KEGG pathway diagrams, systematic
experimental data on protein-protein interactions by
yeast two-hybrid systems, sequence similarity relations
by SSEARCH, expression similarity relations
by microarray gene expression profiles, and crossreference
links between database entries.
7. KEGG Pathway Database
A part of the Kyoto Encyclopedia of Genes and
Genomes, this graphical interface for pathway diagrams
is very user friendly and a boon of information
for any researcher looking for relational information
for a given protein. Two diagrammatical databases
are available, a metabolic pathway database (http://
www.genome.ad.jp/kegg/metabolism.html) and a
regulatory pathway database (http://www.genome.
ad.jp/kegg/regulation.html); each one of these
divided in subsections. In addition to the possibility to
perform searches on particular objects or sequences in
the various pathways, one can also generate possible
8. Yeast Interacting Proteins Database
A companion site to a publication reporting on the
comprehensive two-hybrid analysis of the budding
yeast proteome. One can download the complete
datasets or analyse them as well as previously
reported protein-protein interactions using a graphical
system for viewing gene regulatory networks.
M. Gateways to Scientific Resources
1. The DEAMBULUM-BIONETosphere Thematic
A gateway to useful online resources for molecular
biology, biocomputing, medicine, and biology. It
includes hyperlinks to databases (sequence, bibliographic,
organisms, etc.), sequence analysis tools, software,
and many others.
2. The WI4rW Virtual Library of Cell Biology
A very large repository of cell biology information.
It includes numerous sections with hyperlinks to
various cell biology laboratories, databases, journals,
methods, organizations, and meetings, among others.
3. Pedro's Biomolecular Research Tools
An extensive and quite comprehensive collection
of links to resources useful to molecular and cell
4. The Canadian Bioinformatics Resource
A Web site providing convenient, effective access to
widely used bioinformatic tools and databases.
5. Atelier BioInformatique, aBi Online Analysis
An extensive collection of hyperlinks to various
bioinformatics tools available online. A similar but
complementary Web site is the home page of Dr.
Andrew Kropinski (http://molbiol-tools.ca/).
6. bioWl4rW a Resource for Life Science Researchers
A forum for life science researchers containing
information and links to protocols, news groups, and
many other resources.
7. Molecular Biology Gateway
A gateway to Web resources for molecular biology,
genetics, microbiology, and biochemistry.
N. Sequence Databases and Analysis Tools
This is arguably the largest single group of scientific
Web sites in existence. The number of sites featuring
sequence analysis tools (of proteins as well as nucleic
acids), database queries, and prediction algorithms,
among others, is overwhelming and many times
the hardest task is to choose which one to use. Listing
of even just the most interesting and relevant sites
would exceed by far the scope of this resource section.
We have chosen instead to provide a few select Web
pages of major biology servers containing a large and
well-curated collection of databases and tools that
allow them be used as entry points for broader
1. The European Bioinformatics Institute (EBI)
The European Bioinformatics Institute is a nonprofit
academic organisation that forms part of the European
Molecular Biology Laboratory (EMBL). The EBI
manages databases of biological data and provides a
comprehensive range of very useful bioinformatics
2. The Catalog of Databases (DBCAT)
A near-exhaustive list of existent databases for
various application fields, such as DNA, RNA, and
3. The National Center for Biotechnology
One of the major bioinformatics servers, NCBI
creates public databases, conducts research in computational
biology, develops software tools for analyzing
genome data, and disseminates biomedical information.
It provides an extensive collection of tools and
resources, including, but not limited to, molecular
databases such as GenBank, Entrez, and dbEST; literature
databases such as PubMed and OMIM; and tools
such as BLAST, Cn3D, and LinkOut.
4. Genome Net
A Japanese network of database and computational
services for genome research and related research
areas in molecular and cellular biology. A gateway
providing entry points to resources, including, but
not limited to, DBGET (Integrated Database Retrieval
System), KEGG (Kyoto Encyclopedia of Genes and
Genomes), and SSDB (Sequence Similarity Database)
(http://www.genome.ad.jp / dbget / dbget.links.html).
5. The Protein DataBank at Brookhaven (PDB)
PDB is the repository for the processing and distribution
of 3D biological macromolecular structure data.
In addition to containing structural data deposited by
crystallographers and spectroscopists (NMR), worldwide
PDB also presents a large collection of software
for structural work and educational resources.
6. Center for Biological Sequence Analysis
The server at CBS provides a set of very useful tools
for sequence analysis, such as TMHMM for the identification
of transmembrane helices in proteins; TargetP
for the determination of subcellular location of proteins;
and NetNGlyc for the identification of N-linked
glycosylation sites in human proteins, as well as a very
nice collection of links to other sites of interest.
7. The Expert Protein Analysis System (ExPASy)
Molecular Biology Server
The ExPASy proteomics server of the Swiss Institute
of Bioinformatics (SIB) is dedicated to protein analysis
and contains a large number of tools as well as links
to biology servers. The Amos Bairoch's WWW links
page within the ExPASy server (http://www.expasy.
org/alinks.html) contains pointers to information
sources for life scientists with an interest in biological
macromolecules. Additionally, this site is also home to
Biohunt (http://www.expasy.org/BioHunt), a molecular
biology search engine.
8. The Institute for Genomic Research (TIGR)
A not-for-profit research institute whose primary
research interests are in structural, functional, and comparative analysis of genomes and gene products
from a wide variety of organisms. This site contains
a collection of curated databases containing DNA
and protein sequence, gene expression, cellular role,
protein family, and taxonomic data for microbes,
plants, and humans. Particularly interesting is the
TIGR microarray resources page, where one can find
many software tools available for free download.
A database of human genes, their products, and
their involvement in diseases. A search engine useful
for people who wish to find information about genes
O. Educational and General Information
1. Cell and Molecular Biology Online
A site containing general information and links
for cell and molecular biologists. It features several
hyperlinks to many resources such as online journals,
methods, protocols, and laboratories.
2. The Glossarist
A searchable glossary directory. Looking for the
definition of a term in a particular subject can be difficult
and time-consuming. That is where the Glossarist
can help you look. This Web page contains links to
several online dictionaries and glossaries, including,
but not limited to, the online version of the book published
by Lackie and Dow (1999) (http://on.to/
dictionary) and BioABACUS (http://www.nmsu.
edu/-molbio/bioABACUShome.htm), a searchable
database of abbreviations and acronyms in
3. Kimball's Biology Pages
A Web site containing an online biology textbook.
Even though some of the information in this Web site
has been taken from the sixth edition of the author's
general biology text "Biology" published in 1994 by
Wm. C. Brown, frequent updates make this site well
worth a visit.
4. Online Biology Book
A college-level introduction biology text with an
interesting set of lectures with many illustrations.
5. The Biology Project
An online interactive resource for biology. This site
consists of student-oriented, highly interactive learning
materials that can be used to support lectures for
laboratory meetings, and discussion sessions of
general education courses.
6. Biotech's Scientific Dictionary
A dictionary on general terminology of biochemistry,
biotechnology, botany, cell biology, and genetics,
as well as more specific brief definitions of the cell
7. Biology Online
A source of basic biological information, with tutorials
and a dictionary of biology, as well as links to
hundreds of related biology sites.
8. The Visible Mouse
A Web site providing a very nice introduction to the
anatomy, physiology, histology, and pathology of the
laboratory mouse with emphasis on genetically engineered
9. Lee M. Silver's Mouse Genetics
The electronic version of Silver's book.
10. The Zebrafish Book
A guide for the laboratory use of zebrafish (Danio
11. Mark Blaxter's Home Page
It contains "The Genetics of Caenorhabditis elegans,
an Introduction," a very well-written introduction to
the biology of C. elegans.
A gateway to evaluated internet resources in the
basic biological and biomedical sciences, aimed at
students, researchers, academics, and practitioners in
biological or biomedical science.
P. Safety, Ethical Issues, Legislation, and
1. International Centre for Genetic Engineering and
B io techno lo gy-B io safety
The ICGEB Biosafety Web pages, containing information
on biosafety, international biosafety regulations
(USA, Europe and others), handling of GMOs,
and links to other related sites.
2. European Agency for Safety and Health at Work
This is the corporate Web site of the OSHA. It provides
useful information and access to full-text versions
of all OSHA's publications.
3. European Chemical Bureau (ECB)
The ECB is the focal point in Europe for data and
the assessment procedure on dangerous chemicals.
This site provides information on the classification and
labelling of substances, import/export of dangerous
chemicals, legislation, and a collection of links to other
4. Material Safety Data Sheet (MSDS) Databases
A search engine for MSDS libraries. MSDSSEARCH
is a reliable starting point for obtaining the
most updated MSDS documents from the manufacturer
and provides a single, international, database
with all MSDSs available in text format at no cost to
5. EUROPA Steering Committee on Bioethics
This Web site contains information concerning
meetings and documentation produced by the CDBI as
well as links to other relevant sites.
6. The International Bioethics Committee (IBC)
The Bioethics Programme is part of UNESCO's
Division of the Ethics of Science and Technology in
the Social and Human Sciences Sector and, through its
committees, produces advice, recommendations, and
proposals to submit to the Director-General for consideration
by UNESCO's governing bodies. In addition to
providing access to IBC's documents, this Web site has
various links to legislative institutions, databases of
bioethics institutions, and other related websites.
7. Institutional Animal Care and Use Committee at
University of Iowa
This Web site has a very descriptive collection of
basic biomethodology for mouse, rat, rabbit, and
guinea pig animal husbandry, as well as a large
number of established guidelines/regimens for
various animal uses (e.g., recommendations for the
production of ascitic fluid; regimens for anesthesia and
analgesia of laboratory animals).
8. Animal Care at Johns Hopkins
A lot of useful information on regulations and
polices on animal care and use.
9. UCAR Manual on the Responsible Care and Use
of Laboratory Animals
A resource from the University of Rochester
Medical Center. It includes a manual on care and use
of laboratory animals and links to other resources,
such as the dosage calculator (http://www.fda.gov/cder/cancer/ animalframe.htm).
10. OECD Principles of Good Laboratory Practices
A Web site containing information on OECD guidelines
for GLP, and principles of GLP, as well as links to
national GLP sites.
11. U.S. Environmental Protection Agency (EPA)
EPA's home page to the Good Laboratory Practice
Standards (GLPs) compliance monitoring program.
Europe's network of patent databases. Search
published worldwide patent applications with an
English abstract and title as well as published patent
applications in their original language from various
European countries. A real trove of information,
reagents, and sequences is sometimes buried in patent
5. The Wellcome Library
One of the world's greatest collections of books,
manuscripts, pictures, and films around the meaning
and history of medicine.
A catalog of books, journals, and audiovisuals in the
National Library of Medicine collections.
Q. Literature Datasets
1. BioMed Central
An open access, independent publishing house
committed to providing immediate free access to peerreviewed
PubMed is a service of the National Library of Medicine
providing access to over 12 million MEDLINE
citations back to the mid-1960s and additional life
science journals. PubMed also includes links to many
sites providing full text articles and other related
resources. A similar service is provided by High Wire
3. Online Mendalian Inheritance in Man (OMIM)
A resource provided by NCBI containing curated
reviews on human genes of interest with many references
and embedded hyperlinks to other resources.
4. The Cochrane Library
This site consists of a regularly updated collection
of evidence-based medicine databases, including The
Cochrane Database of Systematic Reviews, which
provide high-quality information to people providing
and receiving care and those responsible for research,
teaching, funding, and administration at all levels. The
Cochrane Library is available on a subscription basis,
but there are several countries that have arranged
national provisions and thus allow all residents to
access The Cochrane Library for free (e.g., Australia,
England, Norway, Finland).
A large medical reference site including an exhaustive
list of medical journals and medical associations
and similar resources in the biological sciences. Other
research tools include medical glossaries, disease databases,
clinical trials and guidelines, and medical journals
offering full-text article.
8. BioMail Service
Biomail is an automatic service that regularly
(weekly by default) searches for articles, that have
recently appeared in the PubMed Medline database
using customized search terms. Then it emails lists of
the found articles to the user.
R. General Protocols
This Web site features a collection of protocols contributed
by scientists from over 125 academic laboratories
covering a variety of life science disciplines.
A large site with a plethora of links and many useful
An initiative by a team of MIT-affiliated researchers
and local software engineers to develop a free Web site
containing research protocols used in biological
A specialized Web site containing a collection of
links to more than 2000 online protocols. You can
discuss these protocols with researchers that share a similar interest. The protocols are indexed into eight
categories: anatomy and histology, biochemistry
and molecular biology, biotechnology, cell biology,
developmental biology, genetics, immunology, and
4. Protocol Online
A database of research protocols in a variety of life
science fields. It features user-submitted protocols as
well as links to other Web sites.
S. General Reagents and Techniques
1. The Biocurrents Research CentermDatabase of
A NIH-funded database providing its user with a
useful forum on the use of pharmacological compounds
in cellular research. It lists over 500 compounds
with details on their mode of action and
employ, including references.
A buying guide for life sciences. Even though this
site is commercially oriented it allows one to search a
wide range of product-related technical information
for the life science researcher in a rather comprehensive
manner. If you need something and do not know where
to buy it and whom to buy it from, this site may be just
what you need. Included is Biocompare's Antibody
Search, which allows you to search over 60,000 antibodies
from various antibody suppliers. A similar service
provider is BioSupplyNet (http://www.biosupplynet.
com/) where you can browse and search for suppliers
in a variety of areas of life science research.
3. Bioresearch Online
A sourcing site for bioresearch. In addition to it
belong a buyer's guide and a free newsletter, it contains
a search engine for product information.
4. LabVelocity's Biowire
A Web site containing user-written laboratory
product reviews pertaining to the life sciences community.
It holds a very large number (ca. 25,000) of
product reviews, which are a good aid not only when
deciding on purchasing a particular item, but also if
you are searching for a specific product. A complementary
site is SciQuest (http://www.sciquest.com/
commerce/CommerceRouter/Index), a site providing
search possibilities for scientific products.
A search engine for finding health sciences
T. Model Organisms
1. The Mouse Genome Resources
A gateway to mouse resources. This site is an entry
point to access information pertaining to the NCBI
mouse genome sequence as well as other extramural
2. Whole Mouse Catalog
A collection of links to internet resources of particular
interest to scientific researchers using mice or rats
in their work.
3. The Jackson Laboratory Home Page
JAX online consists of a series of resources of
interest for mouse researchers, including databases
(http" / / www.jax.org / resources / search_databases.ht
ml) and a mouse strain repository (http://jaxmice.jax.
org/index.html) for the collection and distribution of
genetically engineered mice, as well as a Mouse
Genome Informatics (MGI) site that provides integrated
access to data on the genetics, genomics, and
biology of the laboratory mouse.
4. The Mouse Phenome Database
A collection of comprehensive phenotypic and
genotypic data on inbred laboratory mouse strains.
5. The Edinburgh Mouse Atlas Project (EMAP)
This Web site is the home page of a collaborative
project within the University of Edinburgh aiming at
the creation of a digital atlas of mouse embryonic
development. It consists of a series of interactive threedimensional
computer models of mouse embryos at successive stages of development with defined
anatomical domains linked to a stage-by-stage ontology
of anatomical names. Additionally, the EMAP
atlas underlies an image-mapped gene-expression
database (EMAGE; http://genex.hgu.mrc.ac.uk/
Emage/database/intro.html). These two databases are
This database system provides access to comprehensive
public repositories for genome mapping data
from farmed and other animal species (e.g., cat,
chicken, cow, deer, horse, pig, salmon, sheep, tilapia,
turkey). Data stored include details of loci and
markers, references/papers, authors, genetic linkage
map assignments, cytogenetic map assignments,
experimental techniques, PCR primers and conditions,
and any other data pertaining to genome mapping.
7. Rat Genome Database (RGD)
A Web site providing a large amount of rat genetic
and genomic resources. It includes curated data on rat
genes, quantitative trait loci (QTL), microsatellite
markers, and rat strains used in genetic and genomic
research. In addition, RGD provides a large number of
tools for gene prediction, radiation hybrid mapping,
polymorphic marker selection, and more.
A database of genetic and molecular data for
Drosophila. FlyBase includes data on all species from
the family Drosophilidae, but the primary species represented
is Drosophila melanogaster. This site also contains
several links to resources of interest for Drosophila
9. The Zebrafish Information Network (ZFIN)
ZFIN is a database resource for the laboratory use
of zebrafish. It provides integrated zebrafish genetic,
genomic, and developmental information, together
with links to corresponding data in other model organism
and human databases.
10. The HGMP-RC Fugu Genome Project
In addition to containing the publicly available draft
sequence of the Fugu genome, this site also provides a
collection of protocols, publications, and much data for
the scientific community with an interest in Fugu
rubripes (the Japanese puffer fish).
11. Caenorhabditis elegans WWW Server
A Web site aimed at the community of C. elegans
researchers. This site boasts a large number of
resources, including literature search, methods, a list
of meetings, labs, and researchers, links to Bionet.
celegans, etc. A companion site is WormBase
(http://www.wormbase.org/). A Web site displaying
a large amount of relevant information and hyperlinks
for the C. elegans scientific community.
12. WWW Virtual Library for Xenopus
A site dedicated to Xenopus laevis, a commonly used
model system for studying vertebrate early development.
One of the main uses of this site is as a reference
for researchers looking for molecular probes. It also
contains a collection of whole mount staining patterns
using both antibody and nucleic acid probes, a
methods book, supplier listing, Xenopus scientific
community white pages, and more.
An informatics resource for Dictyostelium discoideum,
it consists of a comprehensive genomic
Dictyostelium database, lab protocols and strain
availability, and a list of researchers, among many
14. The Arabidopsis Information Resource (TAIR)
A comprehensive resource for the scientific community
working with Arabidopsis thaliana, a widely
used model plant. TAIR consists of a searchable relational
database, which includes many different data
types. In addition, pages on news, information on the
Arabidopsis Genome Initiative (AGI), Arabidopsis lab
protocols, and useful links are provided.
Additional sites and nonlisted model organisms can
be found at the following sites:
The WWW Virtual Library: Model Organisms
The Sanger Institute's Model Organisms Resources
Links (http://www.sanger.ac.uk/Info/Links /
Infobiogen's list of genomes and organisms (http://www.infobiogen,fr/services/deambulum/english/genomesl.html)
NIH's Model Organisms for Biomedical Research
III. IMAGING TECHNIQUES
IN CELL BIOLOGY
One of the paramount interests of cell biologists
is to observe cellular themes, temporally as well as
spatially resolved. No longer just structures, but also
proteins and their cellular localisation, dynamics, and
interaction(s). The field of cellular imaging is currently
one of the cornerstones of cell biology and microscopy
constitutes arguably its single most important technique.
For this reason, we have chosen to list and highlight
Web sites dealing with the subject of microscopy
in a more comprehensive manner then hitherto. This
part of the resources section is thus devoted to
microscopy techniques and covers the subject in a
broad manner with sites that should be of great use to
the novice and experienced user alike.
A. Light Microscopy
1. A Brief History of Optics
A part of the laser-optics UK Web site giving a historical
summary of the important discoveries in the
field of optics.
2. Properties of Light and Introductory Optics
The Molecular Expressions Microscopy Primer is an
excellent microscopy Web site from Florida State University
(principal authors: Michael W. Davidson, FSU
and Mortimer Abramowitz-http://micro.magnet.
fsu.edu/). An extensive series of tutorials on light and
colours can be found on this Web site: nature of light
(electromagnetic radiation, duality of light, definition
of colours), physical properties (reflection, refraction,
diffraction, polarisation, interference), and fundamental
tools to generate and direct light (lenses, filters,
sources of light, laser). A good introduction about light
microscopy written by these authors can be downloaded
at: http: //screensavers.magnet.fsu.edu/pdfs/
3. Anatomy of a Light Microscope and Basic
Concepts in Optical Microscopy
The complete description of the different parts of a
microscope can be found within this link: microscope
components configuration, optical train components,
perfect lens characteristics, objectives, and other
important parts of the microscope.
4. Concepts and Formulas in Microscopy
A part of the Nikon's MicroscopyU Web site
(http://www.microscopyu.com/). This Web site was
originally designed to provide an educational forum
for all aspects of optical microscopy, digital imaging,
and photomicrography and complements the Molecular
Expressions Microscopy Primer microscopy Web
site (http://micro.magnet.fsu.edu/). This Web site
part covers concepts and formulas in microscopy and
includes definitions on some very important and often
not well-understood parameters (numerical aperture,
depth of field, resolution, and many others).
5. Sources of Visible Light
Description of various sources of light used for
6. Köhler Illumination
Köhler illumination is a basic requirement of all
modern light microscopy. The purpose is to obtain an
evenly lit field of view and as wide a cone of radiation
as possible in order to achieve maximum resolution.
This Web page explains clearly what the Köhler illumination
is and how to set it up.
7. Specialised Microscopy Techniques
Microscopic techniques can be separated into two
categories: microscopy using polychromatic light
(basic light microscopy) and microscopy using specific
wavelength (fluorescence microscopy) that need
specific filters. Here you will find a description of different nonfluorescent microscopy techniques:
bright-field and dark-field microscopy, Nomarski (or
DIC), phase contrast, and so on.
B. Fluorescence Microscopy
1. What Is Fluorescence? The Stokes Law
Cell biologists want to observe the localisation,
dynamics, and relocalisation of proteins. Unfortunately,
proteins are not directly visible; in order to
monitor their localisation they need to be tagged with
fluorescent probes. This site gives the necessary background
about how fluorescence is generated.
A link about George Gabriel Stokes.
2. Fluorescence Microscopy Tutorials
Fluorescence microscopy is the most common technique
today in medical and biological sciences. This
link focuses on excitation and emission fundamentals,
light sources, lasers, and filter cubes. The section interactive
Java tutorials give very useful information
about fluorochrome data tables, excitation/emission
wavelengths, and filter cube suggestions listed by
3. Laser and Fluorescence Microscopy
Section about laser fundamentals from the Olympus
Web site. Lasers can be found in CD players and
various other commonly used objects. In the field of
microscopy, lasers are used for their monochromatic
properties, light coherence, and power. This link gives
useful and accessible information about laser physics.
Many Java tutorials are also available.
C. Image Acquisition
1. Cameras and CCD Detectors
Originally, mechanisms of image capture were
restricted to photomicrography on film. Currently, the
development of sensitive and low noise cameras gives
the possibility to acquire digitally images from the
microscope. These cameras with high sensitivity are at
the core of the development of video microscopy. Digitalized
images, as an ordered matrix of integers rather
than a series of analog variations in colour and intensity,
give the interesting possibility to post process
images in order to enhance features and extract information.
This section addresses a variety of current
topics in image acquisition and processing.
A part of the Roper scientific Web site
(http://www.roperscientific.com) called encyclopedia
and describing many camera concepts, such as
binning, gain, and dynamic range, among others. A
very useful reference to understand basic principles of
cameras and CCD detectors.
Comparison of technical characteristics of several
D. Filter Sets and Fluorescence Filter Cubes
Filter sets are designed to select a specific wavelength
for specimen illumination with polychromatic
light sources and are essential for selectively collecting
fluorescent light coming from the sample. Proper
selection of filters is the key to successful fluorescence
microscopy. This section describes characteristics of
excitation and emission filters used in combination
with dichroic mirrors to design filter cubes.
The Curvomatic application from the Omega Web
site (http://www.omegafilters.com) is a tool helping
microscopists to choose their filters set according to
fluorophores used. A very useful application.
E. Fluorescence Tables
This link provides a table that summarizes several
peak excitation and emission wavelengths of commonly
used fluorochromes. These different fluorescence
tags can be coupled with proteins or drugs (e.g.,
phalloidin or taxol) to monitor localisation of proteins
The Bio-Rad fluorescence database has been
designed to allow the user to superimpose graphical
fluorochrome data from various fluorochromes onto a
normalised axis. Both emission and excitation spectra
can be plotted from any fluorochrome in the database.
These can subsequently be overlaid with filter data
curves and laser lines, which aids the microscopist in
selection of the correct fluorochrome for use with their
samples and microscope.
The fluorescence spectrum viewer from bdbiosciences.
This can be used as an alternative to Bio-Rad
fluorescent database and the curvomatic application
F. Fluorescent Probes for Light Microscopy
1. Fluorophores and Fluorescents Reagents
An electronic version of the Molecular Probes
Handbook. Molecular Probes is one of the most interesting
providers of fluorescent probes for cell biology.
This Web edition of the handbook is an updated
version of the 9th edition and is presented in two
formats. Very useful information can be found in this
Web handbook, such as cross-linking techniques, photoreactives
reagents, probes for cytoskeletal proteins,
membranes, organelles, and endocytosis, as well as pH
indicators, and ions indicators.
This link points to the complete list of fluorescent
Probes available from Molecular Probes. For each
probe a sheet summarizes some characteristic of the
probe (emission and excitation spectra, physical properties,
etc...). Spectra are also available for download.
A base/dye ratio calculator from molecular probes.
This applet allows the possibility to calculate fluorescence
characteristics (maximum wavelength, extinction
coefficient) of a nucleotide coupled to a
2. Secondary Antibodies for Immunohistochemistry
A part of the analytical imaging facility Web site
from Albert Einstein college of medicine (New York,
http://www.aecom.yu.edu/aif/). This link points to a
troubleshooting guide on immunofluorescence nonspecific
labelling; very useful for understanding staining
problems in immunofluorescence experiments.
Jackon immunoresearch and Zymed are providers
(although not unique) of secondary antibodies used in
fluorescence microscopy. Secondary antibodies are
classical tools used in cell biology to reveal localisation
of proteins by fluorescence microscopy. Molecular
Probes also provides some secondary antibodies.
3. GFP. Background and Properties of GFP and
These Web pages about green fluorescent protein
(GFP) have been developed as a dissertation project for
the principles of protein structure using the internet
You will find the in vivo role of the GFP and some basic
properties. Biosynthesis, chemical structure of the fluorophore,
and spectrum characteristics of this protein
are also available.
4. Commercial Web site of Fluorescent Proteins
This link points to the Clontech Web site, with
emphasis on GFP vectors. Clontech is historically the
first provider of GFP-expressing vectors.
G. Immunohistochemistry and
1. Protocols Database
Protocol Links Web page of IHC world Web site
(http://www.ihcworld.com/; online information
center for immunohistochemistry). An extensive list of
Web sites, pdf files, and protocols covering fields of
general histology, immunohistochemistry, immunofluorescence,
in situ hybridisation, and electron
Link to the protocols database of the IHC Web site.
You can query the protocol database for a specific
2. Immunohistochemistry and in situ Hybridization
Link to a Web site explaining theory and techniques
of immunolabelling. Some protocols are available and
many Powerpoint presentations are downloadable.
Useful teaching resource.
3. Other Immunofluorescence Protocols
Web site of the imaging technology group from the
Beckman Institute for Advanced Science and Technology
(http://www.itg.uiuc.edu/). Link includes technical
bulletin providing an introduction to fluorescent
microscopy and a collection of various protocols for
specific applications of fluorescence.
H. Other Microscopy Techniques
1. Three-Dimensional Laser Confocal Microscopy
Web site from Lance Ladic, Department of Physiology,
University British Columbia, giving a basic introduction
to 3D laser-scanning microscopy.
Link to the course "Looking inside cells and tissues
by optical sectioning with a confocal laser scanning
microscope" prepared by M. Diirrenberger and R. SiRterlin.
Also some basics about confocal microscopy.
Home page of the scanning laser microscopy lab
(also known as the confocal microscopy group) of the
physics department at the University of Waterloo. This
site is designed for researchers who use (or might like
to use) confocal microscopes. This Web site describes
optical design, problems of lateral and axial resolution,
and problems of confocal slicing in confocal
microscopy. Some formulae can also be found.
A complete section about confocal microscopy from
the Molecular Expressions Microscopy Primer Web
site. Basic concepts, imaging modes, specimen preparation
and imaging, laser systems for confocal
microscopy, etc... A very nice interactive java tutorial
showing how a confocal microscope is working. This
tutorial also shows effects of pinhole aperture on the
quality of the confocal image.
2. Spinning Disk Confocal Microscopy
A short Web page that describes differences
between confocal scanning microscopy and the new
technique of spinning disk confocal microscopy.
3. Multiphoton Fluorescence Microscopy and Two
Multiphoton fluorescence microscopy is a powerful
research tool that combines the advanced optical
techniques of laser-scanning microscopy with long
wavelength multiphoton fluorescence excitation. Multiphoton
microscopy is generally used to specifically
excitate fluorophores in a specific Z location. This link
gives much information about this technique complementary
to confocal microscopy.
4. Fluorescence Resonance Energy Transfer (FRET)
FRET microscopy uses the same physical principle
as FRET spectroscopy. FRET is a technique used to
determine the interaction (or proximity) of two fluorescent
labelled molecules. This site gives the mathematical
background necessary to explain FRET
spectroscopy. Observations and equations described
here are applicable to FRET microscopy.
Molecular Probes Web page about fluorescence resonance
energy transfer microscopy. Information about
primary conditions of FRET, F6rster radius, and fluorophore
pairs used for FRET can be found.
5. Fluorescent Lifetime Imaging Microscopy (FLIM)
Time-resolved fluorescence emission spectroscopy
of a photoexcited sample is a powerful tool for the
study of living cells in both space and time of their
internal biochemistry. The Web page of the W.M.
Reck Center for Cellular Imaging (University of Virginia)
provides theory, images, and references about
6. An Archive of Electron Micrographs
A collection of electron micrography images from
the Institute for Molecular Virology, University of
7. Atlas of Microscopy Anatomy
Electronic version of the Atlas of Microscopic
Anatomy: A Functional Approach: Companion to
Histology and Neuroanatomy, second edition.
8. A Video Tour of Cell Motility
Contribution to the EAMNET network (http://
www.embl.de/eamnet) from the John Victor Small
laboratory. An original gallery of video microscopies
describing the phenomenon of cell motility.
9. Free Software for Microscopy
A part from Lance Ladic Web site (Department of
Physiology, University British Columbia) giving many
links for microscopy and image processing softwares.
10. ImageJ-Freeware Java Image Processing Software
ImageJ is a very good image processing software,
written in Java and available for all types of platforms
(Linux/UNIX, Windows and Mac-based computer).
11. Power Point Presentations on Microscopy
General teaching resource about light microscopy
available as powerpoint presentations.
12. The European Advanced Light Microscopy
Network (EAMNET) Network
EAMNET is a EU-funded network of eight European
laboratories and two industrial partners working
in the field of light microscopy. The aim of EAMNET
is to assist scientists in exploiting the power of imaging
by organizing practical teaching courses, creating
online teaching modules, and offering software packages
13. Cell Migration Consortium
Movies and photo from the cell migration consortium
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y.
(2001). A comprehensive two-hybrid analysis to explore the yeast
protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574.
Lachie, J. M., and Dow, J. A. T. (1999). "The Dictionary of Cell and
Molecular Biology," 3rd Ed. Academic Press, London.