Research Resources
Submit a Site | Forums & Blogs | Model Organism & Genome Databases | Methods, Protocols, Tutorials | Simulation and Animation Resources | Equipment Vendors | Reagent and Supply Vendors | Cell Biology Literature | Calendars
Submit a Site
Submit
a Cell Biology Research Site
(include URL and category)
Forums & Blogs
ASCB
Cell Biology Forums
Aetiology:
blog by Tara Smith
BioCompare:
forums onDNA topics, RNA topics, Protein Topics, Immunochemistry and Tissue
Culture
BioForum:
cell biology forum
BIOSCI/Bionet:
usergroups
CellCultureChat:
bulletin board for the discussion of cell lines and methodology
Fellows
Net from EMBO
Journal
Club: blog from Nature
Life
Science: blogs on scienceblogs.com
Methagora
Nature Methods forum
Molecular
Biology: forum from Molecular Station
ScienceRing:
network of scientists
ScientistSolutions:
cell biology forum
Model Organism Community Sites & Genome Databases
Chlamydomonas:
ChlamyCenter resources from Duke University
Dictyostelium discoideum:
DictyBase
Tetrahymena Genome Database:
from Stanford University
Tetrahymena
Weblinks: from Dr. Smith-Sommerville, University of Alabama, Tuscaloosa
Candida Genome
Database: from Stanford
Fission yeast: PombeNet,
Forsburg lab from University Southern California
Saccharomyces cerevisiae
Genome Database: SGD
Arabidopsis:
tThe Arabidopsis Information Resource from TAIR
Gramene: comparative
grass genomics resource
Maize Genetics Database:
MaizeGDB community database about the crop plant Zea mays ssp. mays
Caenorhabditis
elegans databases:
• C
elegans movies
• C elegans
www server
• Wormatlas
• Wormbase
• WormBook
• WormImage
Drosophila:
FlyBase
Mouse Genomics
Informatics: MGI, from Jackson Labs
Puffer fish: Fugu Informatics network
Rat Genome Database:
RGD, from the Medical College of Wisconsin
XenBASE: Xenopus
laevis and tropicalis biology and genomics resource
Zebrafish
resources:
• NCBI
Zebrafish Resources page
• Tubingen
map of the zebrafish genome
• ZFIN: University
of Oregon
• Zfish: zebrafish
genome resources, Washington University, St Louis
Escherichia
coli databases:
• EcoCyc
• International
E. coli Alliance: IECA
Comprehensive microbe databases:
• Bacterial
Genomes: by Welcome Trust Sanger Institute,, concentrates on pathogens
and model organisms
•
Microbe Sequencing Projects: NCBI
• TIGR
Comprehensive Microbial Resource: CMR
All
the Virology on the World Wide Web: from Dr. David Sander, Tulane
University Medical School, New Orleans
Viral
Genomes: NCBI
AAAS
Functional Genomics Resources
ArkDB: from the
Roslin Institute, Scotland
BioMedCentral:
catalog of cell biology databases
Ensembl
list of species
GenomeSeek
database: access to current and completed eukaryal and microbial genome
projects
Model Organisms:
by Welcome Trust Sanger Institute ,br> NCBI
NIAID
BRC Central: a repository linking to eight Bioinformatics Resource
Centers
NIGMS
Genetic and Genomic Resources for Model Organisms
The Gene Ontology
project: controlled vocabulary to describe gene and gene product attributes
in any organism
Organism
Database: by CalTech
US Department of Energy
Joint Genome Institute
Methods, Protocols, Tutorials
Biological
Research Protocol Books: list of protocol books available for purchase
BPO
Biological Procedures Online: open access methods journal
BioVisa.net:
large collection of protocols in the life sciences
Cell
Biological Applications of Fluorescence Microscopy: by Stephen Rogers,
University of Illinois at Urbana-Champaign
Cell
Biology Protocols: from BioCompare
Cell
Biology Lab Manual: for college-level course by Dr. William H. Heidcamp,
Gustavus Adolphus College,St. Peter, MN
Confocal-microscopy.org:
confocal protocols and resources
COPE
Cytokines Online Pathfinder Encyclopedia: by Horst Ibelgaufts, PhD
CSH Protocols:
interactive source of new and classic research techniques
Current
Protocols: contains thousands of basic to advanced research protocols
FlowCytometryProtocols:
from Imperial Cancer Research Fund, UK
Genomics
Methods: links from Davidson College
GFP
Applications: by Wallace Marshall, Yale
Immunohistochemistry
Techniques Database: compiled from published sources and laboratory
submissions
Immunoportal.com:
source IHC and in situ hybridization protocols
Methods
& Protocols: large collection from Cell and Molecular Biology Online
Microarray
Protocols: from National Human Genome Research Institute
Microscopy
Protocols: from Harriet Smith-Sommerville, PhD University of Alabama,
Tuscaloosa
Molecular
Biology Protocols: by Horizon Scientific Press
PCR
Station: numerous protocols and troubleshooting tips
ProSciProtocols:
collection of immunology protocols from ProSci, In.
Protocol
Guide: from Biotechniques
ProtocolsMethodsTechniques:
from Molecular Station
ReBase:
restriction enzyme database
Protocol-Online:
list of categorized procedures
TDG:
Tissue Dissociation Guide theory and technique from Worthington Biochemical
Corp
Tissue
Culture Methods: by Julie Wolf, University of Maryland Baltimore County
WebCutter:
for predicting restriction enzyme digests
Westernblots:
everything you ever wanted to know
Yeast
Protocols: compilation of protocols from numerous labs from Tritech
Research
Animation
Tutorials: tutorials on creating animations using various software
packages form MolecularMovies.org
BIOMS: the Center for
Modeling and Simulation in the Bioscieces site promoting the use of modeling
and simulation in biology
DNATube: scientific
video site, a YouTube for biology
JOVE: Journal of
Visualized Experiments
Lab Action: biology
videos
Nature
Protocols (subscription required)
Simulation and Animation Resources
Adobe
for After Effects, Director and Flash
Amira 3D: visualization
and volume modeling software
BIO
Programming Tools: from University of British Columbia
BioSpice: collaboration
of biologists, engineers and computer scientists at Berkeley to develop
a tool kit of open source software tools to represent and simulate cellular
processes
CellML: from the
University of Auckland
Cell
Illustrator: environment for simulating and representing biological
systems
Cell-O: by Richard
Azevedo, University of Houston and Hans-Peter Meinzer German Cancer Research
Center
CompuCell3D:
tissue and organ simulator based on the Cellular Potts Model from the
University of Notre Dame
Cytosim7:
for modeling the cytoskeleton by Francois Nedelec and Dietrich Foethke,
EMBL, Heidelberg
DIAS: dynamic
image analysis software from David Soll, PhD, University of Iowa
E-Cell: an object-oriented
software suite for modeling, simulation, and analysis of large scale complex
systems, particularly focused on biological details of cellular behavior
Gepasi: software package
for modeling biochemical systems
Java
Macromedia
Director MX
Example
Matlab:
from Mathworks
Maya:
integrated 3D modeling and animation
MCell and DReaMM
(Monte Carlo Cell and Design, Render, and Animate MCell Models): microphysiological
simulations from Pittsburgh Supercomputing Center
TASI
Animation: advice on Vector and animated graphics from Technical Advisory
Service for Images
Virtual Cell: modeling
and simulation framework developed by NRCAM, National Center for Cell
Analysis and Modeling: by University of Connecticut Health Center
Visbox: hardware
display products and solutions for high resolution and immersive 3D applications
VMD Visual
Molecular Dynamics: from the University of Illinois at Urbana-Champaign
VMD Gallery
VTK (Visualization ToolKit):
an open source, freely available software system for 3D computer graphics,
image processing, and visualization, consisting of a C++ class library,
and several interpreted interface layers including Tcl/Tk, Java, and Python.
VTK
Technical Paper: by WJ Schroeder, KM Martin and W Lorensen, GE Corporate
Research & Development
3D Slicer: "point
& click" end-user application based on VTK, for delivering algorithms
to computer scientists and biomedical researchers
Cell
Biology Animation: by John Kyrk
cgbiovisuals:
site of Allan Spong, PhD
Drew
Berry
Drew
Berry's page on CGSociety website
Fairman Studios:
medical and biological illustration and animation
fiVth
Medical Media: site of Graham Johnson
ForgeFX:
interactive 3D simulation and visualization company
ImageCyte: by
Karin Christensen
MolecularMovies:
a portal to cell and molecular animation, includes access to a number
of animations
Molecular
Movies Animation Tutorials: in Maya, After Effects and Cinema4D
Sumanas:
developers of interactive educational animations
XVIVO: creates animations
for biotech companies and educational organizations
s & Professional Organizations
AMI:
Association of Medical Illustrators
Image
Analysis Conferences
ISCB: International
Society for Computational Biology
Medical Imaging
Conferences
PLoS Computational
Biology
Equipment Vendors
Microscope and Optical Component Manufacturers
Cargille Laboratories:
immersion oil several formulations covering a wide spectrum of viscosities
and fluorescence levels
FEI
Fullam
Gatan
Hitachi
High Technologies
JEOL USA, Inc.: maker
of electron beam equipment, including electron beam lithography and ion
beam systems as well as microscopes
Leica Microsystems
Nikon
Olympus
Omega Optical:
makers of precision optical filters
Optiscan: miniature
confocal endomicroscope for clinical use, which permits direct and non-invasive
views of cells inside the human body
Carl Zeiss Microimaging
Software for Microscopy and Digital Imaging
Bitplane:
real time interactive analysis and visualization software
CellProfiler:
image analysis software
Digital
Images & Editing: list of useful sites from Harriet Smith-Sommerville,
PhD University of Alabama, Tuscaloosa
EM
Yellowpages: software for electron microscopy
FreeSFP:
for 3D digital images, especially suitable for single or multi-channel
images from microscopes or MRI
Huygens
Essential: from SVI is an image processing software package tailored
for deconvolution of microscopic images. The software is described at
the Huygens
Essential Wiki
ImageJ: Public
domain Java image processing program inspired by NIH Image that runs on
all operating systems.
IMOD: image processing,
modeling and display programs used for tomographic reconstruction and
for 3D reconstruction of EM serial sections and optical sections
LisPixis: public
domain image analysis program for Windows, written and maintained by David
Bright, formerly of NIST
Metamorph
7: imaging software
NIH Image:
a public domain image processing and analysis program for the Macintosh.
Scion Image for Windows:
a free PC version of Image, is available from Scion Corporation.
VayTek: deconvolution,
volume rendering and image acquisition software
Reagent and Antibody Suppliers
21stCentury
Biochemicals: custom antibodies and peptides
AbCAM: UK company
with over 30,000 antibodies
Abgent: antibodies
targeting protein kinases, phosphatases, methyl and acetyl transferases,
ubiquitin and SUMO, and glycosylases
BioLegend: antibodies
for immunology and cell biology research
Biomeda: immunochemicals
Cedarlane:
monoclonal and polyclonal antibodies
Imgenex: makers
of antibodies, gene and protein expression systems and cell and tissue
arrays
Immuquest: antibodies
against nuclear proteins.
Invitrogen/Molecular
Probes: antibodies tagged with fluorescent molecules or fluorescent
molecules that can be used as antibody tags
Mitoscience:
mitochondria-specific antibodies
Nordic: Dutch
company offering over 1500 antibodies
R&D Systems:
specialty manufacturer of biological products with two operating divisions:
Biotechnology and Hematology
Rockland: immunochemicals
for research
Strategic
Biosolutions: stock antibodies and custom antibody production
SouthernBiotech:
founded in 1982 by scientists from Dr. Max Cooper's Cellular Immunology
Laboratory at the University of Alabama
VectorLabs:
provided the research community with the first set of Biotin-Avidin System
reagents
Antibody
Resource Page: guide to companies that sell catalog and custom antibodies
BIORATING: free public
repository of user ratings and primary data for commercial antibodies
Immunoportal:
source for information on antibody vendors, and protocols
ATCC:
American Type Culture Collection
CABRI: Common Access
to Biological Resources and Information
Cell
Line Database: from Istituto Nazionale per la Ricerca sul Cancro,
Italy
DSMZ: German Collection
of Microorganisms and Cell Cultures
HSRRB:
Human Science Research Resources Bank of the Japanese Collection of Research
Bioresources
UKNCC: United Kingdom
National Culture Collection
Vendors of other Chemicals, Reagents and Supplies
Resources for Searching and Comparing Supplies
BioCompare:
categorized cell biology product guide
BioSupplyNet:
search for supplies
ChemBargains:
search for chemical products
eMolecules: search
for information and suppliers of chemicals
Life Sciences
World: online resource for biotechnology
R&D Chemicals:
directory of chemical suppliers
Used-line: search
for used equipment
Cell Biology Literature
Annual
Review of Cell and Developmental Biology
Current
Opinion in Cell Biology
Nature Reviews Molecular
Cell Biology
Nature Reviews Immunology
Nature Reviews Cancer
Nature Reviews Neuroscience
Nature Reviews Genetics
Nature Reviews Drug
Discovery
Nature Reviews
Microbiology
Signal Transduction
Knowledge Environment
Trends
in Biochemical Sciences
Trends
in Cell Biology
Crossref: gain
access to journals with DOI string
GoogleScholar
PubMed
HighWire
Press: free full-text articles
Hinari site:
from World Health Organization
Online Textbooks and Lab Manuals
Beginning
Molecular Biology Laboratory Manual: University of Maryland, Baltimore
County
College
Cell Biology Lab Manual: by Dr. William H. Heidcamp, Biology Department,
Gustavus Adolphus College,St. Peter, MN:
Kimball's
Biology Pages: online biology textbook
Molecular
Biology of the Cell (4th ed): by Alberts et al
Molecular Biology
Web Book: by Web-books.com
Molecular
Cell Biology (6th ed): by Lodish, et al
NCBI
Bookshelf: collection of free biomedical books
Online
Biology Book: by Michael J. Farabee, PhD, Estrella Mountain Community
College, in sunny Avondale, AZ
Plant Physiology Online:
a Companion to Plant Physiology (4th ed): by Lincoln Taiz and Eduardo
Zeiger
The
Science Creative Quarterly Cell Biology Textbook page: from The University
of British Columbia, Canada
