Software and Services: Microarray Analysis
The Microarray Analysis Facility supports various microarray expression data analysis programs, R (statistical package), and a database archive.
Basic Services Subscription: $1640.00 Annual Fee Sept 1 - Aug 31
GeneSpring: Up to 2 lab copies.
Access and training on R / Bioconductor scripts (including Affy and ABI scripts).
Access to Ingenuity Pathway Assist (gene ontology tool).
Access to Online Protocols (by Wiley Publishing)
Access to Affymetrix MicroArray Analysis workstation (upon request).
2 registrants in any MAF basic class or 1 registrant MAF advanced class.
4 hours personal support (consultation, programming, sys-admin, etc).
GeneSpring
GeneSpring v5.0 by Silicon Genetics is now available to BimCore subscribers. GeneSpring is available for download to local machine. BimCore has licensed three (3) concurrent seats.
R / BioconductorR / Bioconductor (v 1.8, R 2.3.0) is now available to BimCore subscribers. Bioconductor is open source and runs on PC and Linux. BimCore scripts include: quality control, verification of replicates, RMA normalization, ABI analysis and ANOVA and clustering.
Rosetta ResolverRosetta Resolver (currently under evaluation 03/2008) is a scalable gene expression data management and analysis system. Rosetta Resolver provides automated data import, built-in standardized analysis methods, option to create analysis workflows for consistent protocols throughout a lab or core, cross-species analyses, etc.
Ingenuity Pathways AnalysisIngenuity Pathway Analysis by Ingenuity Systems is available to BimCore Microarray subscribers via the web. We have licensed a single concurrent seat, so please use the calendar. Ingenuity Pathways Analysis enables biologists and bioinformaticians to model, analyze and understand the complex biological systems at the core of all life science research. Ingenuity Pathways Analysis leverages the world largest and highest quality knowledge base of biological networks, powerful algorithms and an exceptionally easy-to-use software interface to provide researchers with the insights and confidence to make better and faster decisions at every step of their research.
DAVIDDAVID (Database for Annotation, Visualization and Integrated Discovery) 2007 provides a comprehensive set of funcitonal annotation tools for investigators to understand biological meaning behind large lists of genes. DAVID provides functional annotation, gene functional classification, gene ID conversion and batch viewer.
PantherThe PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System by Applied Biosystems is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. For an increasing number of proteins, detailed biochemical interactions in canonical pathways are captured and can be viewed interactively.
On-line ProtocolsOnLine Current Protocols content from Wiley Publishing is now available to Emory faculty, students and staff .
This agreement, which was developed through the work of BimCore and Emory University Libraries, provides limited access to various protocols. The terms of
our agreement require users to login from an Emory IP or through the Emory VPN.
Emory Protocols include: Bioinformatics, Cell Biology,
Cytometry, Human Genetics, Immunology, Magentic Resonance Imaging,
Neuroscience, Nucleic Acid Chemistry, Pharmacology, Protein Science,
Toxicology, Molecular Biology, Microbiology
The Affymetrix Microarray Suite and workstation are no longer available. Please contact Kim Gernert at 404-727-3501 for assistance with Affymetrix support.
ConfacThe CONFAC software finds the conserved Transcription Factor Binding Sites (TFBS) in the promoter regions of the genes of given Human genes and the corresponding Mouse homolog.
Microarray TechnologiesBimCore has listed local genechip array processing centers and cores, along with additional links to other genechip technologies.