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PhD Program in Computational Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, April 29-May 2, 2008
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Data and databases
Lars Juhl JensenEMBL Heidelberg
a lot of data
a lot of databases
Duncan Hull, nodalpoint.org
genes and proteins
GenBank
UniProt
PDB
genomes
SGDSaccharomyces Genome Database
TAIRThe Arabidopsis Information Resource
GeneDB
Ensembl
and many others
homology
orthology and paralogy
InParanoid
model organism databases
HomoloGene
Entrez
COGClusters of Orthologous Groups
deep orthology
functional classes
OrthoMCL
high resolution
YOGY
meta-database
eggNOG
multiple resolutions
TreeFam
phylogenetic trees
protein domains
CDDConserved Domain Database
NCBI BLAST
Pfam
high coverage
SMART
signal transduction
InterPro
meta-database
structural classification
SCOP
manual assignments
CATH
automatic assignments
cell cycle
evolution of expression
gene expression
microarrays
dynamics
GEOGene Expression Omnibus
ArrayExpress
cell cycle
Cyclebase.org
SCEPTRANS
interactions
affinity purification
yeast two-hybrid
synthetic lethality
repositories
BioGRID
DIPDatabase of Interacting Proteins
IntAct
MINTMolecular Interactions Database
cell cycle
dynamic network
linear motifs
less than 10 residues
Prosite
ELM
Domino
PepCyber P~Pep
Phospho.ELM
PhosphoSite
PhosPhAt
Phosida
cell cycle
evolution of phosphorylation
complexes
CORUM
Gene Ontology
cell cycle
regulation of assembly
pathways
KEGG
broad coverage
iPath
EcoCyc
MetaCyc
metabolism
Reactome
elegant data model
PIDPathway Interaction Database
meta-database
models
BioModels
cell cycle
Cyclonet
CCDB
integration
STRING
benchmarking
transfer by orthology
Bayesian framework
signaling networks
NetworKIN
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