>
Tag
> Links tagged with 'systems biology'

Links tagged with 'systems biology'

RSS FeedCompact ViewList as XMLList as JSON

Found 9 links

Displaying 9 links

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

BioNumbersDatabase Content

http://www.bionumbers.hms.harvard.edu

Literature > Databases

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals biological models cell biology computational biology genetic databases humans molecular biology nucleic acid databases protein databases systems biology theoretical models

BioSystemsDatabase Content

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

Protein > Databases

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals cell membrane computational biology genes genetic databases genomics humans national library of medicine (u.s.) nucleic acid databases protein databases systems biology united states
setsNational Center for Biotechnology Information (NCBI)

FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

KEGGDatabase Content

http://www.genome.ad.jp/kegg

Model Organisms > Databases

The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
4
Average: 4 (1 vote)
tagsalgorithms computational biology genetic databases human genome humans ligands nucleic acid databases pharmaceutical preparations protein databases protein interaction mapping systems biology tertiary protein structure

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

PredUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs

Protein > Interactions, Pathways, Enzymes

PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.

This content is being maintained by cliffzhang.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms artificial intelligence binding sites computational biology conserved sequence molecular models multiprotein complexes protein binding protein conformation protein databases protein interaction domains and motifs protein interaction mapping protein structural homology proteins sequence alignment surface properties systems biology

webPIPSATool Content

http://pipsa.h-its.org

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.

This content is being maintained by wade.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms binding sites biological models chemical models computer simulation electrostatics enzyme activation enzymes kinetics protein binding protein conformation protein interaction mapping proteins research signal transduction static electricity systems biology triose-phosphate isomerase