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Previous page (1-dimensional arterial tree model)
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1-dimensional arterial tree model
3D viewer
AUC Estimation For meta-cluster track (analysis)
About dialog (extension point)
Acknowledgements
Adaptive simulated annealing (analysis)
Add calculated column (analysis)
Add expression values (analysis)
Add genes from CMA (analysis)
Add reactants (analysis)
Affymetrix CEL file
Affymetrix normalization (analysis)
Agilent microarray file
Agilent normalization (analysis)
Algebraic steady state (analysis)
Analyses (extension point)
Analysis (element type)
Analysis method development
Analysis of Binding Regions (analysis)
Analysis of Cis-Regulatory Modules (analysis)
Analyze SNP list (GTRD) (workflow)
Analyze SNP list (TRANSFAC(R)) (workflow)
Analyze any DNA sequence, EMBL (workflow)
Analyze any DNA sequence, Fasta (workflow)
Analyze any DNA sequence, GeneBank (workflow)
Analyze any DNA sequence (GTRD) (workflow)
Analyze any DNA sequence (TRANSFAC(R)) (workflow)
Analyze any DNA sequence for site enrichment (GTRD) (workflow)
Analyze any DNA sequence for site enrichment (TRANSFAC(R)) (workflow)
Analyze miRNA target enrichment (analysis)
Analyze promoters (GTRD) (workflow)
Analyze promoters (TRANSFAC(R)) (workflow)
Annotate diagram (analysis)
Annotate table (analysis)
Annotate track with genes (analysis)
Annotation (extension point)
Antimony
Antimony (file format)
Application log (viewpart)
Apply CMA model to tracks (analysis)
Apply events (analysis)
Apply state to diagram (analysis)
ArticleComparator (analysis)
ArticleTrackCreator (analysis)
Autosome.Ru
BAM filter multi-hits (analysis)
BAM filter strand specific (analysis)
BDK
BED format
BPMN
Beans (extension point)
Binding regions summary (analysis)
BioBlend
BioCloudCentral
BioGears
BioHub
BioNetGen
BioNetGen language format
BioPAX file
BioStore
BioUML
BioUML - systems biology
BioUML Development Kit
BioUML Development history
BioUML Simulation result (file format)
BioUML development history
BioUML development roadmap
BioUML exceptions
BioUML format
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BioUML overview
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BioUML server installation
BioUML team
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BioUML web client
BioUML web edition
BioUML wiki
BioUML workbench
BioUML workbench installation
Biohub (extension point)
Biohub (host object)
Biomodels
Biopath
Biouml.plugins.affymetrix (plugin)
Biouml.plugins.agentmodeling (plugin)
Biouml.plugins.agilent (plugin)
Biouml.plugins.antimony (plugin)
Biouml.plugins.bindingregions (plugin)
Biouml.plugins.bionetgen (plugin)
Biouml.plugins.biopax (plugin)
Biouml.plugins.bkl (plugin)
Biouml.plugins.bowtie (plugin)
Biouml.plugins.ccsignature (plugin)
Biouml.plugins.cellml (plugin)
Biouml.plugins.chebi (plugin)
Biouml.plugins.chemoinformatics (plugin)
Biouml.plugins.chipmunk (plugin)
Biouml.plugins.cma (plugin)
Biouml.plugins.creasemarks (plugin)
Biouml.plugins.cytoscape (plugin)
Biouml.plugins.das (plugin)
Biouml.plugins.download (plugin)
Biouml.plugins.dropbox (plugin)
Biouml.plugins.endonet (plugin)
Biouml.plugins.enrichment (plugin)
Biouml.plugins.ensembl (plugin)
Biouml.plugins.expasy (plugin)
Biouml.plugins.expression (plugin)
Biouml.plugins.fbc (plugin)
Biouml.plugins.genemodels (plugin)
Biouml.plugins.genenet (plugin)
Biouml.plugins.geneways (plugin)
Biouml.plugins.genomeenhancer (plugin)
Biouml.plugins.ginsim (plugin)
Biouml.plugins.glycan (plugin)
Biouml.plugins.gne (plugin)
Biouml.plugins.go (plugin)
Biouml.plugins.googledrive (plugin)
Biouml.plugins.graphml (plugin)
Biouml.plugins.gtrd (plugin)
Biouml.plugins.gxl (plugin)
Biouml.plugins.hemodynamics (plugin)
Biouml.plugins.illumina (plugin)
Biouml.plugins.kegg (plugin)
Biouml.plugins.keynodes (plugin)
Biouml.plugins.lucene (plugin)
Biouml.plugins.machinelearning (plugin)
Biouml.plugins.matlab (plugin)
Biouml.plugins.metabolics (plugin)
Biouml.plugins.microarray (plugin)
Biouml.plugins.mirbase (plugin)
Biouml.plugins.miriam (plugin)
Biouml.plugins.mirprom (plugin)
Biouml.plugins.modelreduction (plugin)
Biouml.plugins.node (plugin)
Biouml.plugins.obo (plugin)
Biouml.plugins.optimization (plugin)
Biouml.plugins.pass (plugin)
Biouml.plugins.pathfinder (plugin)
Biouml.plugins.perfectosape (plugin)
Biouml.plugins.pharm (plugin)
Biouml.plugins.proteinmodel (plugin)
Biouml.plugins.psimi (plugin)
Biouml.plugins.reactome.biohub (plugin)
Biouml.plugins.reactome (plugin)
Biouml.plugins.research (plugin)
Biouml.plugins.riboseqArticleResult (plugin)
Biouml.plugins.riboseq (plugin)
Biouml.plugins.sabiork (plugin)
Biouml.plugins.sbgn (plugin)
Biouml.plugins.sbml (plugin)
Biouml.plugins.sbw (plugin)
Biouml.plugins.sedml (plugin)
Biouml.plugins.seek (plugin)
Biouml.plugins.server (plugin)
Biouml.plugins.simulation-test (plugin)
Biouml.plugins.simulation (plugin)
Biouml.plugins.softberry (plugin)
Biouml.plugins.stochastic (plugin)
Biouml.plugins.svg (plugin)
Biouml.plugins.test (plugin)
Biouml.plugins.transfac (plugin)
Biouml.plugins.transpath (plugin)
Biouml.plugins.uniprot (plugin)
Biouml.plugins.users (plugin)
Biouml.plugins.wiki (plugin)
Biouml.workbench.graph (plugin)
Biouml.workbench (plugin)
Bioumlsim
Blast alignment coverage (analysis)
Bowtie (analysis)
Breakdancer output (file format)
Bsa (host object)
BuildASiteOffsetTable (analysis)
BuildProfileModel (analysis)
Building Flux Balance DataTable (analysis)
C-tau
CMA Result Statistic (analysis)
CNVnator genotype output (file format)
COVID-19 parameters for Intestine
COVID-19 parameters for Lung
COVID-19 parameters for Nasopharynx
CRC Analysis
CRISPR Cas9 and specific oligonucleotides (analysis)
CR cluster selector (analysis)
CWL
Calculate CMA regulation (analysis)
Calculate TFs regulatory score (analysis)
Calculate keynodes ranks (analysis)
Calculate weighted mutation score (analysis)
Categories (reference type)
Categories - BKL
Categories - ExPASy
Categories - GTRD
Categories - Gene ontology
Cdk (host object)
CellML (file format)
Cell - EndoNet
Cell type specific TFBS prediction
Cellular genetic algorithm (analysis)
ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)
ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)
ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow)
ChIP-Seq - Identify and classify target genes (TRANSPATH(R)) (workflow)
ChIP-Seq - Identify and classify target genes (workflow)
ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R)) (workflow)
ChIP-Seq characteristics distribution (analysis)
ChIP-Seq peaks clusterization (analysis)
ChIP-seq Analysis
ChIP-seq Quality control analysis
ChIP-seq peak profile (analysis)
ChIP-seq peaks - GTRD
ChIPHorde (analysis)
ChIPMunk (analysis)
ChIPMunk (perspective)
ChIP experiment - GTRD
Change diagram (analysis)
Change profile cutoffs (analysis)
Check Workflow consistency (analysis)
Check quotas (analysis)
Chipmunk (host object)
ChromatinInfo table creation (analysis)
Chromosome enrichment (analysis)
Cis-module identification (analysis)
Cis-module sets near given genes (analysis)
Cistrom construction (analysis)
Classification analysis
Classification analysis advanced (analysis)
Classification hub
Clean up SQL database (analysis)
CloudBioLinux
CloudMan
Cluster analysis
Cluster analysis by K-means (analysis)
Cluster by path (analysis)
Cluster by shortest path (analysis)
Cluster track (analysis)
Collaborative diagram editing
Colon cancer signature2 (analysis)
Colon cancer signature (analysis)
Color space to nucleotide (analysis)
Com.developmentontheedge.beans (plugin)
Com.developmentontheedge.server (plugin)
Com.developmentontheedge.util (plugin)
Combined track
Common and IPS scores correlation (analysis)
Common class (extension point)
Compare Experiments (analysis)
Compare TFBS mutations (analysis)
Compare analysis results (analysis)
Compare site models (analysis)
Composite module to proteins (analysis)
ComputeProfileSums (analysis)
ComputeTranscriptProfile (analysis)
Compute coverage by window (analysis)
Compute coverage profile (analysis)
Compute differentially expressed genes (Affymetrix probes) (workflow)
Compute differentially expressed genes (Agilent Tox probes) (workflow)
Compute differentially expressed genes (Agilent probes) (workflow)
Compute differentially expressed genes (Illumina probes) (workflow)
Compute differentially expressed genes using EBarrays (workflow)
Compute differentially expressed genes using Hypergeometric test (Affymetrix probes) (workflow)
Compute differentially expressed genes using Hypergeometric test (Agilent probes) (workflow)
Compute differentially expressed genes using Hypergeometric test (Illumina probes) (workflow)
Compute differentially expressed genes using Limma (workflow)
Compute profile thresholds (analysis)
Construct IPS CisModule (analysis)
Construct composite modules (analysis)
Construct composite modules on track (correlation) (analysis)
Construct composite modules on tracks (analysis)
Construct composite modules on tracks (without site search) (analysis)
Construct composite modules on tracks with keynodes (analysis)
Construct composite modules with keynodes (analysis)
Context item (extension point)
Continue CMA (analysis)
Contributors
Convert diagram to Transpath (analysis)
Convert diagram to pairs (analysis)
Convert files to tracks (analysis)
Convert genomic BAM to transcriptomic (analysis)
Convert identifiers for multiple gene sets (workflow)
Convert site models to proteins (analysis)
Convert site search summary (analysis)
Convert table (analysis)
Convert table to VCF track (analysis)
Convert table to track (analysis)
Convert table via homology (analysis)
Convert tracks to VCF (analysis)
Copy data element (analysis)
Copy folder (analysis)
Correlation Analysis
Correlations of best sites (analysis)
Count olig frequencies (analysis)
Count reads in transcripts (analysis)
CoverageCheker (analysis)
Coverage Profiles Cutoff (analysis)
Covid-19 Differential Delay Model
Covid 19
Covid 19 parameters
Creasemarks analysis
Create DAS track (analysis)
Create IPS model (analysis)
Create Match model (analysis)
Create custom project (analysis)
Create database from diagram (analysis)
Create flat files (analysis)
Create folder (analysis)
Create matrix by mixture of normal components (analysis)
Create matrix logo (analysis)
Create miRNA promoters (analysis)
Create per TF flat files (analysis)
Create profile from CMA model (analysis)
Create profile from gene table (analysis)
Create profile from matrix library (analysis)
Create profile from site model table (analysis)
Create random track (analysis)
Create state (analysis)
Create tissue-specific promoter track (analysis)
Create transcript region track (analysis)
Create weight matrix model (analysis)
Creating Galaxy tool
Cross-species identification of enriched motifs in promoters, using orthologue information (TRANSFAC(R)) (workflow)
Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow)
Cross cost grid layout
Cytoscape network format
DAE Models examples
DDMoRe consortium
DNase-seq Group and Profile Generation (Previous version) (analysis)
DNase-seq Group and Profile Generation (analysis)
Dannon et al. Covid-19 transmission in England
Danon et al. Covid-19 transmission in England
Das (host object)
DataFilter (host object)
Data (host object)
Data collection listener (extension point)
Data matrix operations (analysis)
Databases
Databases installation
Default (perspective)
Defines.js
Descrete events
Developed models
DiChIPHorde (analysis)
DiChIPMunk (analysis)
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