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- IPS prediction (analysis) (5 revisions)
- Merge binding regions for cell-lines (analysis) (5 revisions)
- File (element type) (5 revisions)
- Gene set enrichment analysis - select a classification (Gene table) (workflow) (5 revisions)
- Biouml.plugins.node (plugin) (5 revisions)
- Gene Ontology (5 revisions)
- Matching BioHub (5 revisions)
- TRRD (5 revisions)
- Unspecified (reference type) (5 revisions)
- Download (5 revisions)
- Project (5 revisions)
- Enrichment (host object) (5 revisions)
- Biouml.plugins.riboseq (plugin) (5 revisions)
- BioBlend (5 revisions)
- GO installation (5 revisions)
- Virtual rat (5 revisions)
- Combined track (5 revisions)
- Analyze SNP list (TRANSFAC(R)) (workflow) (5 revisions)
- Table (element type) (5 revisions)
- Cis-module identification (analysis) (5 revisions)
- Systems biology - model export (5 revisions)
- Common and IPS scores correlation (analysis) (5 revisions)
- Differential expression with DESeq (analysis) (5 revisions)
- Substances - ChEBI (5 revisions)
- Biouml.plugins.perfectosape (plugin) (5 revisions)
- Visual modeling (5 revisions)
- SDF file (5 revisions)
- Categories - GTRD (5 revisions)
- Fastq format (5 revisions)
- Gathering genome statistics (analysis) (5 revisions)
- Cluster track (analysis) (5 revisions)
- Pathways - Reactome (5 revisions)
- Distinct TF classes (analysis) (5 revisions)
- Data (host object) (5 revisions)
- Pathways - Transpath (5 revisions)
- BioNetGen language format (5 revisions)
- Acknowledgements (5 revisions)
- Institute of Systems Biology (5 revisions)
- Prepare Search by regulation (analysis) (5 revisions)
- Proteins - GenBank (5 revisions)
- Ru.biosoft.graphics (plugin) (5 revisions)
- GeneXplain GmbH (6 revisions)
- Non-merged ChIP-Seq tracks summary (analysis) (6 revisions)
- BioUML server (6 revisions)
- Interval format (6 revisions)
- Search tools (6 revisions)
- Text file (6 revisions)
- Extract ribosomal RNA (analysis) (6 revisions)
- Modular model of the human CVS v.1 (6 revisions)
- CloudMan (6 revisions)
- Systems biology - Get started (6 revisions)
- Biopath (6 revisions)
- ZIP-archive (file format) (6 revisions)
- Find common effectors in networks (TRANSPATH(R)) (workflow) (6 revisions)
- Text output file generated by R (file format) (6 revisions)
- VAT output (file format) (6 revisions)
- Repository (6 revisions)
- Find master regulators in networks (TRANSPATH(R)) (workflow) (6 revisions)
- Biouml.plugins.affymetrix (plugin) (6 revisions)
- Gene Transfer Format (6 revisions)
- Analyze SNP list (GTRD) (workflow) (6 revisions)
- VCF format (6 revisions)
- Modular modeling (6 revisions)
- Gene expression prediction (6 revisions)
- Proteins - RefSeq (6 revisions)
- HTML file (6 revisions)
- Matrix (element type) (6 revisions)
- Probes - Affymetrix (6 revisions)
- Image file (6 revisions)
- General Feature Format (6 revisions)
- Varscan output (file format) (6 revisions)
- Biouml.plugins.pharm (plugin) (6 revisions)
- Biouml.plugins.mirbase (plugin) (6 revisions)
- Pindel output (file format) (6 revisions)
- Transcripts - RefSeq (6 revisions)
- Tabular (file format) (6 revisions)
- Wiggle format (6 revisions)
- Patient-specific cardiovascular model (6 revisions)
- Find master regulators for multiple gene sets (TRANSPATH(R)) (workflow) (6 revisions)
- Count olig frequencies (analysis) (6 revisions)
- Viewpart (6 revisions)
- ROC curves for best sites union (analysis) (7 revisions)
- C-tau (7 revisions)
- TRANSFAC matrices format (7 revisions)
- Proteins - IPI (7 revisions)
- Proteins - UniProt (7 revisions)
- SISSRs output (file format) (7 revisions)
- Graph search (7 revisions)
- Compute differentially expressed genes using Hypergeometric test (Agilent probes) (workflow) (7 revisions)
- TRANSFAC profile (file format) (7 revisions)
- Genome Browser iframe (7 revisions)
- Find common effectors in networks (GeneWays) (workflow) (7 revisions)
- Quasi-steady-state analysis example (7 revisions)
- Find master regulators in networks (GeneWays) (workflow) (7 revisions)
- Compute differentially expressed genes using Hypergeometric test (Illumina probes) (workflow) (7 revisions)
- CNVnator genotype output (file format) (7 revisions)
- Binding regions summary (analysis) (7 revisions)
- SBML(CellDesigner) (file format) (7 revisions)
- Proteins - Reactome (7 revisions)
- Normalize (host object) (7 revisions)
- Perspective (7 revisions)
- Locations of best sites (analysis) (7 revisions)
- Galaxy cloud (7 revisions)
- Genes - Ensembl (7 revisions)
- SBML (file format) (7 revisions)
- Export (extension point) (7 revisions)
- Danon et al. Covid-19 transmission in England (7 revisions)
- Fasta format (7 revisions)
- Genes - Entrez (7 revisions)
- Image (element type) (7 revisions)
- Repository pane toolbar (7 revisions)
- Breakdancer output (file format) (7 revisions)
- Genes - GenBank (7 revisions)
- Biouml.plugins.antimony (plugin) (7 revisions)
- Common class (extension point) (7 revisions)
- Disease - MeSH (7 revisions)
- EMBL format (7 revisions)
- SED-ML file (7 revisions)
- Force directed layout (7 revisions)
- Lucene indexes creation (7 revisions)
- Overall circulation model (7 revisions)
- GenBank format (7 revisions)
- Gene set enrichment analysis (Agilent probes) (workflow) (7 revisions)
- GinSim (file format) (7 revisions)
- Find master regulators for multiple gene sets (GeneWays) (workflow) (7 revisions)
- Correlations of best sites (analysis) (7 revisions)
- ChIP-Seq characteristics distribution (analysis) (7 revisions)
- IPS ROC-curves (analysis) (7 revisions)
- Gene set enrichment analysis (Gene table) (workflow) (7 revisions)
- Expression mapping (7 revisions)
- CellML (file format) (7 revisions)
- SAM or BAM alignment file (7 revisions)
- BED format (7 revisions)
- Mapping to ontologies (Gene table) (workflow) (7 revisions)
- Biouml.plugins.wiki (plugin) (8 revisions)
- Compute differentially expressed genes using Hypergeometric test (Affymetrix probes) (workflow) (8 revisions)
- Ru.biosoft.access.search (plugin) (8 revisions)
- Biouml.plugins.simulation-test (plugin) (8 revisions)
- Biouml.workbench.graph (plugin) (8 revisions)
- Hierarchical layout (8 revisions)
- Biouml.plugins.research (plugin) (8 revisions)
- GC island finder (analysis) (8 revisions)
- Biouml.plugins.obo (plugin) (8 revisions)
- Ru.biosoft.treetable (plugin) (8 revisions)
- Com.developmentontheedge.server (plugin) (8 revisions)
- Transplorer (8 revisions)
- Biouml.plugins.lucene (plugin) (8 revisions)
- ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow) (8 revisions)
- Rbiouml (8 revisions)
- Defines.js (8 revisions)
- Biouml.plugins.gne (plugin) (8 revisions)
- Com.developmentontheedge.util (plugin) (8 revisions)
- Biouml.plugins.chebi (plugin) (8 revisions)
- Diagram view part (extension point) (8 revisions)
- Biouml.plugins.stochastic (plugin) (8 revisions)
- Analyze promoters (TRANSFAC(R)) (workflow) (8 revisions)
- ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow) (8 revisions)
- Biouml.plugins.agentmodeling (plugin) (8 revisions)
- Descrete events (8 revisions)
- Biouml.plugins.matlab (plugin) (8 revisions)
- Biouml.plugins.svg (plugin) (8 revisions)
- Ru.biosoft.works (plugin) (8 revisions)
- Ensembl (8 revisions)
- Biouml.plugins.sbgn (plugin) (8 revisions)
- Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow) (8 revisions)
- Biouml.plugins.test (plugin) (8 revisions)
- Transcripts - Ensembl (8 revisions)
- Biouml.plugins.graphml (plugin) (8 revisions)
- Table document (8 revisions)
- Ru.biosoft.server.servlets (plugin) (8 revisions)
- Mixture of normal components (analysis) (8 revisions)
- ChIP-Seq - Identify and classify target genes (workflow) (8 revisions)
- Upstream analysis (TRANSFAC(R) and GeneWays) (workflow) (8 revisions)
- Ru.biosoft.server.tomcat (plugin) (8 revisions)
- Compute differentially expressed genes (Agilent probes) (workflow) (8 revisions)
- Biouml.plugins.proteinmodel (plugin) (8 revisions)
- ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R)) (workflow) (8 revisions)
- Proteins - Ensembl (8 revisions)
- Biouml.plugins.gxl (plugin) (8 revisions)
- New BioStore (8 revisions)
- BioUML format (8 revisions)
- Upstream analysis (TRANSFAC(R) and TRANSPATH(R)) (workflow) (8 revisions)
- Cross cost grid layout (8 revisions)
- Biouml.plugins.miriam (plugin) (8 revisions)
- Biouml.plugins.uniprot (plugin) (8 revisions)
- Compute differentially expressed genes (Illumina probes) (workflow) (8 revisions)
- Biouml.plugins.genenet (plugin) (8 revisions)
- Biouml.plugins.psimi (plugin) (8 revisions)
- Biouml.plugins.biopax (plugin) (8 revisions)
- Biouml.plugins.hemodynamics (plugin) (8 revisions)
- Ru.biosoft.services (plugin) (8 revisions)
- Biouml.plugins.users (plugin) (8 revisions)
- Biouml.plugins.geneways (plugin) (8 revisions)
- Biouml.plugins.reactome.biohub (plugin) (8 revisions)
- Biouml.plugins.server (plugin) (8 revisions)
- SIF (file format) (8 revisions)
- Databases (9 revisions)
- MGL (9 revisions)
- Analysis method development (9 revisions)
- Ru.biosoft.templates (plugin) (9 revisions)
- Biomodels (9 revisions)
- Ru.biosoft.math (plugin) (9 revisions)
- Mapping to ontologies (TRANSPATH(R)) (workflow) (9 revisions)
- R installation (9 revisions)
- SBGN extension (9 revisions)
- Host object (extension point) (9 revisions)
- Create matrix by mixture of normal components (analysis) (9 revisions)
- Biouml.plugins.sabiork (plugin) (9 revisions)
- Ru.biosoft.plugins.jri (plugin) (9 revisions)
- Biouml.plugins.expasy (plugin) (9 revisions)
- Compute differentially expressed genes (Affymetrix probes) (workflow) (9 revisions)
- Mapping to ontologies for multiple gene sets (workflow) (9 revisions)
- Biouml.plugins.sbw (plugin) (9 revisions)
- BioUML exceptions (9 revisions)
- Diagram (element type) (9 revisions)
- Steady State Examples (9 revisions)
- Ru.biosoft.graph (plugin) (9 revisions)
- Method (extension point) (9 revisions)
- CWL (9 revisions)
- Extend network (analysis) (10 revisions)
- Biouml.plugins.kegg (plugin) (10 revisions)
- Biouml.plugins.ginsim (plugin) (10 revisions)
- Cellular genetic algorithm (analysis) (10 revisions)
- Ru.biosoft.analysis.optimization (plugin) (10 revisions)
- Quadratic Hill-climbing (analysis) (10 revisions)
- Evolution strategy (SRES) (analysis) (10 revisions)
- Biouml.plugins.softberry (plugin) (10 revisions)
- GLBSOLVE (analysis) (10 revisions)
- Analyze promoters (GTRD) (workflow) (10 revisions)
- BioUML team (10 revisions)
- Biouml.plugins.optimization (plugin) (10 revisions)
- Polynomial Regression analysis (10 revisions)
- Up and Down Identification (analysis) (10 revisions)
- Ru.biosoft.plugins.javascript (plugin) (10 revisions)
- Presentations (10 revisions)
- Particle swarm optimization (analysis) (10 revisions)
- Biouml.plugins.expression (plugin) (10 revisions)
- Hypergeometric analysis (10 revisions)
- Meta analysis (10 revisions)
- Biouml.plugins.microarray (plugin) (10 revisions)
- Join diagrams (analysis) (10 revisions)
- Ensembl installation (10 revisions)
- Gene set enrichment analysis (Affymetrix probes) (workflow) (10 revisions)
- Ru.biosoft.galaxy (plugin) (10 revisions)
- Biouml.plugins.sedml (plugin) (10 revisions)
- Biouml.plugins.illumina (plugin) (10 revisions)
- Gene set enrichment analysis (Illumina probes) (workflow) (10 revisions)
- ChIP-seq Analysis (11 revisions)
- Information box (11 revisions)
- Galaxy installation (11 revisions)
- Fold-Change calculation (analysis) (11 revisions)
- Creating Galaxy tool (11 revisions)
- Hadoop (11 revisions)
- Biouml.plugins.fbc (plugin) (11 revisions)
- Map to Transpath (analysis) (11 revisions)
- Tutorials (11 revisions)
- Biouml.plugins.genemodels (plugin) (11 revisions)
- Biouml.plugins.reactome (plugin) (12 revisions)
- Biouml.plugins.bowtie (plugin) (12 revisions)
- Biouml.plugins.keynodes (plugin) (12 revisions)
- Biouml.plugins.simulation (plugin) (12 revisions)
- Biouml.plugins.endonet (plugin) (12 revisions)
- Biouml.plugins.cellml (plugin) (12 revisions)
- Biouml.plugins.pass (plugin) (12 revisions)
- Biouml.plugins.go (plugin) (12 revisions)
- Manual parameter fitting (12 revisions)
- Biouml.plugins.sbml (plugin) (12 revisions)
- Upload from FTP (analysis) (12 revisions)
- GTRD Workflow (12 revisions)
- Fastq mcf (12 revisions)
- Biouml.plugins.bionetgen (plugin) (12 revisions)
- Ru.biosoft.server (plugin) (12 revisions)
- GeneNet (12 revisions)
- Join table (analysis) (12 revisions)
- Biouml.plugins.das (plugin) (12 revisions)
- Biouml.plugins.modelreduction (plugin) (13 revisions)
- Ru.biosoft.table (plugin) (13 revisions)
- Add expression values (analysis) (13 revisions)
- Create folder (analysis) (13 revisions)
- Genome Browser json (13 revisions)
- Biouml.plugins.enrichment (plugin) (13 revisions)
- Ru.biosoft.workbench (plugin) (13 revisions)
- Systems biology - manual model construction (13 revisions)
- Illumina normalization (analysis) (13 revisions)
- Create weight matrix model (analysis) (13 revisions)
- Biouml.plugins.chemoinformatics (plugin) (13 revisions)
- Bowtie (analysis) (13 revisions)
- Site search result optimization (analysis) (13 revisions)
- Construct IPS CisModule (analysis) (13 revisions)
- Select table columns (analysis) (13 revisions)
- Genome coverage (analysis) (13 revisions)
- Annotate table (analysis) (13 revisions)
- Run MACS 1.3.7 on ChiP-Seq (analysis) (13 revisions)
- Site search summary (analysis) (13 revisions)
- CRC Analysis (13 revisions)
- Biouml.plugins.cma (plugin) (13 revisions)
- Biouml.plugins.transfac (plugin) (13 revisions)
- Motif quality analysis (13 revisions)
- Biouml.plugins.bindingregions (plugin) (13 revisions)
- Correlation Analysis (13 revisions)
- Create profile from gene table (analysis) (13 revisions)
- Join several tables (analysis) (13 revisions)
- Create Match model (analysis) (13 revisions)
- Convert site models to proteins (analysis) (13 revisions)
- Adaptive simulated annealing (analysis) (13 revisions)
- IPS motif discovery (analysis) (13 revisions)
- Biouml.plugins.bkl (plugin) (13 revisions)
- Join tracks (analysis) (13 revisions)
- Mass Conservation Analysis (14 revisions)
- Save hits (analysis) (14 revisions)
- Heterozygous site caller (analysis) (14 revisions)
- Save network (analysis) (14 revisions)
- Simulation (14 revisions)
- ChIP-seq peak profile (analysis) (14 revisions)
- SNP matching (analysis) (14 revisions)
- Server ICT (14 revisions)
- Convert table via homology (analysis) (14 revisions)
- Cluster analysis by K-means (analysis) (14 revisions)
- Reactions Analysis (14 revisions)
- Covid 19 parameters (14 revisions)
- Validate Experiments (analysis) (14 revisions)
- Affymetrix normalization (analysis) (14 revisions)
- Merge track statistics (analysis) (14 revisions)
- Biouml.plugins.chipmunk (plugin) (14 revisions)
- Gene set to track (analysis) (14 revisions)
- Cluster by shortest path (analysis) (14 revisions)
- Annotate track with genes (analysis) (14 revisions)
- Create DAS track (analysis) (14 revisions)
- Run MACS 1.4.0 on ChiP-Seq (analysis) (14 revisions)
- Agilent normalization (analysis) (14 revisions)
- Compare Experiments (analysis) (14 revisions)
- BioNetGen (14 revisions)
- Biouml.plugins.creasemarks (plugin) (14 revisions)
- Biouml.plugins.transpath (plugin) (14 revisions)
- Site counts in repeats (analysis) (14 revisions)
- Create IPS model (analysis) (14 revisions)
- Track coverage (analysis) (14 revisions)
- PASS analysis (14 revisions)
- Change profile cutoffs (analysis) (14 revisions)
- Process track with sites (analysis) (14 revisions)
- Building Flux Balance DataTable (analysis) (14 revisions)
- Compare site models (analysis) (14 revisions)
- Track to gene set (analysis) (15 revisions)
- Stoichiometric Matrix (analysis) (15 revisions)
- Mutation effect (analysis) (15 revisions)
- Site search on gene set (analysis) (15 revisions)
- Analysis of Cis-Regulatory Modules (analysis) (15 revisions)
- Convert table to track (analysis) (15 revisions)
- Simulation analysis (15 revisions)
- Site search on track (analysis) (15 revisions)
- Apply state to diagram (analysis) (15 revisions)
- Filter one track by another (analysis) (15 revisions)
- Chromosome enrichment (analysis) (15 revisions)
- Filter table (analysis) (15 revisions)
- SDE model (analysis) (15 revisions)
- Filter track by condition (analysis) (15 revisions)
- Ru.biosoft.proteome (plugin) (15 revisions)
- Export element (analysis) (15 revisions)
- Creasemarks analysis (15 revisions)
- Gene overlap statistics (analysis) (15 revisions)
- Visualize results (analysis) (15 revisions)
- DiChIPMunk (analysis) (15 revisions)
- Venn diagrams (analysis) (15 revisions)
- Landing (15 revisions)
- Site distribution (analysis) (15 revisions)
- BioUML workbench installation (15 revisions)
- Track statistics (analysis) (15 revisions)
- Features (15 revisions)
- GeneXplain (15 revisions)
- Composite module to proteins (analysis) (16 revisions)
- Convert table (analysis) (16 revisions)
- Ru.biosoft.access (plugin) (16 revisions)
- Nonlinear Model (analysis) (16 revisions)
- Biouml.workbench (plugin) (16 revisions)
- Linear Shifted Model (analysis) (16 revisions)
- MicroRNA aligner (analysis) (16 revisions)
- Tools Comparison (16 revisions)
- Biouml.plugins.ensembl (plugin) (16 revisions)
- Gene features (analysis) (16 revisions)
- Systems biology - model import (16 revisions)
- Read counter (analysis) (16 revisions)
- Regulator search (analysis) (16 revisions)
- Copy folder (analysis) (16 revisions)
- Install TRANSFAC(R) database (analysis) (16 revisions)
- Metabolic Control Analysis (16 revisions)
- Install TRANSPATH(R) database (analysis) (16 revisions)
- Repository pane (17 revisions)
- ChIPMunk (analysis) (17 revisions)
- BioUML web edition (17 revisions)
- DiChIPHorde (analysis) (17 revisions)
- BioUML workbench (17 revisions)
- Effector search (analysis) (17 revisions)
- Metabolic control analysis example (17 revisions)
- Sensitivity Analysis (17 revisions)
- Functional classification (analysis) (17 revisions)
- BioStore (17 revisions)
- Preprocess raw reads (analysis) (18 revisions)
- Ru.biosoft.analysis (plugin) (18 revisions)
- Enrichment analysis (18 revisions)
- ChIPHorde (analysis) (18 revisions)
- N-Glycan biosynthesis (18 revisions)
- Steady State (analysis) (18 revisions)
- GTRD comparison (18 revisions)
- BioUML server installation (20 revisions)
- Biouml.plugins.gtrd (plugin) (20 revisions)
- Diagram document (20 revisions)
- Flux Balance Constraint (analysis) (21 revisions)
- Systems biology - model simulation (22 revisions)
- GTRD statistics (22 revisions)
- Construct composite modules (analysis) (23 revisions)
- Construct composite modules on tracks (analysis) (23 revisions)
- Ru.biosoft.bsa (plugin) (24 revisions)
- Workflow (27 revisions)
- Sensitivity analysis example (27 revisions)
- BioUML user interface (29 revisions)
- BioUML development roadmap (31 revisions)
- Antimony (36 revisions)
- BioUML (38 revisions)
- BioUML - systems biology (38 revisions)
- Parameter identifiability example (42 revisions)
- Flux balance analysis (44 revisions)
- Tools Comparison 2022 (45 revisions)
- Optimization problem (46 revisions)
- BioUML development history (70 revisions)
- BioUML wiki (94 revisions)
- GTRD (103 revisions)
- Optimization examples (190 revisions)
- Covid 19 (244 revisions)
