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  1. Covid 19‏‎ (244 revisions)
  2. Optimization examples‏‎ (190 revisions)
  3. GTRD‏‎ (103 revisions)
  4. BioUML wiki‏‎ (94 revisions)
  5. BioUML development history‏‎ (70 revisions)
  6. Optimization problem‏‎ (46 revisions)
  7. Tools Comparison 2022‏‎ (45 revisions)
  8. Flux balance analysis‏‎ (44 revisions)
  9. Parameter identifiability example‏‎ (42 revisions)
  10. BioUML‏‎ (38 revisions)
  11. BioUML - systems biology‏‎ (38 revisions)
  12. Antimony‏‎ (36 revisions)
  13. BioUML development roadmap‏‎ (31 revisions)
  14. BioUML user interface‏‎ (29 revisions)
  15. Sensitivity analysis example‏‎ (27 revisions)
  16. Workflow‏‎ (27 revisions)
  17. Ru.biosoft.bsa (plugin)‏‎ (24 revisions)
  18. Construct composite modules (analysis)‏‎ (23 revisions)
  19. Construct composite modules on tracks (analysis)‏‎ (23 revisions)
  20. Systems biology - model simulation‏‎ (22 revisions)
  21. GTRD statistics‏‎ (22 revisions)
  22. Flux Balance Constraint (analysis)‏‎ (21 revisions)
  23. BioUML server installation‏‎ (20 revisions)
  24. Biouml.plugins.gtrd (plugin)‏‎ (20 revisions)
  25. Diagram document‏‎ (20 revisions)
  26. Ru.biosoft.analysis (plugin)‏‎ (18 revisions)
  27. N-Glycan biosynthesis‏‎ (18 revisions)
  28. Enrichment analysis‏‎ (18 revisions)
  29. ChIPHorde (analysis)‏‎ (18 revisions)
  30. Steady State (analysis)‏‎ (18 revisions)
  31. GTRD comparison‏‎ (18 revisions)
  32. Preprocess raw reads (analysis)‏‎ (18 revisions)
  33. Repository pane‏‎ (17 revisions)
  34. ChIPMunk (analysis)‏‎ (17 revisions)
  35. BioUML web edition‏‎ (17 revisions)
  36. DiChIPHorde (analysis)‏‎ (17 revisions)
  37. Metabolic control analysis example‏‎ (17 revisions)
  38. Sensitivity Analysis‏‎ (17 revisions)
  39. Effector search (analysis)‏‎ (17 revisions)
  40. BioUML workbench‏‎ (17 revisions)
  41. Functional classification (analysis)‏‎ (17 revisions)
  42. BioStore‏‎ (17 revisions)
  43. Biouml.workbench (plugin)‏‎ (16 revisions)
  44. Tools Comparison‏‎ (16 revisions)
  45. MicroRNA aligner (analysis)‏‎ (16 revisions)
  46. Biouml.plugins.ensembl (plugin)‏‎ (16 revisions)
  47. Gene features (analysis)‏‎ (16 revisions)
  48. Systems biology - model import‏‎ (16 revisions)
  49. Read counter (analysis)‏‎ (16 revisions)
  50. Regulator search (analysis)‏‎ (16 revisions)
  51. Install TRANSFAC(R) database (analysis)‏‎ (16 revisions)
  52. Metabolic Control Analysis‏‎ (16 revisions)
  53. Install TRANSPATH(R) database (analysis)‏‎ (16 revisions)
  54. Copy folder (analysis)‏‎ (16 revisions)
  55. Ru.biosoft.access (plugin)‏‎ (16 revisions)
  56. Nonlinear Model (analysis)‏‎ (16 revisions)
  57. Composite module to proteins (analysis)‏‎ (16 revisions)
  58. Convert table (analysis)‏‎ (16 revisions)
  59. Linear Shifted Model (analysis)‏‎ (16 revisions)
  60. Analysis of Cis-Regulatory Modules (analysis)‏‎ (15 revisions)
  61. Convert table to track (analysis)‏‎ (15 revisions)
  62. Apply state to diagram (analysis)‏‎ (15 revisions)
  63. Filter one track by another (analysis)‏‎ (15 revisions)
  64. Chromosome enrichment (analysis)‏‎ (15 revisions)
  65. SDE model (analysis)‏‎ (15 revisions)
  66. Filter table (analysis)‏‎ (15 revisions)
  67. Ru.biosoft.proteome (plugin)‏‎ (15 revisions)
  68. Gene overlap statistics (analysis)‏‎ (15 revisions)
  69. Filter track by condition (analysis)‏‎ (15 revisions)
  70. Export element (analysis)‏‎ (15 revisions)
  71. Visualize results (analysis)‏‎ (15 revisions)
  72. Creasemarks analysis‏‎ (15 revisions)
  73. Venn diagrams (analysis)‏‎ (15 revisions)
  74. DiChIPMunk (analysis)‏‎ (15 revisions)
  75. Site distribution (analysis)‏‎ (15 revisions)
  76. Landing‏‎ (15 revisions)
  77. Track statistics (analysis)‏‎ (15 revisions)
  78. GeneXplain‏‎ (15 revisions)
  79. BioUML workbench installation‏‎ (15 revisions)
  80. Track to gene set (analysis)‏‎ (15 revisions)
  81. Stoichiometric Matrix (analysis)‏‎ (15 revisions)
  82. Features‏‎ (15 revisions)
  83. Mutation effect (analysis)‏‎ (15 revisions)
  84. Site search on gene set (analysis)‏‎ (15 revisions)
  85. Simulation analysis‏‎ (15 revisions)
  86. Site search on track (analysis)‏‎ (15 revisions)
  87. ChIP-seq peak profile (analysis)‏‎ (14 revisions)
  88. Reactions Analysis‏‎ (14 revisions)
  89. Validate Experiments (analysis)‏‎ (14 revisions)
  90. Convert table via homology (analysis)‏‎ (14 revisions)
  91. Cluster analysis by K-means (analysis)‏‎ (14 revisions)
  92. Merge track statistics (analysis)‏‎ (14 revisions)
  93. Gene set to track (analysis)‏‎ (14 revisions)
  94. Affymetrix normalization (analysis)‏‎ (14 revisions)
  95. Covid 19 parameters‏‎ (14 revisions)
  96. Run MACS 1.4.0 on ChiP-Seq (analysis)‏‎ (14 revisions)
  97. Biouml.plugins.chipmunk (plugin)‏‎ (14 revisions)
  98. Cluster by shortest path (analysis)‏‎ (14 revisions)
  99. Site counts in repeats (analysis)‏‎ (14 revisions)
  100. Annotate track with genes (analysis)‏‎ (14 revisions)
  101. Agilent normalization (analysis)‏‎ (14 revisions)
  102. Create DAS track (analysis)‏‎ (14 revisions)
  103. Track coverage (analysis)‏‎ (14 revisions)
  104. Compare Experiments (analysis)‏‎ (14 revisions)
  105. BioNetGen‏‎ (14 revisions)
  106. Biouml.plugins.creasemarks (plugin)‏‎ (14 revisions)
  107. PASS analysis‏‎ (14 revisions)
  108. Biouml.plugins.transpath (plugin)‏‎ (14 revisions)
  109. Create IPS model (analysis)‏‎ (14 revisions)
  110. Process track with sites (analysis)‏‎ (14 revisions)
  111. Heterozygous site caller (analysis)‏‎ (14 revisions)
  112. Change profile cutoffs (analysis)‏‎ (14 revisions)
  113. Mass Conservation Analysis‏‎ (14 revisions)
  114. Save hits (analysis)‏‎ (14 revisions)
  115. Building Flux Balance DataTable (analysis)‏‎ (14 revisions)
  116. Simulation‏‎ (14 revisions)
  117. Compare site models (analysis)‏‎ (14 revisions)
  118. Save network (analysis)‏‎ (14 revisions)
  119. SNP matching (analysis)‏‎ (14 revisions)
  120. Server ICT‏‎ (14 revisions)
  121. Create folder (analysis)‏‎ (13 revisions)
  122. Systems biology - manual model construction‏‎ (13 revisions)
  123. Ru.biosoft.workbench (plugin)‏‎ (13 revisions)
  124. Biouml.plugins.enrichment (plugin)‏‎ (13 revisions)
  125. Illumina normalization (analysis)‏‎ (13 revisions)
  126. Site search result optimization (analysis)‏‎ (13 revisions)
  127. Genome coverage (analysis)‏‎ (13 revisions)
  128. Select table columns (analysis)‏‎ (13 revisions)
  129. Site search summary (analysis)‏‎ (13 revisions)
  130. Run MACS 1.3.7 on ChiP-Seq (analysis)‏‎ (13 revisions)
  131. Create weight matrix model (analysis)‏‎ (13 revisions)
  132. Biouml.plugins.chemoinformatics (plugin)‏‎ (13 revisions)
  133. Bowtie (analysis)‏‎ (13 revisions)
  134. Construct IPS CisModule (analysis)‏‎ (13 revisions)
  135. Annotate table (analysis)‏‎ (13 revisions)
  136. Motif quality analysis‏‎ (13 revisions)
  137. CRC Analysis‏‎ (13 revisions)
  138. Biouml.plugins.transfac (plugin)‏‎ (13 revisions)
  139. Biouml.plugins.cma (plugin)‏‎ (13 revisions)
  140. Join several tables (analysis)‏‎ (13 revisions)
  141. Biouml.plugins.bindingregions (plugin)‏‎ (13 revisions)
  142. Correlation Analysis‏‎ (13 revisions)
  143. Create profile from gene table (analysis)‏‎ (13 revisions)
  144. IPS motif discovery (analysis)‏‎ (13 revisions)
  145. Join tracks (analysis)‏‎ (13 revisions)
  146. Create Match model (analysis)‏‎ (13 revisions)
  147. Ru.biosoft.table (plugin)‏‎ (13 revisions)
  148. Convert site models to proteins (analysis)‏‎ (13 revisions)
  149. Adaptive simulated annealing (analysis)‏‎ (13 revisions)
  150. Biouml.plugins.bkl (plugin)‏‎ (13 revisions)
  151. Biouml.plugins.modelreduction (plugin)‏‎ (13 revisions)
  152. Genome Browser json‏‎ (13 revisions)
  153. Add expression values (analysis)‏‎ (13 revisions)
  154. Biouml.plugins.endonet (plugin)‏‎ (12 revisions)
  155. Biouml.plugins.cellml (plugin)‏‎ (12 revisions)
  156. Biouml.plugins.pass (plugin)‏‎ (12 revisions)
  157. Manual parameter fitting‏‎ (12 revisions)
  158. Biouml.plugins.go (plugin)‏‎ (12 revisions)
  159. Upload from FTP (analysis)‏‎ (12 revisions)
  160. Biouml.plugins.sbml (plugin)‏‎ (12 revisions)
  161. Ru.biosoft.server (plugin)‏‎ (12 revisions)
  162. GeneNet‏‎ (12 revisions)
  163. GTRD Workflow‏‎ (12 revisions)
  164. Fastq mcf‏‎ (12 revisions)
  165. Join table (analysis)‏‎ (12 revisions)
  166. Biouml.plugins.bionetgen (plugin)‏‎ (12 revisions)
  167. Biouml.plugins.das (plugin)‏‎ (12 revisions)
  168. Biouml.plugins.reactome (plugin)‏‎ (12 revisions)
  169. Biouml.plugins.bowtie (plugin)‏‎ (12 revisions)
  170. Biouml.plugins.keynodes (plugin)‏‎ (12 revisions)
  171. Biouml.plugins.simulation (plugin)‏‎ (12 revisions)
  172. Galaxy installation‏‎ (11 revisions)
  173. Hadoop‏‎ (11 revisions)
  174. Fold-Change calculation (analysis)‏‎ (11 revisions)
  175. Creating Galaxy tool‏‎ (11 revisions)
  176. Tutorials‏‎ (11 revisions)
  177. Map to Transpath (analysis)‏‎ (11 revisions)
  178. Biouml.plugins.fbc (plugin)‏‎ (11 revisions)
  179. Biouml.plugins.genemodels (plugin)‏‎ (11 revisions)
  180. ChIP-seq Analysis‏‎ (11 revisions)
  181. Information box‏‎ (11 revisions)
  182. Cellular genetic algorithm (analysis)‏‎ (10 revisions)
  183. Up and Down Identification (analysis)‏‎ (10 revisions)
  184. Ru.biosoft.plugins.javascript (plugin)‏‎ (10 revisions)
  185. Evolution strategy (SRES) (analysis)‏‎ (10 revisions)
  186. Biouml.plugins.softberry (plugin)‏‎ (10 revisions)
  187. GLBSOLVE (analysis)‏‎ (10 revisions)
  188. Analyze promoters (GTRD) (workflow)‏‎ (10 revisions)
  189. Biouml.plugins.optimization (plugin)‏‎ (10 revisions)
  190. Presentations‏‎ (10 revisions)
  191. BioUML team‏‎ (10 revisions)
  192. Particle swarm optimization (analysis)‏‎ (10 revisions)
  193. Hypergeometric analysis‏‎ (10 revisions)
  194. Meta analysis‏‎ (10 revisions)
  195. Biouml.plugins.expression (plugin)‏‎ (10 revisions)
  196. Gene set enrichment analysis (Affymetrix probes) (workflow)‏‎ (10 revisions)
  197. Join diagrams (analysis)‏‎ (10 revisions)
  198. Biouml.plugins.microarray (plugin)‏‎ (10 revisions)
  199. Ru.biosoft.galaxy (plugin)‏‎ (10 revisions)
  200. Ensembl installation‏‎ (10 revisions)
  201. Biouml.plugins.sedml (plugin)‏‎ (10 revisions)
  202. Gene set enrichment analysis (Illumina probes) (workflow)‏‎ (10 revisions)
  203. Biouml.plugins.illumina (plugin)‏‎ (10 revisions)
  204. Extend network (analysis)‏‎ (10 revisions)
  205. Biouml.plugins.kegg (plugin)‏‎ (10 revisions)
  206. Ru.biosoft.analysis.optimization (plugin)‏‎ (10 revisions)
  207. Biouml.plugins.ginsim (plugin)‏‎ (10 revisions)
  208. Quadratic Hill-climbing (analysis)‏‎ (10 revisions)
  209. Polynomial Regression analysis‏‎ (10 revisions)
  210. Ru.biosoft.plugins.jri (plugin)‏‎ (9 revisions)
  211. Create matrix by mixture of normal components (analysis)‏‎ (9 revisions)
  212. Biouml.plugins.sabiork (plugin)‏‎ (9 revisions)
  213. Biouml.plugins.expasy (plugin)‏‎ (9 revisions)
  214. Mapping to ontologies for multiple gene sets (workflow)‏‎ (9 revisions)
  215. Compute differentially expressed genes (Affymetrix probes) (workflow)‏‎ (9 revisions)
  216. Steady State Examples‏‎ (9 revisions)
  217. Biouml.plugins.sbw (plugin)‏‎ (9 revisions)
  218. BioUML exceptions‏‎ (9 revisions)
  219. Ru.biosoft.graph (plugin)‏‎ (9 revisions)
  220. Method (extension point)‏‎ (9 revisions)
  221. Diagram (element type)‏‎ (9 revisions)
  222. CWL‏‎ (9 revisions)
  223. MGL‏‎ (9 revisions)
  224. Ru.biosoft.templates (plugin)‏‎ (9 revisions)
  225. Databases‏‎ (9 revisions)
  226. Analysis method development‏‎ (9 revisions)
  227. Ru.biosoft.math (plugin)‏‎ (9 revisions)
  228. Mapping to ontologies (TRANSPATH(R)) (workflow)‏‎ (9 revisions)
  229. R installation‏‎ (9 revisions)
  230. SBGN extension‏‎ (9 revisions)
  231. Biomodels‏‎ (9 revisions)
  232. Host object (extension point)‏‎ (9 revisions)
  233. Biouml.plugins.obo (plugin)‏‎ (8 revisions)
  234. Rbiouml‏‎ (8 revisions)
  235. Com.developmentontheedge.server (plugin)‏‎ (8 revisions)
  236. Biouml.plugins.lucene (plugin)‏‎ (8 revisions)
  237. ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)‏‎ (8 revisions)
  238. Defines.js‏‎ (8 revisions)
  239. Biouml.plugins.gne (plugin)‏‎ (8 revisions)
  240. Com.developmentontheedge.util (plugin)‏‎ (8 revisions)
  241. Diagram view part (extension point)‏‎ (8 revisions)
  242. Biouml.plugins.stochastic (plugin)‏‎ (8 revisions)
  243. Analyze promoters (TRANSFAC(R)) (workflow)‏‎ (8 revisions)
  244. Ru.biosoft.works (plugin)‏‎ (8 revisions)
  245. Biouml.plugins.chebi (plugin)‏‎ (8 revisions)
  246. ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)‏‎ (8 revisions)
  247. Descrete events‏‎ (8 revisions)
  248. Mapping to ontologies for multiple gene sets (TRANSPATH(R)) (workflow)‏‎ (8 revisions)
  249. Biouml.plugins.agentmodeling (plugin)‏‎ (8 revisions)
  250. Biouml.plugins.matlab (plugin)‏‎ (8 revisions)

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