Features - Revision history

Stan.lo@dote.ru: /* See also */

2013-06-25T07:53:57Z

‎See also

2013-06-25T07:08:43Z

‎Databases

2013-06-24T07:06:27Z

‎See also

2013-06-19T06:11:50Z

‎Search tools

2013-06-19T06:10:42Z

‎See also

2013-05-17T10:34:33Z

wikipedia: namespace used

2013-05-08T04:06:21Z

{{R}} - ‎Supported standards

2013-05-07T09:56:17Z

Links to optimization methods - ‎Parameters fitting

2013-05-04T05:52:52Z

Link to workflows - ‎Other features

2013-05-04T05:52:07Z

BSA link fixed - ‎Analyses

@@ Line 127: / Line 127: @@
 * [[BioUML]]
 * <span class="plainlinks">[http://wiki.biouml.org/index.php/Category:Analyses Analyses]</span>
 * [[Workflows]]

@@ Line 25: / Line 25: @@
 It works with the main biological databases:
-* catalogues: Ensembl, UniProt, ChEBI, GO;
+* catalogues: [[Ensembl]], [http://www.uniprot.org/ UniProt], [http://www.ebi.ac.uk/chebi/ ChEBI], [[Gene Ontology database|GO]];
-* pathways: KEGG, Reactome, EHMN, BioModels, SABIO-RK, TRANSPATH, EndoNet, BMOND.
+* pathways: [http://www.genome.jp/kegg/ KEGG], [[Reactome]], [http://www.ehmn.bioinformatics.ed.ac.uk/ EHMN], [[Biomodels]], [http://sabio.villa-bosch.de/ SABIO-RK], [http://genexplain.com/transpath-1 TRANSPATH], [http://endonet.bioinf.med.uni-goettingen.de/ EndoNet], [[BMOND]].
-−
 == Search tools ==

@@ Line 129: / Line 129: @@
 * <span class="plainlinks">[http://wiki.biouml.org/index.php/Category:Analyses Analyses]</span>
 * [[Workflows]]
 * [[Search tools]]
 * [[BioUML development history]]

@@ Line 31: / Line 31: @@
 BioUML provides powerful search possibilities with such tools as:
-* [[full text search]] ([http://lucene.apache.org/ Apache Lucene] is used),
+* [[Information box#Search|full text search]] ([http://lucene.apache.org/ Apache Lucene] is used),
 * [[graph search]] - finds related pathway components and presents results as an editable graph.
-−
 ==Graph layout engine==

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 * <span class="plainlinks">[http://wiki.biouml.org/index.php/Category:Analyses Analyses]</span>
 * [[Workflows]]
 * [[BioUML development history]]

@@ Line 88: / Line 88: @@
 ==Genome browser==
-* uses [http://en.wikipedia.org/wiki/Ajax_(programming) AJAX] and [http://en.wikipedia.org/wiki/Canvas_element HTML5 <canvas>] technologies (BioUML web edition);
+* uses [[wikipedia:Ajax (programming)|AJAX]] and [[wikipedia:Canvas element|HTML5 <canvas>]] technologies ([[BioUML web edition]]);
 * interactive - dragging, semantic zoom;
 * DAS support (Distributed Annotation System);

@@ Line 20: / Line 20: @@
-BioUML also supports '''JavaScript''' (script console, JavaSsript editor, JavaScript debugger (BioUML workbench only), JavaScript preprocessor (allows to embed easily R expressions), '''R''' (connect to R on local or remote machine, convert BioUML data to R and save R results as BioUML data, R graphics support, R preprocessor for JavaScript) and '''SQL''' (SQL console, direct SQL access to analysis results tables).
+BioUML also supports '''JavaScript''' (script console, JavaSsript editor, JavaScript debugger (BioUML workbench only), JavaScript preprocessor (allows to embed easily R expressions), '''{{R}}''' (connect to R on local or remote machine, convert BioUML data to R and save R results as BioUML data, R graphics support, R preprocessor for JavaScript) and '''SQL''' (SQL console, direct SQL access to analysis results tables).
-−
 == Databases ==

@@ Line 78: / Line 78: @@
 * constraint support;
 * different optimization methods:
-** Adaptive Simulating Annealing,
+** [[Adaptive simulated annealing (analysis)|Adaptive Simulating Annealing]],
-** Cellular genetic algorithm,
+** [[Cellular genetic algorithm (analysis)|Cellular genetic algorithm]],
-** Evolution strategy (SRES),
+** [[Evolution strategy (SRES) (analysis)|Evolution strategy (SRES)]],
-** GLBSOLVE,
+** [[GLBSOLVE (analysis)|GLBSOLVE]],
-** Particle swarm optimization,
+** [[Particle swarm optimization (analysis)|Particle swarm optimization]],
-** Quadratic Hill-climbing;
+** [[Quadratic Hill-climbing (analysis)|Quadratic Hill-climbing]];
 * optimization and parallelization of computations;
 * JavaScript API for parameters fitting;
 ==Genome browser==

@@ Line 109: / Line 109: @@
 ==Other features==
-BioUML also allows for '''workflows, reproducible research'''
+BioUML also allows for '''[[workflows]], reproducible research'''
 * actions journal,
 * Analysis,
@@ Line 125: / Line 125: @@
 * Variables
 * ODE(model as differential equation system).
 ==See also==

@@ Line 101: / Line 101: @@
 BioUML utilizes a wide variety of '''methods for data analyses''':
-* [[:BSA (analyses group)|biosequence analysis]],
+* [[:Category:BSA (analyses group)|biosequence analysis]],
 * [[:Category:Optimization (analyses group)|model optimization]],
 * [[:Category:Statistics (analyses group)|statistics]],