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remove the "chemical" in reaction networks #40
Description
Trac Ticket #40
component: code
owner: martin
reporter: martin
created: 2014-05-08 16:34:01
milestone:
type: task
version:
keywords:
isn't necessarily always a ''chemical'' reaction network..
comment 1
time: 2014-05-11 17:36:53
author: Martin Scharm martin@binfalse.de
In None:
chemical reaction network -> reaction network [see #40]
still todo: documentation of changes & update web pages
comment 2
time: 2014-05-11 19:28:52
author: martin
Updated _comment0 to 1399836722789648
comment 3
time: 2014-05-11 19:28:52
author: martin
Updated _comment1 to 1399836856501467
comment 4
time: 2014-05-11 19:28:52
author: martin
Updated _comment2 to 1399836905016715
comment 5
time: 2014-05-11 19:28:52
author: martin
Updated _comment3 to 1399837004780317
comment 6
time: 2014-05-11 19:28:52
author: martin
Updated _comment4 to 1399837691794576
comment 7
time: 2014-05-11 19:28:52
author: martin
Updated _comment5 to 1399837881270811
comment 8
time: 2014-05-11 19:28:52
author: martin
todo: search for chemical and crn (something else?)
correct modifier resolution in CRN #18CRN entities shouldn't use SBO #16/ReactionNetwork/HierarchyNetworkbives-sbml:add independent markup #7http://sems.uni-rostock.de/trac/bives/wiki//BivesOnCommandLinehttp://sems.uni-rostock.de/trac/bivesws/wiki//BivesWebServiceUsagehttp://sems.uni-rostock.de/trac/bivesws-client/wiki//ComparisonRequest
also grep sources:
#!bash
egrep -rni "crn|chemical" src | sed 's/:/ /' | awk '{print $1}' | sort | uniq
- /src/main/java/de/unirostock/sems/bives/algorithm/GraphProducer.java
- /src/main/java/de/unirostock/sems/bives/api/Diff.java
- /src/main/java/de/unirostock/sems/bives/api/RegularDiff.java
- /src/main/java/de/unirostock/sems/bives/api/Single.java
- /src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslatorDot.java
- /src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslatorGraphML.java
- /src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslator.java
- /src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslatorJson.java
- /src/main/java/de/unirostock/sems/bives/ds/ontology/SBOTerm.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkCompartment.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkEntity.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetwork.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkReaction.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkSubstance.java
- /src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkSubstanceRef.java
- /src/main/java/de/unirostock/sems/bives/markup/MarkupDocument.java
- /src/test/java/de/unirostock/sems/bives/TestGraphs.java
- cellml package:
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/main/java/de/unirostock/sems/bives/cellml/algorithm/CellMLGraphProducer.java
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/main/java/de/unirostock/sems/bives/cellml/api/CellMLDiff.java
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/main/java/de/unirostock/sems/bives/cellml/api/CellMLSingle.java
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/main/java/de/unirostock/sems/bives/cellml/parser/CellMLComponent.java
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/test/java/de/unirostock/sems/TestDiffinterpreter.java
- http://sems.uni-rostock.de/trac/bives-cellml/wiki//src/test/java/de/unirostock/sems/TestForChaste.java
- SBML package:
- http://sems.uni-rostock.de/trac/bives-sbml/wiki//src/main/java/de/unirostock/sems/bives/sbml/algorithm/SBMLConnector.java
- http://sems.uni-rostock.de/trac/bives-sbml/wiki//src/main/java/de/unirostock/sems/bives/sbml/algorithm/SBMLGraphProducer.java
- http://sems.uni-rostock.de/trac/bives-sbml/wiki//src/main/java/de/unirostock/sems/bives/sbml/api/SBMLDiff.java
- http://sems.uni-rostock.de/trac/bives-sbml/wiki//src/main/java/de/unirostock/sems/bives/sbml/api/SBMLSingle.java
- http://sems.uni-rostock.de/trac/bives-sbml/wiki//src/test/java/de/unirostock/sems/TestComparison.java
- framework:
- http://sems.uni-rostock.de/trac/bives/wiki//src/main/java/de/unirostock/sems/bives/Main.java
- http://sems.uni-rostock.de/trac/bives/wiki//src/test/java/de/unirostock/sems/bives/test/sysmoseek/ManchesterTest.java
- web service:
- http://sems.uni-rostock.de/trac/bivesws/wiki//src/main/java/de/unirostock/sems/bives/webservice/WebQueryExecuter.java
- http://sems.uni-rostock.de/trac/bivesws/wiki//src/main/webapp/WEB-INF/Usage.jsp
- http://sems.uni-rostock.de/trac/bivesws/wiki//src/test/java/de/unirostock/sems/bives/webservice/TestWeb.java
- web service client:
- http://sems.uni-rostock.de/trac/bivesws-client/wiki//src/test/java/de/unirostock/sems/bives/webservice/client/ClientComparisonExample.java