Agent-based modeling: A systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 5, Issue 4, 2013, Pages 461-480

  Hunt, C Anthony ^a   Kennedy, Ryan C ^a   Kim, Sean H J ^b   Ropella, Glen E P ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

^c TEMPUS DICTUM INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGENT BASED MODELING AND SIMULATION; CLINICAL RESEARCH; COMPUTER MODEL; DECISION MAKING; DRUG INDUSTRY; INFORMATION TECHNOLOGY; KNOWLEDGE; MODEL; PHARMACEUTICS; PREDICTION; PRODUCTIVITY; REVIEW; SIMULATION; UNCERTAINTY;

DRUG INTERACTIONS; EVIDENCE-BASED MEDICINE; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; RESEARCH; UNCERTAINTY;

EID: 84879287149     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1222     Document Type: Review

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134. Listed below are available, open-source tools of the type that can be used now to begin satisfying the listed interactive Knowledge Repository requirements.
135. Databases
136. PostgreSQL (relational): http://www.postgresql.org/
137. ZOBD: http://zodb.org/
138. NoSQL: http://nosql-database.org/
139. RDF/SPARQL: http://www.w3.org/TR/rdf-sparql-query/
140. Data [de]composition
141. R: http://www.r-project.org/
142. HDF: http://www.hdfgroup.org/HDF5/
143. Semantics
144. Protoge: http://protege.stanford.edu/
145. Ontopia: http://www.ontopia.net/
146. Jena: https://jena.apache.org/
147. Pellet: http://clarkparsia.com/pellet/ (complete)
148. Racer: http://www.sts.tu-harburg.de/~r.f.moeller/racer/ (complete)
149. Hermit: http://hermit-reasoner.com/
150. Executable models
151. Code
152. Eclipse: http://eclipse.org/
153. Netbeans: http://netbeans.org/
154. Graphical programming
155. Ptolemy II: http://ptolemy.eecs.berkeley.edu/ptolemyII/index.htm
156. NetLogo: http://ccl.northwestern.edu/netlogo/
157. ArgoUML: http://argouml.tigris.org/
158. Modeling infrastructure
159. JAMES II: http://wwwmosi.informatik.uni-rostock.de/mosi/projects/cosa/james-ii
160. CC3D: http://www.compucell3d.org/
161. MASON: http://cs.gmu.edu/~eclab/projects/mason/
162. Actor model133
163. Erlang: http://www.erlang.org/
164. Scala: http://www.scala-lang.org/node/242
165. Workflow
166. Kepler: http://kepler-project.org/
167. Taverna: http://www.taverna.org.uk/
168. Galaxy: http://galaxyproject.org/
169. Triana: http://www.trianacode.org/
170. Graphs
171. NetworkX: http://networkx.lanl.gov/
172. JUNG: http://jung.sourceforge.net/