title: JCell--a Java-based framework for inferring regulatory networks from time series data.
abstract: BACKGROUND
  JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers.
  
  
  BACKGROUND
  The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.
authors.affiliation: Centre for Bioinformatics Tübingen (ZBIT), University of Tübingen Sand 1, 72076 Tübingen, Germany. christian.spieth@uni-tuebingen.de
authors.forename: C
authors.initials: C
authors.lastname: Spieth
authors.forename: J
authors.initials: J
authors.lastname: Supper
authors.forename: F
authors.initials: F
authors.lastname: Streichert
authors.forename: N
authors.initials: N
authors.lastname: Speer
authors.forename: A
authors.initials: A
authors.lastname: Zell
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003201:Computers; D020869:Gene Expression Profiling; D020407:Internet; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D012984:Software; D013997:Time Factors; D014584:User-Computer Interface