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News archive

09.08.2006
New Publication: JCell - a Java based framework for inferring regulatory networks from time series data.
Bioinformatics, 22, pp. 2051-2052

02.04.2006
Nomination: Best Paper Award The comparative model study was nomination for the GECCO Best Paper Award.

27.03.2006
New Publication: Comparing Mathematical Models on the Problem of Network Inference.
Genetic and Evolutionary Computation Conference (GECCO 2006), Seattle, USA

27.03.2006
New Publication: Comparing Evolutionary Algorithms on the Problem of Network Inference.
Genetic and Evolutionary Computation Conference (GECCO 2006), Seattle, USA

20.07.2005
Announcing JCell v.1.0.1: Minor Update.
The new version of JCell is with minor bug fixes is available.

09.06.2005
JCell wins the 3rd prize of the the doIT-Award of Baden-Württemberg: doIT Software Award 2005. More information can be found here.

28.04.2005
JCell manual online available. The JCell documentation has been published as a technical report.

09.02.2005
Special Edition on Systems Biology: JCell in BIOspektrum.
JCell is mentioned in an article by Christian Spieth on Systems Biology in the recent edition of BIOspektrum.

02.02.2005
Database of benchmark data sets: JCellDB online.
JCellDB, a database containing artificial regulatory networks for benchmark purposes is online.

20.01.2005
Announcing JCell v.1.0.0: Major Update.
The new version of JCell is here. New features are for example: Multi-Objective EAs, extended KEGG support, Performance improvements, ...

07.01.2005
New Publication: Multi-Objective Model Optimization for Inferring Gene Regulatory Networks.
Conference on Evolutionary Multi-Criterion Optimization (EMO 2005), Guanajuato, Mexico,
LNCS 3410, pp. 607620, 2005, Springer-Verlag

15.11.2004
New algorithm implemented: Multi-Objective EAs.
A new algorithm using multiple optimization objectives.

19.07.2004
Completely redesign of the website: JCell online.
The official website of JCell@ZBIT is online. The design of the "unofficial site" will soon be updated.

07.07.2004
New regulatory model implemented: pseudo-linear weight matrices.
A pseudo-linear, quantitative model based on weight matrices.

27.11.2003
New inference algorithm implemented: bitset inference.
This inference algorithm is a Memetic Algorithm. Global GA optimizing a BitSet representing a topology, local ES-search for parameters.

13.11.03
New inference algorithm implemented: island inference.
The algorithm is using an island strategy to preserve diversity in the population.

30.09.2003
New inference algorithm implemented: iteratively knockout.
The algorithm evaluates the impact of single genes on the current model and suggests new biological experiments toor further reduce the ambiguity.

02.09.2003
New inference algorithm implemented: single gene inference.
This inference algorithm infers a single gene in the context of all other gene expression levels. It can be used to predict the expression changes of a single gene.

15.07.2003
New algorithm implemented: separation strategy.
This enhancement for standard inference processes separates genes and infers them independently. These submodels are merged into a global model, which itself is then optimized.

07.06.2003
New regulatory model implemented: weight matrices.
A linear, quantitative model.

21.05.2003
New regulatory model implemented: S-Systems.
An approximation of arbitrary differential equation systems. A non-linear, qualitative model.

01.05.2003
Basic framework (): JCell v0.8.


Christian Spieth.
http://www.ra.cs.uni-tuebingen.de/software/JCell/archive.html
2004 University of Tübingen, Germany