EvA2 Mailing List

We have installed a mailing list to support users and developers. If you would like to join, please visit EvA-listinfo.

Users

Here is a list of companies using the EvA2 library. If you also use EvA2 and would like to appear on this list, please send us an E-Mail.

Name Description
Daimler AG Automatic transmission optimization.
The Bosch Group Optimization of job-shop-scheduling problems.
Altana Pharma Combinartorial libary design.
INSILICO biotechnology Optimizing kinetic model parameters to fit timeseries of the glucose metabolism of yeast.
BMW During the BMBF-Project Optimization of combustion engines .
hte GmbH During the BMBF-Project Automated Crystallization.

Software using EvA2

Here is a list of software packages using the EvA2 (or former JavaEvA) library.

Name Description
Systems Biology Toolbox for MATLAB Optimization of complex system parameters in Systems Biology.
JCell JCell is a framework to simulate intra-cellular processes based on gene regulatory mechanisms. The project is aiming to model and reconstruct genetic interactions in silico, and helps researchers to gain new insights in the organisational structure of an organism.
joelib JOELib is a platform independent open source computational chemistry package written in Java.

Publications using EvA2/JavaEvA

[1] Markus Beck, Peter Bayer, Michael de Paly, Jozsef Hecht-Mendez, and Andreas Zell. Geometric arrangement and operation mode adjustment in low enthalpy geothermal borehole fields for heating. Energy, 49:434-443, 2013. [ details ]
[2] Jozsef Hecht-Mendez, Michael de Paly, Markus Beck, and Peter Bayer. Optimization of energy extraction for vertical closed-loop geothermal systems considering groundwater flow. Energy Conversion and Management, 66:1-10, 2013. [ details ]
[3] Markus Beck, Michael de Paly, Jozsef Hecht-Mendez, Peter Bayer, and Andreas Zell. Evaluation of the Performance of Evolutionary Algorithms for Optimization of Low-Enthalpy Geothermal Heating Plants. In Genetic and Evolutionary Computation Conference, GECCO-2012, pages 1047-1054, Philadelphia, USA, July 2012. [ details ]
[4] Michael de Paly, Jozsef Hecht-Mendez, Markus Beck, Philipp Blum, Andreas Zell, and Peter Bayer. Optimization of energy extraction for closed shallow geothermal systems using linear programming. Geothermics, 43:57-65, 2012. [ DOI | details ]
[5] Markus Beck, Jozsef Hecht-Mendez, Michael de Paly, Peter Bayer, Philipp Blum, and Andreas Zell. Optimization of the energy extraction of a shallow geothermal system. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 3622-3628, Barcelona, Spain, July 2010. [ DOI | details ]
[6] Marcel Kronfeld and Andreas Zell. Towards scalability in niching methods. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 4409-4416, Barcelona, Spain, July 2010. [ details | pdf ]
[7] Michael de Paly, Niels Schuetze, and Andreas Zell. Determining crop-production functions using multi-objective evolutionary algorithms. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 1870 - 1877, Barcelona, Spain, July 2010. [ DOI | details ]
[8] Marcel Kronfeld, Hannes Planatscher, and Andreas Zell. The EvA2 optimization framework. In Christian Blum and Roberto Battiti, editors, Learning and Intelligent Optimization Conference, Special Session on Software for Optimization (LION-SWOP), number 6073 in Lecture Notes in Computer Science, LNCS, pages 247-250, Venice, Italy, January 2010. Springer Verlag. [ details | pdf ]
[9] Marcel Kronfeld and Andreas Zell. Gaussian process assisted particle swarm optimization. In Christian Blum and Roberto Battiti, editors, Learning and Intelligent Optimization Conference (LION IV), number 6073 in Lecture Notes in Computer Science, LNCS, pages 139-153, Venice, Italy, January 2010. Springer Verlag. [ details ]
[10] Marcel Kronfeld, Andreas Dräger, Moritz Aschoff, and Andreas Zell. On the Benefits of Multimodal Optimization for Metabolic Network Modeling. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter Stadler, editors, German Conference on Bioinformatics (GCB 2009), volume P-157 of Lecture Notes in Informatics, pages 191-200, Halle (Saale), Germany, September 2009. German Informatics Society. [ details | link | pdf ]
[11] Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Systems Biology, 3(5):5, January 2009. [ DOI | details | link | pdf ]
[12] Michael de Paly and Andreas Zell. Optimal irrigation scheduling with evolutionary algorithms. In Lecture Notes in Computer Science (EvoWorkshops 2009), volume 5484, pages 142-151, Tübingen, Germany, 2009. Springer-Verlag Berlin Heidelberg. [ link ]
[13] Marcel Kronfeld, Christian Weiss, and Andreas Zell. A dynamic swarm for visual location tracking. In 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), pages 203-210, Brussels, Belgium, September 2008. [ details | pdf ]
[14] Marcel Kronfeld. EvA2 Short Documentation. Center for Bioinformatics Tuebingen, University of Tuebingen, Sand 1, 72076 Tübingen, Germany, 2008 edition, 2008. [ link | pdf ]
[15] Andreas Dräger, Marcel Kronfeld, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, and Andreas Zell. Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum. In Dipti Srinivasan and Lipo Wang, editors, IEEE Congress on Evolutionary Computation (CEC 2007), pages 896-903, Singapore, September 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI | details | link | pdf ]
[16] Felix Streichert. Evolutionary Algorithms in Multi-Modal and Multi-Objective Environments. PhD thesis, University of Tübingen, Tübingen, Germany, 2007.
[17] Patrick Heinemann, Felix Streichert, Frank Sehnke, and Andreas Zell. Automatic calibration of camera to world mapping in robocup using evolutionary algorithms. In IEEE International Congress on Evolutionary Computing (CEC 2006), pages 4459-4466, 2006. [ pdf ]
[18] Felix Streichert and Holger Ulmer. JavaEvA: a Java based framework for evolutionary algorithms. Technical Report WSI-2005-06, Center for Bioinformatics Tuebingen (ZBIT) of the Eberhard Karls University, Tuebingen, Germany, April 2005. [ link ]
[19] Christian Spieth, Felix Streichert, Nora Speer, and Andreas Zell. Multi-objective model optimization for inferring gene regulatory networks. In Carlos A. Coello Coello, Arturo Hernández Aguirre, and Eckart Zitzler, editors, Conference on Evolutionary Multi-Criterion Optimization (EMO 2005), volume 3410 of Lecture Notes in Computer Science, pages 607-620, Guanajuato, Mexico, March 2005. Springer. [ pdf ]
[20] Felix Streichert, Holger Ulmer, and Andreas Zell. Parallelization of multi-objective evolutionary algorithms using clustering algorithms. In Carlos A. Coello Coello, Arturo Hernández Aguirre, and Eckart Zitzler, editors, Conference on Evolutionary Multi-Criterion Optimization (EMO 2005), volume 3410 of Lecture Notes in Computer Science, pages 92-107, Guanajuato, Mexico, March 2005. Springer. [ pdf ]
[21] Christian Spieth, Felix Streichert, Nora Speer, and Andreas Zell. Optimizing topology and parameters of gene regulatory network models from time-series experiments. In Genetic and Evolutionary Computation (GECCO 2004), volume 3102, pages 461-470, Seattle, USA, June 2004. Springer. [ pdf ]
[22] Felix Streichert, Hannes Planatscher, Christian Spieth, Holger Ulmer, and Andreas Zell. Comparing genetic programming and evolution strategies on inferring gene regulatory networks. In Genetic and Evolutionary Computation (GECCO 2004), volume 3102 of Lecture Notes in Computer Science, pages 471-480, Seattle, USA, June 2004. Springer. [ pdf ]
[23] Christian Spieth, Felix Streichert, Nora Speer, and Andreas Zell. A memetic inference method for gene regulatory networks based on s-systems. In IEEE Congress on Evolutionary Computation (CEC 2004), volume 1, pages 152-157, Portland, USA, 2004. IEEE Press. [ pdf ]
[24] Christian Spieth, Felix Streichert, Nora Speer, and Andreas Zell. Utilizing an island model for ea to preserve solution diversity for inferring gene regulatory networks. In IEEE Congress on Evolutionary Computation (CEC 2004), volume 1, pages 146-151, Portland, USA, 2004. IEEE Press. [ pdf ]
[25] Christian Spieth, Felix Streichert, Nora Speer, and Andreas Zell. Iteratively inferring gene regulatory networks with virtual knockout experiments. In European Workshop on Evolutionary Bioinformatics (evoBIO), volume 3005 of Lecture Notes in Computer Science, pages 102-111, Coimbra, Portugal, 2004. Springer. [ pdf ]
[26] Felix Streichert, Christian Spieth, Holger Ulmer, and Andreas Zell. How to evolve the head-tail pattern from reaction-diffusion systems. In NASA/DoD Conference on Evolvable Hardware, pages 261-268, Seattle, WA, USA, 2004. IEEE Press. [ pdf ]
[27] Felix Streichert, Holger Ulmer, and Andreas Zell. Evaluating a hybrid encoding and three crossover operators on the constrained portfolio selection problem. In Evolutionary Computation (CEC 2004), volume 1, pages 932-939, Portland, OR, USA, 2004. IEEE Press. [ pdf ]
[28] Felix Streichert, Holger Ulmer, and Andreas Zell. Comparing discrete and continuous genotypes on the constrained portfolio selection problem. In Genetic and Evolutionary Computation Conference (GECCO 2004), volume 2 of Lecture Notes in Computer Science, pages 1239-1250, Seattle, WA, USA, 2004. Springer. [ pdf ]
[29] Holger Ulmer, Felix Streichert, and Andreas Zell. Knowledge Incorporation in Evolutionary Computation, volume 167 of Studies in Fuzziness and Soft Computing Series, chapter Model Assisted Evolution Strategies, pages 333-358. Springer, 2004.
[30] Holger Ulmer, Felix Streichert, and Andreas Zell. Evolution strategies with controlled model assistance. In Congress on Evolutionary Computation (CEC 2004), volume 2, pages 1569-1576, Portland, OR, USA, 2004. IEEE Press. [ pdf ]
[31] Felix Streichert, Christian Spieth, Holger Ulmer, and Andreas Zell. Evolving the ability of limited growth and self-repair for artificial embryos. In 7th European Conference on Artificial Life (ECAL), volume 2801 of Lecture Notes in Artificial Intelligence, pages 289-298, Dortmund, Germany, 2003. Springer. [ pdf ]
[32] Felix Streichert, Gunnar Stein, Holger Ulmer, and Andreas Zell. A clustering based niching method for evolutionary algorithms. In E. Cantú-Paz, J. A. Foster, K. Deb, D. Davis, R. Roy, U.-M. O'Reilly, H.-G. Beyer, R. Standish, G. Kendall, S. Wilson, M. Harman, J. Wegener, D. Dasgupta, M. A. Potter, A. C. Schultz, K. Dowsland, N. Jonoska, and J. Miller, editors, Genetic and Evolutionary Computation Conference (GECCO 2003), volume 1 of Lecture Notes in Computer Science, pages 644-645, Chicago, IL, USA, 2003. Springer. [ pdf ]
[33] Felix Streichert, Holger Ulmer, and Andreas Zell. Evolutionary algorithms and the cardinality constrained portfolio selection problem. In Operations Research Proceedings 2003, pages 253-260, Heidelberg, Germany, 2003. Springer. [ pdf ]
[34] Holger Ulmer, Felix Streichert, and Andreas Zell. Model-assisted steady-state evolution strategies. In Genetic and Evolutionary Computation Conference (GECCO 2003), volume 1 of Lecture Notes in Computer Science, pages 610-621, Chicago, IL, USA, 2003. Springer. [ pdf ]
[35] Holger Ulmer, Felix Streichert, and Andreas Zell. Optimization by gaussian processes assisted evolution strategies. In Selected Papers of the International Conference on Operations Research (OR 2003), pages 435-442, Heidelberg, Germany, 2003. Springer. [ pdf ]
[36] Holger Ulmer, Felix Streichert, and Andreas Zell. Evolution strategies assisted by gaussian processes with improved pre-selection criterion. In 2003 Congress on Evolutionary Computation (CEC 2003), volume 1, pages 692-699. IEEE Press, 2003. [ pdf ]
[37] Jürgen Wakunda and Andreas Zell. EvA: A Tool for Optimization with Evolutionary Algorithms. In 23rd EUROMICRO Conference '97 New Frontiers of Information Technology, volume 0, pages 644-651, Los Alamitos, CA, USA, September 1997. IEEE Computer Society. [ DOI | details | link | pdf ]

External publications:

Comparison of evolutionary algorithms in gene regulatory network model inference
Sirbu A, Ruskin HJ., Crane M
BMC Bioinformatics 2010, 11:59 (27 January 2010)

The EvA2 Optimization Framework
M. Kronfeld, H. Planatscher, and A. Zell
Learning and Intelligent Optimization Conference, LION IV
Special Session on Software for Optimization, LION-SWOP, January 2010 (accepted).

Optimal Irrigation Scheduling with Evolutionary Algorithms
M. de Paly and A. Zell
Lecture Notes in Computer Science (EvoWorkshops 2009)
Springer-Verlag Berlin Heidelberg, 2009, 5484, pp. 142-151

On the Benefits of of Multimodal Optimization for Metabolic Network Modeling.
M. Kronfeld, M. Aschoff, A. Dräger, and A. Zell
German Conference on Bioinformatics (GCB 2009), Halle (Saale), Germany,
September 28-30 2009, pp. 191-200.

Modeling Metabolic Networks: a Comparison of Rate Laws in Combination with Various Parameter Optimization Strategies
A. Dräger, M. Kronfeld, M. Ziller, J. Supper, H. Planatscher, J. Magnus, M. Oldiges, O. Kohlbacher, and A. Zell
BMC Systems Biology 2009, 3:5 (14 January 2009).
Supplemental download: The Langevin model

A Dynamic Swarm for Visual Location Tracking
M. Kronfeld, C. Weiss, and Andreas Zell.
6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008).
Sept. 22-24, 2008. Brussels, Belgium.

Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum
A. Dräger, M. Kronfeld, J. Supper, H. Planatscher, J. Magnus, M. Oldiges and A. Zell
IEEE Congress on Evolutionary Computation, Singapore
September 25-28, 2007

Automatic Calibration of Camera to World Mapping in RoboCup using Evolutionary Algorithms
P. Heinemann, F. Sehnke, F. Streichert, and A. Zell
Proceedings of the IEEE International Congress on Evolutionary Computing (CEC 2006),
pp. 4459-4466, 2006

Parallelization of Multi-Objective Evolutionary Algorithms using Clustering Algorithms
F. Streichert, H. Ulmer, and A. Zell
Conference on Evolutionary Multi-Criterion Optimization - EMO 2005,
Guanajuato, Mexico, March 9-11, 2005

Multi-Objective Model Optimization for Inferring Gene Regulatory Networks
C. Spieth, F. Streichert, N. Speer, and A. Zell
Conference on Evolutionary Multi-Criterion Optimization - EMO 2005,
Guanajuato, Mexico, March 9-11, 2005

Comparing Discrete and Continuous Genotypes on the Constrained Portfolio Selection Problem
F. Streichert, H. Ulmer, and A. Zell
Genetic and Evolutionary Computation Conference - GECCO 2004,
Seattle, WA, USA, June 26-30, 2004, Proceedings, Part II. pp. 1239-1250, © Springer-Verlag (LNCS 3103), ISBN 3-540-22343-6
Abstract: [pdf]

Optimizing Topology and Parameters of Gene Regulatory Network Models from Time-Series Experiments
C. Spieth, F. Streichert, N. Speer, and A. Zell
Genetic and Evolutionary Computation Conference - GECCO 2004,
Seattle, WA, USA, June 26-30, 2004, Proceedings, Part I. pp. 461-470, © Springer-Verlag (LNCS 3102), ISBN 3-540-22344-4
Abstract: [pdf]

Comparing Genetic Programming and Evolution Strategies on Inferring Gene Regulatory Networks
F. Streichert, H. Planatscher, C. Spieth, H. Ulmer, and A. Zell
Genetic and Evolutionary Computation Conference - GECCO 2004,
Seattle, WA, USA, June 26-30, 2004, Proceedings, Part I. pp. 471-480, © Springer-Verlag (LNCS 3102), ISBN 3-540-22344-4
Abstract: [pdf]

How to evolve the Head-Tail Pattern from Reaction-Diffusion Systems
F. Streichert, C. Spieth, H. Ulmer, and A. Zell
Proceedings of the 2004 NASA/DoD Conference on Evolvable Hardware
Seattle, WA, USA, June 24-26, 2004, Proceedings pp. 261-268, IEEE Press, ISBN 0-7695-2145-2
Abstract: [pdf]

Evaluating a Hybrid Encoding and Three Crossover Operators on the Constrained Portfolio Selection Problem
F. Streichert, H. Ulmer, and A. Zell
Congress on Evolutionary Computation (CEC 2004)
Portland, OR, USA, June 19-23, 2004, Proceedings Part I pp. 932-939, IEEE Press, ISBN 0-7803-8515-2
Abstract: [pdf]

A Memetic Inference Method for Gene Regulatory Networks Based on S-Systems
C. Spieth, F. Streichert, N. Speer, and A. Zell
Congress on Evolutionary Computation (CEC 2004)
Portland, OR, USA, June 19-23, 2004, Proceedings Part I pp. 152-157, IEEE Press, ISBN 0-7803-8515-2
Abstract: [pdf]

Utilizing an Island Model for EA to Preserve Solution Diversity for Inferring Gene Regulatory Networks
C. Spieth, F. Streichert, N. Speer, and A. Zell
Congress on Evolutionary Computation (CEC 2004)
Portland, OR, USA, June 19-23, 2004, Proceedings Part I pp. 146-151, IEEE Press, ISBN 0-7803-8515-2
Abstract: [pdf]

Evolution Strategies with Controlled Model Assistance
H. Ulmer, F. Streichert, and A. Zell
Congress on Evolutionary Computation (CEC 2004)
Portland, OR, USA, June 19-23, 2004, Proceedings Part II pp. 1569-1576, IEEE Press, ISBN 0-7803-8515-2
Abstract: [pdf]

Iteratively Inferring Gene Regulatory Networks with Virtual Knockout Experiments
C. Spieth, F. Streichert, N. Speer and A. Zell
Proceedings of the 2nd European Workshop on Evolutionary Bioinformatics (evoBIO)
Applications of Evolutionary Computing: EvoWorkshops2004, LNCS, vol. 3005, pp. 102-111
Abstract: [pdf]

Evolution Strategies assisted by Gaussian Processes with improved Pre-Selection Criterion
H. Ulmer, F. Streichert, and A. Zell
Congress on Evolutionary Computation, CEC 2003,
Canberra, Australia, December 8-12, 2003, Proceedings, Part I. pp. 692-699, IEEE-Press, ISBN 0-7803-7804-0
Abstract: [pdf]

A Clustering Based Niching EA for Multimodal Search Spaces
F. Streichert, G. Stein, H. Ulmer, and A. Zell
Evolution Artificielle 6th International Conference (EA 2003)
Marseille, France, October 27-30, 2003, Proceedings pp. 169-180, ISBN 2-72261-12667-8
Evolution Artificielle, pp. 293-304, © Springer-Verlag (LNCS 2936), ISBN 3-540-21523-9
Abstract: [pdf]

Evolutionary Algorithms and the Cardinality Constrained Portfolio Selection Problem
F. Streichert, H. Ulmer, and A. Zell
Selected Papers of the International Conference on Operations Research (OR 2003)
Heidelberg, Germany, September 3-5, 2003, pp. 253-260, Springer, ISBN 3-540-21445-3
Abstract: [pdf]

Optimization by Gaussian Processes Assisted Evolution Strategies
H. Ulmer, F. Streichert, and A. Zell
Selected Papers of the International Conference on Operations Research (OR 2003)
Heidelberg, September 3-5, 2003, pp. 435-442, Springer, ISBN 3-540-21445-3
Abstract: [pdf]

Evolving the Ability of Limited Growth and Self-Repair for Artificial Embryos
F. Streichert, C. Spieth, H. Ulmer, and A. Zell
Advances in Artificial Life - Proceedings of the 7th European Conference on Artificial Life (ECAL)
Dortmund, Germany, September 14-17, 2003, Proceedings pp. 289-298, © Springer-Verlag (LNAI 2801), ISBN 3-540-20057-6
Abstract: [pdf]

Model-Assisted Steady-State Evolution Strategies
H. Ulmer, F. Streichert, and A. Zell
Genetic and Evolutionary Computation Conference - GECCO 2003,
Chicago, IL, USA, July 12-16, 2003. Proceedings, Part I. pp. 610-621, © Springer-Verlag (LNCS 2723), ISBN 3-540-40602-6
Abstract: [pdf]

Book Chapters

Model Assisted Evolution Strategies
H. Ulmer, F. Streichert, and A. Zell
in "Knowledge Incorporation in Evolutionary Computation", in Studies in Fuzziness and Soft Computing Series, Springer, to appear 2004.

Posters

A Clustering Based Niching Method for Evolutionary Algorithms
F. Streichert, G. Stein, H. Ulmer, and A. Zell
Genetic and Evolutionary Computation Conference - GECCO 2003,
Chicago, IL, USA, July 12-16, 2003. Proceedings, Part I. pp. 644-645, © Springer-Verlag (LNCS 2723), ISBN 3-540-40602-6
Abstract: [pdf]