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Heitzmann J, Thoma Y, Bricca R, Gagnieu M-C, Leclerc V, Roux S, Conrad A, Ferry T and Goutelle S (2022), "Implementation and Comparison of Two Pharmacometric Tools for Model-Based Therapeutic Drug Monitoring and Precision Dosing of Daptomycin", Pharmaceutics. Vol. 14(1)

[Abstract] [BibTeX] [DOI] [URL]
Abstract: Daptomycin is a candidate for therapeutic drug monitoring (TDM). The objectives of this work were to implement and compare two pharmacometric tools for daptomycin TDM and precision dosing. A nonparametric population PK model developed from patients with bone and joint infection was implemented into the BestDose software. A published parametric model was imported into Tucuxi. We compared the performance of the two models in a validation dataset based on mean error (ME) and mean absolute percent error (MAPE) of individual predictions, estimated exposure and predicted doses necessary to achieve daptomycin efficacy and safety PK/PD targets. The BestDose model described the data very well in the learning dataset. In the validation dataset (94 patients, 264 concentrations), 21.3% of patients were underexposed (AUC24h < 666 mg.h/L) and 31.9% of patients were overexposed (Cmin > 24.3 mg/L) on the first TDM occasion. The BestDose model performed slightly better than the model in Tucuxi (ME = −0.13 ± 5.16 vs. −1.90 ± 6.99 mg/L, p < 0.001), but overall results were in agreement between the two models. A significant proportion of patients exhibited underexposure or overexposure to daptomycin after the initial dosage, which supports TDM. The two models may be useful for model-informed precision dosing.
BibTeX: 
@article{heitzmann22implementation,
  author = {Heitzmann, Justine and Thoma, Yann and Bricca, Romain and Gagnieu, Marie-Claude and Leclerc, Vincent and Roux, Sandrine and Conrad, Anne and Ferry, Tristan and Goutelle, Sylvain},
  title = {Implementation and Comparison of Two Pharmacometric Tools for Model-Based Therapeutic Drug Monitoring and Precision Dosing of Daptomycin},
  journal = {Pharmaceutics},
  year = {2022},
  volume = {14},
  number = {1},
  url = {https://www.mdpi.com/1999-4923/14/1/114},
  doi = {10.3390/pharmaceutics14010114}
}
Drennan PG, Thoma Y, Barry L, Matthey J, Sivam S and van Hal SJ (2021), "Bayesian Forecasting for Intravenous Tobramycin Dosing in Adults With Cystic Fibrosis Using One Versus Two Serum Concentrations in a Dosing Interval", Therapeutic Drug Monitoring. Vol. 43(4)

[Abstract] [BibTeX] [URL]
Abstract: Background:
BibTeX: 
@article{drennan21bayesian,
  author = {Drennan, Philip G. and Thoma, Yann and Barry, Lucinda and Matthey, Johan and Sivam, Sheila and van Hal, Sebastiaan J.},
  title = {Bayesian Forecasting for Intravenous Tobramycin Dosing in Adults With Cystic Fibrosis Using One Versus Two Serum Concentrations in a Dosing Interval},
  journal = {Therapeutic Drug Monitoring},
  year = {2021},
  volume = {43},
  number = {4},
  url = {https://journals.lww.com/drug-monitoring/Fulltext/2021/08000/Bayesian_Forecasting_for_Intravenous_Tobramycin.10.aspx}
}
Narayan SW, Thoma Y, Drennan PG, Yejin Kim H, Alffenaar J-W, Van Hal S and Patanwala AE (2021), "Predictive Performance of Bayesian Vancomycin Monitoring in the Critically Ill", Critical Care Medicine. Vol. 49(10), pp. 952-960.

[Abstract] [BibTeX] [URL]
Abstract: OBJECTIVES:
BibTeX: 
@article{narayan21predictive,
  author = {Narayan, Sujita W. and Thoma, Yann and Drennan, Philip G. and Yejin Kim, Hannah and Alffenaar, Jan-Willem and Van Hal, Sebastiaan and Patanwala, Asad E.},
  title = {Predictive Performance of Bayesian Vancomycin Monitoring in the Critically Ill},
  journal = {Critical Care Medicine},
  year = {2021},
  volume = {49},
  number = {10},
  pages = {952-960},
  url = {https://journals.lww.com/ccmjournal/Fulltext/2021/10000/Predictive_Performance_of_Bayesian_Vancomycin.36.aspx}
}
Wertenbroek R, Thoma Y, Mor FM, Grassi S, Heuschkel MO, Roux A and Stoppini L (2021), "SpikeOnChip : A Custom Embedded Platform for Neuronal Activity Recording and Analysis", IEEE Transactions on Biomedical Circuits and Systems. Vol. 15(4), pp. 743-755.

[BibTeX] [DOI]
BibTeX: 
@article{wertenbroek21spikeonchip,
  author = {Wertenbroek, Rick and Thoma, Yann and Mor, Flavio Maurizio and Grassi, Sara and Heuschkel, Marc Olivier and Roux, Adrien and Stoppini, Luc},
  title = {SpikeOnChip : A Custom Embedded Platform for Neuronal Activity Recording and Analysis},
  journal = {IEEE Transactions on Biomedical Circuits and Systems},
  year = {2021},
  volume = {15},
  number = {4},
  pages = {743-755},
  doi = {10.1109/TBCAS.2021.3097833}
}
Buclin T, Thoma Y, Widmer N, André P, Guidi M, Csajka C and Decosterd LA (2020), "The Steps to Therapeutic Drug Monitoring: A Structured Approach Illustrated With Imatinib", Frontiers in Pharmacology. Vol. 11, pp. 177.

[Abstract] [BibTeX] [DOI] [URL]
Abstract: Pharmacometric methods have hugely benefited from progress in analytical and computer sciences during the past decades, and play nowadays a central role in the clinical development of new medicinal drugs. It is time that these methods translate into patient care through therapeutic drug monitoring (TDM), due to become a mainstay of precision medicine no less than genomic approaches to control variability in drug response and improve the efficacy and safety of treatments. In this review, we make the case for structuring TDM development along five generic questions: 1) Is the concerned drug a candidate to TDM? 2) What is the normal range for the drug's concentration? 3) What is the therapeutic target for the drug's concentration? 4) How to adjust the dosage of the drug to drive concentrations close to target? 5) Does evidence support the usefulness of TDM for this drug? We exemplify this approach through an overview of our development of the TDM of imatinib, the very first targeted anticancer agent. We express our position that a similar story shall apply to other drugs in this class, as well as to a wide range of treatments critical for the control of various life-threatening conditions. Despite hurdles that still jeopardize progress in TDM, there is no doubt that upcoming technological advances will shape and foster many innovative therapeutic monitoring methods.
BibTeX: 
@article{buclin20steps,
  author = {Buclin, Thierry and Thoma, Yann and Widmer, Nicolas and André, Pascal and Guidi, Monia and Csajka, Chantal and Decosterd, Laurent A.},
  title = {The Steps to Therapeutic Drug Monitoring: A Structured Approach Illustrated With Imatinib},
  journal = {Frontiers in Pharmacology},
  year = {2020},
  volume = {11},
  pages = {177},
  url = {https://www.frontiersin.org/article/10.3389/fphar.2020.00177},
  doi = {10.3389/fphar.2020.00177}
}
Emery J, Andersson P, Roncarolo F and Thoma Y (2019), "A low fluctuation control strategy for PMSM direct drive system targeting Particle Beam Instrumentation Application", In 2019 IEEE Conference on Control Technology and Applications (CCTA)., Aug, 2019. , pp. 437-443.

[Abstract] [BibTeX] [DOI]
Abstract: Particle accelerators have a singular environment where multiple constraints are driving the engineering of equipment. Designers have to deal with the destructive effects of charged particles, high vacuum requirements, large temperatures and particular system architectures due to large-scale installations such as the Large Hadron Collider (LHC) at the CERN laboratory. At the same time, there is a continuous challenge to produce, measure and control smaller particle beams to increase the discovery potentials of large physics experiments. In this context, an innovative actuator has been built to measure precisely the size of beams down to 150um sigma, by moving a thin carbon wire of 30um at about 20m·s-1 through particle beams. Called Beam Wire Scanner (BWS), this system uses direct drive coupling to actuate a shaft inside a vacuum vessel without moving parts outside it. We are reporting on the design and validation of its control system based on torque control feedback as the only on-line closedloop system to operate this instrument. The proposed strategy keeps the smoothest action as possible on the system avoiding speed and position corrections that would lead to undesired torque variations, increasing the uncertainty of the carbon wire position.
BibTeX: 
@inproceedings{emery19low,
  author = {J. Emery and P. Andersson and F. Roncarolo and Y. Thoma},
  title = {A low fluctuation control strategy for PMSM direct drive system targeting Particle Beam Instrumentation Application},
  booktitle = {2019 IEEE Conference on Control Technology and Applications (CCTA)},
  year = {2019},
  pages = {437-443},
  doi = {10.1109/CCTA.2019.8920688}
}
Wertenbroek R and Thoma Y (2019), "Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK", In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)., Nov, 2019. , pp. 534-541.

[Abstract] [BibTeX] [DOI]
Abstract: The Pair-HMM forward algorithm is an essential algorithm found in many genomic related analyses. The high number of floating point operations in the algorithm makes it one of the main contributors to the compute time of analysis pipelines. To speed-up computations we propose an FPGA-based hardware accelerator for the Amazon AWS F1 Cloud platform. The accelerator is open source and has been tested within the popular Genomic Analysis Toolkit (GATK) pipeline. The accelerator achieved up to 15 × speed-up against the software implementation when used in-pipeline. The accelerator has also been tested in the experimental Spark (distributed) version of the GATK HaplotypeCaller tool. An in-depth analysis of the compute time contributions allowed to point out the main bottlenecks for accelerators in the GATK pipeline, resulting in a hybrid CPU-FPGA solution to best exploit both resources.
BibTeX: 
@inproceedings{wertenbroek19acceleration,
  author = {R. Wertenbroek and Y. Thoma},
  title = {Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK},
  booktitle = {2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  year = {2019},
  pages = {534-541},
  doi = {10.1109/BIBM47256.2019.8983189}
}
Wertenbroek R and Thoma Y (2018), "k-mer Counting with FPGAs and HMC In-Memory Operations", In 2018 NASA/ESA Conference on Adaptive Hardware and Systems (AHS)., Aug, 2018. , pp. 233-240.

[Abstract] [BibTeX] [DOI]
Abstract: k-mer counting is an essential algorithm found in many genomic related processes. It may seem like a rather trivial task but is in fact computationally expensive due to the sheer amount of data. The ever growing rate at which data is generated in genomics requires the creation of novel solutions leveraging new technologies to keep up the pace. In this paper we explore the use of in-memory operations of Hybrid Memory Cubes (HMC) to accelerate k-mer counting. The resulting accelerator is compared to an existing accelerator also using HMC memory, as well as state of the art k-mer counting software. The use of in-memory operations resulted in a 14.6% to 16.9% performance improvement over using the HMC without them. The accelerator showed a speed-up of 3-4x over software when running with a single FPGA and HMC and a speed-up of 16-17x when using 4 FPGAs and 4 HMCs.
BibTeX: 
@inproceedings{wertenbroek18kmer,
  author = {R. Wertenbroek and Y. Thoma},
  title = {k-mer Counting with FPGAs and HMC In-Memory Operations},
  booktitle = {2018 NASA/ESA Conference on Adaptive Hardware and Systems (AHS)},
  year = {2018},
  pages = {233-240},
  doi = {10.1109/AHS.2018.8541417}
}
Dubovitskaya A, Buclin T, Schumacher M, Aberer K and Thoma Y (2017), "TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back", In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics. New York, NY, USA , pp. 223-232. ACM.

[BibTeX] [DOI] [URL]
BibTeX: 
@inproceedings{dubovitskaya17tucuxi,
  author = {A. Dubovitskaya and T. Buclin and M. Schumacher and K. Aberer and Y. Thoma},
  title = {TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back},
  booktitle = {Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics},
  publisher = {ACM},
  year = {2017},
  pages = {223--232},
  url = {http://doi.acm.org/10.1145/3107411.3107439},
  doi = {10.1145/3107411.3107439}
}
Petraglio E, Wertenbroek R, Capitao F, Guex N, Iseli C and Thoma Y (2017), "Genomic Data Clustering on FPGAs for Compression", In Applied Reconfigurable Computing: 13th International Symposium, ARC 2017, Delft, The Netherlands, April 3-7, 2017, Proceedings. Cham , pp. 229-240. Springer International Publishing.

[Abstract] [BibTeX] [DOI] [URL]
Abstract: Current sequencing machine technology generates very large and redundant volumes of genomic data for each biological sample. Today data and associated metadata are formatted in very large text file assemblies called FASTQ carrying the information of billions of genome fragments referred to as ``reads'' and composed of strings of nucleotide bases with lengths in the range of a few tenths to a few hundreds bases. Compressing such data is definitely required in order to manage the sheer amount of data soon to be generated. Doing so implies finding redundant information in the raw sequences. While most of it can be mapped onto the human reference genome and fits well for compression, about 10% of it usually does not map to any reference [1]. For these orphan sequences, finding redundancy will help compression. Doing so requires clustering these reads, a very time consuming process. Within this context this paper presents a FPGA implementation of a clustering algorithm for genomic reads, implemented on Pico Computing EX-700 AC-510 hardware, offering more than a $$1000backslashtimes $$  speed up over a CPU implementation while reducing power consumption by a 700 factor.
BibTeX: 
@inproceedings{petraglio17genomic,
  author = {E. Petraglio and R. Wertenbroek and F. Capitao and N. Guex and C. Iseli and Y. Thoma},
  editor = {Wong, Stephan and Beck, Antonio Carlos and Bertels, Koen and Carro, Luigi},
  title = {Genomic Data Clustering on FPGAs for Compression},
  booktitle = {Applied Reconfigurable Computing: 13th International Symposium, ARC 2017, Delft, The Netherlands, April 3-7, 2017, Proceedings},
  publisher = {Springer International Publishing},
  year = {2017},
  pages = {229--240},
  url = {http://dx.doi.org/10.1007/978-3-319-56258-2_20},
  doi = {10.1007/978-3-319-56258-2_20}
}
Wertenbroek R, Petraglio E and Thoma Y (2017), "Pipelined Multi-FPGA Genomic Data Clustering", In Algorithms and Architectures for Parallel Processing. Cham , pp. 558-568. Springer International Publishing.

[Abstract] [BibTeX]
Abstract: High throughput DNA sequencing made individual genome profiling possible and produces very large amounts of data. Today data and associated metadata are stored in FASTQ text file assemblies carrying the information of genome fragments called reads. Current techniques rely on mapping these reads to a common reference genome for compression and analysis. However, about 10% of the reads do not map to any known reference making them difficult to compress or process. These reads are of high importance because they hold information absent from any reference. Finding overlaps in these reads can help subsequent processing and compression tasks tremendously. Within this context clustering is used to find overlapping unmapped reads and sort them in groups. Clustering being an extremely time consuming task a modular multi-FPGA pipeline was designed and is the focus of this paper. A pipeline with 6 FPGAs was created and has shown a speed-up of $$backslashtimes 5$$ compared to existing FPGA implementations. Resulting enriched files encoding reads and clustering results show file sizes within a 10% margin of the best DNA compressors while providing valuable extra information.
BibTeX: 
@inproceedings{wertenbroek17pipelined,
  author = {R. Wertenbroek and E. Petraglio and Y. Thoma},
  editor = {Ibrahim, Shadi and Choo, Kim-Kwang Raymond and Yan, Zheng and Pedrycz, Witold},
  title = {Pipelined Multi-FPGA Genomic Data Clustering},
  booktitle = {Algorithms and Architectures for Parallel Processing},
  publisher = {Springer International Publishing},
  year = {2017},
  pages = {558--568}
}
Thoma Y, Dassatti A, Molla D and Petraglio E (2015), "FPGA-GPU communicating through PCIe", Microprocessors and Microsystems., March, 2015. Vol. 39, pp. 565-575.

[BibTeX] [DOI]
BibTeX: 
@article{thoma15fpga,
  author = {Y. Thoma and A. Dassatti and D. Molla and E. Petraglio},
  title = {FPGA-GPU communicating through PCIe},
  journal = {Microprocessors and Microsystems},
  year = {2015},
  volume = {39},
  pages = {565-575},
  doi = {{http://dx.doi.org/10.1016/j.micpro.2015.02.005}}
}
Damavandi YB, Mohammadi K, Upegui A and Thoma Y (2014), "On Feasibility of Adaptive Level Hardware Evolution for Emergent Fault Tolerant Communication", International Journal of Engineering., jan, 2014. Vol. 27(1), pp. 101-112.

[Abstract] [BibTeX]
Abstract: A permanent physical fault in communication lines usually leads to a failure. The feasibility of evolution of a self-organized communication is studied in this paper to mitigate this problem. In this case a communication protocol may emerge between blocks and also can adapt itself to environmental changes like physical faults and defects. In spite of the faults, blocks may continue to function, since a self-organized nature can provide self-healing capabilities. In the present paper, Evolvable Hardware is to create such a fault tolerant communication without any predefined protocol using a GA algorithm. Evolvable Hardware is a concept that aims the application of evolutionary algorithms to hardware design. The feasibility of this idea is studied in simulation of two reconfigurable blocks that are intended to transmit video streams through their communication lines. Permanent physical faults are induced in the communication lines between Evolvable Hardware blocks. Although the results show the emergence of fault tolerant protocols among Evolvable Hardware blocks without human intervention, there are some limitations in functional and gate level evolution of the blocks. Thus, a new adaptive approach is presented in this paper to defeat some limitations like the stalling effect of GA in faulty conditions.
BibTeX: 
@article{baleghi14feasibility,
  author = {Y. Baleghi Damavandi and K. Mohammadi and A. Upegui and Y. Thoma},
  title = {On Feasibility of Adaptive Level Hardware Evolution for Emergent Fault Tolerant Communication},
  journal = {International Journal of Engineering},
  year = {2014},
  volume = {27},
  number = {1},
  pages = {101-112}
}
Dassatti A, Auberson O, Bornet R, Messerli E, Stadelmann J and Thoma Y (2014), "REPTAR: A universal platform for codesign applications", In Education and Research Conference (EDERC), 2014 6th European Embedded Design in., Sept, 2014. , pp. 109-113.

[Abstract] [BibTeX] [DOI]
Abstract: Embedded systems are shaping a new world. There is no sector immune to their adoption and the effects in the long term are unpredictable and fascinating. Embedded systems are designed by embedded system engineers. What technical education and what kind of practical skills these new engineers will need? This is a complex and unanswered question. In this paper we describe our proposal to equip engineering students with knowledge and experience: REPTAR. REPTAR (Reconfigurable Embedded Platform for Training And Research) is a feature rich complex embedded system designed for giving the opportunity to tomorrow's engineers of having hands-on experience on modern technologies and learning by doing. As a side effect REPTAR revealed itself as an invaluable tool for rapid prototyping and research explorations.
BibTeX: 
@inproceedings{dassatti14reptar,
  author = {Dassatti, A. and Auberson, O. and Bornet, R. and Messerli, E. and Stadelmann, J. and Thoma, Y.},
  title = {REPTAR: A universal platform for codesign applications},
  booktitle = {Education and Research Conference (EDERC), 2014 6th European Embedded Design in},
  year = {2014},
  pages = {109-113},
  doi = {10.1109/EDERC.2014.6924369}
}
Simalatsar A, Bornet R, You W, Thoma Y and De Micheli G (2014), "Safe Implementation of Embedded Software for a Portable Device Supporting Drug Administration", In Bioinformatics and Bioengineering (BIBE), 2014 IEEE International Conference on., Nov, 2014. , pp. 257-264.

[Abstract] [BibTeX] [DOI]
Abstract: Poor adherence to medical regimen causes approximately 33% to 69% of medication-related hospitalizations and accounts for $100 billion in annual health care costs. In this paper we address the problem of unintentional non adherence, when patient fails to take a medication due to forgetfulness or carelessness. We present the safe approach to software implementation of a portable reminder device with enabled personalization of medical regimen. The presented prototype is designed for imatinib administration, a drug used to treat Chronic Myeloid Leukemia (CML). However, thanks to the component-based structure of the software, the method can be applied to other cases by replacing implementation of certain components.
BibTeX: 
@inproceedings{simalatsar14safe,
  author = {Simalatsar, A. and Bornet, R. and Wenqi You and Thoma, Y. and De Micheli, G.},
  title = {Safe Implementation of Embedded Software for a Portable Device Supporting Drug Administration},
  booktitle = {Bioinformatics and Bioengineering (BIBE), 2014 IEEE International Conference on},
  year = {2014},
  pages = {257-264},
  doi = {10.1109/BIBE.2014.55}
}
Thoma Y, Dassatti A and Molla D (2013), "FPGA2: An Open Source Framework for FPGA-GPU PCIe Communication", In Reconfigurable Computing and FPGAs (ReConFig), 2013 International Conference on. , pp. 1-6. IEEE.

[Abstract] [BibTeX]
Abstract: In recent years two main platforms emerged as powerful key players in the domain of parallel computing: GPUs and FPGAs. Many researches investigate interaction and benefits of coupling them with a general purpose processor (CPU), but very few, and only very recently, integrate the two in the same computational system. Even less research are focusing on direct interaction of the two platforms. This paper presents an open source framework enabling easy integration of GPU and FPGA resources; Our work provides direct data transfer between the two platforms with minimal CPU coordination at high data rate and low latency. Finally, at the best of our knowledge, this is the first proposition of an open source implementation of a system including an FPGA and a GPU that provides code for both sides. Notwithstanding the generality of the presented framework, we present in this paper an actual implementation consisting of a single GPU board and a FPGA board connected through a PCIe link. Measures on this implementation demonstrate achieved data rate that are close to the theoretical maximum.
BibTeX: 
@inproceedings{thoma13fpga,
  author = {Y. Thoma and A. Dassatti and D. Molla},
  title = {FPGA2: An Open Source Framework for FPGA-GPU PCIe Communication},
  booktitle = {Reconfigurable Computing and FPGAs (ReConFig), 2013 International Conference on},
  publisher = {IEEE},
  year = {2013},
  pages = {1-6}
}
Fuchs A, Csajka C, Thoma Y, Buclin T and Widmer N (2012), "Benchmarking Therapeutic Drug Monitoring Software: A Review of Available Computer Tools", Clinical Pharmacokinetics. Vol. 52(1), pp. 9-22.

[BibTeX] [DOI] [URL]
BibTeX: 
@article{fuchs12benchmarking,
  author = {A. Fuchs and C. Csajka and Y. Thoma and T. Buclin and N. Widmer},
  title = {Benchmarking Therapeutic Drug Monitoring Software: A Review of Available Computer Tools},
  journal = {Clinical Pharmacokinetics},
  year = {2012},
  volume = {52},
  number = {1},
  pages = {9-22},
  url = {http://dx.doi.org/10.1007/s40262-012-0020-y},
  doi = {10.1007/s40262-012-0020-y}
}
Thoma Y, Messerli E, Starkier M, Molla D, Masle S, Bianchi C, Gubler O, Magliocco C, Crausaz P, Tâche S, Prêtre D and Trolliet G (2012), "Math2Mat: from Octave/Matlab to VHDL", In Proc. of 2012 NASA/ESA Conference on Adaptive Hardware and Systems (AHS-2012)., jun, 2012. , pp. 264-271.

[Abstract] [BibTeX] [DOI]
Abstract: Math2Mat aims at automatically generating a VHDL description of a mathematical description written in Octave/Matlab. The generation creates a synthesizable RTL description using floating point operators (32 or 64 bits) combined in a fully pipelined way. Emphasis is put on the throughput attainable by the design, especially in the #x201D;for loop #x201D; implementation. The software also offers a graphical user interface, letting the developer manage the different parameters before generation. Verification can also be launched from the software, a SystemVerilog testbench being automatically generated.
BibTeX: 
@inproceedings{thoma12math2mat,
  author = {Y. Thoma and E. Messerli and M. Starkier and D. Molla and S. Masle and C. Bianchi and O. Gubler and C. Magliocco and P. Crausaz and S. Tâche and D. Prêtre and G. Trolliet},
  title = {Math2Mat: from Octave/Matlab to VHDL},
  booktitle = {Proc. of 2012 NASA/ESA Conference on Adaptive Hardware and Systems (AHS-2012)},
  year = {2012},
  pages = {264-271},
  doi = {10.1109/AHS.2012.6268661}
}
Upegui A, Thoma Y, Satizábal H, Mondada F, Retornaz P, Graf Y, Perez-Uribe A and Sanchez E (2010), "Ubichip, Ubidule, and MarXbot: A Hardware Platform for the Simulation of Complex Systems", In Evolvable Systems: From Biology to Hardware. Vol. 6274, pp. 286-298. Springer Berlin / Heidelberg.

[BibTeX] [URL]
BibTeX: 
@incollection{upegui10ubichip,
  author = {A. Upegui and Y. Thoma and H. Satizábal and F. Mondada and P. Retornaz and Y. Graf and A. Perez-Uribe and E. Sanchez},
  editor = {Tempesti, Gianluca and Tyrrell, Andy and Miller, Julian},
  title = {Ubichip, Ubidule, and MarXbot: A Hardware Platform for the Simulation of Complex Systems},
  booktitle = {Evolvable Systems: From Biology to Hardware},
  publisher = {Springer Berlin / Heidelberg},
  year = {2010},
  volume = {6274},
  pages = {286-298},
  note = {10.1007/978-3-642-15323-525},
  url = {http://dx.doi.org/10.1007/978-3-642-15323-5_25}
}
Jorand O, Perez-Uribe A, Volken H, Upegui A, Thoma Y, Sanchez E, Mondada F and Retornaz P (2009), "Noise and bias for free : PERPLEXUS as a material platform for embodied thought-experiments", In Proc. of the 2ns Symposium on Computing and Philosophy. Edinburgh, apr, 2009. , pp. 28-34.

[Abstract] [BibTeX]
Abstract: There is a growing interest in attempting to study cognitive and social phenomena under the umbrella of "complex theory". We are indeed immersed in so-called "complex systems", but we are still a long way from a clear understanding of the concepts and principles that underlie the "complexity thinking". The purpose of this paper to provide a simple (and too short) conceptual framework to understand the basic ideas that allow us to think and speak of complexity in the context of PERPLEXUS as a physical substratum for the embodiment of questions related to cognition (individual and/or social) and the material realization of philosophical thought-experiments. To do so, we will notice the controversies concerning the very existence of such a thing as a "theory of complexity". We also will capture some features that can be considered as characterizations (or fingerprints) of "complexity thinking" by contrasting them with a classical Cartesian-Newtonian mode of thinking. Then, we will stress the key role of embodiment as a necessary ingredient to be incorporated in the explanatory efforts of different domains dealing with cognition, development and evolution. We will finally explain how the platform PERPLEXUS can represent such an ideal locus1for reformatting and tackling conceptual and philosophical questions grounded in aspects of complexity and embodiment.
BibTeX: 
@inproceedings{jorand09noise,
  author = {O. Jorand and A. Perez-Uribe and H. Volken and A. Upegui and Y. Thoma and E. Sanchez and F. Mondada and P. Retornaz},
  title = {Noise and bias for free : PERPLEXUS as a material platform for embodied thought-experiments},
  booktitle = {Proc. of the 2ns Symposium on Computing and Philosophy},
  year = {2009},
  pages = {28-34}
}
Peev M, Pacher C, Alleaume R, Barreiro C, Bouda J, Boxleitner W, Debuisschert T, Diamanti E, Dianati M, Dynes JF, Fasel S, Fossier S, Furst M, Gautier JD, Gay O, Gisin N, Grangier P, Happe A, Hasani Y, Hentschel M, Hubel H, Humer G, Langer T, Legre M, Lieger R, Lodewyck J, Lorunser T, Lutkenhaus N, Marhold A, Matyus T, Maurhart O, Monat L, Nauerth S, Page JB, Poppe A, Querasser E, Ribordy G, Robyr S, Salvail L, Sharpe AW, Shields AJ, Stucki D, Suda M, Tamas C, Themel T, Thew RT, Thoma Y, Treiber A, Trinkler P, Tualle-Brouri R, Vannel F, Walenta N, Weier H, Weinfurter H, Wimberger I, Yuan ZL, Zbinden H and Zeilinger A (2009), "The SECOQC quantum key distribution network in Vienna", New Journal of Physics. Vol. 11, pp. 075001.

[Abstract] [BibTeX] [DOI]
Abstract: In this paper, we present the quantum key distribution (QKD) network designed and implemented by the European project SEcure COmmunication based on Quantum Cryptography (SECOQC) (2004-2008), unifying the efforts of 41 research and industrial organizations. The paper summarizes the SECOQC approach to QKD networks with a focus on the trusted repeater paradigm. It discusses the architecture and functionality of the SECOQC trusted repeater prototype, which has been put into operation in Vienna in 2008 and publicly demonstrated in the framework of a SECOQC QKD conference held from October 8 to 10, 2008. The demonstration involved one-time pad encrypted telephone communication, a secure (AES encryption protected) video-conference with all deployed nodes and a number of rerouting experiments, highlighting basic mechanisms of the SECOQC network functionality. The paper gives an overview of the eight point-to-point network links in the prototype and their underlying technology: three plug and play systems by id Quantique, a one way weak pulse system from Toshiba Research in the UK, a coherent one-way system by GAP Optique with the participation of id Quantique and the AIT Austrian Institute of Technology (formerly ARC(21)), an entangled photons system by the University of Vienna and the AIT, a continuous-variables system by Centre National de la Recherche Scientifique (CNRS) and THALES Research and Technology with the participation of Universite Libre de Bruxelles, and a free space link by the Ludwig Maximillians University in Munich connecting two nodes situated in adjacent buildings (line of sight 80 m). The average link length is between 20 and 30 km, the longest link being 83 km. The paper presents the architecture and functionality of the principal networking agent-the SECOQC node module, which enables the authentic classical communication required for key distillation, manages the generated key material, determines a communication path between any destinations in the network, and realizes end-to-end secure transport of key material between these destinations. The paper also illustrates the operation of the network in a number of typical exploitation regimes and gives an initial estimate of the network transmission capacity, defined as the maximum amount of key that can be exchanged, or alternatively the amount of information that can be transmitted with information theoretic security, between two arbitrary nodes.
BibTeX: 
@article{peev09secoqc,
  author = {M. Peev and C. Pacher and R. Alleaume and C. Barreiro and J. Bouda and W. Boxleitner and T. Debuisschert and E. Diamanti and M. Dianati and J. F. Dynes and S. Fasel and S. Fossier and M. Furst and J. D. Gautier and O. Gay and N. Gisin and P. Grangier and A. Happe and Y. Hasani and M. Hentschel and H. Hubel and G. Humer and T. Langer and M. Legre and R. Lieger and J. Lodewyck and T. Lorunser and N. Lutkenhaus and A. Marhold and T. Matyus and O. Maurhart and L. Monat and S. Nauerth and J. B. Page and A. Poppe and E. Querasser and G. Ribordy and S. Robyr and L. Salvail and A. W. Sharpe and A. J. Shields and D. Stucki and M. Suda and C. Tamas and T. Themel and R. T. Thew and Y. Thoma and A. Treiber and P. Trinkler and R. Tualle-Brouri and F. Vannel and N. Walenta and H. Weier and H. Weinfurter and I. Wimberger and Z. L. Yuan and H. Zbinden and A. Zeilinger},
  title = {The SECOQC quantum key distribution network in Vienna},
  journal = {New Journal of Physics},
  year = {2009},
  volume = {11},
  pages = {075001},
  doi = {10.1088/1367-2630/11/7/075001}
}
Stucki D, Barreiro C, Fasel S, Gautier J-D, Gay O, Gisin N, Thew R, Thoma Y, Trinkler P, Vannel F and Zbinden H (2009), "Continuous high speed coherent one-way quantum key distribution", Optics Express., aug, 2009. Vol. 17(16), pp. 13326-13334.

[Abstract] [BibTeX]
Abstract: Quantum key distribution (QKD) is the first commercial quantum technology operating at the level of single quanta and is a leading light for quantum-enabled photonic technologies. However, controlling these quantum optical systems in real world environments presents significant challenges. For the first time, we have brought together three key concepts for future QKD systems: a simple high-speed protocol; high performance detection; and integration both, at the component level and for standard fibre network connectivity. The QKD system is capable of continuous and autonomous operation, generating secret keys in real time. Laboratory and field tests were performed and comparisons made with robust InGaAs avalanche photodiodes and superconducting detectors. We report the first real world implementation of a fully functional QKD system over a 43dB-loss (150km) transmission line in the Swisscom fibre optic network where we obtained average real-time distribution rates over 3 hours of 2.5bps.
BibTeX: 
@article{stucki09continuous,
  author = {D. Stucki and C. Barreiro and S. Fasel and J.-D. Gautier and O. Gay and N. Gisin and R. Thew and Y. Thoma and P. Trinkler and F. Vannel and H. Zbinden},
  title = {Continuous high speed coherent one-way quantum key distribution},
  journal = {Optics Express},
  year = {2009},
  volume = {17},
  number = {16},
  pages = {13326--13334}
}
Brousse O, Sassatelli G, Gil T, Guillemenet Y, Robert M, Grize F, Sanchez E, Thoma Y, Upegui A, Moreno J-M and Madrenas J (2008), "BAF: A Bio-Inspired Agent Framework for Distributed Pervasive Applications", In Proceeding of GEM08. , pp. 115-121.

[BibTeX]
BibTeX: 
@inproceedings{brousse08baf,
  author = {O. Brousse and G. Sassatelli and T. Gil and Y. Guillemenet and M. Robert and F. Grize and E. Sanchez and Y. Thoma and A. Upegui and J.-M. Moreno and J. Madrenas},
  title = {BAF: A Bio-Inspired Agent Framework for Distributed Pervasive Applications},
  booktitle = {Proceeding of GEM08},
  year = {2008},
  pages = {115-121}
}
Brousse O, Sassatelli G, Gil T, Robert M, Grize F, Sanchez E, Upegui A and Thoma Y (2008), "The Perplexus Programming Framework: Combining Bio-inspiration and Agent-Oriented Programming for the Simulation of Large Scale Complex Systems", In Evolvable Systems: From Biology to Hardware. Berlin, Heidelberg Vol. 5216, pp. 402-407. Springer Verlag.

[BibTeX] [DOI]
BibTeX: 
@inproceedings{brousse08perplexus,
  author = {O. Brousse and G. Sassatelli and T. Gil and M. Robert and F. Grize and E. Sanchez and A. Upegui and Y. Thoma},
  editor = {G.S. Hornby and L. Sekanina and P.C. Haddow},
  title = {The Perplexus Programming Framework: Combining Bio-inspiration and Agent-Oriented Programming for the Simulation of Large Scale Complex Systems},
  booktitle = {Evolvable Systems: From Biology to Hardware},
  publisher = {Springer Verlag},
  year = {2008},
  volume = {5216},
  pages = {402-407},
  doi = {10.1007/978-3-540-85857-7\_36}
}
Stucki D, Barreiro C, Fasel S, Gautier J, Gay O, Gisin N, Thew R, Thoma Y, Trinkler P, Vannel F and Zbinden H (2008), "High Speed Coherent One-way Quantum Key Distribution Prototype", arXiv.org.

[BibTeX]
BibTeX: 
@article{stucki08high,
  author = {D. Stucki and C. Barreiro and S. Fasel and J.D. Gautier and O. Gay and N. Gisin and R. Thew and Y. Thoma and P. Trinkler and F. Vannel and H. Zbinden},
  title = {High Speed Coherent One-way Quantum Key Distribution Prototype},
  journal = {arXiv.org},
  year = {2008}
}
Thoma Y and Upegui A (2008), "UbiManager: A software Tool for Managing Ubichips", In Proceedings of the 3rd NASA/ESA Conference on Adaptive Hardware and Systems. , pp. 213-219. IEEE Computer Society.

[Abstract] [BibTeX] [DOI]
Abstract: This paper introduces the UbiManager, a tool for managing the ubichip reconfigurable circuit. The ubichip is a custom reconfigurable electronic device for implementing circuits featuring bio-inspired mechanisms like growth, learning, and evolution. The ubichip has been developed in the framework of Perplexus, a European project that aims to develop a scalable hardware platform made of bio-inspired custom reconfigurable devices for simulating large-scale complex systems. In this paper, we present the software tool used for designing, simulating, emulating, debugging, configuring, and monitoring the systems to be implemented in the ubichip. This paper also presents the dissemination plans of the UbiManager, that consist in a web platform allowing researchers to access the hardware platform from any remote base station.
BibTeX: 
@inproceedings{thoma08ubimanager,
  author = {Y. Thoma and A. Upegui},
  editor = {D. Keymeulen and T. Arslan and M. Suess and A. Stoica and A.T. Erdogan and D. Merodio},
  title = {UbiManager: A software Tool for Managing Ubichips},
  booktitle = {Proceedings of the 3rd NASA/ESA Conference on Adaptive Hardware and Systems},
  publisher = {IEEE Computer Society},
  year = {2008},
  pages = {213-219},
  doi = {10.1109/AHS.2008.39}
}
Upegui A, Thoma Y, Perez-Uribe A and Sanchez E (2008), "Dynamic Routing on the Ubichip: Toward Synaptogenetic Neural Networks", In Proceedings of the 3rd NASA/ESA Conference on Adaptive Hardware and Systems. , pp. 228-235. IEEE Computer Society.

[Abstract] [BibTeX] [DOI]
Abstract: The ubichip is a bio-inspired reconfigurable circuit developed in the framework of the european project Perplexus. The ubichip offers special reconfigurability capabilities, being the dynamic routing one of them. This paper describes how to exploit the dynamic routing capabilities of the ubichip in order to implement synaptogenetic neural networks. We present two techniques for dynamically generating the network topology, we describe their implementation in the ubichip, and we analyse the resulting topology. This work constitutes a first step toward neural circuits exhibiting more realistic neural plasticity features.
BibTeX: 
@inproceedings{upegui08dynamic,
  author = {A. Upegui and Y. Thoma and A. Perez-Uribe and E. Sanchez},
  editor = {D. Keymeulen and T. Arslan and M. Suess and A. Stoica and A.T. Erdogan and D. Merodio},
  title = {Dynamic Routing on the Ubichip: Toward Synaptogenetic Neural Networks},
  booktitle = {Proceedings of the 3rd NASA/ESA Conference on Adaptive Hardware and Systems},
  publisher = {IEEE Computer Society},
  year = {2008},
  pages = {228-235},
  doi = {10.1109/AHS.2008.39}
}
Upegui A, Perez-Uribe A, Thoma Y and Sanchez E (2008), "Neural Development on the Ubichip by Means of Dynamic Routing Mechanisms", In Evolvable Systems: From Biology to Hardware. Berlin, Heidelberg Vol. 5216, pp. 392-401. Springer Verlag.

[BibTeX] [DOI]
BibTeX: 
@inproceedings{upegui08neural,
  author = {A. Upegui and A. Perez-Uribe and Y. Thoma and E. Sanchez},
  editor = {G.S. Hornby and L. Sekanina and P.C. Haddow},
  title = {Neural Development on the Ubichip by Means of Dynamic Routing Mechanisms},
  booktitle = {Evolvable Systems: From Biology to Hardware},
  publisher = {Springer Verlag},
  year = {2008},
  volume = {5216},
  pages = {392-401},
  doi = {10.1007/978-3-540-85857-7\_35}
}
Upegui A, Thoma Y, Sanchez E, Perez-Uribe A, Moreno J, Madrenas J and Sassatelli G (2008), "The PERPLEXUS bio-inspired hardware platform: A flexible and modular approach", International Journal of Knowledge-Based and Intelligent Engineering Systems (KES). Vol. 12(3), pp. 201-212. IOS Press.

[BibTeX]
BibTeX: 
@article{upegui08perplexus,
  author = {A. Upegui and Y. Thoma and E. Sanchez and A. Perez-Uribe and J.M. Moreno and J. Madrenas and Gilles Sassatelli},
  title = {The PERPLEXUS bio-inspired hardware platform: A flexible and modular approach},
  journal = {International Journal of Knowledge-Based and Intelligent Engineering Systems (KES)},
  publisher = {IOS Press},
  year = {2008},
  volume = {12},
  number = {3},
  pages = {201-212}
}
Barker W, Halliday DM, Thoma Y, Sanchez E, Tempesti G and Tyrrell AM (2007), "Fault Tolerance using Dynamic Reconfiguration on the POEtic Tissue", IEEE Transactions on Evolutionary Computation. Vol. 11(5), pp. 666-684.

[BibTeX] [DOI]
BibTeX: 
@article{barker07fault,
  author = {W. Barker and D. M. Halliday and Y. Thoma and E. Sanchez and G. Tempesti and and A. M Tyrrell},
  title = {Fault Tolerance using Dynamic Reconfiguration on the POEtic Tissue},
  journal = {IEEE Transactions on Evolutionary Computation},
  year = {2007},
  volume = {11},
  number = {5},
  pages = {666-684},
  doi = {10.1109/TEVC.2007.896690}
}
Sanchez E, Perez-Uribe A, Upegui A, Thoma Y, Moreno J, Villa A, Volken H, Napieralski A, Sassatelli G and Lavarec E (2007), "PERPLEXUS: Pervasive Computing Framework for Modeling Complex Virtually-Unbounded Systems", In AHS 2007 - Proceedings of the 2nd NASA/ESA Conference on Adaptive Hardware and Systems. Los Alamitos, CA, USA, aug, 2007. , pp. 600-605. IEEE Computer Society.

[BibTeX]
BibTeX: 
@inproceedings{sanchez07perplexus,
  author = {E. Sanchez and A. Perez-Uribe and A. Upegui and Y. Thoma and J.M. Moreno and A. Villa and H. Volken and A. Napieralski and G. Sassatelli and E. Lavarec},
  editor = {T. Arslan and A. Stoica and M. Suess and D. Keymeulen and T. Higuchi and R. Zebulum and A. T. Erdogan},
  title = {PERPLEXUS: Pervasive Computing Framework for Modeling Complex Virtually-Unbounded Systems},
  booktitle = {AHS 2007 - Proceedings of the 2nd NASA/ESA Conference on Adaptive Hardware and Systems},
  publisher = {IEEE Computer Society},
  year = {2007},
  pages = {600-605}
}
Stucki D, Fasel S, Gisin N, Thoma Y and Zbinden H (2007), "Coherent One-way Quantum Key Distribution", In Proceedings of SPIE. Vol. 6583

[BibTeX] [DOI]
BibTeX: 
@inproceedings{stucki07coherent,
  author = {D. Stucki and S. Fasel and N. Gisin and Y. Thoma and H. Zbinden},
  editor = {I. Prochazka and A. L. Migdall and A. Pauchard and M. Dusek and M. S. Hillery and W. P. Schleich},
  title = {Coherent One-way Quantum Key Distribution},
  booktitle = {Proceedings of SPIE},
  year = {2007},
  volume = {6583},
  doi = {10.1117/12.722952}
}
Thoma Y, Upegui A, Perez-Uribe A and Sanchez E (2007), "Self-Replication Mechanism by Means of Self-Reconfiguration", In 20th International Conference on Architecture of Computing Systems 2007 (ARCS '07), Workshop proceedings., mar, 2007. , pp. 105-112. VDE Verlag.

[BibTeX]
BibTeX: 
@inproceedings{thoma07self,
  author = {Y. Thoma and A. Upegui and A. Perez-Uribe and E. Sanchez},
  editor = {M. Platzner and K.-E. Grosspietsch and C. Hochberger and A. Koch},
  title = {Self-Replication Mechanism by Means of Self-Reconfiguration},
  booktitle = {20th International Conference on Architecture of Computing Systems 2007 (ARCS '07), Workshop proceedings},
  publisher = {VDE Verlag},
  year = {2007},
  pages = {105-112}
}
Upegui A, Thoma Y, Sanchez E, Perez-Uribe A, Moreno J and Madrenas J (2007), "The Perplexus Bio-inspired Reconfigurable Circuit", In Proceedings of the 2nd NASA/ESA Conference on Adaptive Hardware and Systems. Los Alamitos, CA, USA, aug, 2007. , pp. 600-605. IEEE Computer Society.

[BibTeX]
BibTeX: 
@inproceedings{upegui07perplexus,
  author = {A. Upegui and Y. Thoma and E. Sanchez and A. Perez-Uribe and J.M. Moreno and J. Madrenas},
  editor = {T. Arslan and A. Stoica and M. Suess and D. Keymeulen and T. Higuchi and R. Zebulum and A. T. Erdogan},
  title = {The Perplexus Bio-inspired Reconfigurable Circuit},
  booktitle = {Proceedings of the 2nd NASA/ESA Conference on Adaptive Hardware and Systems},
  publisher = {IEEE Computer Society},
  year = {2007},
  pages = {600-605}
}
Moreno J-M, Thoma Y, Sanchez E, Eriksson J, Iglesias J and Villa A (2006), "The POEtic Electronic Tissue and its Role in the Emulation of Large-Scale Biologically Inspired Spiking Neural Networks Models", In ComPlexus., aug, 2006. Vol. 3, pp. 32-47.

[Abstract] [BibTeX]
Abstract: One of the major obstacles found when trying to construct artefacts derived from principles observed in living beings is the lack of actual dynamic hardware with autonomous capabilities. Even if programmable devices offer the possibility of modifying the functionality implemented in the device, they rely on external hardware and software elements to provide its physical confi guration. In this paper we present a new family of electronic devices, called POEtic, whose architecture has been derived from the basic properties that can be extracted from the three major organization principles present in living beings: phylogenesis, ontogenesis and epigenesis. We will demonstrate that the capabilities present in these new programmable devices make them an ideal candidate for the real-time emulation of large-scale biologically inspired spiking neural network models.
BibTeX: 
@inproceedings{moreno06poetic,
  author = {J.-M. Moreno and Y. Thoma and E. Sanchez and J. Eriksson and J. Iglesias and A. Villa},
  title = {The POEtic Electronic Tissue and its Role in the Emulation of Large-Scale Biologically Inspired Spiking Neural Networks Models},
  booktitle = {ComPlexus},
  year = {2006},
  volume = {3},
  pages = {32-47}
}
Rossier J, Thoma Y, Mudry P-A and Tempesti G (2006), "MOVE Processors That Self-replicate and Differentiate", In Proc. Biologically Inspired Approaches to Advanced Information Technology (BioADIT 2006). Berlin Heidelberg (3853), pp. 160-175. Springer-Verlag.

[Abstract] [BibTeX]
Abstract: This article describes an implementation of a basic multiprocessor system that exhibits replication and differentiation abilities on the POEtic tissue, a programmable hardware designed for bio-inspired applications [1, 2] . As for a living organism, whose existence starts with only one cell that first divides, our system begins with only one totipotent processor, able to implement any of the cells required by the final organism, which can also fully replicate itself, using the functionalities of the POEtic substrate. Then, analogously to the cells in a developing organism, our just replicated totipotent processors differentiate in order to execute their specific part of the complete organism functionality. In particular, we will present a working realization using MOVE processors whose instructions define the flow of data rather than the operations to be executed [3]. It starts with one basic MOVE processor that first replicates itself three times; the four resulting processors then differentiate and connect together to implement a multi-processor modulus-60 counter.
BibTeX: 
@inproceedings{rossier06move,
  author = {J. Rossier and Y. Thoma and P.-A. Mudry and G. Tempesti},
  editor = {A.J. Ijspeert and others},
  title = {MOVE Processors That Self-replicate and Differentiate},
  booktitle = {Proc. Biologically Inspired Approaches to Advanced Information Technology (BioADIT 2006)},
  publisher = {Springer-Verlag},
  year = {2006},
  number = {3853},
  pages = {160-175}
}
Moreno J, Thoma Y and Sanchez E (2005), "POEtic: A Prototyping Platform for Bio-inspired Hardware", In Evolvable Systems: From Biology to Hardware (ICES 2005). Berlin Heidelberg Vol. 3637, pp. 177-187. Springer-Verlag.

[BibTeX]
BibTeX: 
@inproceedings{moreno05poetic,
  author = {J.M. Moreno and Y. Thoma and E. Sanchez},
  editor = {J.M. Moreno and J. Madrenas and J. Cosp},
  title = {POEtic: A Prototyping Platform for Bio-inspired Hardware},
  booktitle = {Evolvable Systems: From Biology to Hardware (ICES 2005)},
  publisher = {Springer-Verlag},
  year = {2005},
  volume = {3637},
  pages = {177-187}
}
Thoma Y and Sanchez E (2005), "An Adaptive FPGA and its Distributed Routing", In Proc. ReCoSoc '05 Reconfigurable Communication-centric SoC. Montpellier - France, June, 2005. , pp. 43-51.

[Abstract] [BibTeX]
Abstract: Every commercially available FPGA supplies high routing capabilities. However, placement and routing are processed by a computer before being sent to the chip. This nonadaptive feature does not fit well with bio-inspired applications such as growing systems or neural networks with changing topology. Therefore we propose a new kind of routing, built in hardware and totally distributed. Unlike previous works about routing, our approach does not need a central control over the process. In this paper we present a new FPGA embedding this algorithm, as well as the basic idea of our architecture, based on a parallel implementation of Lee shortest path algorithm. We then present a second algorithm that decreases the number of possible congestions, a third that reduces the execution time, and a fourth that combines both techniques. Finally we introduce different neighborhoods and compare all these algorithms in terms of area, speed, path length and congestion.
BibTeX: 
@inproceedings{thoma05adaptive,
  author = {Y. Thoma and E. Sanchez},
  title = {An Adaptive FPGA and its Distributed Routing},
  booktitle = {Proc. ReCoSoc '05 Reconfigurable Communication-centric SoC},
  year = {2005},
  pages = {43-51}
}
Thoma Y (2005), "Tissu Numérique Cellulaire à Routage et Configuration Dynamiques". Thesis at: EPFL. 1015 Lausanne, April, 2005.

[BibTeX]
BibTeX: 
@phdthesis{thoma05tissu,
  author = {Y. Thoma},
  title = {Tissu Numérique Cellulaire à Routage et Configuration Dynamiques},
  school = {EPFL},
  year = {2005},
  note = {Thesis N°3226. http://lslwww.epfl.ch/ thoma/research/these}
}
Moreno J-M, Thoma Y, Sanchez E, Torres O and Tempesti G (2004), "Hardware Realization of a Bio-inspired POEtic Tissue", In Proc. 2004 NASA/DoD Conference on Evolvable Hardware. Los Alamitos, California , pp. 237-244. IEEE Computer Society.

[Abstract] [BibTeX]
Abstract: This paper will present the physical hardware realization of a novel bio-inspired architecture, called POEtic tissue. This electronic tissue provides a platform for the efficient implementation in actual hardware of evolutionary, epigenetic (learning) and ontogenetic (growth, self-repair, self-replication) mechanisms. After a brief introduction the overall organization of the tissue will be presented. Then its main building blocks will be reviewed. Finally, the implementation details of the first hardware prototype of the tissue, constructed in the form of an ASIC, will be outlined. The implementation results demonstrate that the proposed architecture constitutes a good candidate when considering the electronic realization of bio-inspired principles.
BibTeX: 
@inproceedings{moreno04hardware,
  author = {J.-M. Moreno and Y. Thoma and E. Sanchez and O. Torres and G. Tempesti},
  editor = {R. S. Zebulum and D. Galtney and G. Hornby and D. Keymeulen and J. Lohn and A. Stoica},
  title = {Hardware Realization of a Bio-inspired POEtic Tissue},
  booktitle = {Proc. 2004 NASA/DoD Conference on Evolvable Hardware},
  publisher = {IEEE Computer Society},
  year = {2004},
  pages = {237-244}
}
Roggen D, Thoma Y and Sanchez E (2004), "An Evolving and Developing Cellular Electronic Circuit", In Proc. Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9). Cambridge, Massachusetts, USA , pp. 33-38. The MIT Press.

[Abstract] [BibTeX]
Abstract: A novel multi-cellular electronic circuit capable of evolution and development is described here. The circuit is composed of identical cells whose shape and location in the system is arbitrary. Cells all contain the complete genetic description of the final system, as in living organisms. Through a mechanism of development, cells connect to each other using a fully distributed hardware routing mechanism and differentiate by expressing a corresponding part of the genetic code thereby taking a specific functionality and connectivity in the system. The configuration of the system is found by using artificial evolution and intrinsic evolution at the schematic level is possible. Applications include the approximation of boolean functions and the evolution of a controller capable of navigating a Khepera robot while avoiding obstacles. The circuit is suited for a custom chip called POEtic, which is a generic platform to implement bio-inspired applications.
BibTeX: 
@inproceedings{roggen04evolving,
  author = {D. Roggen and Y. Thoma and E. Sanchez},
  editor = {J. Pollack and others},
  title = {An Evolving and Developing Cellular Electronic Circuit},
  booktitle = {Proc. Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9)},
  publisher = {The MIT Press},
  year = {2004},
  pages = {33-38}
}
Thoma Y, Tempesti G, Sanchez E and Moreno Arostegui J-M (2004), "POEtic: An Electronic Tissue for Bio-Inspired Cellular Applications", BioSystems., August-October, 2004. Vol. 74(1-3), pp. 191-200.

[Abstract] [BibTeX]
Abstract: In this paper, we introduce the general architecture of a new electronic tissue called POEtic. This reconfigurable circuit is designed to ease the implementation of bio-inspired systems that bring cellular applications into play. It contains special features that allow a developer to realize systems that require evolution (Phylogenesis), development (Ontogenesis), and/or learning (Epigenesis). A dynamic routing algorithm has been added to a structure similar to that of common commercial FPGAs, in order to allow the creation of data paths between cells. As the creation of these paths is dynamic, it is possible to add new cells or to repair faulty ones at runtime.
BibTeX: 
@article{thoma04poetic,
  author = {Y. Thoma and G. Tempesti and E. Sanchez and J.-M. Moreno Arostegui},
  title = {POEtic: An Electronic Tissue for Bio-Inspired Cellular Applications},
  journal = {BioSystems},
  year = {2004},
  volume = {74},
  number = {1-3},
  pages = {191-200}
}
Thoma Y, Roggen D, Sanchez E and Moreno J-M (2004), "Prototyping with a Bio-inspired Reconfigurable Chip", In Proc. 15th IEEE International Workshop on Rapid System Prototyping (RSP 2004). Los Alamitos, California , pp. 239-246. IEEE Computer Society.

[Abstract] [BibTeX]
Abstract: In this paper we explain how the POEtic chip can be used for rapid prototyping. The POEtic chip, currently in the test phase, is a system-on-chip (SoC) containing a microprocessor and a reconfigurable array. Special features allow the dynamic creation of data paths in the reconfigurable array at runtime. It has been specially designed to ease the development of bio-inspired systems such as neural networks, but can serve as a general purpose platform, or as a prototype for hardware/software codesign. An AMBA bus allows POEtic chips to be connected to each other, or to external devices. After describing the hardware SoC, we discuss the software tools that have been created to design and test different applications. Three of these applications are described in order to demonstrate the utility of the POEtic chip’s special features.
BibTeX: 
@inproceedings{thoma04prototyping,
  author = {Y. Thoma and D. Roggen and E. Sanchez and J.-M. Moreno},
  editor = {F. Titsworth},
  title = {Prototyping with a Bio-inspired Reconfigurable Chip},
  booktitle = {Proc. 15th IEEE International Workshop on Rapid System Prototyping (RSP 2004)},
  publisher = {IEEE Computer Society},
  year = {2004},
  pages = {239-246}
}
Thoma Y and Sanchez E (2004), "A Reconfigurable Chip for Evolvable Hardware", In Proc. Genetic and Evolutionary Computation COnference (GECCO 2004), Part I. Berlin, Heidelberg (3102), pp. 816-827. Springer Verlag.

[Abstract] [BibTeX]
Abstract: In the recent years, Xilinx devices, like the XC6200, were the preferred solutions for evolving digital systems. In this paper, we present a new System-On-Chip, the POEtic chip, an alternative for evolvable hardware. This chip has been specifically designed to ease the implementation of bio-inspired systems. It is composed of a microprocessor, and a programmable part, containing basic elements, like every standard Field Programmable Gate Array, on top of which sits a special layer implementing a dynamic routing algorithm. Online on-chip evolution can then be processed, as every configuration bit of the programmable array can be accessed by the microprocessor. This new platform can therefore replace the Xilinx XC6200, with the advantage of having a processor inside.
BibTeX: 
@inproceedings{thoma04reconfigurable,
  author = {Y. Thoma and E. Sanchez},
  editor = {K. Deb and others},
  title = {A Reconfigurable Chip for Evolvable Hardware},
  booktitle = {Proc. Genetic and Evolutionary Computation COnference (GECCO 2004), Part I},
  publisher = {Springer Verlag},
  year = {2004},
  number = {3102},
  pages = {816-827}
}
Roggen D, Hofmann S, Thoma Y and Floreano D (2003), "Hardware Spiking Neural Network with Run-Time Reconfigurable Connectivity in an Autonomous Robot", In Proc. 2003 NASA/DoD Conference on Evolvable Hardware. Los Alamitos, California , pp. 189-198. IEEE Computer Society.

[Abstract] [BibTeX]
Abstract: A cellular hardware implementation of a spiking neural network with run-time reconfigurable connectivity is presented. It is implemented on a compact custom FPGA board which provides a powerful reconfigurable hardware platform for hardware and software design. Complementing the system, a CPU synthesized on the FPGA takes care of interfacing the network with the external world. The FPGA board and the hardware network are demonstrated in the form of a controller embedded on the Khepera robot for a task of obstacle avoidance. Finally, future implementations on new multi-cellular hardware are discussed.
BibTeX: 
@inproceedings{roggen03hardware,
  author = {D. Roggen and S. Hofmann and Y. Thoma and D. Floreano},
  editor = {J. Lohn and R. Zebulum and J. Steincamp and D. Keymeulen and A. Stoica and M. I. Ferguson},
  title = {Hardware Spiking Neural Network with Run-Time Reconfigurable Connectivity in an Autonomous Robot},
  booktitle = {Proc. 2003 NASA/DoD Conference on Evolvable Hardware},
  publisher = {IEEE Computer Society},
  year = {2003},
  pages = {189-198}
}
Tempesti G, Mange D, Petraglio E, Stauffer A and Thoma Y (2003), "Developmental Processes in Silicon: An Engineering Perspective", In Proc. 2003 NASA/DoD Conference on Evolvable Hardware. Los Alamitos, California , pp. 255-264. IEEE Computer Society.

[Abstract] [BibTeX]
Abstract: In this article, we try to analyze the requirements of developmental processes from the perspective of their implementation in digital hardware. After recalling the motivations for such an implementation, we concentrate separately on the two mechanisms (cellular division and cellular differentiation) that are exploited by biological systems to realize development. We then describe some of the current and projected solutions to implement such mechanisms in hardware, and conclude by analyzing the most interesting features of developmental approaches.
BibTeX: 
@inproceedings{tempesti03developmental,
  author = {G. Tempesti and D. Mange and E. Petraglio and A. Stauffer and Y. Thoma},
  editor = {J. Lohn and R. Zebulum and J. Steincamp and D. Keymeulen and A. Stoica and M. I. Ferguson},
  title = {Developmental Processes in Silicon: An Engineering Perspective},
  booktitle = {Proc. 2003 NASA/DoD Conference on Evolvable Hardware},
  publisher = {IEEE Computer Society},
  year = {2003},
  pages = {255-264}
}
Tempesti G, Roggen D, Sanchez E, Thoma Y, Canham R and Tyrell A (2003), "Ontogenetic Development and Fault Tolerance in the POEtic Tissue", In Evolvable Systems: From Biology to Hardware. Proc. 5th Int. Conf. on Evolvable Hardware (ICES 2003). Berlin, Heidelberg (2606), pp. 141-152. Springer Verlag.

[Abstract] [BibTeX]
Abstract: In this article, we introduce the approach to the realization of ontogenetic development and fault tolerance that will be implemented in the POEtic tissue, a novel reconfigurable digital circuit dedicated to the realization of bio-inspired systems. The modelization in electronic hardware of the developmental process of multi-cellular biological organisms is an approach that could become extremely useful in the implementation of highly complex systems, where concepts such as self-organization and fault tolerance are key issues. The concepts presented in this article represent an attempt at finding a useful set of mechanisms to allow the implementation in digital hardware of a bio-inspired developmental process with a reasonable overhead.
BibTeX: 
@inproceedings{tempesti03ontogenetic,
  author = {G. Tempesti and D. Roggen and E. Sanchez and Y. Thoma and R. Canham and A.M. Tyrell},
  editor = {A.M. Tyrrell and P.C. Haddow and J. Torresen},
  title = {Ontogenetic Development and Fault Tolerance in the POEtic Tissue},
  booktitle = {Evolvable Systems: From Biology to Hardware. Proc. 5th Int. Conf. on Evolvable Hardware (ICES 2003)},
  publisher = {Springer Verlag},
  year = {2003},
  number = {2606},
  pages = {141-152}
}
Thoma Y, Sanchez E, Moreno Arostegui J-M and Tempesti G (2003), "A Dynamic Routing Algorithm for a Bio-Inspired Reconfigurable Circuit", In Proc. of the 13th International Conference on Field Programmable Logic and Applications (FPL'03). Berlin, Heidelberg Vol. 2778, pp. 681-690. Springer Verlag.

[Abstract] [BibTeX]
Abstract: In this paper we present a new dynamic routing algorithm specially implemented for a new electronic tissue called POEtic. This reconfigurable circuit is designed to ease the implementation of bio-inspired systems that bring cellular applications into play. Specifically designed for implementing cellular applications, such as neural networks, this circuit is composed of two main parts: a two-dimensional array of basic elements similar to those found in common commercial FPGAs, and a two-dimensional array of routing units that implement a dynamic routing algorithm which allows the creation of data paths between cells at runtime.
BibTeX: 
@inproceedings{thoma03dynamic,
  author = {Y. Thoma and E. Sanchez and J.-M. Moreno Arostegui and G. Tempesti},
  editor = {P. Y. K. Cheung and others},
  title = {A Dynamic Routing Algorithm for a Bio-Inspired Reconfigurable Circuit},
  booktitle = {Proc. of the 13th International Conference on Field Programmable Logic and Applications (FPL'03)},
  publisher = {Springer Verlag},
  year = {2003},
  volume = {2778},
  pages = {681-690}
}
Thoma Y, Sanchez E, Arostegui J-MM and Tempesti G (2003), "Un Sistema de Enrutamiento Dinàmico para un Circuito Reconfigurable Bio-Inspirado", In Computacion Reconfigurable & FPGAs. Universided Autonoma de Madrid , pp. 27-37.

[Abstract] [BibTeX]
Abstract: En este artículo presentamos un nuevo algoritmo de enrutamiento dinámico, dise nado especialmente para un nuevo tejido electrónico llamado POEtic. Este circuito reconfigurable tiene como finalidad la simplificación del diseño de sistemas bio-inspirados para aplicaciones celulares (circuitos neuronales artificiales, por ejemplo). El circuito se compone de dos partes: una matriz bidimensional de elementos básicos, similares a las células de base de los circuitos FPGA comerciales, y una matriz bidimensional de unidades de enrutamiento, que implementan un algoritmo de enrutamiento dinámico que permite la creación de caminos de datos entre las células, sin interrumpir el funcionamiento del sistema.
BibTeX: 
@inproceedings{thoma03sistema,
  author = {Y. Thoma and E. Sanchez and J.-M. Moreno Arostegui and G. Tempesti},
  editor = {E. B. Scalvinoni and F. G. Arribas and S. Lopez-Buedo and G. S. Capristo},
  title = {Un Sistema de Enrutamiento Dinàmico para un Circuito Reconfigurable Bio-Inspirado},
  booktitle = {Computacion Reconfigurable & FPGAs},
  year = {2003},
  pages = {27-37}
}
Tempesti G, Roggen D, Sanchez E, Thoma Y, Canham R, Tyrrell A and Moreno J-M (2002), "A POEtic Architecture for Bio-Inspired Systems", In Proc. 8th Int. Conf. of Artificial Life VIII. Cambridge, Massachusetts, December, 2002. , pp. 111-115. MIT Press.

[Abstract] [BibTeX]
Abstract: The implementation of bio-inspired systems in hardware has traditionally been more a matter of artistry than of method. The reasons are multiple, but one of the main problems has always been the lack of a universal platform, of a standardized architecture, and of a proper methodology for the implementation of such systems. The ideas presented in this article are the first results of a new research project, "Reconfigurable POEtic Tissue". The goal of the project is the development of a hardware platform capable of implementing systems inspired by all the three major axes (phylogenesis, ontogenesis, and epigenesis) of bio-inspiration in digital hardware. A novel cellular architecture, capable of exploiting the main features of the future POEtic tissue and compatible with a relatively automatic design methodology, is then presented.
BibTeX: 
@inproceedings{tempesti02poetic,
  author = {G. Tempesti and D. Roggen and E. Sanchez and Y. Thoma and R. Canham and A. Tyrrell and J.-M. Moreno},
  editor = {R.K. Standish and M.A. Bedau and H.A. Abbass},
  title = {A POEtic Architecture for Bio-Inspired Systems},
  booktitle = {Proc. 8th Int. Conf. of Artificial Life VIII},
  publisher = {MIT Press},
  year = {2002},
  pages = {111-115}
}
Thoma Y and Sanchez E (2002), "CoDeNios: A Function Level Co-Design Tool", In Workshop on Computer Architecture Education, WCAE 2002, Workshop Proceedings. Anchorage, Alaska , pp. 73-78.

[Abstract] [BibTeX]
Abstract: The need of co-design systems, along with the FPGA complexity, is increasing dramatically, both in industrial and academic settings. New tools are necessary to ease the development of such systems. Altera supplies a development kit with a 200’000 equivalent gates FPGA; combined with its proprietary Nios configurable processor, it allows co-design and multi-processor architecture creation. In this paper, we present a new tool, CoDeNios, which lets a developer partition a C program at the function level, and automatically generates the whole system.
BibTeX: 
@inproceedings{thoma02codenios,
  author = {Y. Thoma and E. Sanchez},
  title = {CoDeNios: A Function Level Co-Design Tool},
  booktitle = {Workshop on Computer Architecture Education, WCAE 2002, Workshop Proceedings},
  year = {2002},
  pages = {73-78}
}