Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation

Gorka Epelde, Andoni Mujika, Roberto Alvarez, Peter Leškovský, Alessandro de Mauro, Finn Krewer, Axel Blau

Abstract

This paper discusses a Caenorhabditis elegans (C. elegans) nematode behavioral experiment input encoding. It proposes a common digital representation for behavioral studies with C. elegans. This work is a step forward towards the reproducibility and comparability of in silico simulations of the nematode with real-world experiments. The digital representation is divided into environmental and experimental configurations. The behavioral input is structured by duration-based behavioral experiment types at the top level (i.e. interaction at a specific time, interaction from t0 – t1 and overall duration) and by interaction type (i.e. mechanotaxis, chemotaxis, thermotaxis, galvanotaxis and phototaxis) for each duration-based type. The environment configuration is composed of the identification of the worm’s mutation type, worm crowding, initial location, configuration of the assay plate, and obstacle settings. Parameters are defined by an XML schema to ensure the interoperability with other simulation solutions. It is being implemented and tested in the context of the Si elegans project

References

  1. Cannon, Robert C., Gewaltig, Marc-Oliver, Gleeson, Padraig, Bhalla, Upinder S., Cornelis, Hugo, Hines, Michael L., Howell, Fredrick W., Muller, Eilif, Stiles, Joel R., Wils, Stefan and Schutter, Erik De (2007), Interoperability of Neuroscience Modeling Software: Current Status and Future Directions. Neuroinformatics, 5(2): 127-138.
  2. Crook, Sharon M., Davison, Andrew P. and Plesser, Hans E. (2013), Learning from the Past: Approaches for Reproducibility in Computational Neuroscience, 73- 102, in: Bower, J. M. (Ed.), 20 Years of Computational Neuroscience. Springer Series in Computational Neuroscience. Springer New York. available at http://link.springer.com/chapter/10.1007/ 978-1-4614-1424-7_4 [23 September 2015].
  3. Dada, Joseph O., Spasic, Irena, Paton, Norman W. and Mendes, Pedro (2010), SBRML: A Markup Language for Associating Systems Biology Data with Models. Bioinformatics, 26(7): 932-938.
  4. Davison, Andrew P., Brüderle, Daniel, Eppler, Jochen, Kremkow, Jens, Muller, Eilif, Pecevski, Dejan, Perrinet, Laurent and Yger, Pierre (2009), PyNN: A Common Interface for Neuronal Network Simulators. Frontiers in Neuroinformatics, 2. available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC26345 33/ [23 September 2015].
  5. Dräger, Andreas and Palsson, Bernhard Ø. (2014), Improving Collaboration by Standardization Efforts in Systems Biology. Frontiers in Bioengineering and Biotechnology, 2. available at http://www.ncbi.nlm nih.gov/pmc/articles/PMC4259112/ [22 September 2015].
  6. Gabel, Christopher V., Gabel, Harrison, Pavlichin, Dmitri, Kao, Albert, Clark, Damon A. and Samuel, Aravinthan D. T. (2007), Neural Circuits Mediate Electrosensory Behavior in Caenorhabditis Elegans. The Journal of Neuroscience, 27(28): 7586-7596.
  7. Ghosh, Samik, Matsuoka, Yukiko, Asai, Yoshiyuki, Hsin, Kun-Yi and Kitano, Hiroaki (2011), Software for Systems Biology: From Tools to Integrated Platforms. Nature Reviews Genetics. available at http://www.nature.com/doifinder/10.1038/nrg3096 [22 September 2015].
  8. Gleeson, P, Crook, S, Cannon, RC, Hines, ML, Billings, GO, Farinella, M, Morse, TM, Davison, AP, Ray, S and Bhalla, US (2010), NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail. PLoS Computational Biology, 6(6): e1000815.
  9. Hart, Anne C (2005), Behavior (July 3, 2006), WormBook, Ed. The C. Elegans Research Community, WormBook, doi/10.1895/wormbook. 1.87. 1.
  10. Iersel, Martijn P. van, Villéger, Alice C., Czauderna, Tobias, Boyd, Sarah E., Bergmann, Frank T., Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I., Mi, Huaiyu, Moodie, Stuart L., Kitano, Hiroaki, Novère, Nicolas Le and Schreiber, Falk (2012), Software Support for SBGN Maps: SBGN-ML and LibSBGN. Bioinformatics, 28(15): 2016-2021.
  11. Le Novère, Nicolas, Finney, Andrew, Hucka, Michael, Bhalla, Upinder S, Campagne, Fabien, Collado-Vides, Julio, Crampin, Edmund J, Halstead, Matt, Klipp, Edda, Mendes, Pedro, Nielsen, Poul, Sauro, Herbert, Shapiro, Bruce, Snoep, Jacky L, Spence, Hugh D and Wanner, Barry L (2005), Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM). Nature Biotechnology, 23(12): 1509- 1515.
  12. Lloyd, Catherine M., Halstead, Matt D. B. and Nielsen, Poul F. (2004), CellML: Its Future, Present and Past. Progress in Biophysics and Molecular Biology, 85(2- 3): 433-450.
  13. Mueller, Shane T. and Piper, Brian J. (2014), The Psychology Experiment Building Language (PEBL) and PEBL Test Battery. Journal of Neuroscience Methods, 222: 250-259.
  14. Neurobehavioral Systems (2015), Precise, Powerful Stimulus Delivery. available at http://www.neurobs .com/ [23 September 2015].
  15. NuML Project (2015), NuML - Numerical Markup Language. available at https://github.com/numl/numl [23 September 2015].
  16. OpenWorm Project (2015), OpenWorm Movement Validation Project. available at https://github. com/openworm/movement_validation [22 September 2015].
  17. Schindelman, Gary, Fernandes, Jolene S., Bastiani, Carol A., Yook, Karen and Sternberg, Paul W. (2011), Worm Phenotype Ontology: Integrating Phenotype Data within and beyond the C. Elegans Community. BMC bioinformatics, 12: 32.
  18. Si elegans Consortium (2015a), Behavioural Experiment Input Definition XML Schema. available at https://github.com/Si-elegans/behavioural_experiment _definition/blob/master/behaviourDesc.xsd.
  19. Si elegans Consortium (2015b), Behavioral Experiment Input Encoding Example. available at https://github. com/Si-elegans/behavioural_experiment_definition/ blob/master/Examples/example_nebica2015.xml.
  20. Szigeti, Balazs, Gleeson, Padraig, Vella, Michael, Khayrulin, Sergey, Palyanov, Andrey, Hokanson, Jim, Currie, Michael, Cantarelli, Matteo, Idili, Giovanni and Larson, Stephen (2014), OpenWorm: An OpenScience Approach to Modelling Caenorhabditis Elegans. Frontiers in Computational Neuroscience, 8. available at http://www.frontiersin.org/Journal /Abstract.aspx?s=237&name=computational_neurosci ence&ART_DOI=10.3389/fncom.2014.00137.
  21. Teeters, Jeffrey L., Harris, Kenneth D., Millman, K. Jarrod, Olshausen, Bruno A. and Sommer, Friedrich T. (2008), Data Sharing for Computational Neuroscience. Neuroinformatics, 6(1): 47-55.
  22. Waltemath, Dagmar, Adams, Richard, Bergmann, Frank T., Hucka, Michael, Kolpakov, Fedor, Miller, Andrew K., Moraru, Ion I., Nickerson, David, Sahle, Sven, Snoep, Jacky L. and Novère, Nicolas Le (2011), Reproducible Computational Biology Experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Systems Biology, 5(1): 198.
  23. Ward, Alex, Liu, Jie, Feng, Zhaoyang and Xu, X Z Shawn (2008), Light-Sensitive Neurons and Channels Mediate Phototaxis in C. Elegans. Nature Neuroscience, 11(8): 916-922.
  24. Wimalaratne, S. M., Halstead, M. D. B., Lloyd, C. M., Cooling, M. T., Crampin, E. J. and Nielsen, P. F. (2009), A Method for Visualizing CellML Models. Bioinformatics, 25(22): 3012-3019.
Download


Paper Citation


in Harvard Style

Epelde G., Mujika A., Alvarez R., Leškovský P., de Mauro A., Krewer F. and Blau A. (2015). Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation . In Proceedings of the 3rd International Congress on Neurotechnology, Electronics and Informatics - Volume 1: NeBICA, (NEUROTECHNIX 2015) ISBN 978-989-758-161-8, pages 115-120. DOI: 10.5220/0005701801150120


in Bibtex Style

@conference{nebica15,
author={Gorka Epelde and Andoni Mujika and Roberto Alvarez and Peter Leškovský and Alessandro de Mauro and Finn Krewer and Axel Blau},
title={Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation},
booktitle={Proceedings of the 3rd International Congress on Neurotechnology, Electronics and Informatics - Volume 1: NeBICA, (NEUROTECHNIX 2015)},
year={2015},
pages={115-120},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005701801150120},
isbn={978-989-758-161-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 3rd International Congress on Neurotechnology, Electronics and Informatics - Volume 1: NeBICA, (NEUROTECHNIX 2015)
TI - Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation
SN - 978-989-758-161-8
AU - Epelde G.
AU - Mujika A.
AU - Alvarez R.
AU - Leškovský P.
AU - de Mauro A.
AU - Krewer F.
AU - Blau A.
PY - 2015
SP - 115
EP - 120
DO - 10.5220/0005701801150120