The Multiscale Systems Immunology project: software for cell-based immunological simulation

<p>Abstract</p> <p>Background</p> <p>Computer simulations are of increasing importance in modeling biological phenomena. Their purpose is to predict behavior and guide future experiments. The aim of this project is to model the early immune response to vaccination by an agent based immune response simulation that incorporates realistic biophysics and intracellular dynamics, and which is sufficiently flexible to accurately model the multi-scale nature and complexity of the immune system, while maintaining the high performance critical to scientific computing.</p> <p>Results</p> <p>The Multiscale Systems Immunology (MSI) simulation framework is an object-oriented, modular simulation framework written in C++ and Python. The software implements a modular design that allows for flexible configuration of components and initialization of parameters, thus allowing simulations to be run that model processes occurring over different temporal and spatial scales.</p> <p>Conclusion</p> <p>MSI addresses the need for a flexible and high-performing agent based model of the immune system.</p

A Newcomer's Guide to EICS, the Engineering Interactive Computing Systems Community

[EN] Welcome to EICS, the Engineering Interactive Computing Systems community, PACMHCI/EICS journal, and annual conference! In this short article, we introduce newcomers to the field and to our community with an overview of what EICS is and how it positions with respect to other venues in Human-Computer Interaction, such as CHI, UIST, and IUI, highlighting its legacy and paying homage to past scientific events from which EICS emerged. We also take this opportunity to enumerate and exemplify scientific contributions to the field of Engineering Interactive Computing Systems, which we hope to guide researchers and practitioners towards making their future PACMHCI/EICS submissions successful and impactful in the EICS community.We acknowledge the support of MetaDev2 as the main sponsor of EICS 2019. We would like to thank the Chairs of all the tracks of the EICS 2019 conference, the members of the local organization team, and the web master of the EICS 2019 web site. EICS 2019 could not have been possible without the commitment of the Programme Committee members and external reviewers. This work was partially supported by the Spanish Ministry of Economy, Industry and Competitiveness, State Research Agency / European Regional Development Fund under Vi-SMARt (TIN2016-79100-R), the Junta de Comunidades de Castilla-La Mancha European Regional Development Fund under NeUX (SBPLY/17/180501/000192) projects, the Generalitat Valenciana through project GISPRO (PROMETEO/2018/176), and the Spanish Ministry of Science and Innovation through project DataME (TIN2016-80811-P).López-Jaquero, VM.; Vatavu, R.; Panach, JI.; Pastor López, O.; Vanderdonckt, J. (2019). A Newcomer's Guide to EICS, the Engineering Interactive Computing Systems Community. Proceedings of the ACM on Human-Computer Interaction. 3:1-9. https://doi.org/10.1145/3300960S193Bastide, R., Palanque, P., & Roth, J. (Eds.). (2005). Engineering Human Computer Interaction and Interactive Systems. Lecture Notes in Computer Science. doi:10.1007/b136790Beaudouin-Lafon, M. (2004). Designing interaction, not interfaces. Proceedings of the working conference on Advanced visual interfaces - AVI ’04. doi:10.1145/989863.989865Bodart, F., & Vanderdonckt, J. (Eds.). (1996). Design, Specification and Verification of Interactive Systems ’96. Eurographics. doi:10.1007/978-3-7091-7491-3Gallud, J. A., Tesoriero, R., Vanderdonckt, J., Lozano, M., Penichet, V., & Botella, F. (2011). Distributed user interfaces. Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems - CHI EA ’11. doi:10.1145/1979742.1979576Graham, T. C. N., & Palanque, P. (Eds.). (2008). Interactive Systems. Design, Specification, and Verification. Lecture Notes in Computer Science. doi:10.1007/978-3-540-70569-7Proceedings of the 1st ACM SIGCHI symposium on Engineering interactive computing systems - EICS ’09. (2009). doi:10.1145/1570433Lawson, J.-Y. L., Vanderdonckt, J., & Vatavu, R.-D. (2018). Mass-Computer Interaction for Thousands of Users and Beyond. Extended Abstracts of the 2018 CHI Conference on Human Factors in Computing Systems. doi:10.1145/3170427.3188465Lozano, M. D., Galllud, J. A., Tesoriero, R., Penichet, V. M. R., Vanderdonckt, J., & Fardoun, H. (2013). 3rd workshop on distributed user interfaces. Proceedings of the 5th ACM SIGCHI symposium on Engineering interactive computing systems - EICS ’13. doi:10.1145/2494603.2483222Proceedings of the 2014 Workshop on Distributed User Interfaces and Multimodal Interaction - DUI ’14. (2014). doi:10.1145/2677356Proceedings of the ACM SIGCHI Symposium on Engineering Interactive Computing Systems. (2019). doi:10.1145/3319499Tesoriero, R., Lozano, M., Vanderdonckt, J., Gallud, J. A., & Penichet, V. M. R. (2012). distributed user interfaces. CHI ’12 Extended Abstracts on Human Factors in Computing Systems. doi:10.1145/2212776.2212704Vanderdonckt, J. (2005). A MDA-Compliant Environment for Developing User Interfaces of Information Systems. Active Flow and Combustion Control 2018, 16-31. doi:10.1007/11431855_2Vatavu, R.-D. (2012). User-defined gestures for free-hand TV control. Proceedings of the 10th European conference on Interactive tv and video - EuroiTV ’12. doi:10.1145/2325616.2325626Vatavu, R.-D. (2017). Beyond Features for Recognition: Human-Readable Measures to Understand Users’ Whole-Body Gesture Performance. International Journal of Human–Computer Interaction, 33(9), 713-730. doi:10.1080/10447318.2017.1278897Wobbrock, J. O., & Kientz, J. A. (2016). Research contributions in human-computer interaction. Interactions, 23(3), 38-44. doi:10.1145/290706

Agreement technologies and their use in cloud computing environments

The final publication is available at Springer via http://dx.doi.org/10.1007/s13748-012-0031-9[EN] Nowadays, cloud computing is revolutionizing the services provided through the Internet to adapt itself in order to keep the quality of its services. Recent research foresees the advent of a new discipline of agent-based cloud computing systems that can make decisions about adaption in an uncertain environment. This paper discusses the role of argumentation in the next generation of agreement technologies and its use in cloud computing environments.This work is supported by the Spanish government (MICINN), project reference: TIN2012-36586-C03-01.Heras Barberá, SM.; De La Piedra, F.; Julian Inglada, VJ.; Rodríguez, S.; Botti Navarro, VJ.; Bajo, J.; Corchado, JM. (2012). Agreement technologies and their use in cloud computing environments. Progress in Artificial Intelligence. 1(4):277-290. https://doi.org/10.1007/s13748-012-0031-9S27729014European Comission: The Future of Cloud Computing. Technical report (2010)Barham, P., Dragovic, B., Fraser, K., Hand, S., Harris, T., Ho, A., Neugebauer, R., Pratt, I., Warfield, A.: Xen and the art of virtualization. In: SOSP03 Proceedings of the Nineteenth ACM Symposium on Operating Systems Principles, pp. 164–177. ACM, New York (2003)Wang, L., et. al.: Scientific cloud computing: early definition and experience. In: 10th IEEE International Conference on High Performance Computing and Communications (HPCC-08), pp. 825–830. IEEE Press (2008)Talia, D.: Clouds meet agents: toward intelligent cloud services. Internet Comput. IEEE 16(2), 78–81 (2012). doi: 10.1109/MIC.2012.28Heras, S.: Case-Based Argumentation Framework for Agent Societies. PhD thesis, Universitat Politècnica de València. http://hdl.handle.net/10251/12497 (2011)Ashton, K.: That ‘internet of things’ thing. RFID J. (2009). http://www.rfidjournal.com/article/view/4986Klusch, M.: Information agent technology for the Internet: a Survey. Data Knowl. Eng. 36, 337–372 (2001)Schaffer, H.E.: X as a Service. Cloud Computing, and the Need for Good Judgment IT Professional 11(5), 4–5 (2009). doi: 10.1109/MITP.2009.112Richardson, L., Ruby, S.: RESTful Web Services, Web services for the real world O’Reilly, Media, May, p. 454 (2007)GlusterFS Developers. The Gluster web site. http://www.gluster.org (2012)Chodorow, K., Dirolf, M.: The Definitive Guide. O’Reilly Media, MongoDB (2010)Fuentes-Fernandez, R., Hassan, S., Pavon, J., Galan, J.M., Lopez-Paredes, A.: Metamodels for role-driven agent-based modelling. Comput. Math. Organ. Theory 18(1), 91–112 (2012)Jordán, J., et al.: A customer support application using argumentation in multi-agent systems. In: 14th International Conference on, Information Fusion, pp. 772–778 (2011)Heras, S., Jordán, J., Botti, V., Julián, V.: Argue to agree: a case-based argumentation approach. Int. J. Approx. Reasoning (2012, in press)Walton, D., Reed, C., Macagno, F.: Argumentation Schemes. Cambridge University Press, Cambridge (2008)Bench-Capon, T., Sartor, G.: A model of legal reasoning with cases incorporating theories and values. Artif. Intell. 150(1–2), 97–143 (2003)Dignum, F., Weigand, H.: Communication and deontic logic. In: Information Systems Correctness and Reusability, pp. 242–260. World Scientific, Singapore (1995)Wooldridge, M., Jennings, N.R.: Intelligent agents: theory and practice. Knowl. Eng. Rev. 10(2), 115–152 (1995)Lopez-Rodriguez, I., Hernandez-Tejera, M.: Software agents as cloud computing services. In: 9th International Conference on Practical Applications of Agents and Multiagent Systems. Advances in Intelligent and Soft Computing, vol. 88, pp. 271–276. Springer, Berlin (2011)Sim, K.M.: Towards complex negotiation for cloud economy. In: 5th International Conference on Advances in Grid and Pervasive Computing. LNCS, vol. 6104, pp. 395–406. Springer, Berlin (2010)Aversa, R., et al.: Cloud agency: a mobile agent based cloud system. In: International Conference on Complex, Intelligent and Software Intensive Systems, pp. 132–137. IEEE Computer Society Press, Washington, DC (2010)Cao, B., et al.: A service-oriented qos-assured and multi-agent cloud computing architecture. In: 1st International Conference on Cloud Computing. LNCS, vol. 5931, pp. 644–649. Springer, Berlin (2009)Rahwan, I., Simari, G. (eds.): Argumentation in Artificial Intelligence. Springer, Berlin (2009

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

Utah Science Vol. 44 No. 1, Spring 1983

1 CANNED RAINBOW TROUT D. T. Bartholomew, C. A. Ernstrom, and V. T. Mendenhall Canned trout is nudging canned tuna on grocery shelves thanks to a cooperative venture at USU. Trout meat that used to be lost to human consumption has been made available. 4 GRAPES TO MAKE YOUR OWN RAISINS J. L. Anderson, M. G. Weeks, W. A. Varga, G. Scott, and C. P. Brennand All grapes are not equal when it comes to converting them into raisins. Utah\u27s climate makes local testing of varieties especially crucial. There are, however, varieties and raisin,-making techniques that can be recommended for the home gardener. 9 APPLE GROWING-A BLEND OF ART AND SCIENCE D. R. Walker Science has given the apple grower several production tools, none more valuable than the ability to dwarf the trees. Research is now defining the best spacing and rootstocks for optimizing early and prolonged productivity. 12 VEGETABLE VARIETIES FOR UTAH A. R. Hamson and W. A. Varga Seed Catalogues just aren\u27t enough if you want your garden to thrive. You need the recommendations that are coming from a varietal testing program at Farmington, Utah. 17 A VEGETABLE GARDENER\u27S GUIDE TO IRRIGATION R. W. Hill, I. Agulto, M. D. Miah, and A. A. Ramalan A scientific evaluation of varied irrigation frequencies determines the most efficient watering procedures for improved crop production. 20 COMPUTING NUTRITION G. C. Lauritzen and B. W. Wyse A new diet aid is available through your County Extension Office. A computerized analysis of your daily diet identifies insufficient required nutrients as well as selects foods to insure a healthy weight loss in a prescribed time period

Trusted CI Experiences in Cybersecurity and Service to Open Science

This article describes experiences and lessons learned from the Trusted CI project, funded by the US National Science Foundation to serve the community as the NSF Cybersecurity Center of Excellence. Trusted CI is an effort to address cybersecurity for the open science community through a single organization that provides leadership, training, consulting, and knowledge to that community. The article describes the experiences and lessons learned of Trusted CI regarding both cybersecurity for open science and managing the process of providing centralized services to a broad and diverse community.Comment: 8 pages, PEARC '19: Practice and Experience in Advanced Research Computing, July 28-August 1, 2019, Chicago, IL, US