{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T10:50:05Z","timestamp":1743072605164,"version":"3.40.3"},"publisher-location":"Cham","reference-count":35,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030856328"},{"type":"electronic","value":"9783030856335"}],"license":[{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021]]},"DOI":"10.1007\/978-3-030-85633-5_16","type":"book-chapter","created":{"date-parts":[[2021,9,12]],"date-time":"2021-09-12T23:04:33Z","timestamp":1631487873000},"page":"245-253","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols"],"prefix":"10.1007","author":[{"given":"David","family":"Doty","sequence":"first","affiliation":[]},{"given":"Eric","family":"Severson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,9,13]]},"reference":[{"key":"16_CR1","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1007\/978-3-319-66799-7_11","volume-title":"DNA Computing and Molecular Programming","author":"D Alistarh","year":"2017","unstructured":"Alistarh, D., Dudek, B., Kosowski, A., Soloveichik, D., Uzna\u0144ski, P.: Robust detection in leak-prone population protocols. In: Brijder, R., Qian, L. (eds.) DNA 2017. LNCS, vol. 10467, pp. 155\u2013171. Springer, Cham (2017). https:\/\/doi.org\/10.1007\/978-3-319-66799-7_11"},{"key":"16_CR2","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1007\/978-3-662-47666-6_38","volume-title":"Automata, Languages, and Programming","author":"D Alistarh","year":"2015","unstructured":"Alistarh, D., Gelashvili, R.: Polylogarithmic-time leader election in population protocols. In: Halld\u00f3rsson, M.M., Iwama, K., Kobayashi, N., Speckmann, B. (eds.) ICALP 2015. LNCS, vol. 9135, pp. 479\u2013491. Springer, Heidelberg (2015). https:\/\/doi.org\/10.1007\/978-3-662-47666-6_38"},{"issue":"4","key":"16_CR3","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1007\/s00446-005-0138-3","volume":"18","author":"D Angluin","year":"2006","unstructured":"Angluin, D., Aspnes, J., Diamadi, Z., Fischer, M.J., Peralta, R.: Computation in networks of passively mobile finite-state sensors. Distrib. Comput. 18(4), 235\u2013253 (2006)","journal-title":"Distrib. Comput."},{"issue":"2","key":"16_CR4","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/s00446-008-0059-z","volume":"21","author":"D Angluin","year":"2008","unstructured":"Angluin, D., Aspnes, J., Eisenstat, D.: A simple population protocol for fast robust approximate majority. Distrib. Comput. 21(2), 87\u2013102 (2008)","journal-title":"Distrib. Comput."},{"key":"16_CR5","doi-asserted-by":"publisher","unstructured":"Berenbrink, P., Giakkoupis, G., Kling, P.: Optimal time and space leader election in population protocols. In: STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing, STOC 2020, pp. 119\u2013129. Association for Computing Machinery, New York (2020). https:\/\/doi.org\/10.1145\/3357713.3384312","DOI":"10.1145\/3357713.3384312"},{"key":"16_CR6","unstructured":"Berenbrink, P., Hammer, D., Kaaser, D., Meyer, U., Penschuck, M., Tran, H.: Simulating population protocols in sub-constant time per interaction. In: ESA 2020: 28th Annual European Symposium on Algorithms, vol. 173, pp. 16:1\u201316:22 (2020). https:\/\/drops.dagstuhl.de\/opus\/volltexte\/2020\/12882"},{"key":"16_CR7","unstructured":"Berenbrink, P., Kaaser, D., Kling, P., Otterbach, L.: Simple and efficient leader election. In: 1st Symposium on Simplicity in Algorithms (SOSA 2018), vol. 61, pp. 9:1\u20139:11 (2018)"},{"key":"16_CR8","doi-asserted-by":"crossref","unstructured":"Bilke, A., Cooper, C., Els\u00e4sser, R., Radzik, T.: Brief announcement: population protocols for leader election and exact majority with $${O}(\\log ^2 n)$$ states and $${O}(\\log ^2 n)$$ convergence time. In: PODC 2017: Proceedings of the ACM Symposium on Principles of Distributed Computing, pp. 451\u2013453. ACM (2017)","DOI":"10.1145\/3087801.3087858"},{"key":"16_CR9","doi-asserted-by":"crossref","unstructured":"Burman, J., et al.: Time-optimal self-stabilizing leader election in population protocols. In: PODC 2021: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (2021)","DOI":"10.1145\/3465084.3467898"},{"key":"16_CR10","doi-asserted-by":"crossref","unstructured":"Cao, Y., Gillespie, D.T., Petzold, L.R.: Efficient step size selection for the tau-leaping simulation method. J. Chem. Physi. 124(4), 044109 (2006)","DOI":"10.1063\/1.2159468"},{"key":"16_CR11","doi-asserted-by":"publisher","unstructured":"Cardelli, L., Kwiatkowska, M., Laurenti, L.: Stochastic analysis of chemical reaction networks using linear noise approximation. Biosystems 149, 26\u201333 (2016). https:\/\/doi.org\/10.1016\/j.biosystems.2016.09.004, https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0303264716302039, selected papers from the Computational Methods in Systems Biology 2015 conference","DOI":"10.1016\/j.biosystems.2016.09.004"},{"issue":"10","key":"16_CR12","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1038\/nnano.2013.189","volume":"8","author":"YJ Chen","year":"2013","unstructured":"Chen, Y.J., et al.: Programmable chemical controllers made from DNA. Nat. Nanotechnol. 8(10), 755\u2013762 (2013)","journal-title":"Nat. Nanotechnol."},{"issue":"1","key":"16_CR13","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/s11047-019-09756-4","volume":"19","author":"A Condon","year":"2020","unstructured":"Condon, A., Hajiaghayi, M., Kirkpatrick, D., Ma\u0148uch, J.: Approximate majority analyses using tri-molecular chemical reaction networks. Nat. Comput. 19(1), 249\u2013270 (2020)","journal-title":"Nat. Comput."},{"key":"16_CR14","unstructured":"Doty, D., Severson, E.: ppsim: A software package for efficiently simulating and visualizing population protocols. Technical Report 2105.04702, arXiv (2021). arXiv:2105.04702"},{"key":"16_CR15","doi-asserted-by":"crossref","unstructured":"Doty, D., Soloveichik, D.: Stable leader election in population protocols requires linear time. Distrib. Comput. 31(4), 257\u2013271 (2018), special issue of invited papers from DISC 2015","DOI":"10.1007\/s00446-016-0281-z"},{"key":"16_CR16","doi-asserted-by":"crossref","unstructured":"Dudek, B., Kosowski, A.: Universal protocols for information dissemination using emergent signals. In: Proceedings of the 50th Annual ACM SIGACT Symposium on Theory of Computing, pp. 87\u201399 (2018)","DOI":"10.1145\/3188745.3188818"},{"key":"16_CR17","unstructured":"Els\u00e4sser, R., Radzik, T.: Recent results in population protocols for exact majority and leader election. Bull. EATCS 3(126) (2018)"},{"issue":"11","key":"16_CR18","doi-asserted-by":"publisher","first-page":"5624","DOI":"10.1073\/pnas.1912980117","volume":"117","author":"G Fanti","year":"2020","unstructured":"Fanti, G., Holden, N., Peres, Y., Ranade, G.: Communication cost of consensus for nodes with limited memory. Proc. Natl. Acad. Sci. 117(11), 5624\u20135630 (2020)","journal-title":"Proc. Natl. Acad. Sci."},{"key":"16_CR19","doi-asserted-by":"crossref","unstructured":"Ga\u0327sieniec, L., Stachowiak, G.: Fast space optimal leader election in population protocols. In: SODA 2018: ACM-SIAM Symposium on Discrete Algorithms, pp. 2653\u20132667. SIAM (2018)","DOI":"10.1137\/1.9781611975031.169"},{"key":"16_CR20","doi-asserted-by":"crossref","unstructured":"Ga\u0327sieniec, L., Stachowiak, G., Uzna\u0144ski, P.: Almost logarithmic-time space optimal leader election in population protocols. In: SPAA 2019: 31st ACM Symposium on Parallelism in Algorithms and Architectures, pp. 93\u2013102 (2019)","DOI":"10.1145\/3323165.3323178"},{"issue":"9","key":"16_CR21","doi-asserted-by":"publisher","first-page":"1876","DOI":"10.1021\/jp993732q","volume":"104","author":"MA Gibson","year":"2000","unstructured":"Gibson, M.A., Bruck, J.: Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104(9), 1876\u20131889 (2000)","journal-title":"J. Phys. Chem. A"},{"issue":"25","key":"16_CR22","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340\u20132361 (1977)","journal-title":"J. Phys. Chem."},{"issue":"4","key":"16_CR23","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1063\/1.1378322","volume":"115","author":"DT Gillespie","year":"2001","unstructured":"Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting systems. J. Phys. Chem. 115(4), 1716\u20131733 (2001)","journal-title":"J. Phys. Chem."},{"key":"16_CR24","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","volume":"58","author":"DT Gillespie","year":"2007","unstructured":"Gillespie, D.T.: Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35\u201355 (2007)","journal-title":"Annu. Rev. Phys. Chem."},{"key":"16_CR25","unstructured":"GillesPy2. https:\/\/github.com\/StochSS\/GillesPy2"},{"issue":"7","key":"16_CR26","doi-asserted-by":"publisher","first-page":"2976","DOI":"10.1063\/1.1678692","volume":"57","author":"TG Kurtz","year":"1972","unstructured":"Kurtz, T.G.: The relationship between stochastic and deterministic models for chemical reactions. J. Phys. Chem. 57(7), 2976\u20132978 (1972)","journal-title":"J. Phys. Chem."},{"key":"16_CR27","doi-asserted-by":"publisher","unstructured":"Lathrop, J.I., Lutz, J.H., Lutz, R.R., Potter, H.D., Riley, M.R.: Population-induced phase transitions and the verification of chemical reaction networks. In: Geary, C., Patitz, M.J. (eds.) DNA 26: 26th International Conference on DNA Computing and Molecular Programming. Leibniz International Proceedings in Informatics (LIPIcs), vol.\u00a0174, pp. 5:1\u20135:17. Schloss Dagstuhl\u2013Leibniz-Zentrum f\u00fcr Informatik, Dagstuhl (2020). https:\/\/doi.org\/10.4230\/LIPIcs.DNA.2020.5","DOI":"10.4230\/LIPIcs.DNA.2020.5"},{"key":"16_CR28","unstructured":"ppsim Python package. source code (2021). https:\/\/github.com\/UC-Davis-molecular-computing\/ppsim API documentation, https:\/\/ppsim.readthedocs.io\/ Python package for installation via pip: https:\/\/pypi.org\/project\/ppsim\/"},{"issue":"2","key":"16_CR29","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1016\/j.jcp.2006.10.034","volume":"224","author":"M Rathinam","year":"2007","unstructured":"Rathinam, M., El Samad, H.: Reversible-equivalent-monomolecular tau: a leaping method for \u201csmall number and stiff\u2019\u2019 stochastic chemical systems. J. Comput. Phys. 224(2), 897\u2013923 (2007)","journal-title":"J. Comput. Phys."},{"key":"16_CR30","doi-asserted-by":"crossref","unstructured":"Sanft, K.R., Wu, S., Roh, M., Fu, J., Rone, K.L., Petzold, L.R.: Stochkit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics 27(17), 501\u2013522 (2011). https:\/\/academic.oup.com\/bioinformatics\/article\/27\/17\/2457\/224105","DOI":"10.1093\/bioinformatics\/btr401"},{"issue":"20","key":"16_CR31","doi-asserted-by":"publisher","first-page":"05B618","DOI":"10.1063\/1.2919546","volume":"128","author":"A Slepoy","year":"2008","unstructured":"Slepoy, A., Thompson, A.P., Plimpton, S.J.: A constant-time kinetic monte carlo algorithm for simulation of large biochemical reaction networks. J. Chem. Phys. 128(20), 05B618 (2008)","journal-title":"J. Chem. Phys."},{"issue":"3","key":"16_CR32","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1089\/cmb.2008.0063","volume":"16","author":"D Soloveichik","year":"2009","unstructured":"Soloveichik, D.: Robust stochastic chemical reaction networks and bounded tau-leaping. J. Comput. Biol. 16(3), 501\u2013522 (2009)","journal-title":"J. Comput. Biol."},{"issue":"6369","key":"16_CR33","doi-asserted-by":"publisher","first-page":"eaal2052","DOI":"10.1126\/science.aal2052","volume":"358","author":"N Srinivas","year":"2017","unstructured":"Srinivas, N., Parkin, J., Seelig, G., Winfree, E., Soloveichik, D.: Enzyme-free nucleic acid dynamical systems. Science 358(6369), eaal2052 (2017)","journal-title":"Science"},{"issue":"01","key":"16_CR34","doi-asserted-by":"publisher","first-page":"2050005","DOI":"10.1142\/S012962642050005X","volume":"30","author":"Y Sudo","year":"2020","unstructured":"Sudo, Y., Masuzawa, T.: Leader election requires logarithmic time in population protocols. Para. Process. Lett. 30(01), 2050005 (2020)","journal-title":"Para. Process. Lett."},{"issue":"11","key":"16_CR35","doi-asserted-by":"publisher","first-page":"2620","DOI":"10.1109\/TPDS.2020.2991771","volume":"31","author":"Y Sudo","year":"2020","unstructured":"Sudo, Y., Ooshita, F., Izumi, T., Kakugawa, H., Masuzawa, T.: Time-optimal leader election in population protocols. IEEE Trans. Parallel Distrib. Syst. 31(11), 2620\u20132632 (2020). https:\/\/doi.org\/10.1109\/TPDS.2020.2991771","journal-title":"IEEE Trans. Parallel Distrib. Syst."}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-85633-5_16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,12]],"date-time":"2021-09-12T23:06:10Z","timestamp":1631487970000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-85633-5_16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"ISBN":["9783030856328","9783030856335"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-85633-5_16","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2021]]},"assertion":[{"value":"13 September 2021","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"CMSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Computational Methods in Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Bordeaux","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"France","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2021","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"22 September 2021","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"24 September 2021","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"19","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cmsb2021","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/cmsb2021.labri.fr\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}