Modeling Biological Systems Using Crowdsourcing

[1] An G., Mi Q., Dutta-Moscato J., and Vodovotz Y. Agent-based models in translational systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 1(2):159{171, 2009.10.1002/wsbm.45364033320835989Search in Google Scholar

[2] Ansari S., Binder J., Boue S., Fabio A. D., Hayes W., Hoeng J., Iskandar A., Kleiman R., Norel R., O'neel B., Peitsch M. C., Poussin C., Pratt D., Rhrissorrakrai K., Schlage W. K., Stolovitzky G., and Talikka M. On crowd-verification of biological networks. Bioinformatics and Biology Insights, 7:BBI.S12932, 2013.10.4137/BBI.S12932379829224151423Search in Google Scholar

[3] Bae J. A., Mu S., Kim J. S., Turner N. L., Tartavull I., Kemnitz N., Jordan C. S., Norton A. D., Silversmith W. M., Prentki R., et al. Digital museum of retinal ganglion cells with dense anatomy and physiology. bioRxiv, page 182758, 2018.10.1101/182758Search in Google Scholar

[4] Barone J., Bayer C., Copley R., Barlow N., Burns M., Rao S., Seelig G., Popovic Z., Cooper S., and Players N. Nanocrafter: Design and evaluation of a dna nanotechnology game. In Proceedings of the 10th International Conference on the Foundations of Digital Games, pages 1{5, 2015.Search in Google Scholar

[5] Barrett T., Wilhite S. E., Ledoux P., Evangelista C., Kim I. F., Tomashevsky M., Marshall K. A., Phillippy K. H., Sherman P. M., Holko M., et al. Ncbi geo: archive for functional genomics data sets|update. Nucleic acids research, 41(D1):D991{D995, 2012.Search in Google Scholar

[6] Bladek I., Chojnacki T., Miazga K., and Szwachla J. Platform for evaluation of algorithms estimating real paremeters in biological systems (Platforma do oceny algorytmow wyznaczania paramterow rzeczywistych w systemach biologicznych). Master's thesis, Faculty of Computing, Poznan University of Technology, 2014.Search in Google Scholar

[7] Bonabeau E. Decisions 2.0: The power of collective intelligence. MIT Sloan management review, 50(2):45, 2009.Search in Google Scholar

[8] Bruggeman F. J. and Westerhoff H. V. The nature of systems biology. Trends in Microbiology, 15(1):45{50, 2007.10.1016/j.tim.2006.11.00317113776Search in Google Scholar

[9] Cookson C. Online gaming yields first results for alzheimer's research. Financial Times, 2017.Search in Google Scholar

[10] Cooper S., Khatib F., Treuille A., Barbero J., Lee J., Beenen M., Leaver-Fay A., Baker D., Popović Z., et al. Predicting protein structures with a multiplayer online game. Nature, 466(7307):756, 2010.10.1038/nature09304295641420686574Search in Google Scholar

[11] Costello J. C. and Stolovitzky G. Seeking the Wisdom of Crowds Through Challenge-Based Competitions in Biomedical Research. Clinical Pharmacology & Therapeutics, 93(5):396{398, feb 2013.10.1038/clpt.2013.3623549146Search in Google Scholar

[12] Dahari H., Ribeiro R. M., and Perelson A. S. Triphasic decline of hepatitis C virus RNA during antiviral therapy. Hepatology, 46(1):16{21, 2007.10.1002/hep.2165717596864Search in Google Scholar

[13] Dawson R. and Bynghall S. Getting Results From Crowds: The definitive guide to using crowdsourcing to grow your business. Advanced Human Technologies Incl, 2012.Search in Google Scholar

[14] Deng N., Galliers R., and Joshi K. Crowdworking|a new digital divide? is design and research implications. In ECIS Conference Proceedings, 2016.Search in Google Scholar

[15] Derry J. M. J., Mangravite L. M., Suver C., Furia M. D., Henderson D., Schildwachter X., Bot B., Izant J., Sieberts S. K., Kellen M. R., and Friend S. H. Developing predictive molecular maps of human disease through communitybased modeling. Nature Genetics, 44(2):127{130, jan 2012.10.1038/ng.1089364381822281773Search in Google Scholar

[16] DiStefano III J. Dynamic systems biology modeling and simulation. Academic Press, 2015.Search in Google Scholar

[17] Doan A., Ramakrishnan R., and Halevy A. Y. Crowdsourcing systems on the world-wide web. Commun. ACM, 54(4):86{96, Apr. 2011.10.1145/1924421.1924442Search in Google Scholar

[18] Eiben C. B., Siegel J. B., Bale J. B., Cooper S., Khatib F., Shen B. W., Stoddard B. L., Popovic Z., and Baker D. Increased Diels-Alderase activity through backbone remodeling guided by foldit players. Nature biotechnology, 30(2):190, 2012.10.1038/nbt.2109356676722267011Search in Google Scholar

[19] Estellés-Arolas E. and González-Ladrón-De-Guevara F. Towards an integrated crowdsourcing definition. J. Inf. Sci., 38(2):189{200, Apr. 2012.10.1177/0165551512437638Search in Google Scholar

[20] Fratczak F. Design of the algorithm for estimating values of parameters in biological models (Opracowanie algorytmu wyznaczajacego wartosci parametrow w modelach biologicznych). Master's thesis, Faculty of Computing, Poznan University of Technology, 2016.Search in Google Scholar

[21] Fries P. A mechanism for cognitive dynamics: neuronal communication through neuronal coherence. Trends in Cognitive Sciences, 9(10):474 {480, 2005.Search in Google Scholar

[22] Frings M., Berkels B., Behr M., and Elgeti S. Comparison of optimization algorithms for the slow shot phase in hpdc. AIP Conference Proceedings, 1960(1):110005, 2018.10.1063/1.5034962Search in Google Scholar

[23] Galton F. Vox populi (the wisdom of crowds). Nature, 75(7):450{451, 1907.10.1038/075450a0Search in Google Scholar

[24] Good B. M. and Su A. I. Crowdsourcing for bioinformatics. Bioinformatics, 29(16):1925{1933, 2013.10.1093/bioinformatics/btt333372252323782614Search in Google Scholar

[25] Haklay M. and Weber P. Openstreetmap: User-generated street maps. Ieee Pervas Comput, 7(4):12{18, 2008.Search in Google Scholar

[26] Helmstaedter M., Briggman K. L., Turaga S. C., Jain V., Seung H. S., and Denk W. Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature, 500(7461):168, 2013.10.1038/nature1234623925239Search in Google Scholar

[27] Hill S. M., Heiser L. M., Cokelaer T., Unger M., Nesser N. K., Carlin D. E., Zhang Y., Sokolov A., Paull E. O., Wong C. K., et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature methods, 13(4):310, 2016.Search in Google Scholar

[28] Hirschman L., Fort K., Boué S., Kyrpides N., Islamaj Doğan R., and Cohen K. B. Crowdsourcing and curation: perspectives from biology and natural language processing. Database, 2016:baw115, 2016.Search in Google Scholar

[29] Ho C. C. and Ting C.-Y. Measuring crowd sourced analytics: A review. Inter- national Information Institute (Tokyo). Information, 19(10B):4891, 2016.Search in Google Scholar

[30] Hodgkin A. L. and Huxley A. F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol, 117(4):500{544, Aug 1952.10.1113/jphysiol.1952.sp004764139241312991237Search in Google Scholar

[31] Horowitz S., Koepnick B., Martin R., Tymieniecki A., Winburn A. A., Cooper S., Flatten J., Rogawski D. S., Koropatkin N. M., Hailu T. T., et al. Determining crystal structures through crowdsourcing and coursework. Nature communica- tions, 7:12549, 2016.10.1038/ncomms13392509333327779204Search in Google Scholar

[32] Howe J. The rise of crowdsourcing. Wired magazine, 14(6):1{4, 2006.Search in Google Scholar

[33] Kawrykow A., Roumanis G., Kam A., Kwak D., Leung C., Wu C., Zarour E., players P., Sarmenta L., Blanchette M., and WaldispĀ(Ehl J. Phylo: A citizen science approach for improving multiple sequence alignment. PLOS ONE, 7(3):1{9, 03 2012.10.1371/journal.pone.0031362329669222412834Search in Google Scholar

[34] Kim J. S., Greene M. J., Zlateski A., Lee K., Richardson M., Turaga S. C., Purcaro M., Balkam M., Robinson A., Behabadi B. F., et al. Space{time wiring specificity supports direction selectivity in the retina. Nature, 509(7500):331, 2014.10.1038/nature13240407488724805243Search in Google Scholar

[35] Kitano H. Foundations of Systems Biology. The MIT Press, 2001.10.7551/mitpress/3087.001.0001Search in Google Scholar

[36] Kittur A., Chi E. H., and Suh B. Crowdsourcing user studies with mechanical turk. In Proceedings of the SIGCHI conference on human factors in computing systems, pages 453{456. ACM, 2008.10.1145/1357054.1357127Search in Google Scholar

[37] Lee J., Kladwang W., Lee M., Cantu D., Azizyan M., Kim H., Limpaecher A., Gaikwad S., Yoon S., Treuille A., Das R., and . Rna design rules from a massive open laboratory. Proceedings of the National Academy of Sciences, 111(6):2122{ 2127, 2014.10.1073/pnas.1313039111392605824469816Search in Google Scholar

[38] Lee J. and Seo D. Crowdsourcing not all sourced by the crowd: An observation on the behavior of wikipedia participants. Technovation, 55:14{21, 2016.Search in Google Scholar

[39] Liang J., Qu B., Suganthan P., and Hernández-Díaz A. G. Problem definitions and evaluation criteria for the CEC 2013 special session on real-parameter optimization. Computational Intelligence Laboratory, Zhengzhou University, Zhengzhou, China and Nanyang Technological University, Singapore, Technical Report, 201212:3{18, 2013.Search in Google Scholar

[40] Logas H., Whitehead J., Mateas M., Vallejos R., Scott L., Shapiro D., Murray J., Compton K., Osborn J., Salvatore O., and others. Software Verification Games: Designing Xylem, The Code of Plants. In Foundations of Digital Games 2014 (FDG2014), pages 1{8. Center for Games and Playable Media, 2014.Search in Google Scholar

[41] Luengo-Oroz A. M., Arranz A., and Frean J. Crowdsourcing malaria parasite quantification: An online game for analyzing images of infected thick blood smears. J Med Internet Res, 14(6):e167, Nov 2012.10.2196/jmir.2338351072023196001Search in Google Scholar

[42] Marbach D., Costello J. C., Küffner R., Vega N. M., Prill R. J., Camacho D. M., Allison K. R., Aderhold A., Bonneau R., Chen Y., et al. Wisdom of crowds for robust gene network inference. Nature methods, 9(8):796, 2012.10.1038/nmeth.2016351211322796662Search in Google Scholar

[43] Mavandadi S., Feng S., Yu F., Dimitrov S., Yu R., and Ozcan A. Biogames: A platform for crowd-sourced biomedical image analysis and telediagnosis. Games for Health Journal, 1(5):373{376, 2012. PMID: 23724363.Search in Google Scholar

[44] Mesarovic M. Systems Theory and Biology. Springer Verlag, 1968.Search in Google Scholar

[45] Meyer P., Cokelaer T., Chandran D., Kim K. H., Loh P.-R., Tucker G., Lipson M., Berger B., Kreutz C., Raue A., Steiert B., Timmer J., Bilal E., Sauro H. M., Stolovitzky G., and Saez-Rodriguez J. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology, 8(1):13, Feb 2014.10.1186/1752-0509-8-13392787024507381Search in Google Scholar

[46] Mietchen D., Wodak S., Wasik S., Szostak N., and Dessimoz C. Submit a topic page to plos computational biology and wikipedia. PLOS Computational Biology, 14(5):1{4, 05 2018.10.1371/journal.pcbi.1006137597887729851950Search in Google Scholar

[47] Nurse P. Reductionism: The ends of understanding. Nature, 387(6634):657, 1997.Search in Google Scholar

[48] Peer E., Samat S., Brandimarte L., and Acquisti A. Beyond the turk: An empirical comparison of alternative platforms for crowdsourcing online behavioral research. NA - Advances in Consumer Research, 43:18{22, 2016.Search in Google Scholar

[49] Pico A. R., Kelder T., van Iersel M. P., Hanspers K., Conklin B. R., and Evelo C. Wikipathways: Pathway editing for the people. PLOS Biology, 6(7):1{4, 07 2008.10.1371/journal.pbio.0060184247554518651794Search in Google Scholar

[50] Powell M. J. A view of algorithms for optimization without derivatives. Math- ematics Today-Bulletin of the Institute of Mathematics and its Applications, 43(5):170{174, 2007.Search in Google Scholar

[51] Prejzendanc T., Wasik S., and Blazewicz J. Computer representations of bioinformatics models. Current Bioinformatics, 11(5):551{560, 2016.10.2174/1574893610666150928193510Search in Google Scholar

[52] Prelec D., Seung H. S., and McCoy J. A solution to the single-question crowd wisdom problem. Nature, 541(7638):532, 2017.10.1038/nature2105428128245Search in Google Scholar

[53] Saez-Rodriguez J., Costello J. C., Friend S. H., Kellen M. R., Mangravite L., Meyer P., Norman T., and Stolovitzky G. Crowdsourcing biomedical research: leveraging communities as innovation engines. Nature Reviews Genetics, 17(8):470{486, jul 2016.10.1038/nrg.2016.69591868427418159Search in Google Scholar

[54] Schmidt M. and Lipson H. Distilling Free-Form Natural Laws from Experimental Data. Science, 324(5923):81{85, apr 2009.10.1126/science.116589319342586Search in Google Scholar

[55] Schrier K. Investigating typologies of games as research environments. In Pro- ceedings of International Conference on the Foundations of Digital Games, pages 1{4, 2017.Search in Google Scholar

[56] Szostak N., Synak J., Borowski M., Wasik S., and Blazewicz J. Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution. PLOS ONE, 2017.10.1371/journal.pone.0180827550727928700697Search in Google Scholar

[57] Szostak N., Wasik S., and Blazewicz J. Hypercycle. PLOS Computational Biol- ogy, 12(4):e1004853, apr 2016.10.1371/journal.pcbi.1004853482441827054759Search in Google Scholar

[58] Szuba T. T., Polański P., Schab P., and Wielicki P. On efficiency of collective intelligence phenomena. In Transactions on computational collective intelligence III, pages 50{73. Springer, 2011.10.1007/978-3-642-19968-4_3Search in Google Scholar

[59] Tellioglu U., Xie G. G., Rohrer J. P., and Prince C. Whale of a crowd: Quantifying the effectiveness of crowd-sourced serious games. In 2014 Computer Games: AI, Animation, Mobile, Multimedia, Educational and Serious Games (CGAMES), pages 1{7, July 2014.10.1109/CGames.2014.6934151Search in Google Scholar

[60] Tomita, Hashimoto, Takahashi, Shimizu, Matsuzaki, Miyoshi, Saito, Tanida, Yugi, Venter, and Hutchison. E-CELL: Software environment for whole cell simulation. Genome Inform Ser Workshop Genome Inform, 8:147{155, 1997.Search in Google Scholar

[61] Tyagi M., Hashimoto K., Shoemaker B. A., Wuchty S., and Panchenko A. R. Large-scale mapping of human protein interactome using structural complexes. EMBO reports, 13(3):266{271, 2012.10.1038/embor.2011.261329691322261719Search in Google Scholar

[62] Van Pelt C. and Sorokin A. Designing a scalable crowdsourcing platform. In Pro- ceedings of the 2012 ACM SIGMOD International Conference on Management of Data, SIGMOD '12, pages 765{766, New York, NY, USA, 2012. ACM.10.1145/2213836.2213951Search in Google Scholar

[63] Von Ahn L., Maurer B., McMillen C., Abraham D., and Blum M. recaptcha: Human-based character recognition via web security measures. Science, 321(5895):1465{1468, 2008.Search in Google Scholar

[64] Wang Z., Monteiro C. D., Jagodnik K. M., Fernandez N. F., Gundersen G. W., Rouillard A. D., Jenkins S. L., Feldmann A. S., Hu K. S., McDermott M. G., et al. Extraction and analysis of signatures from the gene expression omnibus by the crowd. Nature communications, 7:12846, 2016.10.1038/ncomms12846505268427667448Search in Google Scholar

[65] Wasik S., Antczak M., Badura J., and Laskowski A. Evaluation as a service architecture and crowdsourced problems solving implemented in optil. io platform. arXiv preprint arXiv:1807.06002, 2018.Search in Google Scholar

[66] Wasik S., Antczak M., Badura J., Laskowski A., and Sternal T. Optil.io: Cloud Based Platform For Solving Optimization Problems Using Crowdsourcing Approach. In Proceedings of the 19th ACM Conference on Computer Supported Cooperative Work and Social Computing Companion, pages 433{436, San Francisco, CA, USA, 2016. ACM, ACM Digital Library.10.1145/2818052.2869098Search in Google Scholar

[67] Wasik S., Antczak M., Badura J., Laskowski A., and Sternal T. A survey on online judge systems and their applications. ACM Comput. Surv. 51(1):3:1{3:34, Jan. 2018.10.1145/3143560Search in Google Scholar

[68] Wasik S., Fratczak F., Krzyskow J., and Wulnikowski J. Inferring Mathematical Equations Using Crowdsourcing. PLOS ONE, 10(12):e0145557, dec 2015.10.1371/journal.pone.0145557470100126713846Search in Google Scholar

[69] Wasik S., Jackowiak P., Figlerowicz M., and Blazewicz J. Multi-agent model of hepatitis C virus infection. Artificial Intelligence in Medicine, 60(2):123{131, feb 2014.10.1016/j.artmed.2013.11.00124309221Search in Google Scholar

[70] Wasik S., Prejzendanc T., and Blazewicz J. ModeLang - a new approach for experts-friendly viral infections modeling. Computational and Mathematical Methods in Medicine, 2013:8, 2013.10.1155/2013/320715387841524454531Search in Google Scholar

[71] Wawrzyniak P. Methods of integrating micro-tasking websites with crowdsourced serious games (Metody integracji serwisow mikro-zadaniowych z grami komputerowymi adresowanymi do tlumow). Master's thesis, Faculty of Computing, Poznan University of Technology, 2018.Search in Google Scholar

[72] Wulnikowski J. and Krzyskow J. Design and implementation of the game utilizing crowdsourcing to model dynamic systems (Opracowanie gry wykorzystujacej crowdsourcing do modelowania systemow dynamicznych). Master's thesis, Faculty of Computing, Poznan University of Technology, 2016.Search in Google Scholar

[73] Xintong G., Hongzhi W., Song Y., and Hong G. Brief survey of crowdsourcing for data mining. Expert Systems with Applications, 41(17):7987{7994, 2014.10.1016/j.eswa.2014.06.044Search in Google Scholar

[74] Zhan C. and Yeung L. F. Parameter estimation in systems biology models using spline approximation. BMC Systems Biology, 5(1):14, Jan 2011.10.1186/1752-0509-5-14375010721255466Search in Google Scholar