{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T13:24:43Z","timestamp":1787232283094,"version":"build-2736575974"},"reference-count":51,"publisher":"Society for Industrial & Applied Mathematics (SIAM)","issue":"4","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["RO1GM117138"],"award-info":[{"award-number":["RO1GM117138"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1662305"],"award-info":[{"award-number":["DMS-1662305"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-1936770"],"award-info":[{"award-number":["MCB-1936770"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1707400"],"award-info":[{"award-number":["DBI-1707400"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["SIAM Rev."],"published-print":{"date-parts":[[2023,11]]},"abstract":"<jats:p>Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced level can be challenging. Students often arrive with different mathematical backgrounds, different interests, and divergent reasons for wanting to learn the material. Here we describe a course on stochastic processes in biology delivered between September and December 2020 to a mixed audience of mathematicians and biologists. In addition to traditional lectures and homework, we incorporated a series of weekly computational challenges into the course. These challenges served to familiarize students with the main modeling concepts and provide them with an introduction on how to implement the concepts in a research-like setting. In order to account for the different academic backgrounds of the students, they worked on the challenges in small groups and presented their results and code in a dedicated discussion class each week. We discuss our experience designing and implementing an element of problem-based learning in an applied mathematics course through computational challenges. We also discuss feedback from students and describe the content of the challenges presented in the course. We provide all materials, along with example code for a number of challenges.<\/jats:p>","DOI":"10.1137\/21m1445545","type":"journal-article","created":{"date-parts":[[2023,11,7]],"date-time":"2023-11-07T04:48:50Z","timestamp":1699332530000},"page":"1152-1170","source":"Crossref","is-referenced-by-count":0,"title":["Incorporating Computational Challenges into a Multidisciplinary Course on Stochastic Processes"],"prefix":"10.1137","volume":"65","author":[{"given":"Mark Jayson","family":"Cortez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan Eric","family":"Akil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1975-3913","authenticated-orcid":true,"given":"Kre\u0161imir","family":"Josi\u0107","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander J.","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"351","published-online":{"date-parts":[[2023,11,7]]},"reference":[{"key":"atypb1","doi-asserted-by":"publisher","DOI":"10.1201\/b12537"},{"key":"atypb2","doi-asserted-by":"publisher","DOI":"10.1201\/9780429283321"},{"key":"atypb3","volume-title":"Problem-Based Learning: An Approach to Medical Education","author":"Barrows H. S.","year":"1980"},{"key":"atypb4","first-page":"1","volume":"12","author":"Berrett D.","year":"2012","journal-title":"Chronicle Higher Educ."},{"key":"atypb5","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/2018.001.0001","volume-title":"Computational Modeling of Genetic and Biochemical Networks","author":"Bower J. M.","year":"2001"},{"key":"atypb6","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-08488-6"},{"key":"atypb7","doi-asserted-by":"publisher","DOI":"10.1080\/00131911.2014.929565"},{"key":"atypb8","volume-title":"Dynamical Systems, and Control","author":"Brunton S. 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Galarnyk,\n                      Python Tutorials\n                      ,https:\/\/github.com\/mGalarnyk\/Python_Tutorials(accessed 2021-08-29)."},{"key":"atypb19","doi-asserted-by":"publisher","DOI":"10.1038\/35002131"},{"key":"atypb20","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9781107447615"},{"key":"atypb21","volume-title":"Markov Processes: An Introduction for Physical Scientists","author":"Gillespie D.","year":"1991"},{"key":"atypb22","doi-asserted-by":"publisher","DOI":"10.1021\/j100540a008"},{"key":"atypb23","doi-asserted-by":"publisher","DOI":"10.1137\/S0036144500378302"},{"key":"atypb24","doi-asserted-by":"publisher","DOI":"10.1137\/060666457"},{"key":"atypb25","doi-asserted-by":"publisher","DOI":"10.1023\/B:EDPR.0000034022.16470.f3"},{"key":"atypb26","first-page":"485","volume":"3","author":"Hung W.","year":"2008","journal-title":"Handb. Res. Educ. Commun. Technol."},{"key":"atypb27","volume-title":"Cooperative Learning Methods: A Meta-Analysis","author":"Johnson D. W.","year":"2000"},{"key":"atypb28","doi-asserted-by":"publisher","DOI":"10.1016\/j.physd.2019.02.001"},{"key":"atypb29","doi-asserted-by":"publisher","DOI":"10.1007\/s11538-005-9046-8"},{"key":"atypb30","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.76.051917"},{"key":"atypb31","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.75.021904"},{"key":"atypb32","doi-asserted-by":"publisher","DOI":"10.3102\/00346543071003449"},{"key":"atypb33","doi-asserted-by":"publisher","DOI":"10.3126\/kumj.v10i4.11002"},{"key":"atypb34","series-title":"Series on Higher Education","volume-title":"Cooperative Learning for Higher Education Faculty","author":"Millis B. J.","year":"1997"},{"key":"atypb35","doi-asserted-by":"publisher","DOI":"10.1159\/000163038"},{"key":"atypb36","doi-asserted-by":"publisher","DOI":"10.2307\/j.ctvjghw98"},{"key":"atypb37","first-page":"9","volume":"2","author":"Oakley B.","year":"2004","journal-title":"J. Student Centered Learning"},{"key":"atypb38","unstructured":"R. D. Peng,\n                      Advanced Statistical Computing\n                      ,https:\/\/bookdown.org\/rdpeng\/advstatcomp\/rejection-sampling.html(accessed 2021-07-26)."},{"key":"atypb39","volume-title":"Numerical Recipes: The Art of Scientific Computing","author":"Press W. H.","year":"2007","edition":"3"},{"key":"atypb40","doi-asserted-by":"publisher","DOI":"10.1002\/j.2168-9830.2006.tb00884.x"},{"key":"atypb41","unstructured":"L. Raviv and B. Thompson,\n                      A Short Tutorial on Agent Based Modeling in Python\n                      ,https:\/\/github.com\/Limor-Raviv\/Tutorial_Agent_Based_Models(accessed 2021-07-26)."},{"key":"atypb42","doi-asserted-by":"publisher","DOI":"10.1038\/nature06095"},{"key":"atypb43","doi-asserted-by":"publisher","DOI":"10.1186\/s40594-020-00208-5"},{"key":"atypb44","doi-asserted-by":"publisher","DOI":"10.2307\/j.ctt6wq6fh.6"},{"key":"atypb45","doi-asserted-by":"publisher","DOI":"10.1080\/0022250X.1971.9989794"},{"key":"atypb46","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.324.7330.153"},{"key":"atypb47","doi-asserted-by":"publisher","DOI":"10.3102\/00346543069001021"},{"key":"atypb48","doi-asserted-by":"publisher","DOI":"10.1007\/s40571-015-0082-3"},{"key":"atypb49","doi-asserted-by":"publisher","DOI":"10.1201\/9781420010664"},{"key":"atypb50","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2509"},{"key":"atypb51","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.326.7384.328"}],"container-title":["SIAM Review"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/epubs.siam.org\/doi\/pdf\/10.1137\/21M1445545","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T12:31:07Z","timestamp":1787229067000},"score":1,"resource":{"primary":{"URL":"https:\/\/epubs.siam.org\/doi\/10.1137\/21M1445545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11]]},"references-count":51,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,11]]}},"alternative-id":["10.1137\/21M1445545"],"URL":"https:\/\/doi.org\/10.1137\/21m1445545","relation":{},"ISSN":["0036-1445","1095-7200"],"issn-type":[{"value":"0036-1445","type":"print"},{"value":"1095-7200","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11]]}}}