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  1. The ODD protocol: A review and first update

    01 Aug 2015 | Teaching & Reference Material | Contributor(s): Volker Grimm, Uta Berger, Donald L. DeAngelis, J. Gary Polhill, Jarl Giske, Steven F. Railsback

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/865The ‘ODD’ (Overview, Design concepts, and Details) protocol was published in 2006 to standardize the published descriptions of individual-based and agent-based...

  2. The preferential attachment model

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar, Ying Xin

    Many empirically studied networks have approximately so-called power-law or scale-free degree distributions. In Section 1 we formally define such distributions and explore some of their properties. We also introduce and briefly compare two methods for constructing random...

  3. The replacement number

    10 May 2015 | Teaching & Reference Material | Contributor(s): Winfried Just, Hannah Lea Callender, Drew LaMar, Ying Xin

    In this module we introduce the important notion of the replacement number, which generalizes the basic reproductive number R0. We investigate how this number behaves near the start of an outbreak in models based on the uniform mixing assumption and in models that assume a contact network that is...

  4. The Tree of Life

    19 Jun 2015 | Teaching & Reference Material | Contributor(s): Arietta Fleming-Davies, Julie Morris, Sarah Orlofske, Ellen Wisner

         Transforming the "parade of phyla" into an integrated curriculum emphasizing evolutionary concepts, tree-thinking, and quantitative reasoning skills Our goal is to create an integrated curriculum that emphasizes evolutionary concepts, tree-thinking,...

  5. Theory, models and biology

    28 Aug 2015 | Teaching & Reference Material | Contributor(s): Wenying Shou, Carl T Bergstrom, Arup K Chakraborty, Frances K Skinner

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/861Theoretical ideas have a rich history in many areas of biology, and new theories and mathematical models have much to offer in the future.

  6. Tools: New tools for new science

    06 Feb 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/891A collection of computational, modeling and data analysis tools developed at Microsoft Research Labs.

  7. Towards better modelling and decision support: Documenting model development, testing, and analysis using TRACE

    20 Feb 2015 | Teaching & Reference Material | Contributor(s): Jacqueline Augusiak, Andreas Focks, Béatrice M. Frank, Faten Gabsi, Alice S.A. Johnston, Chun Liu, Benjamin T. Martin, Mattia Meli, Viktoriia Radchuk, Pernille Thorbek, Steven F Railsback, Volker Grimm

    This resource has been updated - find the current version  here: https://qubeshub.org/qubesresources/publications/829Highlights• We introduce TRACE, a framework for documenting model testing and analysis.• TRACE is based on the recently proposed framework...

  8. Training In-Service Teachers to Think Deeply About Modeling in the Common Core Movement

    11 Oct 2016 | Teaching & Reference Material | Contributor(s): Talitha Washington

    This resource has been updated - find the current version here: https://qubeshub.org/publications/242Over the years, I have conducted in-service teacher training sessions and workshops organized by the Capstone Institute at Howard University. My role has been to enhance teacher content...

  9. Two themes, one talk: Distributing quantitative faculty expertise to classrooms that need it in real-time & measuring professional contributions to undergraduate education

    25 Jul 2015 | Teaching & Reference Material | Contributor(s): Jeremy M Wojdak, Sam S Donovan, Tom Gower, Kristin Jenkins

    This resource has been updated - find the current version here: https://qubeshub.org/publications/230Have you ever wanted to add a quantitative project to your course, but lacked the expertise with some aspect of the software, computation, modeling, or statistics?  Have you ever wished...

  10. Undergraduate Research Experiences in Computational Science at a Community College

    13 Jun 2015 | Teaching & Reference Material | Contributor(s): Tony Sena

    This resource has been updated - find the current version here: https://qubeshub.org/publications/320We will present our experiences doing undergraduate research in the area of parallel computing and distributed systems on a multidisciplinary environment with STEM students. We show that...

  11. Understanding the Quantitative and Computational Skills of Incoming Biology Students

    27 Oct 2015 | Teaching & Reference Material | Contributor(s): Charles Umbanhowar Jr, Jason M Belitsky, P. Brodfuehrer, Gregory Davis, T. Haque, L. Lee, C. McFadden, Paul Overvoorde, M. Preest, Liz Stanhope, M. Vinces, Andrew Zieffler, Laura Ziegler

    This resource has been updated - find the current version here: https://qubeshub.org/publications/244Insufficient mathematical preparation has been linked to the failure of incoming students to persist in STEM-related majors.  In addition, recent advances in computation allow biologists...

  12. Understanding the Quantitative and Computational Skills of Incoming Biology Students

    27 Oct 2015 | Teaching & Reference Material | Contributor(s): Charles Umbanhowar Jr, Jason M Belitsky, P. Brodfuehrer, Gregory Davis, T. Haque, L. Lee, C. McFadden, Paul Overvoorde, M. Preest, Liz Stanhope, M. Vinces, Andrew Zieffler, Laura Ziegler

    This resource has been updated - find the current version here: https://qubeshub.org/publications/244Insufficient mathematical preparation has been linked to the failure of incoming students to persist in STEM-related majors.  In addition, recent advances in computation allow biologists...

  13. Using Evolutionary Data in Developing Phylogenetic Trees: A Scaffolded Approach with Authentic Data

    01 Oct 2015 | Teaching & Reference Material | Contributor(s): Kd Davenport, Kirsten Jane Milks, Rebecca Van Tassell

    Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships...

  14. Using gross parasites to sneak even grosser equations into the introductory biology classroom

    19 Jul 2015 | Teaching & Reference Material | Contributor(s): Jeremy M Wojdak

    This resource has been updated - find the current version here: https://qubeshub.org/publications/234This was an oral presentation at the 2015 Annual Meeting of the American Society of Parasitologists in Omaha, NE. "College faculty that teach introductory courses often struggle to...

  15. Using Online Materials/Videos to Enrich Linear Algebra for Scientists

    08 Jul 2015 | Teaching & Reference Material | Contributor(s): Sarah Hews

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/785Linear algebra is an important course for biology majors but it is usually designed for math majors (emphasizing proofs) or engineers (focusing more on matrix algebra and...

  16. Using Online Materials/Videos to Enrich Linear Algebra for Scientists

    21 Oct 2015 | Teaching & Reference Material | Contributor(s): Sarah Hews

    This resource has been updated - find the current version here: https://qubeshub.org/publications/250Linear algebra is an important course for biology majors but it is usually designed for math majors (emphasizing proofs) or engineers (focusing more on matrix algebra and algorithms)....

  17. Using Online Materials/Videos to Enrich Linear Algebra for Scientists

    21 Oct 2015 | Teaching & Reference Material | Contributor(s): Sarah Hews

    This resource has been updated - find the current version here: https://qubeshub.org/publications/250Linear algebra is an important course for biology majors but it is usually designed for math majors (emphasizing proofs) or engineers (focusing more on matrix algebra and algorithms)....

  18. Vision and Change in Undergraduate Biology Education: A Call to Action

    25 May 2015 | Teaching & Reference Material

    This is the final report of a national conference organized by the American Association for the Advancement of Science with support from the National Science Foundation in an effort to show how the undergraduate biology education system needs to be improved: "Given the radical changes in the...

  19. Visualization: Quantitative reasoning via image analysis, networks, topology, generative models, and 3D rendering

    10 Jun 2015 | Teaching & Reference Material | Contributor(s): Sam S Donovan, John R Jungck

    This resource has been updated - find the current version here: https://qubeshub.org/publications/321Additional resources for:"Visualization: Quantitative reasoning via image analysis, networks, topology, generative models, and 3D rendering" by John R. JungckDate and Time:...

  20. Wellesley College Study Packet for the Quantitative Reasoning Assessment

    27 Mar 2015 | Teaching & Reference Material

    This resource has been updated - find the current version here: https://qubeshub.org/qubesresources/publications/782This packet contains a set of 24 practice questions and 2 full-length practice assessments for the Quantitative Reasoning Assessment for Wellesley College.