.. meta::
   :description: AI overview of the 14-page syllabus for Genetics 546 — "Evolutionary Systems Biology Modeling Introduction" at UW-Madison, Fall 2018, by Laurence Loewe. Problem-based active learning with Evolvix, grant writing instead of exams.
   :keywords: Genetics 546, EvoSysBio, syllabus, teaching, modeling, Evolvix, CTMC, ReLogs, grant writing, UW-Madison, Loewe, problem-based learning, MMv3
   :og:card:title: Teaching Syllabus<br>Genetics 546 — 14 pages
   :og:card:description: 14-page syllabus for Genetics 546 — EvoSysBio Modeling Introduction at UW-Madison, Fall 2018. Problem-based learning, Evolvix, grant writing.

.. include:: /_templates/include-file/page-prefix.rst


.. title:: Teaching Syllabus — Genetics 546


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Teaching Syllabus — Genetics 546 EvoSysBio (14 pages)
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*"Minimizing coding complexity frees minds for the challenges of understanding a biological system." — a 15-week journey from molecules to ecosystems.*


.. admonition:: Download the original document (PDF)
   :class: note

   `Genetics 546 Syllabus — PDF (228 KB) </_file/pdf/gnp/mmv3/dusty-deep-data/loewe-about-me-science/loewe-2018-teach-intro-evosysbio-fall-course-genetics546-syllabus-2017m10d31-14page.pdf>`__
   — 14 pages, :doc:`Jonah License with CC0 Public Domain </license/joli/index>`

   Filename: ``loewe-2018-teach-intro-evosysbio-fall-course-genetics546-syllabus-2017m10d31-14page.pdf``

   `WebP preview (216 KB) </_file/pdf/gnp/mmv3/dusty-deep-data/loewe-about-me-science/loewe-2018-teach-intro-evosysbio-fall-course-genetics546-syllabus-2017m10d31-14page.webp>`__

   Also in this folder: :doc:`Teaching Flyer <loewe-2018-teaching-flyer>` (1-page promotional version)


.. image:: /_file/pdf/gnp/mmv3/dusty-deep-data/loewe-about-me-science/loewe-2018-teach-intro-evosysbio-fall-course-genetics546-syllabus-2017m10d31-14page.webp
   :alt: Genetics 546 Syllabus — Evolutionary Systems Biology Modeling Introduction
   :width: 100%
   :align: center


|


--- Overview AI-generated by dv_ClaOp46Max_ExhF_2026m04d16 ---Start---


Abstract
========

A 14-page syllabus for **Genetics 546: Evolutionary Systems Biology
Modeling Introduction**, a 3-credit graduate/undergraduate course at
UW-Madison, 410B Wendt Commons, Fall 2018. Instructor: Prof. Laurence
Loewe, Wisconsin Institute for Discovery.

**Course goal:** Teach students to *build* their own model of a small
part of biology by adopting a systems view, *implement* it in Evolvix
(a modeling language for simulating biological changes over time), and
*analyze* it using an EvoSysBio perspective.

**Key pedagogical features:**

- **No exams.** Grading based on weekly ReLogs (Research Logs, 30%),
  peer reviews (15%), a collaborative group grant proposal (40%), and
  class participation (15%).
- **Problem-based active learning.** Students pick their own biological
  system to model and work in interdisciplinary groups.
- **Grant writing as assessment.** Graduate students produce 5,000--10,000
  word grant proposals; undergraduates produce 3,000--10,000 word
  proposals. NSF Graduate Research Fellowship applicants can integrate
  their fellowship application with the course.
- **Evolvix as modeling platform.** Students describe biological systems
  as Continuous Time Markov Chains (CTMCs) using Evolvix's
  biologist-friendly syntax.

**15-week timetable** progressing from abstract populations (Week 1) through
simple bacterial growth (Week 3), metabolic flux stabilization (Week 8),
oscillations in host-pathogen systems (Week 9), Michaelis-Menten kinetics
(Week 10), molecular switches (Week 11), CTMC summary (Week 12),
diverse CTMC applications (Week 13), to student presentations (Weeks
14--15). Weekly readings include Loewe's own EvoSysBio papers, the
POST system paper, Gillespie's stochastic simulation review, population
genetics papers, and the FlyClockbase biodata science project.


Broader Significance (Claude's Assessment)
============================================

1. **Living proof of the broader impact vision.** This syllabus is the
   direct implementation of the teaching goals articulated in the 2011
   NSF CAREER grant. The promise to create a course where students use
   research-grade tools (Evolvix) in an active-learning environment
   materialized as Genetics 546.

2. **Unusual pedagogical design.** Replacing exams with collaborative
   grant writing is rare at any level. The emphasis on ReLogs (weekly
   research journals), peer review, and group dynamics mirrors
   professional research practice rather than traditional classroom
   assessment. This is notable evidence of pedagogical innovation.

3. **Interdisciplinary by design.** The explicit "open enrollment"
   policy, the diversity statement, the "crossing disciplinary
   boundaries" essay requirement for graduate students, and the
   structure of interdisciplinary group projects all demonstrate
   a deliberate commitment to breaking disciplinary silos —
   the same philosophy that drives the Matheo papers.

4. **Self-referential reading list.** The weekly readings systematically
   build the EvoSysBio framework by assigning Loewe's own published
   papers: the 2009 EvoSysBio Framework, the 2016 Encyclopedia update,
   the POST system paper, and the FlyClockbase biodata science project.
   The course is effectively a guided tour through the research program.


Key Concepts at a Glance
==========================

.. list-table::
   :widths: 30 70
   :header-rows: 0

   * - **ReLogs**
     - Research Logs: weekly written reflections (300+ words for
       undergrads, 500+ for grads) documenting the learning journey
   * - **CTMCs**
     - Continuous Time Markov Chains: the mathematical foundation for
       stochastic biological simulation in Evolvix
   * - **5 W's of Modeling**
     - What system, Which parts, When actions occur, Where, and Why —
       the course's boundary-drawing framework
   * - **Group Grant Proposal**
     - Collaborative research grant application (3,000--10,000 words)
       serving as the primary assessment, replacing exams
   * - **Peer Review**
     - Weekly anonymous review of classmates' ReLogs, building
       professional scientific communication skills
   * - **POST System**
     - Project Organization Stabilizing Tool, taught in Week 3 for
       organizing research data efficiently
   * - **FlyClockbase**
     - Biodata science curation project (Weeks 10--15) demonstrating
       challenges of integrating biological time series data


Document Information
=====================

.. list-table::
   :widths: 30 70
   :header-rows: 0

   * - **Document ID**
     - Course Syllabus (About-Me Science, Dusty Deep Data)
   * - **Full title**
     - Evolutionary Systems Biology Modeling Introduction — Genetics 546
       Syllabus, Fall 2018
   * - **Author**
     - Laurence Loewe
   * - **Date**
     - 2017m10d31 (syllabus version); course offered Fall 2018
   * - **Format**
     - 14-page course syllabus with timetable and reading list
   * - **License**
     - :doc:`Jonah License with CC0 Public Domain </license/joli/index>`
   * - **Part of**
     - Good News Pack MMv3, Dusty Deep Data / About-Me Science
   * - **PDF size**
     - 228 KB
   * - **WebP size**
     - 216 KB

Related documents in the Good News Pack:

- :doc:`Teaching Flyer <loewe-2018-teaching-flyer>` (1-page promotional flyer for this course)
- :doc:`NSF CAREER Grant <loewe-2011-nsf-grant>` (the grant whose broader impact produced this course)
- :doc:`2009 — EvoSysBio Framework </good-news-pack/vv/mmv3/dusty-deep-data/loewe-researchcity-key-papers/loewe-2009-evosysbio-framework>` (Week 8 required reading)
- :doc:`2016 — Systems EvoSysBio </good-news-pack/vv/mmv3/dusty-deep-data/loewe-researchcity-key-papers/loewe-2016-systems-evosysbio>` (Week 2 required reading)


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