Gaining Insight through Systems Thinking and Computational Modeling

Getting Started:  Learn and Do

Sequence of Activities

Introduction to Systems Thinking and Modeling

Today's problems often take the form of complex systems - climate change, cancer, politics. Tackling these problems requires a systems approach. Learn about what a system is, how feedback loops are part of most systems, and how we can model complex systems with modern tools.

Once you are in the mindset of a systems thinker, move through the modules of varying difficulties - Introductory (easiest), Intermediate, Advanced (hardest) - at your own pace. You can start anywhere, but keep in mind that some of the modules build on each other.

Share Your Model

These projects give you the tools to be creative and design your own models. Within the scientific community, we value collaboration in order to further our knowledge of the world. Please share your model with us so that the community has access to your ideas!


Your Day as a System

TOOL: Loopy

TIME (est.):  1 - 1.5 hours


Your overall well-being is weighted by different elements of your day. If you treat your day as a system, you can start to determine where you can improve your future days to achieve wellness. What steps can you take toward wellness?

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What do rabbit populations, The Lorax and epidemics have in common?

TOOL: SageModeler

TIME (est.):  0.5  - 1 hours

SYSTEM PROPERTIES: Cause and Effect, Interconnection, Accumulation

The world contains a multitude of complex systems, and as diverse as they may seem, their similarities far outweigh their differences. Learn about using models to help understand simple systems while gaining familiarity with an intuitive modeling tool.

Octopus Population Dynamics

TOOL: Stella Online

TIME (est.):  1 - 1.5 hours

SYSTEM PROPERTIES: Feedback Loops, Behavior Over Time Graphs

Octopuses  have been called the Geniuses of the Ocean.  How can we predict their population numbers with a dynamic, quantitative model?  

HIV Disease Dynamics

TOOL: Loopy

TIME (est.):  0.5 - 1 hours


Four superhero scientists at ISB use their superpowers to study HIV using systems biology! Why does an HIV patient's T cell count affect their viral susceptibility? Let's create a simple model using Loopy to find out, then, you can build your own HIV gene regulatory model!


Exploring Disease Epidemics

TOOL: SageModeler

TIME (est.): 1 hour

SYSTEMS PROPERTIES: Cause and Effect, Interconnection, Feedback Loops, Rates and Accumulations, Behavior over Time

Use your modeling skills to investigate disease epidemics. You will also learn the basics of systems dynamics while exploring the fundamental structures and behaviors found in systems.

Predator-Prey Dynamics

TOOL: Stella Online

TIME (est.):  0.5 - 1 hrs

SYSTEM PROPERTIES: Tipping Points, Feedback Loops, Behavior Over Time Graphs

Our oceans house a wondrous array of organisms.  How are populations of predator and prey connected?  

Exploring and Visualizing Ocean Data

TOOL: Ocean Data View

TIME (est.):  0.5 - 1 hrs

The oceans are experiencing great change as part of climate change. How can we use computational tools to visualize and understand data about the oceans?

Identifying Gene Targets for Malaria with Excel

TOOL: Excel

TIME (est.): 1-2 hours

SYSTEMS PROPERTIES: Cause and Effect, Interconnection, Feedback Loops, Rates and Accumulations

 Use Excel as a statistical tool to determine which proteins would be good targets for a malaria vaccine.

Characterizing GBM Cell Heterogeneity in Response to Drug Treatment Using Excel

TOOL: Excel

TIME (est.): 2-3 hours

SYSTEMS PROPERTIES: Wicked Problems, Systems within Systems, Dynamic Systems

 Use Excel to analyze the variances between two glioblastoma tumor treatments and learn how certain stem cell markers are expressed in over 300 tumor cells.


Effects of Ocean Acidification on Clownfish

TOOL: NetLogo

TIME (est.): 1 - 2 hrs

SYSTEM PROPERTIES: Environmental Effects, Feedback Loops, Behavior Over Time Graphs

Ocean acidification is increasing as climate change progresses. What effects might ocean acidification have on clownfish survival?

 Effects of Caffeine on Yeast

TOOLS: R, Github, Trimmomatic, STAR, Cufflinks, Kallisto

Time (est): 1 - 2 hrs

SYSTEM PROPERTIES: Environmental Effects, Differential Expression

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How organisms adapt to different environmental stressors can be tracked through which genes are expressed or not. How does yeast adapt to caffeine?

How do genes linked to mitosis and repair relate to each other? Learn techniques for finding and grouping clusters in big data sets.

Analyzing the Presence of GBM Stem Cell Markers in the Tumor Microenvironment


TIME (est.): 3-4 hrs

SYSTEMS PROPERTIES: Wicked Problems, Systems within Systems, Dynamic Systems

Use R to analyze and visualize single-cell data from various tumors to better understand cell proliferation pathways in cancer.

Final Project: Create Your Own Model

TOOL: Your choice!

Apply what you have learned to create a model of a system of your choice. 

Learn more and/or contact us through email - or through our main websites - and

Funding to support the development of these lessons was provided by National Science Foundation Award DBI-1565166 & 0640950 and Institute for Systems Biology Innovator Award (ISB Project #10520010000).  The content of these pages was created by students for students with the help of teachers, scientists and the Jones Family Foundation.  The views expressed herein are those of the authors and do not necessarily reflect the views of ISB, NSF or JFF.