Author Archives: Cynthia McIntyre

Total solar eclipse and other awe-inspiring celestial activities

When you’re looking up at the solar eclipse on August 21 (wearing appropriate eye protection, of course), you might also be wondering: What else is out there? Black holes, dark energy, life forms? Are we really alone in the universe?

This is one of the great unanswered questions for scientists, which is why it’s in the 125th anniversary issue of Science dedicated to the topic of “What Don’t We Know” — a list of questions scientists still puzzle over.

At the Concord Consortium, we were fascinated by these questions, and it got us thinking … how can we generate that kind of curiosity and excitement among students, especially those who see science as dry facts and a long list of crazy vocabulary words like azimuth and hypernova and transneptunians?

The goal of our High-Adventure Science project is aimed at just that — engaging students in the same way scientists approach unanswered questions. In collaboration with National Geographic Education, we’ve developed six week-long units for middle and high school students on compelling, unanswered questions, including “Is there life in space?

This free online investigation helps students see how scientists use modern tools to locate planets around distant stars and explore the probability of finding extraterrestrial life. The curriculum incorporates dynamic computer models, including planet hunting models and Molecular Workbench models, real-world data, and and a video about planet hunters. What could be more cool?

As students search for habitable places beyond Earth, they hunt for planets using a model to explore how the brightness of a star changes over time as a planet orbits around it. This is known as the transit method. Students learn how the size of the planet and the angle of the orbit relative to the viewer each play a role in the light intensity that reaches Earth. This is similar to the solar eclipse when the moon will block the light of the sun as it transits between the sun and Earth.

Planet hunting model. Explore how combining data from the velocity of a star and the light intensity of a star can be used to find planets. Adjust the orbital angle (tilt) of the model by clicking in the grid area and dragging, so that you can see star movement in the velocity graph. As the planet passes in front of the star, watch what happens to the light intensity on the light intensity graph.

While the excitement of this eclipse may last just a few minutes (until the next total solar eclipse in North America in 2024), students can use High-Adventure Science to conduct other awe-inspiring celestial investigations, like the search for life in space!



Summer intern dives deep into someone else’s code

In his spare time, Saul Amster likes to program. He’s currently working on a project to turn a tablet into a magic mirror. Yes, like Snow White’s evil stepmother (“Mirror, mirror on the wall…”), except imagine asking the mirror for the day’s forecast or the score of last night’s game. “Programming is an interesting hobby,” he says. “It’s basically free. All you need is a computer. Other hobbies require you to keep sinking money into them.”

This summer, Saul turned his programming hobby into an internship at the Concord Consortium. But while he’s used other external software libraries before, he had to teach himself to work with other people’s preexisting code, plus learn the push and pull requests of contributing code on GitHub. And although he was new to the code base underlying the Seismic Explorer software, which displays earthquakes and volcanoes worldwide using real-time data from the USGS, he didn’t let that stop him from jumping in. In fact, he’s enhanced an existing feature by redrawing the plate boundaries to make them more noticeable and added a new feature that shows arrows to display the movement of the tectonic plates. He’s now reworking how the animation is done in the model.

“I have been really impressed with Saul,” says Amy Pallant, Principal Investigator of the Geological Models for Explorations of Dynamic Earth (GEODE) project, which developed Seismic Explorer. “He has been able to add new data into the model, think about the user experience, and help me make decisions about layout, design, and data representation. His vast experience with programming, computer games and educational environments meant that I could learn from him, too.”

Saul is sure this first experience working with someone else’s code will serve him well when he heads off to Ithaca College as a freshman computer science major. “This has been super helpful for classes and for future jobs,” he says. He’s not at all worried about his freshman Java course, since he has already learned the language. It’s one of his favorites, along with C#, which he uses in his videogame programming.

Saul is excited about some high-end virtual reality gear he spotted in the computer department at Ithaca. He’s already made some small VR apps for the Google cardboard, and he’s looking forward to research opportunities. So along with clothes and toothpaste, he’s packing his laptop and external graphics box—with better cooling and more power, it’s perfect for developing (and playing) games, and getting his homework done, of course.


Introducing summer intern, data science major Maya Haigis

Before interning with senior scientist Charles Xie this summer, Maya Haigis had no idea how many solar panel manufacturers there are—“There’s a ton!”

A data science major at the University of Rochester, Maya put her analytic skills to work at the Concord Consortium collecting data on solar panels (dimensions, weight, maximum wattage, etc.) and designed a panda solar power plant with Energy3D, an engineering design and simulation tool for renewable energy and energy efficiency. She used Energy3D to create a power plant in the shape of a bald eagle, too.

“Charles heard about the giant panda power plant in Datong, China, in the news, and asked me to replicate it in Energy3D.” Maya says, “It was a good introduction to the features of Energy3D. Charles suggested I do something relevant to the U.S.—like our own national symbol! It was fun imagining flying across the country and seeing a giant bald eagle out of the window instead of the generic rectangles or circles of traditional solar farms.”

She also worked with the Energy3D team modeling local schools and other community buildings for the Solarize Your World curriculum they are designing.

“Maya is a real genius in 3D modeling,” said Charles. “I didn’t expect her to come up with sophisticated 3D structures within a couple of hours with a piece of software that she had never used before. But she did it elegantly. It is remarkable that she has created scores of highly accurate 3D models for school buildings with incredible details.”

Bald eagle solar power in Energy3D (left) and close-up of bald eagle (right).

As a sophomore, Maya is currently on the same path as computer science students, but her curriculum path will soon diverge with a focus on data mining and database systems plus more statistics. She’s always been “a math person,“ she says, but credits her high school AP statistics teacher’s enthusiasm for data and statistics for consolidating her interest.

At the University of Rochester she’s already taken courses in Java, data structures and algorithms, discrete math, calculus, and linear algebra with differential equations. “All data is interesting,” she says, but notes sports stats are particularly fascinating. No surprise, since Maya is a student athlete who plays field hockey at the Division III school where her schedule includes practice six days a week.

She notes, “My brother and I used to have a collection of baseball cards and I would try to memorize the stats of my favorite players. It’s a bit ironic because before games, coaches always say that once you step onto the field, the statistics don’t mean anything and what matters is which team plays the hardest, but I still look through other team stats.”

Recently, Maya had a pivotal experience. She spent half a day at Pfizer working with a business analyst, who serves as a connection between scientists and programmers. “The business analyst would explain to the scientists what the data meant,” she explains. “And if the scientists wanted their data displayed in a certain way, she would talk to the programmers.” Maya can imagine filling a similar liaison role working as data scientist, though she also admits, “I’m not exactly sure what I want to do after college, but I’m looking forward to the data science courses at Rochester, and I’m excited to see what opportunities will arise with big data!”

Chinese translation of SageModeler systems dynamics modeling tool

In June, Professor Silvia Wen-Yu Lee and her team at the National Changhua University of Education in Central Taiwan offered a 10-hour modeling curriculum to approximately 100 seventh grade students. Students used a new Chinese language version of SageModeler to model the relationship between marine biology and human activity in a unit about environmental conservation.

SageModeler is a free, web-based systems dynamics modeling tool for middle and high school students to construct dynamic models. SageModeler is being developed by the Building Models project, a collaboration between the Concord Consortium and the CREATE for STEM Institute at Michigan State University (MSU).

Professor Lee met Joe Krajcik, one of the lead writers of the Next Generation Science Standards and Principal Investigator (PI) of the Building Models project at MSU, where she had served as a visiting professor in 2014. Dan Damelin is the project’s PI at the Concord Consortium. Thanks to this fortuitous collaboration, Lee and her team translated SageModeler into Chinese, and her students are now taking advantage of this easy-to-use tool to create dynamic systems models.

Students building models with SageModeler. 

“The students learned how to draw models instantly after a brief demonstration,” Lee noted. “Our teachers were amazed by the students’ level of engagement and by the students’ attention to the relationships when they are working together on the SageModeler. ” Professor Lee and her colleagues at the National Changhua University of Education hope to understand how the students develop competencies in model building and whether they develop clear understandings of the causal and dynamic relationships in marine biology and human activity (fishing) through modeling.

Sample student model from a seventh grade Taiwanese student.

You can build your own model in five easy steps.

  1. Open SageModeler (in English or Chinese)

  2. Add variables to the canvas First, brainstorm factors that affect marine biology. What contributes to it and what is affected by it? Now, add images for each variable to the canvas.

  3. Link variables and set relationships Draw links from one variable to another and select from a menu to set the relationships between those variables. By using words and pictures of graphs, students can define the underlying equations that will be used to run the model.

  4. Run the model Open the simulation controls and run the model to collect data. Adjust the model settings to see how changing the variables affects the outcome. Does the model output data make sense? Does it match real-world data? Are the relationships between variables set up appropriately?

  5. Revise and expand your model Revise your model to better match the phenomenon you are modeling. For example, you may want to add more variables. As you continue to ask new questions, you can revise your model and deepen your understanding of the system.

We are currently working on additional internationalization efforts, including Turkish and Spanish translations. Interested in learning more or contributing a translation? Contact us.

Why dragons?

Breeding virtual dragons is all in a day’s work in biology classrooms using Geniverse, our free, web-based genetics software. Although Geniverse is a game-like environment, it’s far more than child’s play. Indeed, students dive into genetics on a quest to heal a beloved dragon. Students use a model species (drakes) to explore the fundamental mechanisms of heredity and genetic diseases and get a taste of careers in genetics. (Drakes are essentially a smaller version of a dragon, and are a model species in much the same way as the mouse is a model species for human genetic disease.)

But why did we choose dragons and drakes? To start, they are just plain fun! And since they’re mythical, we can bring together into one animal any and all real-world genes we’d like to teach with—without having to be restricted to a specific species’ genome. So, while our dragons and drakes are fantastical, their genes are very much real, gathered from mice, fruit flies, lizards, and other organisms we study in laboratories all over the world. When students learn genetics with Geniverse, they’ll encounter the genes again, should they venture into a real genetics lab later in life.

Students begin their Geniverse adventure as a student in the Drake Breeder’s Guild, where they move through four levels of progressively more difficult genetics challenges and unlock new chapters of the narrative. Try Geniverse now and learn how fun (and educational) dragons can be!

The real genes of Geniverse

Did you know that while dragons and their model species drakes are fictional and fanciful, the genetics of these virtual Geniverse creatures is based firmly on the real-world genetics of model organisms?

The drake genes and traits have been carefully compiled from the actual genes and associated traits of the anole lizard, mouse, fruit fly, zebrafish, and other model species. The genes for forelimbs, wings, color, and other drake traits are genes that are involved in the development of those traits in real organisms. There’s real biology behind the Geniverse narrative as well: the disease that plagues our hero’s dragon friend is modeled on a rare human metabolic disorder, ornithine transcarbamylase (OTC) deficiency. In fact, since the genes of humans are similar to the genes of the model organisms we use in real life—that’s why we can learn so much about human genetics from them—the genes of the Geniverse drakes are quite similar to human genes.

In addition, the interactive models that students use to conduct virtual experiments in Geniverse are powered by genetics programming that accurately simulates real-life patterns of inheritance in humans as well as model organisms. Students who learn with Geniverse are learning to analyze experimental results that would be obtained from these genes in a laboratory.

Nomenclature Genomic Location
Symbol w Chromosome 1
Name wingless Linkage map 70 cM
Species Dracomimus familiaris Genome coordinates unknown


Summary information
Phenotype: The wingless gene affects wing development in drakes. Homozygotes for the wingless allele (w/w) lack externally visible wings entirely. The skeleton of wingless drakes has a vestigial dorsal shoulder and a remnant of the proximal wing bone. Note: This gene and phenotype are taken from the fruit fly, d. Melanogaster, and the human correlate gene, called Wnt1, is 80% similar to the wingless DNA sequence.
W/W or W/w w/w


Alleles and Phenotypes
Allele Summary
W Presumptive wild-type allele
w Recessive allele
Genotype Phenotype
W/W Normal wings
W/w Normal wings
w/w wingless


Nomenclature Genomic Location
Symbol Wnt1 Chromosome 1
Name Proto-oncogene Wnt-1 Linkage map unknown
Species Dracomimus familiaris Genome Coordinates 1: 70 Mbp

At the University of Massachusetts at Amherst, students are utilizing bioinformatics tools to build new drake genes, mutant alleles, and phenotypes based on investigations of the scientific literature. In an exploration of multiple genetic mechanisms, students have created drakes whose genotypes give rise to deafness and dwarfism, cancer and cold tolerance, polydactyly, and the ability to spit spider silk. We’re thrilled to see these additions to our drake genome!

National Teacher Appreciation Day & Teaching System Modeling with SageModeler

We are delighted to highlight the work of Erin Cothran from Hudson (Massachusetts) High School, for National Teacher Appreciation Day! Erin is teaching a 10th grade chemistry unit she developed based on the driving question, “How can something that can’t be seen crush a 67,000 lb. oil tanker made of half-inch steel?” The unit includes four activities:

  • Why do my ears hurt when I dive in the deep end of the pool?
  • Why do I have to let air out of my car tires in the summer but add more air to my tires in the winter?
  • Why does a soda can explode if it is left unopened and in a hot car?
  • How can a big metal drum be crushed using air pressure?

Each activity includes opportunities for students to build, test, and revise systems models using our free, web-based SageModeler dynamic modeling software.

Erin said, “Using SageModeler has changed how I teach about systems modeling. With the the Next Generation Science Standards being adopted by many schools, modeling has become a main focus of lessons. Working with SageModeler over the past year has allowed me insight into how computer models can be used to help answer questions.”

“I am able to facilitate my students’ learning about the components that make good models effective,” she noted. “Even more importantly, students are discovering that models need to be adjusted as science evolves, that it is okay to not get it correct on the first attempt. Through learning how to build models they are able to define relationships between variables and test their ideas. They love picking custom images, making links, and running the simulation to see the outcomes.”

Dan Damelin, a Principal Investigator of our Building Models project, which is developing SageModeler, reports, “Erin is a very thoughtful teacher who engages students by using the models they generate to drive class discussion.”

The Building Models project is a collaboration between the Concord Consortium and the CREATE for STEM Institute at Michigan State University. The project is researching how the use of a semi-quantitative systems dynamics tool to construct external models helps students build mental models as well as how teachers and curriculum materials can support and scaffold student learning with respect to the interplay between external and internal models. We look forward to learning more from Erin and all the Building Models research teachers.

Evo-Ed Integrative Cases will be enriched to address NGSS

A new collaborative research project at the Concord Consortium and Michigan State University will develop and research learning materials on the molecular and cellular basis for genetics and the process of evolution by natural selection. These two areas are both difficult to teach and learn, and although they have been historically taught separately, they are interlinked and span multiple levels of organization. The goal of Connected Biology: Three-dimensional learning from molecules to populations is to design, develop, and examine the learning outcomes of a new connected curriculum unit for biology that embodies the conceptual framework of the Next Generation Science Standards.

Peter White, science education researcher and entomologist at Michigan State University (MSU); Louise Mead, Education Director at the BEACON Center for the Study of Evolution in Action at MSU; and postdoctoral fellow Alexa Warwick at the BEACON Center visited the Concord Consortium recently to plan our joint work together. Frieda Reichsman and Paul Horwitz will serve as the Principal Investigator and Co-PI at the Concord Consortium.

The new units will leverage the contextually rich Evo-Ed Integrative Cases, which build directly on the interlinked nature of evolution and genetics and connect the science ideas with meaningful real-world examples. The Evo-Ed case studies track the evolution of traits from their origination in DNA mutation, to the production of different proteins, to the fixation of alternate macroscopic phenotypes in reproductively isolated populations. For example, the Evolution of Lactase Persistence case study examines the genetics, cell biology, anthropology, and biogeography of this system.

The human lactase gene (LCT) is a 55 kilo-base pair segment of the second chromosome.

The curriculum will integrate the three dimensions of science—the core ideas of biology, the science and engineering practices, and the crosscutting concepts—to support all students in building toward deep understandings of biological phenomena. The project will be guided by two main research questions:

  1. How does learning progress when students experience a set of coherent biology learning materials that employ the principles of three-dimensional learning?
  2. How do students’ abilities to transfer understanding about the relationships between molecules, cells, organisms, and evolution change over time and from one biological phenomenon to another?

Note: If you’ve used the Evo-Ed cases in your classroom, we’d love to get your feedback! Please respond to this short survey to be entered into a drawing to receive a $50 Amazon gift card.

Welcome to our three Google Summer of Code students

Google Summer of Code 2013Three international students will spend the summer coding for our open source projects. Through Google Summer of Code (GSoC), they’ll earn stipends from Google, plus get a coveted GSoC t-shirt and certificate.

Expansion of SPARKS HTML5 circuit simulator

Our HTML5 breadboard simulator allows students to experiment with basic DC and AC circuits using linear components (resistors, capacitors, inductors) and to perform measurements with a function generator, a digital multimeter and an oscilloscope.

Sabareesh Nikhil C, from Hyderabad, India, will extend our existing circuit-solving code to handle non-linear components such as diodes, op amps and transistors. Instead of treating each circuit as a lumped impedance and computing its response to a single frequency, the new code will perform a more realistic time-based computation, which will enable it to model the behavior of more complex circuits. Sabareesh also plans to implement a communication protocol that will enable circuits on different computers to communicate with each other.

Sabareesh will work with Concord Consortium mentors Paul Horwitz, Sam Fentress and Richard Klancer.

Probe your browser!

Science classrooms use probes and sensors to enable real-time data collection by students. Currently we use Java applets to support communication between sensors and web-based applications in the browser. Increasingly limited support for Java is making it difficult to integrate probes and sensors that use Java software for use in the classroom.

Lingliang Zhang from New York, NY, and Abu Dhabi, United Arab Emirates, will design a native application for desktops, which will make the data from probes and sensor hardware available to our browser-based JavaScript applications. The native application will use an embedded webserver to connect to our existing sensor library. This approach will enable browsers on desktops and laptops to use our currently supported Pasco and Vernier sensor devices without a Java applet.

He will work under the mentorship of our Senior Software Engineer Scott Cytacki.

Port HTML5 interactives to phones and tablets

Our HTML5 interactives are rendered using a semantic layout system. With a modified UI, they could work on phones, allowing students to interact with them on multiple devices. Additionally, with an iOS and Android application created using Cordova, users could install the interactives and use them offline. This app could also allow parts of the engine behind the interactives to run natively in order to get better performance on these devices.

Apoorv Narang from New Delhi, India, will measure performance on various devices to determine which of our HTML5 interactives can be run on these devices. He will improve our lab framework, which is the system that displays and runs interactives, with the goal of making our interactives look—and run!—better on phones.

Director of Technology Stephen Bannasch will mentor Apoorv.


During summer 2012, we were fortunate to have two fabulous GSoC students, including Piotr Janik, who continues coding for us as a consultant. Watch Piotr describe his experience with Google Summer of Code.

We can’t wait to see the code that our three new GSoC students will develop this summer!


Share and embed—easily!

One of the key features of our Next-Generation Molecular Workbench is the ability to easily share and embed interactives in blog posts, learning management systems, emails and more—wherever you can paste a weblink or HTML code. Just two simple steps will have you sharing your favorite interactives with all your friends and colleagues in no time flat!

  1. Click the Share link at the top of an interactive.
  2. Copy and paste the link into Facebook, Google+, Twitter, Pinterest or wherever you want to share the interactive.

Want to embed the interactive in your own blog or web page instead?

  1. Click the Share link at the top of an interactive.
  2. Copy the HTML and paste the iframe code where you want the interactive to appear.

Sharing and embedding Next-Generation Molecular Workbench interactives

Learn more about how easy it is to share interactives.

We want to make it easy for you to learn and teach with accurate scientific models.  We’ve gotten it down to two steps. Now it’s up to you to share your favorite interactives far and wide. 🙂

Explore currently available interactives.

Share with us: which are your favorite interactives and why? What interactives do you want to see?