Award Abstract # 1324753
DIP: Collaborative Research: Taking Hands-on Experimentation to the Cloud: Comparing Physical and Virtual Models in Biology on a Massive Scale

NSF Org: IIS
Division of Information & Intelligent Systems
Recipient: THE LELAND STANFORD JUNIOR UNIVERSITY
Initial Amendment Date: September 9, 2013
Latest Amendment Date: July 20, 2015
Award Number: 1324753
Award Instrument: Standard Grant
Program Manager: Sushil K Prasad
IIS
 Division of Information & Intelligent Systems
CSE
 Directorate for Computer and Information Science and Engineering
Start Date: September 15, 2013
End Date: August 31, 2018 (Estimated)
Total Intended Award Amount: $1,350,000.00
Total Awarded Amount to Date: $1,356,500.00
Funds Obligated to Date: FY 2013 = $1,350,000.00
FY 2015 = $6,500.00
History of Investigator:
  • Hans Riedel-Kruse (Principal Investigator)
    ingmar@arizona.edu
  • Paulo Blikstein (Co-Principal Investigator)
Recipient Sponsored Research Office: Stanford University
450 JANE STANFORD WAY
STANFORD
CA  US  94305-2004
(650)723-2300
Sponsor Congressional District: 16
Primary Place of Performance: Stanford
318 Campus Drive
Stanford
CA  US  94305-5014
Primary Place of Performance
Congressional District:
16
Unique Entity Identifier (UEI): HJD6G4D6TJY5
Parent UEI:
NSF Program(s): TUES-Type 2 Project,
Cyberlearn & Future Learn Tech
Primary Program Source: 01001516DB NSF RESEARCH & RELATED ACTIVIT
01001314DB NSF RESEARCH & RELATED ACTIVIT

04001314DB NSF Education & Human Resource
Program Reference Code(s): 9251, 8842, 8045
Program Element Code(s): 751100, 802000
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.070

ABSTRACT

In this Cyberlearning: Transforming Education DIP project, the PIs are building and evaluating a technological and curricular infrastructure to empower scalable, low-cost experimentations for undergraduates and K-12 students in the life sciences. The infrastructure exploits two technologies that have been developed by the PIs: biotic systems, which enable low-cost remote experimentation in biology, and bifocal modeling, which motivates students to engage in deep scientific inquiry by comparing physical and virtual models in real time. Using a low-cost local or remote Biological Printing Unit (BPU), learners will 'print' organisms into petri dishes and run experiments with live materials. Each learner will have control over the empirical apparatus for as long as needed, due to the low cost and scalability of the system. The living material itself has a small footprint, and ever-advancing high-throughput technologies, such as automated microscopy and DNA sequencing, enable cost-effective, automated multiplexing of massive numbers of simple, learner-guided experiments, allowing learners to each personally carry out successions of experiments. The second innovation is juxtaposition, in real time, of the physical experimentation with computer modeling, known as Bifocal Modeling, allowing students to observe and explore the real-world growth, interactions, and characteristics of their organisms in parallel with observing outcomes of models representing their understanding of the biological phenomena underlying organism activity and subsequently refine their explanations and understanding. Research focuses on cognitive affordances and constraints of this new bifocal epistemic form, the supports needed by learners to handle the complexities of this potentially powerful approach, and the progressions in student proficiency in design and execution of experiments when they have both real and virtual models available.

The PIs are addressing the significant challenge of how to bring modern bioscience into classrooms and informal learning environments, at low cost and with substantial variety. The platform they are creating, which integrates Biological Printing Devices with Bifocal Modeling, provides for more open exploration and realism in what learners can experience than is possible simply with simulations and virtual experiments. Schools and universities will be able to integrate more advanced biology experiments into their lab curricula as a result of this investigation, broadening exposure of all students, especially the less privileged, to the life sciences.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 15)
Cira, Nate J and Chung, Alice M and Denisin, Aleksandra K and Rensi, Stefano and Sanchez, Gabriel N and Quake, Stephen R and Riedel-Kruse, Ingmar H "{A Biotic Game Design Project for Integrated Life Science and Engineering Education}" PLoS biology , v.13 , 2015 , p.e1002110-
Cira, N J and Chung, A M and Denisin, A K and Rensi, S and Sanchez, G N and Quake, S.R. and Riedel-Kruse, I. H. "{A Biotic Game Design Project for Integrated Life Science and Engineering Education}" PLoS biology , 2015
Gerber, Lukas C and Calasanz-Kaiser, Agnes and Hyman, Luke and Voitiuk, Kateryna and Patil, Uday and Riedel-Kruse, Ingmar H "{Liquid-handling Lego robots and experiments for STEM education and research}" PLoS biology , v.15 , 2017 , p.e2001413-
Gerber, Lukas C and Kim, Honesty and Riedel-Kruse, Ingmar H "{Microfluidic assembly kit based on laser-cut building blocks for education and fast prototyping.}" Biomicrofluidics , v.9 , 2015 , p.064105
Hossain, Zahid and Bumbacher, Engin and Blikstein, Paulo and Riedel-Kruse, Ingmar H "{Authentic Science Inquiry Learning at Scale Enabled by an Interactive Biology Cloud Experimentation Lab}" Proceedings of the first ACM conference on Learning scale conference. ACM , 2017
Hossain, Zahid and Bumbacher, Engin W and Chung, Alice M and Kim, Honesty and Litton, Casey and Walter, Ashley D and Pradhan, Sachin N and Jona, Kemi and Blikstein, Paulo and Riedel-Kruse, Ingmar H "{Interactive and scalable biology cloud experimentation for scientific inquiry and education}" Nature Biotechnology , v.34 , 2016 , p.1293--129
Hossain, Zahid and Bumbacher, Engin W and Diaz, M and Saltarelli, A and Blikstein, P. and Riedel-Kruse, I "{Interactive Biology Cloud Lab Enables Authentic Inquiry-Based Science Learning At MOOC Scale}" International Journal of Artificial Intelligence in Education, in press (see bioRxiv) , 2017
Kim, Honesty and Gerber, Lukas Cyrill and Chiu, Daniel and Lee, Seung Ah and Cira, Nate J and Xia, Sherwin Yuyang and Riedel-Kruse, Ingmar H "{LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education}" PLoS ONE , v.11 , 2016 , p.e0162602-
Lam, Amy T and Samuel-Gama, Karina G and Griffin, Jonathan and Loeun, Matthew and Gerber, Lukas C and Hossain, Zahid and Cira, Nate J and Lee, Seung Ah and Riedel-Kruse, Ingmar H "{Device and programming abstractions for spatiotemporal control of active micro-particle swarms}" Lab on a Chip , v.17 , 2017 , p.1442--145
Nate J. Cira, Alice M. Chung, Aleksandra K. Denisin, Stefano Rensi, Gabriel N. Sanchez, Stephen R. Quake, Ingmar H. Riedel-Kruse "A Biotic Game Design Project for Integrated Life Science and Engineering Education" PLoS Biology , v.13 , 2015 10.1371/journal.pbio.1002110
Orloff, Nathan D and Truong, Cynthia and Cira, Nathan and Koo, Stephen and Hamilton, Andrea and Choi, Sean and Wu, Victoria and Riedel-Kruse, Ingmar H "{RSC Advances}" RSC Advances , v.4 , 2014 , p.34721--34
(Showing: 1 - 10 of 15)

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Computer technology has evolved from large number-crunching machines in the 1950s to today's interactive devices of ubiquitous professional and personal use. People like Douglas Engelbart, Joseph Licklider, Ralph Baer, and Seymour Papert made computing interactive, accessible, intuitive, affordable, and fun. We are inspired to enable equivalent devices and human-computer interactions for the life-sciences by utilizing constantly advancing technologies like microfluidics, lab robotics, and genetic engineering.

Many access barriers to life-science experimentation currently exist for education as well as for research, e.g., due to training needs, equipment costs, and safety considerations. The goal of this Cyberlearning project was to conceptualize, implement, and user test biology cloud labs (BCL) that could significantly lower these access barriers. Akin to the cloud computation paradigm, a BCL enables remote users, e.g., students or scientists, to perform biology experiments through a web interface on an automated lab that is housed at a different location and which can be time-shared between many users.

Our project leadership consisted of Bioengineering Professor Ingmar Riedel-Kruse and Education Professor Paulo Blikstein. Specifically, we were driven to develop BCLs that could resolve substantial educational needs: Familiarity with advanced scientific practices and 'authentic inquiry' are imperative for K12 and college education (see Next Generation Science Standards, NGSS) but are difficult to achieve in real-world classrooms given logistics and cost. In addition to traditional physical hands-on labs, virtual and remote labs have recently been successfully deployed in various STEM disciplines. But remote labs for life science education did not exist - in large part because of the associated logistics of handling living specimen. We set out to solve this challenge and to develop the corresponding concepts and technologies for biology education. We also rationalized that our work will be applicable for professional and citizen science research.

Our project Outcomes and Intellectual Merits fall into engineering and educational components:

First, we developed foundational hardware and programming concepts to make interaction with biology accessible: (i) In analogy to CPUs/GPUs, we conceptualized Biotic Processing Units (BPUs) that house, actuate, and measure microbiological systems robustly long term, and where digital stimulus instructions convert to digital output of analog biological behavior. We then investigated different domain-specific BPU designs suited for different biology experiments. (ii) We implemented programming languages to instruct such BPUs to enable the development of versatile real-time interactive applications such experiments, art, and games.

We then developed and implemented two BCLs that also demonstrate the two major (and fundamentally different) biology interaction paradigms: (i) Turn-based batch experimentation, where 1-day long experiments on slime-mold (Physarum) chemotaxis from multiple users are executed in parallel on one BPU. (ii) Real-time interactive experimentation, where 1-minute long experiments on microswimmer (Euglena) phototaxis are executed sequentially on one BPU. In both cases, we set up a cluster of BPUs to increase throughput. Especially the Euglena based cloud lab could scale cost-effectively to millions of phototaxis experiments/year (~1 cent/ experiment) - sufficient to support a nation-wide educational impact.

We then developed lesson plans and instructional materials around these BCL, furthermore a modeling platform that allows students to develop quantitative mathematical and biophysical models to compare to their experiments, i.e., to engage in Bifocal Modeling. We deployed and user-tested these BCL in various educational settings: (i) We run multiple user studies in K12 and university settings. (ii) We delivered the first massive open online course (MOOC) that enabled students globally to execute key scientific practices including real biology experiments and open-ended, self-driven inquiry. (iii) In collaborated with Prof. Kemi Jona (Northwestern University) we evaluated BCL integration into third-party platforms (iLab) and ran teacher training workshops. (iv) We let three teachers design their own lesson plans and integrate the BCL into their regular curriculum.

Regarding Broader Impact, more than 1,000 students (from over 40 countries) and more than 10 instructors (teachers) have participated in these studies; ~100 teachers have been reached during training - demonstrating scalability, versatility, and educational effectiveness of BCLs. Logging of diverse user data enabled large-scale learning analytics to understand more generally how students learn, perform experiments, and build computational models. Students were enabled to perform self-guided investigations, and increased student motivation compared to usage of simulations alone was found. We also derived general recommendations for cloud lab design and deployment.

We published 14 peer-reviewed journal and conference papers (more are pending) and 1 invited review in the monograph 'Cyber-Physical Laboratories in Engineering and Science Education.' About 40 presentation were given at conferences and university seminars by the project participants. 11 undergraduate students, 3 high-school students, and 1 science teacher gained research experience working in our labs and received co-authorship on peer-reviewed publications.

Synergistically, we developed educational NSF-funded spin-off projects on interactive biology museum exhibits and liquid handling robots.

Overall, this project established a paradigm shift from observational biology experimentation towards truly realtime interactive experiences between macroscopic humans and microscopic living cells.


Last Modified: 12/18/2018
Modified by: Hans I Riedel-Kruse

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