Team:UPenn/Human Practices

Human Practices in the OptoReader

Determining our project is responsible and will better the world

Human practices is an integral aspect of research and one that we integrated into all phases of research. One particular aspect of conducting and implementing research that we valued was access. Often, cost is a barrier to access for individuals in all fields whether it be finance or research. Ideas may abound in the most intelligent individuals, but without access to the proper equipment, grants, or other fundering, certain groundbreaking ideas in research may never come to fruition. One such tool that has the potential to make waves in the fields of medicine, genetics, and metabolic engineering is optogenetics. Unfortunately, current research methods are costly and time-consuming, requiring high-quality plate readers, equipment, and ample time to collect data over the course of an experiment.

We strongly believe that: Firstly, Optogenetics is an important tool that will uncover key scientific discoveries in the coming years. Secondly, all researchers should have access to high-quality, high-throughput equipment at an affordable price in order to champion inquiry and insight using optogenetics. This was a strong foundation for building the OptoReader, an affordable and open access device that enables optogenetic experiments. We hope our device contributes to expanding the depth and breadth of discoveries in science, medicine, and countless other fields.

We are honored to be able to have the opportunity to conduct our research, and as a team we are committed to working towards a more equitable and equal research environment.

Our Values

Accessibility | Equity | Innovation | Responsibility

Our Actions in response to Reflection, Research, and Engagement

A. ENGAGEMENT/RESEARCH

→ We engaged with stakeholders in optogenetic research such as Dr. Jose Avalos and Saurabh Malani. We learned that their applications of metabolic engineering in bacteria and yeast required different cell densities.

REFLECTION/ACTION → The impact of our discussions with Dr. Avalos and Saurabh led to the selection of our hardware components to ensure that both low and high ranges of optical densities can be read in order to allow other researchers to use their biological system of choice.

B. ENGAGEMENT/RESEARCH

→ We engaged with the staff of the Stephensen Foundation Educational Laboratories to discuss how users may interact with our device. Initially, protocols for our device were manually set in the python and Arduino scripts.

REFLECTION/ACTION → In response to learning that there was sometimes limited software acumen among researchers, we designed an interactive and comprehensive Graphical User Interface. This will vastly increase accessibility and equality in use of our device by allowing researchers to utilize our high-throughput OptoReader without needing extensive software and hardware background.

C. ENGAGEMENT/RESEARCH

→ As we are near the completion of our device, we returned to initial conversations with stakeholders, including the Avalos Lab and Dr. Brian Chow. With current optogenetic research being carried out to mitigate harmful toxins and fuels in labs across the world, we saw the importance of creating methods of making the research more dynamic and efficient. The Avalos Lab informed us that they were curious about stimulating cells during different growth phases.

REFLECTION/ACTION → An untapped potential in optogenetic research currently is feedback algorithms in response to monitoring certain conditions like growth phase. In order for our team to do our part in impacting biofuels and organic compound alternatives, we took on the goal of implementing feedback mechanisms in our device. Now, the user can monitor a condition (like optical density), and subsequently adjust a second condition (such as stimulating light intensity) for all 96 wells separately.

D. ENGAGEMENT/RESEARCH

→ We reached out to other iGEM teams using optogenetics for their research. Our intention was to make sure that our device would be able to support the work of a variety of optogenetic applications. We learned that one team was using red light as a kill-switch and having our robust fluorescence reading mechanism with programmable light intensity would be useful for timing the killing mechanism.

REFLECTION/ACTION → In response to this information, we added a red light stimulating LED. We also learned that another team wanted to be able to test their optogenetic construct and find optimal light doses. We ensured that we had a proper feedback function for researchers to easily program mechanisms such as a kill-switch light dose once optical density reaches a certain threshold. Moreover, we added review panels and created a more straightforward graphical user interface for researchers to optimize their optogenetic tools.