Interactive Cloud Experimentation for Biology

Abstract

Interacting with biological systems via experiments is important for academia, industry, and education, but access barriers exist due to training, costs, safety, logistics, and spatial separation. High-throughput equipment combined with web streaming could enable interactive biology experiments online, but no such platform currently exists. We present a cloud experimentation architecture (paralleling cloud computation), which is optimized for a class of domain-specific equipments (biotic processing units -BPU) to share and execute many experiments in parallel remotely and interactively at all time. We implemented an instance of this architecture that enables chemotactic experiments with a slime mold Physarum Polycephelum. A user study in the blended teaching and research setting of a graduate-level biophysics class demonstrated that this platform lowers the access barrier for non-biologists, enables discovery, and facilitates learning analytics. This architecture is flexible for integration with various biological specimens and equipments to facilitate scalable interactive online education,

Device and programming abstractions for spatiotemporal control of active micro-particle swarms

“…The synergistic integration of global and local stimulus modalities (side LEDs, projector, and microfluidic chip mazes) combinatorically increased the possibilities to manipulate and interact with microscopic swarms compared to previous systems. 7,30,31,[37][38][39]50 Having multiple stimulus modalities can also greatly accelerate specific tasks compared to single modality stimulation, e.g. the command fastCompress, which combines the LED stimulus with a projected barrier, is at least an order of magnitude faster than the command compress, which only uses a shrinking projected barrier (Fig.…”

“…8,10,15,[17][18][19][20] Algorithms for efficient control and programming of such swarms have been extensively studied via theory 20,21 and experiment in both synthetic 22 and natural systems, from motor proteins and filaments 23,24 to single-celled organisms 2,8,25,26 to insects 27 to macroscopic robots. 20,21,28 For microbiological swarms, "interactive biology" setups have enabled both professionals and non-experts to interact and experiment with swarm agents in real-time for research and edutainment purposes, e.g., through biology cloud experimentation laboratories, 29,30 museum exhibits, 31 or biotic games. 32,33,38 While most of these platforms had been developed ground-up to support a single application, more expressive, general purpose setups with a larger degree of programmability are desirable for applications involving swarm control of microscopic agents.…”

“…magnetic or light fields) to control directionality of many agents, but this precludes local control over subgroups of agents. 1,27,30,[34][35][36] Other setups capitalize on local stimuli (e.g. projection of images 31,37 ) to control individual Fig.…”

“…1). We combined several existing biotic processing units (BPUs 30,38 ) from other experimental 7,37 and interactive biology 31,39 setups to create a single highly expressive BPU (Fig. 2).…”

An interactive programming paradigm for realtime experimentation with remote living matter

“…exhibits [33], biology cloud labs [19,20,21], biotic games [5,40], and Do-It-Yourself Biology (DIYbio) kits [26]. Future engineering applications such as for biological swarm control have been demonstrated [30], and applications for discovery research are in reach [9,32,20].…”