We aim to introduce a non-narrative (no textual, verbal or video) approach to communicate scientific processes.
challenges at biological laboratory
Translation of basic stem-cell research into therapeutics demands reproducibility and identification of subsequent experimental processes variations, in order to assure cellular quality and efficacy. However, many methodologies of stem cell research remain highly idiosyncratic; and the traditional narrative (textual, verbal or video) approaches still lack the ability to identify or assess process variations.
capturing laboratory process variations
ProtocolNavigator, which is a virtual laboratory environment where researchers can emulate their laboratory activities, and the software automatically annotates the practice or activities and depicts a time-integrated interactive experimental map, that includes action patterns, manipulations and data acquisition icons. Interlinking and traversing through this map, a provenance trail for samples becomes apparent and the underlying process emerges visualised across a timeline. Learn more about ProtocolNavigator
converting to OSC messages
We have developed algorithms that automatically converts ProtocolNavigator captured laboratory processes into open sound control (OSC) messages. Through ProtocolNavigator we basically capture the provenance information of the sample (stem cell). Provenance embodies the history of an object or data with chronological description of the 5Ws – who, where, when, what and why. Provenance has been extensively used in the manufacturing industry to determine the quality of a product, by providing better interpretation, assessment, attribution and authentication via these 5Ws.
parameter mapping and sonification
Extensive parameter mapping were undertaken on the multi-dimensional provenance information (eg. activity, location) into auditory dimensions (eg. pitch and rhythm) to facilitate the auditory perception for laboratory process interpretation. The goal has been to generate a language independent approach so that researchers from any discipline can abstract knowledge and discover relationships between process variation and sample quality.
An interdisciplinary team consists of sonification experts, musicians, biologists, social scientists and bioinformaticists converged and mapped laboratory activities and the interactive musical system. We have developed algorithms that sonify these provenance trails and map them into compositions. Basic musical process have been designed that respond to the OSC messages and process or generate new musical material.
Bellow are some common laboratory activities and their associated music. All examples are in relation to six well plate.
Seed: Cells are put into wells with certain density (mapping)
Incubate: whole plate is placed in incubator at particular temperature and time period (mapping)
Label: labelling cells with chemical labels (mapping)
Wash: cells washed with fresh medium (mapping)
Transfer: samples are transferred from one location (well) to another (tube). (mapping)
Measure: experimental effect on the sample measured via instruments. In this case by flow cytometer. (mapping)
Labelling with Quantum Dots
Two alternate experimental designs for the labelling stem cells with quantum dots -Continuous sampling vs. Staggered seeding. For continuous sampling cells were seeded in all 6 wells at time 0h and then labelled with quantum dots and measured at different time intervals. For staggered approach cells were seeded at different time intervals while measurement was carried out at the end of the experiment.
In the video, top panel shows the design of the experiments captured and depicted via ProtocolNavigator, while the bottom panel shows the status of the wells (orange colour) where activity is undertaken.