This Interactive Laboratory Notebook (ILN) mimics conventional laboratory notebook. But unlike conventional laboratory notebooks and common e-books, ILS establishes a two-way communication mode. Here readers not only have access to all level of experiment related information, but also can upload the modified information to communicate their ideas or variations. This two-way communication is outlined bellow -
Read through the Interactive Laboratory Notebook.
Download different entities (e.g. sample, instruments, sub-processes etc.) or the whole experiment from this ILN as ProtocolNavigator readable files.
Open files in ProtocolNavigator.
Edit according to individual understanding and practice using ProtocolNavigator Interface.
Upload ^(email) and append file to ILN as a thread to the original.
Other readers will recycle and expand current knowledge Through this approach our aim is to engage the research community into two different levels -
- First, readers can engage and contribute any level within the experiment they wish to - from instrument settings to whole experiment.
-Secondly, in addition to conventional written comments, readers can include their own experience or activities to the thread by using ProtocolNavigator and this Interactive Laboratory Notebook.

The team is essentially made up of a

• cancer cell biology group
• mathematicians
• physicists

with collectively high expert knowledge in the handling of the biology, the assay, the data acquisition, data analysis, data interpretation and signal processing.

An example from our laboratory involves collecting flow cytometry data from a population of tumor cells. Figure 1 show maps representing two different approaches to the experiment. The goal is to determine how a fluorescent signal changes over time as a tumor population proliferates, or in biophotonics terms, how cell division leads to the reduction or dilution of a fluorescent readout over time. The principal difference between these two experiments is that one represents a continuously sampled culture set up at the start of the experiment (i.e., t = 0) and then sampled on five subsequent days (continuous experiment); while the other (staggered experiment) represents a time course with a staggered start so that all the samples are analyzed at a single time point (an endpoint assay). In both cases, the cell culture is sampled after 1, 2, 3, 4, and 5 days of growth. Either approach allows the biologist to adequately monitor the growth parameters of the cultures, and each allows users to logistically setup their experiments. Also in both scenarios, the nanoparticle readout (per cell), acquired by flow cytometry, becomes attenuated over time; in other words as the cells have an opportunity to go through more division after 5 days each cell will have less signal compared to day 1. The staggered approach is classically used when the perturbing agent to be added is a small molecule or 'drug', where delivery to the cell is assumed to be invariant each time. It might also be preferred if it is important for data acquisition to occur on the same day for convenience or to control for variability in the instrument.

However there is a fundamental flaw in the staggered approach from the physics/biophotonics perspective. This arises because 'particulate' labelling is innately variable and as a result the effective cellular labeling is not constant. This presents unreliability of the nanoparticle signal leading to a misinterpretation of the cellular system growth. The mathematical assumption of a conserved readout over time becomes computationally buried in this variability of labeling. Since in this study it is essential to determine the inheritance of a nanoparticle signal as a result of cell division, a continuous sampling approach allows the mathematical modeler to apply the assumption of signal conservation (since loading variability is no longer a problem); in other words the sum of nanoparticle signal at 144h = the signal at 24h. It became clear that for the mathematical modeler to appropriately use these datasets (FCS files in this case) for this purpose, details and provenance of the experiment set-up was critical. This book provides the environment for ensuring that communication is unambiguous and accessible across the technical and discipline environments.