Open-source software for
designing, documenting and reproducing
biological experiments

"In the long history of humankind (and animal kind, too) those who learned to collaborate and improvise most effectively have prevailed" - Charles Darwin (1809 - 1882)

On this desk sits the Interactive Laboratory Notebook (ILN), where an interdisciplinary group can share their research ideas, practice and experiment related information. Challenges and motivation for effective communication and collaboration within a multi-disciplinary environment are as follows

Please use     to browse through Interactive Laboratory Notebook (ILN)

Understanding the processing of nanoparticles in tumour population - establishing the methodology

Here the goal is to determine how a fluorescent signal from the nanoparticles 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 purpose is to establish the appropriate regimens and the experimental designs that enable us to measure a conserved process with relevance to the biology and the underlying biophotonics principles.
This book contains the optimized methods underpinned by different assumptions.
Methods >> Staggered biology approach
This has a practical and logistics advantage in that it delivers all of the cell analysis on the same day. To achieve this, the cells are seed in separate flasks on sequential dates to emulate the time series. At the same time the quantum dot labelling is undertaken also in a staggered approach. Thus producing sampling at 24, 48, 72 hrs after quantum dot loading.

The problem with this approach is that both the biology or the quantum dot labelling (biophotonics) is non-parallel and therefore quantitatively non-comparable. The experimenter achieves an overall view of fluorescence signal changes over time. However, the process is not robust enough to model these signal changes. The problem probably originates from the fact that quantum dot labelling is a highly variable process, the biology however can be staggered to reflect and quantify tumour growth. So, another method needs to be optimised.

Methods >> Continuous time series approach
The biology is established in separate flask with the same seeding start point. The quantum dot labelling is prepared and added to each of the flask at same time and same day. The readout is then obtained is sequential days. This enables the experimenter to quantify the fluorescence signal change for sequential days and thus enables modelling and time series analysis. The main benefit is that the biology is not disturbed and the conserved nature of biophotonics is applicable. Note: This is a fully optimised, highly reproducible method and used routinely in the lab.
Methods >> Transfer approach
In this method, the biology and the quantum dot labelling are completely synchronised. In other words, a single flask of cells are labelled with quantum dots. These cells are then scooped up (harvested) and re-seeded into other flasks (other vessels), and left to establish and grow. These new flasks can then be sampled and measured for a fluorescence readouts to provide completely comparable and analytically stable signals.

The advantage of this transfer approach is that different growth conditions, perturbations and intractable conditions for labelling can now be analysed and modelled. For instance, cells grown in normoxic and hypoxic environments, or cells grown in 2D or as spheroids can be analysed and modelled. This makes the time series able to cope with complex perturbation and growth environments.

Experiments >> Typical continuous time series approach
This represents the practice of continuous method, with further analysis. Published paper.