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From 2014.igem.org

Contents 1 Introduction 1.1 Lay out your plan, then record what you did 1.2 You decide the level of detail 1.3 Propagation and Backtracking 1.4 Version control 1.5 The web 2 References

Introduction

Documentation is one of the most important aspects of any scientific project. Nevertheless, maintaining a detailed log of all experiments performed can often be a daunting task, especially when consistency and standardization across multiple persons is required. This consistency is particularly important in the context of iGEM, where group work is of paramount importance. Also, as many iGEM projects build upon results of preceding teams, a standardized way of documenting would further enhance this interaction. Reproducibility of projects would also be increased. Thus, a consistent, semi-automated, documentation method could help solve many of the problems faced by iGEM teams, but also researchers in general.

For these reasons, we created a software which does just that. Our MidnightDoc enables reproducibility by making sure that documenting experimental methods becomes a fun activity; a natural extension of normal lab routine. In the following, we will describe the main design principles behind this fine piece of software.

Lay out your plan, then record what you did

The most important design principle behind MidnightDoc is the fact that it accompanies lab work and in fact makes it easier. In order to illustrate this, consider the simple example of a restriction or ligation experiment: The user will first look up for the concentrations of his fragments, as measured for example by a spectrophotometer. Then, based on these concentration measurements and the manufacturer guidelines, which might specify the required amount of each fragment (e.g. in micromol or nanograms) or the ratio between them, the user will calculate the necessary volumina. Only after these calculation have been done, will the user be able to mix these components and then start the reactions. Once this has been done, he will document some of the aforementioned numbers (e.g. the volumina used) in his labbook for future reference.

Now, notice that there are several ways in which a software tool can assist in the previous process. First of all, an integrated database with information on all available plasmid, PCR amplified DNA fragments, etc. would make the retrieval of the concentration information a lot easier. Then, this can be immediately used for subsequent calculations, which also should be done by the software.

To achieve this, you have to pre-specify your plan: the experimental guidelines and procedures which you want to follow. The rules, such as ratios of fragments, will then be integrated in order to automate calculations. Thus, MidnightDoc, will help with your calculations, but at the same time document what you did. Also, once you have created the protocol for an experimental procedure, such as a ligation with different fragments, you will be able to reuse it with new details, such as the new fragments or the different concentrations.

You decide the level of detail

We took special care in making sure that MidnightDoc would conform to the different requirements of different labs.

Propagation and Backtracking

Version control

The biostatistics community has recently embraced the idea of [http://cran.r-project.org/web/views/ReproducibleResearch.html Reproducible research], by introducing standards which should be followed when reporting any computational task. Thus, other researchers will be able to verify methods used in diverse publications, but also modify and improve upon them. We believe, that documentation of wet lab work, should also try to make use some of these concepts (and vice versa!).

The main concept of the reproducible research community which inspired us for MidnightDoc are the version control systems, such as [http://git-scm.com/ git]. In computational tasks and programming in general, the basic idea is that you should be able to look at the code you had previously written, which over many iterations lead to the final production code. Similarly, in the context of wet lab documentation, you should be able to easily revert to the state of the documentation at a particular date. This would allow one to explore protocols that were used by the lab previously and got replaced or modified over time. In addition, it would allow to explore the PCR fragments which were available at a particular point in time.

In summary, version control, is very exciting indeed, even if it is centralized!

The web

References