Organizing your PhD work in SciNote

Your lab is similar to this scenario:

Your laboratory hosts PhD students on a regular or occasional basis. The PhD project is typically part of a bigger picture, bigger research project or initiative. At the same time it is separate enough that it can be managed separately, also due to the nature of PhD projects, as they often include novel, risky research areas that may have unpredictable results. However, this does not mean the PhD project is unstructured. It still has an outline, a structure, a long term plan and set of goals, which in time become more and more concrete. Usually, one PhD student is working on a PhD project, with at least one supervisor. 

Size: You are a small/medium sized academic or industrial research lab within the larger organization

Work focus: basic research, applied research, planning, executing experiments, reporting, publishing articles 

Keywords describing the example: PhD, doctorate thesis, research, young researcher, menthor, supervisor

Suggested SciNote structure:

1. Team: In the beginning, a team is defined, consisting of different researchers e.g. investigation of environmental toxins as polycyclic aromatic compounds (PAC analysis). You can create a Project folder (PAC analysis), where all the related project work and experiments will be gathered.

3. Experiments: Experiment can be e.g. UV/VIS Spectroscopy, Quantification etc.


2. Project: Researchers can create projects, and within those projects, individual experiments are created that consist of multiple tasks. Projects can be private (e.g. your PhD work), or shared if you need to collaborate. Within the PAC analysis team, projects would be e. g. Characterization, LC-MS/MS, MALDI-TOF MS

4. Tasks: Each task has its own protocol, which can be self-written or imported from – a collection of freely available protocols. For each task, you can set start and due dates, add comments, and assign them as completed. Besides that, you can add the results of a completed protocol directly to the respective task.

“We created a “PAC analysis” team and projects for individual tasks (e. g. Characterization, LC-MS/MS, MALDI-TOF MS). To get to know the system, we decided to make a simple UV/Vis characterization of 16 different standards within two 96-well microtiter plates (MTP). So, we created a protocol within the ELN and linked it to a task in the experiment “UV/Vis spectroscopy” and the project “Characterization.” Read the entire case study and explanations by Liane Kober, Molecular Biotechnology and Functional Genomics, TU Wildau, Germany here. 

To sum it up, your SciNote structure could be

SciNote structure

Team 1: PAC Analysis

Project(s): MALDI – TOF MS (Mass Spectrometry)

PAC analysis

Experiment(s): Testing matrices, Quantification, UV/Vis spectroscopy

Task(s): Protocol to follow, and results once the work is done

Maldi-TOF MS

Examples of additional functionalities that are helpful:

Inventory management

Inventories in SciNote are lists (repositories, libraries) of whatever you need e.g., files, samples, equipment, reagents or something completely different. They are completely editable so your columns can contain names, ID codes, barcodes, files, dates and more.  You can always add a new item to the inventory and then assign it to the task within the experiment. This means you will always have the full history of what has been done with each inventory item, one click away.

Integration with

You can search the public database of directly from SciNote Protocol repository, preview protocols, and if you like a protocol, you can seamlessly import it into SciNote. SciNote will get the protocol from, parse it to SciNote protocol format which you will be able to preview and store into your SciNote Protocol repository.

More about SciNote functionalities

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