Research integrity (data storage)

[tentative policy]

Where to save data

All data will be saved on our file server (Cronus), which is a redundant, fully backuped and maintained storage system. Although you might have material in your user share (private), all data, analyses, notes and presentations should be stored on Cronus.

Your data and documents should be stored with a logical file structure. The next guidelines might seem a bit too complex or rigid at first read. In fact, it is simple and it will help us to work effectivly as a team and, equally important, it will ensure we respect terms&condition of funders, basic requirements for scientific reporting and effective long-term archiving of our data. Your Cronus folder will have to be organized in logical collections of files. I mandate the use of the following collections, but you can add others if necessary:

  • PRJ_short_project_identifier | to store all data and analysis related to a specific project. This folder may or may not be further organized, but I advise to use clearly identifieable sub-folders with prefix DATA_ , ANALYSIS_ , SOFTWARE_ , MANUSCRIPT_ to identify different types of collections:
    • For instance, you may wish to organize all imaging data in one folder and all western blots in another, or all results belonging to a task within the project in one folder. The important thing is that there is a logic in your organization. If experiments are made of different files, which is often the case, create a folder for each collection of data. Either the data file, or the folder containing a collection of data files, must store the date of the experiment and basic experimental notes (see below).
    • Simple data analysis might be stored within DATA folders; however, you might have more complex analysis that tap into different data. In this case, save also folders for data analysis (excel files, matlab code, etc…)
    • Similarly, you might need to develop software do analyse your data and you can have code within DATA or ANALYSIS sub-folder. However, if your software grows large and it is of general use, you might wish to create a dedicated SOFTWARE subfolder.
    • You might identify a number of different collections, one could be all files to assemble a MANUSCRIPT
  • LITERATURE (optional) | you can be flexible with this folder, but I advise to have a dedicated folder where you store all your pdfs, at the level of organizaion you prefer. I also really advise to store notes about papers, or to prepare for yourself literature reviews. Here, you could also save your EndNote database.
  • PRESENTATIONS | Store here all internal presentations such as Work-in-Progress talks, Friday lab meetings talks, posters or talks prepared for conferences or retreats, in other terms, everything that was presented internally or publicly. I advise to structure the folder as in collections of files for CONFERENCES, LABMEETINGS and POSTERS. Clearly date all presentations. Feel free to add journal clubs or those more articulated slides you may prepare for our Wednsday meetings, but these are optional
  • RESOURCES | Store here all files related to plamids, cell lines, or other materials you need to inventorise and that could be important for the group. Also, create here a LAB_BOOKS folder. You will store here all your digital lab books, or pdf exports. Would you wish to have a distinct lab book per project, feel free to do so, but ensure that every project folder contains its own LAB_BOOK collection.
  • Collect all other non-organized material in a OTHER folders, or create other collections. However, make sure that are clearly identifiable. Once you left the lab, I would probably delete the OTHER folder to avoid archiving unnecessary files.

Confused? Search for the folder ‘FOLDER_STRUCTURE_DEMO’ in the SysMic group and you will see how simple this is.

How to save data

It is probably impossible to give a policy for each data type or file you will handle. Once you stored files in the right place, half of the job is already done. The next step is to ensure that we can easily identify a logical link between data, analysis, lab books and, eventually, manuscripts. Therefore, date experiments, store source data names in the analysis files and in the documents you create to disseminate our work.

File names

Experimental data, or the folder containing them when multple files are generated should be of the format:

YYYYMMDD_brief_description_[v#] or, for example, 20180131_mTagBFP_1.sdt or 20180131_SW48_ERK_sensor (folder)

We use the YYYYMMDD format because when you order files, or folder, alphabetically, they will be ordered chronologically. We do not rely on the OS time stamp.

For analysis file, manuscritps or other files you will update, but you wished to keep a record of, version them adding a ‘v#’ at the end, where # is a progressive number.

Experimental notes [additional to lab books]

Please read the guidelines of lab book keeping. We are transitioning to fully digital note keeping (read specific guidance). Do have an entry for each experiment in your lab book. However, there are a number of experimental parameters or observations that might more convinently stored within a sub-folder containing data. For instance, when we do imaging, we do not enter imaging parameters within lab books, but we rather have a ‘readme.txt’ or ‘notes.txt’ file. Usually, we use similar settings from experimental to experimental sessions and, therefore, we can simply copy and paste these files and update what is necessary to update. Mind you that if you use a confocal or a motorized microscope, most information is stored in the metadata of your experiment. However, some instrument does not perform this operation. The bottom line is, either in your digital lab book, or within the data folder, there should be enough information to understand how the sample was prepared and how the experiment was executed.