C - 2 Exercise: Write a DMP (part 1) : Introduction to Data Management practices

Overview

Teaching: 5 min
Exercises: 35 min

Questions

What does a typical DMP look like?

Objectives

Using information provided in a scenario, create a data management plan using the Data Stewardship wizard Links to an external site..

Instructions

Follow the instructions below in order to get started

Go to DS wizard Links to an external site. and log in with your university credentials by clicking on the orange button.

dsw-homepage

Click on Projects in left-hand margin

projects

Click on Create in top right corner, name the project <your_name>_test_DMP, select template named Intro DM course Template and click on Save

create_project

Note

For the purpose of this learning module, a special project template has been created, in order to better demonstrate tool. It is not suitable for creating a real data management plan. We recommend using a template called Vetenskapsrådet DMP Template, when writing a full DMP.

We will (eventually) delete all projects using this course-specific knowledge model.

There is a more thourough guide of the wizard in the left-side margin Guide - Write a DMP Links to an external site.

About the tool

The answers will be saved automatically.
Under most of the questions you will find guidance or advice on how to answer or what to consider.
For some questions you may provide more than one answer. If you want to add a new answer click the Add button at the end of your last answer.
- When using Add button you might need scroll up in order to get to the first field to be filled.
The DSW provides a filtering feature that allows you to see questions relevant only to a particular phase of a research project.
- Make sure the phase Before Submitting the Proposal is selected.
- Answer the questions in red (these are the questions that should be answered during the selected phase, questions which belong to other phases are in black).

You are now ready to answer the questions using the provided scenario below.

Scenario

SARS-CoV-2 genomic surveillance in Italy

Principal investigator Sam Smith (sam.smith@example.com) at Uppsala University and [you; as a researcher and contact person], wish to do RNA sequencing of nasopharyngeal swab samples taken at a hospital in Italy as part of genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Dr Smith has applied for funding at Vetenskapsrådet. The project is planned to start 2021-10-30 and continue until 2022-05-31. [you] will attend the course ‘Introduction to data management practices’ given by NBIS in order to ensure the data management quality.

The RNA sequencing will be done at the national sequencing facility NGI on Illumina NextSeq 500, a well described and known instrument. The sequencing will be made on 91 samples, producing .fastq files with a total size of ~50 GB.
In addition to the sequence datasets, the sequences will be mapped to a reference genome of SARS-CoV-2 from isolate Wuhan-Hu-1, available at https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2 Links to an external site.

In order to ensure experiment quality, calibrating measurements and repeat samples will be done. The steps of the analysis will be documented using R Notebooks. The research team will use the ENA virus pathogen reporting standard checklist ERC000033 Links to an external site., which is a minimum metadata standard developed for submission of virus surveillance and outbreak. In addition, the file organisation and naming conventions will be documented in a README text file that will be put in the root folder of the project, and a dictionary of the sample metadata will be created.

The analysis will be done by the research group at the SNIC center Uppmax, for which a project will be applied for.

This project adheres to Open Science and FAIR principles, so the sequencing datasets will be published in European Nucleotide Archive (ENA) at the time of arrival, and will be put under an embargo for one year until the analysis has been done and a paper has been submitted to a publisher. This way the datasets will be backed-up at a remote location, separate from the Uppmax account.

Note

Notice that once a question has been answered, it becomes green and the chapter display becomes ticked instead of showing the number of questions that should be answered.

Add a TODO (optional)

The tool has a TODO function, which lets you mark questions where an action is necessary.

Click on V. Storage and backup in the Chapters display menu and scroll down to the question 3.b.1.a.3 Is and application for SNIC project done?

Click on the + sign next to the question.

Notice that you now have 1 TODOs in top of the page.

Solution

Please find a pre-filled DMP here: https://dsw.scilifelab.se/projects/07d3fb1c-5941-4ac4-98c2-39409573bbb0 Links to an external site.

Key Points

There are tools that make the writing process easier.

Do not feel over-whelmed by the time spent on writing/answering questions, it is time well spent since it will save time in the long-run, just as good project planning does.