SSSSLEEPING

Summer School Study on Sleep & Learning Entailing Every Participant In Nijmegen, Gelderland

The idea

We want YOU as an author on our paper. We hope that together with all participants, organizers as well as all speakers, we will create a paper during and as part of the Summer School program. Data will be collected on you, analyzed and written up by you, and ultimately published with all 70+ participants as coauthors! We hereby aim to teach you how to properly run and publish a sleep study from A-Z using free and open tools, including sleep study design, data collection, sleep and behavioural analysis and statistics, writing a research paper and publishing as a preprint (and eventually a journal article). In addition, an important emphasis will be placed on open-science practices, such as pre-registration and data/code sharing and using open science tools.

 

The plan

We all together will collect the data and collaboratively create a paper as part of the Neuroscience of Sleep Summer School. You can be one of 40 study subjects with their memory, attention and sleep being tracked during 3 lectures and 3 nights. In addition to being a participant, you can take part in the analysis of the data (questionnaires evaluation, sleep scoring, biosignal evaluation for sleep quality and drowsiness during the lecture). You can also help in writing the manuscript and help in the submission and publishing process. Importantly, we will give enough opportunities for everyone taking part in the Summer School to reach the level of authorship. We expect that if everyone will take part and help, our results will be of high scientific quality and we can publish a great paper on bioRxiv.org at least. The main work of analysing and writing a first draft of the paper will be done in two hands-on session on the afternoon and evening during Thursday and Friday. There, everyone will analyse the data, write the manuscript, and get it ready for the final results of the memory test a week later. We will work in dedicated groups that focus one one aspect of the project. We plan to prepare all data to mainly do a correlative/exploratory study without manipulation of any conditions.

 

The question

The main question we will try to answer is:

“Is long-term memory of lecture affected by daytime drowsiness or nighttime sleep?”

We will also discuss if other questions can be answered by the data and decide on a final set of main and secondary hypotheses together. Finally we will pre-register our hypothesis online at osf.io before the final results and data collection are in. If you have any good ideas that do not conflict with feasibility of our project, please note them down, there will be a chance to discuss them during the Summer School.

 

The data

Over the course of the Summer School we will collect plenty of data. To test all participants’ long-term memory we will ask questions about the content of the lectures and what happened there. The questions will be multiple choice and the lecturers help us in creating them. The questions are answered online at least a week after the Summer School. This will likely be the weekend of 20-21th of July 2019. So please keep some free time for this weekend. Besides this memory test, we will also have some more additional questionnaires during the summer school that will help in addressing confounds or align with other measures we will take.

For recording the EEG signal of all the participants during the lectures and nights we will use a sleep EEG headband that measures brain and body signals (ZMax from hypnodynecorp.org). This will give us objective data on what the brain and the body was engaged on and leaves plenty of room to practice and do some typical sleep analysis with it. Please be aware that your anonymized raw data will be shared publicly at one point down the line.

 

The analysis

For the analysis of the data we will use free and open-source software where possible (e.g. R, python, FieldTrip, SleepTrip/SpiSOP, JASP). For the analysis, the most important and critical part is to get the results correct. Therefore we use both cutting-edge but also approved methods to work on the data. Some analysis pipelines will be provided by us as templates. We will complete and extend the pipeline during the hands-on session so we will get our results as soon and reliable as possible.

There are a lot of things to be done. That is: scoring and cleaning the sleep and wake data, organizing the data, double checking the completeness and correctness of the results, aggregating results, detecting sleep spindles and slow waves, finding the spectral composition of sleep states, implementing measures to detect drowsiness in the lecture recording, calculating scores for the questionnaires etc.

Also we will plot the fruits of this analysis and make some figures that support our findings best or are supplementary. We will also prepare and implement the necessary statistical strategies and models to answer our research questions and hypotheses as well as possible.

The analysis will be held to best practices in sleep research and you are welcome to bring it further. A goal of the analysis is to construct it so that it can be repeated with little effort with new data, i.e. make it replicable. Also we have some measures at our disposal to increase anonymity of the data is also assured during the analysis. This will also make you able to apply those methods directly to your research after the Summer School.

 

The writing

For the writing part, and to further foster replication of this study, we will track the progress with online tools. This will also be helpful in tracking author contributions. We aim for using google docs in collaborative writing on the manuscript, github.org in publishing the analysis pipeline and versions, and osf.io as a repository for all parts and data of the study and results being published. In addition, the data will be available on the Donders Data Repository. The final paper is then ready for publishing and submission in bioRxiv.org. From then, and as a bonus, every author is invited to bring the publishing further into a peer-reviewed journal, but that is not our immediate goal.

We will provide already a manuscript draft and templates that include major parts of the Methods section, and a proposed outline and structure of the Introduction, Results and Discussion and References. This template will include suggestions on style, format and structure of the paper, so it will not be a mess if many people will work on it. At each step, everyone of the Summer School is able to see the progress of the paper. Dedicated groups will focus on different sections of the paper and revision of the entirety. We aim to get the important part of the manuscript done during the Summer School, and at least most be ready before the final results are checked (i.e., the results from the memory test a week later). The Manuscript should be ready in such a way that the incoming results will only change a few (but important) parts of the paper. This means we will aim to write it so open that if the results fall in either way of our hypotheses we are able to adapt the manuscript easily, and have an easy time to finalize a Discussion.

In case you have not much experience in writing, seeing how others write the paper will likely teach you a few things about paper writing in the process.

 

The rules

Perhaps the question arises, who will be on the paper, and on which position, etc.?

Needless to say, that authorship does not come for free and just being at the Summer School does not grant you authorship. You really need to contribute: in planning and designing the study and the paper, aiding or being part in data collection, analysing the data, writing things up, do critical revision of these processes and other things that grant authorship. We will try to track contribution of everyone, online as well as offline.

In the end we aim for a fair process to acknowledge everyone’s contribution. The “Author Contribution” section of the final paper will be as accurate as we can manage to do. We will also make sure that it will not be hard to reach the status of authorship and give everyone a chance to reach it regardless of their background. Furthermore, everyone will have the chance to excel, and we will take great effort that everyone will be treating each other with equal measures. In the end, the organizers of the study will decide who contributed, but we will have an open ear for anyone that disagrees.

Importantly, we want the whole project to be as much fun as possible. The last thing we want is that people feel badly treated. Thus, we already made a plan how to keep you motivated and acknowledge contributing in a transparent way. We will announce this plan and other rules and discuss them with you at the Summer School. Then you can confirm if you are happy with it before the real work starts.

Finally, the data, including raw data, will be publicly shared on publication of the paper, but of course anonymized. Each author that was also a subject will know what is their own raw and public data. No one knows to whom of the other study subjects the data belongs to, but everyone will have access to the anonymized data.

 

The goals

Besides answering an important research question and publish it as a paper, there is more to it. Especially we plan this experience to be helpful for the early career scientist in this field. They will gain some more research skills in the course of this activity: design a study, conduct a study, introduce blinding procedures where necessary, do pre-registration, perform a cutting-edge sleep analysis, write a research paper, perform statistics, and see the publishing process etc.

Thus, while the paper will be the most visible outcome, everyone should have fun and learn something while working on it.

 

The roles

The roles that can be taken during the Summer School are mentioned here for an overview and might change later or new ones will be added. You can AND should take more than one role if possible:

• Study subject: The data is collected on you. 40 of you will have the opportunity to wear a sleep EEG head-band during 3 lectures and the 3 following nights. Data on your memory for all lectures will be asked a week later, and potentially a month later.
• Data collector: You will aid the collection of the data, see that it is converted, and put in the right study folders, you will ensure that the other study subjects do their job well.
• Data analyzer: You score the sleep and lecture data and get valuable information of the quality of sleep and the level of attention out of the raw data.
• Statistical analyzer: You need to assure that the study analysis is sound and close to the hypotheses, also you need to advise and plan the tests using free statistical software (e.g. R or JASP)
• Results writer: You write up the results, and bring them in a logical and complete form to answer the research questions. You assure that they fit a narrative and proper structure.
• Discussion writer: You evaluate the results and look for literature to confirm, support or contradict our findings, also you aid in adapting and completing the Introduction.
• Revisioner: you will correct the “mistakes” the others make in analysis and in writing to not hinder publishing and keep the process smoothly running. You assure everything looks good and give constructive feedback to others, and aid to adapt code and text accordingly.
• Submissioner: You help in getting the versions and all parts of the data, manuscript and necessary steps ready for submission to bioRxiv.org

 

Please pick a role that you either are confident to take, or are confident to learn. We will make sure that anyone is able to contribute to each of those roles, so be bold.

 

The organisation

More information on the organisation will follow at a later update.

 

But for now:

If you take part in our study, there are some things that you will need to bring or are needed for making the writing and analysis part work.

 

Please bring:

• A good attitude. Stay positive and help everyone to make this work. 🙂
• Your laptops
• (optional) external drive of USB stick

 

Please get accounts at:

• https://github.com
• https://osf.io
• https://accounts.google.com/signup

… (if you do not already have an account to spare).

 

Please install on your laptops

• R (https://www.r-project.org/)
• Rstudio (https://www.rstudio.com/products/rstudio/download/)
• (optional) Matlab 2013b or later.

 

These things are also useful besides the project.

 

If you do not want to get an account on these websites, or cannot install the software we will try to help out at the summer school. We will try to provide you with the necessary materials (PC, pen, paper, etc.) to participate as an author and a study subject. We however have a limited amount of PCs available.

 

We will try to organize food, snacks and drinks in case the hands-on and hackathon part will be intensive. Coffee will be omnipresent.

 

The sign-up

Please sign up as early as possible and indicate what role you would be willing to take (you can still change your mind at any time later).

 

At least one additional email will follow in the 2 weeks before the Summer School. This will include updates on the project and some instructions on what to prepare. Also, this will include some necessary Consent and Approval Forms. Until then, this sign-up is more of a gathering of how much people are interested on this project so we can plan better.

 

Of note, if you think your participation as a subject could potentially confound the results of the study (e.g. physical or health reasons) please do not volunteer as study subject but choose another role. This is because we intend to represent a typical study population without major obvious confounds. In the end every author will want a quality paper and not everyone can be a subject.

 

Finally, please note, that by signing up, you are visible to all the other participants and organizers of the Neuroscience of Sleep Summer School.

 

Please do not be shy, if you have any questions and concerns or feedback, let us know and send us an email with the subject “[SSSSLEEPING]”.

 

Please sign-up with your name and affiliation, this makes it easier later on to make you appear as an author on the paper. Thank you for considering this.

 

We count on your contribution!

 

SIGN-UP SHEET

 

The organizers

Freddy – research@frederikweber.com

Leonore – leonore.bovy@radboudumc.nl