“Publish My Protocol”
During this 5-session workshop, participants will deposit a protocol on protocols.io and prepare a companion “Lab protocol” publication to submit to PLoS One. This new article type is designed to make research methods more transparent and reproducible by pairing a living protocol, deposited on protocols.io, with a brief Lab Protocol publication. This also allows authors to obtain credit for their methods development work by obtaining a peer-reviewed, published article. The method does not have to be a completely new invention but can be a variation or extension for a traditional or existing method that will benefit the research community.
What is the advantage of this approach, compared to a publication in a methods journal?
Publications in methods journals reflect what one lab is doing at a single point in time. They can quickly become outdated, as most protocols continue to evolve after publication. Protocols.io is a protocol repository, which allows authors to deposit detailed protocols with additional features like pictures or short video clips, or timings for individual steps. The repository allows authors to create updated versions of their protocol at any time, so people who read your article can then go to protocols.io to find the latest version. This allows you to maintain a living protocol, which will make it easier for research within and outside your lab to follow your methods. Scientists outside your lab group can also “fork” your protocol by sharing their own modified version. New versions and forks link back to your original protocol, and protocols are citable with a DOI. This means that you get credit when others re-use your protocol.
The course is open to all researchers (any career stage) at Berlin research institutions (also BUA institutions) who want to develop, apply and disseminate appropriate scientific methods, tests, operational procedures in this way.
Can I still participate if I want to deposit a protocol, without preparing a Lab Protocol publication?
Participants who only want to deposit a protocol can choose to skip Session 4 (please indicate this when registering).
What do I need to bring?
Bring a list of materials for your protocol – you will use this information to look up research resource identifiers (RRIDs) for antibodies, cell lines, model organisms, plasmids, software and tools to make it easier for others to determine exactly what was used.
Bring your protocol, including a comprehensive list of materials with RRIDs. If you would like to include videos or pictures for any protocol steps (optional, file size limit 100 MB), you will need video or picture files for these steps. If you need more file space, contact the instructors early on.
To prepare the “Expected results” section, you will either need prior publications using the protocol, or new sample datasets demonstrating that the protocol worked.
Feedback from co-authors and/or classmates, anything needed to complete unfinished items
Will I be able to finish everything in 5 sessions?
The workshops provide an overview of important points, dedicated work time to get started, and access to instructors who can help if you have questions. Participants should make substantial progress during the sessions, but will likely need to additional time outside of class to complete their protocol and paper.
Commitment to Openness
All course participants must commit to sharing their full, step-by-step protocol. Steps cannot be omitted.
Where can I find examples of published articles/protocols?
Is my protocol eligible?
Are welcome for all research areas covered by PLOS One. The workshop organizers recommend consulting the author guidelines for further details (see Lab Protocols in the “Guidelines for specific study types” section: journals.plos.org/plosone/s/submission-guidelines).
The Q&A session in this explanatory video (https://www.youtube.com/watch?v=unhqD4j0TRQ) notes that modifications and extensions of existing methods are welcome, however the author instructions note that protocols describing routine methods, or extensions or modifications of routine methods, will not be considered for publication. Authors who are working on protocols for routine methods may still benefit from depositing protocols (Sessions 1-3).
This course is not recommended for researchers working on systematic review protocols, as these are traditionally deposited in PROSPERO. Researchers working on preclinical systematic reviews may want to take QUEST courses on preclinical systematic reviews.
Can I sign up with a colleague?
One person can attend the workshop and prepare materials on behalf of a group who worked on the protocol. However, we also welcome people to work in small groups, with others who will be listed as co-authors on the protocol and publication. If you plan to do this, please list the names of your team members who plan to attend when registering. These workshops focus on drafting materials; participants should ensure that all co-authors have had an opportunity to comment on and approve the protocol and paper prior to submission.
When registering, you will be asked whether others who were involved in developing the protocol support your participation in this workshop series.
Do I have to publish my protocol or submit my article?
No – decisions about protocol publication and article submission rest solely with the authorship team. Other members of your research group can still benefit from your deposited protocol if you decide to keep it private within your team.
Does participation guarantee article acceptance?
No – the workshop organizers are not affiliated with protocols.io or PLOS One. Editorial decisions are the responsibility of the journal.
ECTS & Course Credit
Participants who complete the workshop series will receive a certificate. Graduate students should talk to staff for their degree programs, prior to enrollment, to determine whether ECTS acquired during this course will count towards graduation requirements. Graduate students who would like to use the Lab Protocol publication as a paper in their dissertation should check with their program in advance to determine whether this type of paper counts towards degree requirements. 0.5 ECTS points for participants who prepare and article, 0.25 ECTS points for participants who only deposit a protocol.
The cost for publishing a Lab Protocols article in PLOS One is $1,100. This cost may be reduced if the corresponding author is primarily affiliated with FU or MDC, as these organizations have partnerships with PLOS One to reduce publishing costs. Charité participants can obtain up to 500 Euros towards publication costs for open access articles through the Open Access Fund. Charité course participants can ask QUEST for funds to cover the remaining publication costs for one Lab Protocols article. Available funds will be allocated on a first-come, first-served basis until allocated funding is used. To qualify for this opportunity, Lab Protocols articles must be accepted within 6 months of the course end date. Participants from other institutions should consult institutional open access funds requirements to determine whether they are eligible for partial or full reimbursement of publication charges for open access publications.
Course participants who are also lab members of current NeuroCure PIs, NeuroCure group leaders or are NeuroCure fellows will receive reimbursement for APCs upon application.
Tracey L. Weissgerber, PhD
Group Leader, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany
QUEST – Quality | Ethics | Open Science | Translation
Dr. Weissgerber is a meta-researcher at QUEST (Quality | Ethics | Open Science | Translation) in Berlin. Her team focuses on improving transparency, reproducibility and rigor in scientific publications. Her 2015 paper on bar graphs has been viewed more than 395,000 times. This paper contributed to policy changes in many journals that encourage authors to replace bar graphs of continuous data with more informative graphics (dot plots, box plots, violin plots).
René Bernard, PhD (zum Kontakt verlinken)
Coordinator for Value and Open Science
NeuroCure Cluster of Excellence
Charité – Universitätsmedizin Berlin
Dr. Bernard is a trained pharmacist, pharmacologist, and currently works as Coordinator for Research Value and Open Science in the NeuroCure Cluster of Excellence. In addition to neuroscientific research, he worked for several years in an academica-industry collaboration and helped to develop two quality management systems designed for preclinical research. He is committed to promoting good research practice, as laid out in this open access book, to which he contributed.
This is a joint course from BIH-QUEST Center and NeuroCure Cluster of Excellence. NeuroCure is funded within the Excellence Strategy by the GERMAN FEDERAL and BERLIN STATE GOVERNMENTS through DFG Grant EXC 2049 / project number: 39068808.
Date: January 6 – February 3, 2022
- Session 1 (January 6, 2-3:30pm) – Planning (1.5 hours): This session will include an overview of the process for depositing a protocol and preparing and article, and identify materials needed for the remaining sessions.
- Session 2 (January 13, 2-4pm) - Protocol depositing work session (2 hours): Participants will upload their protocol on protocols.io. Protocols may relate to any topic covered by PLoS One.
- Session 3 (January 20, 2-4pm) Feedback (2 hours): Participants will share their protocols with the class and obtain feedback. Homework: Participants will likely need additional time outside of class to finish uploading their protocol. After sessions 2 and 3, participants are encouraged to solicit feedback from co-authors. They may also exchange protocols with classmates working on similar topics to get feedback.
- Session 4 (January 27, 2-4pm) – Publication work session (2 hours): Participants will begin drafting the companion Lab Protocol publication, using the PLoS One template. The article has four sections: title, introduction, methods and materials (this section consists of a link to the protocol deposited on protocols.io), and expected results. Homework: Participants will likely need additional time outside of class to finish drafting their paper. Participants are encouraged to solicit feedback from co-authors. They may also exchange papers with classmates working on similar topics to get feedback.
- Session 5 (February 3, 2-3:30pm) – Unfinished business (optional – 1.5 hours): This session provides dedicated work time for participants to complete unfinished items, or integrate feedback from co-authors.
Workshop language: English
Location: The workshop will be held online via MS Teams or gotomeeting. The access data will be sent by e-mail approximately one week before the seminar.