Write and/or Publish My Protocol Working Group

Description

This is a self-paced working group course, where participants will write a protocol and deposit that protocol on protocols.io (Write my protocol course), or deposit a protocol on protocols.io and prepare an accompanying Lab Protocols article to submit to PLOS One (Publish my protocol course).  Participants will watch YouTube videos prior to working group meetings to guide them through the process of writing a protocol, depositing it on protocols.io, and/or preparing a Lab Protocols article.

This course is appropriate for anyone working with a reusable step-by-step protocol, and is not limited to wet lab protocols. This course is not designed for participants who are writing protocols for systematic reviews and meta-analyses (these should be deposited on PROSPERO), or clinical study protocols that describe a design for a specific study. Clinical studies may include reusable step-by-step protocols (e.g. protocols for performing a specific measurement or intervention) that would be a good fit for this course.

What is the advantage of a Lab Protocols article, compared to a methods article in a 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 They can quickly become outdated, as most protocols continue to evolve after publication.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.

Target group

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 and operational procedures in this way.

Can I still participate if I want to deposit a protocol, without preparing a Lab Protocol publication?

Yes; register for Write My Protocol, and not Publish My Protocol. You can register for Publish My Protocol later if you change your mind.

What do I need to get started?

Write My Protocol:

• A list of materials needed to complete your protocol
• A protocols.io account 
• Sign up for free here: protocols.io
• A draft of your protocol, if you have one

Publish My Protocol:

• A list of materials needed to complete your protocol
• A protocols.io account (sign up for free)
• Your protocol
• Data showing that your protocol yields the expected results (you do not need data from a full research study; you only need data to show that your protocol produces what you say it produces – see videos for more information)

Commitment to openness

All course participants must commit to sharing their full, step-by-step protocol. Steps cannot be omitted.

Published protocols from past course participants

Generation of full-length circular RNA libraries for Oxford Nanopore long-read sequencing, see Article

State-of-the-art methods of viral infections in human lung organoids – collection of 5 protocols, see Article

Does my protocol meet the criteria for Lab Protocols articles?

Protocols 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.

Can I sign up with a colleague?

One person can attend the working group 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 organisers 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.

Write my protocol: 0.5 ECTS. Participants must provide a link to the protocol deposited on protocols.io or a PDF of a private protocol to receive a certificate.

Publish my protocol: 1.0 ECTS. Participants must provide a link to the protocol deposited on protocols.io and a draft of the Lab Protocols article to obtain a certificate.

Publication fees

The cost for publishing a Lab Protocols article in PLOS One is $ 1,135. This cost may be reduced if the corresponding author is primarily affiliated with FU or MDC, as these organisations have partnerships with PLOS One to reduce publishing costs. Charité participants can obtain funding for publication costs of open access articles in PLOS One through the Open Access Fund.

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.

Instructors

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
Coordinator for Value and Open Science NeuroCure Cluster of Excellence Charité – Universitätsmedizin Berlin  orcid.org/0000-0003-3265-2372

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.

Course support

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.