Finding What Works: Locating Resources and Reproducible Protocols
Over the course of 26 years Richard Lenski, a professor at Michigan State University, watched the E. coli bacteria used in his lab multiply through over 59,000 generations. He used his lab freezer as a “time machine” and collected samples after every 75 days, roughly every 500 generations. Over time, he saw some lines double in size, mutate more quickly, and become more efficient at using the glucose in the solution they were grown. He even witnessed one of the bacterial lines develop into what he believes to be a new species. Click here to read the whole story.
What if you were to do this same experiment, but instead of looking at E. coli cultures you looked at the evolution of lab protocols over the course of your career? Which evolves quicker?
Protocols are constantly changing within labs. When searching for protocols it is easy to fall into information overload. How do you choose which protocols are right to suit your needs? If you do find protocols related to what you are trying to do...are any of them detailed enough for you to be able to replicate in your lab?
Often the know-how needed to implement research protocols remains restricted to the research group that developed the method or technology. The materials and methods section of the manuscript is not always enough to allow for scientific reproducibility and it can be challenging to find protocols that are.
Journals That Address the Need for Detailed Protocols
Scientific reproducibility of experiments is a crucial issue. To help address the need for more detailed protocols, demand for journals reporting detailed methods has increased. Journals such as Nature Protocols, JOVE, Current Protocols, and MethodsX have helped to fill the void. Here we introduce a few of the different journals and websites that are helping scientists share and access detailed protocols.
Current Protocols in Plant Biology
"Sound and reproducible laboratory methods are the foundation of scientific discovery. Yet nuances that are critical for an experiment's success are not captured in the primary literature but exist only as part of a lab's oral tradition. Current Protocols in Plant Biology provides reproducible step-by-step instructions for protocols relevant to plant research. Written by experts in the field and extensively edited to our exacting standards, the protocols include all of the information necessary to complete an experiment in the laboratory—introduction, materials lists with supplier information, detailed step-by-step procedures with helpful annotations, recipes for reagents and solutions, illustrative figures and information-packed tables. Each article also provides invaluable discussions of background information, applications of the methods, important assumptions, key parameters, time considerations, and tips to help avoid common pitfalls and troubleshoot experiments. Furthermore, Current Protocols content is thoughtfully organized by topic for optimal usage and to maximize contextual knowledge. Quarterly issues allow Current Protocols in Plant Biology to constantly evolve to keep pace with the newest discoveries and developments." - from Current Protocols website
Recently there has been a rise in the development of open-access communities where protocols can be crowd-sourced. Some examples include bio-protocol, Open Wet Ware, Nature Protocol Exchange and protocols.io.
What makes bio-protocol unique? - from Renate Weizbauer, Ph.D. Carnegie Institution for Science, Department for Plant Biology, at Stanford University, California
Most of us Life scientists have a biological question in mind that we want to probe, and we want to spend little time reinventing a method or troubleshooting an experiment. To use a method developed by a fellow scientist, we need detailed, reproducible protocols.
bio-protocol, a free-to-access, free-to-publish journal run mostly by early career scientists at the bench, provides protocols that have undergone a peer review process to ensure high quality, detailed step-by-step protocols. Being an online journal, we can utilize images and movies to highlight parts of an experimental procedure. An interactive platform allows the protocol user to communicate with the author, or to leave feedback. With the later option, we envision science community sourced updates on a protocol, for example an adaption of a protocol to a different tissue or plant species.
Being a platform from scientists for scientists, we have received overwhelming review and editorial support from junior faculty, post-doctoral fellows, and senior graduate students who have in many cases experienced first hand the frustration of establishing protocols in their projects. For them, and us, reproducibility and transparency in Life sciences really matters.
Bio-protocol currently hosts about 2,200 protocols complementing research articles from more than 145 different journals including eLife, Science, Cell, the PLoS journals, PNAS, the EMBO Journal and journals under many societies; i.e. ASPB, ASCB, ASM, AACR.
So far, most of our protocols are commissioned by our team of Editors, although we now encourage direct submission after a pre-submission inquiry or after recommendation from one of our collaborating journals. In addition, we host topic specific special issues, and are currently assembling a Plant Cell Biology special issue in parallel with the Focus Issue on Cell Dynamics published in Plant Physiology earlier this year.
What make Protocols.io unique? - from Steven Burgess, Visiting Scholar at the University of Illinois at Urbana-Champaign
For me there are two things which are very important: Every lab has it's own protocols, with slight variations and tweaks to those published in the literature. These small hints and tips can often make the difference between succesfully repeating someone's experiment or not. Protocols.io provides a platform for publishing complete protocols, going into much more detail than published methods, You get a digitial object identifier, so it can be cited in publications and a number of journals are partnering with the site.
In addition, for me what makes protocols.io particulary useful, is that unlike other platforms for publishing detailed methods, which tend to be publications, it allows protocols to be updated through version control. Many lab protocols evolve overtime, and this site enables you to keep up to date. Further it helps you to easily share and disseminate protocols with lab members and collaborators, it is possible to see which methods are commonly used, and commenting section allows discussion with the scientists who published a procedure to try and solve common problems.
To best utlise the site, I would advise joining a community or group, such as the one we set up for Plantae! (or perhaps CyanoWorld for those working with cyanobacteria). Check to see if any of the protocols you currently use are there already, and share any that are not listed (you can import protocols from word files). If a protocol you are using is present, have a look, if you have a modified version consider copying the protocol and amending. Discussion with other members in the community is encouraged! One of the potentially revolutionary aspects is that through sharing protocols openly, and working as a community to refine and standardize techniques it may help improve scientific rigor and address some of the problems with reproducible research.
Utilizing the Plantae Community
Plantae is also here to help! If you have ideas for ways to utilize Plantae to find and troubleshoot protocols we would love to hear them. Most of us understand the struggles associated with finding protocols and have experienced the frustration of investing time and resources trying to follow a set of instructions that just won’t work.
David Horvath has initiated a “Methods and Protocols” network https://community.plantae.org/organization/methods-and-protocols/dashboard to serve as a site to ask about, store, and discuss protocols that should be useful for members of the plant biology community. Upload additional protocols of your own and check out the protocols already available.
What is the goal of the Methods and Protocols Network? -from David Horvath, Research Plant Physiologist with the Sunflower and Plant Biology Research Unit, Red River Valley Agricultural Research Center, Fargo, ND
“The goal of this group is to provide visual aids to compliment written protocols for all lab procedures - from the simple to the complex, and to provide a venue for comments and suggested improvements for posted protocols.
Too often, sufficient details are impossible to include in the written protocols submitted with publications- things like pellet appearance, physical manipulations of samples, etc. These make repeating experiments or techniques one might read about in a manuscript difficult- and sometimes impossible.
For example, there is a short video of me collecting sunflower root material that will likely be described in the manuscript as - "We collected root material from sunflowers growing with or without weeds." There is no mention that I had to pound the root mass to remove enough soil to get at the roots. There is no mention of the fact that the roots I collected were the smaller roots snipped off from the outside of the root mass and that very few if any of the thicker root sections near the base of the plant were collected. There is no mention of how or if I removed the soil from the roots prior to freezing. All of this is lost without the accompanying video, and it is unlikely that someone trying to repeat my work would collect the same type of material or treat it in the same way without watching me do it.
Once there are enough protocols uploaded, we will try to tag them so that they someone looking for a particular procedure could easily find those that are pertinent.”