Abstract
In the August 2009 issue of Autophagy, I indicated that we were launching a new category of article, Protocols. At that time, I noted that we would ultimately be placing these articles on a new site online. Well, that time has finally arrived (see www.landesbioscience.com/journals/autophagy/protocols/ for links to these papers). Therefore, it seems appropriate for me to briefly distinguish among three types of community-oriented papers, Protocol, Toolbox and Resource.
Protocols are just what they sound like. These papers provide step-by-step detailed procedures for particular experimental approaches. We all know that typical procedures described in even the most complete Materials and Methods, or Experimental Procedures sections of research papers leave out enough information to choke an autophagosome. The chance of actually repeating such an experiment successfully, based solely on that information, can be slim, depending on its difficulty. In contrast, Protocols are meant to provide all of the details, so that even a novice would have a fair chance of carrying out a similar analysis. Accordingly, the Protocols do not have to describe new (that is, unpublished) methods, and they should not include unpublished data. Instead, they need to have a clearly stated methodology including all of the necessary reagents, as well as notes indicating potential problems and solutions.
Toolbox articles are more like standard research papers rather than Protocols. That is, they must contain previously unpublished data that demonstrate a new method, and the utility of that method relative to what is already available. Accordingly, Toolbox articles do not have to include detailed protocols, although they may. The overall purpose of the Toolbox category is to let you know about a new technology, even if it has not yet been used to provide a “groundbreaking” result—the focus here is on the method, not the outcome. I view this type of article as providing a service to the community, because other researchers may be able to apply the method to address a question they are asking in their own particular system. If the method proves to be particularly useful, it would be appropriate to subsequently publish a Protocol.
Resource papers are distinct from Protocols and Toolboxes, but I include them here because they are in a separate category from research papers, and they again provide information that may be of general use to the community. Resource papers are meant to provide previously unpublished data, for example from large-scale screens, which may be very useful even though they do not by themselves lead to a mechanistic insight. There are many examples of such screens that generate a huge amount of information—more than one lab can handle in a reasonable amount of time. Rather than hiding these data away, perhaps forever, the Resource article allows other researchers to access them, and potentially pursue in-depth studies on some portion that is relevant to their own interests.
Toolbox and Resource papers are subject to standard peer review because they contain previously unpublished data. Protocols are also reviewed, but in this case more like a Review article. That is, the review of a Protocol is meant to ensure that there are no obvious errors, and that the details are adequate to allow the method to be reproduced.
In summary, I note once again that the online Protocols, and also the Toolbox articles, are available at the following URL: www.landesbioscience.com/journals/autophagy/protocols/. Our goal will be to continue to add to these articles, and to update them as needed. Therefore, we need your help. I encourage you to submit Protocol and Toolbox articles for publication in Autophagy, to expand the resources available to the autophagy community.