Protocol publishing and collecting – systems and advice wanted

UntitledOne of our goals this year for microBEnet is to start to build a protocol library for members of the community.  This library would hopefully include methods for carrying out all sorts of different kinds of work – from how to sample dust in a building (e.g., do you use a shop vac or a small filter?; if you use a shop vac, which one and how?) to how to do bioinformatics analyses of microbiome data.

So I have been asking around and sniffing around and searching around for ways to build such a library.  And this question is likely of interest to anyone out there who would like to publish, share, or access various protocols.

In my brief looking around I have found four systems that have features that are similar to what I am imagining.

Ideally any system would have the following features

  • Open (e.g., open source software running it)
  • Free (i.e., no charge for the user)
  • Have rewards for posting (e.g., getting a DOI / citable publication)
  • Good links to published literature
  • Links to ways to order reagents and supplies
  • Versioning
  • Easy access / printing for using during work

Some people in my lab have been arguing that most of the features I am looking for could come from GitHub.  I think this is an interesting idea but I just do not see most of the non-computational people in a field using GitHub to share lab protocols.

So – I am writing here to seek input from the community.

3 thoughts on “Protocol publishing and collecting – systems and advice wanted

  1. We have had protocols on OpenWetWare for a long time (8 years) and it’s not terribly hard to set it up with a DOi system (and comes standard with permalinks to edits). So the only thing missing is the links to suppliers, and that’s not hard to automate if you think it’s important.

  2. There is a need for standardized methods that can be available to newcomers to a field, and nowhere is this more evident than in studies of the indoor microbiome. However, many researchers studying the indoor environment favor developing their own methods and do not commonly use standard methods.

    A significant contribution of researchers is in the development of methods, and many peer-reviewed publications report the results of methods evaluation and application, a necessary activity for progress in science and in its application in the field.

    ASTM International, formerly The American Society for Testing and Materials ( has a committee on sampling and analysis of air (D22 on Air Quality —

    There is no fee for attendance at and participation in ASTM Committee D22 and its subcommittees, although only members may vote on ballots for adoption of standards. Anyone can contribute to the development of standards and their revision.

    Most university and major research institutions provide access to all ASTM standards. As a volunteer non-profit society, ASTM charges for copies of standards to cover the cost of staff support and publication.

    D22 has several subcommittees including one on indoor air (D22.05 on Indoor Air –

    In the interest of full disclosure, Subcommittee D22.05 was founded in 1985 by me, Hal Levin, who served as its chair for it first 20 years.

    Under D22.05 on Indoor Air standards have been developed relevant to the collection of dust and some of these methods have been used for investigation of the microbial content of dust. The primary focus has been on chemicals, especially volatile organic chemicals, but also on semi-volatiles, PAHs, and some inorganic chemicals. A complete list of active standards and standards under development is available at

    There is also Subcommittee D22.08 on Sampling and Analysis of Mold. A complete list of active standards and work items can be seen at

    One of the standards under D22.08 jurisdiction ios ASTM D7338 – 10 Standard Guide for Assessment Of Fungal Growth in Buildings. The “Significance and Use sections can be viewed here – where there is also information on how to obtain a copy. A revision is currently proposed and under discussion. This would be a great opportunity for those studying the indoor microbiome to get involved in the practical application of the knowledge developed through work done under Sloan Foundation funding or any other relevant work.

    Another of the standards under D22.08 jurisdiction is D5952-08 Standard Guide for the Inspection of Water Systems for Legionella and the Investigation of Possible Outbreaks of Legionellosis (Legionnaires’ Disease or Pontiac Fever). The “Significance and Use sections can be viewed here – where there is also information on how to obtain a copy.

  3. One of the most important contributions of ASTM committees is often their Special Technical Publications (STPs), not necessarily the standards they produced. I am proud of the many symposia and resulting STPs we produced while I chaired the committee.

    Early in the life of the ASTM Subcommittee D22.05 on Indoor Air, we sponsored a symposium on Bioaerosols. The Symposium, Biological Contaminants in Indoor Environments, took place July 16-19, 1989, in Boulder, Colorado, at the University of Colorado Conference Center. (I don’t know whether Norm Pace was there.)

    The organizers of the Symposium, James Otten, Phil Morey, and the late James Feeley, Sr., invited speakers who had generally devoted most of their career to the study of a single organism or type of organism. They asked each presenter to identify the best methods to sample and analyze for that organism in air. Most did not do air sampling and did not write about it, but the symposium organizers/editors pressed them to respond, even if only speculative regarding air sampling.

    A hardbound copy of the Special Technical Publication (STP 1071) with all the papers is available from ASTM –

    In the interest of full disclosure, I am the author of the least important contribution included in the STP.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.