[Terrapreta] Charcoal Specification

[Sean K. Barry]

Hi Christelle,

This all sounds very good.  I think the "bread(proof) is in the pudding".  Should we nominate reviewers, and/or take turns?  Should all of the reviewers be members, database subscribers, or contributors?  Will their be some formal submission rules for the reviewers to use when deciding about full publication of a submission in the database?

Could we have an "open review" phase, first, for the whole group of subscribers with database access?  Perhaps we could all first vote for submissions, after an "open" presentation to the whole group, with an experiment description and summary results at minimum?   We could tally votes from the group, "yes/no" for more formal review by the review committee (or not), and with a quorum of votes deciding (majority of the subscriber-ship), then send the data on to the review committee.  This could save the review committee members from having to review "dogs that don't hunt".  This might also help the database administrator, if the group "weeds out" experiments before the fully detailed experimental data needs to be entered into the database.

That was a question I had too. ... Should the submission be entered into the database before the review committee reviews it?
I think yes, but this might depend on how busy the database administrator is?  Or, on the rate of contributions, etc.?

I like your plan otherwise, so far, especially that it will be based on such a successful database template as the Stanford Microarray Database.  The provisions for access with data privileges and the use of Non-Disclosure/Non-Compete documents, where appropriate, should be able handle the data protection issues, I would think.

Thanks you so much for doing this bit of research and being willing to set up, at least, an initial database, Christelle.  I think you are being very helpful.

Regards,

SKB

  ----- Original Message ----- 
  From: ch braun<mailto:brauncch at gmail.com> 
  To: Terrapreta<mailto:terrapreta at bioenergylists.org> 
  Sent: Wednesday, September 05, 2007 2:16 PM
  Subject: Re: [Terrapreta] Charcoal Specification


  Hello,

  Thanks a lot for your answers and suggestions. I had indeed feared that the idea of an open-source database would quite soon come across data protection issues, but that came sooner as expected. So better address that first. 

  1. DATA PROTECTION
  I googled a little bit and found a description of the Stanford Microarray Database. Here a small abstract:
  """ One of the most successful, proven, and heavily utilized microarray databases is the Stanford Microarray Database (SMD – http://genome-www.stanford.edu/microarray<http://genome-www.stanford.edu/microarray>) [5]. SMD currently archives more than 34,500 microarray experiments including 4500 from more than a hundred different publications and supports approximately 700 users [6]. It has a great breadth of features that include data filtering, data analysis, visualization toolsets, and constantly updated biological annotations for many organisms. Additionally, SMD features a strict hierarchical user and group model of user accounts such that experiments can be collaboratively shared or protected as desired by individual researchers. """ 
  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=12930545<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=12930545>

  So I guess that would be the direction to follow, right ? Promote as far as possible the open-source approach while still supporting the development of private "branches" without public access but with the same facilities and formats for the data registration so that it can be easily integrated to the main trunk if the protection can be removed in a future stage. 
  So a traditional user-level access control should actually suffice to solve the proprietary issues, right ? Or am I missing something ?

  2. DATA CONSISTENCY
  I agree there should be a reviewing process. A list of "volunteered experts" could for instance be maintained, and every new submission sent for review alternatively to 2 or 3 of them ? 

  3. EXISTING DATA
  The more comprehensive, the better...And I have no doubt that the databases maintained by the TP list owners, Danny Day or at Cornell are of pretty good quality! 
  On the other hand it is probably more reasonable to start small and expand gradually the base so that it doesn't get messy ( i.e. buggy). 

  4. ACTION
  By the way, since the success of the project depends for a large part on the amount and motivation of the participants and contributors, I guess it's not worth starting an endless metaphysical debate on the pros and cons... let's rather try it out directly and see what happens, right ? 

  So I don't have terabytes free space available, but I still can set up a minimal database and provide an online form that can be fulfilled with the corresponding data and added to the DB if the submission makes sense. 
  That would be an initial test phase, on which will depend further development. 

  And last point, concerning the budget problem: well I am quite happy with my PhD student salary for now...on the other hand, there is no way I can provide myself financial support to something! But I believe for now something really great and useful is already achievable without investing something else than a lot of motivation and effort. 

  Sincerely yours,
  Christelle 






  On 9/5/07, Tom Miles <tmiles at trmiles.com<mailto:tmiles at trmiles.com>> wrote: 
    Jon,



    Soil biology and root development are two objectives I have heard most from growers.



    Thanks for the run down on fertilizers.  It sounds like it will be important to distinguish between farming regimes. I've heard from Midwestern farmers that they believe that the earthworms of their youth disappeared with extensive use of anhydrous ammonia. 



    Tom







       



    From: terrapreta-bounces at bioenergylists.org<mailto:terrapreta-bounces at bioenergylists.org> [mailto:terrapreta-bounces at bioenergylists.org<mailto:terrapreta-bounces at bioenergylists.org>] On Behalf Of Jon C. Frank
    Sent: Tuesday, September 04, 2007 10:30 AM
    To: Terrapreta
    Subject: Re: [Terrapreta] Charcoal Specification



    Two specifications to look at would be more at its affect in soil.  These would be:



    Charcoal/biochars impact on stimulating soil biology



    Charcoal/biochars impact on building humus



    And a 3rd one:



    Charcoa/biochars impact on stimulating root development



    Just a few ideas,



    Jon

      -----Original Message-----
      From: terrapreta-bounces at bioenergylists.org<mailto:terrapreta-bounces at bioenergylists.org> [mailto:terrapreta-bounces at bioenergylists.org<mailto:terrapreta-bounces at bioenergylists.org>]On Behalf Of ch braun
      Sent: Monday, September 03, 2007 4:35 AM
      To: terrapreta at bioenergylists.org<mailto:terrapreta at bioenergylists.org>
      Subject: [Terrapreta] Charcoal Specification

      Hello,

      I have been trying to get an overview on the current stand of the research on biochar in the world and have been following the TP list discussions for a little while now. 

      My feeling is that a lot of work/discussions/questions could be spared if all the various experiments performed by biochar adepts all around the world could be registered in some central repository which could be publicly consulted anytime by people who would like to have quick answers to questions as "easy" as e.g.: has already somebody made charcoal with feedstock X ? Where ? How ? What were the results ? Any publication/project about that ? and so on...

      All these pieces of information should actually not only be collected together, but also in a uniformed format, a kind of "biochar standard" which would, on one hand, simplify the description of the experiments and their results for people who perform them and, on the other hand, improve the efficiency of the search for infos concerning a precise trial. 

      Storing these infos in the form of a "formal specification" has also the advantage of allowing the use of tools for data processing in order, for instance, to retrieve statistical analysis or to find interesting correlations between parameters. 

      I have started a list of the different parameters I could find in the literature or discussions about charcoal, which could be part of such a "charcoal specification". I also tried to classify them, but since my knowledge in chemistry and experience in the field are quite limited, there are probably inconsistencies, errors or redundancies. And a lot is still missing. So I would really appreciate help for developing this specification! 

      I have no idea how many people would be, like me, interested in such a project... I principally see 2 steps before it can be really useful:
      1. Formalization: completion/correction of the draft, to get a proper model (possibly as soon as possible, with maybe additional changes later on) 
      2. Instantiation: registration of experiments according to this model (of course not limited in time!)

      The best method for step 2 is probably to set up a database whose schema corresponds to 1 and that people can easily populate with their data online. 

      So I put the current draft here:
      http://bionecho.org/terrapreta/charcoalspec.txt<http://bionecho.org/terrapreta/charcoalspec.txt>

      Anyone is welcome to contribute! Maybe the easiest way to proceed is to discuss the changes and additions here and I merge them and update the draft gradually? 

      I am really curious to know what you all think of this idea...

      Sincerely yours,
      Christelle 


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