[Terrapreta] Charcoal Specification

[ch braun]

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) [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

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> 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] *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]*On Behalf Of *ch braun
> *Sent:* Monday, September 03, 2007 4:35 AM
> *To:* 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
>
> 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
>
>
> _______________________________________________
> Terrapreta mailing list
> Terrapreta at bioenergylists.org
> http://tech.groups.yahoo.com/group/biochar/
> http://terrapreta.bioenergylists.org
> http://info.bioenergylists.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: /pipermail/terrapreta_bioenergylists.org/attachments/20070905/95fd8366/attachment.html