[Terrapreta] Charcoal Specification
Tom Miles
tmiles at trmiles.com
Wed Sep 5 20:38:55 EDT 2007
Most organizations and journals have standard procedures for review. On
professional organization sites presentations or papers that are not peer
reviewed are sometimes tagged with a term like "not reviewed for
publication."
Tom
From: terrapreta-bounces at bioenergylists.org
[mailto:terrapreta-bounces at bioenergylists.org] On Behalf Of Sean K. Barry
Sent: Wednesday, September 05, 2007 5:33 PM
To: Terrapreta; ch braun
Subject: Re: [Terrapreta] Charcoal Specification
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) [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
<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=12930
545> &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
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