Miscellaneous ideas - e-mail extend and forum / mailing list table

[Pierre Poulain]

Dear all,

This message gathers few other ideas concerning "ten rules for
contributing to mailing lists and forums"
that probably do not worth a separate message for each of them.

Is it relevant to extend the discussion to e-mail? I understand
sending an e-mail is
not a mean to contribute to, neither to ask for, any "community
knowledge". However, it is also really important
to sometimes "dare" write an e-mail to an author of a paper or to any
scientist you want
to discuss with. As posting in mailing lists and in forums, sending an
e-mail is also
guided by few simple rules, that are -- in my opinion -- very similar
to the ones explained
so far in your draft.

In structural bioinformatics (especially for molecular dynamics
simulations), there are very active and well organized mailing lists
dedicated to the GROMACS software. Few rules are also proposed here
http://www.gromacs.org/Support/Mailing_Lists
They are similar to the ones already written in the draft. The only
slight difference is regarding the quantity of details provided. Yes,
it is really good (and somewhat compulsory) to give details of the
input / ouput / error messages (actual rule 6). No, it is not a good
idea to join a bunch of 2 Mb files. As a matter of fact, the word
SNIPPET (rule 6) should really be emphasized. The question has to be
posed with enough but not too much data.
The R mailing list has also a nice posting guide:
http://www.r-project.org/posting-guide.html

A short paragraph on common language abbreviation could also be
useful, see for instance
http://lists.gromacs.org/pipermail/gmx-users/2002-December/003613.html

Also note the famous CCP4 mailing list (since January 2007), for X-ray
crystallography, https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccp4bb
that could be included in references.
In a extend to this, it could be a good idea to list in a table
interesting mailing lists / forums related to bioinformatics. It is
not an attempt to be comprehensive, rather a list of tails for the
beginner. The table format does not fit the mail so here is a starting
list:

Name: gmx_users
Since: 01/2000
Mail / article number: ??
Description: GROMACS molecular dynamics software
URL: http://lists.gromacs.org/mailman/listinfo/gmx-users

Name: CCP4 bulletin board
Since: 01/2007
Mail / article number: ??
Description: CCP4 suite, and macromolecular crystallography in general
URL: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4BB

Name: R-help
Since: 04/1997
Mail / article number: ??
Description: help about the R statistical analysis/programming
language
URL: https://stat.ethz.ch/mailman/listinfo/r-help

Name: BioStar
Since: 12/2009
Mail / article number: ??
Description: Questions and answers on bioinformatics, computational
genomics and systems biology
URL: http://biostar.stackexchange.com/

Do you have any other?
As you can see, it is not obvious to get the number of mails / posts.
If you think this is useful, I can write a small script to get the
figures of, at least, gmx_user and R-help. In the same idea, it would
be a very convincing argument to represent the cumulative number of
article / mail versus time (month + year).

Regards,

Pierre
--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/

[Giovanni Marco Dall'Olio]

On Tue, Mar 29, 2011 at 3:59 PM, Pierre Poulain <pierre....@univ-paris-diderot.fr> wrote:

Dear all,

This message gathers few other ideas concerning "ten rules for
contributing to mailing lists and forums"
that probably do not worth a separate message for each of them.

Is it relevant to extend the discussion to e-mail? I understand
sending an e-mail is
not a mean to contribute to, neither to ask for, any "community
knowledge". However, it is also really important
to sometimes "dare" write an e-mail to an author of a paper or to any
scientist you want
to discuss with. As posting in mailing lists and in forums, sending an
e-mail is also
guided by few simple rules, that are -- in my opinion -- very similar
to the ones explained
so far in your draft.

This is a good point, but I would prefer to keep the document oriented to mailing lists and online communities. Some of the rules, like 'Search the archives before posting', and 'The archive of your discussion can be useful to other people' apply only to mailing lists & web forums; on the other side, for what I have learned so far (unfortunately :-( ) writing a mail to a PI or a scientist can be much more difficult, and would require a 'Ten Simple Rules' document.

In any case, we can add, in the body of the document, a line saying that these rules apply also to sending emails in general.
 

In structural bioinformatics (especially for molecular dynamics
simulations), there are very active and well organized mailing lists
dedicated to the GROMACS software. Few rules are also proposed here
http://www.gromacs.org/Support/Mailing_Lists
They are similar to the ones already written in the draft. The only
slight difference is regarding the quantity of details provided. Yes,
it is really good (and somewhat compulsory) to give details of the
input / ouput / error messages (actual rule 6). No, it is not a good
idea to join a bunch of 2 Mb files. As a matter of fact, the word
SNIPPET (rule 6) should really be emphasized. The question has to be
posed with enough but not too much data.
The R mailing list has also a nice posting guide:
http://www.r-project.org/posting-guide.html 

 

Thank you very much for the links.
I know that there are already a lot of "How to post to this mailing list" documents, and this is one of the reasons why I decided to make this document publicly editable.
Do you think we can involve the authors of these documents in this manuscript? Could you make circulate the link to this initiative to some of these mailing lists?
I sent a message to the Biostar community, and was planning to send it to the R-help as well.

In any case, these documents will have to be included in the references.

 

I am not sure whether we are allowed to include tables in a Ten Simple Rules document; we will have to talk with the editors about it. I hope they will at least allow us to include a supplementary Table.

We can add the Bio:* mailing lists:

Name: biopython mailing lists
Since:

Mail / article number: ??

Description: the biopython project (users and developers mailing lists)
URL: http://www.biopython.org/wiki/Mailing_lists

Name: bioperl mailing lists
Since:

Mail / article number: ??

Description: the bioperl project (users and developers mailing lists)
URL: http://www.bioperl.org/wiki/Mailing_lists


 

A short paragraph on common language abbreviation could also be
useful, see for instance
http://lists.gromacs.org/pipermail/gmx-users/2002-December/003613.html

This could be useful, but I would give the precedence to other rules. Let's see if we will be allowed to include tables and how many.

 

Pierre
--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/

--
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it

[Pierre Poulain]

Dear all,

> In any case, we can add, in the body of the document, a line saying that
> these rules apply also to sending emails in general.

I agree. Dealing with mailing lists and forums is already enough.
As an opening, in the discussion part, a line about e-mail could be
inserted.

> Do you think we can involve the authors of these documents in this
> manuscript? Could you make circulate the link to this initiative to some of
> these mailing lists?

Yes. I can try to contact them.

> I am not sure whether we are allowed to include tables in a Ten Simple Rules
> document; we will have to talk with the editors about it. I hope they will
> at least allow us to include a supplementary Table.

Apparently, there is no table nor figure in a "Ten Simple Rules"
article.
Until recently, there was neither supplementary data.
But in "Ten Simple Rules for Getting Ahead as a Computational
Biologist in Academia"
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002001
P. E. Bourne added a file as Supporting Information.
So, we could in principle add something as supplementary info :-)

> > A short paragraph on common language abbreviation could also be
> > useful, see for instance
> >http://lists.gromacs.org/pipermail/gmx-users/2002-December/003613.html
>
> This could be useful, but I would give the precedence to other rules. Let's
> see if we will be allowed to include tables and how many.

Maybe it should not be a rule on its own but could be included in one
of the actual rule
(for instance in rule 2).

Cheers

[Giovanni Marco Dall'Olio]

On Wed, Mar 30, 2011 at 10:02 AM, Pierre Poulain <pierre....@univ-paris-diderot.fr> wrote:

Dear all,

> In any case, we can add, in the body of the document, a line saying that
> these rules apply also to sending emails in general.

I agree. Dealing with mailing lists and forums is already enough.
As an opening, in the discussion part, a line about e-mail could be
inserted.

ok. By the way, this document may be interesting:
- "how to send a mail to a researcher" - Nature/Scitable  http://www.nature.com/scitable/topicpage/e-mail-13953985
 

> Do you think we can involve the authors of these documents in this
> manuscript? Could you make circulate the link to this initiative to some of
> these mailing lists?

Yes. I can try to contact them.

perfect.. I will send the invitation to the R-help list and the biopython/open-bio ones.

> I am not sure whether we are allowed to include tables in a Ten Simple Rules
> document; we will have to talk with the editors about it. I hope they will
> at least allow us to include a supplementary Table.

Apparently, there is no table nor figure in a "Ten Simple Rules"
article.
Until recently, there was neither supplementary data.
But in "Ten Simple Rules for Getting Ahead as a Computational
Biologist in Academia"
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002001
P. E. Bourne added a file as Supporting Information.
So, we could in principle add something as supplementary info :-)

ok, I have created a document for this supplementary table here:
- http://www.wikigenes.org/e/art/e/139.html

we can do the formatting later.
 

> > A short paragraph on common language abbreviation could also be
> > useful, see for instance
> >http://lists.gromacs.org/pipermail/gmx-users/2002-December/003613.html
>
> This could be useful, but I would give the precedence to other rules. Let's
> see if we will be allowed to include tables and how many.

Maybe it should not be a rule on its own but could be included in one
of the actual rule
(for instance in rule 2).

ok; as it has been said in another mail, let's collect all the possible rules and then choose the how to organize them later.

 

Cheers

Pierre

--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/

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