status of the manuscript after two weeks
Giovanni Marco Dall'Olio
here is a resume on what has been achieved during these first two weeks of work.
First of all, I would like to thank you all for your contributions. Honestly, I didn't expect this initiative to proceed so fast, and I am very happy to have seen so many contributions and feedback :-).
It seems that the collaborative open approach has paid, this time!
Deadlines and submission date
----------------------------------------------------------------
The manuscript is already almost complete now.
The original deadline was for the end of May; however, I was thinking that we could probably finish it and submit it earlier.
What do you think? What about the end of April?
Title
---------
Some people have proposed to remove 'mailing lists' and 'scientific' from the title.
However, I would prefer to keep both words in the final version.
Mailing lists are by far the most popular medium of communication used by researchers. Most old school scientists are familiar with the concept of mailing lists and are subscribed to at least a few lists or newsletter.
Thus, using the term 'mailing list' in the title can help getting the attention of this audience.
The word 'scientific' can be included or not in the title, it is just a matter of what sounds better.
Abstract and introduction
--------------------------------------------------
I am surprised of how much these two sections have improved compared to the original draft. Apart from some minor revisions, these sections can be considered as finished.
We should work a bit more on the supplementary table 1, 'list of popular scientific mailing lists and communities', which is now cited in the introduction.
A minor issue is the fact that the PLoS CompBiol 'Ten Simple Rules' articles do not have abstracts. Therefore, we will have to merge these two sections together, probably by removing or reducing the first paragraph in the 'Introduction section'.
In any case, it is good to have an abstract ready, in case we decide or have to submit it to other journals.
The first three rules
--------------------------------------
Currently, there are three candidates for the first three rules in the document:
- How to start -> hints on how to find online communities, how to register, how to post
- Don't be afraid of asking a question -> rule to convince people that asking a question in a forum is not bad
- Define your problem clearly
It is difficult to choose here. We may include some parts of the 'How to start' rule in the Introduction, and define better the 'Define your problem clearly' question.
"don't rush" rule and abbreviations
--------------------------------------------------
I don't like much Internet abbreviations like 'BTW', 'IMHO', 'RTM', etc.. so I don't like very much to include them in the paper. However, if you feel it is necessary, these should be included.
Rule 3,4,5,6
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These rules seems to be complete.
Rule 8 "Remember that the archive of your discussion can be useful to other people. "
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For those of you who have not been following the wiki lately, this rule has seen much editing in these two weeks. Congratulations to all the contributers. I think that this rule is ready now.
Rule 9 Be polite, avoid cross-posting on different forums and heated arguments.
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This rule has been added after discussion on the wiki and this mailing list. As Kevin noted, it encompass a range of good netiquette rules and is a bit too generic, but I think it is fine.
Rule 10. Give back to the community
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This rule has also been added after discussion on the wiki. I like very much the idea of putting this rule as the last one. Colin Gillespie pointed out that we should look for a better word than "community"; let's see if we can find a better one soon.
Other suggestions
-------------------------------------
There is a list of minor suggestions that are not general enough to be included as separate rules. Some of them are similar to rules already posted.
I am afraid we will have to remove some of these details if we want to stay in the 'ten rules' limits, but the rules written so far are already sufficient for a divulgative article.
--
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
My blog on bioinformatics: http://bioinfoblog.it
J M
I am also fine with the idea of submitting it earlier if everything is ready.
TITLE: I agree in keeping "mailing lists" and "scientific".
Abstract and introduction: if we want to submit it to PloS, we should keep the abstract and change the page, so that we have only the possibility to work on the introduction. Is that ok if we remove the abstract from the draft?
I would also work a bit in improving Table 1 and the references.
Cheers,
Jacopo Marino.
Jacopo Marino
Organic chemistry institute
Universitat Zurich
Switzerland
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J M
I have started editing the introduction so that it is more suitable for the final format of PloS.
Regards,
Jacopo.
Giovanni Marco Dall'Olio
I would prefer if we can include the hints in the rule 'How to start'
in the text of the introduction, so we can leave rule 0 and 1 as they
were before.
- Introduction: the same as before, plus explaining how to find
communities on google and how do they work
- rule 0: Don't be afraid of asking
- rule 1: Clearly define your problem
This is because I think that 'Clearly define your problem' deserves to
be a separate rule; but if we separate it, we will exceed the limit of
10 rules (which in fact are alread 11).
On Tue, Apr 12, 2011 at 12:42 PM, J M <disapp...@gmail.com> wrote:
> Hi,
>
> I have started editing the introduction so that it is more suitable for the
> final format of PloS.
>
> Regards,
>
> Jacopo.
>
>
>
> 2011/4/12 J M <disapp...@gmail.com>
Pierre Poulain
> we could probably finish it and submit it earlier.
> What do you think? What about the end of April?
I agree. End of April seems OK. No need to wait more if we feel ready.
> Some people have proposed to remove 'mailing lists' and 'scientific' from
> the title.
> However, I would prefer to keep both words in the final version.
I got your point. I also suggested to add a flavour of "in silico" in
the title but I am
afraid this will narrow too much the scope of the article. The funny
things with the "ten simple rules"
series is that articles are published in PLoS CB but actually address
a broader scope than just computational biology.
Am I wrong here ?
> - How to start -> hints on how to find online communities, how to register,
> how to post
> - Don't be afraid of asking a question -> rule to convince people that
> asking a question in a forum is not bad
> - Define your problem clearly
>
> It is difficult to choose here. We may include some parts of the 'How to
> start' rule in the Introduction, and define better the 'Define your problem
> clearly' question.
Maybe the "dare" rule should be number 1.
The rule "Define your problem clearly' could be merged with the next
rule "don't rush".
Indeed, "don't rush" could mean two things. 1/ Take time to define
clearly your problem.
2/ Browse around to know how to ask question.
> "don't rush" rule and abbreviations
> --------------------------------------------------
> I don't like much Internet abbreviations like 'BTW', 'IMHO', 'RTM', etc.. so
> I don't like very much to include them in the paper. However, if you feel it
> is necessary, these should be included.
I don't like these abbreviations neither but at least someone new on
mailing lists
will be able to understand them.
Regarding Table 1 in supplementary material, this was pretty easy to
get the total number
of mails providing the archives were in "pipermail" format. (I can
send the Python script to those
who are interested)
For others (mainly forums), we will have to ask site administrators for
the number of message statistics.
Regards
Pierre
--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/
J M
I have put the old rule n.0 (how to start) in the introduction as Dall'Olio was suggesting. It can be improved, just a question of time.
Then, what do you think to change the example in rule n.1? Are you ok with what I propose in the comment or should we think to another example?
Cheers,
Jacopo.
Giovanni Marco Dall'Olio
> Hi,
> I have put the old rule n.0 (how to start) in the introduction as Dall'Olio
> was suggesting. It can be improved, just a question of time.
ok, thank you.
> Then, what do you think to change the example in rule n.1? Are you ok with
> what I propose in the comment or should we think to another example?
Do you refer to this example:
"""
Dear all, I am experiencing some troubles with the purification of my
protein from E.coli. During the washing step with 50mM imidazole I
loose quite a lot of protein. Now, I know that this concentration of
imidazole is quite high, but if I use less I have more contaminants in
my elution. Therefore I ask you if you have an idea of how to solve
this little problem. Thanks everyone.
"""
ok, I think it is a good example; maybe we should pair it with a
bioinformatics-oriented one.
Maybe we can prepare another supplementary table with examples of good
and bad questions.
--
Melanie Stefan
On 11/04/11 08:47, Giovanni Marco Dall'Olio wrote:
Deadlines and submission date
----------------------------------------------------------------
The manuscript is already almost complete now.
The original deadline was for the end of May; however, I was thinking that we could probably finish it and submit it earlier.
What do you think? What about the end of April?
Rule 3,4,5,6
----------------------------------------------------------------------------------------------------------------------------
These rules seems to be complete.
Other suggestions
-------------------------------------
There is a list of minor suggestions that are not general enough to be included as separate rules. Some of them are similar to rules already posted.
I am afraid we will have to remove some of these details if we want to stay in the 'ten rules' limits, but the rules written so far are already sufficient for a divulgative article.
All the best,
Melanie