earlier closing of the editing phase?
Giovanni Marco Dall'Olio
If we do not proceed with the second table, then we should take a decision: the manuscript is already finished, and it is in a state where each further modification may be more harmful than useful. I don't think that it is worth to spend more time trying to improve it, as it is already clear and well written. What do you think, should we close the initiative now?
Please notice that WikiGenes has a feature for the version control of the document; so, if you believe that a certain version of the manuscript is well written and should not be modified, I invite you to bookmark it, and possibly export it so we can compare it with other versions later.
Let's keep the wiki document open for a few days, and then close the editing phase. Do you all agree?
Thanks
--
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
My blog on bioinformatics: http://bioinfoblog.it
Colin Gillespie
> Hello everybody,
>
> If we do not proceed with the second table, then we should take a decision:
> the manuscript is already finished, and it is in a state where each further
> modification may be more harmful than useful. I don't think that it is worth
> to spend more time trying to improve it, as it is already clear and well
> written. What do you think, should we close the initiative now?
>
> Please notice that WikiGenes has a feature for the version control of the
> document; so, if you believe that a certain version of the manuscript is
> well written and should not be modified, I invite you to bookmark it, and
> possibly export it so we can compare it with other versions later.
>
> Let's keep the wiki document open for a few days, and then close the editing
> phase. Do you all agree?
Colin
>
> Thanks
>
>
> --
> Giovanni Dall'Olio, phd student
> Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
>
> My blog on bioinformatics: http://bioinfoblog.it
>
> --
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe from this group, send email to
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>
--
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/
J M
Rule n.1 needs modifications since is quite hard to understand some phrases...
J
Pierre Poulain
>> phase. Do you all agree?
> Good idea.
Fine by me too. Maybe we should use these last days to enhance / correct
the English (that is already very good) and clean the manuscript from comments.
If you have mailing list / forum in mind do not forgot to fill the
Table 1 in supplementary material.
http://www.wikigenes.org/e/art/e/139.html
No need to be exhaustive, major examples will be enough. I am currently working
on the total number of messages in BioStar and Stackoverflow.
Pierre
--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/
J M
--
Melanie Stefan
I'm all for getting it done as soon as possible. There are a couple of
things that would need to be done before that, though.
- I still want to bring up rule number 6 (about posting code), which I
think should not be a rule by itself, because it relates to coding
questions only (and many questions even on bioinformatics fora aren't).
I would be in favour of copying the text into whatever rule it was (1?)
that deals with stating the question, and then re-numbering the
remaining rules from 1 to 10.
- The manuscript needs a thorough reading with respect to language. Who
are the native English speakers in this group? That's your job!
Other than that, I'm happy with it. Good job everyone!
Melanie
Khader Shameer
I think we should add Stats http://stats.stackexchange.com/ and MetaOptimize http://metaoptimize.com/qa/ and Blue Oblesik http://blueobelisk.shapado.com/ and sites which will be useful for bioinformatics community interested in statistics, machine learning and chemoinformatics. Giovanni - please insert few additional rows in the table. CSG: I think that stats, MO and BO should be added with suitable descriptions to the table.
Please see if you can add them,
Thanks,
KS
Giovanni Marco Dall'Olio
Giovanni:
I think we should add Stats http://stats.stackexchange.com/ and MetaOptimize http://metaoptimize.com/qa/ and Blue Oblesik http://blueobelisk.shapado.com/ and sites which will be useful for bioinformatics community interested in statistics, machine learning and chemoinformatics. Giovanni - please insert few additional rows in the table. CSG: I think that stats, MO and BO should be added with suitable descriptions to the table.
Hello,
I am a bit in a hurry now, but I can add them tomorrow.
Melanie: I would like to look better at rule 6, in principle what you propose seems fair.
Kevin and Brandon, two native English-speaker, will double check the manuscript before submission :-)
J M
just few considerations about the manuscript:
- I also agree about removing table 2. We are trying to submit this paper on PloS, so I assume that people reading this journal already know how to write an understandable, polite question. Therefore I would not spend too much time on that. I think there are more interesting parts that can be modified or improved.
- For this reason I have shortened a bit rule n.1. The concept was repeated too much in my point of view. What do you think?
Thanks,
Jacopo.
J M
I think that this paper should be as general as possible, although it was born with a bioinformatic imprinting.
Shall we change rule n.6 as Melanie was suggesting?
J.
Michael Schubert
- The overall quality of the text is good, but there are phrases that
should be improved.
- Also, I think we should keep it general and match the actual number
of points with the one in the titel, thus merging point 6 into
another.
And who has removed the sentence that defining a problem sometimes
leads to a solution on its own? In my mind, that should be included or
at least a comment be left on why someone thinks it's inappropriate.
On 16 Apr., 13:22, J M <disappunto...@gmail.com> wrote:
> Hi,
>
> I think that this paper should be as general as possible, although it was
> born with a bioinformatic imprinting.
>
> Shall we change rule n.6 as Melanie was suggesting?
>
> J.
>
>
>
>
>
>
>
> > Hi all,
>
> > just few considerations about the manuscript:
>
> > - I also agree about removing table 2. We are trying to submit this paper
> > on PloS, so I assume that people reading this journal already know how to
> > write an understandable, polite question. Therefore I would not spend too
> > much time on that. I think there are more interesting parts that can be
> > modified or improved.
>
> > - For this reason I have shortened a bit rule n.1. The concept was repeated
> > too much in my point of view. What do you think?
>
> > Thanks,
>
> > Jacopo.
>
> >> On Fri, Apr 15, 2011 at 9:02 PM, Khader Shameer <skha...@gmail.com>wrote:
>
> >>> Giovanni:
>
> >>> I think we should add Statshttp://stats.stackexchange.com/and
> >>>http://blueobelisk.shapado.com/and sites which will be useful for
> >>> chemoinformatics. Giovanni - please insert few additional rows in the
> >>> table. CSG: I think that stats, MO and BO should be added with suitable
> >>> descriptions to the table.
>
> >> Hello,
> >> I am a bit in a hurry now, but I can add them tomorrow.
> >> Melanie: I would like to look better at rule 6, in principle what you
> >> propose seems fair.
> >> Kevin and Brandon, two native English-speaker, will double check the
> >> manuscript before submission :-)
>
> >>> Please see if you can add them,
> >>> Thanks,
> >>> KS
>
> >>>>> .
> >>>> --
> >>>> You received this message because you are subscribed to the Google
> >>>> Groups "ten rules for contributing to mailing lists and forums" group.
> >>>> To post to this group, send email to
> >>>> ten-rules-for-contrib...@googlegroups.com.
> >>>> To unsubscribe from this group, send email to
> >>>> ten-rules-for-contributing-...@googlegroups.com
> >>>> .
> >>>> For more options, visit this group at
> >>>> .
> >>> --
> >>> You received this message because you are subscribed to the Google Groups
> >>> "ten rules for contributing to mailing lists and forums" group.
> >>> To post to this group, send email to
> >>> ten-rules-for-contrib...@googlegroups.com.
> >>> To unsubscribe from this group, send email to
> >>> ten-rules-for-contributing-...@googlegroups.com
> >>> .
> >>> For more options, visit this group at
> >>> .
> >> --
> >> Giovanni Dall'Olio, phd student
> >> Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
>
> >> My blog on bioinformatics:http://bioinfoblog.it
>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "ten rules for contributing to mailing lists and forums" group.
> >> To post to this group, send email to
> >> ten-rules-for-contrib...@googlegroups.com.
> >> To unsubscribe from this group, send email to
> >> ten-rules-for-contributing-...@googlegroups.com.
> >> For more options, visit this group at
> >> .
J M
"who has removed the sentence that defining a problem sometimes
leads to a solution on its own? In my mind, that should be included or
at least a comment be left on why someone thinks it's inappropriate"
J.
For more options, visit this group at http://groups.google.com/group/ten-rules-for-contributing-to-ml-and-forums?hl=en.
J M
when is the new deadline for closing the paper?
J
Pierre Poulain
The proposition of Melanie is fair. We could for instance merge and
lighten rule 6 into rule 5 since it is also your job to provide
sufficient code/input/output details to be understood.
As a consequence, removing rule 6 will also reduce the total number of
rules to exactly 10 that is perfectly in line with the "10 simple
rules" series.
I was also wondering if we could / should invert rules 8 and 9. Actual
rule 9 "Be polite, avoid cross-posting on different forums and heated
arguments" and still belongs to the process of asking a question while
actual rule 8 "Remember that the archive of your discussion can be
useful to other people" seems to me closer to rule 10 and its
community feedback.
What do you think of this rule swapping?
P.
Melanie Stefan
I agree with Pierre, swapping rules 8 and 9 seems like an excellent idea.
Melanie
Pierre Poulain
> I agree with Pierre, swapping rules 8 and 9 seems like an excellent idea.
Giovanni and I did it in the exact same time (and the Wikigene engine
solved the editing conflict very well).
I guess we now have our 10 rules in a rational order.
Cheers
Melanie Stefan
J M
I am not really convinced about the real need of the examples in rule n.2. What about deleting them?
J.
--
Pierre Poulain
> I am not really convinced about the real need of the examples in rule n.2.
> What about deleting them?
I like these two since the first one is an beautiful example of
self-answering question
where as the second is an example of a clear and well posed question.
However, we have to keep in mind that the "Ten Simple Rules" series
http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v03.i01
is made of short articles.
I agree with JM that to lighten a bit more our "Ten Simple Rules"
manuscript, we could indeed remove those two examples.
By the way, shouldn't the title become
"Ten simple rules for getting help from mailing lists and online communities"
(with the simple inside)?
Cheers
Pierre
J M
We should always consider the target of the journal, that's why I think that the examples are nice, but nor really usefull.
The title should be:
"Ten simple rules for getting help from mailing lists and on-line scientific communities"
Regards,
Jacopo.
Jacopo Marino
Organic Chemistry Institute
Universitat Zurich
Winterturerstrasse 190
8057 Zurich
CH
+41 44 63 53940
--
J M
I think that rule n.2 should be fixed a bit. We have already discussed about removing the examples, what do you think about that?
Jacopo.
Pierre Poulain
> I think that rule n.2 should be fixed a bit. We have already discussed about
> removing the examples, what do you think about that?
I have just did it. It was 11.45 am in France but maybe changes have
not been updated yes.
I also think we should avoid negative terms into rules names.
For instance, could we rename?
rule 1. Do not be afraid of asking a question
into
rule 1. Dare asking your question
("Dare" is quite strong here but it is intended)
rule 6. Do not expect other people to do your homework
into
rule 6. Do your homework
(and then we explain what we mean by "homework" in the rule itself)
I did not find how to remove the do ... not in rule 4 but the negation
here has its meaning.
J M
I think rule n.2 is better now. I think Giovanni Marco was happy with the idea of having examples, but as I said, I don't know how useful they are.
About removing negative terms in the titles: do you really think it's so bad? Probably without negative terms everything could have a more positive mood, I don't know.
Have a nice Easter time,
Jacopo.
Giovanni Marco Dall'Olio
(sorry, I was traveling)
ok, rule 2 looks better now. I suppose it is better to be concise in a academic paper.
About the negations:
rule 1 -> I prefer the current title
rule 4 -> what about 'Avoid asking what has already been asked before' ?
rule 6 -> If we want to remove the negation, we have to use a longer title.Maybe something on the line of 'Do your homework before posting'.
In any case, I think that the paper is fine... we should be careful not to change too much if not necessary.
Pierre Poulain
> ok, rule 2 looks better now. I suppose it is better to be concise in a
> academic paper.
Indeed.
> rule 1 -> I prefer the current title
OK. My point was that "positive" sentence are usually better perceived
than "negative" ones.
But this is actually true in French and my English is somewhat approximative ;-)
> rule 4 -> what about 'Avoid asking what has already been asked before' ?
Funny. I'll keep the negative form here since "avoid" and "do not" are really
different.
> rule 6 -> If we want to remove the negation, we have to use a longer
> title.Maybe something on the line of 'Do your homework before posting'.
OK. Done.
> In any case, I think that the paper is fine... we should be careful not to
> change too much if not necessary.
I agree.
One last thing. Regarding the supplementary data, table 1 is almost completed.
I am a bit puzzled with the PyMOL wiki that is indeed an online community
but is really different from previous examples. So, should we keep it ?
Cheers
P.
J M
I agree with Giovanni Marco in the changes of the titles he proposes.
Have a nice Easter time!
Jacopo.
J M
What do you think?
J.
Pierre Poulain
> About the Pymol Wiki, we can also remove it, I don't mind. I think it is
> important because many people now need to use Pymol and probably they don't
> know that there is a wiki.
PyMOL and its wiki are definitely great!
Let's remove it for the purpose of the article.
> Concerning table 1, I have tried to write an
> email to the administrators of "molecular station" in order to know when the
> forum was founded, but I have received back all the emails from the email
> address they give. At this point I don't know.
Me too. No answer from "molecular station". I also tried to contact admin
from BlueObelisk and MetaOptimize. Waiting for answers...
Cheers
P.
Giovanni Marco Dall'Olio
Hi,
PyMOL and its wiki are definitely great!
> About the Pymol Wiki, we can also remove it, I don't mind. I think it is
> important because many people now need to use Pymol and probably they don't
> know that there is a wiki.
Let's remove it for the purpose of the article.
ok, as you prefer.
Me too. No answer from "molecular station". I also tried to contact admin
> Concerning table 1, I have tried to write an
> email to the administrators of "molecular station" in order to know when the
> forum was founded, but I have received back all the emails from the email
> address they give. At this point I don't know.
from BlueObelisk and MetaOptimize. Waiting for answers...
Thank you for all the hard work you are doing! :-)
Cheers
P.
--
Dr. Pierre Poulain
DSIMB team
Inserm U665 and Univ. Paris Diderot-Paris 7, France
http://www.dsimb.inserm.fr/~poulain/
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