JChemInf paper

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Pablo Echenique

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May 7, 2011, 1:11:18 PM5/7/11
to Quixote mail list
Dear friends,

I attach you here the present version of the paper that we are preparing for the Journal of Cheminformatics. Also, you have the sources at https://bitbucket.org/echeniquep/2011_quixotenewsletter1st_jci

As you can see, the abstract, the introduction and the conclusions are in pretty good shape, and we mostly need to write the methods section and the results one. We have envisioned the methods section as starting by a description of the Quixote way of working, followed by a brief summary of the whole Quixote architecture (some old-ish versions of possible diagrams attached), and then a description of each of the components. The results section consists of use cases.

We need to organize to write these sections (which shouldn't take too long). This is the important point.

My proposal is that we give a one-week time for people to volunteer to write each of the parts. I could tackle them all, but the result would be suboptimal, since I am not an expert in all the points. So, anyone can:

1. Write any of the sections that remain to be written, and/or produce figures, tables, etc.
2. Modify/add things to the already written parts.
3. Suggest changes to the overall structure of the paper.
4. Produce use cases.

You can do this directly by pulling and pushing to the bitbucket repo (I can give you permissions to push), or you can send me the text by email and I add it to the manuscript.

As you can see, I have written in bold face some points in the manuscript where you can complete things, but obviously everything is modifiable.

Finally, if you want to participate, don't forget to add or tell me your affiliation and grants data.

By the way, how are we about deadlines with JChemInf?

Best,
  Pablo. 

annotatedOverview.png
overview1.png
PublishingSystem.png
quixote.svg
workflow.png
2011_QuixoteNewsletter1st_JCI.pdf

Peter Murray-Rust

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May 31, 2011, 8:24:50 AM5/31/11
to quixot...@googlegroups.com, Charlotte Bolton
I have now added a substantiv chunk to the Methods section and committed to Hg.


On Sat, May 7, 2011 at 6:11 PM, Pablo Echenique <echen...@gmail.com> wrote:
Dear friends,

I attach you here the present version of the paper that we are preparing for the Journal of Cheminformatics. Also, you have the sources at https://bitbucket.org/echeniquep/2011_quixotenewsletter1st_jci

I have renamed this quixotepaper.tex
 
As you can see, the abstract, the introduction and the conclusions are in pretty good shape, and we mostly need to write the methods section and the results one. We have envisioned the methods section as starting by a description of the Quixote way of working, followed by a brief summary of the whole Quixote architecture (some old-ish versions of possible diagrams attached), and then a description of each of the components. The results section consists of use cases.

We need to organize to write these sections (which shouldn't take too long). This is the important point.

My proposal is that we give a one-week time for people to volunteer to write each of the parts. I could tackle them all, but the result would be suboptimal, since I am not an expert in all the points. So, anyone can:

We need collaborators to edit this urgently. I have written most of what I intend but the style needs tightening

so PLEASE CONTRIBUTE.

1. Write any of the sections that remain to be written, and/or produce figures, tables, etc.
2. Modify/add things to the already written parts.
3. Suggest changes to the overall structure of the paper.
4. Produce use cases.

WE NEED FIGURES NOW
 
You can do this directly by pulling and pushing to the bitbucket repo (I can give you permissions to push), or you can send me the text by email and I add it to the manuscript.

As you can see, I have written in bold face some points in the manuscript where you can complete things, but obviously everything is modifiable.

Finally, if you want to participate, don't forget to add or tell me your affiliation and grants data.

By the way, how are we about deadlines with JChemInf?

WE ARE GETTING VERY CLOSE - MUST SUBMIT BY END OF WEEK
 
Best,
  Pablo. 




--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

Pablo Echenique

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Jun 1, 2011, 6:15:21 AM6/1/11
to quixot...@googlegroups.com, Charlotte Bolton
Peter, and Charlotte, and everybody,

I have read what you added and I think the paper is in pretty good shape!

We can do this:

 * I will give it a thorough read now and correct any typos I see, add things which may be missing, etc. I will finish this before this afternoon's meeting.
 * In the same timeframe, I will try to add a use case about my peptide calculations.
 * Although the timing is a bit tight, maybe two more things can be added:
   - Maybe Marcus can write a small paragraph about the integration with Avogadro
   - Maybe Pablo De Castro can describe the basic ideas behind a possible use of a D-Space-based solution for storing the most 'human' metadata associated to the files
 * Jorge can provide some diagrams about the overall Quixote infrastructure and the accompanying text
 * After all that, no later than Thursday night, maybe we could handle the paper to Charlotte, whose English must indeed be better than mine, and maybe she could improve the flow of the discourse and check any inappropriate use of the language.

What do you think?

Contributors can send the text and figures to me before tomorrow night and I can integrate everything. Also don't forget to provide affiliation, aknowledgement and grants data.

About the order of the authors? I would say alphabetic, but my opinion on this is extremely weak, almost non-existent. As for the corresponding author, I would say Peter is the appropriate choice, if he wants to.

Best,
  Pablo. 

Peter Murray-Rust

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Jun 1, 2011, 6:28:07 AM6/1/11
to quixot...@googlegroups.com, Charlotte Bolton
On Wed, Jun 1, 2011 at 11:15 AM, Pablo Echenique <echen...@gmail.com> wrote:
Peter, and Charlotte, and everybody,

I have read what you added and I think the paper is in pretty good shape!

Good
We can do this:

 * I will give it a thorough read now and correct any typos I see, add things which may be missing, etc. I will finish this before this afternoon's meeting.
 * In the same timeframe, I will try to add a use case about my peptide calculations.

This would be very nice
 
 * Although the timing is a bit tight, maybe two more things can be added:
   - Maybe Marcus can write a small paragraph about the integration with Avogadro

PLEASE! The XML is an exciting feature
 
   - Maybe Pablo De Castro can describe the basic ideas behind a possible use of a D-Space-based solution for storing the most 'human' metadata associated to the files

Sure.
 
 * Jorge can provide some diagrams about the overall Quixote infrastructure and the accompanying text

Yes
 * After all that, no later than Thursday night, maybe we could handle the paper to Charlotte, whose English must indeed be better than mine, and maybe she could improve the flow of the discourse and check any inappropriate use of the language.


I think Charlotte and I can hack this!
 


What do you think?

Contributors can send the text and figures to me before tomorrow night and I can integrate everything. Also don't forget to provide affiliation, aknowledgement and grants data.

About the order of the authors? I would say alphabetic, but my opinion on this is extremely weak, almost non-existent. As for the corresponding author, I would say Peter is the appropriate choice, if he wants to.

You are welcome to do it if you wish.

BTW Same and I have a rough spine for a compchem dictionary and he will posit it before the meeting or we will put it in the Etherpad

P.

 

Pablo Echenique

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Jun 2, 2011, 11:54:45 AM6/2/11
to Charlotte Bolton, quixot...@googlegroups.com
On Thu, Jun 2, 2011 at 3:13 PM, Charlotte Bolton <charlott...@gmail.com> wrote:
>>  * Jorge can provide some diagrams about the overall Quixote
>> infrastructure and the accompanying text
>
> Yes

A number of figures were attached to the original email of 2011-05-07
(annotatedOverview.png, overview1.png,PublishingSystem.png,
workflow.png and quixote.svg; I can re-send these if necessary) but
without any indication of their position in the text, or accompanying
figure captions. Please can you clarify?

Charlotte, tonight before midnight or tomorrow early in the morning I'll commit the version with all the included material.
 
Otherwise the paper looks great. I am just tidying up small typos and
adding citations/footnotes.

Are you using the latest version in bitbucket, right?

Best,
  Pablo.

 
Cheers,
Charlotte.

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