Rules


 * Rules**


 * Disclaimer:**
 * These rules ARE NOT completely perfect and DO NOT cover all possible cases, which one could imagine**
 * If you feel, that your particular case is not covered by the rules, than TURN ON YOUR BRAIN and CREATE THE NEW RULE**

Here are the rules we agreed to follow. We must put all the documents generated in MPI into the folders.

As we decided we now store shared information on the root folder of our shared disk.

I.
First, all the presentations must be stored in the folder: Presentations
 * Presentations**

NOTE: with the presentations we denote: presentations or posters on conferences, invited talks, faculty lectures etc ...

For a single presentation one creates a folder: Surname_Meeting_Place_MonthYear (example: Frolov_ACS_Anaheim_Mar2011, below i describe everything based on the example)

The folder should contain: Frolov_ACS_Anaheim_Mar2011.ppt,
 * //1) Presentation files PPT and PDF (with the same name)://**

Frolov_ACS_Anaheim_Mar2011.pdf all authors, and text of the submitted abstract. " Presenter: Andrey Frolov Title: Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions Meeting: 241st American Chemical Society National Meeting & Exposition (ACS) Country: USA Place: Anaheim Date: 27 March 2011 Keywords: Nanotube PL aqueous ions Type: poster Comments: " where type can be: presentation or poster. where one field MUST contain NO newline signs: (eg: "Title: Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions" is correct, "Title: Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions" is NOT correct.)
 * //2) If applicable: Abstract.doc or Abstract.txt: file containing Title,//**
 * //3) README file with the following content://**

One line MUST contain only one field: (eg: "Country: USA Place: Anaheim" is correct, "Country: USA Place: Anaheim" is NOT correct.)


 * //4) Optional: subfolder "misc" which contains any useful data: figures etc.//**

II.

 * Working with the papers:**

Upon performing the first submission of a manuscript the following folder must be created in the Manuscripts folder: (example: Palmer_Dec2010_3DRISMDRUGS, below i describe everything based on the example)
 * Surname_MonthYear_Keyword**

For the first submission the folder must contain the following subfolder: Submission_1_JournalAbbr (example: Submission_1_JACS )

where the index after the the "Submission_" indicates the index of submission (the count of the number a "submit" button is pressed for the manuscript)

If the the paper is rejected and we submit to another journal then a new subfolder is created upon submitting to another journal: (eg: Submission_2_MolPharm)

If the paper is gets comments of reviewers then, upon submitting a reply to reviewers the new submission folder is created: (eg: Submission_3_MolPharm)

If a submission is accepted for publication then the folder is renamed: (eg: from "Submission_3_MolPharm" to "Submission_3_MolPharm_a" ) where "_a" denotes accepted.

Any changes after acceptance are performed on the files of the last submission without renaming them.

Any submission folder must contain the following subfolders: contains everything to compile PDF file of the paper: = article.tex (or article.doc) = bash script "compile.sh", which compiles "article.pdf" by typing "./compile.sh article.tex", eg: code #!/bin/bash texname=$1 name=`echo $texname | sed "s/.tex//g"` latex $name bibtex $name latex $name latex $name dvipdf "$name".dvi "$name".pdf code
 * 1) article:**

contains "cover_letter.doc"
 * 2) cover_letter:**

contains everything to compile PDF file of the SI similar to subfolder "article" (or SI.doc file)
 * 3) SI:**

file reviewers.dat file
 * 4) publishing_agreement:**
 * 5) reviewers:**
 * 6) reply_reviewers (if applicable):**

file. Usually a pdf file of all the submitted documents which is generated by the publisher webpage upon submission.
 * 7) proofs:**

this subfolder must contain the initial data and script which creates a certain figure in the article and the SI. the initial data for a figure must be stored in the corresponding subfolder: fig_1: fig_2: ... fig_N: fig_1_SI: ... fig_M_SI:
 * 8) gfx:**

each of the subfolders must contain a bash script "compile_fig.sh" to make the figure typing "./compile_fig.sh" for any simple figure. (plus any supplementary files: *.dat, *.txt, *.xvg, ...) Notation: simple figure - can be created by a single script (eg: g(r)), supplementary figure - a figure (picture) which cannot be created by a single script (eg photo of samples), complex figure - others (combination of simple/supplementary figures).

Allowed languages and editors to create simple figures: matlab, R, xmgrace, matplotlib, gnuplot.

For each complex figure (eg: plot of g(r) on top of a simulation snapshot). One has to create a complex figure in a PPT format: - the first slide must contain the complex figure itself - next slides entitled "subfigN" must contain the subfigure N (N - is an index) used to create the complex figure. = If the subfigure is a simple figure (like g(r)) then the folder must contain the script "compile_subfigN.sh", and the figure itself "subfigN.png". If a subfigure is changed by an external editor (NOT in PowerPoint) then there should be two slides "subfigN initial", "subfigN modified". = If the subfigure is a supplementary figure then the folder must contain "subfigN.png". Note: simulation snapshots are considered as supplementary figures. But it is highly appreciated if there is a script, which generates the snapshot figure: like "vmd -e script". Note: any manipulations with the figures in PowerPoint (cut the edges, hide a peace of figure by a white box ...) need not to be explained.


 * 9) misc (optional)**


 * Articles**

When the manuscript becomes an article (it has page numbers) a folder is created in the "Articles" with the name: Surname_JournalAbbr_MonthYear_Keyword (example: Palmer_MolPharm_May2011_3DRISMDRUGS) This should contain everything as the accepted submission ( eg "Submission_3_MolPharm_a") plus an additional subfolder: - data: where any relevant data for the paper is present (trajectories (size of trajectory file should not exceed 10 mb => just a few random frames), input files etc ...) additional bib file: "eg: Palmer_MolPharm_May2011_3DRISMDRUGS.bib"

If a manuscript is written by an external group, we must contact them to have all the necessary data.

III.

 * Proposals**

Submitted proposals must be stored in the following folder: "Proposals"

For a proposal one creates the subfolder (Mind !!! the permissions to read must have only authors of the proposal. In some grant agencies there are very strict rules about confidentiality.): Type_Keyword_MonthYear (eg: MarieCurie_BioSol_Mar2009)

The subfolder should contain the following folders: proposal: proposal.tex (proposal.doc), script "compile.sh" (similar to manuscripts) supplementary_docs: any documents, forms related to the proposal gfx (if applicable): similar to manuscripts

IV.

 * Theses**

Submitted theses must be stored in the following folder: "Theses"

For a proposal one creates the subfolder: Surname_MonthYear (eg: Ratkova_May2011) Mind !!! the permissions to read must have only the author of the proposal and the supervisor.)

The subfolder should contain the following folders: theses: theses.tex (proposal.doc), script "compile.sh" (similar to manuscripts) supplementary_docs: any documents, forms related to the proposal gfx: similar to manuscripts.