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--- instructions_for_authors [2010/03/22 17:39]
Christophe Dessimoz
+++ instructions_for_authors [2013/01/10 18:05] (current)
Christophe Dessimoz
@@ Line 2: / Line 2: @@
 This page provides instructions for authors.
+===== Overview =====
+In this course, the writing process is structured into three successive stages and associated deadlines:
+  - Write an "extended" outline. The outline is due on the Monday following the presentation. We will discuss it during the consultation hours. Usually, the extended outline has 4-levels: title, sections, subsections, paragraphs.
+  - Write your manuscript. It is due 2 weeks after the presentation, and should be submitted electronically using the web interface.
+  - Revise your manuscript based on the feedback from the peer-reviews. Your revision is due 1 week after you obtain the peer-reviews.
 ===== Editorial Policy =====
-In the context of this course, a review is a synthesis of a current computational biology research topic. The target readership is students in the computational biology master program. The typical length of a review is between 1,200 and 1,800 words.
+In the context of this course, a review is a synthesis of a current computational biology research area. The target readership is composed of research and masters students in the computational biology. The typical length of a review is between 1800-2000 words.
+===== Authorship =====
+In this course, the policy for authorship follows the guidelines of the [[http://www.admin.cam.ac.uk/offices/research/documents/research/good_research_practice.pdf|CAM Good research practice]].
+If the manuscript builds upon the seminar presentation---as is generally the case---the (guest) lecturer who presented the topic is included in the list of authors.
-===== LaTeX Templates and utilities =====
-  * {{:revcompbiol_latex_template.zip|LaTeX templates for the course}} (V1.0)
-  * [[http://www.latex-project.org/|LaTeX]] (Try installing it through your usual package manager first)
-  * [[http://hutchinson.belmont.ma.us/tth/|TTH]], tool to convert .tex to .html (for final version)
 ===== Initial Submission =====
+==== Format ====
+The guiding principle for the formatting of your initial submission is that it should ease peer-review:
+  * At a minimum, the heading (or title page) should include the title, name of authors, date, and abstract.
+  * The text should be double-space, single column text.
+  * Citations should be in [[http://en.wikipedia.org/wiki/Parenthetical_referencing|author-date]] format (e.g. APA-style).
+  * Figures (or tables) should be provided alongside the text with appropriate captions (titles).
+  * Pages should be numbered.
+As word processor, most students like to use Word, OpenOffice, or LaTeX. Perhaps of interest for some is the WYSIWYG editor for Latex/Tex [[http://www.lyx.org|Lyx]].
+==== Submission Process ====
 Submit your review in PDF format directly on the [[http://revcompbiol.ethz.ch/journal/revcompbiol|article management system]].
-If you have not already, you will need to start by  [[http://revcompbiol.ethz.ch/journal/revcompbiol/user/register|creating an account]]. Note that you have to explicitly select author and reviewer roles upon registration:
+If you have not already, you will need to start by  [[http://revcompbiol.ethz.ch/journal/revcompbiol/user/register|creating an account]]. Note that you have to explicitly select author __and__ reviewer roles upon registration:
 {{:screenshot.png?400|}}
-If you missed these options upon registration, you can activate the author/reviewer roles later by changing your [[http://revcompbiol.ethz.ch/journal/revcompbiol/user/profile|profile settings]] (Home > User > Edit Profile).
+If you missed these options upon registration, you can still activate the author or reviewer roles by changing your [[http://revcompbiol.ethz.ch/journal/revcompbiol/user/profile|profile settings]] (Home > User > Edit Profile).
 **Check-list**
-  * Spelling: use automated spell-checker (e.g. ispell) and proofread your text carefully.
+  * Spelling: use an automated spell-checker (e.g. ispell) and use British English and proofread your text carefully.
   * Verify one more time
-    * that references are accurate and complete
+    * that the references are accurate and complete
-    * that each claim backed by citation
+    * that each claim is backed by citation(s)
-    * that your narrative is coherent
+    * that your narrative is coherent (with a beginning, middle and conclusion)
-    * that the article meets editorial policy
+    * that the article meets our editorial policy
-  * Ask a colleague for feedback on draft (thank for his/her help in Acknowledgement section)
+  * Ask a colleague for feedback on the draft (thank them for their help in the Acknowledgements section)
 ===== Revision =====
 Submit your revision directly on the [[http://revcompbiol.ethz.ch/journal/revcompbiol|article management system]]. Include the following files:
-  * PDF (typeset by LaTeX with {{:revcompbiol_latex_template.zip|course template}})
+  * PDF (if you use LaTeX, you can use the {{:revcompbiol_latex_template.zip|course template}})
-  * Images sources (most likely PDF or EPS)
+  * Original document, i.e. Word or LaTeX file with all sources (e.g. bibliography, .tex, .bib, images, and any other file required to produce your manuscript)
-  * Images converted to JPG or PNG
+  * Cover letter that explains how you addressed the concerns of the referees (and of the editor, if any).
-  * LaTeX sources (.tex and .bib files)
-  * HTML version, which can be generated using [[http://hutchinson.belmont.ma.us/tth/|TTH]]. You may have to fix the image paths by hand, and a cover letter answering all critiques raised by referees.
+===== LaTeX Templates and utilities =====
+  * {{:revcompbiol_latex_template.zip|LaTeX templates for the course}} (V1.0)
+  * [[http://www.latex-project.org/|LaTeX]] (Try installing it through your usual package manager first)