Fwd: Genome Research -- Manuscript Decision

[Benedict Paten]

Good news - looks like we have provisional (it's very wordy) acceptance of the Alignathon manuscript. Still a few small formatting changes to make, but otherwise we're (probably) in!  Good work everyone, especially Dent!

---------- Forwarded message ----------
From: Laura DeMare <lde...@cshl.edu>
Date: Tue, Sep 23, 2014 at 1:14 PM
Subject: Genome Research -- Manuscript Decision
To: Benedict Paten <bene...@soe.ucsc.edu>


RE:  GENOME/2014/174920

Dear Dr. Paten,

Your revised manuscript entitled, "Alignathon: A competitive assessment of whole
genome alignment methods," has been reviewed.  Please visit http://submit.genome.org
to view the referees' comments.

As you will see, the referee found the work improved, but they did suggest an
addition to the text and there are some Editorial points that still need to be
addressed before the work would be suitable for publication.

The Abstract is not in journal format. Please rewrite, removing "Background:"
"Results:" and "Conclusions:"

Please reduce the number of figures, by removing redundancy, focusing on the main
novel points of interest to our readers and moving supporting material to the
supplement.

Please correct the following in text, tables, and figures:
Vista Browser -> VISTA Browser
UCSC genome browser -> UCSC Genome Browser
Multiz -> MULTIZ
AutoMz - >AutoMZ
de-novo -> de novo
mod ENCODE -> modENCODE
ENCODE pilot project -> ENCODE Pilot Project

Please relocate the following at the beginning of Methods to a new section entitled
"Data access" at the end of Methods and just above the Acknowledgments: "The project
website is available at http://compbio.soe.ucsc.edu/alignathon/. The website links to
all of the datasets, submissions and benchmarking code."

Please modify (ENCODE Project Consortium 2012) to (The ENCODE Project Consortium
2012) in text and remove additional authors following "Consortium" from the
reference. Please include a citation for modENCODE.

Once again, please reformat references in journal style, including titles and "et
al." after 10 authors (see Instructions to Authors.)

Please fix text wrapping in Tables.

Given that you can make these changes to the manuscript, we will be happy to accept
your manuscript in principle for publication in Genome Research.  Please read the
referee's comments and address the point.


Additionally check below to go through each point as these are required for prompt
publication of the manuscript:


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1) Please also go through your work once more to make sure it is written in as
streamlined a fashion as possible.  This is the best way to be sure the main points
of the work are highlighted and the general interest for the work is at its peak.
Any redundancies in the text should be removed, and only points of main interest
should be included in results and discussion.  Material not essential to the direct
understanding of the manuscript should be considered carefully for online-only
supplemental material; all lengthy tables should be reduced to a single page where
possible, and the complete table be made available as an online supplement. If
English is your second language, a native English speaker should proofread the work
prior to resubmission.

2) Check our Author Instructions at http://submit.genome.org to make sure you are
following all data availability and fair-use rules AND to format your manuscript in
our house style.  Putting your manuscript in the appropriate format will serve to
expedite your manuscript for publication as well as save substantially on possible
production fees incurred during the processing of your manuscript by the printer, who
charges for any changes made during galley stages. Pay special attention to the
appropriate ORDER of the sections (or obtain permission from the editor to alter the
format), and also be absolutely sure figures and tables are SEPARATE from the text
and figure legends are SEPARATE from figures.

PLEASE be reminded that you MUST use current and approved nomenclature for gene and
protein names and symbols (including appropriate use of italics [using italics is a
standard for genes, so put ALL gene symbols and loci, in italics] and capitalization
as it applies for each organism's standard nomenclature format, in text, tables, and
figures. For web site links for data submission, nomenclature rules, or for
submission of gene or protein names, see Web Site Links for Data Submission and
Appropriate Nomenclature at http://www.genome.org/misc/ifora_weblinks.shtml. Failure
to use appropriate nomenclature for manuscripts that have been accepted can result in
change fees and significant delays at the time of manuscript processing.

All data utilized in this manuscript must be made available by posting it in the
accepted public databases.  In the absence of an appropriate database, the data must
be submitted as supplementary material to be posted at the Genome Research website
(you may also, of course, post it at your own website).


3) From your Author Area at submit.genome.org please download, fill out, sign, and
return the 2 PRODUCTION FORMS: COLOR APPROVAL FORM and the LICENSE TO PUBLISH. We now
absolutely require EACH author to agree to the online AUTHOR DECLARATION and for any
conflicts or competing interests to be disclosed in the online DISCLOSURE DECLARATION
so please ensure EACH and every author is contacted regarding these items prior to
submission of a revised manuscript. Please e-mail (preferred) or fax PRODUCTION FORMS
to: Peggy Calicchia, Genome Research, Administrative Assistant, Tel: 516-422-4012;
Fax: 516-422-4092; e-mail: cali...@cshlbp.org). Any delay in sending these forms
will cause a delay in the production of your manuscript for publication.

More information on our OPEN ACCESS and the ACCEPTED PREPRINT options can be found
online at www.genome.org.

4) All data or information obtained through personal communication also requires a
letter of approval for use.   Authors are responsible for obtaining permission from
the rights holder to adapt or reproduce material previously published elsewhere
(typically, this will be the publisher) and for including any required permission
statement alongside the citation.  Please e-mail (preferred) or fax PERMISSIONS to:
Peggy Calicchia, Genome Research, Editorial Secretary, Tel: 516-422-4012; Fax:
516-422-4092; e-mail: cali...@cshlbp.org). Any delay in sending this will cause a
delay in the production of your manuscript for publication.

5) Please note we accept electronic art files created in TIFF, EPS, PDF, JPEG, or AI
when the digital file specifications are adhered to (see parameters online in
Submission of Electronic Figures for Accepted Manuscripts: Detailed Instructions
available in Author Info at www.genome.org).  Please provide appropriately formatted
art files in the system and indicate that correct art files are available online on
the manuscript checklist.

To aid you in submitting your digital files in the correct format, we have a digital
art analysis program associated with our online submission system called Digital Expert:

There are no image files for Digital Expert to analyze.

If "Fail" is returned in the report the art file is unusable must be revised to
satisfy the art specifications above and detailed in Instructions to Authors.


----------

When you submit your revised manuscript to our online system, please use the "submit
a revised manuscript" button. Note, at this stage, the text and tables must be
submitted online as WORD files (.doc) so that we have source files from which the
production team can process your manuscript (the system will convert these to a
single PDF for editorial reviewing purposes- and production will use the WORD source
file for turning your manuscript into galleys). If absolutely necessary, we can use
.tex files - but will use the PDF to double-check formatting - and also require a
bibliography (.bbl) file for the references.  In cases where the source file is in
LaTex, BE ABSOLUTELY SURE the PDF of your manuscript is correct as this will be our
only source for creating properly formatted galleys, and all changes made at galley
stages incur fees.  NO mailed hardcopy of manuscript is required.  Only the requested
art files for figures should be uploaded and Production Forms and Permissions emailed
or faxed to the office.

I look forward to receiving your revised manuscript.


With kind regards,

Laura DeMare, Ph.D
Assistant Editor
Genome Research




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