The Open Bioinformatics Journal
ISSN: 1875-0362 - Volume 6, 2012
Instructions
for Authors
The Open Bioinformatics Journal is an
Open Access online journal which publishes Research articles and Letters in the field of bioinformatics and computational biology, aiming at providing the most complete and reliable source of information on current developments in the field.
Manuscripts may be submitted directly to tobioij@benthamopen.org.
Each peer-reviewed article that is published in a Bentham
OPEN Journal is universally and freely accessible via
the Internet in an easily readable and printable PDF format.
Online Manuscript Submission: An online submission
and tracking service via Internet facilitates a speedy
and cost-effective submission of manuscripts.1
The full manuscript has to be submitted online via
Bentham's Content Management System (CMS) at http://www.bentham-editorial.org/
View
Instructions
Alternatively, you may also submit your full manuscript by
e-mail to tobioij@benthamopen.org
Manuscripts must be submitted by one of the authors of the
manuscript, and should not be submitted by anyone on their
behalf. The principal/corresponding author will be required
to submit a Covering Letter along with the manuscript, on
behalf of all the co-authors (if any). The author(s) will
confirm that the manuscript (or any part of it) has not been
published previously or is not under consideration for publication
elsewhere. Furthermore, any illustration, structure or table
that has been published elsewhere must be reported, and copyright
permission for reproduction must be obtained.
For all online submissions, please provide soft copies of all the materials (main text in MS Word or Tex/LaTeX), figures / illustrations in TIFF, PDF or JPEG, and chemical structures drawn in ChemDraw (CDX) / ISISDraw (TGF) as separate files, while a PDF version of the entire manuscript must also be included, embedded with all the figures / illustrations / tables / chemical structures etc. It is advisable that the document files related to a manuscript submission should always have the name of the corresponding author as part of the file name, i.e., "Cilli MS text.doc" , "Cilli MS Figure 1", etc.
A successful electronic submission of a manuscript will be
followed by a system-generated acknowledgement to the principal/corresponding
author within 72 hours of the dispatch of
the manuscript. Any questions with regards to the preparation
of and submission of your manuscript to the journal should
be addressed to tobioij@benthamopen.org
and copied to managingeditor@benthamopen.org
NOTE: Any queries therein should be addressed
to oa@benthamscience.org
and copied to Jalil@benthamscience.org
Manuscript Preparation: The manuscript should
be written in English in a clear, direct and active style.
All pages must be numbered sequentially, facilitating in the
reviewing and editing of the manuscript.
For further convenience, the customer support team available
at Bentham Publishing Services (www.benthampublishingservices.com)
can provide assistance to authors for the preparation of manuscripts.
Manuscript Length:
Research Articles: The total number of words
for a published research article is from 4000 to 8000 words.
Letter Articles: The total number of words for a
published letter/short communication article is from 3000
to 6000 words.
There is no restriction on the number of figures, tables or additional files e.g. video clips, animation and datasets, that can be included with each article online. Authors should include all relevant supporting data with each article.
Manuscripts Published:
The Journal accepts research articles and letter articles, written in English. Proceedings of conferences and book reviews may also be considered for publication.
Conference Proceedings: The journal will
consider for publication proceedings of relevant conferences
in the field. Proposals for publishing conference proceedings
should be submitted to the Editor at e-mail tobioij@benthamopen.org
with a copy to oa@benthamscience.org
Open Access Book Reviews: This journal publishes
open access reviews on recently published books (both print
and electronic) relevant to the journal. Publishers and authors
of books are invited to contact our book reviews editor at
tobioij@benthamopen.org
with book review requests. All submitted books will be reviewed
by an independent expert in the field.
MANUSCRIPT SECTIONS FOR PAPERS: Manuscripts
for research articles and letters submitted to the respective
journals should be divided into the following sections.
Covering letter
Title
Title page
Abstract
Key words
Text organization
List of abbreviations (if any)
Conflict of interest (if any)
Acknowledgements (if any)
References
Appendices
Figures/illustrations (if any)
Mathematical Expressions (if any)
Tables (if any)
Supportive/supplementary material (if any)
Source Code/Algorithms (if any)
COVERING LETTER: It is a mandatory requirement
that a signed covering letter also be submitted along with
the manuscript by the author to whom correspondence is to
be addressed, delineating the scope of the submitted article
declaring the potential competing interests, acknowledging
contributions from authors and funding agencies, and certifying
that the paper is prepared according to the 'Instructions
for Authors'. All inconsistencies in the text
and in the reference section, and any typographical errors
must be carefully checked and corrected before the submission
of the manuscript. The article contains no such material or
information that may be unlawful, defamatory, fabricated,
plagiarized, or which would, if published, in any way whatsoever,
violate the terms and conditions as laid down in the agreement.
The authors acknowledge that the publishers have the legal
right to take appropriate action against the authors for any
such violation of the terms and conditions as laid down in
the agreement. Download
the Covering letter
TITLE: The title should be precise and brief
and must not be more than 120 characters. Authors should avoid
the use of non-standard abbreviations. The title must be written
in title case except for articles, conjunctions and prepositions.
Authors should also provide a short ‘running title’.
TITLE PAGE: Title page should include paper
title, author(s) full name and affiliation, corresponding
author(s) names complete affiliation/address, along with phone,
fax and email.
ABSTRACT: The abstract
should not exceed 250 words for research papers and should
be limited to only 150 words for letters, summarizing the
essential features of the article. The use of abbreviations
should be reduced to a minimum and the references should not
be cited in the abstract.
KEYWORDS: Please provide 6-8 keywords
in alphabetical order.
TEXT ORGANIZATION: The main text should
begin on a separate page and should be divided into separate
sections. For Research articles, the preparation of the main
text must be structured into separate sections as Introduction,
Materials and Methodology, Results, Discussion and Conclusion.
For Letter articles, the manuscript should be divided into
title page, abstract and the main text. The text may be subdivided
further according to the areas to be discussed, which should
be followed by the Acknowledgement (if any) and Reference
sections.The manuscript style must be uniform throughout the
text and 10 pt Times New Roman fonts should be used. The full
term for an abbreviation should precede its first appearance
in the text unless it is a standard unit of measurement. The
reference numbers should be given in square brackets in the
text. Italics should be used for Binomial names of organisms
(Genus and Species), for emphasis and for unfamiliar words
or phrases. Non-assimilated words from Latin or other languages
should also be italicized e.g. in vivo, in vitro, per
se, et al. etc. Protein and Nucleic acid sequences may
be included and should conform to International databases.
Genomic and Proteomic studies may be included and should conform
to International databases.
Protection of Human Subjects and Animals in Research:
When reporting experiments involving human subjects, authors
should indicate whether the procedures followed were in accordance
with the ethical standards of the responsible committee on
human experimentation (institutional and national) and with
the Helsinki Declaration of 1975, as revised in 2000.
For research involving animals, authors should indicate whether the procedures followed were in accordance with the standards set forth in the Guide for the Care and Use of Laboratory Animals(published by the National Academy of Science, National Academy Press, Washington, D.C.).
Nomenclature:
The authors are encouraged to use standardized nomenclature
wherever necessary:
•The SI units should be used; if not exclusively, please
provide the SI value in parentheses after each value.
•Species names should be italicized (e.g., Homo sapiens).
The generic name of a species should be given in full the
first time it appears in the text.
•The author authority for each species is desirable
on its first mention.
Chemical formulae may not be used as abbreviations in the
text.
•Genes, mutations, genotypes, and alleles should also
be indicated in italics but the protein product of a gene
should be in Roman type. Use the recommended name by consulting
the appropriate genetic nomenclature database, e.g., HUGO
for human genes. It is sometimes advisable to indicate the
synonyms for the gene the first time it appears in the text.
Gene prefixes such as those used for oncogenes or cellular
localization should be shown in roman: v-fes, c-MYC, etc.
•The Recommended International Non-Proprietary Name
(rINN) of drugs should be provided.
•In case of usage of symbols that do not conform to
those that have previously appeared in the literature, their
aliases may be obtained from the approved nomenclature in
the HGNC (HUGO Gene Nomenclature Committee) [http://www.genenames.org/]
and LocusLink, to allow retrieval of all the information available
for each gene.
Taxonomic nomenclature: The Latin name and
taxonomic authority (e.g. Linnaeus) should be given for all
experimental species. Chemical nomenclature must conform to
the Subject Index of Chemical Abstracts.
Greek Symbols and Special Characters: Greek
symbols and special characters play a prominent role in the
manuscript. These symbols often undergo formatting changes
and get corrupted or lost during preparation of a manuscript
for publication. To ensure that all special characters used
are embedded in the text, these special characters should
be inserted as a symbol but should not be a result of any
format styling (Symbol font face) otherwise they
will be lost during conversion to PDF/XML2.
Authors are encouraged to consult reporting guidelines. These
guidelines provide a set of recommendations comprising a list
of items relevant to their specific research design. All kinds
of measurements should be reported only in International System
of Units (SI).
LIST OF ABBREVIATIONS: If abbreviations
are used in the text either they should be defined in the
text where first used, or a list of abbreviations can be provided.
CONFLICT OF INTEREST: Financial contributions
to the work being reported should be clearly acknowledged,
as should any potential conflict of interest.
ACKNOWLEDGEMENTS: Please acknowledge anyone
(individual/company/institution) who has contributed to the
study by making substantial contributions to conception, design,
acquisition of data, or analysis and interpretation of data,
or who was involved in drafting the manuscript or revising
it critically for important intellectual content. Please list
the source(s) of funding for the study, for each author, and
for the manuscript preparation in the acknowledgements section.
This journal complies with the International Committee of
Medical Journal Editors' Uniform Requirements for Manuscripts
Submitted to Biomedical Journals www.icmje.org
and the FDA's Good Reprint Practices for the Distribution
of Medical Journal Articles and Medical or Scientific Reference
Publications on Unapproved New Uses of Approved Drugs and
Approved or Cleared Medical Devices http://www.fda.gov/oc/op/goodreprint.html
REFERENCES: References must be listed in
IEEE style only. All references should be numbered sequentially
[in square brackets] in the text and listed in the same numerical
order in the reference section. The reference numbers must
be finalized and the bibliography must be fully formatted
before submission.
The author will be responsible for the accuracy and completeness
of the references.
See below few examples of references listed in the correct
IEEE style:
Journal Articles:
[1] G. Liu, K. Y. Lee, and H. F. Jordan, "TDM and TWDM
de Bruijn networks and shufflenets for optical communications", IEEE Trans. Comp., vol. 46, pp. 695-701, June 1997.
Books:
[2] S. M. Hemmingsen, Soft Science. Saskatoon: University
of Saskatchewan Press, 1997.
[3] A. Rezi and M. Allam, "Techniques in array processing
by means of transformations," in Control and Dynamic
Systems, Vol. 69, Multidimensional Systems,
C. T. Leondes, Ed. San Diego: Academic Press, 1995, pp. 133-180.
Edited Book:
[4] D. Sarunyagate, Ed., Lasers. New York: McGraw-Hill,
1996.
Conference Proceedings:
[5] N. Osifchin and G. Vau, “Power considerations for
the modernization of telecommunications in Central and Eastern
European and former Soviet Union (CCE/FSU) countries”,
in Second International Telecommunication Energy Special Conference
Special Conference, 1997, pp. 9-16.
Patent:
[6] K. Kimura and A. Lipeles, "Fuzzy Controller Component,"
U. S. Patent 14,860,040, December 14, 1996.
Thesis:
[7] H. Zhang, "Delay-insensitive networks", M.S.
thesis, University of Waterloo, Waterloo, ON, Canada, 1997.
Electronic Publication:
E-Books:
[8] L. Bass, P. Clements, and R. Kazman. Software Architecture
in Practice, 2nd ed. Reading, MA: Addison Wesley, 2003.
[E-book] Available: Safari e-book.
E-Journals:
[9] P. H. C. Eilers and J. J. Goeman, "Enhancing scatterplots
with smoothed densities", Bioinformatics, vol.
20, no. 5, pp. 623-628, March 2004. [Online] Available: www.oxfordjournals.org.
[Accessed Sept. 18, 2004].
E-citations:
[10] Citations for articles/material published exclusively
online or in open access (free-to-view) , must contain the
exact Web addresses (URLs) at the end of the reference(s),
except those posted on an author’s Web site unless editorially
essential, e.g. ‘Reference: Available from: URL’
Some important points to remember:
*References must be complete and accurate.
*Online citations should include the date of access.
*Journal titles should conform to the IEEE Transactions, Journals
and Letters abbreviations.
*All authors of referenced papers must be cited and there
must be no use of the short hand version of et al.
*Take special care of the punctuation convention as described
in the above-mentioned examples.
*Avoid using superscript in the in-text citations and reference
section.
*Abstracts, unpublished data and personal communications (which
can only be included if prior permission has been obtained)
should not be given in the reference section but they may
be mentioned in the text and details provided as footnotes.
*The authors are encouraged to use a recent version of EndNote
(version 5 and above) or Reference Manager (version 10) when
formatting their reference list, as this allows references
to be automatically extracted.
APPENDICES: In case there is a need to present
lengthy, but essential methodological details, use appendices,
which can be a part of the article. An appendix must not exceed
three pages (Times New Roman, 12 point fonts, 900 max. words
per page).The information should be provided in a condensed
form, ruling out the need of full sentences. A single appendix
should be titled APPENDIX, while more than one can be titled
APPENDIX A, APPENDIX B, and so on.
FIGURES/ILLUSTRATIONS: The authors should
provide the illustrations as separate files, as well as embedded
in the text file, numbered consecutively in the order of their
appearance. Each figure should include a single illustration.
No charges will be levied on the use of color figures except
in the reprints. Each figure should be closely cropped to
minimize the amount of white space surrounding the illustration.
If a figure consists of separate parts, it is important that
a single composite illustration file be submitted, containing
all parts of the figure.
Photographs should be provided with a scale bar if appropriate,
as well as high-resolution component files.
Scaling/Resolution:
For Line Art image type, which is generally an image based
on lines and text and does not contain tonal or shaded areas,
the preferred file format is TIFF or EPS, with colour mode
being Monochrome 1-bit or RGB, in a resolution of 900-1200
dpi.
For Halftone image type, which is generally a continuous tone photograph and contains no text, the preferred file format is TIFF, with colour mode being or RGB or Grayscale, with a minimum resolution of 300 dpi.
For Combination image type, which is generally an image containing
halftone in addition to text or line art elements, the preferred
file format is TIFF, with colour mode being or RGB or Grayscale,
in a resolution of 500-900 dpi.
Formats:
For illustrations, the following file formats are acceptable:
• Illustrator
• EPS (preferred format for diagrams)
• PDF (also especially suitable for
diagrams)
• PNG (preferred format for photos
or images)
• Microsoft Word (version 5 and above;
figures must be a single page)
• PowerPoint (figures must be a single
page)
• TIFF
• JPEG (conversion should be done using
the original file)
• BMP
• CDX (ChemDraw)
• TGF (ISISDraw)
Bentham OPEN does not process figures submitted in
GIF format.
If the large size of TIFF or EPS figures acts as an obstacle
to online submission, authors may find that conversion to
JPEG format before submission results in significantly reduced
file size and upload time, while retaining acceptable quality.
JPEG is a ‘lossy’ format, however in order to maintain acceptable
image quality, it is recommended that JPEG files are saved
at High or Maximum quality.
Files should not be compressed with tools such as Zipit or
Stuffit prior to submission as these tools will in any case
produce negligible file-size savings for JPEGs and TIFFs,
which are already compressed.
Image Conversion Tools:
There are many software packages, many of them freeware or
shareware, capable of converting to and from different graphics
formats, including PNG.
Good general tools for image conversion include GraphicConverter
on the Macintosh, PaintShop Pro, for Windows, and ImageMagick,
which is available on Macintosh, Windows and UNIX platforms.
Note that bitmap images (e.g. screenshots) should not be converted
to EPS, since this will result in a much larger file size
than the equivalent JPEG, TIFF, PNG or BMP, with no increase
in the quality. EPS should only be used for images produced
by vector-drawing applications such as Adobe Illustrator or
CorelDraw. Most vector-drawing applications can be saved in,
or exported as, EPS format. In case the images have been originally
prepared in an Office application, such as Word or PowerPoint,
then the original Office files should be directly uploaded
to the site, instead of being converted to JPEG or another
format that may be of low quality.
Chemical Structures: Chemical structures must be prepared according to the guidelines below.
Structures should be prepared in ChemDraw and provided as separate file, submitted both on disk and in printed formats.
Structure Drawing Preferences:
[As according to the ACS style sheet]
Drawing Settings:
Chain angle 120°
Bond spacing 18% of width
Fixed length 14.4 pt (0.500cm, 0.2in)
Bold width 2.0 pt (0.071cm, 0.0278in)
Line width 0.6 pt (0.021cm, 0.0084in)
Margin width 1.6 pt (0.096cm)
Hash spacing 2.5 pt (0.088cm, 0.0347in)
Text settings:
Font Times New Roman
Size 8 pt
Under the Preference Choose:
Units points
Tolerances 3 pixels
Under Page Setup Use:
Paper US letter
Scale 100%
TABLES:
*Data tables should be submitted in Microsoft Word table
format.
*Each table should include a title/caption being explanatory
in itself with respect to the details discussed in the table.
Detailed legends may then follow.
*Table number in bold font i.e. Table 1,
should follow a title. The title should be in small case with
the first letter in caps. A full stop should be placed at
the end of the title.
*Tables should be embedded in the text exactly according
to their appropriate placement in the submitted manuscript.
*Columns and rows of data should be made visibly distinct
by ensuring that the borders of each cell are displayed as
black lines.
*Tables should be numbered in Arabic numerals sequentially
in order of their citation in the body of the text.
*If a reference is cited in both the table and text, please
insert a lettered footnote in the table to refer to the numbered
reference in the text.
*Tabular data provided as additional files can be submitted
as an Excel spreadsheet.
SUPPORTIVE/SUPPLEMENTARY MATERIAL:
We do encourage to append supportive material, for example
a PowerPoint file containing a talk about the study, a PowerPoint
file containing additional screenshots, a Word, RTF, or PDF
document showing the original instrument(s) used, a video,
or the original data (SAS/SPSS files, Excel files, Access
Db files etc.) provided it is inevitable or endorsed by the
journal's Editor.
Supportive/Supplementary material intended for publication
must be numbered and referred to in the manuscript but should
not be a part of the submitted paper. In-text citations as
well as a section with the heading "Supportive/Supplementary
Material" before the "References" section should
be provided. Here, list all Supportive/Supplementary Material
and include a brief caption line for each file describing
its contents.
Any additional files will be linked into the final published
article in the form supplied by the author, but will not be
displayed within the paper. They will be made available in
exactly the same form as originally provided only on our Web
site. Please also make sure that each additional file is a
single table, figure or movie (please do not upload linked
worksheets or PDF files larger than one sheet). Supportive/Supplementary
material must be provided in a single zipped file not larger
than 4 MB.
Authors must clearly indicate if these files
are not for publication but meant for the reviewers'/editors'
perusal only.
PERMISSION FOR REPRODUCTION: Published/reproduced
material should not be included unless you have obtained written
permission from the copyright holder, which should be forwarded
to the Editorial Office in case of acceptance of your article
for publication.
For obtaining permission for reproducing any material published
in an article by Bentham Science Publishers, please fill in
the request FORM
and send to tobioij@benthamopen.org
for consideration.
AUTHORS AND INSTITUTIONAL AFFILIATIONS:
The author will be required to provide their full names, the
institutional affiliations and the location, with an asterisk
in front of the name of the principal/corresponding author.
The corresponding author(s) should be designated and their
complete address, business telephone and fax numbers and e-mail
address must be stated to receive correspondence and galley
proofs.
REVIEWING AND PROMPTNESS OF PUBLICATION:
All manuscripts submitted for publication will be immediately
subjected to peer-reviewing, usually in consultation with
the members of the Editorial Advisory Board and a number of
external referees. Authors may, however, provide in their
Covering Letter the contact details (including e-mail addresses)
of four potential peer reviewers for their paper. Any peer
reviewers suggested should not have recently published with
any of the authors of the submitted manuscript and should
not be members of the same research institution.
All peer-reviewing will be conducted via the Internet
to facilitate rapid reviewing of the submitted manuscripts.
Every possible effort will be made to assess the manuscripts
quickly with the decision being conveyed to the authors in
due course.
LANGUAGE AND EDITING: Manuscripts must be
written in good English in a clear and correct style. In order
to maintain uniformity throughout the text, the manuscript
should be written in either American or British English. Submitted
manuscripts will not be edited for style or language, and
reviewers may advise rejection of a manuscript if it is compromised
by grammatical errors. Non-native speakers of English may
choose to make use of a copyediting and language editing service
such as that provided by Bentham
Publishing Services (please contact at email: info@benthampublishingservices.com).
PROOF CORRECTIONS: Authors are required
to proofread the PDF versions of their manuscripts before
submission. To avoid delays in publication, proofs should
be checked immediately for typographical errors and returned
within 48 hours. Major changes are not acceptable
at the proof stage. If unable to send corrections within 48
hours due to some reason, the author(s) must at least
send an acknowledgement on receiving the galley proofs or
the article will be published exactly as received and the
publishers will not be responsible for any error occurring
in the manuscript in this regard.
The corresponding author will be solely responsible for ensuring
that the revised version of the manuscript incorporating all
the submitted corrections receives the approval of all the
authors of the manuscript.
COPYRIGHT: Authors who publish in Bentham
OPEN Journals retain copyright to their work. Submission
of a manuscript to the respective journals implies that all
authors have read and agreed to the content of the Covering
Letter or the Terms and Conditions. It is a condition of publication
that manuscripts submitted to this journal have not been published
and will not be simultaneously submitted or published elsewhere.
Plagiarism is strictly forbidden, and by submitting the article
for publication the authors agree that the publishers have
the legal right to take appropriate action against the authors,
if plagiarism or fabricated information is discovered. Once
submitted to the journal, the author will not withdraw their
manuscript at any stage prior to publication.
Articles are licensed under the terms of the Creative Commons
Attribution non-commercial License (http://creativecommons.org/licenses/by-nc/3.0/)
which permits unrestricted, non-commercial use, distribution
and reproduction in any medium, providing that the work is
properly cited.
Plagiarism Prevention:
Bentham Science Publisher uses the iThenticate software to detect instances of overlapping and similar text in submitted manuscripts. iThenticate software checks content uploaded by a journal editorial office against a database of periodicals, the Internet, and a comprehensive article database. It generates a similarity report, including the percentage overlap between the uploaded article and published material. Any instances of content overlap are treated according to a journal's peer review integrity statement and the policies recommended by the editorial Committee. You are assured that the publisher, where you are submitting your manuscript, is committed to actively combating plagiarism and publishing original research.
PUBLICATION FEES: The publication fee details
for each article published in the journal are given below:
Letters: The publication fee for each published
Letter article submitted is US $600.
Research Articles: The publication fee for
each published Research article is US $800.
Book Reviews: The open access fee for a published
book review is US $450.
Once the paper is accepted for publication, the author will
receive by email an electronic invoice. The fee form is also
available on the Web site at www.benthamscience.com/open/feeform
.
MEMBERSHIP: Join as a member of Bentham OPEN
today to obtain great discounts on your article publication
fees! For details click
here.
REPRINTS: High quality printed reprints
of published articles are available for purchase, if ordered,
with a minimum number of 100 reprints.
1 The submission process
is compatible with version 3.0 or later of Internet Explorer
and Netscape Navigator, and with most other modern Web browsers.
It can be used from PC, Mac, or Unix platforms.
2 In this connection, we
recommend the use of Microsoft Word version 2000 and above.
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