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Submission Preparation Checklist

As part of the submission process, authors are required to check off their submission's compliance with all of the following items, and submissions may be returned to authors that do not adhere to these guidelines.
  • The manuscript is original and has not been previously published (in electronic or print version) in any other peer-reviewed journal, is not under consideration by any other journal and does not infringe any existing copyright or any other third party rights.
  • Authors have read and adhere with the Journal Policies described in About the Journal.
  • The submission adheres with the Author Guidelines.
  • The submission file is a Portable Document Format (PDF) file including figures, tables and Digital Object Identifiers (DOIs) for the references where available.
  • After peer review and upon acceptance, the publication will be free of charge.
  • Before publication, authors agree to sign the license agreement.
  • A cover letter in simple text format will be provided in Comments to the Editor and will include names and contact information of 3 potential peer reviewers.

Author Guidelines

  1. 1. General
    1. Article types (journal sections)
    2. Files or data required for submission
    3. Language
  2. 2. Basic format requirements
  3. 3. Section guidelines
  4. 4. Source code
  5. 5. Template document

1.General

Genomics and Computational Biology is an open-access journal publishing peer-reviewed articles using computational approaches to answer biological questions, especially in the field of genome biology. The journal publishes articles of the following types (journal sections): Research Articles, Resources, Analytical Workflows, Reviews or Short Comminications. These general guidelines apply to all types of articles. Please read these instructions carefully and follow them strictly so that the publication process is as efficient and rapid as possible. The Editors reserve the right to return submissions that are not prepared in accordance with the following instructions. This is an "on-line only" publication, although article length is not limited we encourage authors to be concise. We also encourage authors to make freely available their research materials (e.g. data or source code).

If you are unsure as to whether or not your manuscript meets the journal’s scope, please send a pre-submission inquiry to the Editor-in-Chief (Fontaine@GenomicsComputBiol.org).

1.1 Article types (journal sections)

  • Research articles: Research Articles present research works using computational biology methods to gain new insight into genome biology. They provide a novel and original contribution to the field. Paper acceptance depends more on scientific quality than on general interest levels.
  • Resource articles: Resources articles describe new software, databases or on-line tools performing tasks related to the field and useful to the scientific community. Authors should provide concrete examples making use of the tool for a specific task and comparing its performance with respect to previous related tools. Resources should be freely available and provide example datasets and enough methodological details, including the algorithms used or the dependencies with commercial platforms.
  • Analytical Workflows: Analytical Workflows articles describe in depth the steps, methods and tools required to solve a complex analytical problem. The article should provide a conceptual description, enough methodological details to understand and reproduce the workflow, critical decision points, etc. A real example with a freely available dataset should be provided to aid users. Software or programs used within the implementation of the Analytical Workflow should be freely available when possible. Articles targeting an audience of non-specialists are welcome.
  • Reviews: Reviews provide an accurate and balanced overview of the "state of the art" and future developments on topics related to the use of bioinformatic/computational tools in genome biology. Review articles should be important for researchers in the field and could also target researchers from other areas.
  • Short communications: Short Communications are articles limited to 2500 words and could be written as Research Articles, Resources or Analytical Workflows.

1.2 Files or data required for submission

All submitted articles require:

  • a cover letter
  • a PDF document file including manuscript text, tables, figures and references (with DOIs where available)
  • supplementary files, if relevant

Upon acceptance the following files or data will be required:

  • Document source files (DOCX, ODT or TEX files)
  • Bibliographic data including DOIs as a BIB file
  • One independent high-resolution file for each figure (see guidelines for figure preparation)

Please include a the cover letter : i) a brief explanation of the background, results and the biological insight provided by the paper, ii) the type of article that you are submitting and iii) three potential reviewers including name, email address, and institutional affiliation. Potential reviewers must be scientists working independently (not recent collaborators) and have knowledge on the area. The cover letter has to be provided in simple text format directly in the online submission system as "Comments to the editors".

1.3 Language

Articles must be submitted in English. Spelling may be done according to US English or British English, but it must be consistent throughout the entire manuscript. Please note that we do not copy-edit manuscripts, so the language in the manuscript should be clear and concise. If necessary, we will encourage authors to seek help from native English colleagues or to use a professional copy editing service. The quality of English should not detract from scientific content; therefore, we may reject submissions in which the English is insufficient to convey the scientific meaning in a clear manner.

2. Basic format requirements

In Genomics and Computational Biology we aim to facilitate the road to academic publishing. Authors can choose to submit articles using the Template document or to submit articles in any format or layout given that they follow a set of basic format requirements. After peer review and acceptance, the authors are required to format the article following the sections guidelines described below. Please note that before final publication, minor changes may be applied to the layout of an article by the journal team. All submissions must adhere to the following guidelines designed to ensure a clear structure and to facilitate evaluation by reviewers:

  • Figures and tables are submitted together with the article “main text” in a single PDF file. Tables and figures include title and legend, and are of enough quality to be evaluated during the peer review process.
  • The document includes at least the following sections or information: Title, Authors list, Author affiliations, Corresponding Author, Keywords, Abstract, Conflicts of interest, Author contributions, and References.
  • The document body should include the following sections although it may be customized by authors: Introduction, Methods, Results, and Discussion (results and discussion sections may be combined).
  • Other sections may be included if relevant: e.g. Avalibility and requirements or List of supplementary files.
  • Supplementary data is submitted as independent files (e.g. tables, figures or text).
  • Authors are free to choose the style of the bibliographic list, but all references must be consistently formatted using a uniform style.
  • Text is preferably formatted as “double-space”.

3. Section guidelines

Authors can choose to submit articles following these guidelines or the basic formatting principles described above. However, upon article acceptance after the peer review proccess, the authors will be requested to submit the manuscript according to the guidelines described below.

3.1 Title

The title (150 characters or less) should be comprehensible for non-specialists and avoid specialist abbreviations, if possible.

3.2 Author list

The author list should provide:

  • an author list and affiliations where the first name, middle name initials (if used), surname and full affiliation from all authors should be provided including department, university/institution and its location, including city, ZIP code, state/province (if applicable), and country
  • corresponding author including full contact information such as phone and email

If the article has been submitted on behalf of a consortium, all author names and affiliations should be listed at the end of the article.

3.3 Abstract

The abstract should:

  • summarize the objective and main results of the study
  • describe how the study was performed without a deep methodological description
  • be written in a single paragraph
  • be succinct and not exceed 250 words
  • minimize the use of abbreviations (if possible)
  • not cite references

3.4 Availability and requirements

This section should provide readers with relevant data about availability of a resource or an implementation of a described method. It is mandatory for Resources articles but optional for other types of articles. A bullet list should provide the following details: project name, home page, operating system(s), programming language(s), main dependencies, and license. This section is intended to provide a brief overview and more extended information should be provided in the related documentation.

3.5 Keywords

A list of 3 to 10 keywords separated by semi-columns must be provided in a single paragraph.

3.6 Introduction

The introduction should:

  • state the background of the research and its aims
  • end with a brief statement of what is being reported in the article
  • be comprehensible for non-specialists in the field

3.7 Methods

This section must explain the study design, materials used and the analysis performed. Enough methodological details must be provided to ensure that the results can be reproduced by others. If the study is using already established methods, the authors may cite articles where the methods are described in detail. However, the information provided should give a clear idea of the method independently of the previous publications.

Manuscripts involving human and/or animal studies must include an ethics statement including the name of the corresponding board or committee that approved the study. In human studies an additional declaration of informed consent is required (see editorial policies).

This section may be divided into sub-sections with corresponding sub-headers.

3.8 Results

This section may be divided into sub-sections with corresponding sub-headers.

3.9 Discussion

This section should recapitulate the conclusions from the article and explain their significance in a broader context. Relevant studies should be cited and discussed in the context of the novel results presented in the study. Limitations of the study should also be discussed.

3.10 Acknowledgments

The Acknowledgments should list the study's funding sources and all non-authors who additionally contributed to the work.

3.11 Author contributions

In this section, a statement indicating the tasks performed by each author should be included, with authors referred to by their initials.

3.12 Conflict of Interest Declaration

Authors must declare conflicts of interest on the present work (see Editorial policies). When there are no conflicts of interest, authors must declare the following statement: “The author(s) declare(s) no conflicts of interest”.

3.13 Abbreviations

Authors should introduce abbreviations in parenthesis after the first mention of the term. If multiple abbreviations are used they should additionally be listed in this section using the following format:

Abbreviation: Full name.

3.14 References

Only articles that are published or in press should be included in the references. References to unpublished work or personal communications are not allowed. All references will appear in the text as consecutive numbers in square brackets and numerically sorted in the reference section. Journal abbreviations follow Index Medicus/MEDLINE. Examples below come from BioMed Central (BMC Genomics) as Genomics and Computational Biology uses the same style (based on SpringerVancouverNumber):

Article within a journal by DOI (prefered option)
Slifka MK, Whitton JL. Clinical implications of dysregulated cytokine production. Dig J Mol Med. 2000;78(2):74-80 doi:10.1007/s001090000086.

Book chapter, or an article within a book
Wyllie AH, Kerr JFR, Currie AR. Cell death: the significance of apoptosis. In: Bourne GH, Danielli JF, Jeon KW, editors. International review of cytology. London: Academic; 1980. p. 251-306.

Complete book, authored
Blenkinsopp A, Paxton P. Symptoms in the pharmacy: a guide to the management of common illness. 3rd ed. Oxford: Blackwell Science; 1998.

Online document
Doe J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 1999. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.

Online database
Healthwise Knowledgebase. US Pharmacopeia, Rockville. 1998. http://www.healthwise.org. Accessed 21 Sept 1998.

Supplementary material/private homepage
Doe J. Title of supplementary material. 2000. http://www.privatehomepage.com. Accessed 22 Feb 2000.

FTP site
Doe, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (1999). Accessed 12 Nov 1999.

Organization site
ISSN International Centre: The ISSN register. http://www.issn.org (2006). Accessed 20 Feb 2007.

Dataset with persistent identifier
Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, et al. Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. 2011. http://dx.doi.org/10.5524/100012.

3.15 Endnotes

Endnotes should be in lowercase letters and cited in superscript position. Please do not use footnotes.

3.16 Figures and tables

All figures and tables must be embedded in the manuscript itself, if possible close to the location in the text in which they are being referred. Figures and tables must be either one-column wide or two-columns wide. To facilitate the insertion of figures and tables into the manuscript, please see the manuscript template.

3.17 Figures

Figures should be numbered using Arabic numerals (e.g., Figure 1, 2, 3) and panels identified by capital letters (e.g., A, B, C). Figure Legends must contain a concise title not longer than 15 words that describes the whole figure, followed by a short description of each panel. If a bibliographic reference is included in a figure legend, it must follow the journal style and be included in the references section.

Upon acceptance of the manuscript for publication, authors will be required to provide high-resolution figures (600 d.p.i. for line drawings in black and white and 300 d.p.i. for colour or grayscale). Color figures must be supplied in RGB colors. Please ensure that any text or numbers in the figures is large enough to be readable on the screen and on a printed version (with lettering of at least 2 mm). High resolution figures must be submitted in Portable Network Graphic (PNG) or Portable Document Format (PDF).

If primary experimental data are presented, such as a PhosphorImager or digital camera images, any editing or modification must be indicated. The image will be considered to be un-edited unless otherwise stated. Adjustments of brightness, contrast, or color balance are acceptable if applied to the whole image and if these adjustments do not eliminate or misrepresent features present in the original file. The grouping of images from different experiments or from different parts of the same experiment must be declared.

3.18 Tables

Tables should be numbered using Arabic numerals (e.g., Table 1, 2, 3). Tables should include a short title not longer than 15 words and may include a concise legend. Please avoid extensive methodological details. All abbreviations within a table must be defined in the legend. Please do not paste spreadsheet or image files (e.g., .jpg .tif) into the manuscript as tables.

3.19 Supplementary data

All text and figures in the supplementary data should be prepared according to the journal guidelines. Preferred file formats are TXT and DOCX for text documents, and TSV and XLSX for tables or spreadsheets. Guidelines for figures also apply here. Supplementary data files must not exceed 10MB altogether. We encourage authors to make available any large dataset used in the study through public repositories or in a publicly accessible web site. In the Supplementary Data section of the manuscript, a description of each supplementary file should be provided in a paragraph with the following format:

Title. Name; Description. (e.g. Document S1. Supplementary methods and results; This file includes a detailed description of the algorithm and benchmark results for simulated datasets.)

4. Source code

We encourage authors to make their source code freely available under an Open Source Initiative (OSI) compliant license. Source code should be provided with appropriate documentation for developers and users. It could be deposited in a publicly accessible repository such as Github or Source Forge. If relevant, binaries for common operating systems should be provided for peer reviewers and users.

5. Template document

Genomics and Computational Biology provides Latex template files for formatting an article as a PDF file. Although the template may not be used for article submission and peer review, it is used to produce the final article layout. Upon acceptance authors are required to provide the source files of their article (main text as DOCX/ODT/TEX, figures in high resolution, tables and bibliography as BIB file including DOIs where available). Latex template files include a .tex file for the manuscript content, a .bst file for bibliography style, and example figures and bibliography records in a BIB file.

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