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Author Guidelines

  1. General
    1. Language
    2. Files required for submission
    3. Pre-submission inquiries
  2. Content is first!
  3. Guidelines for Research Articles
    1. Main manuscript
    2. Figures
    3. Supplementary data
  4. Special Sections
    1. Resources: software, on-line tools and database articles
    2. Analytical Workflows
    3. Reviews
    4. Short Communications
  5. Suggested data repositories
  6. Source code
  7. 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 in the following sections (or article types): Research Articles, Resources, Analytical Workflows, Reviews or Short Comminications. These general guidelines apply to all types of articles. Additional requirements specific for each article type are described below.

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.

If you are unsure as to whether or not your manuscript meets the journal’s scope, please contact the Editor-in-Chief in the form of a pre-submission inquiry.

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.

Files or data required for submission

All submitted articles require:

  • a cover letter
  • a Microsoft Word DOCX or PDF document file including manuscript text, tables, figures and references

Upon acceptance the following files or data will be required:

Please include in 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 text format directly in the online submission system.

Pre-submission inquiries

Pre-submission inquiries are not required for Genomics and Computational Biology. However, authors may submit a pre-submission inquiry in order to evaluate if an article is of interest to the journal.

A pre-submission inquiry must be sent by email to Fontaine@GenomicsComputBiol.org and consists of an abstract and a cover letter indicating the significance and the type of article being considered (see section policies).

The journal can not guarantee the speed of response but normally you will get a response within a week. Additionally editors can not guarantee that a paper will be sent to review before seeing the complete manuscript.

2. Content is first!

In Genomics and Computational Biology we aim to facilitate the road to academic publishing. Authors can choose to follow the strict formatting guidelines described here, 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 journal formatting guidelines.

Basic format requirements

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 DOCX or PDF file. Tables and figures include title and legend, are inserted in the corresponding position where they are described in the text (not all at the end of the document), and are of enough quality to be evaluated during the peer review process. Please note that high resolution figure files will be required later for publication of accepted articles.
  • The document includes the following sections: Title, Authors list, Author affiliations, Corresponding Author, Keywords, Abstract, Introduction, Methods, Results, Discussion (results and discussion sections can be combined), References, List of supplementary files, and Bibliography. An extra section “Avalibility and requirements” is required for resources and analytical workflows.
  • 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. Preferably, the following minimum data should be provided for each citation: the full article title, first author, journal/book/proceedings title, volume, page and DOIs. Please note that DOIs of cited references will be required for the published version of the artile.
  • Text is formatted as “double-space”.

3. Guidelines for Research Articles.

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

Main manuscript

All manuscripts have to be submitted using the template document provided below (see Template document section), which is divided into the following sections: Title, Author list, Abstract, Availability and requirements (optional), Keywords, Introduction, Methods, Results, Discussion, Supplementary Data (optional), Acknowledgements, Author Contributions, Conflict of Interest Declaration, Abbreviations (optional), References and Endnotes (optional). Figures, tables and legends have to be embedded in the text. This is an "on-line only" publication, although article length is not limited we encourage authors to be concise.

We encourage authors to read carefully the instructions for the correct use of the template document. Adherence to these guidelines will ensure that your submission has the required format and is quickly processed. Please note that before publication, the layout of an article may be modified by the journal team.

Title

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

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, state/province (if applicable), and country
  • corresponding author including full contact information (phone, fax 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.

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

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.

Keywords

A list of 3 to 10 keywords separated by semi-columns must be provided in a single paragraph. If available, keywords from the MeSH vocabulary are preferred.

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

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. Please follow source code guidelines described below if relevant.

Results

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

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.

Acknowledgments

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

Author contributions

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

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”.

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.

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. If available, DOI numbers must be displayed and set as active hyperlinks for references to journal articles. Note that active DOIs will be required for all referenced articles prior to publication.

Web links and URLs should be given in full in the endnote section.

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. Please see the following examples:

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.

Article within a journal
Smith JJ. The world of science. Am J Sci. 1999;36:234-5.

Article within a journal (no page numbers)
Rohrmann S, Overvad K, Bueno-de-Mesquita HB, Jakobsen MU, Egeberg R, Tjønneland A, et al. Meat consumption and mortality - results from the European Prospective Investigation into Cancer and Nutrition. BMC Medicine. 2013;11:63.

Article within a journal supplement
Frumin AM, Nussbaum J, Esposito M. Functional asplenia: demonstration of splenic activity by bone marrow scan. Blood 1979;59 Suppl 1:26-32.

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.

OnlineFirst chapter in a series (without a volume designation but with a DOI)
Saito Y, Hyuga H. Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Top Curr Chem. 2007. doi:10.1007/128_2006_108.

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.

University site
Doe, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (1999). Accessed 25 Dec 1999.

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.

Examples above come from BioMed Central (BMC Genomics) as Genomics and Computational Biology uses the same style (based on SpringerVancouverNumber). Style files are available for the following programs:

  • EndNote
    • Note that DOIs may be displayed as full URLs and the first part of the URLs (http://dx.doi.org/) should be manually removed in the generated References list
  • Latex

Authors using other bibliographic management programs may choose to adapt close styles such as the followings althoug DOIs may not be displayed for journal articles:

Endnotes

Endnotes should be used to provide electronic links (e.g. full URLs) and included in a separate section. Endnotes should be in lowercase letters and cited in superscript position. Please do not use footnotes.

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.

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 Tagged Image File Format (.tif), Joint Photographic Experts Group (.jpg), or Portable Network Graphic (PNG).

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.

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 create tables using the special table function in your text processor in the same style as the tables in the template document. Please do not paste spreadsheet or image files (e.g., .jpg .tif) into the manuscript as tables.

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 (see also our policy about distribution of materials and data) 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; File: file name. Description. (e.g. Document S1. Supplementary methods and results; File: Methods.Results.pdf. This file includes a detailed description of the algorithm and benchmark results for simulated datasets.)

4. Special sections

Special Sections contain Reviews, Resources, Analytical Workflows and Short Communications with the aim of making them widely accessible and useful for the scientific community. The proposed articles should be relevant to the field, focus on applicability and provide biological insight.

All articles should provide applied examples showing how the proposed resource, method or workflow can be used to perform a concrete task. It is mandatory for authors to make the datasets that were analyzed in the article freely available, to ensure that the datasets can be re-used as reference datasets in the future. Deposition of reference datasets in the appropriate on-line repositories, together with providing the corresponding accession number, is encouraged. Please see example repositories in this list. Please follow source code guidelines if relevant.

All formatting requirements described in the General and in the Research Articles guidelines are valid for Special Sections articles unless otherwise specified.

Resources: software, on-line tools and database articles

The journal publishes articles describing new on-line resources enabling the analysis or the access to biological data. The following aspects should be considered when submitting a Resources article:

  • Free access. The journal is committed to the maximum dissemination and wide use of the resource reported. Thus, the reported resource must be freely available with no registration requirement at the time of publication. A statement indicating a complete URL address where the resource is available must be included in the abstract. We encourage authors to associate a non-restrictive license to their resource such as GNU GPL, GNU LGPL, BSD, Free BSD or Creative Commons if relevant.
  • Utility. The proposed resource should be useful to the scientific community. Authors should show that the resource outperforms related resources in a specific way or provide new biological insight. If related/similar resources exist, a comparison with the proposed resource is required. If this is not possible authors should discuss the utility of the reported resource. Combination or linking utilities from different resources may be considered for publication, given that it provides new biological insight.
  • Validation. Authors should show that the resource actually accomplishes the task for which it is intended. The article should show a practical example making use of the resource for a specific task. Software articles should assess the performance and accuracy of the software on a test dataset, which should be based on real data although simulated datasets could be additionally tested.

Resources papers should describe implementation details in the Methods section, and the resulting resource and tests in the Results section.

Papers should provide full details of the data collection and curation process, the algorithms used, the platform requirements to run the resource (Windows, Linux, etc) and the main dependencies with other platforms or tools. For software, full details on dependencies must be provided in the associated documentation.

Additionally, by publishing in Genomics and Computational Biology, the authors agree to maintain the resource for at least 2 years after publication of the article. Please note that providing the source code and documentation would allow the community to use or evaluate the resource any time in the future.

Analytical Workflows

These articles provide a practical guide for readers aiming to perform a complex bioinformatic analysis. Please consider the following aspects when preparing an Analytical Workflows paper:

  • Target audience. Authors should state in the abstract if the proposed workflow is intended for experts or novices in the field. The depth of detail in general aspects of the workflow should be in accordance to the target audience. Workflows targeting novices are welcome and should assume basic bioinformatics skills.
  • Detailed. Sufficient conceptual and methodological details should be provided, including a conceptual flowchart describing the different steps and options, description of the independent tools used, system requirements, instructions to install or use the software/tool, tools parameters and commands, file formats, processing time and memory requirements, troubleshooting, etc.
  • Applicability. The article should be a practical guide and describe the analysis of a freely available dataset and the results obtained.
  • Accessibility. We recommend authors to deposit the workflow implementation in relevant on-line repositories such as myExperiment.
  • Open access. Although the use of commercial tools will not preclude the publication of a paper, the use of open source tools is strongly recommended.
  • Decision points and critical steps. Authors should indicate critical steps that may lead to failure or have major effects on the final output. When alternative routes exist to perform the task, arguments should be provided to enable informed decision-making.
Reviews

Reviews articles should provide a systematic and updated overview of the subject under consideration and include a speculation of the future development of the field. These articles should contain the following sections: Introduction, Body, Conclusions, Acknowledgements, Web Resources (as necessary), and References. The body may be divided in sections and subsections with a corresponding header.

Short communications

Short Communications are articles limited to 2500 words and could be written as Research Articles, Resources or Analytical Workflows. Authors have to refer to the corresponding guidelines.

5. Suggested repositories

An updated and more extended list of repositories can be found in the DataCite website.

6. 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 (e.g., JavaDoc or Perl POD) 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.

7. Template document

Genomics and Computational Biology provides template files for submitting and formatting an article as a DOCX or PDF file. Upon acceptance, authors will be required to provide the source files (manuscript, figures, tables and bibliography). Please note that final publication layout may differ from outputs generated from the template files.

Latex template

Latex template files include a .tex file for the manuscript content, a .bst file for bibliography style, and example figures and bibliography records. As the Latex template files are in Beta version, authors may adapt them as needed and notify the editor of such changes.

Microsoft Word template

The Word template file is provided as a .dot file for submitting a DOCX or a PDF file.

The template is composed of page headers, a title section, a body, and page footers. Authors should not edit page headers and footers. Text highlighted in grey will be filled in by the journal and should not be edited by authors. Text in brackets indicates some guidelines for authors to follow and should be deleted (together with the brackets) by the authors before submission to the journal. When copying text from another document, please paste the text using the "Paste Special / unformatted text" option of your word processor in order to preserve the format. No blank lines should remain in the article as space between paragraphs or objects are coded in the custom formatting styles. Authors must use these styles as shown in the template or described below.

Figures, tables, legends and mathematical equations have to be embedded in the text. Tables, mathematical equations and endnotes have to be created using the word processor special tool. Figures should be inserted from image files (e.g. jpg, png or tiff).

By default, tables or figures will be displayed as a single column item. When a figure or a table is too large to be correctly displayed in a single column, there is the option of displaying it as a double column item. In order to do this:

  1. Insert a “continuous section break” at the desired location between paragraphs
  2. Insert a second “continuous section break”
  3. Create or copy the table or the figure between both “section breaks”
  4. Format this section as one column in the Page Layout settings

Title section

The title section has a single column of text and the following styles are used:

  • GCB Article Type: article type
  • GCB Title: title of the article
  • GCB Author names: list of authors
  • GCB Author Affiliations: list of affiliations
  • GCB Author Correspondence: information for correspondence
  • GCB Article Dates: dates related to the article such as date of reception, revision and acceptance.

Authors must update this section with relevant information as described in the instructions and as shown in the template. Please do not edit text highlighted in grey.

Article body

The article body has two columns of text and contains the main sections of the article (e.g. abstract, introduction, methods, etc...). Sections described as optional in the instructions (e.g. Abbreviations and Endnotes) should be deleted from the manuscript if they are not used. The following styles are used:

  • GCB Normal Text: normal text to be applied by default
  • GCB Heading 1: main headings (e.g. Abstract, Introduction and Keywords)
  • GCB SubHeading: subheadings (or level 2 headings)
  • GCB Paragraph As List: lists of the Keywords, Supplementary Data, and Abbreviations sections where each item of a list is represented by a new paragraph.
  • GCB References: list of references (see details below)
  • GCB Endnotes: list of endnotes

The following styles related to figures and tables are also used:

  • GCB Caption: figure or table captions composed of a label, a title and a legend in a paragraph just following the figure or table (in captions, only figure title and label have a bold font effect. Remove manually the effect where necessary.)
  • GCB Table Text: text in tables
  • GCB Normal Text Before Table: to be applied to a paragraph of normal text displayed on the same page just before a table
  • GCB Bitmap Figure: images as figures (select the image representing the figure, apply the style, and if necessary set the paragraph alignment)

Bullet and numbered lists

To add a bullet list using the journal format you can use the following procedure: write each item of the list in its own consecutive paragraph without indentation or tabulation, select these paragraphs, apply paragraph style "Normal" to the selection, apply list style "GCB Bullet List" from the Multilevel List settings. To indent some items, place your cursor at the beginning of the line to be indented and press the TAB key.

Numbered lists are not defined or restricted by the journal.

References section

The References section contains a numerically sorted list of References where each reference is represented by a new paragraph formatted with the GCB References style (Arial 8pt; Hanging Indent of 0.5cm). References are numbered in the same order as they appear in the text. Each paragraph is composed as follows: the Reference number directly followed by a dot, an indent (just type the TAB key once), and the detailed reference as described above. Users of Bibliographic manager software may generate automatically the References list and manually change the font to Arial 8 points and the hanging indent to 0.5 cm.

 

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. Submissions that do not adhere to these guidelines may be rejected.

  1. 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. When submitting extended versions of previously published work, an explanation has been provided in the cover letter and the previous related publication has been appropriately cited.
  2. Authors have read and adhere with the Journal Policies.
  3. The text adheres to the format requirements described the journal formatting guidelines.
  4. If submitting a Resources article, authors agree to maintain the resource(s) (e.g. software or databases) for at least 2 years after publication of the related article.
  5. After peer review and upon acceptance, authors agree to pay the article processing charge.
 

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