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INSTRUCTIONS TO AUTHORS

Aims and Scope

Submission

Instructions for Specific Article Types

Preparing Main Manuscript Text

Preparing Figures

Preparing Tables

Preparing Additional Files

Preparing Supporting Information

Ethics

Aims and Scope

GigaScience is an online open access, open data, open peer-review journal. Our focus covers ‘big data’ research from the life and biomedical sciences, including the growing range of work that uses difficult-to-access large-scale data, such as imaging, neuroscience, ecology, cohort, systems biology, and other new types of sharable data. We are unique in the publishing industry as we publish ALL research objects (data, software tools, source code, workflows, bioboxes/docker and other elements related to the work underpinning the findings in the article). We do this within the context of a variety of article types, including Research, Data Notes, Technical Notes, Reviews and Commentaries. Our goal is to revolutionize publishing by improving research reproducibility and data dissemination, organization, understanding, and re-use. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data, provides data analysis tools and cloud-computing resources. Coupled with this, we have also built a Galaxy-based data analysis platform to host computational methods and workflows, maximizing use of the data, tools and workflows in our articles in a more accessible and reproducible environment.

Submission

All manuscripts are submitted and reviewed via the journal's manuscript submission system. New authors should create an account prior to submitting a manuscript for consideration. Questions about submitting to the journal should be sent to the editorial office at editorial@gigasciencejournal.com.

Instructions for Specific Article Types

Specific instructions for each distinct article type are available at the following links:

Preparing Main Manuscript Text

  • Use double line spacing
  • Include line and page numbering
  • Use SI units: Please ensure that all special characters used are embedded in the text, otherwise they will be lost during conversion to PDF
  • Do not use page breaks in your manuscript

File formats

The following word processor file formats are acceptable for the main manuscript document:

  • Microsoft word (DOC, DOCX)
  • Rich text format (RTF)
  • TeX/LaTeX

Please note: editable files are required for processing in production. If your manuscript contains any non-editable files (such as PDFs) you will be required to re-submit an editable file if your manuscript is accepted.

Note that figures must be submitted as separate image files, not as part of the submitted manuscript file. For more information, see Preparing figures below.

Additional information for TeX/LaTeX users

Please use OUP’s TeX template and BibTeX stylefile if you use TeX format. When submitting TeX submissions, please submit your TeX file as the main manuscript file and your bib/bbl file as a dependent file. Please also convert your TeX file into a PDF and submit this PDF as an additional file with the name 'Reference PDF'. This PDF will be used by our production team as a reference point to check the layout of the article as the author intended. Please also note that all figures must be coded at the end of the TeX file and not inline.

All relevant editable source files must be uploaded during the submission process. Failing to submit these source files will cause unnecessary delays in the production process.

Style and language

For editors and reviewers to accurately assess the work presented in your manuscript you need to ensure the English language is of sufficient quality to be understood. If you need help with writing in English you should consider:

Language editing

Please note that the use of a language editing service is not a requirement for publication in the journal and does not imply or guarantee that the article will be selected for peer review or accepted. More information on language editing services can be found here.

Data and materials

GigaScience requires authors to deposit the data set(s) supporting the results reported in submitted manuscripts in a publicly-accessible data repository, such as GigaDB (see GigaDB database terms of use for complete details). This section should be included when supporting data are available and must include the name of the repository and the permanent identifier or accession number and persistent hyperlinks for the data sets (if appropriate). The following format is recommended:

"The data set(s) supporting the results of this article is(are) available in the [repository name] repository, [cite unique persistent identifier]."

Submission of data into GigaDB does NOT serve as a substitution for submission of data to community-mandated databases. E.g. genome sequence data must still be submitted to GenBank, ENA, or DDBJ. For a complete list of community available databases please see the Reporting Standards section of our Editorial Policies.

Following the Joint Declaration of Data Citation Principles, where appropriate, we ask that the data sets be cited where it is first mentioned in the manuscript, and included in the reference list. If a DOI has been issued to a dataset please always cite it using the DOI rather than the less stable URL the DOI resolves to (e.g. http://dx.doi.org/10.5524/100044 rather than http://gigadb.org/dataset/100044). For more see:

Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. Martone M. (ed.) San Diego CA: FORCE11; 2014 [https://www.force11.org/datacitation]

A list of available scientific research data repositories can be found in res3data and BioSharing.

GigaScience requires that source-code from software/papers with supporting code be made openly available. The source-code needs to be under an Open Source Initiative approved license where practicable compiled running software is made available. If the code is not hosted in a repository, the GigaScience GitHub repository is also available for this purpose. The information on the software should include the following information in the manuscript:

Availability and requirements

Lists the following:

  • Project name: e.g. My bioinformatics project
  • Project home page: e.g. https://github.com/ISA-tools
  • Operating system(s): e.g. Platform independent
  • Programming language: e.g. Java
  • Other requirements: e.g. Java 1.3.1 or higher, Tomcat 4.0 or higher
  • License: e.g. GNU GPL, FreeBSD etc.


You must also state the specific version of the computer program you are using, not just citing a paper that has the most recent description of an earlier version of the software.

References

All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. The reference numbers must be finalized and the reference list fully formatted before submission. For further information including example references please read our reference preparation guidelines. 

What should be cited?

Articles, clinical trial registration records, abstracts that have been published or are in press, the products of public e-print/preprint servers, should be cited. Scientific datasets, protocols and code should be considered legitimate, citable products of research, and accorded the same importance in the scholarly record as citations of other research objects, such as publications. Therefore we follow the guidelines of the Data Citation and Software Citation Principles. We strongly recommend the use of community preprint servers such as arXiv, bioRxiv, OSF Preprints, and PeerJ Preprints. We encourage the citation of preprints where appropriate in the reference list, and will not consider them in the evaluation of the conceptual advance of a manuscript submitted for publication.

Unpublished papers and personal communications should not be included in the reference list, but may be included in the text and referred to as "unpublished observations" or "personal communications" giving the names of the involved researchers. For work under review in another journal, submitting to pre-print servers allows them to be cited. Obtaining permission to quote personal communications and unpublished data from the cited colleagues is the responsibility of the author. Footnotes are not allowed, but endnotes are permitted. Journal abbreviations follow Index Medicus/MEDLINE.

Any in press articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office. 

Note that comprehensive, unbiased and accurate citation of the relevant literature is an essential part of the scientific process. Articles must cite appropriate and relevant literature in support of the claims made. Excessive and inappropriate self-citation or coordinated efforts among several authors to collectively self-cite is strongly discouraged. The editors may contact authors if extensive use of inappropriate citations are suspected.

Authors should consider the following guidelines when preparing their manuscript:

  • Any statement in the manuscript that relies on external sources of information (i.e. not the authors' own new ideas or findings or general knowledge) should use a citation.
  • Authors should avoid citing derivations of original work. For example, they should cite the original work rather than a review article that cites an original work.
  • Authors should ensure that their citations are accurate (i.e. they should ensure the citation supports the statement made in their manuscript and should not misrepresent another work by citing it if it does not support the point the authors wish to make).
  • Authors should not cite sources that they have not read.
  • Authors should not preferentially cite their own or their friends’, peers’, or institution’s publications.
  • Authors should avoid citing work solely from one country.
  • Authors should not use an excessive number of citations to support one point.
  • Ideally, authors should cite sources that have undergone peer review where possible.
  • Authors should not cite advertisements or advertorial material.


How to format your references

Examples of the GigaScience reference style are shown below. Please ensure that the reference style is followed precisely; if the references are not in the correct style, they may need to be retyped and carefully proofread.

References

All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. The reference numbers must be finalized and the reference list fully formatted before submission. For further information including example references please read our reference preparation guidelines. 

Web links and URLs

All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: 

The PANGAEA Database. https://pangaea.de/. Accessed 15 Jan 2015. 

If an author or group of authors can clearly be associated with a web link (e.g. for blogs) they should be included in the reference.

Only articles and abstracts that have been published or are in press, or are available through public e-print/preprint servers, may be cited; unpublished abstracts, unpublished data and personal communications should not be included in the reference list, but may be included in the text and referred to as "unpublished observations" or "personal communications" giving the names of the involved researchers. Obtaining permission to quote personal communications and unpublished data from the cited colleagues is the responsibility of the author. 

Examples of the GigaScience reference style are shown below.

Example reference style:

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 Med. 2013;11:63.

Article within a journal by DOI
Slifka MK, Whitton JL. Clinical implications of dysregulated cytokine production. Dig J Mol Med. 2000; doi:10.1007/s801090000086.

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.

Preparing Figures

When preparing figures, please follow the formatting instructions below.

  • Figures should be provided as separate files, not embedded in the main manuscript file.
  • Each figure of a manuscript should be submitted as a single file that fits on a single page in portrait format.
  • Tables should NOT be submitted as figures but should be included in the main manuscript file.
  • Multi-panel figures (those with parts a, b, c, d etc.) should be submitted as a single composite file that contains all parts of the figure.
  • Figures should be numbered in the order they are first mentioned in the text, and uploaded in this order.
  • Figures should be uploaded in the correct orientation.
  • Figure titles (max 15 words) and legends (max 300 words) should be provided in the main manuscript, not in the graphic file.
  • Figure keys should be incorporated into the graphic, not into the legend of the figure.
  • Each figure should be closely cropped to minimize the amount of white space surrounding the illustration. Cropping figures improves accuracy when placing the figure in combination with other elements when the accepted manuscript is prepared for publication on our site. For more information on individual figure file formats, see our detailed instructions.
  • Individual figure files should not exceed 10 MB. If a suitable format is chosen, this file size is adequate for extremely high quality figures.
  • Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures (or tables) that have previously been published elsewhere. In order for all figures to be open access, authors must have permission from the rights holder if they wish to include images that have been published elsewhere in non-open access journals. Permission should be indicated in the figure legend, and the original source included in the reference list.

Figure file types

We accept the following file formats for figures:

  • EPS (suitable for diagrams and/or images)
  • PDF (suitable for diagrams and/or images)
  • Microsoft Word (suitable for diagrams and/or images, figures must be a single page)
  • PowerPoint (suitable for diagrams and/or images, figures must be a single page)
  • TIFF (suitable for images)
  • JPEG (suitable for photographic images, less suitable for graphical images)
  • PNG (suitable for images)
  • BMP (suitable for images)
  • CDX (ChemDraw - suitable for molecular structures)

For information and suggestions of suitable file formats for specific figure types, please see our author handbook.

Figure size and resolution

Figures are resized during publication of the final full text and PDF versions to conform to the GigaScience standard dimensions, which are detailed below.

Figures on the web:

  • width of 600 pixels (standard), 1200 pixels (high resolution).

Figures in the final PDF version:

  • width of 85 mm for half page width figure
  • width of 170 mm for full page width figure
  • maximum height of 225 mm for figure and legend
  • image resolution of approximately 300 dpi (dots per inch) at the final size

Figures should be designed such that all information, including text, is legible at these dimensions. All lines should be wider than 0.25 pt when constrained to standard figure widths. All fonts must be embedded.

Figure file compression

  • Vector figures should if possible be submitted as PDF files, which are usually more compact than EPS files.
  • TIFF files should be saved with LZW compression, which is lossless (decreases file size without decreasing quality) in order to minimize upload time.
  • JPEG files should be saved at maximum quality.
  • Conversion of images between file types (especially lossy formats such as JPEG) should be kept to a minimum to avoid degradation of quality.

Preparing Tables

When preparing tables, please follow the formatting instructions below.

  • Tables should be numbered and cited in the text in sequence using Arabic numerals (i.e. Table 1, Table 2 etc.).
  • Tables less than one A4 or Letter page in length can be placed in the appropriate location within the manuscript.
  • Tables larger than one A4 or Letter page in length can be placed at the end of the document text file. Please cite and indicate where the table should appear at the relevant location in the text file so that the table can be added in the correct place during production.
  • Larger datasets, or tables too wide for A4 or Letter landscape page can be uploaded as additional files. Please see [below] for more information.
  • Tabular data provided as additional files can be uploaded as an Excel spreadsheet (.xls ) or comma separated values (.csv). Please use the standard file extensions.
  • Table titles (max 15 words) should be included above the table, and legends (max 300 words) should be included underneath the table.
  • Tables should not be embedded as figures or spreadsheet files, but should be formatted using ‘Table object’ function in your word processing program.
  • Color and shading may not be used. Parts of the table can be highlighted using superscript, numbering, lettering, symbols or bold text, the meaning of which should be explained in a table legend.
  • Commas should not be used to indicate numerical values.

Preparing Additional Files

As the length and quantity of data is not restricted for many article types, authors can provide datasets, tables, movies, or other information as additional files.

All additional files will be published along with the accepted article. Do not include files such as patient consent forms, certificates of language editing, or revised versions of the main manuscript document with tracked changes. Such files, if requested, should be sent by email to the journal’s editorial email address, quoting the manuscript reference number. Please do not send patient consent forms unless requested.

Results that would otherwise be indicated as "data not shown" should be included as additional files. Since many web links and URLs rapidly become broken, Oxford University Press requires that supporting data are included as additional files, or deposited in a recognized repository. Please do not link to data on a personal/departmental website. Do not include any individual participant details. The maximum file size for additional files is 20 MB each, and files will be virus-scanned on submission. Each additional file should be cited in sequence within the main body of text.

If additional material is provided, please list the following information in a separate section of the manuscript text:

File name (e.g. Additional file 1)

File format including the correct file extension for example .pdf, .xls, .txt, .pptx (including name and a URL of an appropriate viewer if format is unusual)

Title of data

Description of data

Additional files should be named "Additional file 1" and so on and should be referenced explicitly by file name within the body of the article, e.g. 'An additional movie file shows this in more detail [see Additional file 1]'.

Preparing Supporting Information

Please make sure you have the following information available before you submit your manuscript:

Author information
Full names and email addresses of all co-authors on your manuscript.

Cover letter
A cover letter that includes the following information, as well as any additional information requested in the instructions for your specific article type (see main manuscript section above):

An explanation of why your manuscript should be published in GigaScience

An explanation of any issues relating to journal policies

A declaration of any potential competing interests

Confirmation that all authors have approved the manuscript for submission

Confirmation that the content of the manuscript has not been published, or submitted for publication elsewhere

If you are submitting a manuscript to a particular special issue, please refer to its specific name in your covering letter

Ethics

Authors should observe high standards with respect to publication ethics as set out by the Commission on Publication Ethics (COPE). Falsification or fabrication of data, plagiarism, including duplicate publication of the authors’ own work without proper citation, and misappropriation of the work are all unacceptable practices. Any cases of ethical misconduct are treated very seriously and will be dealt with in accordance with the COPE guidelines.

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