Information For Authors

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@gigabytejournal.com.

All associated data and other research objects should be submitted to the GigaDB curation team. The manuscript submission system includes a section specifically for data. To prepare your data in advance to speed completion of article submission and assessment see Instructions For Data Submission.   

Submission through Overleaf

For creating manuscripts in LaTeX, GigaByte recommends the use of its own LaTeX class files. Our class files are available online at Overleaf and also as a downloadable package via the links below. Please replace and remove the template content when you create the manuscript.

Overleaf is a free, collaborative online LaTeX editor that allows you to write your manuscript in a TeX or rich text environment, to generate PDF outputs as you write, and to share your manuscript with co-authors and collaborators. When ready for submission, the manuscript files can be downloaded from Overleaf and submitted to the journal’s online submission system. Please use either of the following Overleaf templates for the specific article types below:

Data Release Overleaf Template

Technical Release Overleaf Template.

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 file formats are acceptable for the main manuscript document:

  • Microsoft word (DOC, DOCX)
  • TeX/LaTeX
  • PDF

Please note: GigaByte has a pure XML workflow and can only currently convert from word and LaTex files. If your manuscript contains any non-editable files (such as PDFs) you will be required to re-submit an editable/convertible 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.

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. 

Data and Materials

GigaByte 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). See also Instructions For Data Submission.

The Data and Materials 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 FAIRsharing.

GigaByte 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. 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.
  • RRID: if applicable, e.g. RRID: SCR_014986

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.

GigaScience also follows the Software Citation Principles, and recommendations of the FORCE11 Software Citation Implementation Working Group. Software citation elevates software to the level of a first-class object in the digital scholarly ecosystem, consistent with its immense significance. The software should be cited in the references and include the version (if unknown the date of access should be used) and identifier (a persistent identifier like a DOI or a URL to where the software exists). If an article exists that describes the software, it should be cited as an additional reference, as well as citing the software itself.

For more see: Katz, D. S., et al., (2020) Recognizing the value of software: a software citation guide. F1000 Research. https://doi.org/10.12688/f1000research.26932.2

For machine learning papers, please also include the model and information to re-run it, such as computational resources and time taken to train it. 

For any article that presents software, in addition to making the source code available, we encourage submission to Code Ocean, a cloud-based computational reproducibility platform. Code Ocean supports any open-source programming language (as well as MATLAB and Stata). Authors should upload their code and data, specifying the appropriate languages and dependencies within the computational environment, to create a “compute capsule” that reproduces the results.

Once the code is published on Code Ocean, you will be issued DOI, which should be used to cite the compute capsule in the software section and any other relevant reference in the paper. Readers will then be able to view and verify the article’s results without needing to download or install anything. To submit, sign up here https://codeocean.com/signup.

GigaByte encourages and assists with the submission of detailed protocols to the open access repository protocols.io. Please enter the details into protocols.io, issue a DOI, and cite the protocols.io record from the Methods section. Protocols.io now includes the ability to put in bioinformatics protocols in addition to wetlab protocols. (See https://www.youtube.com/watch?v=BJONcAC21-A)

Authors benefit greatly by posting their methods in protocols.io as these are presented in a formatted form, allow inclusion of all the details, are fully searchable unlike supplementary files, and can be updated to new versions as basic methodology changes over time. Doing this saves authors extensive time in the future as the methods do not need to be rewritten in future manuscripts as they need only be cited. Please register any new software application in the SciCrunch.org database to receive a RRID (Research Resource Identification Initiative ID) number, and include this in your manuscript. This will facilitate tracking, reproducibility and re-use of your tool.

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, and Software Citation Guide. We strongly recommend the use of community preprint servers such as arXiv, bioRxiv,medRxiv, and OSF 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 work discussed in the manuscript ideally should be deposited and cited from preprint servers, but authors can include citations to papers in-press so long as those papers are not essential for validation or understanding the manuscript submitted here. A typical reason to cite papers in press would be for highlighting the rationale or presenting a use case for the data or tools submitted here. Effectively: the data or software needs to be able to be reviewed as a stand-alone. 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' and curators 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.
  • It is preferable that authors cite sources that have undergone peer review where possible.
  • Authors should not cite advertisements or advertorial material.
  • Authors should cite any software in the references, and if an article exists that describes the software, it should be cited as an additional reference.

How to format your references

Examples of the GigaByte 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 2020. 

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 GigaByte 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.

Online First 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
Joe D. 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 2010.

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.

Software without persistent identifier but with version and identifier (URL)
SAMtools (2020). SAMtools (Version 1.1)
https://github.com/samtools/samtools/releases/tag/1.11

Software with persistent identifier
Piccolo S, Hill K, Suh E, Dayton J. (2019, November 15). srp33/ShinyLearner: Gigascience (Version 1). Zenodo. http://doi.org/10.5281/zenodo.3543724

Protocol with persistent identifier
Mofiz E, Holt D, Seemann T, Currie BJ, Fischer K, Papenfuss AT. Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment. protocols.io. 2016 http://dx.doi.org/10.17504/protocols.io.exwbfpe.

Code Ocean integration with persistent identifier
Geib SM, Hall B, Derego T et al. Genome Annotation Generator NCBI for submission [Source Code] [Database]. CodeOcean. 2018; https://doi.org/10.24433/CO.fceb0521-a26d-441f-9fe0-bccc6a250fc9.

Certificate of executable computation with persistent identifier
Eglen SJ. (2020, February 18). CODECHECK Certificate 2020-001. Zenodo. http://doi.org/10.5281/zenodo.3674056

Preparing Figures

When preparing figures, please follow the formatting instructions below.

  • Files should contain all relevant informations in the front matter such as:
    • Full title of the article
    • Running title (Short title)
    • Author name(s) with complete affiliations 
    • Corresponding author details (emails, correspondence address)
  • Equations should be submitted in MathType or Microsoft equation (NOT as figures), if manuscript is submitted in Microsoft Word.
  • Tables should NOT be submitted as figures but should be included in the main manuscript file.
  • Each figure should be submitted as a single file that fits on a single page in portrait format.
  • Multi-panel figures (with parts such as a, b, c, d etc.) should be submitted as a single composite file that contains all parts of the figure.
  • The figures should be named/numbered and supplied as per the order they are first mentioned in the text.
  • Figure resolution should be adequate for high quality production.
  • Copyright permission on figures/tables should be obtained by the author from the copyright holder to reproduce in the article, if they have been previously published elsewhere. Permission must be obtained from the rights holder by the author if the author wishes to include any image from a non-open access journals to be open access and the permissions must be indicated in the figure legends. 
  • All cited references in the text should be listed in the references section and vice versa, and should contain all the available details in the reference.

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)
  • SVG (suitable for diagrams)
  • TIFF (suitable for images)
  • JPEG (suitable for photographic images, less suitable for illustrations)
  • PNG (suitable for images)
  • BMP (suitable for images)
  • PSD (Photoshop)
  • AI (Adobe Illustrator)

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 should be formatted using ‘Table object’ function in your word processing program.
  • 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.
  • 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. , 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.

Preparing Supplementary Information

GigaByte does not accept PDF supplementary files. Data from Supplementary Information will be included in GigaDB. Supplementary Text, with some exceptions, should either be included in the main text as part of the main document, or included as an Appendix section in the main article. The editors and reviewers will provide guidance in cases of uncertainty of how additional text should be handled. (See Instruction for Data Submission for how to provide supplementary information in a usable format and what text files are suitable for inclusion in GigaDB)

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 in GigaDB or deposited in a recognized repository. Since many web links and URLs rapidly become broken, please do not include links to data on a personal/departmental website. 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.

File format including the correct file extension for example .pdf, .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 GigaByte
An explanation of any issues relating to journal policies
A declaration of any potential competing interests
Details on preprint versions of the submitted work
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

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.