Technical Release Description

Reporting standards

GigaByte supports efforts promoting the use of reporting guidelines (see more in our editorial, FAIRsharing recommendations, and our Editorial Policies and Reporting Standards page).

Criteria

Technical Release articles are short structured reports presenting an open-source software tool or an experimental or computational method, test or procedure for the analysis or handling of research data. Web servers and database articles are also considered. The tool or method described may be new, or an update or adaptation of an existing one (GigaByte will shortly have a specific template for Update papers). For software, this includes new functionality, improvements in performance or its interface, or a release on a new platform. The tool or method should have undergone some testing, and this should be summarised in the report. It does not necessarily have to outperform existing approaches, but it should show innovation in the approach, implementation, or have added benefits that have been needed in this arena (e.g., easier, simpler, faster). Authors must clearly acknowledge work upon which they are building, both published and unpublished.

Detailed written documentation is not required in the report but should be included alongside the software and highlighted (e.g. as a detailed readme or readthedocs).

Availability of software to reviewers and other researchers

A distinctive characteristic of GigaByte is its focus on the availability of all supporting materials, high quality documentation and testing, the availability of test input and output data, and reproducibility. It is expected that reviewers, editors, and readers of the journal will be in a position to freely download and/or deploy tools and examine the source code, test the application on defined datasets, and reproduce all examples given in the text of the paper. Submissions that do not meet these requirements will be rejected without review.

In broad terms, the requirements for submission are that all supporting information, source code and test data of a clearly defined version are available in a recognised and appropriate repository (e.g. GitHub, DockerHub, CodeOcean, Galaxy, myExperiment, Bioinformatics.org).  Users must have the right to examine, compile, run and modify the code for any purpose. All software must therefore be provided under a license that is approved by the Open Source Initiative where practicable compiled running software is made available. See choosealicense.com for a useful resource for selecting a license. Examples of test data and expected outputs should be provided that enable readers to reproduce examples given in the paper. Documentation is expected to be consistent with best practice for the language and/or discipline, and highlighted in the paper. Upon acceptance, a snapshot of the version of code used in the manuscript can be hosted in GigaDB, Software Heritage or Zenodo to maintain reproducibility and integrated into the manuscript with a DOI.

Test datasets described in the manuscript must be available for our reviewers to assess along with the manuscript. This can be done either on your own website, an open repository or temporarily in the private data hosting region in our GigaDB repository.

If you wish to make a presubmission enquiry about the suitability of your manuscript, please email the editors at editorial@gigabytejournal.com who will respond to your enquiry as soon as possible.

Manuscript File formats

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

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

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 text when you put your manuscript together.

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 the following Overleaf template:

Technical Release Overleaf Template.

Data Access Requirements and Submission

Any test dataset(s) described in the Technical Release must be available for our reviewers to assess along with the manuscript. This can be done either on your own website, an open repository or temporarily in the private data hosting region in our GigaDB repository. If your manuscript is considered suitable for review, after an initial editorial assessment for scope and scale, a member of the GigaDB database team will contact you to help any associated data available to the reviewers.

GigaByte is able to host very large datasets of all types (there is no Data Processing Charge for datasets below 1TB. Contact the editors if you require more), including test input and output data. The journal provides a direct link from the published manuscripts to the journal’s affiliated database, GigaDB. On acceptance for publication, snapshots of the code and the datasets linked by GigaDB are given a DOI, which allows easy and more permanent access to the data, provides a format suitable for citing data in the reference section of future articles that use these data, and enables data tracking and credit*.

If your manuscript is considered suitable for review, after an initial editorial assessment for scope and scale, a member of the GigaScience database team will contact you to help make your data available to the reviewers.

At data submission, you need to include information about the data, not just submission of the data alone. For this, please provide our curators the following information about the data:

  1. A title that is specific to the data itself. (Typically such titles include a phrase like "The data for…").
  2. Abstract- a brief description of the dataset(s) included and their potential use for the scientific community.
  3. Author list for the dataset (This can differ from that of the submitted manuscript).
  4. Data types (e.g., sequence assembly, transcriptome, imaging, movies, etc.).
  5. Organism(s) and/or tissue(s) for each data type.
  6. Estimate of dataset size.
  7. Readme file: This file should contain information about the files (to be) hosted in a dataset, including any file naming convention used and the directory structure of any compressed archive (.tar) files. For more general information about Readme Files, the following links may be useful: http://en.wikipedia.org/wiki/README and http://www.wikihow.com/Write-a-Read-Me.
  8. Link(s) to any relevant data that is publicly available, or any related accession numbers in other repositories (Note that any data being submitted to GigaByte that has a community-approved data repository must also be submitted there. We will be happy to help you with this process.)
  9. Acknowledgements, if any, and be sure to include a list of grants and funding agencies and information on (URL links to) consortium or projects if there are any associated with these data.

Template Text 

Title and author information

This should list: the title of the article, which should include an accurate, clear and concise description of the reported work, avoiding abbreviations; and the full names, institutional addresses, e-mail addresses for all authors, and ORCID IDs. The contact/ corresponding author should also be indicated. It is suitable, should the authors of the work prefer to designate authorship as a Consortium or Project. In such a case, a contact author must still be provided, and a complete author list/institutions/emails/etc should be included in the author contribution section. The name of the software should ideally be included in the title of the manuscript.

Abstract

Recommended 150 words
The Abstract must succinctly describe the high-level functionality and purpose of the software for a diverse, non-specialist audience. At the end, please include an Availability & Implementation section; this must include the availability and licensing of the Technical Release presented, including links to any relevant code repository and website. Please minimize the use of abbreviations and do not cite references in the abstract. 

Research Area (choose one from list of 10)
Classifications (choose multiple from list of 90)

Statement of Need 

This illustrates the research purpose of the work and helps highlight and define the audience. The background and purpose of the work presented should be presented here for a non-specialist audience, If applicable, mention and cite any research that this work would help support.

Implementation

This should include a description of the overall architecture of the software implementation, along with details of any critical issues and how they were addressed, and should be presented in a reproducible manner. 

Information on how to reproduce results/figures described in the manuscript is very useful. If the study is built upon already published methods, the corresponding software should also be open and accessible to allow for reproducibility of the results described in the manuscript.

For papers presenting a database, you should include a brief description of the protocol for data collection, data curation and quality control, and what is being reported in the article. The user interface should be described and a discussion of the intended uses of the database, and the benefits that are envisioned, should be included, together with data on how its performance and functionality compared with functionally similar existing databases. A case study of the use of the database may be presented. The planned future development of new features, if any, should be mentioned.

Web server and workflow papers must add significant value to a simple command line execution of the underlying software, and include a simple mechanism to try out sample data. Web servers should operate through a well-designed graphical user interface, provide help pages or a tutorial, and work on common operating systems. 

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. 

Availability of supporting source code and requirements

List 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

This needs to be under an Open Source Initiative approved license where practicable compiled running software is made available in a code repository. 

Data Availability Statement

All authors must include a “Data Availability” statement in the endmatter of their manuscript detailing where the data supporting their findings can be found or stating "not applicable" in this section if no data needs to be declared. GigaByte requires authors to deposit the test data set(s) supporting the results reported in submitted manuscripts in a publicly-accessible data repository such as GigaDB (see submission details below and the 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). Any archived code snapshots should also be cited here. The following format is recommended:

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

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 the FAIRsharing website.

Declarations

List of abbreviations (if applicable)

If abbreviations are used in the text they should be defined in the text at first use, and a list of abbreviations should be provided in alphabetical order.

Ethics approval and consent to participate

Manuscripts reporting studies involving newly produced human or animal data must include a statement on ethics approval and consent including the name of the ethics committee that approved the study and reference number if appropriate. 

If your manuscript does not report on or involve the use of any animal or human data this section is not applicable to your submission. Please state “Not applicable” in this section.

Competing interests

All financial and non-financial competing interests must be declared in this section. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.

Authors' contributions

The individual contributions of authors to the manuscript should be specified in this section. Guidance and criteria for authorship can be found in our editorial. We would recommend you follow some kind of standardised taxonomy like the NISO/CASRAI CRediT (Contributor Roles Taxonomy).

Acknowledgements

Please acknowledge any financial support including the grant code, as well as anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section. If you do not have anyone to acknowledge, please write "Not applicable" in this section.

See our editorial for a full explanation of acknowledgements and authorship criteria.

Authors' information

You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.

Endnotes

Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.

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. GigaByte believes that data, software and protocols should be treated as legitimate, citable objects 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.

GigaScience follows the 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 following information: Creator (the authors or project that developed the software); Title (the name of the software); Publication venue (ideally an archive or repository); Date (when the software was published), Version (if unknown the date of access should be used); and Identifier (a president 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

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 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)
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013;2:10

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
Bloggs J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 2015. http://www.rsc.org/dose/title of subordinate document. Accessed 20 May 2015.

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

Supplementary material/private homepage
Bloggs J. Title of supplementary material. 2014. http://www.privatehomepage.com. Accessed 20 Sept 2015.

University site
Bloggs, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (2015). Accessed 15 Dec 2015.

FTP site

Bloggs, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (2015). Accessed 17 Jan 2015.

Organization site
ISSN International Centre: The ISSN register. http://www.issn.org (2006). Accessed 18 Jan 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.

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

See Information for Authors for information on how to format figures, tables and additional files.

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