Standard operating procedure
Standard operating procedures (SOPs) should follow a general format of title, overview and procedures used, and should categorize the type(s) of processes involved. SOPs should also describe the title, authors, institutions, origins, revision versions, dates and any underlying dependencies. SIGS encourages submission of details such as command-line arguments or other run-time parameters, and operational thresholds. The sequential procedure of computational and manual operations for data capture and calculation should describe the: 1) assumptions involved; 2) steps for reproducibility; 3) points at which the quality of the process and its output may be evaluated. SIGS encourages authors of genome reports to reference SOPs used for processing. SIGS aims to provide a repository of best practices in analyzing genomics data and transparency for methods used to produce data in genome reports. For more information, please read:
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008;12(2):137-41. (Pubmed, DOI)
Preparing your manuscript
A concise and meaningful title should convey to readers the nature of the article.
Title, Authors, Abstract, Introduction, Requirements, Procedure, Implementation, Discussion
The institutional affiliation(s) of each author should be identified with a superscripted number in the order of first appearance in the author list. Author affiliations should be numbered, using Vancouver style.
The author responsible for the submission and coordination of communication with the editorial office during peer review and with readers post publication should be identified along with their institutional email address. The editorial office will deal with only one corresponding author on a given manuscript.
Abstract (Heading 1)
Authors should provide a concise, non-redundant and meaningful abstract that describes the nature of the article. It should summarize the rationale, the objectives and the findings of the report and provide key details (e.g., relevant INSDC identifiers, culture collection identifiers, other project metadata that is accessible in standardized form).
Key words (Heading 1)
Authors should include five to seven descriptive keywords. These may include the name(s) of the organism(s) sequenced, the name of the next higher taxonomic rank, the sampling site and other significant details about the nature of the study.
Abbreviations (Heading 1)
Authors should include any non-standard abbreviations that are used throughout the article. Do not include well-known abbreviations (e.g., NCBI, EMBL, DNA, RNA) and do not use non-standard abbreviations for organism names. Species and subspecies names must be fully spelled out on first use as binomials (genus name and species epithet) or trinomials (genus name, species epithet subsp. subspecies epithet). Following first usage, the genus name may be abbreviated by using the first letter of the genus name, followed by a period and the epithets.
Main article body
In order to strike a balance between readability and level of detail, we provide guidelines for SOP documentation at two levels of detail. This distinction between levels occurs entirely within the Procedure section. Both documentation levels should describe a process so that a domain expert can understand the method and process flow. The Level 2 SOP provides additional detail required that would be required to replicate or implement the SOP.
Level 1 SOP:
A general description of the steps in a procedure including listing of software packages used, critical cutoffs, and important decision points. A description of the input and outputs from each step should be provided.
Level 2 SOP:
A detailed description of the procedure that allows for replication or implementation by a domain expert. This description should specifically name relevant software executables and parameters that are necessary for replication of the procedure by an operator of the SOP.
- The Introduction section should provide the goals and scope of the SOP. Related SOPs can also be referenced in this section
- Descriptions of software options should be limited to parameters and cutoffs that impact results, deviate from standard defaults, or are commonly customized as part of executing the SOP
- Troubleshooting information should be provided where appropriate following the relevant steps in the procedure section or more generally described in the Discussion.
- Technical references that are internal to an institution and not public should be excluded. Examples include intranet URLs, file system paths, and computer server names that are not publicly accessible on the Internet
- A description of the primary output or outputs, including file formats, should be included at the end of the Procedures section or as part of the Implementation section
- In some cases, an institution will have an SOP that is written and targeted entirely for institution staff rather than the general public
- These internal SOPs may contain information only relevant to institution staff, such as file system path or intranet URLs. Before submission to SIGs, we encourage institutions to revise SOPs intended for an internal audience so that are of general interest and are accessible to a wide audience.
All manuscripts must contain the following sections under the heading 'Declarations':
- Ethics approval and consent to participate
- Consent for publication
- Availability of data and material
- Competing interests
- Authors' contributions
- Authors' information (optional)
Please see below for details on the information to be included in these sections.
If any of the sections are not relevant to your manuscript, please include the heading and write 'Not applicable' for that section.
Ethics approval and consent to participate
Manuscripts reporting studies involving human participants, human data or human tissue must:
- include a statement on ethics approval and consent (even where the need for approval was waived)
- include the name of the ethics committee that approved the study and the committee’s reference number if appropriate
Studies involving animals must include a statement on ethics approval.
See our editorial policies for more information.
If your manuscript does not report on or involve the use of any animal or human data or tissue, please state “Not applicable” in this section.
Consent for publication
If your manuscript contains any individual person’s data in any form (including any individual details, images or videos), consent for publication must be obtained from that person, or in the case of children, their parent or legal guardian. All presentations of case reports must have consent for publication.
You can use your institutional consent form or our consent form if you prefer. You should not send the form to us on submission, but we may request to see a copy at any stage (including after publication).
See our editorial policies for more information on consent for publication.
If your manuscript does not contain data from any individual person, please state “Not applicable” in this section.
Availability of data and materials
All manuscripts must include an ‘Availability of data and materials’ statement. Data availability statements should include information on where data supporting the results reported in the article can be found including, where applicable, hyperlinks to publicly archived datasets analysed or generated during the study. By data we mean the minimal dataset that would be necessary to interpret, replicate and build upon the findings reported in the article. We recognise it is not always possible to share research data publicly, for instance when individual privacy could be compromised, and in such instances data availability should still be stated in the manuscript along with any conditions for access.
Data availability statements can take one of the following forms (or a combination of more than one if required for multiple datasets):
- The datasets generated and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS]
- The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
- All data generated or analysed during this study are included in this published article [and its supplementary information files].
- The datasets generated and/or analysed during the current study are not publicly available due [REASON WHY DATA ARE NOT PUBLIC] but are available from the corresponding author on reasonable request.
- Data sharing is not applicable to this article as no datasets were generated or analysed during the current study.
- The data that support the findings of this study are available from [third party name] but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of [third party name].
- Not applicable. If your manuscript does not contain any data, please state 'Not applicable' in this section.
More examples of template data availability statements, which include examples of openly available and restricted access datasets, are available here.
BioMed Central also requires that authors cite any publicly available data on which the conclusions of the paper rely in the manuscript. Data citations should include a persistent identifier (such as a DOI) and should ideally be included in the reference list. Citations of datasets, when they appear in the reference list, should include the minimum information recommended by DataCite and follow journal style. Dataset identifiers including DOIs should be expressed as full URLs. For example:
Hao Z, AghaKouchak A, Nakhjiri N, Farahmand A. Global integrated drought monitoring and prediction system (GIDMaPS) data sets. figshare. 2014. http://dx.doi.org/10.6084/m9.figshare.853801
With the corresponding text in the Availability of data and materials statement:
The datasets generated during and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS].[Reference number]
All financial and non-financial competing interests must be declared in this section.
See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.
Please use the authors initials to refer to each authors' competing interests in this section.
If you do not have any competing interests, please state "The authors declare that they have no competing interests" in this section.
All sources of funding for the research reported should be declared. The role of the funding body in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript should be declared.
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 policies.
Please use initials to refer to each author's contribution in this section, for example: "FC analyzed and interpreted the patient data regarding the hematological disease and the transplant. RH performed the histological examination of the kidney, and was a major contributor in writing the manuscript. All authors read and approved the final manuscript."
Please acknowledge 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.
See our editorial policies for a full explanation of acknowledgements and authorship criteria.
If you do not have anyone to acknowledge, please write "Not applicable" in this section.
Group authorship (for manuscripts involving a collaboration group): if you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records, please ensure that the title of the collaboration Group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “Acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.
Please note that individual names may not be present in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.
This section is optional.
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 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.
Examples of the Vancouver reference style are shown below.
See our editorial policies for author guidance on good citation practice
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 Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link, such as for weblogs, then they should be included in the reference.
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 Medicine. 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.
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.
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.
Doe, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (1999). Accessed 25 Dec 1999.
Doe, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (1999). Accessed 12 Nov 1999.
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.
Figures, tables and additional files
See General formatting guidelines for information on how to format figures, tables and additional files.
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