This guide is also available in pdf format. Do contact the Editorial Office (protocols@nature.com) if anything is unclear.

Manuscript Tracking System

Please use our Manuscript Tracking System to submit your protocol. Specific links for submitting your protocol are supplied in e-mails from the Editors.

General submission guidelines

Unless we are notified otherwise in a cover letter on submission, submission to Nature Protocols is taken to imply that there is no significant overlap between the submitted protocol and any other protocols from the same authors under consideration or in press elsewhere.

Submission is also taken to imply that all coauthors have approved the contents of the protocol and its submission by the corresponding author, and that the corresponding author is authorized to represent all coauthors in pre-publication discussions with the journal. (The corresponding author for editorial purposes need not be the senior author, nor the person to whom correspondence is addressed after publication.) The primary affiliation for each author should be the institution where the majority of their work was done. If an author has subsequently moved, the current address may also be stated.

A high priority of Nature Protocols is that all protocols be accessible to nonspecialists. The commissioned protocols are subject to substantial editing to achieve this goal. After acceptance, a copy editor will make further changes to ensure that the text and figures are readable and clear to those outside the field and that papers conform to our style. Contributors are sent proofs and are welcome to discuss proposed changes with the editors, but Nature Protocols reserves the right to make the final decision about matters of style and the size of figures. Commissioned protocols will typically undergo peer review, thus commissioning does not guarantee publication. The editors also reserve the right to retract a protocol, even after it has been accepted, if it becomes apparent that there are serious problems with the scientific content or with violations of our publishing policies.

Protocol format

We recommend that the authors of commissioned protocols follow these guidelines wherever possible to facilitate the refereeing and editorial process. The Editorial Office welcomes feedback regarding the practicality of these guidelines and the format in general, as Nature Protocols is a new product and we are keen for it to be as amenable as possible to researchers.

As we use Microsoft Word in the Editorial office, this is our preferred format for text; however, we can also accept plain ASCII text (.txt).

Title

The title should succinctly describe the method and, if appropriate, its application. It should be no longer than 30 words.

Authors

Include those who have contributed intellectually and practically to the development of the technique. For all authors please include first name, middle initial (if appropriate), last names, postal address and e-mail address. Also include the telephone number and fax number for the corresponding author. If appropriate, a link to a lab home page or staff information page can also be included for appropriate authors.

Abstract/Summary

Include a summary of the protocol (maximum 150 words), briefly describing the protocol and its applications. The suggested format is to include one or two sentences summarising the protocol; then to explain more specifically the stages of the protocol, and if appropriate, how these compare with other protocols; and then to include one or two sentences describing the results that can be expected. If possible, include a final sentence indicating how long the whole protocol takes.

Introduction (use heading ‘INTRODUCTION’)

The purpose of the introduction is to enable readers to make a decision as to the suitability of the protocol to their experimental problem. Initially you should introduce the technique under discussion. You should also discuss the diversity of applications of the protocol, whilst making the limitations of the present technique clear. Where applicable, reference should be made to alternative methods that are commonly used to achieve the result of the protocol. If you think that the protocol could be adapted for use in a wider range of applications than presented you should discuss this. For protocols describing the preparation of organic molecules, a scheme showing the sequence of reactions should be included. Use subheadings where appropriate. Include reference to key papers where the protocol has been used previously or to reviews that discuss applications of the protocol (see below for how to cite references). You are actively encouraged, where appropriate, to reference other protocols in Nature Protocols.

Materials (use heading ‘MATERIALS’)

Include a list of the essential materials, split into reagents (use heading ‘REAGENTS’) and equipment (use heading ‘EQUIPMENT’). This should include the recipes for buffers and the suppliers used for reagents. If you have found that deviations from a particular reagent, or its source, have adverse effects on the outcome of the protocol this should be made clear by the word ‘CRITICAL’ followed by, if necessary, a brief explanation. Toxic or harmful agents should be made clear by the word ‘CAUTION’ followed by, if necessary, a brief explanation. Please also highlight any specialist equipment required. The information you provide about the sources of reagents and equipment will enable us to link your protocol to Nature Product Finder to help users obtain the equipment and materials they need. Please provide as much information as you can to help us successfully identify the product, e.g. company name, company website, product code. If you need to include detailed information about specific reagents or equipment, please list in additional, optional, sections, called ‘REAGENT SETUP’ and ‘EQUIPMENT SETUP’. These sections are suitable for details of composition of buffers or the setup of equipment.

Step by step methodology (use heading ‘PROCEDURE’)

This is the major part of the protocol. Include as a numbered list, ideally with numbers in bold; do not follow the numbers with a period (full stop). Use the active tense rather than the passive tense, for example, “Pipette 20ml of buffer A into the flask”. If the protocol naturally breaks into separate stages, then include subheadings and resume the numbered list. This is particularly appropriate if there are stages in the protocol where the procedure can be stopped (pause point), e.g. overnight. Any pause points should be indicated with the heading ‘PAUSE POINT’, followed by a brief description of the options available, for example “Can be left overnight at 4_oC or frozen for up to a month at -20_oC”.

Highlight critical steps in the protocol that must be included for success, and provide user hints to maximise the likelihood of success. Make these clear with the heading ‘CRITICAL STEP’, followed by a brief explanation.

Highlight any toxic or harmful chemicals that are used so appropriate cautionary information can be linked. Make these clear by preceding them with the wording ‘CAUTION’ prior to their first mention.

Include diagrams of equipment set-up, where appropriate. If the protocol is complicated you should consider including a flow diagram to demonstrate how the stages fit together.

Include information on how to troubleshoot the most likely problems users will encounter with the protocol. Please provide this information in the form of a table with the columns ‘problem’, ‘possible reason’, ‘solution’ with problematic steps flagged in the main text by the heading ‘TROUBLESHOOTING’. Include figures where appropriate.

Where there are alternative routes to reach the next stage of the protocol, please break down the appropriate steps using i), ii), etc. For example:

1. This step can be performed using option A or option B.
1. First option
1. First part
2. Second part, etc.
2. Second option
1. First part
2. Second part, etc.

Timing (use heading ‘TIMING’)

If possible, please include a timeline indicating the approximate time a step, or set of steps, will take e.g. Steps 1–3, 30 min.; Steps 6+7, 2 h. Provide this information as a summary at the end of the procedure, as a list. If you think it would be more user friendly you could refer to time needed for each section or detail what needs to be performed on each day of the protocol.

Anticipated results (use heading ‘ANTICIPATED RESULTS’)

Include information about, or examples of, the likely outcome to users, for example, likely yield of protein, typical microscopy images, etc.

References (use heading ‘REFERENCES’)

List all references mentioned in the protocol. References are numbered sequentially as they appear in the text, tables and figure legends. Use superscript numbers to indicate a reference, for example 1. Only one publication is given for each number, and footnotes are not used. Only papers that have been published or accepted by a named publication should be in the numbered list; meeting abstracts and papers in preparation should be mentioned in the text with a list of authors (or initials if any of the authors are co-authors of the present contribution). Published conference abstracts and URLs for web sites should be cited parenthetically in the text, not in the reference list; articles in formal, peer-reviewed online journals should be included in the reference list. Grant details and acknowledgments are not permitted as numbered references.

All authors should be included in reference lists unless there are more than five, in which case only the first author should be given, followed by 'et al.'. Authors should be listed last name first, followed by a comma and initials of given names. Titles of cited articles are required and should be in Roman text and titles of books in italics; the first word of the title is capitalized, the title written exactly as it appears in the work cited, ending with a period. Journal names are italicized and abbreviated (with periods) according to common usage; refer to the National Library of Medicine for details. Volume numbers appear in bold. For book citations, the publisher and city of publication are required (e.g. John Wiley & Sons, Hoboken, New Jersey, USA, 2003).

List all references mentioned in the protocol. Use the format given in the examples below:

1. Helms, C. et al. A putative RUNX1 binding site variant between SLC9A3R1 and RAT9 is associated with susceptibility to psoriasis. Nat. Genet. 35, 349-356 (2003).
2. Lovett, M. Direct selection of cDNAs with large genomic DNA clones. In Molecular Cloning: A Laboratory Manual Edn. 3 Vol. 2 (eds. Sambrook., J. & Russell, D.W.) 11.98-11.133 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).

Nomenclature

Authors should use approved nomenclature for gene symbols. The full name should be provided at first mention, the gene symbol in brackets i.e. titin (Ttn). Thereafter, the gene symbol should be used. Please consult the appropriate nomenclature databases for correct gene names, symbols and formatting. A useful resource is LocusLink. Approved human gene symbols are provided by HUGO Gene Nomenclature Committee (HGNC), e-mail: nome@galton.ucl.ac.uk. Approved mouse symbols are provided by The Jackson Laboratory, e-mail: nomen@informatics.jax.org. Another useful site is the Gene Ontology Project.

Avoid listing multiple names of genes (or proteins) separated by a slash, as in 'Oct4/Pou5f1', as this is ambiguous (it could mean a ratio, a complex, alternative names or different subunits). Use one name throughout and include the other at first mention: 'Pou5f1 (also known as Oct4)'.

Guides for Digital Images

Images submitted with a manuscript for review should be minimally processed (for instance, to add arrows to a micrograph). Authors should retain their unprocessed data and metadata files, as editors may request them. If unprocessed data are unavailable, manuscript evaluation may be stalled until the issue is resolved. All digitized images submitted with the final revision of the manuscript must be of high quality and have resolutions of at least 300 dpi.

A certain degree of image processing is acceptable for publication (and for some experiments, fields and techniques is unavoidable), but the final image must correctly represent the original data and conform to community standards. The guidelines below will aid in accurate data presentation at the image processing level; authors must also take care to exercise prudence during data acquisition, where misrepresentation must equally be avoided. Figure legends should include the pertinent instrument settings, acquisition conditions and processing changes, as described in this guide.

1. Authors should list all image acquisition tools and image processing software packages used.
2. Authors should document key image-gathering settings and processing manipulations.
3. Images gathered at different times or from different locations should not be combined into a single image, unless it is stated that the resultant image is a product of time-averaged data or a time-lapse sequence. If juxtaposing images is essential, the borders should be clearly demarcated in the figure and described in the legend.
4. The use of touch-up tools, such as cloning and healing tools in Photoshop, or any feature that deliberately obscures manipulations, is to be avoided.
5. Processing (such as changing brightness and contrast) is appropriate only when it is applied equally across the entire image and is applied equally to controls. Contrast should not be adjusted so that data disappear. Excessive manipulations, such as processing to emphasize one region in the image at the expense of others (for example, through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control.
6. When submitting revised final figures upon conditional acceptance, authors may be asked to submit original, unprocessed images.

Electrophoretic gels and blots

Positive and negative controls, as well as molecular size markers, should be included on each gel and blot - either in the main figure or an expanded data supplementary figure. A citation must be provided for antibodies.

The display of cropped gels and blots in the main paper is encouraged if it improves the clarity and conciseness of the presentation. In such cases, the cropping must be mentioned in the figure legend and the supplementary information should include full-length gels and blots wherever possible. These uncropped images should be labeled as in the main text and placed in a single supplementary figure. The manuscript's figure legends should state that "full-length blots/gels are presented in Supplemental Figure X."

• Vertically sliced gels that juxtapose lanes that were not contiguous in the experiment must have a clear separation or a black line delineating the boundary between the gels.
• Cropped gels in the paper must retain important bands.
• Cropped blots in the body of the paper should retain at least six band widths above and below the band.
• High-contrast gels and blots are discouraged, as overexposure may mask additional bands. Authors should strive for exposures with gray backgrounds. Multiple exposures should be presented in supplementary information if high contrast is unavoidable. Immunoblots should be surrounded by a black line to indicate the borders of the blot, if the background is faint.
• For quantitative comparisons, appropriate reagents, controls and imaging methods with linear signal ranges should be used.

Microscopy

Authors should be prepared to supply the editors with original data upon request, at the resolution collected, from which their images were generated. Cells from multiple fields should not be juxtaposed in a single field; instead multiple supporting fields of cells should be shown as supplementary information.

Specific guidelines: Adjustments should be applied to the entire image. Threshold manipulation, expansion or contraction of signal ranges and the altering of high signals should be avoided. If 'Pseudo-coloring' and nonlinear adjustment (for example 'gamma changes') are used, this must be disclosed. Adjustments of individual color channels are sometimes necessary on 'merged' images, but this should be noted in the figure legend.

We encourage inclusion of the following with the final revised version of the manuscript for publication:

• In the Materials, specify the type of equipment (microscopes/objective lenses, cameras, detectors, filter model and batch number) and acquisition software used. Although we appreciate that there is some variation between instruments, equipment settings for critical measurements should also be listed.
• The following should be included in each figure legend: acquisition information, including time and space resolution data (xyzt and pixel dimensions); image bit depth; experimental conditions such as temperature and imaging medium; and fluorochromes (excitation and emission wavelengths or ranges, filters, dichroic beamsplitters, if any).
• The display lookup table (LUT) and the quantitative map between the LUT and the bitmap should be provided, especially when rainbow pseudocolor is used. If the LUT is linear and covers the full range of the data, that should be stated.
• Processing software should be named and manipulations indicated (such as type of deconvolution, 3D reconstructions, surface and volume rendering, 'gamma changes', filtering, thresholding and projection).

Authors should state the measured resolution at which an image was acquired and any downstream processing or averaging that enhances the resolution of the image.

Submission of Figures, Tables, and other additional protocol components

Tables

Please submit tables in Word format at the end of your text document, or as a separate file. Tables should be created using the Microsoft Word table editor, where possible.

Figure format for initial submission

All figures should be uploaded upon submission via our online submission system, in one of our preferred formats [see below]. On initial submission all panels of a figure or table (e.g., Fig. 1a, b and c) should be combined into one file; please do not send as separate files. Please include a brief title and legend (preferably incorporated into the image file to appear near the image) as part of every electronic figure submitted, and a title as part of every table. Please ensure that both axes of all graphs are labelled appropriately.

When a paper is accepted, we might request high-resolution files suitable for publication. Thus, please bear in mind our guidelines for the figures for accepted manuscripts [see below] when preparing your figures, so that it is easier to provide publication-standard figures when they are required.

Figure appearance and layout

Whilst Nature Protocols is an online only product, many users will print your protocol prior to use. Thus figures should be sized to be legible to users and to facilitate printing. Unnecessary figures and parts (panels) of figures and tables should be avoided. Figures should not contain more than one panel unless the parts are logically connected; each panel of a multipart figure should be sized so that the whole figure can be reduced by the same amount and reproduced on the printed page at the smallest size at which essential details are visible. When a protocol is accepted for publication, we might ask for high-resolution figure files, possibly in a different electronic format. This information will be included in the acceptance letter.

Lettering on figures should be in a clear, sans-serif typeface (for example, Helvetica); if possible, the same typeface and approximate font size (no smaller than 7 point) should be used for all figures in a paper. Use symbol font for Greek letters. Figures should be on a white background, and should avoid excessive boxing, unnecessary color, spurious decorative effects (such as three-dimensional 'skyscraper' histograms) and highly pixelated computer drawings. The vertical axis of histograms should not be truncated to exaggerate small differences. Labelling must be of sufficient size and contrast to be readable after appropriate size reduction. The thinnest lines in the final figure should be no smaller than 0.5 point wide. Authors will see a proof of figures. Reasonable requests to enlarge figures will be considered, but editors will make the final decision on figure size.

Figures divided into parts should be labelled with a lower-case, bold a, b, and so on, in the same typesize as used elsewhere in the figure. Lettering in figures should be in lower-case type, with only the first letter of each label capitalized. Units should have a single space between the number and the unit, and follow SI nomenclature (for example, ms rather than msec) or the nomenclature common to a particular field. Thousands should be separated by commas (1,000). Unusual units or abbreviations should be spelled out in full or defined in the legend. Scale bars should be used rather than magnification factors, with the length of the bar defined in the legend rather than on the bar itself. In general, please use visual cues rather than verbal explanations, such as "open red triangles", in the legend.

Figure format

Image types

Images fall into two basic categories: photographic or scanned images, and graphs and schematic diagrams. Rasterized formats are best for photographs, scans, and composite figures containing photographic or scanned images with minimal or relatively simple labelling, whereas line or vector formats are best for graphs and schematic diagrams, and for composite figures containing a mixture of photographs or scans and detailed text or line artwork. The best format for any particular figure therefore depends partly on what kind of images it contains.

Electronic image formats

A wide variety of software is available to generate and manipulate images, and a huge range of graphics file formats exist. Rasterized (or bitmapped) formats such as TIFF are composed of an array of dots (pixels). The quality is determined by the resolution, usually measured in dots per inch (dpi; also referred to as 'pixels per inch'). For adequate reproduction we need a minimum of 300 dpi at the size the image is to appear. Size and resolution are linked so that, for example, enlarging an image to twice its original size will halve the resolution. If the resolution is too low, individual pixels become visible to the eye, the edges of lines begin to appear 'stepped' and the image may look blurred or pixelated.

Line (or vector) formats such as Postscript, EPS and PDF preserve individual lines and text as separate, editable components. This makes them easier and quicker to reletter or edit as necessary, reducing the chance of errors, and gives sharper results in print and online. Also, because these images have no 'resolution' as such, they may be enlarged without any reduction in quality.

Preferred formats

Adobe Photoshop (layered .psd file only) or TIFF format (high resolution, minimum 300 dpi) for photographic images.

Adobe Illustrator, Postscript, EPS or PDF format for figures containing line drawings and graphs, including figures combining text and line art with photographs or scans. If these formats are not possible, we can also accept Microsoft Word, Microsoft Excel, Microsoft PowerPoint or JPEG (high-resultion, 300 dpi, as separate files (not embedded in your text file):

Please do not send figures prepared in the following formats, as we cannot use them: Canvas, Freehand, CorelDraw

Movies and audio files

We welcome you to submit appropriate movies or audio files, if these would be useful for our users. Movies could include examples of the results obtained, or footage of researchers performing critical parts of the protocol. Please use QuickTime movie (.mov) or Flash movie (.swf) format for movies, or audio files (.wav).

Notes on particular formats

In Photoshop, please send the Photoshop file (.psd) with the layers intact. Individual components of the figure cannot be edited on flattened Photoshop files.

Although PowerPoint can export JPEGs, the resulting files are low resolution and not suitable for printing. The only way to obtain a high-quality graphics format from Microsoft Office applications is to generate Postscript using 'Print to file'.

JPEG is a compressed format, which achieves smaller file sizes by discarding information. As a result, saving in JPEG format may cause a noticeable reduction in quality, so we prefer Photoshop or TIFF format for rasterized images. When JPEG is the only option available, the quality should be set to the highest possible to minimize loss of information.

TIFF files are larger than JPEGs, but it is possible to reduce the file size by saving with compression (LZW compression is preferred), which does not degrade the quality of the image. Alternatively, compression software such as DropStuff or ZipIt can be used to reduce the file sizes.

How to send files

Because we may have difficulties with your digital files, it is important to send them to us on disks with the final version of your manuscript. Figures may be sent on Zip disk, Jaz disk, or CD. We have an FTP site, if you wish to use this, please let us know so we can send you further details. Wherever possible, we prefer to use original digital figures to ensure the highest quality reproduction. We do ask that you always send two sets of high-quality printouts of your figures along with your accepted manuscript in the event that we cannot use your digital files.

Other requirements

Authors are responsible for obtaining before publication permissions for tables, figures, images or movies previously published elsewhere, direct quotes of ?200 words or scattered quotes from a single source of ?400 words in total. Citations of personal communications must be authorized by the correspondent involved, with signed permission to cite being sent to the editorial office by mail or fax. This is also relevant to figures that have been altered in any way. Please note that it is courteous to inform the author of the original material of your intent to use their published work, in addition to contacting the copyright holder.

Copyright

Authors of manuscripts accepted for publication will be sent a copyright transfer form, please contact us if you need further information at this stage.

Self archiving

Authors are able to self-archive the author version of their accepted manuscript six months after publication. By “author’s version” we are referring to Word or Tex files produced by the author, not a PDF or HTML downloaded from nature.com. The article will have been developmentally edited and peer reviewed, but it will not have been copyedited into the final published version. This policy has been developed to meet the needs of authors and the evolving policies of funding agencies that may wish to archive the research they fund. It is also designed to protect the integrity of the scientific record, with the published version clearly identified as the definitive version of the article.

Abbreviation

The correct abbreviation for abstracting and indexing purposes is Nat. Protocols.

ISSN

The international standard serial number (ISSN) for Nature Protocols is ISSN 1750-2799.

Human and Animal subjects

For protocols that use live vertebrates or higher invertebrates, authors must include mention that all experiments should be performed in accordance with relevant guidelines and regulations. For manuscripts reporting experiments on human subjects, authors must also include a statement confirming that informed consent must be obtained from all subjects. These statements should appear as CAUTIONS. Referees may be asked to comment specifically on any cases in which concerns arise.

Competing financial interests

In the interests of transparency and to help readers form their own judgements about possible bias, the Nature journals now require authors of primary and secondary research articles to declare any competing financial interests relating to papers accepted for publication. A detailed explanation of why this policy has been adopted can be found at the end of the statement. The policy applies to all protocols published in Nature Protocols.

Authors are required, before final acceptance of their contribution, to return a declaration of competing financial interests. If appropriate, this is published as part of the protocol. Authors may use the form to decline to disclose their financial interests, but we will publish the fact that they have declined to provide information.

The declaration form will be sent to the corresponding author only at the time of acceptance and the corresponding author is asked to reply on behalf of all the authors.

Definition

For the purposes of this statement, competing interests are defined as those of a financial nature that, through their potential influence on behaviour or content or from perception of such potential influences, could undermine the objectivity, integrity or perceived value of a publication.

They may include any of the following:

• Funding: research support (including salaries, equipment, supplies, reimbursement for attending symposia, and other expenses) by organizations that may gain or lose financially through publication of the protocol.
• Employment: recent (while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through publication of the protocol.
• Personal financial interests: stocks or shares in companies that may gain or lose financially through publication; consultation fees or other forms of remuneration from organizations that may gain or lose financially; patents or patent applications whose value may be affected by publication.

It is difficult to specify a threshold at which a financial interest becomes significant, but note that many US universities require faculty members to disclose interests exceeding $10,000 or 5% equity in a company (see, for example, B. Lo et al. New Engl. J. Med. 343, 1616-1620; 2000). Any such figure is necessarily arbitrary, so we offer as one possible practical alternative guideline: "Any undeclared competing financial interests that could embarrass you were they to become publicly known after your work was published."

We do not consider diversified mutual funds or investment trusts to constitute a competing financial interest.

Application to authors

Unless/until the protocol is published, authors' declarations will be considered confidential, and will not be disclosed to referees.

The published protocol indicates the authors' response using one of the following standard wordings:

• The authors declare that they have no competing financial interests.
• The authors declare competing financial interests (see the HTML version of this article for details).
• The authors decline to provide information about competing financial interests.
• The authors declare that their competing financial interests in this work are too numerous to itemize.
• The authors are bound by confidentiality agreements that prevent them from disclosing their financial interests in this work.

For contributions with more than one author, the corresponding author (the person responsible for communication with the journal) should provide a declaration on behalf of all authors.

We recognize that a comprehensive declaration could become unwieldy if a protocol has too many authors or an author has numerous financial interests. If this is the case and itemized disclosure is unfeasible, editors may invite authors to use the following standard wording as an alternative: "The authors declare that their competing financial interests in this work are too numerous to itemize."

We also recognize that some authors may be bound by confidentiality agreements. In such cases the authors may be invited to use the following standard wording as an alternative to itemized disclosure: "The authors declare that they are bound by confidentiality agreements that prevent them from disclosing their financial interests in this work".

We do not require authors to state the monetary value of their financial interests.

Application to referees

We invite referees to exclude themselves in cases where there is a significant conflict of interest, financial or otherwise. However, just as financial interests need not invalidate the usefulness of a protocol, nor do they automatically disqualify a referee from evaluating it. Referees are asked to inform the editors of any related interests, including financial interests as defined above, which might be perceived as relevant. Editors will consider these statements when weighing referees' recommendations.

Application to editors

All editorial staff are required to declare to their employer any interests —financial or otherwise—that might influence, or be perceived to influence, their editorial practices. Failure to do so is a disciplinary offence.

Application to publishing policy

All of the Nature Publishing Group (NPG) journals thrive on their independence. Their strict policy is that editorial independence, decisions and content should not be compromised by commercial or financial interests, or by any specific arrangements with advertising clients or sponsors. Our policy is to disclose such arrangements where there is any risk of a perception of compromise on this issue. Please see a list of all sponsors associated with Nature Publishing Group at http://npg.nature.com/npg/servlet/Content?data=xml/10_clients.xml&style=xml/10_clients.xsl.

Reasons for policy

The introduction of this policy is based on recognition of potential problems for three principal reasons.

• First, there is suggestive evidence in the literature that publication practices in biomedical research have been influenced by the commercial interests of authors. Several related discussions that contain the relevant references can be found in the Journal of the American Medical Association, 1 November 2000 (for example, A D DeAngelis Conflict of interest and the public trust. J. Am. Med. Assoc. 284, 2237-2238; 2000; see also Nature Neuroscience 3, 299; 2000). This evidence is consistent with the truism that, although, in principle, science may be objective and its findings independent of other interests, scientists can be imperfect and subjective. There are circumstances where selection of evidence, interpretation of results or emphasis of presentation might be inadvertently or even deliberately biased by a researcher's other interests.
• Second, there is a more general concern among researchers and others about the possible undermining of the integrity of scientific research by increasing commercial links and consequent influences. We believe that the best way to maintain readers' trust in the integrity of the research we publish is through a policy of transparency. If financial interests are disclosed, readers will be able to make an informed judgment about their significance or lack of significance. We believe this will be to the benefit of readers and authors alike.
• Third, many institutions have introduced policies on competing interests that require authors to include descriptions of financial and other interests in publications. We are happy to support them.

We do not expect to police this policy ourselves: we believe that primary responsibility for ensuring that researchers' conduct is appropriate lies with their employers, rather than with journal editors. However, where we believe trust has been significantly compromised by an author's actions, we will seek to redress the matter by an appropriate combination of sanctions and communications to readers and employers.

We welcome comments and suggestions about this policy, which should be sent to nature@nature.com, marked "Competing interests policy".
Dr Philip Campbell
Editor, Nature
Editor-in-Chief, Nature publications

Availability of materials and data

An inherent principle of publication is that others should be able to replicate and build upon the authors' published protocols. Therefore, a condition of publication in Nature Protocols is that materials, data and associated protocols must be available to readers. Any restrictions on the availability of materials or information must be disclosed at the time of submission of the manuscript, and the materials section of the manuscript itself should include details of how materials and information may be obtained, including any restrictions that may apply. One preferred form of disclosure is a link from the materials section to a copy of the relevant Material Transfer Agreement (MTA) form, which will be hosted as supplementary information on the journal's web site. Authors may charge a reasonable fee to cover the costs of producing and distributing materials. If materials are to be distributed by a for-profit company, this should be stated.

For materials such as mutant and genetically modified organisms and cells, authors are expected to use established public repositories (for example, Jackson Laboratory, Mutant Mouse Regional Resource Centers, American Type Culture Collection, UK Stem Cell Bank, and so on) wherever possible.

Referees may be asked to comment on the terms of access to materials, methods and/or datasets, and we reserve the right to refuse publication in cases where authors are unable to provide adequate assurances that essential resources will be made freely available to the community.

Policy on biosecurity issues

Editors may seek advice about submitted protocols not only from technical referees but also on any aspect that raises concerns. These may include, for example, ethical issues. Very occasionally, concerns may also relate to the societal implications of publishing a protocol, including threats to security. In such circumstances, advice will usually be sought simultaneously with the refereeing process. As in all publishing decisions, the ultimate decision whether to publish is the responsibility of the editor of the journal concerned.

The threat posed by bioweapons raises the unusual need to assess the balance of risk and benefit in publication. Editors are not necessarily well qualified to make such judgements unassisted, and so we reserve the right to take expert advice in cases where we believe that concerns may arise. We recognize the widespread view that openness in science helps to alert society to potential threats and to defend against them, and we anticipate that only very rarely (if at all) will the risks be perceived as outweighing the benefits of publishing a protocol that has otherwise been deemed appropriate for Nature Protocols. Nevertheless, we think it appropriate to consider such risks and to have a formal policy for dealing with them if need arises.

The editorial staff of Nature journals maintain a network of advisers on biosecurity issues. All concerns on that score, including the commissioning of external advice, will be shared within an editorial monitoring group consisting of the Editor-in-Chief of Nature publications, the Executive Editor of the Nature research journals, the Chief Biological Sciences Editor of Nature, and the chief editor of the journal concerned.

Once a decision has been reached, authors will be informed if biosecurity advice has informed that decision.

Refutations and Complaints

We recognize our responsibility to correct errors that we have previously published. Our policy is to consider refutations of protocols, and to publish them (in concise form) if and only if the author provides compelling evidence that a major claim of the original protocol was incorrect. Refutations are peer-reviewed, and where possible they are sent to the same referees who reviewed the original paper. A copy is normally also sent to the corresponding author of the original paper for signed comments. Complaints, disagreements over interpretation and other matters arising should be addressed to the editor. Editorial decisions in such cases are based on considerations of reader interest, novelty of arguments, integrity of the publication record and fairness to the parties involved. Publication may take various forms (Correspondence, Corrigendum from the original author, Statement by Editors, etc), and the right of reply is at the discretion of the editor.

Corrections

Errata: errors introduced by the journal during editing or production and for which the journal takes responsibility. Our policy is to correct such errors in cases where they distort the scientific meaning or the bibliographic record, or where they have significant potential to damage the reputation of the authors, the journal and/or third parties.

Corrigenda: errors introduced by authors, for which they take responsibility. Our policy is to allow authors to correct such errors in cases where they distort the scientific meaning or the bibliographic record, or where they have significant potential to damage the reputation of the journal or third parties.

Addenda: additional information from authors that, while not correcting a specific error, nevertheless alters the interpretation of a paper. Publication of addenda is at the discretion of the editor.

Authors should note that publication online represents definitive publication. Authors should therefore make every effort to check for errors in their proofs before the paper is published online.

Supplementary information online is subject to the same policies as the main article. In order to maintain the integrity of the publication record, corrections must be accompanied by an erratum, corrigendum or addendum.

More detailed information on our corrections policy is available here.