Submitting to the Web Server Issue

All articles published in NAR are made freely available online immediately upon publication, under an Open Access model partially funded by author charges. Please visit the Open Access Initiative page for more information. The NAR Web Server Issue is published online only, and no print copies are available for purchase.

Contents

Nucleic Acids Research devotes a single issue in July to papers describing web-based software resources of value to the biological community. The Web Server Issue contains papers describing software programs that run on the web and provide useful computations on DNA, RNA and protein sequences or structures; analysis of high throughput sequencing data and microarray data; metagenomic and microbiome analysis, network and pathway analysis; biological text mining; tools for synthetic biology; and innovative visualizations. In addition, there is a special section for Web Services. This category includes short papers describing websites that implement useful web services, i.e. automated analyses that are accessed programmatically rather than through manual interaction with a web server.

Stand-Alone applications for high-throughput data analysis are no longer covered by the Web Server Issue, please submit them as Standard articles to the ‘Computational Biology’ section.

Web Servers must:

• be functional on the date of the proposal submission. Access to the server must be through a web browser.
• use the HTTPS protocol and run on the http standard port (443).
• Must provide a cookie consent form when cookies are used.
• include a simple mechanism to try out sample data provided by the authors, for example, a button for automatic loading of the data. Sample data must be accessible to users so that they can confirm data formatting requirements.
• contain help pages and/or a tutorial with links to sample output that performs interactively in the same way as real output. The help pages must include information on how to interpret the results returned by the web server.
• keep every user's submitted data private and not viewable by anyone other than the user or those given permission by the user.
• provide a web link to the results if the website is not able to return results immediately. The link should be provided at the time of data submission and allow the user to bookmark and access the results later. Ideally, the link will report the status of the job (queued, running, or finished). Any request for an email must state that it is optional.
• provide a clear benefit over similar applications or over using R packages.
• provide rich data output (e.g. hyperlinks and visualisations).
• have a free access statement or a licence link on the landing page.

Web Servers must not:

• require users to log in, to register, or to leave an email address unless they handle sensitive human data (see below). Any registration must be optional e.g. for data sharing or access restriction to the user's own data.
• be restricted to a single (or few) species except for humans and common model organisms.
• require excessive data preprocessing with other tools (e.g. by creating Rdata frames) before it can be used.
• cover single steps in the middle of a pipeline.
• be new classifiers which do not produce rich output.
• be mere portals for download or visualisation of static data without the option to analyse user data.
• be updates/enhancements/copies of web servers which have been published within the last two years.
• use Flash and/or Java plugins due to security risks.
• use tracking cookies

Websites that use a guest login will not be approved.

Web Services must:

• provide a help page which contains a comprehensive list of the web services available along with a clear description and the access URL of each.
• provide a template script in python or another commonly used programming language, that can be run to access several of the web services and parse the output data. The goal is to give the user (and the reviewers) a working template for web services access. Ideally, the program should be easily modifiable so that it can be used for all the web services available.
• provide a prominent link to the template script on the home page.
• have a free access statement or a licence link on the landing page

Web Servers that handle sensitive human data (e.g. health records or genetic data) may require registration and login. In these cases, users must be able to register themselves without providing their email address. Registration must be handled automatically by the website. Access to non-human data must be possible without registration.

Submission

Authors wishing to submit manuscripts for the Web Server Issue MUST read and follow these instructions. See also the editorial from the 2017 issue and the NAR policy on software availability.

Authors must upload a one-page summary at http://nar.bihealth.de/ to check the suitability of their proposed submission by 20 December at the latest. Proposals sent in before 10 November will not be reviewed until after that date.

Proposals that are discouraged:

1. Servers that primarily aggregate data from several sources or assemble together existing third-party tools.
2. Servers that employ third-party software that has more restrictive usage terms than the "free and open to all…" statement.
3. Analysers of large data files, such as high-throughput sequencing data files.
4. Servers that produce primarily downloadable files without corresponding data visualisation in the browser.
5. Yes/No decision predictors, multi-state classifiers, or producers of numerical scores meant to inform classification, that lack additional useful supporting information or further analysis.
6. Web servers using new methods that have not been previously validated in a separate peer-reviewed publication or that have been published for less than a year.
7. New predictors based on machine learning unless the predictors have been validated in a separate peer-reviewed publication.

Note that servers that provide an interface into a single database will not normally be considered for this issue, but instead should be described as part of an article devoted to the database and submitted for consideration in the annual Database Issue.

For web servers, or essentially similar web servers, that have been the subject of a previous publication, including publication in journals other than NAR, there is a minimum two-year interval before re-publication in the Web Server Issue.

The ONE PAGE SUMMARY MUST:

• contain, at the top, one of the following affirmative statements:

1. "This website is free and open to all users and there is no login requirement."
2. "This website is free and open to all users. Upload and analysis of sensitive personal information requires a login."

• provide descriptions of the input data, the output, and the processing method; complete citations for previous publications of the method or the web server; and two to four keywords.
• include a notification if this is an update from a previous publication in the Web Server issue or elsewhere, and in that case, include an estimate of the number of users and the number of citations.
• include a notification if this is a resubmission of a proposal or a paper rejected in a previous year.

Additionally, any third-party software employed by the website that has more restrictive usage terms must be listed.

On the upload page, the following must be specified:

• website address.
• website name.
• names, affiliations, and email addresses of all authors.
• the Pubmed ID(s) of peer-reviewed manuscripts that describe the method (if applicable).
• the browsers and/or operating systems under which the software was tested.

Free access to the website will be checked during submission.

IF THE WEB SERVER IS PREDICTIVE, authors MUST include, within the summary, details on validation of predictions from new data not used in training. N-fold cross validation studies will not be considered sufficient. Details should include size and composition of the validation data set (number of positive and negative cases), and several measures of predictive performance, including sensitivity, specificity, and precision.

IF THE WEBSITE IMPLEMENTS A META-SERVER OR COMPUTATIONAL WORKFLOW, the summary MUST describe 1) significant added value beyond the simple chaining together of existing third party software or the calculation of a consensus prediction from third party predictors and classifiers; and at least one of the following: 2) how user time for data gathering and multi-step analysis is significantly reduced, or 3) how the website offers significantly enhanced display of the data and results.

IF THE WEB SERVER DEALS WITH PROTEIN STRUCTURE TOPICS, the summary MUST report performance on recent CASP experiments.

IF THE WEB SERVER DEALS WITH PROTEIN OR PEPTIDE DOCKING, the summary MUST report performance on recent CAPRI experiments.

IF THE WEB SERVER DEALS WITH PROTEIN FUNCTION PREDICTION, the summary MUST report performance on recent CAFA experiments

It is expected that the website will be maintained for at least five years.

Authors should restrict themselves to a maximum of three proposals.

Manuscripts

For proposals given approval, the manuscript submission deadline will be 3 weeks after the date of the approval email or 15 January, whichever is later. (Authors are encouraged to be patient. Proposal reviews take up most of January.) Manuscripts will undergo an initial round of editorial review before being sent to reviewers and may be rejected at that time if they are determined to be inappropriate for the journal. The deadlines for revision of manuscripts are tight, typically only two or three weeks are allowed.

• The manuscript MUST contain one of the following affirmative statements:

1. "This website is free and open to all users and there is no login requirement."
2. "This website is free and open to all users. Upload and analysis of sensitive personal information requires a login."  

• Authors should submit their manuscript electronically through ScholarOne Manuscripts. In case of difficulty, queries should be addressed to [email protected].
• All submissions to NAR must include at least one named author, who will serve as the corresponding author. If a paper was authored by a collaborator group, one author must be chosen as the corresponding author and will be listed as the author "on behalf of" the collaborator group
• Authors are encouraged to use the NAR Word and LaTeX templates. The manuscript text (including references, figure legends and simple tables) may be in .pdf, .doc, .rtf, or LaTeX format. For the initial submission a .pdf file is acceptable.
• In the submission form box titled Key Points, include up to three short sentences (bullet points) briefly describing the key features of the submission.
• As an additional file, include a graphical abstract (this is due only with the first manuscript revision, but may be included with the original manuscript). Follow this link for guidelines for graphical abstracts.
• At the time of manuscript submission authors MUST include a cover letter listing other websites that do similar or identical computations, along with their URLs.
• Authors must supply the names, institutes, and email addresses of six suggested referees. They should be scientists working independently (i.e. not a recent collaborator) who have relevant expertise or who would be likely users of the web server.
• Authors should try to use the name(s) of the software as the first word(s) in the title of the article and should include within the abstract a valid URL from which the software can be accessed. NAR is available in full-text form on the web, and each article will contain a link to its web server URL.
• The manuscript should include a description of the software including the required input, the range of computations it can perform, and examples of the output returned to the user. Comparison with existing methods should also be included. One or more use case studies should be presented to illustrate how the website can provide new biological insights. Submissions should typically be 4-5 printed journal pages in length, but authors are urged to be succinct in their writing, given the tight page constraints of this special issue.
• Manuscripts that contain only a cursory description of the web server and are instead mainly devoted to use of the server for some particular data analyses are not appropriate.
• Manuscripts that provide a first description of a new algorithmic method are generally inappropriate for the Web Server issue and should be submitted instead for consideration as a Computational Biology Standard paper.
• Authors should submit supplementary data if appropriate. Such material could include a description of the mathematics behind an algorithm used by the web server or a tutorial describing how the software should be used if it is non-intuitive. All supplementary data must be available at the time of submission, for editorial review, and the final material will be archived on the NAR web site.
• The software must be completely functional and have been extensively tested at the time of submission. Reviewers should not be expected to debug the software and significant problems that should have been picked up during testing will be grounds for rejection.
• References must be in the correct journal format and should be cited in the text by sequential number only, in order of appearance, and listed numerically in the References section. Manuscripts 'submitted' or 'in preparation', URLs, and personal communications should not be cited. Please note that references include the full titles of each paper. For more specific information, please consult the NAR web site.
• The references section must include active electronic DOI and PubMed Central links for each cited paper (where available). Please include a PubMed abstract link if the PMC link is not available. Programs to help insert the links into the references section are available.
• The home page for the software should not be used as a figure in the article unless an explanation of the page is required. A more appropriate figure would include the result of a typical computation.
• Authors whose native language is not English are encouraged to ask a native English speaker to check the text prior to submission. Follow this link for a list of English language service providers.
• For more specific information, please consult the general Instructions to Authors.

To help authors evaluate their manuscripts, the instructions to reviewers are included below:

When reviewing papers for the NAR Web Server Issue, please be aware of the following points:

• The purpose of this software issue is to provide a single location where potential users of web-based software can find out what is available and what the software actually does.
• While originality is not necessarily an issue, if software with similar functionality is available from other sources, then there must be something significant and new in this contribution. Comparison to existing methods should be included in the manuscript.
• A key consideration on acceptability will be whether the software described in the manuscript is useful and whether it works over the web as described. It is important that the package be tested thoroughly, preferably on at least two commonly used web browsers to make sure that it works as advertised and has an interface that is user-friendly.
• The software should provide analysis of wide interest. A program that is relevant to only a few individuals is unlikely to make it into the issue.
• Some web servers are predictive. In this case the manuscript must provide evidence of validation independent of any training data. Details should include size and composition of the validation data set (number of positive and negative cases), and several measures of predictive performance, such as sensitivity, specificity, precision, and any others that are appropriate.
• Some web servers are meta-servers or computational pipelines. In this case, the manuscript must describe 1) significant added value beyond the simple chaining together of existing third party software or the calculation of a consensus prediction from third party predictors and classifiers; and at least one of the following: 2) how user time for data gathering and multi-step analysis is significantly reduced or 3) how the website offers significantly enhanced display of the data and results.
• Some web servers deal with protein structure topics. In this case, the manuscript must report performance on recent relevant CASP experiments.
• Some web servers deal with protein and peptide docking. In this case, the manuscript must report performance on recent relevant CAPRI experiments.
• Some web servers deal with protein function prediction. In this case, the manuscript must report performance on recent relevant CAFA experiments.
• The software may have been described in an earlier publication. In this case, the paper should include the appropriate reference(s) and should contain a description of what is new and different. In such cases, brevity is essential.
• The author has stated that the website is free and open to all and that there is no login requirement (unless sensitive data is transmitted). Guest login must not be required. Additionally, while the website may request an email address, the address must be optional and not be required to obtain results. Please notify me in your review if this is not the case.
• Constructive comments that will lead to an improved manuscript or an improved piece of software on the web will be the most helpful. Most manuscripts describing a server that is significantly different from anything else available will be acceptable eventually, unless the piece of software does not work, gives erroneous results, or is simply of no practical use.

Schedule

The Web Server Issue receives several hundred proposals and manuscripts. Due to the crush around deadlines, authors should be patient about responses from the editor. Reply to proposals will typically be made by mid-February. Reviews of manuscripts should be received by mid-April.

For further information please contact Dr. Dominik Seelow at [email protected].