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Submitting to the Web Server Issue

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Since 2005 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 http://www.oxfordjournals.org/our_journals/nar/announce_openaccess.html 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; network and pathway analysis; biological text mining; analysis of high throughput sequencing data, metagenomics data and microarray data; tools for synthetic biology; and innovative visualizations.

Special Categories for 2014

Most articles in the Web Server issue describe access to tools through a web browser. However, there are two special sections for Web Services and stand-alone programs for high-throughput data analysis.

Web Services. This category includes short papers describing websites that implement useful web services, that is, multiple task, automated analyses that are accessed programmatically rather than through manual interaction with a web server. To be considered, a website must:

  • Implement a large collection of web services. These services may be for general bioinformatics use, or focused on a single data domain, such as microarray data.
  • 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 program in python, perl, 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 of the web services available.
  • Provide a prominent link to the template program on the home page.

High-Throughput Data Analysis. This section includes papers describing stand-alone (non-web server) programs that analyze very high volume experimental data (typically in excess of 500 Mb), such as that produced by the new sequencing technologies. To be considered, a program must:

  • Operate through a well-designed graphical user interface, similar to that of a web browser, which can be used to access the local data, select the parameters, run the program, and store and view the results. The program MUST add value to a simple command line execution of the underlying software.
  • Include extensive help information.
  • Run properly on a computer which is not connected to the internet (since many laboratory computers holding sensitive data may be off the internet to satisfy legal requirements).
  • Run properly on at least two of the three common operating systems (Linux, Mac, and PC).
  • Be self-installing, that is, have a well tested, "one click"-type installation.

For stand alone-programs, virtual machines will not be accepted.

Submission

Authors wishing to submit manuscripts for the 2014 Web Server Issue MUST read and follow these instructions. See also the editorial from the 2013 issue.

  • Authors must contact Dr. Gary Benson at narwbsrv@bu.edu to check the suitability of their proposed submission by 31 December, 2013 at the latest. A summary (maximum one page) should be submitted for this purpose. Proposals sent in before 30 November 2013 will not be reviewed until after that date.
  • The WEB SERVER MUST BE FUNCTIONAL on the date of the proposal submission. Access to the server must be through a web browser. Non-server application programs will only be considered for high-throughput data (see above).
  • The website MUST include a simple mechanism to try out sample data provided by the authors, for example, a button for automatic loading of the data.
  • The website MUST contain help pages 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.
  • The output MUST be primarily web-based and viewable on the website. Use of browser plugins for data visualization is encouraged.
  • If the website is not able to return results immediately, it MUST provide a web link to the results, at the time of data submission, which the user can then bookmark and access at a later time. Ideally, this link will report the status of the job (queued, running, or finished). Do not assume that users will provide an email address for results notification. Any request for an email must state that it is optional. Websites that use a guest login will not be approved.
  • Every user’s submitted data MUST be private and not viewable by anyone other than the user or those given permission by the user.
  • The one page summary MUST contain, at the top, the following affirmative statement. "This website is free and open to all users and there is no login requirement."
  • The one page summary MUST include the website address; website name; and the names, affiliations, and email addresses of all authors.
  • The one page summary MUST 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. Additionally, authors must indicate how long the server has been running, the number of inputs analyzed during testing, and an estimate of the number of individuals outside of the authors' group who have been involved in the testing.
  • The one page summary MUST include a notification if this is an update from a previous publication in the Web Server issue, and in that case, include an estimate of the number of users and the number of citations.
  • The one page summary MUST include a notification if this is a resubmission of a proposal or a paper rejected in a previous year.
  • 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 WEB SERVER DEALS WITH PROTEIN STRUCTURE TOPICS (structure prediction, binding site prediction, etc.) the one page summary MUST report performance on recent CASP experiments.
  • It is expected that the website will be maintained for at least five years.

In general, proposals should describe web servers that are novel. Proposals for tasks that are already handled by many servers are unlikely to be accepted. The following types of proposals are discouraged: 1) meta-servers, which combine the output of programs not developed by the proposal authors, 2) servers that aggregate data from several sources, 3) pipelines, unless they primarily link methods developed by the authors, 4) analyzers of large data files, such as next-generation sequencing data files, unless submitted as a stand-alone program, 5) servers that produce primarily downloadable files without corresponding data visualization in the browser, 6) simple yes/no decision predictors or classifiers that lack additional useful supporting information or further analysis, and 7) new methods that have not been previously validated in a separate 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.

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 31 January 2014, 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.

  • Authors should submit their manuscript electronically through ScholarOne Manuscripts (http://mc.manuscriptcentral.com/nar). In case of difficulty, queries should be addressed to nar@soton.ac.uk
  • The manuscript MUST be uploaded as a .doc, .rtf, or .tex file. It must NOT be uploaded as a .pdf file.
  • 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 (http://nar.oxfordjournals.org), 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. 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 analysis 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 paper.
  • The online version of the Web Server Issue will afford authors the opportunity to provide readers with 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, unpublished results 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 are available upon request to help insert the links into the references section.
  • 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.
  • 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.
  • A key consideration on acceptability will be whether the software described in the manuscript is useful and whether it actually 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.
  • 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. Guest login should 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 Gary Benson at narwbsrv@bu.edu.