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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.nar.oxfordjournals.org/openaccess for more information.

From 2009 the NAR Web Server Issue will be published online only, and no print copies will be available for purchase.

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 perform useful computations on DNA, RNA and protein sequences or structures as well as servers for text mining and other aspects of biological data processing such as the analysis of microarray data sets and biological networks.
  • a summary of web servers produced by Francis Ouellette and his colleagues at the Ontario Institute for Cancer Research.

The 2009 Web Server Issue, in addition to topics generally related to DNA, RNA and Proteins will have a special emphasis on network and pathway analysis, biological text mining and metagenomics.

Submission

Authors wishing to submit manuscripts for the 2009 Web Server Issue MUST read and follow these instructions:

  • Authors must contact Dr. Gary Benson at narwbsrv@bu.edu to check the suitability of their proposed submission by 31 December, 2008 at the latest. A maximum one page summary of the web server function should be submitted for this purpose. Proposals sent in before 24 November 2008 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. Servers which require access through a separate application program will be rejected.
  • 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 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; names, affiliations, and emails of all authors; a notification if this is an update from a previous publication in the Web Server issue; literature references for previous descriptions of the method or the web server; descriptions of the input data, the output, and the processing method; and two to four keywords. Additionally, authors must indicate how long the server has been running, the number of input sequences analyzed during testing and an estimate of the number of individuals outside of the authors' group who have been involved in the testing.
  • 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.

Note that servers that merely 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. However, servers that interface with multiple databases that are not normally queried together will be considered.

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 2009, whichever is later. (Authors are encouraged to be patient. Proposal reviews take up most of January.)

  • Authors should submit their manuscript electronically through Manuscript Central (http://mc.manuscriptcentral.com/nar). In case of difficulty, queries should be addressed to nar@neb.com.
  • 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 hotlink 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 a description of the processing method or to the use of the server for some particular data analysis are not appropriate.
  • 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. A recommended way to organize any supplementary data is to include, within the main text of the printed article, a short table of its contents (one line per item). Each topic could then be expanded as appropriate within the supplement. Authors are encouraged to be innovative in their use of such supplementary data, taking advantage of the fact that electronic material, unlike printed material, need not be static. 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 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 2009 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 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. 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 the end of January. Reviews of manuscripts should be received by late March.

For further information please contact Dr Gary Benson at narwbsrv@bu.edu.