Cold Spring Harbor Protocols Bioinformatics and Computational Biology Instructions for Authors

To submit a protocol, please use the CSH Protocols online manuscript submission system. For presubmission inquiries, please e-mail the editor.

Please follow the instructions below when preparing your protocol for submission. These guidelines are intended to serve as a general template for writing Bioinformatics and Computational Biology Protocols, Information Panels, and Topic Introductions. Based on the nature of these subject areas, we wish to allow authors to retain flexibility in the presentation of this material. It is not necessary to include all sections in a submitted protocol. But as it is the goal of CSH Protocols to provide practical information to researchers in as clear and concise a manner as is possible, we ask that authors do not add additional sections.

In some instances, authors may feel it is preferable to submit bioinformatics protocols and approaches as other article types, such as Topic Introductions or Information Panels. We recommend that authors contact CSH Protocols by a presubmission inquiry to discuss these options prior to submitting any such manuscripts. All Protocols, Topic Introductions, and Information Panels will be peer-reviewed.

Please submit all text as Microsoft Word (.doc) documents.

Overall length: 2-8 printed pages, or 1000-4000 words. This does not include the Title, Author Information, Figure/Table Legends, Acknowledgments, or References.

Title: Titles should not exceed 20 words. Please include in titles any terms likely to enhance search results.

Author Information: Full author name(s) and affiliation(s). The corresponding author should supply a valid e-mail address, which will appear within the protocol.

Introduction: Approximately 150-200 words; should be a brief summary of the technique's principles and scope. The Introduction will be deposited into Medline as the Abstract; therefore, citations to other work should not be included in this section. Additional information may be included in the Discussion.

Related Information: Indicate other Protocols, Topic Introductions, and Information Panels to which the protocol should be linked. See below for a description of each file type; include each additional file separately with your submission. References to other publications that would normally appear in the abstract—such as those from which the protocol is derived—may also be placed here.

Background: This section should present an overview of the biological questions that the Protocol is meant to address. Also appropriate here is a brief historical synopsis of the technique(s) in the protocol, and authors are encouraged to include display items such as Figures that broadly illustrate the goals of the technique(s). We ask authors to keep in mind that the intent of a Protocol is to serve more as a user’s guide than as a comprehensive summary. The Background section should therefore not exceed 1,000 words nor contain more than two subheadings. Comparisons of alternative protocols should not be present in the Background, but are appropriate for the Discussion.

Materials: Authors should specify the computing resources and equipment (hardware and software) required by the technique as well as indicate what type of networking (if any) is necessary. Materials should be listed in alphabetical order. It is appropriate (and desirable) to include URLs in this section, such as those linking to sites for download of bioinformatics tools, but we strongly prefer that these links correspond to relatively "permanent" sites that are unlikely to become quickly outdated.

Method: Briefly describe, in linear and numbered sequence, the precise instructions to perform the action(s) required. Divide the procedure with subheadings (fewer than eight words) corresponding to major stages of the process. The numbering of steps should be continuous from one stage to the next. Each step is limited to one paragraph.

•Include notes to steps for critical information. The text of each note should be italicized and inserted below the step to which it refers.

•Include screenshots and output samples as Figures or Tables, if appropriate.

•Note references to the Parameters section (below).

Include alternatives to performing specific steps (optional). Where two or more alternatives exist, they should be numbered as sets of consecutive steps, and a brief statement outlining each alternative should be incorporated. For example: choose procedure A (Steps 1-10) or procedure B (Steps 11-20), then continue with Step 21 and so on.

Parameters: The Parameters section is roughly equivalent to the Troubleshooting section of a standard protocol. Authors should indicate what variables exist and how they may be used to refine the results of a given bioinformatics approach. As in the Method, screenshots and output samples as Figures or Tables may be included, and examples should be cross-referenced to other sections where appropriate.

Discussion: Address advantages, limitations, and special considerations of the technique. Discuss use for various applications in comparison to alternative techniques and/or provide specific examples (if applicable) and cross-reference to the appropriate section(s). Limit the Discussion to 1,000 words, and include citations where appropriate.

Acknowledgments: Include any acknowledgments here, as briefly as possible.

References: Include key reviews and/or a hypothesis-driven paper in which the technique has been used. Brief citations in the text should correspond to full references in the list.

Figures: Figures that illustrate the technique, example results, etc. are welcome, but should be limited to no more than five with accompanying legends. Indicate whether a figure is critical to performing the experiment; it will then be included in the protocol at the appropriate step. If a figure is more informational in nature, then please indicate that it can be included as a "call-out" that links to a pop-up window display. In either case, figures will be printed with the printer-friendly version of the protocol. If possible, include a flow-chart diagram that illustrates the procedure or a figure that illustrates its application (see Digital Art Guidelines for acceptable file formats).

Tables: Small tables that are critical to the Method section should be included within the protocol steps. (All tables must be created using MS Word's table format, which can be found from MS Word's Table pull-down menu. Do not "tab over" to align columns visually, giving the appearance of a table.) Informational tables providing background or alternative material that may pertain to one or more protocols should be included as Information Panels and linked to and from the Related Information section and/or a link from within the appropriate step.

Movies: In the Related Information section, indicate that a movie is available, and include the movie's title and/or give a description. The movie may also be cited at the appropriate protocol step, if desired.

Other Article Types:

Topic Introduction: This material usually pertains to more than one protocol and provides general and background information, theory, and applications about the technique(s) to which it is linked. Please reference Topic Introductions in the Related Information section(s) of relevant protocols (if any) and provide these documents as separate MS Word files. Topic Introductions should have an Introduction section that will serve as the abstract, and they may also contain figures, tables, and movies.

Information Panels: These articles provide functional and/or practical information about a particular topic that is in a protocol, but they do not contain either information that is critical to performing the method or historical, encyclopedic-type background details. Please reference Information Panels in the Related Information section(s) of relevant protocols (if any) and provide these documents as separate MS Word files. Information Panels should have an Introduction section that will serve as the abstract, and they may also contain figures, tables, and movies.