Instructions to Authors 

Articles. Articles are full length (max. 5000 words, with 5 page equivalents of figures and tables) and peer-reviewed reports presenting original research on novel biological methods and techniques or significant modifications to existing protocols. An article has the following major sections: abstract, introduction, materials and methods, results, discussion and references.

Protocols. Protocols are step-by-step guide and instructions to a new technique or a commonly used technique with significant modification for improvement. Protocols can also cover existing techniques for which prior protocols have not been published. To be considered for publication in Theoretical Biology Forum, Protocols need to bring a significant added value to their respective biological or biomedical fields. Protocols presenting very succinct procedures, minor variations/additions to previously published protocols or a combination of previously documented procedures that do not represent a substantial innovation or bring obvious benefits will generally not be considered. Protocols are peer-reviewed and contain the following major sections: abstract, background, materials, procedure, anticipated results, troubleshooting and references.

Benchmarks. Benchmarks present studies designed to objectively compare two or more methods with original data and discuss their pros and cons.

Resources. Resources present information on innovative and useful online tools, services and databases that hold broad appeal for the community at large.

Reviews. Reviews are peer-reviewed articles that aim to provide a timely, comprehensive and insightful overview of a particular technique or techniques for the study of a particular aspect of biology.

Application Notes. Application notes are product specific technical guides which are of general interest to readers of the Journal. This type of articles is considered as advertisements and will not be submitted to indexing service.

Commentaries. Commentaries have a flexible format, mainly to provide a personal perspective on a published manuscript or a topic of scientific importance. They should be of interest to a broader readership and be written in layman’s terms. The length is typically 1-2 printed pages. Commentaries are usually commissioned by the journal. Authors who wish to submit an unsolicited commentary should contact the editorial office.

General Guidelines for Formatting Manuscripts

Manuscripts must be written in clear and concise English and be in accordance with the following length and formatting guidelines. The Editors reserve the right to return manuscripts that are not in accordance with the guidelines.

Text

The Editorial Office currently only accepts text files in MS Word format. Please submit the full text (including figures and their accompanying legends, tables, and references) as a single MS Word file.

Manuscripts should be presented in the following order: (i) Title page, (ii) Abstract and Key words, (iii) Main text, (iv) Acknowledgments, (v) References, (vi) Figure and Figure legends, (vii) Tables (with title and footnotes if any). Footnotes to the text are not allowed and such materials should be incorporated into the text. For the convenience of the reviewers, figures should be embedded in MS Word file and their legends should appear immediately below their corresponding figures.

Title page Title page should contain (i) the title of the paper. Title should be short, informative and contain major key words of the manuscript. Abbreviations should be avoided in the title. ii) the full names of the authors, (iii) authors’ affiliations. (iv) full postal and email address of corresponding author(s), (v) a short running title (less than 40 characters), (vi) abbreviations used.

Abstract and Keywords Abstract should be a single paragraph not exceeding 250 words. Abbreviations should be avoided where possible. Reference citations within the abstract are not permitted. The abstract should describe all key novel findings of the study (Research Articles) or key concept and steps (Protocols). Up to five keywords should be given in alphabetical order, below the abstract, each separated by a comma.

Graphical abstract For accepted papers in the section of “Articles” “Protocols”, “Resources” and “Benchmarks”, a graphical abstract summarizing the method or protocol of the article in a concise and pictorial form should be provided. The image must clearly represent the work described in the article and should be submitted upon acceptance of the article. The image should be 600 (w) × 400 (h) pixels in size and have a resolution of no more than 150 pixels/inch (ppi) or dpi. Lettering in the image should use Arial font with a size of 12-16 points. Preferred file type is JPEG.

Figures

Figures and supplementary figures should be presented in the order they are mentioned in the text. All figures should be cited in consecutive order in consecutive Arabic numerals in the text (such as Figure 1, Figure 2 and 3, Figure 3A and 3B, Figure 2A-2C). When figures are cited in parenthesis, figures name should be shortened as Fig. (such as Fig. 1).

The final dimensions of figures will be between 82 mm and 172 mm wide on the printed page. Figures divided into panels should be labeled with an upper-case, bold letter (Helvetica or Arial Font, such as A, B, C). Multi-panel figures should be composed as one single image and be in proportion, with consistently sized lettering so that the whole figure can be proportionally scaled down to the smallest size possible at which the essential details are visible.

For initial submission, apart from embedded in MS Word file (see “Text” above), figures should also be submitted as separate TIFF files with a resolution of at least 300 dpi.

Figure legends

Figure legends should start with a caption for each figure followed by a brief description of the methods for conducting the experiments and the data presented in the figure. When a figure contains multiple panels, each panel should be mentioned as A., B., C., etc.

Tables

Tables should be typed on separate pages and numbered consecutively with Arabic numerals (Table 1, Table 2, etc.). Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables indicated by lower-case superscript letters are acceptable, but extensive experimental details should be avoided. Tables should be cited in the text as Table 1, Table 1-3, etc.

Mathematics and Equations

Mathematical characters and equations should be prepared using MS Word’s Equation Editor or MathType version 6.0 or higher (available from Design Science, Inc.).

References

Only articles that have been published or that are accepted for publication at a named publication should be cited in the reference list. The Vancouver system (also known as “author-number” system) of referencing should be used. References should be numbered consecutively in order of appearance in the text in square brackets. If cited in tables or figure legends, number according to the first identification of the table or figure in the text. Reference to unpublished data and personal communications should not appear in the list but should be cited in the text only (e.g., Smith A, 2000, unpublished data). Names of journals should be abbreviated in the style used in PubMed. Authors are responsible for the accuracy of the references.

The number of cited references should not exceed the limit specified for each type of manuscripts (see section specific guidelines).

Authors are not required to provide doi or Pubmed ID numbers for cited references.

If EndNote program is used for formatting references, please use the PLoS-Public Library of Science Style which can be downloaded from this link from the EndNote web site: http://endnote.com/styles/PLoS.ens

Examples of reference listing:

Journal articles

  1. Ting AH, Schuebel KE, Herman JG, Baylin SB (2005) Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 37: 906-910.
  2. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, et al. (2012) Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol 13: R48.

Books

  1. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia: University of Pennsylvania Press. 435 p.

Book Chapters

  1. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21-28.

Websites

Website citations should be formatted to include the following components: name of the web page or entire site, the organization creating or owning the site, date of the site is cited, and the URL to the page or site. For example:

  1. MethPrimer. Li Lab, Department of Urology, University of California San Francisco. Cited on May 30, 2012. Available from: http://www.urogene.org/methprimer

Supplementary Information

Supplementary information is peer-reviewed material directly relevant to the conclusions of an article that cannot be included in the printed version owing to space or format constraints. Supplementary information should enhance, but not be essential to, a reader’s understanding of the paper and may consist of additional text, materials, figures, tables and movies.

Supplementary information should be combined into a single PDF file except for large Excel tables (see below) and movies (see above). This PDF file should be labeled “Supplementary Information” and should start with a title page containing the title of the paper, authors, a table of content that provides a clear and easy access to the sections of supplementary information, as cited in the main text.

All supplementary figures and supplementary tables should be cited as “Figure S1”, “Figure S2”, “Table S1”, “Table S2”, etc., throughout the text. Each figure legend should be typed beneath its figure.

Large supplementary tables (more than 50 rows) can be submitted as MS Excel spreadsheet documents (.xls or .xlsx).

A list of supplementary data with a brief legend for each piece of data (e.g., supplementary materials, figures, tables, movies, etc.) should be included at the end of the main manuscript.

File sizes must be as small as possible. In general, a supplementary information file should not exceed 20 MB.

Supplementary information is not copy-edited, so authors should ensure that it is supplied ready for publication. It cannot be modified, nor new supplementary information added, after the paper has been accepted for publication.

Section Specific Guidelines for Formatting Manuscripts

Research Articles

Research Articles are full length (max. 5000 words, up to 6 display items including figures and tables) and peer-reviewed reports presenting original research on novel biological methods and techniques or significant modifications to existing protocols. An article has the following major sections: Abstract, Introduction, Materials and Methods, Results, Discussion and References (max.30 references).

Protocols

Protocols are step-by-step guide and instructions to a new technique or a commonly used technique with significant modification for improvement. Protocols can also cover existing techniques for which prior protocols have not been published. To be considered for publication in Theoretical Biology Forum, Protocols need to bring a significant added value to their respective biological or biomedical fields. Protocols presenting very succinct procedures, minor variations/additions to previously published protocols or a combination of previously documented procedures that do not represent a substantial innovation or bring obvious benefits will generally not be considered. Protocols are peer-reviewed and contain the following major sections: abstract, background, materials, procedure, anticipated results, troubleshooting and references (max. 20 references).

Protocols should be formatted to include the following sections (where applicable):

Background: Background serves as an introduction to the protocol with brief history for the development of the protocol, the theory and principle behind the methodology and applications of the protocol. Figures depicting protocol principle, diagram or flowchart are encouraged.

Materials: Materials section should in general include the following three components.

  • REAGENTS: List all reagents used in the protocol with the vendor name, vendor location and preferably a catalog number.
  • RECIPES: List the recipes of solutions used in the protocol. Purchased ready-to-use solutions and recipes do not need to be listed.
  • EQUIPMENT: List major equipment used with the accompanying vendor name, vendor location and preferably a catalog number.

Procedure: Procedure can be divided into major sections with a heading for each section (such as cell culture, chromatin cross linking, chromatin isolation, etc.) and each step numbered below. Numbers should be contiguous throughout the procedure. For example, the first heading may include steps 1-4 and the second heading steps 5-7.

Under each step or section, the following headings may be included where needed:

  • TIPS/HINTS: Provide any tips or hints that will be helpful for readers to follow the protocol.
  • CAUTION: Draw attention to any steps where mistakes or problems can occur.
  • NOTES: Anything else the readers should be aware of.
  • CRITICAL STEP: Draw attention to important steps.

Anticipated results: Describe yield and other outcome that can be regularly achieved by following the protocol. Examples of typical results in the forms of figures, images or tables can be presented.

Troubleshooting: List commonly encountered problems, caveats and solution if known for any step of the protocol. Troubleshooting should preferably listed in a table with the following 4 columns: (1) Step # (referring to the step in protocol), (2) Problem (describing potential problems), (3) Cause (causes of the problems) and (4) suggestions (measures to prevent and correct the problem).

RESOURCES

Resources are full length (max. 3000 words, up to 4 display items including figures and tables) and peer-reviewed reports presenting information on innovative and useful online tools, services and databases that hold broad appeal for the community at large.

Resources reporting online tools/services should include the following sections: Abstract, Highlight/Feature, Introduction, Implementation, Troubleshooting or Debugging, Discussion and References (maximum of 20 references).

Resources reporting databases should include the following major sections: Abstract, Introduction, Data generation, Utility and Discussion, and References (max. 20 references).

Benchmarks

Benchmarks are full length (max. 4000 words, up to 4 display items including figures and tables) and peer-reviewed reports presenting studies designed to objectively compare two or more methods with original data and discuss their pros and cons. A benchmark article has the following major sections: Abstract, Introduction, Materials and Methods, Results, Discussion and References (max. 30 references).

Reviews

Reviews are peer-reviewed articles that aim to provide a timely, comprehensive and insightful overview of a particular technique or techniques for the study of a particular aspect of biology. The main text should be about 5,000 words. References should be limited to 50.

Application Notes

Application Notes are generally 2000 words, excluding abstract and references, and can include up to 3 display items. Application notes can be submitted as a word document. The content of the Application Notes should focus on technical performance and evaluation of a new product or technology.