Article types

Regular Papers

Regular Papers are original scientific articles describing research in any of the above areas irrespective of length. They are standard contributions to BEST.

Application Notes

Applications Notes are short original articles describing novel algorithms only specifically for software implementations devoted to Systems Biology. The aim of this section is to accelerate the publication process and to increase the visibility of software enabling the mathematical modelling and analysis of biological processes. Each Application note must be accompanied by sample data and relevant documentation (user manual, tutorial), ideally in the form of a dedicated website maintained by the author(s). All this material, including the software itself, must be freely available to academic user for at least two years after the publication date. Availability must be specified in the abstract of the article, along with the addresses where to obtain the material. The software should be extensively tested and run under on a wide range of machines. Application Notes should focus on the description of the main characteristics of the software itself, but can be accompanied by a few illustrative applications. The description of extensive biological applications can be submitted in the regular article section of the journal.

Book Reviews

Book reviews are typically short reviews of recently published books in the scientific literature within the interest of the readership of BEST and its scope as indicated above. Prior to submitting a book review, please contact the Editor-in-chief to determine if the book review is suitable or warranted for BEST. Requests for book reviews will be considered on an individual basis through contact with the Editor.

Review Articles

Review articles are typically longer contributions focusing on one topic within the scope of BEST. Authors interested in writing review articles for BEST should contact the Editor-in-Chief before submitting their contribution. Review articles will be printed on an irregular basis in BEST and are not meant to replace regular papers. Similarly, length regular papers should not be represented as review articles. Review articles are meant to survey a particular topic of interest and present a position on current and future directions of research for the community.

Hypothesis Papers

Hypothesis Papers provide an option for authors to advance new ideas, hypotheses, or theories. Such novel concepts are typically based primarily on previously published data, findings, or observations and a strong line of reasoning, rather than on extensive new experiments. Ideally, a way of testing the hypothesis or theory being proposed should be developed as part of the submission.

Peer review

This journal follows a single anonymized review process. Your submission will initially be assessed by our editors to determine suitability for publication in this journal. If your submission is deemed suitable, it will typically be sent to a minimum of two reviewers for an independent expert assessment of the scientific quality. The decision as to whether your article is accepted or rejected will be taken by our editors.

Special issues and article collections

The peer review process for special issues and article collections follows the same process as outlined above for regular submissions, except, a guest editor will send the submissions out to the reviewers and may recommend a decision to the journal editor. The journal editor oversees the peer review process of all special issues and article collections to ensure the high standards of publishing ethics and responsiveness are respected and is responsible for the final decision regarding acceptance or rejection of articles.

Authorship

All authors should have made substantial contributions to all of the following:

1. The conception and design of the study, or acquisition of data, or analysis and interpretation of data.
2. Drafting the article or revising it critically for important intellectual content.
3. Final approval of the version to be submitted.

All authors should agree to be accountable for all aspects of the work to ensure that the questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Changes to authorship

The editors of this journal generally will not consider changes to authorship once a manuscript has been submitted. It is important that authors carefully consider the authorship list and order of authors and provide a definitive author list at original submission.

The policy of this journal around authorship changes:

• All authors must be listed in the manuscript and their details entered into the submission system.
• Any addition, deletion or rearrangement of author names in the authorship list should only be made prior to acceptance, and only if approved by the journal editor.
• Requests to change authorship should be made by the corresponding author, who must provide the reason for the request to the journal editor with written confirmation from all authors, including any authors being added or removed, that they agree with the addition, removal or rearrangement.
• Only in exceptional circumstances will the journal editor consider the addition, deletion or rearrangement of authors post acceptance.
• Publication of the manuscript may be paused while a change in authorship request is being considered.
• Any authorship change requests approved by the journal editor will result in a corrigendum if the manuscript has already been published.
• Any unauthorised authorship changes may result in the rejection of the article, or retraction, if the article has already been published.

 

Funding sources

Authors must disclose any funding sources who provided financial support for the conduct of the research and/or preparation of the article. The role of sponsors, if any, should be declared in relation to the study design, collection, analysis and interpretation of data, writing of the report and decision to submit the article for publication. If funding sources had no such involvement this should be stated in your submission.

List funding sources in this standard way to facilitate compliance to funder's requirements:

Funding: This work was supported by the National Institutes of Health [grant numbers xxxx, yyyy]; the Bill & Melinda Gates Foundation, Seattle, WA [grant number zzzz]; and the United States Institutes of Peace [grant number aaaa].

It is not necessary to include detailed descriptions on the program or type of grants, scholarships and awards. When funding is from a block grant or other resources available to a university, college, or other research institution, submit the name of the institute or organization that provided the funding.

If no funding has been provided for the research, it is recommended to include the following sentence:

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

 

Writing and formatting

File format

We ask you to provide editable source files for your entire submission (including figures, tables and text graphics). Some guidelines:

• Save files in an editable format, using the extension .doc/.docx for Word files and .tex for LaTeX files. A PDF is not an acceptable source file.
• Lay out text in a single-column format.
• Use spell-check and grammar-check functions to avoid errors.

Title page

You are required to include the following details in the title page information:

• Article title. Article titles should be concise and informative. Please avoid abbreviations and formulae, where possible, unless they are established and widely understood, e.g., DNA).
• Author names. Provide the given name(s) and family name(s) of each author. The order of authors should match the order in the submission system. Carefully check that all names are accurately spelled. If needed, you can add your name between parentheses in your own script after the English transliteration.
• Affiliations. Add affiliation addresses, referring to where the work was carried out, below the author names. Indicate affiliations using a lower-case superscript letter immediately after the author's name and in front of the corresponding address. Ensure that you provide the full postal address of each affiliation, including the country name and, if available, the email address of each author.
• Corresponding author. Clearly indicate who will handle correspondence for your article at all stages of the refereeing and publication process and also post-publication. This responsibility includes answering any future queries about your results, data, methodology and materials. It is important that the email address and contact details of your corresponding author are kept up to date during the submission and publication process.
• Present/permanent address. If an author has moved since the work described in your article was carried out, or the author was visiting during that time, a "present address" (or "permanent address") can be indicated by a footnote to the author's name. The address where the author carried out the work must be retained as their main affiliation address. Use superscript Arabic numerals for such footnotes.

Abstract

You are required to provide a concise and factual abstract which does not exceed 250 words. The abstract should briefly state the purpose of your research, principal results and major conclusions. Some guidelines:

• Abstracts must be able to stand alone as abstracts are often presented separately from the article.
• Avoid references. If any are essential to include, ensure that you cite the author(s) and year(s).
• Avoid non-standard or uncommon abbreviations. If any are essential to include, ensure they are defined within your abstract at first mention.

Keywords

You are required to provide 1 to 7 keywords for indexing purposes. Keywords should be written in English. Please try to avoid keywords consisting of multiple words (using "and" or "of").

We recommend that you only use abbreviations in keywords if they are firmly established in the field.

Highlights

You are encouraged to provide article highlights at submission.

Highlights are a short collection of bullet points that should capture the novel results of your research as well as any new methods used during your study. Highlights will help increase the discoverability of your article via search engines. Some guidelines:

• Submit highlights as a separate editable file in the online submission system with the word "highlights" included in the file name.
• Highlights should consist of 3 to 5 bullet points, each a maximum of 85 characters, including spaces.

We encourage you to view example article highlights and read about the benefits of their inclusion.

Stereochemistry abstract

For each important chiral compound, you are requested to supply a stereochemistry abstract detailing structure, name, formula and all available stereochemical information for eventual incorporation into a database. An abstract for only one enantiomer per compound is required.

Math formulae

• Submit math equations as editable text, not as images.
• Present simple formulae in line with normal text, where possible.
• Use the solidus (/) instead of a horizontal line for small fractional terms such as X/Y.
• Present variables in italics.
• Denote powers of e by exp.
• Display equations separately from your text, numbering them consecutively in the order they are referred to within your text.

Tables

Tables must be submitted as editable text, not as images. Some guidelines:

• Place tables next to the relevant text or on a separate page(s) at the end of your article.
• Cite all tables in the manuscript text.
• Number tables consecutively according to their appearance in the text.
• Please provide captions along with the tables.
• Place any table notes below the table body.
• Avoid vertical rules and shading within table cells.

We recommend that you use tables sparingly, ensuring that any data presented in tables is not duplicating results described elsewhere in the article.

Figures, images and artwork

Figures, images, artwork, diagrams and other graphical media must be supplied as separate files along with the manuscript. We recommend that you read our detailed artwork and media instructions. Some excerpts:

When submitting artwork:

• Cite all images in the manuscript text.
• Number images according to the sequence they appear within your article.
• Submit each image as a separate file using a logical naming convention for your files (for example, Figure_1, Figure_2 etc).
• Please provide captions for all figures, images, and artwork.
• Text graphics may be embedded in the text at the appropriate position. If you are working with LaTeX, text graphics may also be embedded in the file.

Artwork formats

When your artwork is finalized, "save as" or convert your electronic artwork to the formats listed below taking into account the given resolution requirements for line drawings, halftones, and line/halftone combinations:

• Vector drawings: Save as EPS or PDF files embedding the font or saving the text as "graphics."
• Color or grayscale photographs (halftones): Save as TIFF, JPG or PNG files using a minimum of 300 dpi (for single column: min. 1063 pixels, full page width: 2244 pixels).
• Bitmapped line drawings: Save as TIFF, JPG or PNG files using a minimum of 1000 dpi (for single column: min. 3543 pixels, full page width: 7480 pixels).
• Combinations bitmapped line/halftones (color or grayscale): Save as TIFF, JPG or PNG files using a minimum of 500 dpi (for single column: min. 1772 pixels, full page width: 3740 pixels).

Please do not submit:

• files that are too low in resolution (for example, files optimized for screen use such as GIF, BMP, PICT or WPG files).
• disproportionally large images compared to font size, as text may become unreadable.

Figure captions

All images must have a caption. A caption should consist of a brief title (not displayed on the figure itself) and a description of the image. We advise you to keep the amount of text in any image to a minimum, though any symbols and abbreviations used should be explained.

Provide captions in a separate file.

Color artwork

If you submit usable color figures with your accepted article, we will ensure that they appear in color online.

Please ensure that color images are accessible to all, including those with impaired color vision. Learn more about color and web accessibility.

For articles appearing in print, you will be sent information on costs to reproduce color in the printed version, after your accepted article has been sent to production. At this stage, please indicate if your preference is to have color only in the online version of your article or also in the printed version.

Supplementary material

We encourage the use of supplementary materials such as applications, images and sound clips to enhance research. Some guidelines:

• Cite all supplementary files in the manuscript text.
• Submit supplementary materials at the same time as your article. Be aware that all supplementary materials provided will appear online in the exact same file type as received. These files will not be formatted or typeset by the production team.
• Include a concise, descriptive caption for each supplementary file describing its content.
• Provide updated files if at any stage of the publication process you wish to make changes to submitted supplementary materials.
• Do not make annotations or corrections to a previous version of a supplementary file.
• Switch off the option to track changes in Microsoft Office files. If tracked changes are left on, they will appear in your published version.

We recommend you upload research data to a suitable specialist or generalist repository. Please read our guidelines on sharing research data for more information on depositing, sharing and using research data and other relevant research materials.

Video

This journal accepts video material and animation sequences to support and enhance your scientific research. We encourage you to include links to video or animation files within articles. Some guidelines:

• When including video or animation file links within your article, refer to the video or animation content by adding a note in your text where the file should be placed.
• Clearly label files ensuring the given file name is directly related to the file content.
• Provide files in one of our recommended file formats. Files should be within our preferred maximum file size of 150 MB per file, 1 GB in total.
• Provide "stills" for each of your files. These will be used as standard icons to personalize the link to your video data. You can choose any frame from your video or animation or make a separate image.
• Provide text (for both the electronic and the print version) to be placed in the portions of your article that refer to the video content. This is essential text, as video and animation files cannot be embedded in the print version of the journal.

We publish all video and animation files supplied in the electronic version of your article.

For more detailed instructions, we recommend that you read our guidelines on submitting video content to be included in the body of an article.

Research data

We are committed to supporting the storage of, access to and discovery of research data, and our research data policy sets out the principles guiding how we work with the research community to support a more efficient and transparent research process.

Research data refers to the results of observations or experimentation that validate research findings, which may also include software, code, models, algorithms, protocols, methods and other useful materials related to the project.

Please read our guidelines on sharing research data for more information on depositing, sharing and using research data and other relevant research materials.

For this journal, the following instructions from our research data guidelines apply.

Option B: Research data deposit, citation and linking

You are encouraged to:

• Deposit your research data in a relevant data repository.
• Cite and link to this dataset in your article.
• If this is not possible, make a statement explaining why research data cannot be shared.

Data statement

To foster transparency, you are encouraged to state the availability of any data at submission.

Ensuring data is available may be a requirement of your funding body or institution. If your data is unavailable to access or unsuitable to post, you can state the reason why (e.g., your research data includes sensitive or confidential information such as patient data) during the submission process. This statement will appear with your published article on ScienceDirect.

Read more about the importance and benefits of providing a data statement.

Article structure

Article sections

• Divide your article into clearly defined and numbered sections. Number subsections 1.1 (then 1.1.1, 1.1.2, ...), then 1.2, etc.
• Use the numbering format when cross-referencing within your article. Do not just refer to "the text."
• You may give subsections a brief heading. Headings should appear on a separate line.
• Do not include the article abstract within section numbering.

Theory and calculation

The theory section should lay the foundation for further work by extending the background you provided in the introduction to your article. The calculation section should represent a practical development from a theoretical basis.

Glossary

Please provide definitions of field-specific terms used in your article, in a separate list.

Acknowledgements

Include any individuals who provided you with help during your research, such as help with language, writing or proof reading, in the acknowledgements section. Acknowledgements should be placed in a separate section which appears directly before the reference list. Do not include acknowledgements on your title page, as a footnote to your title, or anywhere else in your article other than in the separate acknowledgements section.

Author contributions: CRediT

Corresponding authors are required to acknowledge co-author contributions using CRediT (Contributor Roles Taxonomy) roles:

• Conceptualization
• Data curation
• Formal analysis
• Funding acquisition
• Investigation
• Methodology
• Project administration
• Resources
• Software
• Supervision
• Validation
• Visualization
• Writing – original draft
• Writing – review and editing

Not all CRediT roles will apply to every manuscript and some authors may contribute through multiple roles.

Funding sources

Authors must disclose any funding sources who provided financial support for the conduct of the research and/or preparation of the article. The role of sponsors, if any, should be declared in relation to the study design, collection, analysis and interpretation of data, writing of the report and decision to submit the article for publication. If funding sources had no such involvement this should be stated in your submission.

List funding sources in this standard way to facilitate compliance to funder's requirements:

Funding: This work was supported by the National Institutes of Health [grant numbers xxxx, yyyy]; the Bill & Melinda Gates Foundation, Seattle, WA [grant number zzzz]; and the United States Institutes of Peace [grant number aaaa].

It is not necessary to include detailed descriptions on the program or type of grants, scholarships and awards. When funding is from a block grant or other resources available to a university, college, or other research institution, submit the name of the institute or organization that provided the funding.

If no funding has been provided for the research, it is recommended to include the following sentence:

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Appendices

We ask you to use the following format for appendices:

• Identify individual appendices within your article using the format: A, B, etc.
• Give separate numbering to formulae and equations within appendices using formats such as Eq. (A.1), Eq. (A.2), etc. and in subsequent appendices, Eq. (B.1), Eq. (B. 2) etc. In a similar way, give separate numbering to tables and figures using formats such as Table A.1; Fig. A.1, etc.

References

Since our journal aims to reach a broad international audience, it is highly encouraged to use references from well-known highly-ranked journals and preferably in the English language.

Citation in text

Please ensure that every reference cited in the text is also present in the reference list (and vice versa). Any references cited in the abstract must be given in full. Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list, they should follow the standard reference style of the journal and should include a substitution of the publication date with either 'Unpublished results' or 'Personal communication'. Citation of a reference as 'in press' implies that the item has been accepted for publication.

Web references

As a minimum, the full URL should be given and the date when the reference was last accessed. Any further information, if known (DOI, author names, dates, reference to a source publication, etc.), should also be given. Web references can be listed separately (e.g., after the reference list) under a different heading if desired, or can be included in the reference list.

Data references

This journal encourages you to cite underlying or relevant datasets in your manuscript by citing them in your text and including a data reference in your Reference List. Data references should include the following elements: author name(s), dataset title, data repository, version (where available), year, and global persistent identifier. Add [dataset] immediately before the reference so we can properly identify it as a data reference. The [dataset] identifier will not appear in your published article.

Preprint references

Where a preprint has subsequently become available as a peer-reviewed publication, the formal publication should be used as the reference. If there are preprints that are central to your work or that cover crucial developments in the topic, but are not yet formally published, these may be referenced. Preprints should be clearly marked as such, for example by including the word preprint, or the name of the preprint server, as part of the reference. The preprint DOI should also be provided.

Reference management software

Most journals have their reference template available in many of the most popular reference management software products. These include all products that support Citation Style Language styles, such as EndNote. Using citation plug-ins from these products, authors only need to select the appropriate journal template when preparing their article, after which citations and bibliographies will be automatically formatted in the journal's style. If no template is yet available for this journal, please follow the format of the sample references and citations as shown in this Guide. If you use reference management software, please ensure that you remove all field codes before submitting the electronic manuscript.

Reference style

Text: Citations in the text should follow the referencing style used by the American Psychological Association. You are referred to the Publication Manual of the American Psychological Association, Sixth Edition, ISBN 1-4388-0559-6, copies of which may be ordered from http://books.apa.org/books.cfm?id=4200067 or APA Order Dept., P.O.B. 2710, Hyattsville, MD 20784, USA or APA, 3 Henrietta Street, London, WC3E 8LU, UK. Details concerning this referencing style can also be found at

https://booksite.elsevier.com/9780081019375/content/Elsevier%20Standard%20Reference%20Styles.pdf.

DOI addresses should be used in the reference list where they are available.

List: references should be arranged first alphabetically and then further sorted chronologically if necessary. More than one reference from the same author(s) in the same year must be identified by the letters "a", "b", "c", etc., placed after the year of publication.

Examples

Reference to a journal publication:

Van der Geer, J., Hanraads, J. A. J., & Lupton R. A. (2000). The art of writing a scientific article. Journal of Scientific Communications, 163, 51-59.

Reference to a book:

Strunk, W., Jr., & White, E. B. (1979). The elements of style. (3rd ed.). New York: Macmillan, (Chapter 4).

Reference to a chapter in an edited book:

Mettam, G. R., & Adams, L. B. (1994). How to prepare an electronic version of your article. In B. S. Jones, & R. Z. Smith (Eds.), Introduction to the electronic age (pp. 281-304). New York: E-Publishing Inc.

Reference to a dataset:

[dataset] 5. Oguro, M., Imahiro, S., Saito, S., Nakashizuka, T. (2015). Mortality data for Japanese oak wilt disease and surrounding forest compositions. Mendeley Data, v1. http://dx.doi.org/10.17632/xwj98nb39r.1.

Reference to conference proceedings published in a journal:

Duckworth, A. L., Quirk, A., Gallop, R., Hoyle, R. H., Kelly, D. R., & Matthews, M. D. (2019). Cognitive and noncognitive predictors of success. Proceedings of the National Academy of Sciences, USA, 116(47), 23499–23504. https://doi.org/10.1073/pnas.1910510116

Reference to an abstract of a conference presentation:

Cacioppo, S. (2019, April 25–28). Evolutionary theory of social connections: Past, present, and future [Conference presentation abstract]. Ninety-ninth annual convention of the Western Psychological Association, Pasadena, CA, United States. https://westernpsych.org/wp-content/uploads/2019/04/WPA-Program-2019-Final-2.pdf

For APA style references in the text the following rules apply (note the use of ‘and’ and ‘&’):

• For publications by one author, when the name is mentioned in the text, use [...] Smith (1999) [...]; when the name is not directly part of the text use [...] (Smith, 1999).
• For publications by two authors, when the names are mentioned in the text, use [...] Smith and Jones (1999) [...]; when the names are not part of the text use [...] (Smith & Jones, 1999).
• For publications by three or more authors, when the names are mentioned in the text, use [...] Smith et al. (1999) [...]; when the names are not mentioned use [...] (Smith et al., 1999).
• For references with the same first author surname and year, cite as many names of co-authors as are necessary to distinguish the two references (rather than using ‘a’ and ‘b’ after the year, as in other reference systems). Use ‘a’ and ‘b’ after the year only if all authors. names as well as the year are identical.
• If just one name precedes it, no comma should appear before ‘and’, ‘&’ or ‘et al.’.. In the other case a comma should appear.
• For works without an author, list the title of the work instead of the author.

Abbreviate journal names according to the List of Title Word Abbreviations (LTWA).

Submitting your manuscript

Submission checklist

Before completing the submission of your manuscript, we advise you to read our submission checklist:

• One author has been designated as the corresponding author and their full contact details (email address, full postal address and phone numbers) have been provided.
• All files have been uploaded, including keywords, figure captions and tables (including a title, description and footnotes) included.
• Spelling and grammar checks have been carried out.
• All references in the article text are cited in the reference list and vice versa.
• Permission has been obtained for the use of any copyrighted material from other sources, including the Web.