In Silico Biology

Journal of Biological Systems Modeling and Multi-Scale Simulation



15, 4 issues

Latest issue

15:1-2 online 17 November 2023

Next issue

15:3 scheduled for February 2024

Back volumes

From volume 1, 1998

ISSN print


ISSN online

Open Access

Aims & Scope

In Silico Biology is a scientific research journal for the advancement of computational models and simulations applied to complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e., "in silico") modeling and analysis tools are developed and utilized to predict and elucidate dynamics of biological systems, their design and control, and their evolution. Experimental support may also be provided to support the computational analyses.

In Silico Biology aims to advance the knowledge of the principles of organization of living systems. We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. In particular, we seek for integrative formalisms to decipher cross-talks underlying systems level properties, ultimate aim of multi-scale models.

Studies published in In Silico Biology generally use theoretical models and computational analysis to gain quantitative insights into regulatory processes and networks, cell physiology and morphology, tissue dynamics and organ systems. Areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others. Multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations, interface between -omics integration and modeling, and development of algorithms for modeling purposes are of particular interest.

In Silico Biology also publishes foundational research in which novel algorithms are developed to facilitate modeling and simulations. Such research must demonstrate application to a concrete biological problem.

The term "in silico" is a pendant to "in vivo" (in the living system) and "in vitro" (in the test tube) biological experiments, and implies the gain of insights by computer-based simulations and model analyses.

In Silico Biology frequently publishes special issues on seminal topics and trends. Special issues are handled by Special Issue Editors appointed by the Editor-in-Chief. Proposals for special issues should be sent to the Editor-in-Chief.

Editorial Board

Matteo Barberis, PhD
Systems Biology
School of Biosciences and Medicine
Faculty of Health and Medical Sciences
University of Surrey
Stag Hill Campus, 07 AX 01 Edward Jenner Building
Guildford, Surrey GU2 7XH
United Kingdom

Advisory Board
Dennis Bray
University of Cambridge, UK

Roland Eils
University of Heidelberg, Germany

Albert Goldbeter
Université Libre de Bruxelles, Belgium

Hiroaki Kitano
The Systems Biology Institute, Japan

Michael Mackey
McGill University, Canada

John Tyson
Virginia Tech, USA

Hans Westerhoff
University of Manchester, UK

Former Editors-in-Chief
Mads Kaern

Edgar Wingender

Jack Leunissen †
The Netherlands 

Editorial Board
John Aitchison
Institute for Systems Biology, USA

Ilya Akberdin
Institute of Cytology and Genetics, Russia

Gabor Balazsi
University of Texas, Houston, USA

Diego di Bernardo
Telethon Institute for Genetics and Medicine, Italy

Daniel Charlebois
Stony Brook University, USA

Sangdun Choi
Ajou University, Korea

Daniel Coombs
University of British Columbia, Canada

Eldon Emberly
Simon Fraser University, Canada

Brian Ingalls
University of Waterloo, Canada

Johannes Jaeger
Centre for Genomic Regulation, Spain

Yves Lussier
University of Chicago, USA 

Ion Mandoiu
University of Connecticut, USA

William Mather
Virginia Tech, USA

Nicolas Mermod
University of Lausanne, Switzerland

David Gómez Míguez
Universidad Autónoma de Madrid, Spain

Theodore Perkins
Ottawa Hospital Research Institute, Canada

Andre Ribeiro
Tampere University of Technology, Finland

Moises Santillan
Centre for Research and Advanced Studies, Mexico

Kumar Selvarajoo
Keio University, Japan

Narayanaswamy Srinivasan 
Indian Institute of Science, India

Peter Swain
University of Edinburgh, Scotland, UK

Jose Vilar
University of the Basque Country, Spain

Xiao Wang
Arizona State University, USA 

Author Guidelines


By submitting my article to this journal, I agree to the Author Copyright Agreement, the IOS Press Ethics Policy, and the IOS Press Privacy Policy.

Authors are requested to submit their manuscript electronically to the journal’s editorial management system.
Note that the manuscript should be uploaded as one file with tables and figures included. This file can be a Word document, a PDF, or a zip file.



To be considered for publication, submitted manuscripts must satisfy the following criteria:

  • The research must be consistent with the Aims and Scope of In Silico Biology and be of relevance to contemporary biological problems.
  • The manuscript must be accessible to a broad readership, and must clearly highlight the relevance to a contemporary biological problem in the introduction.
  • The research must be solid in design, method and analysis, and conclusions supported by solid data. The manuscript must contain sufficient details for others to reproduce this data.
  • The submitted work must not be published or submitted for publication elsewhere in any form, in whole or in part.

A letter must accompany all submissions from the corresponding author addressed to the Editor-in-Chief. The cover letter must:

  • Explain why the submitted work meets the criteria for publication and declare that the submitted work, in whole or in part, is not published or submitted for publication elsewhere.
  • Identify an Editor and five potential reviewers with the relevant expertise necessary to assess whether or not the submitted work meets the criteria for publication.
  • Confirm that all results contained in the submission is described in sufficient detailed to be reproduced, and that the corresponding author agrees to provide any and all materials required for independent validation.
  • Attest that all co-authors listed have approved the submission, and that all authors have contributed in significant ways to the submitted work.
  • Declare the absence of existing or potential conflicts of interest on behalf of all contributing authors. Conflicts of interest will not negatively impact the publication of the submitted work but must be noted.

Open Access

In Silico Biology is an open acces journal with articles published under the Creative Commons Attribution License (CC BY-NC 4.0). The article publication charges (APCs) are waived for papers submitted before December 31, 2023.


Direct submissions
Authors of unsolicited manuscripts are requested to submit their manuscript electronically to the journal’s editorial management system.
 Note that the manuscript should be uploaded as one file with tables and figures included. This file can be a Word document, a PDF, or a zip file.

In most cases, the Editor-in-Chief will assign an Editor to handle the peer review of a submitted work. Based on reports from at least two independent referees, the Editor will provide to the Editor-in-Chief a recommendation of Accept, Accept after minor revisions, Accept after major revisions, Reject with an invitation to re-submit, or Reject. The Editor-in-Chief is responsible for ensuring that the submitted work is fairly and objectively reviewed, and communicates the final decision to the corresponding author.

Once accepted, the corresponding author must provide the following files: a source file of the text written in Word, WordPerfect, Open Office, Pages, LateX (If using LaTeX, please use the standard article.sty as a style file) and separate files of all figures. The required file formats for figures are described in “Preparation of manuscripts”.


Manuscripts must be written in English. Authors whose native language is not English are advised to consult a professional English language editing service or a native English speaker prior to submission. Poorly written manuscript or manuscript with excessive grammatical errors will be rejected without review.

Style of presentation
Manuscripts should be prepared with wide margins and double spacing throughout, including the abstract, footnotes and references. Every page of the manuscript, including the title page, references, tables, etc., should be numbered. However, no reference should be made to page numbers in the text; if necessary, one may refer to sections. Avoid excessive use of italics and bold face.

SI units should be used, i.e., the units based on the meter, kilogram, second, etc. 

Headings and subheadings should be numbered and typed on a separate line, without indentation. Manuscripts should be organized in the following order:

  • Title page
  • Abstract
  • Main text (see below)
  • Acknowledgements
  • Author contributions
  • References
  • Tables and Table captions
  • Figure captions
  • Figures 

Title page
The title page should provide the following information:

  • Title (should be clear, descriptive and short)
  • Name(s) of author(s); please indicate who is the corresponding author with an asterisk (*)
  • Full affiliations of all authors
  • Present address of author(s), if different from affiliation
  • Complete address of corresponding author, including telephone and fax numbers and e-mail address
  • Keywords (five words or sentences identifying the main topics discussed)

Author contributions
Any author included in the author list should have contributed significantly to the paper, and no person who has made a significant contribution should be omitted from the list of authors. Please read the IOS Press authorship policy for further information.

The abstract summarizes the motivation, methods and key findings of the study. The abstract should be clear, descriptive, self-explanatory and not exceeding 200 words. It must be suitable for publication in abstracting services.

Main text
The main body of the manuscript typically contains the following:

1. Introduction
2. Results & Discussion
3. Conclusion
4. Methods
5. Appendices

The Introduction, Results and Discussion and Conclusion should not exceed five journal pages in total. Although there is no page limit on Methods and Appendices, these sections should be kept short and concise.

Subsections (if any) should be enumerated and accompanied by a brief descriptive title. 

In Silico Biology currently does not publish supplemental material. Sufficient information to fully reproduce the submitted work must be described within the main body of the manuscript with details, if necessary, provided in an appendix. For computational datasets and analyses, the submitted work must include sufficiently detailed descriptions of procedures (e.g., pseudo-codes). These descriptions should be provided in an appendix. Appendices are published in print.

Large experimental datasets must be submitted to the appropriate public repository and the details of their analyses described in one or more appendices.

Footnotes should only be used if absolutely essential. In most cases it is possible to incorporate the information in the text. If used, they should be numbered in the text, indicated by superscript numbers and kept as short as possible.

We recognize that the typical organization may not always be the best representation, and minor deviations are acceptable if adequately explained in the cover letter.


  • Number as Table 1, Table 2 etc. All tables must be referenced in the main text.
  • Each table should be provided on a separate page at the end of the manuscript. Tables should not be inserted into the main text.
  • Each table should have a brief and self-explanatory title.
  • Column headings should be brief, but sufficiently explanatory. Standard abbreviations of units of measurement should be added between parentheses.
  • Vertical lines should not be used to separate columns. Leave some extra space between the columns instead.
  • Any explanations essential to the understanding of the table should be given in footnotes at the bottom of the table.

Number figures as Fig. 1, Fig. 2, etc. . All figures must be referred to in the main text.

Each figure should be provided on a separate page in the initial submission and as a separate file once accepted for publication.

Color figures can be included, provided the author pays for the cost of their reproduction.

Once accepted, all figures must be provided as separate files with the following specifications:

  • Figure should fill a single column or spanning two columns of the printed journal. White spaces to the left and right of the figure body should be minimal.
  • Figures should be of such a size as to allow a reduction of 50% without compromising its quality
  • Line art should have a minimum resolution of 600 dpi. Only EPS or TIFF formats are accepted.
  • Grayscales (incl photos) should have a minimum resolution of 300 dpi (no lettering), or 500 dpi (when there is lettering). Only TIFF format is accepted.
  • CMYK encoding should be used for color figures.
  • Do not use color in your figures if they are to be printed in black & white, as this will reduce the print quality.

On figures where a scale is needed, use bar scales rather than numerical ones, i.e., do not use scales of the type 1:10,000. This avoids problems if the figures need to be slightly resized during reproduction.

Each figure should have a self-explanatory caption. The captions to all figures should be typed on a separate sheet of the manuscript.

Photographs are only acceptable if they have good contrast and intensity.

Place citations as numbers in square brackets in the text. All publications cited in the text should be presented in the list of references at the end of the manuscript, in the sequential order they appear in the main text, in the following style:

[1] B. Newman and E.T. Liu, Perspective on BRCA1, Breast Disease 10 (1998), 3-10.
[2] D.F. Pilkey, Happy conservation laws, in: Neural Stresses, J. Frost, ed., Controlled Press, Georgia, 1995, pp. 332-391.
[3] E. Wilson, Active vibration analysis of thin-walled beams, Ph.D. Dissertation, University of Virginia, 1991.


Copyright of your article
Authors submitting a manuscript do so on the understanding that they have read and agreed to the terms of the IOS Press Author Copyright Agreement.

Article sharing
Authors of journal articles are permitted to self-archive and share their work through institutional repositories, personal websites, and preprint servers. Authors have the right to use excerpts of their article in other works written by the authors themselves, provided that the original work is properly cited. The consent for sharing an article, in whole or in part, depends on the version of the article that is shared, where it is shared, and the copyright license under which the article is published. Please refer to the IOS Press Article Sharing Policy for further information.

Quoting from other publications
Authors, when quoting from someone else's work or when considering reproducing figures or tables from a book or journal article, should make sure that they are not infringing a copyright. Although in general authors may quote from other published works, permission should be obtained from the holder of the copyright if there will be substantial extracts or reproduction of tables, plates, or other figures. If the copyright holder is not the author of the quoted or reproduced material, it is recommended that the permission of the author should also be sought. Material in unpublished letters and manuscripts is also protected and must not be published unless permission has been obtained. Submission of a paper will be interpreted as a statement that the author has obtained all the necessary permission. A suitable acknowledgement of any borrowed material must always be made.


The corresponding author will receive a PDF proof and is asked to check this proof carefully (the publisher will execute a cursory check only). Corrections other than printer's errors, however, should be avoided. Costs arising from such corrections will be charged to the authors.

The corrected proof is published online in the journal’s pre-press module shortly after the proof is created and author corrections are implemented. This is not the final version. As soon as the article is assigned to an issue, the final bibliographic information will be added and the pre-press file will be replaced by the updated, final version. Pre-press articles are fully citable by using their DOI number.


How to order reprints, a PDF file, journals, or IOS Press books
The corresponding author of a contribution to the journal will receive a complimentary PDF Author’s Copy of the article, unless otherwise stated. This PDF copy is watermarked and for personal use only. A free PDF copy will not be provided for conference proceedings and abstract issues. An order form for a PDF file without watermark, reprints or additional journal copies will be provided along with the PDF proof.

If you wish to order reprints of an earlier published article, please contact the publisher for a quotation. IOS Press, Fax: +31 20 687 0019. Email:

An author is entitled to 25 % discount on IOS Press books. See Author’s discount (25%) on all IOS Press book publications.


Authors of published articles (non-prepress, final articles) will be contacted by Kudos. Kudos is a service that helps researchers maximize the impact and visibility of their research. It allows authors to enrich their articles with lay metadata, add links to related materials and promote their articles through the Kudos system to a wider public. Authors will receive no more than three emails: one invitation and a maximum of two reminders to register for the service and link the published article to their profile. Using and registering for Kudos remains entirely optional. For more information, please have a look at our authors section.


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Abstracted/Indexed in

Academic Source Complete
CAB Abstracts
Cabell's Guide or Directory
Chemical Abstracts Service
Chemical Abstracts Service (CAS)
EBSCO databases
Google Scholar
Inspec IET
Microsoft Academic Search
Ulrich's Periodicals Directory
Web of Science: Biological Abstracts
Web of Science: BIOSIS Previews

Peer Review

In Silico Biology Peer Review Policy

In Silico Biology is a peer-reviewed journal. All articles submitted to the journal undergo a single blind peer review process. This means that the identity of the authors is known with the reviewers but the identity of the reviewers is not communicated to the authors. Please visit our reviewer guidelines for further information about how to conduct a review.

After automatic plagiarism screening through iThenticate, all submitted manuscripts are subject to initial appraisal by the Editor-in-Chief, and, if found suitable for further consideration, to rigorous peer-review by independent, anonymous expert referees. Reasons to reject a paper in the pre-screening process could for example be because the work does not fall within the aims and scope, the writing is of poor quality, the instructions to authors were not followed or the presented work is not novel.

Papers deemed suitable to be reviewed will be assigned a handling editor. The handling editor will then invite reviewers to comment on the work. Typically decisions are based on three reviews, in some circumstances a minimum of two reviews may be deemed sufficient to make a decision on a paper. The Editor-in-Chief strives to ensure a typical turnaround time of 3 months from submission until first decision.

Reviewers are asked to judge a paper on at least:

  • Originality, novelty and significance of results
  • Technical quality of work
  • Comprehensibility and presentation of the paper
  • Overall impression

Based on the received reviews the handling editor will propose to the Editor-in-Chief a recommendation:

  1. Accept as is
  2. Accept pending minor revisions
  3. Resubmit after major revisions
  4. Reject outright

They mean the following:

  1. Accept as is: The manuscript is suitable for publication and only requires minor polishing; thus, no further reviews are requested.
  2. Accept pending minor revisions: The authors are required to make moderate changes to their manuscript. The manuscript becomes acceptable for publication if the changes proposed by the reviewers and editors are successfully addressed. The revised manuscript will be examined by the Editor-in-Chief and possibly sent back to all (or a selection of) reviewers for a second round of reviews. Authors are requested to provide a letter to the reviewers detailing the improvements made for the resubmission.
  3. Resubmit after major revisions: The manuscript cannot be accepted for publication in its current form. However, a major revision which addresses all issues raised by the reviewers may be acceptable for publication. The revised manuscript will undergo a full second round of review. Authors are requested to provide a letter to the reviewers detailing the improvements made for the resubmission.
  4. Reject outright: The manuscript is rejected as it is deemed to be out of scope, not relevant, or not meeting the journal’s quality standards in terms of significance, novelty, and/or presentation.

Authors are notified by the Editor-in-Chief, whose decision is final.

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Free open access will be provided to all papers submitted for review prior to Dec 31, 2023.

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