In Silico Biology
Journal of Biological Systems Modeling and Multi-Scale Simulation
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. Special areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others, and the use of multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations.
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.
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.
About In Silico Biology
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 (ISB) was founded in 1998 as a purely online journal. IOS Press became the publisher of the printed journal shortly after. Today, ISB is dedicated exclusively to biological systems modeling and multi-scale simulations and is published solely by IOS Press. The previous online publisher, Bioinformation Systems, maintains a website containing studies published between 1998 and 2010 for archival purposes.
We strongly support open communications and encourage researchers to share results and preliminary data with the community. Therefore, results and preliminary data made public through conference presentations, conference proceeding or posting of unrefereed manuscripts on preprint servers will not prohibit publication in ISB. However, authors are required to modify a preprint to include the journal reference (including DOI), and a link to the published article on the ISB website upon publication.
Mads Kaern, PhD
Jack Leunissen †
Diego di Bernardo
David Gómez Míguez
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.
IOS Press is committed to support the computational biology community and will provide free open access to all papers submitted for review prior to Dec 31, 2017. A fee may be applied for open access after that date (the current fee is €900 or US$1250).
Open access publishing in In Silico Biology is governed by the IOS Press Open Library policy and adheres to the Creative Commons Attribution License.
EDITING AND PEER-REVIEW
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.
The Editor-in-Chief, members of the Editorial Board and Special Issue Editors may solicit submissions. The soliciting Editor handles the peer review of such invited contributions in the same way as direct submissions, and the corresponding author should interact directly with this Editor. Authors of manuscripts solicited by the Editor-in-Chief are requested to submit their work directly to email@example.com
Once the criteria for publication are satisfied, the Editor shall submit to the Editor-in-Chief a cover letter explaining why these criteria are satisfied, supporting reports from at least two independent referees, and typeset-ready material.
PREPARATION OF MANUSCRIPTS
Manuscripts must be written in English. Poorly written manuscript or manuscript with excessive grammatical errors will be rejected without review. Peerwith offers a language and copyediting service to all scientists who want to publish their manuscript in scientific peer-reviewed periodicals and books.
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
- Main text (see below)
- Author contributions
- Tables and Table captions
- Figure captions
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)
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.
The main body of the manuscript typically contains the following:
2. Results & Discussion
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:
 B. Newman and E.T. Liu, Perspective on BRCA1, Breast Disease 10 (1998), 3-10.
 D.F. Pilkey, Happy conservation laws, in: Neural Stresses, J. Frost, ed., Controlled Press, Georgia, 1995, pp. 332-391.
 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.
Quoting from other publications
An author, when quoting from someone else’s work or when considering reproducing figures or table from a book or journal article, should make sure that he is not infringing a copyright. Although in general an author may quote from other published works, he should obtain permission from the holder of the copyright if he wishes to make substantial extracts or to reproduce 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.
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”.
Note that the corresponding author must pay for the cost of color figure reproduction. Estimates of reproduction cost should be requested from the Editorial Office at the time of submission.
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.
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: firstname.lastname@example.org.
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.
HOW TO PROMOTE YOUR WORK
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