Algorithms — Instructions for Authors
1) read the Aims & Scope to gain an overview and assess if your manuscript is suitable for this journal;
4) ensure that all authors have approved the content of the submitted manuscript.
Types of Publications
Algorithms has no restrictions on the length of manuscripts, provided that the text is concise and comprehensive. Full experimental details must be provided so that the results can be reproduced by other groups. Algorithms encourages authors to publish all experimental controls and full datasets as supplementary files (please read the guidelines about Supplementary Materials carefully and references to unpublished data).
The different types of articles published in Algorithms are indicated in the first section of the Aims & Scope. The main types are:
- Articles: research manuscripts report new evidence or new conclusions which have neither been published before nor are under consideration for publication in another journal. MDPI considers all original research manuscripts provided that the work reports scientifically sound experiments and provides a substantial amount of new information. We strongly recommend authors not to unnecessarily divide their work into several related manuscripts.
- Short communications of preliminary, but significant, results will also be considered.
- Reviews: review manuscripts provide concise and precise updates on the latest progress made in a given area of research.
- Papers that have been previously presented at a conference are also highly welcome. If the conference has published proceedings, then these should be cited and noted on the first page of the paper. Also, the authors are asked to disclose this circumstance in their cover letter and include a statement on what has been changed compared to the original conference paper.
Manuscripts for Algorithms should be submitted online at susy.mdpi.com. The submitting author, who is generally the corresponding author, is responsible for the manuscript during the submission and peer-review process. The submitting authors must ensure that all co-authors have been included in the author list (read the criteria to qualify for authorship) and that they all have read and approved the submitted version of the manuscript. To submit your manuscript, register and log in to this website. Once you are registered, click here to go to the submission form for Algorithms. All co-authors can see the manuscript details in the submission system, if they register and log in using the e-mail address provided during manuscript submission.
Accepted File Formats
Authors must use the Microsoft Word template or LaTeX template to prepare their manuscript. Using the template file will substantially shorten the time to complete copy-editing and publication of accepted manuscripts. Accepted file formats are:
- Microsoft Word: Manuscripts prepared in Microsoft Word must be converted into a single file before submission. When preparing manuscripts in Microsoft Word, the Algorithms Microsoft Word template file must be used. Please insert your graphics (schemes, figures, etc.) in the main text after the paragraph of its first citation.
- LaTeX: Manuscripts prepared in LaTeX must be collated into one ZIP folder (include all source files and images, so that the Editorial Office can recompile the submitted PDF). When preparing manuscripts in LaTeX, please use the Algorithms LaTeX template files. You can now also use the online application writeLaTeX to submit articles directly to Algorithms. The MDPI LaTeX template file should be selected from the writeLaTeX template gallery.
A cover letter must be included with each manuscript submission. It should be concise and explain why the content of your paper is significant, placing your findings in the context of existing work and why it fits the scope of the journal. Please confirm that neither the manuscript nor any parts of its content are currently under consideration or published in another journal. Any prior submissions of the manuscript to MDPI journals must be acknowledged. The names of proposed and excluded reviewers should be provided in the submission system, not in the cover letter.
- Research manuscripts should comprise:
- Review manuscripts should comprise the front matter, literature review sections and the back matter. The template file can also be used to prepare the front and back matter of your review manuscript. It is not necessary to follow the remaining structure.
- Abstract Graphic: Authors are encouraged to provide a graphical abstract as a self-explanatory image to appear alongside with the text abstract in the Table of Contents, if you have not done so already. Figures should be a high quality image in any common image format. Note that images displayed online will be up to 11 by 9 cm on screen and the figure should be clear at this size.
- "Data not shown" should be avoided in research manuscripts. We encourage our authors to publish all observations related to the submitted manuscript as Supplementary Materials. "Unpublished data" intended for publication in a different manuscript, i.e., in a manuscript that is either planned, "in preparation" or that have been "submitted" but not yet accepted, should be cited in the text and a reference should be added in the References section. "Personal Communications" should also be cited in the text and reference added in the References section. (see also the MDPI reference list and citations style guide).
- Abbreviations should be defined in parentheses the first time they appear in the abstract, main text and in figure captions.
- SI Units (International System of Units) should be used for this journal. Imperial, US customary and other units should be converted to SI units whenever possible before submission of a manuscript to the journal.
- Equations: If you are using Word, please use either the Microsoft Equation Editor or the MathType add-on in your paper. Equations should be editable by the editorial office and not appear in a picture format.
- Supplementary Materials and Research Data: To maintain the transparency and reproducibility of research results, authors are encouraged to make their experimental and research data openly available either by depositing into data repositories or by publishing the data and files as "Supplementary Materials". Large datasets and files should be deposited in specialized data repositories. Small datasets, spreadsheets, images, video sequences, conference slides, software source code, etc. can be uploaded as "Supplementary Files" during the manuscript submission process. The supplementary files will also be made available to the referees during the peer-review process and be published online alongside the manuscript. Please read the information about Supplementary Materials and Data Deposit for additional guidelines.
These sections should appear in all manuscript types
- Title: The title of your manuscript should be concise, specific and relevant.
- Author List and Affiliations: Authors' full first and last names must be provided. The initials of any middle names can be added. The PubMed/MEDLINE standard format is used for affiliations: complete address information including city, zip code, state/province, country, and all email addresses. At least one author should be designated as corresponding author, and his or her email address and other details should be included at the end of the affiliation section. Please read the criteria to qualify for authorship.
- Abstract: The abstract should be a total of about 200 words maximum. The abstract should be a single paragraph and should follow the style of structured abstracts, but without headings: 1) Background: Place the question addressed in a broad context and highlight the purpose of the study; 2) Methods: Describe briefly the main methods or treatments applied; 3) Results: Summarize the article's main findings; and 4) Conclusion: Indicate the main conclusions or interpretations. The abstract should be an objective representation of the article: it must not contain results which are not presented and substantiated in the main text and should not exaggerate the main conclusions.
- Keywords: Three to ten pertinent keywords need to be added after the abstract. We recommend that the keywords are specific to the article, yet reasonably common within the subject discipline.
- Introduction: The introduction should briefly place the study in a broad context and highlight why it is important. It should define the purpose of the work and its significance. The current state of the research field should be reviewed carefully and key publications should be cited. Please highlight controversial and diverging hypotheses when necessary. Finally, briefly mention the main aim of the work and highlight the main conclusions. As far as possible, please keep the introduction comprehensible to scientists outside your particular field of research.
- Experimental Section: This section should be divided by subheadings. Materials and Methods should be described with sufficient details to allow others to replicate and build on published results. Please note that publication of your manuscript implies that you must make all materials, data, and protocols associated with the publication available to readers. Please disclose at the submission stage any restrictions on the availability of materials or information. New methods and protocols should be described in detail while well-established methods can be briefly described and appropriately cited. Give the name and version of any software used.
- Research manuscripts reporting large datasets that are deposited in a publicly available database should specify where the data have been deposited and provide the relevant accession numbers. If the accession numbers have not yet been obtained at the time of submission, please state that they will be provided during review. They must be provided prior to publication.
- Results: This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation as well as the experimental conclusions that can be drawn.
- Discussion: This section may be divided by subheadings. Authors should discuss the results and how they can be interpreted in perspective of previous studies and of the working hypotheses. The findings and their implications should be discussed in the broadest context possible. Future research directions may also be highlighted.
- Conclusions: This section is not mandatory, but can be added to the manuscript if the discussion is unusually long or complex.
- Supplementary Materials: This section should be included when supplementary information is published online alongside the manuscript. Please indicate the name and title of each supplementary file as follows Figure S1: title, Table S1: title, etc.
- Acknowledgments: All sources of funding of the study should be disclosed. Please clearly indicate grants that you have received in support of your research work. Clearly state if you received funds for covering the costs to publish in open access. Note that some funders will not refund article processing charges (APC) if the funder and grant number are not clearly identified in the paper. Funding information can be entered separately into the submission system by the authors during submission of their manuscript. Such funding information, if available, will be deposited to FundRef if the manuscript is finally published. Authors must have obtained specific permission from individuals and institutions to mention their names in the Acknowledgements.
- Author Contributions: For research articles with several authors, a short paragraph specifying their individual contributions must be provided. The following statements should be used "X and Y conceived and designed the experiments; X performed the experiments; Y analyzed the data; W contributed reagents/materials/analysis tools; Y wrote the paper." Authorship must be limited to those who have contributed substantially to the work reported. Please read the section concerning the criteria to qualify for authorship carefully.
- Conflicts of Interest: Authors must identify and declare any personal circumstances or interest that may be perceived as inappropriately influencing the representation or interpretation of reported research results. If there is no conflict of interest, please state "The authors declare no conflict of interest." Any role of the funding sponsors in the design of the study; in the collection, analyses or interpretation of data; in the writing of the manuscript, or in the decision to publish the results must be declared in this section. If there is no role, please state “The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results”.
- References: References must be numbered in order of appearance in the text (including tables and legends) and listed individually at the end of the manuscript. We recommend preparing the references with a bibliography software package, such as EndNote, ReferenceManager or Zotero to avoid typing mistakes and duplicated references. Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list.
- In the text, reference numbers should be placed in square brackets [ ], and placed before the punctuation; for example , [1–3] or [1,3]. For embedded citations in the text with pagination, use both parentheses and brackets to indicate the reference number and page numbers; for example  (p. 10). or  (pp. 101–105).
- The Reference list should include the full title as recommended by the ACS style guide. The style file for endnote, MDPI.ens, can be found at http://endnote.com/downloads/style/mdpi
- References should be described as follows depending on the type of work:
- Journal Articles:
1. Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal Name Year, Volume, page range, DOI or other identifier. Available online: URL (accessed on Day Month Year).
- Books and Book Chapters:
2. Author 1, A.; Author 2, B. Book Title, 3rd ed.; Publisher: Publisher Location, Country, Year; pp. 154–196.
3. Author 1, A.; Author 2, B. Title of the chapter. In Book Title, 2nd ed.; Editor 1, A.; Editor 2, B., Eds.; Publisher: Publisher Location, Country, Year; Volume 3, pp. 154–196.
- Unpublished work, submitted work, personal communication:
4. Author 1, A.B.; Author 2, C. Title of Unpublished Work. status (unpublished; manuscript in preparation).
5.Author 1, A.B.; Author 2, C. Title of Unpublished Work. Abbreviated Journal Name stage of publication (under review; accepted; in press).
6.Author 1, A.B. (University, City, State, Country); Author 2, C. (Institute, City, State, Country). Personal communication, Year.
- Conference Proceedings:
7. Author 1, A.B.; Author 2, C.D.; Author 3, E.F. Title of Presentation. In Title of the Collected Work (if available), Proceedings of the Name of the Conference, Location of Conference, Country, Date of Conference; Editor 1, Editor 2, Eds. (if available); Publisher: City, Country, Year (if available); Abstract Number (optional), Pagination (optional).
8. Author 1, A.B. Title of Thesis. Level of Thesis, Degree-Granting University, Location of University, Date of Completion.
9.Title of Site. Available online: URL (accessed on Day Month Year).
Unlike published works, websites may change over time or disappear, so we encourage you create an archive of the cited website using a service such as WebCite. Archived websites should be cited using the link provided as follows:
10. Title of Site. URL (archived on Day Month Year).
- All figure files should be separately uploaded during submission.
- Figures and schemes must be provided at a sufficiently high resolution (minimum 1000 pixels width/height, or a resolution of 300 dpi or higher). All Figure file formats are accepted. However, TIFF, JPEG, EPS and PDF files are preferred.
- Algorithms can publish multimedia files in articles or as supplementary materials. Please get in touch with the Editorial office for further information.
- All Figures, Schemes and Tables should also be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Scheme I, Figure 2, Scheme II, Table 1, etc.).
- All Figures, Schemes and Tables should have a short explanatory title and a caption.
- All table columns should have an explanatory heading. To facilitate the copy-editing of larger tables, smaller fonts may be used, but in no less than 8 pt. in size. Authors should use the Table option of Microsoft Word to create tables.
- For multi-panel figures, the file must contain all data in one file. For tips on creating multi-panel figures, please read the helpful advice provided by L2 Molecule.
- Authors are encouraged to prepare figures and schemes in color (RGB at 8-bit per channel). Full color graphics will be published free of charge.
Authorship must include and be strictly limited to researchers who substantially contributed to the design of the study, the production, analysis, or interpretation of the results, and/or preparation of the manuscript. Those who contributed to the work but do not qualify for authorship should be listed in the acknowledgments. More detailed guidance on authorship is given by the International Council of Medical Journal Editors (ICMJE). The journal also adheres to the standards of the Committee on Publication Ethics (COPE) that "all authors should agree to be listed and should approve the submitted and accepted versions of the publication. Any change to the author list should be approved by all authors including any who have been removed from the list. The corresponding author should act as a point of contact between the editor and the other authors and should keep co-authors informed and involve them in major decisions about the publication (e.g. answering reviewers’ comments)." 
- Wager, E.; Kleinert, S. Responsible research publication: international standards for authors. A position statement developed at the 2nd World Conference on Research Integrity, Singapore, July 22-24, 2010. In Promoting Research Integrity in a Global Environment; Mayer, T., Steneck, N., eds.; Imperial College Press / World Scientific Publishing: Singapore; Chapter 50, pp. 309-16.
It is the authors' responsibility to identify and declare any personal circumstances or interests that may be perceived as inappropriately influencing the representation or interpretation of clinical research. If there is no conflict, please state here "The authors declare no conflict of interest." This should be conveyed in a separate "Conflicts of Interest" section preceding the "References" sections at the end of the manuscript.
All submitted manuscripts received by the Editorial Office will be checked by a professional in-house Managing Editor to determine whether it is properly prepared and whether the manuscript follows the ethical policies of the journal. Manuscripts that do not fit the journals ethical policy will be rejected before peer-review. Manuscripts that are not properly prepared will be returned to the authors for revision and resubmission. After these checks, the Managing Editor will consult the journals’ Editor-in-Chief or the Guest Editor (or an Editorial Board member in case of a conflict of interest) to determine whether the manuscript fits the scope of the journal and whether it is scientifically sound. No judgment on the significance or potential impact of the work will be made at this stage. Reject decisions at this stage will be verified by the Editor-in-Chief.
Once a manuscript passes the initial checks, it will be assigned to at least two independent experts for peer-review. A single-blind review is applied, where authors' identities are known to reviewers. Peer review comments are confidential and will only be disclosed with the express agreement of the reviewer.
In the case of regular submissions, in-house assistant editors will invite experts, including recommendations by an academic editor.
These experts may also include Editorial Board members and Guest Editors of the journal.
In the case of a special issue, the Guest Editor will advise in the selection of reviewers.
Potential reviewers suggested by the authors may also be considered. Reviewers should not have published with any of the co-authors during the past five years and should not currently work or collaborate with one of the institutes of the co-authors of the submitted manuscript.
Editorial Decision and Revision
Based on the comments and advice of the peer-reviewers, an external editor – usually the Editor-in-Chief or a Guest Editor – will make a decision to accept, reject, or to ask authors to revise the manuscript.
For Minor Revisions the authors will have one week to resubmit their revised manuscript. For Major Revisions the authors will have two weeks to resubmit their revised manuscript. However, authors should contact the editorial office if extended revision time is anticipated.
Authors may appeal a rejection by sending an e-mail to the Editorial Office of the journal. The appeal must provide a detailed justification, including point-by-point responses to the reviewers' and/or Editor's comments. The Managing Editor of the journal will forward the manuscript and relating information (including the identities of the referees) to an Editorial Board member who was not involved in the initial decision-making process. If no appropriate Editorial Board member is available, the editor will identify a suitable external scientist. The Editorial Board member will be asked to give an advisory recommendation on the manuscript and may recommend acceptance, further peer-review, or uphold the original rejection decision. A reject decision at this stage will be final and cannot be revoked.
In the case of a special issue, the Managing Editor of the journal will forward the manuscript and relating information (including the identities of the referees) to the Editor-in-Chief who will be asked to give an advisory recommendation on the manuscript and may recommend acceptance, further peer-review, or uphold the original rejection decision. A reject decision at this stage will be final and cannot be revoked.
Production and Publication
Once accepted, the manuscript will undergo professional copy-editing, English editing, proofreading by the authors, final corrections, pagination, and, publication on the www.mdpi.com website.
During the submission process, authors are pre encouraged to list five names of potential reviewers with the appropriate expertise to review the manuscript. The editors will not necessarily approach these referees. Please provide detailed contact information (address, homepage, phone, e-mail address). The proposed referees should neither be current collaborators of the co-authors nor have published with any of the co-authors of the manuscript within the last five years. Proposed reviewers should be from different institutions to the authors. You may identify appropriate Editorial Board members of the journal as potential reviewers. You may also suggest reviewers from among the authors that you frequently cite in your paper.
This journal is published in English. To facilitate proper peer-reviewing of your manuscript, it is essential that it is submitted in grammatically correct English. If you are not a native English speaker, we strongly recommend that you have your manuscript professionally edited before submission or read by a native English-speaking colleague. Professional editing will mean that reviewers and future readers are better able to read and assess the content of your manuscript. An additional fee of 250 CHF (Swiss Francs) will be charged to authors if extensive English corrections must be done by the Editorial Office. For additional information see the English Editing Guidelines for Authors.
The editors of this journal take the responsibility to enforce a rigorous peer-review process together with strict ethical policies and standards to ensure to add high quality scientific works to the field of scholarly publication. Unfortunately, cases of plagiarism, data falsification, image manipulation, inappropriate authorship credit, and the like, do arise. The editors of Algorithms take such publishing ethics issues very seriously and are trained to proceed in such cases with a zero tolerance policy.
Authors wishing to publish their papers in Algorithms are asked to abide to the following rules:
- Any facts that might be perceived as a possible conflict of interest of the author(s) must be disclosed in the paper prior to submission.
- Authors should accurately present their research findings and include an objective discussion of the significance of their findings.
- Data and methods used in the research need to be presented in sufficient detail in the paper, so that other researchers can replicate the work.
- Raw data should preferably be publicly deposited by the authors before submission of their manuscript. Authors need to at least have the raw data readily available for presentation to the referees and the editors of the journal, if requested. Authors need to ensure appropriate measures are taken so that raw data is retained in full for a reasonable time after publication.
- Simultaneous submission of manuscripts to more than one journal is not tolerated.
- Republishing content that is not novel is not tolerated (for example, an English translation of a paper that is already published in another language will not be accepted).
- If errors and inaccuracies are found by the authors after publication of their paper, they need to be promptly communicated to the editors of this journal so that appropriate actions can be taken. Please refer to our policy regarding publication of publishing addenda and corrections.
- Your manuscript should not contain any information that has already been published. If you include already published figures or images, please obtain the necessary permission from the copyright holder to publish under the CC-BY license.
- Plagiarism, data fabrication and image manipulation are not tolerated.
- Plagiarism is not acceptable in Algorithms submissions.
Plagiarism includes copying text, ideas, images, or data from another source, even from your own publications, without giving any credit to the original source.
Reuse of text that is copied from another source must be between quotes and the original source must be cited. If a study's design or the manuscript's structure or language has been inspired by previous works, these works must be explicitly cited.
If plagiarism is detected during the peer review process, the manuscript may be rejected. If plagiarism is detected after publication, we may publish a correction or retract the paper.
- Image files must not be manipulated or adjusted in any way that could lead to misinterpretation of the information provided by the original image.
Irregular manipulation includes: 1) introduction, enhancement, moving, or removing features from the original image; 2) grouping of images that should obviously be presented separately (e.g., from different parts of the same gel, or from different gels); or 3) modifying the contrast, brightness or color balance to obscure, eliminate or enhance some information.
If irregular image manipulation is identified and confirmed during the peer review process, we may reject the manuscript. If irregular image manipulation is identified and confirmed after publication, we may correct or retract the paper.
Our in-house editors will investigate any allegations of publication misconduct and may contact the authors' institutions or funders if necessary. If evidence of misconduct is found, appropriate action will be taken to correct or retract the publication. Authors are expected to comply with the best ethical publication practices when publishing with MDPI.
In order to maintain the integrity, transparency and reproducibility of research records, authors are strongly encouraged to make their experimental and research data openly available either by depositing into data repositories or by publishing the data and files as supplementary information in this journal.
For papers in which new computer code (e.g., analytical bioinformatics tools or computer simulations) is of central importance, the authors are encouraged to release custom computer code either by depositing in public source code repositories or by publishing the source code as supplementary information to the publication.
Additional data and files can be uploaded as "Supplementary Files" during the manuscript submission process. The supplementary files will also be available to the referees as part of the peer-review process, although referees are not specifically asked to review these files. Accepted file formats include (but are not limited to):
- data tables and spreadsheets (text files, MS Excel, OpenOffice, CSV, XML, etc.)
- text documents (text files, PDF, MS Word, OpenOffice, etc.; text documents will usually be converted to PDF files for publication)
- images (JPEG, PNG, GIF, TIFF, BMP, etc.)
- videos (AVI, MPG, QuickTime, etc.)
- executables (EXE, Java, etc.)
- software source code
Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list.
Large data sets and files should be deposited to specialized service providers (such as Figshare) or institutional/subject repositories, preferably those that use the DataCite mechanism. For a list of specialized repositories for the deposit of scientific and experimental data, please consult databib.org or re3data.org. The data repository name, link to the data set (URL) and accession number, doi or handle number of the data set must be provided in the paper. The journal Data (ISSN 2306-5729) also accepts submissions of data set papers, and the publication of small data sets along with the paper, and/or software source codes is encouraged.