Algorithms for Molecular Biology strongly encourages that all datasets on which the conclusions of the paper rely should be available to readers. We encourage authors to ensure that their datasets are either deposited in publicly available repositories (where available and appropriate) or presented in the main manuscript or additional supporting files whenever possible. Please see Springer Nature’s information on recommended repositories. Where a widely established research community expectation for data archiving in public repositories exists, submission to a community-endorsed, public repository is mandatory. A list of data where deposition is required, with the appropriate repositories, can be found on the Editorial Policies Page.
Manuscripts must be submitted by one of the authors of the manuscript, and should not be submitted by anyone on their behalf. The corresponding author takes responsibility for the article during submission and peer review.
Please note that Algorithms for Molecular Biology levies an article-processing charge on all accepted Research articles; if the corresponding author's institution is a BioMed Central member the cost of the article-processing charge may be covered by the membership (see About page for detail). Please note that the membership is only automatically recognised on submission if the corresponding author is based at the member institution.
To facilitate rapid publication and to minimize administrative costs, Algorithms for Molecular Biology prefers online submission.
Files can be submitted as a batch, or one by one. The submission process can be interrupted at any time; when users return to the site, they can carry on where they left off.
See below for examples of word processor and graphics file formats that can be accepted for the main manuscript document by the online submission system. Additional files of any type, such as movies, animations, or original data files, can also be submitted as part of the manuscript.
During submission you will be asked to provide a cover letter. Use this to explain why your manuscript should be published in the journal, to elaborate on any issues relating to our editorial policies in the 'About Algorithms for Molecular Biology' page, and to declare any potential competing interests.
Assistance with the process of manuscript preparation and submission is available from BioMed Central customer support team.
The following word processor file formats are acceptable for the main manuscript document:
- Microsoft word (DOC, DOCX)
- Rich text format (RTX)
- Portable document format (PDF)
- TeX/LaTeX (use BioMed Central's TeX template)
- DeVice Independent format (DVI)
TeX/LaTeX users: Please use BioMed Central's TeX template and BibTeX stylefile if you use TeX format. During the TeX submission process, please submit your TeX file as the main manuscript file and your bib/bbl file as a dependent file. Please also convert your TeX file into a PDF and submit this PDF as an additional file with the name 'Reference PDF'. This PDF will be used by internal staff as a reference point to check the layout of the article as the author intended. Please also note that all figures must be coded at the end of the TeX file and not inline.
If you have used another template for your manuscript, or if you do not wish to use BibTeX, then please submit your manuscript as a DVI file. We do not recommend converting to RTF.
For all TeX submissions, all relevant editable source must be submitted during the submission process. Failing to submit these source files will cause unnecessary delays in the publication procedures.
Through a special arrangement with LabArchives, LLC, authors submitting manuscripts to Algorithms for Molecular Biology can obtain a complimentary subscription to LabArchives with an allotment of 100MB of storage. LabArchives is an Electronic Laboratory Notebook which will enable scientists to share and publish data files in situ; you can then link your paper to these data. Data files linked to published articles are assigned digital object identifiers (DOIs) and will remain available in perpetuity. Use of LabArchives or similar data publishing services does not replace preexisting data deposition requirements, such as for nucleic acid sequences, protein sequences and atomic coordinates.
Instructions on assigning DOIs to datasets, so they can be permanently linked to publications, can be found on the LabArchives website. Use of LabArchives’ software has no influence on the editorial decision to accept or reject a manuscript.
Authors linking datasets to their publications should include an Availability of supporting data section in their manuscript and cite the dataset in their reference list.
Preparing main manuscript text
The information below details the section headings that you should include in your manuscript and what information should be within each section.
Please note that your manuscript must include a 'Declarations' section including all of the subheadings (please see below for more information).
General guidelines of the journal's style and language are given below.
Overview of manuscript sections for Research articles
Manuscripts for Research articles submitted to Algorithms for Molecular Biology should be divided into the following sections (in this order):
- Title page
- Main text
- List of abbreviations used (if any)
- Competing interests
- Authors' contributions
- Authors' information (if any)
- Illustrations and figures (if any)
- Tables and captions
- Preparing additional files
The Accession Numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets and include the corresponding database name; for example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845, PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].
The databases for which we can provide direct links are: EMBL Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan (DDBJ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).
For reporting standards please see the information in the About section.
The title page should:
- provide the title of the article
- list the full names, institutional addresses and email addresses for all authors
- indicate the corresponding author
- abbreviations within the title should be avoided
- if a collaboration group should be listed as an author, please list the Group name as an author. If you would like the names of the individual members of the Group to be searchable through their individual PubMed records, please include this information in the “acknowledgements” section in accordance with the instructions below. Please note that the individual names may not be included in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.
The Abstract of the manuscript should not exceed 350 words and must be structured into separate sections: Background, the context and purpose of the study; Results, the main findings; Conclusions, brief summary and potential implications. Please minimize the use of abbreviations and do not cite references in the abstract.
Three to ten keywords representing the main content of the article.
The Background section should be written in a way that is accessible to researchers without specialist knowledge in that area and must clearly state - and, if helpful, illustrate - the background to the research and its aims. The section should end with a brief statement of what is being reported in the article.
This section should contain the main body of the article, and can be divided into sections with short informative headings. The manuscript should be organized so as to be as succinct and as clear as possible, but details of structure will depend on the nature of the work being described.
This should state clearly the main conclusions of the research and give a clear explanation of their importance and relevance. Summary illustrations may be included.
List of abbreviations
If abbreviations are used in the text they should be defined in the text at first use, and a list of abbreviations can be provided, which should precede the competing interests and authors' contributions.
A competing interest exists when your interpretation of data or presentation of information may be influenced by your personal or financial relationship with other people or organizations. Authors must disclose any financial competing interests; they should also reveal any non-financial competing interests that may cause them embarrassment were they to become public after the publication of the manuscript.
Authors are required to complete a declaration of competing interests. All competing interests that are declared will be listed at the end of published articles. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'.
When completing your declaration, please consider the following questions:
Financial competing interests
- In the past three years have you received reimbursements, fees, funding, or salary from an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Is such an organization financing this manuscript (including the article-processing charge)? If so, please specify.
- Do you hold any stocks or shares in an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? If so, please specify.
- Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? If so, please specify.
- Do you have any other financial competing interests? If so, please specify.
Non-financial competing interests
Are there any non-financial competing interests (political, personal, religious, ideological, academic, intellectual, commercial or any other) to declare in relation to this manuscript? If so, please specify.
If you are unsure as to whether you, or one your co-authors, has a competing interest please discuss it with the editorial office.
In order to give appropriate credit to each author of a paper, the individual contributions of authors to the manuscript should be specified in this section.
According to ICMJE guidelines, An 'author' is generally considered to be someone who has made substantive intellectual contributions to a published study. To qualify as an author one should 1) have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) have been involved in drafting the manuscript or revising it critically for important intellectual content; 3) have given final approval of the version to be published; and 4) agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.
We suggest the following kind of format (please use initials to refer to each author's contribution): AB carried out the molecular genetic studies, participated in the sequence alignment and drafted the manuscript. JY carried out the immunoassays. MT participated in the sequence alignment. ES participated in the design of the study and performed the statistical analysis. FG conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.
All contributors who do not meet the criteria for authorship should be listed in an acknowledgements section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, a department chair who provided only general support, or those who contributed as part of a large collaboration group.
You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.
Please acknowledge anyone who contributed towards the article by making substantial contributions to conception, design, acquisition of data, or analysis and interpretation of data, or who was involved in drafting the manuscript or revising it critically for important intellectual content, but who does not meet the criteria for authorship. Please also include the source(s) of funding for each author, and for the manuscript preparation. Authors must describe the role of the funding body, if any, in design, in the collection, analysis, and interpretation of data; in the writing of the manuscript; and in the decision to submit the manuscript for publication. Please also acknowledge anyone who contributed materials essential for the study. If a language editor has made significant revision of the manuscript, we recommend that you acknowledge the editor by name, where possible.
If you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records, please ensure that the title of the collaboration Group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.
Please note that individual names may not be present in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.
Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.
Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.
All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. Each reference must have an individual reference number. Please avoid excessive referencing. If automatic numbering systems are used, the reference numbers must be finalized and the bibliography must be fully formatted before submission.
Only articles and abstracts that have been published or are in press, or are available through public e-print/preprint servers, may be cited; unpublished abstracts, unpublished data and personal communications should not be included in the reference list, but may be included in the text and referred to as "unpublished observations" or "personal communications" giving the names of the involved researchers. Obtaining permission to quote personal communications and unpublished data from the cited colleagues is the responsibility of the author. Footnotes are not allowed, but endnotes are permitted. Journal abbreviations follow Index Medicus/MEDLINE. Citations in the reference list should include all named authors, up to the first six before adding 'et al.'..
Any in press articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.
An Endnote style file is available.
Examples of the Algorithms for Molecular Biology reference style are shown below. Please ensure that the reference style is followed precisely; if the references are not in the correct style they may have to be retyped and carefully proofread.
All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link, such as for weblogs, then they should be included in the reference.
Authors may wish to make use of reference management software to ensure that reference lists are correctly formatted. An example of such software is Papers, which is part of Springer Science+Business Media.
Examples of the Algorithms for Molecular Biology reference style
Article within a journal
Smith JJ. The world of science. Am J Sci. 1999;36:234-5.
Article within a journal (no page numbers)
Rohrmann S, Overvad K, Bueno-de-Mesquita HB, Jakobsen MU, Egeberg R, Tjønneland A, et al. Meat consumption and mortality - results from the European Prospective Investigation into Cancer and Nutrition. BMC Medicine. 2013;11:63.
Article within a journal by DOI
Slifka MK, Whitton JL. Clinical implications of dysregulated cytokine production. Dig J Mol Med. 2000; doi:10.1007/s801090000086.
Article within a journal supplement
Frumin AM, Nussbaum J, Esposito M. Functional asplenia: demonstration of splenic activity by bone marrow scan. Blood 1979;59 Suppl 1:26-32.
Book chapter, or an article within a book
Wyllie AH, Kerr JFR, Currie AR. Cell death: the significance of apoptosis. In: Bourne GH, Danielli JF, Jeon KW, editors. International review of cytology. London: Academic; 1980. p. 251-306.
OnlineFirst chapter in a series (without a volume designation but with a DOI)
Saito Y, Hyuga H. Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Top Curr Chem. 2007. doi:10.1007/128_2006_108.
Complete book, authored
Blenkinsopp A, Paxton P. Symptoms in the pharmacy: a guide to the management of common illness. 3rd ed. Oxford: Blackwell Science; 1998.
Doe J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 1999. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.
Healthwise Knowledgebase. US Pharmacopeia, Rockville. 1998. http://www.healthwise.org. Accessed 21 Sept 1998.
Supplementary material/private homepage
Doe J. Title of supplementary material. 2000. http://www.privatehomepage.com. Accessed 22 Feb 2000.
Doe, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (1999). Accessed 25 Dec 1999.
Doe, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (1999). Accessed 12 Nov 1999.
ISSN International Centre: The ISSN register. http://www.issn.org (2006). Accessed 20 Feb 2007.
Dataset with persistent identifier
Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, et al. Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. 2011. http://dx.doi.org/10.5524/100012.
Preparing illustrations and figures
Illustrations should be provided as separate files, not embedded in the text file. Each figure should include a single illustration and should fit on a single page in portrait format. If a figure consists of separate parts, it is important that a single composite illustration file be submitted which contains all parts of the figure. There is no charge for the use of color figures.
The following file formats can be accepted:
- PDF (preferred format for diagrams)
- DOCX/DOC (single page only)
- PPTX/PPT (single slide only)
- PNG (preferred format for photos or images)
The legends should be included in the main manuscript text file at the end of the document, rather than being a part of the figure file. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals - i.e. Figure 1, 2, 3 etc); short title of figure (maximum 15 words); detailed legend, up to 300 words.
Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.
Preparing a personal cover page
If you wish to do so, you may submit an image which, in the event of publication, will be used to create a cover page for the PDF version of your article. The cover page will also display the journal logo, article title and citation details. The image may either be a figure from your manuscript or another relevant image. You must have permission from the copyright to reproduce the image. Images that do not meet our requirements will not be used.
Images must be 300dpi and 155mm square (1831 x 1831 pixels for a raster image).
Allowable formats - EPS, PDF (for line drawings), PNG, TIFF (for photographs and screen dumps), JPEG, BMP, DOC, PPT, CDX, TGF (ISIS/Draw).
Each table should be numbered and cited in sequence using Arabic numerals (i.e. Table 1, 2, 3 etc.). Tables should also have a title (above the table) that summarizes the whole table; it should be no longer than 15 words. Detailed legends may then follow, but they should be concise. Tables should always be cited in text in consecutive numerical order.
Smaller tables considered to be integral to the manuscript can be pasted into the end of the document text file, in A4 portrait or landscape format. These will be typeset and displayed in the final published form of the article. Such tables should be formatted using the 'Table object' in a word processing program to ensure that columns of data are kept aligned when the file is sent electronically for review; this will not always be the case if columns are generated by simply using tabs to separate text. Columns and rows of data should be made visibly distinct by ensuring that the borders of each cell display as black lines. Commas should not be used to indicate numerical values. Color and shading may not be used; parts of the table can be highlighted using symbols or bold text, the meaning of which should be explained in a table legend. Tables should not be embedded as figures or spreadsheet files.
Larger datasets or tables too wide for a landscape page can be uploaded separately as additional files. Additional files will not be displayed in the final, laid-out PDF of the article, but a link will be provided to the files as supplied by the author.
Tabular data provided as additional files can be uploaded as an Excel spreadsheet (.xls ) or comma separated values (.csv). As with all files, please use the standard file extensions.
Preparing additional files
Although Algorithms for Molecular Biology does not restrict the length and quantity of data included in an article, we encourage authors to provide datasets, tables, movies, or other information as additional files.
Please note: All Additional files will be published along with the article. Do not include files such as patient consent forms, certificates of language editing, or revised versions of the main manuscript document with tracked changes. Such files should be sent by email to firstname.lastname@example.org, quoting the Manuscript ID number.
Results that would otherwise be indicated as "data not shown" can and should be included as additional files. Since many weblinks and URLs rapidly become broken, Algorithms for Molecular Biology requires that supporting data are included as additional files, or deposited in a recognized repository. Please do not link to data on a personal/departmental website. The maximum file size for additional files is 20 MB each, and files will be virus-scanned on submission.
Additional files can be in any format, and will be downloadable from the final published article as supplied by the author. We recommend CSV rather than PDF for tabular data.
Certain supported files formats are recognized and can be displayed to the user in the browser. These include most movie formats (for users with the Quicktime plugin), mini-websites prepared according to our guidelines, chemical structure files (MOL, PDB), geographic data files (KML).
If additional material is provided, please list the following information in a separate section of the manuscript text:
- File name (e.g. Additional file 1)
- File format including the correct file extension for example .pdf, .xls, .txt, .pptx (including name and a URL of an appropriate viewer if format is unusual)
- Title of data
- Description of data
Additional files should be named "Additional file 1" and so on and should be referenced explicitly by file name within the body of the article, e.g. 'An additional movie file shows this in more detail [see Additional file 1]'.
Additional file formats
Ideally, file formats for additional files should not be platform-specific, and should be viewable using free or widely available tools. The following are examples of suitable formats.
- Additional documentation
PDF (Adode Acrobat)
SWF (Shockwave Flash)
MP4 (MPEG 4)
- Tabular data
XLS, XLSX (Excel Spreadsheet)
CSV (Comma separated values)
As with figure files, files should be given the standard file extensions.
Small self-contained websites can be submitted as additional files, in such a way that they will be browsable from within the full text HTML version of the article. In order to do this, please follow these instructions:
- Create a folder containing a starting file called index.html (or index.htm) in the root.
- Put all files necessary for viewing the mini-website within the folder, or sub-folders.
- Ensure that all links are relative (ie "images/picture.jpg" rather than "/images/picture.jpg" or "http://yourdomain.net/images/picture.jpg" or "C:\Documents and Settings\username\My Documents\mini-website\images\picture.jpg") and no link is longer than 255 characters.
- Access the index.html file and browse around the mini-website, to ensure that the most commonly used browsers (Internet Explorer and Firefox) are able to view all parts of the mini-website without problems, it is ideal to check this on a different machine.
- Compress the folder into a ZIP, check the file size is under 20 MB, ensure that index.html is in the root of the ZIP, and that the file has .zip extension, then submit as an additional file with your article.
Style and language
Currently, Algorithms for Molecular Biology can only accept manuscripts written in English. Spelling should be US English or British English, but not a mixture.
There is no explicit limit on the length of articles submitted, but authors are encouraged to be concise.
Algorithms for Molecular Biology will not edit submitted manuscripts for style or language; reviewers may advise rejection of a manuscript if it is compromised by grammatical errors. Authors are advised to write clearly and simply, and to have their article checked by colleagues before submission. In-house copyediting will be minimal. Non-native speakers of English may choose to make use of a copyediting service.
Help and advice on scientific writing
The abstract is one of the most important parts of a manuscript. For guidance, please visit our page on Writing titles and abstracts for scientific articles.
Abbreviations should be used as sparingly as possible. They should be defined when first used and a list of abbreviations can be provided following the main manuscript text.
- Please use double line spacing.
- Type the text unjustified, without hyphenating words at line breaks.
- Use hard returns only to end headings and paragraphs, not to rearrange lines.
- Capitalize only the first word, and proper nouns, in the title.
- All pages should be numbered.
- Use the Algorithms for Molecular Biology reference format (see above-listed "Examples of the Algorithms for Molecular Biology reference style").
- Footnotes are not allowed, but endnotes are permitted.
- Please do not format the text in multiple columns.
- Greek and other special characters may be included. If you are unable to reproduce a particular special character, please type out the name of the symbol in full. Please ensure that all special characters used are embedded in the text, otherwise they will be lost during conversion to PDF.
- Genes, mutations, genotypes, and alleles should be indicated in italics, and authors are required to use approved gene symbols, names, and formatting. Protein products should be in plain type.
SI units should be used throughout (liter and molar are permitted, however).