About Biology Direct

This page includes information about the aims and scope of Biology Direct, editorial policies, open access and article-processing charges, the peer review process and other information. For details of how to prepare and submit a manuscript through the online submission system, please see the instructions for authors.

Aims & scope

Biology Direct serves the life science research community as an open access, peer-reviewed online journal, providing authors and readers with an alternative to the traditional model of peer review. Biology Direct considers original research articles, hypotheses, comments, discovery notes and reviews in selected subject areas, and will eventually cover the full spectrum of biology.

Subject areas already launched include:

•  Genomics, Bioinformatics and Systems Biology - Edited by Eugene Koonin, Laura Landweber, & David Lipman.
•  Immunology - Edited by Neil S Greenspan & David R Kaplan.
•  Mathematical Biology - Edited by Marek Kimmel.

The key aim of Biology Direct is to provide authors and readers with a novel system of peer review. This includes making the author responsible for selecting potentially suitable reviewers for their manuscript, from the journal's Editorial Board; making the peer review process open rather than anonymous; and making the reviewers' reports public, thus increasing the responsibility of the referees and eliminating sources of abuse in the refereeing process.

Edited by Eugene V Koonin, Laura F Landweber and David J Lipman, Biology Direct is supported by an international Editorial Board.

Open access

All articles published by Biology Direct are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. Further information about open access can be found here.

Authors of articles published in Biology Direct are the copyright holders of their articles and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate the article, according to the BioMed Central copyright and license agreement.

Article-processing charges

Open access publishing is not without costs. Biology Direct therefore levies an article-processing charge of £1250/$1975/€1555 for each article accepted for publication. We routinely waive charges for authors from low-income countries. Generally, if the submitting author's institution is a Member the cost of the article-processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are Supporter Members, however, a discounted article-processing charge is payable by the author. For further details, see our article-processing charge page. A limited number of waivers for article-processing charges are also available at the editors' discretion, and authors wishing to apply for these waivers should contact the editors.

Indexing services

Following publication in Biology Direct, the full-text of each article is deposited immediately and permanently archived in PubMed Central, the US National Library of Medicine's full-text repository of life science literature, and also in repositories in e-Depot, the National Library of the Netherlands' digital archive of electronic publications. Biology Direct is included in PubMed and all major bibliographic databases. A complete list of indexing web services that include BioMed Central's journals can be found here.

Biology Direct is tracked by Thomson Reuters (ISI) and has an impact factor of 3.74

Publication and peer review process

Content overview

Biology Direct aims to publish original research articles, hypotheses, and reviews from the full spectrum of biology; the first subject areas launched are Genomics, Bioinformatics, Systems Biology and Immunology and Mathematical Biology. Further subject areas will be launched from time to time until the full spectrum of biology is covered. Subjects covered will include any aspect of molecular, cellular, organismal or population biology, as well as methods, theoretical and computational biology, comparative biology, and evolution. The journal aims to publish primarily articles that address salient aspects of fundamental problems in biology and, ideally, offer new perspectives on such problems.

Biology Direct considers the following types of articles:

Research: reports of data from original research.

Reviews: authoritative, critical discussions of any subject within the scope of the journal. These articles are usually written by opinion leaders that have been invited by the Editorial Board, but proposals (directed to one of the Editors in Chief) are welcome.

Hypotheses: short articles presenting an untested original hypothesis backed solely by previously published results rather than any new evidence.

Opinions: brief articles that express expert opinions and new views on major subjects within the scope of the journal.

Discovery notes: brief reports of specific discoveries made by computational analysis of nucleic acid and/or protein sequences, structures or other data, with novel observations and conclusions about the function, organization, or evolution of proteins, genes or genomes.

Peer-review policies

Biology Direct aims to provide a unique service to authors and readers of research articles, with a novel system of peer review. Key peer review aims are:

• To remove the journal's role in reviewer selection, making the author responsible for suggesting suitable reviewers from the journal's Editorial Board.
• To make the process of peer review open, rather than anonymous, thus eliminating the principal sources of abuse in the refereeing process.
• By making the reviewers' reports public, to increase the responsibility of the referees and to provide readers with pointers as to the content and value of a publication.

These aims will be put into practice as follows.

1. The Editors-in-Chief will assemble, for each subject area, a panel of potential reviewers who have agreed in advance to serve the journal and will form the Editorial Board.
2. An author submitting a research article to the journal will consult the relevant subject panel and suggest appropriate Editorial Board members to peer-review the article. The peer review process will then be coordinated by BioMed Central staff, who will invite the reviewers on the author's behalf. In order to be eligible for publication in Biology Direct, three Editorial Board members are required to agree to assume responsibility for reviewing the manuscript.
3. The journal will insist that the initially requested reviewers are drawn from the Editorial Board, however Editorial Board members can nominate a reviewer in their place. Only reviewers directly nominated by an Editorial Board member are eligible for review.
4. In essence, an article is rejected from the journal if three Editorial Board members do not agree to review it.
5. Any reviewer-author pair (both directions) will be allowed to appear in the journal no more than four times a year.
6. Any author will be allowed to publish no more than two articles per year with the same three reviewers.
7. Reviewers are asked to undertake a two-stage review, because once they agree formally to review an article they are essentially recommending eventual acceptance and publication. The first step for a reviewer is to skim-read the article so as to allow the reviewer to form an overall opinion of the article; if they feel they cannot have their name associated with the publication of this article, they can decline to provide a formal review. But if they agree to review, the second step is for the reviewer to prepare comments for the author but also, if they wish, to prepare 'public' comments, however critical, that will appear alongside the final version of the article when it is published. The reviewer comments to be published can take into account any revisions to the manuscript and therefore might differ substantially from the original comments to the authors, at the reviewer's discretion. The reviewer can also choose to publish no comments with the manuscript in which case it will be indicated, under the reviewer's name, that "This reviewer made no comments for publication".
8. There will be a fairly tight time frame for the review process: if an Editorial Board member does not respond to a request for review within 72 hours, this will be considered to be a 'decline to review' and another reviewer will be sought. However, once an Editorial Board member agrees to review a manuscript, s/he will have 3 weeks to deliver the review. If the reviewer does not deliver comments promptly, the author will be in a position to elect to publish the manuscript accompanied by the name of the reviewer but without comments.
9. The authors will be in a position to withdraw the manuscript if they do not wish to see it published alongside the reviews that have been received. The same article may not then be submitted through other Editorial Board members.
10. As a safeguard against pseudoscience as well as manuscripts that have no significant scientific substance, an Editorial Board member reviewing a manuscript will have the option, in addition to writing a negative review, to alert the Editors-in-Chief that, in his/her opinion, a particular manuscript is not a legitimate scientific work and therefore should not be published in any form. The Editors-in-Chief will make the final decision in such cases. For further information, please see the instructions on how to proceed with Biology Direct's system of peer review. Please note the peer review requirements for discovery notes differ slightly from the process outlined above; please click here for full details.

Authors will be able to check the progress of their manuscript through the submission system at any time by logging into My Biology Direct, a personalized section of the site.

Portability of peer review

In order to support efficient and thorough peer review, we aim to reduce the number of times a manuscript is re-reviewed after rejection from Biology Direct, thereby speeding up the publication process and reducing the burden on peer reviewers. Therefore, please note that, if a manuscript is not accepted for publication in Biology Direct and the authors choose to submit a revised version to another BioMed Central journal, we will pass the reviews on to the other journal's editors at the authors' request. We will reveal the reviewers' names to the handling editor for editorial purposes unless reviewers let us know when they return their report that they do not wish us to share their report with another BioMed Central journal.

Reprints

High-quality, bound reprints can be purchased for all articles published. Please see our reprints website for further information about ordering reprints, and to enquire about further details, including fees, please contact BioMed Central's reprint service.

Supplements

Biology Direct will consider supplements based on proceedings (full articles or meeting abstracts), reviews or research. All articles submitted for publication in supplements are subject to peer review. Published supplements are fully searchable and freely accessible online and can also be produced in print. All full length articles (proceedings, reviews or research articles) are indexed by PubMed. PubMed displays the title of the supplement only in the case of meeting abstract collections. For further information, please contact us.

Editorial policies

Any manuscript, or substantial parts of it, submitted to the journal must not be under consideration by any other journal. In general, the manuscript should not have already been published in any journal or other citable form, although it may have been deposited on a preprint server. Information on duplicate/overlapping publications can be found here. Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party.

Correspondence concerning articles published in Biology Direct is encouraged. A 'post a comment' feature is available on all articles published by Biology Direct. Comments will be moderated by the editorial office (see our Comment policy for further information) and linked to the full-text version of the article, if suitable.

Editorial standards

BioMed Central is a member of the Committee on Publication Ethics (COPE) and endorses the World Association of Medical Editors (WAME) Policy Statement on Geopolitical Intrusion on Editorial Decisions.

Ethical guidelines

Submission of a manuscript to Biology Direct implies that all authors have read and agreed to its content, and that any experimental research that is reported in the manuscript has been performed with the approval of an appropriate ethics committee. Research carried out on humans must be in compliance with the Helsinki Declaration, and any experimental research on animals must follow internationally recognized guidelines. A statement to this effect must appear in the Methods section of the manuscript, including the name of the body which gave approval, with a reference number where appropriate. Informed consent must also be documented. Manuscripts may be rejected if the editorial office considers that the research has not been carried out within an ethical framework, e.g. if the severity of the experimental procedure is not justified by the value of the knowledge gained.

For all articles that include information or clinical photographs relating to individual patients, written and signed consent from each patient to publish must also be made available if requested by the editorial staff.

Biology Direct's publisher, BioMed Central, has a legal responsibility to ensure that its journals do not publish material that infringes copyright, or that includes libellous or defamatory content. If, on review, your manuscript is perceived to contain potentially libellous content the journal Editors, with assistance from the publisher if required, will work with authors to ensure an appropriate outcome is reached.

The involvement of scientific (medical) writers or anyone else who assisted with the preparation of the manuscript content should be acknowledged, along with their source of funding, as described in the European Medical Writers Association (EMWA) guidelines on the role of medical writers in developing peer-reviewed publications. If medical writers are not listed among the authors, their role should be acknowledged explicitly.

Standards of reporting

Biology Direct supports initiatives aimed at improving the reporting of biomedical research. We recommend authors refer to the EQUATOR network website for further information on the available reporting guidelines for health research, and the MIBBI Portal for prescriptive checklists for reporting biological and biomedical research where applicable. Authors are requested to make use of these when drafting their manuscript and peer reviewers will also be asked to refer to these checklists when evaluating these studies. Checklists are available for a number of study designs, including randomized controlled trials (CONSORT), systematic reviews (PRISMA), observational studies (STROBE), meta-analyses of observational studies (MOOSE), diagnostic accuracy studies (STARD) and qualitative studies (RATS). For authors of systematic reviews, an additional file, linked from the Methods section, should reproduce all details concerning the search strategy. For an example of how a search strategy should be presented, see the Cochrane Reviewers' Handbook.

For mutation nomenclature please use the guidelines suggested by the Human Genome Variation Society, and the recommended gene name by consulting the appropriate genetic nomenclature database, e.g., HUGO for human genes, and the International Committee on Standardized Genetic Nomenclature for Mice. We encourage the use of standardized terms for human phenotypes, such as those proposed by the Elements of Morphology working group (see: http://research.nhgri.nih.gov/morphology/index.cgi).

Data and materials release

Submission of a manuscript to Biology Direct implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article.

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.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

The accession numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets with 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).

Mass spectrometry

Mass spectrometry data should be supplied in the mzML format recommended by the HUPO Protein Standards Initiative Mass Spectrometry Standards Working Group guidelines (http://www.psidev.info/index.php?q=node/80). We also recommend that the data is deposited in the ProteomeExchange (http://proteomexchange.org/) through the PRIDE website (http://www.ebi.ac.uk/pride/), and protein interaction data can be submitted to members of the IMEx consortium (http://www.imexconsortium.org/submit-your-data).

Structures

Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

Chemical structures and assays

Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

Functional genomics data (such as microarray, RNA-seq or ChIP-seq data)

Where appropriate, authors should adhere to the standards proposed by the Functional Genomics Data Society and must deposit microarray data in MIAME-compliant format in one of the public repositories, such as ArrayExpress or Gene Expression Omnibus (GEO). Deposition of high-throughput functional genomics sequencing data (such as RNA-Seq or ChIP-Seq data) with ArrayExpress or GEO in compliance with MINSEQE is also required.

Computational modeling

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.

Plasmids

We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.

Appeals and complaints

Authors who wish to appeal a rejection or make a complaint should, in the first instance, contact the Editor-in-Chief who will provide details of the journal's complaints procedure.

Competing interests

Biology Direct requires authors to declare any competing financial or other interest in relation to their work. 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'.

Plagiarism detection

Biology Direct's publisher, BioMed Central, is a member of the CrossCheck plagiarism detection initiative. In cases of suspected plagiarism CrossCheck is available to the editors of Biology Direct to detect instances of overlapping and similar text in submitted manuscripts. CrossCheck is a multi-publisher initiative allowing screening of published and submitted content for originality.

Citing articles in Biology Direct

Articles in Biology Direct should be cited in the same way as articles in a traditional journal. Because articles are not printed, they do not have page numbers; instead, they are given a unique article number.

Article citations follow this format:

Authors: Title. Biol Direct [year], [volume number]:[article number].

e.g. Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, Griffin JL: Increased hepatic oxidative metabolism distinguishes the action of Peroxisome Proliferator-Activated Receptor delta from Peroxisome Proliferator-Activated Receptor gamma in the Ob/Ob mouse. Biol Direct 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Biology Direct?

High visibility

Biology Direct's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience. Articles that have been especially highly accessed are highlighted with a 'Highly accessed' graphic, which appears on the journal's contents pages and search results.

Speed of publication

Biology Direct offers a fast publication schedule whilst maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles are published with their final citation immediately upon acceptance in a provisional PDF form. The article will subsequently be published in both fully browsable web form, and as a formatted PDF; the article will then be available through Biology Direct, BioMed Central and PubMed Central and will also be included in PubMed.

Flexibility

Online publication in Biology Direct gives authors the opportunity to publish large datasets, large numbers of color illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other papers).

Promotion and press coverage

Articles published in Biology Direct are included in article alerts and regular email updates. Some may be included in abstract books mailed to academics and are highlighted on Biology Direct's pages and on the BioMed Central homepage.

In addition, articles published in Biology Direct may be promoted by press releases to the general or scientific press. These activities increase the exposure and number of accesses for articles published in Biology Direct. A list of articles recently press-released by journals published by BioMed Central is available here.

Copyright

Authors of articles published in Biology Direct retain the copyright of their articles and are free to reproduce and disseminate their work (for further details, see the BioMed Central copyright and license agreement).

For further information about the advantages of publishing in a journal from BioMed Central, please click here.