Content we consider
Aims and scope
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles describing novel computational algorithms and software, models and tools, including statistical methods, machine learning and artificial intelligence, as well as systems biology.
BMC Bioinformatics does not make editorial decisions on the basis of the interest of a study or its likely impact. Studies must be scientifically valid; for research articles this includes a scientifically sound research question, the use of suitable methods and analysis, and following community-agreed standards relevant to the research field.
All articles published by BMC Bioinformatics 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.
As authors of articles published in BMC Bioinformatics you are the copyright holders of your article and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate your article, according to the BMC license agreement.
For those of you who are US government employees or are prevented from being copyright holders for similar reasons, BMC can accommodate non-standard copyright lines. Please contact us if further information is needed.
BMC Bioinformatics follows the policies of the BMC journals, unless otherwise noted below which are designed to support our commitment to open data sharing.
Availability of datasets
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, can be found on the Editorial Policies Page.
BMC Bioinformatics 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. If a dataset is not able to be deposited in any of the above repositories due to legal guidelines or ethical reasons, this must be clearly stated in the “Availability of Data and Materials” section.
BMC endorses the Force 11 Data Citation Principles and requires that all publicly available datasets be fully referenced in the reference list with an accession number or unique identifier such as a digital object identifier (DOI).
Authors are required to formally cite any datasets stored in external repositories that are mentioned within their manuscript, including the main datasets that are the focus of the submission, as well as any other datasets that have been used in the work. For previously published datasets, we ask authors to cite both the related research articles and the datasets themselves. All methods, software, and code developed for the manuscript should include a citation on the reference list.
All Springer Nature journals, including BMC Bioinformatics, are participants in the Initiative for Open Citations. As such, data citations are included in full in the formal reference list, exported to Crossref and are openly available.
An author list and title for the dataset should be included in the data citation, and should reflect the author(s) and dataset title recorded at the repository. If author or title is not recorded by the repository, these should not be included in the data citation. The name of the data-hosting repository, URL to the dataset and year the data were made available are required for all data citations. For DOI-based (e.g. figshare or Dryad) repositories the DOI URL should be used. For repositories using accessions (e.g. SRA or GEO) an identifiers.org URL should be used where available. Please refer to the following examples of data citation for guidance:
- Zhang, Q-L., Chen, J-Y., Lin, L-B., Wang, F., Guo, J., Deng, X-Y. Characterization of ladybird Henosepilachna vigintioctopunctata transcriptomes across various life stages. figshare https://doi.org/10.6084/m9.figshare.c.4064768.v3 (2018).
- NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP121625 (2017).
- Barbosa, P., Usie, A. and Ramos, A. M. Quercus suber isolate HL8, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:PKMF00000000 (2018).
- DNA Data Bank of Japan https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004814 (2016).
Availability of computer code and software
Authors must make available upon request, to editors and reviewers, any previously unreported custom computer code or algorithm used to generate the data presented in the manuscript. If published, the software application/tool should be readily available to any scientist wishing to use it for non-commercial purposes, without restrictions (such as the need for a material transfer agreement). If the implementation is not made freely available, then the manuscript should focus clearly on the development of the underlying method and not discuss the tool in any detail.
A statement describing how software or custom code can be accessed must be included in the Declaration section “Availability of Data and Materials". License information for the software or method should also be stated clearly in the “Availability of Data and Materials section” and on the repository site.
This section should include a link to the most recent version of your software or code (e.g. GitHub or Sourceforge or Code Ocean) as well as a link to the archived version referenced in the manuscript. The software or code should be archived in an appropriate repository with a DOI or other unique identifier. For software in GitHub, we recommend using Zenodo.
Code with an assigned DOI must be formally cited and listed in the References section of the manuscript.
Availability of research materials
BMC Bioinformatics follows the BMC editorial policies for the sharing of research materials.
Submission of a manuscript to a BMC journal implies that 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. It is acceptable to request reasonable payment to cover costs of distribution and reagents may be made available via commercial or non-commercial third party providers. Any restrictions on materials availability, including if materials are to be distributed by a for-profit company, must be clearly stated in the paper. As per our policy on authorship responsibilities, it is expected that the corresponding author (or relevant designated authors) will be responsible for materials availability unless otherwise stated.
BMC Bioinformatics encourages study pre-registration and pre-registration of analysis plans in public repositories; details of pre-registration should be provided in the manuscript.
BMC Bioinformatics welcomes submission of replication studies that provide new insights into previously published results and will evaluate these submissions with the same editorial standards we apply to other submissions.
Standards of reporting
BMC Bioinformatics advocates complete and transparent reporting of research and follows the BMC editorial policies on standards of reporting. Additional information is available through the journal’s submission guidelines.
Helpful resources for sharing your research data
We are committed to supporting researchers in sharing their research data, and getting the credit they deserve. Here are some useful resources to help:
Open access publishing is not without costs. BMC Bioinformatics therefore levies an article-processing charge of £1990.00/$2790.00/€2290.00 for each article accepted for publication, plus VAT or local taxes where applicable.
If the corresponding author's institution participates in our open access membership program, some or all of the publication cost may be covered (more details available on the membership page). We routinely waive charges for authors from low-income countries. For other countries, article-processing charge waivers or discounts are granted on a case-by-case basis to authors with insufficient funds. Authors can request a waiver or discount during the submission process. For further details, see our article-processing charge page.
Visit Springer Nature’s open access funding & support services for information about research funders and institutions that provide funding for APCs.
Springer Nature offers agreements that enable institutions to cover open access publishing costs. Learn more about our open access agreements to check your eligibility and discover whether this journal is included.
For more information on APCs please see our Journal Pricing FAQs
All articles published in BMC Bioinformatics are included in:
- Biological Abstracts
- Science Citation Index Expanded
The full text of all articles is deposited in digital archives around the world to guarantee long-term digital preservation. You can also access all articles published by BioMed Central on SpringerLink.
Peer-review is the system used to assess the quality of a manuscript before it is published. Independent researchers in the relevant research area assess submitted manuscripts for originality, validity and significance to help editors determine whether the manuscript should be published in their journal. You can read more about the peer-review process here.
In cases where the journal is unable to find sufficient peer reviewers, the services of a publishing partner, Research Square, may be used to identify suitable reviewers and provide reports to avoid further delays for authors. Reviewers recruited by Research Square are paid a small honorarium for completing the review within a specified timeframe. Honoraria are paid regardless of the reviewer recommendation. With Research Square, a double-anonymous peer review system is in operation.
In cases where reports have been obtained by Research Square, the peer review reports will be unsigned unless the reviewer opts in to sign the report.
BMC Bioinformatics operates a transparent peer-review system, where, if the article is published, the reviewer reports are published online alongside the article under a Creative Commons Attribution License 4.0 but the reviewer is not named.
The benefit of transparent peer review is that it increases transparency. In addition, published reports can serve an educational purpose in helping facilitate training and research into peer review.
Manuscripts submitted to BMC Bioinformatics are assessed by our editors and/or peer reviewers. Editor(s) are expected to obtain a minimum of two peer reviewers for manuscripts reporting primary research or secondary analysis of primary research. It is recognized that in some exceptional circumstances, particularly in niche and emerging fields, it may not be possible to obtain two independent peer reviewers. In such cases, Editor(s) may wish to make a decision to publish based on one peer review report. When making a decision based on one report, Editor(s) are expected to only do so if the peer review report meets the standards set out in the Springer Nature Code of Conduct (section Peer-Review). Senior Editorial Board Members of BMC Bioinformatics handle manuscripts in a broad range of topics within their general areas of expertise, in addition to advising on editorial board and journal development. The Senior Editorial Board is selected based on exceptional contributions to the journal. The Editorial Board Members manage the peer review process and make final decisions on whether papers should be accepted.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We do not make editorial decisions on the basis of the interest of a study or its likely impact. Studies must be scientifically valid; for research articles this includes a scientifically sound research question, the use of suitable methods and analysis, and following community-agreed standards relevant to the research field.
Specific criteria for other article types can be found in the submission guidelines.
All articles submitted to Collections and Special issues are peer reviewed in line with the journal’s standard peer review policy and are subject to all of the journal’s standard editorial and publishing policies. This includes the journal’s policy on competing interests. The Editors declare no competing interests with the submissions which they have handled through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editor who has no competing interests.
All manuscripts submitted to BMC Bioinformatics should adhere to BioMed Central's editorial policies.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Authors who wish to appeal a rejection or make a complaint should follow the procedure outlined in the BMC Editorial Policies.
Articles in BMC Bioinformatics 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. BMC Bioinformatics [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. BMC Bioinformatics 2009, 1:115.
refers to article 115 from Volume 1 of the journal.
Benefits of publishing with BMC
BMC Bioinformatics's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience.
Speed of publication
BMC Bioinformatics 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 will be published with their final citation after acceptance, in both fully browsable web form, and as a formatted PDF.
Online publication in BMC Bioinformatics gives you 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 articles).
Promotion and press coverage
Articles published in BMC Bioinformatics are included in article alerts and regular email updates. Some may be highlighted on BMC Bioinformatics’s pages and on the BMC homepage.
In addition, articles published in BMC Bioinformatics 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 BMC Bioinformatics. A list of articles recently press-released by journals published by BMC is available here.
As an author of an article published in BMC Bioinformatics you retain the copyright of your article and you are free to reproduce and disseminate your work (for further details, see the BMC license agreement).
For further information about the advantages of publishing in a journal from BMC, please click here.
Annual Journal Metrics
15 days to first decision for all manuscripts (Median)
56 days to first decision for reviewed manuscripts only (Median)
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