About Plant Methods

This page includes information about the aims and scope of Plant Methods, 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

Plant Methods is an open access, peer-reviewed online journal that encompasses all aspects of technological innovation in the plant sciences.

There is no doubt that we have entered an exciting new era in plant biology. The completion of the Arabidopsis genome sequence, and the rapid progress being made in other plant genomics projects are providing unparalleled opportunities for progress in all areas of plant science. Nevertheless, enormous challenges lie ahead if we are to understand the function of every gene in the genome, and how the individual parts work together to make the whole organism. Achieving these goals will require an unprecedented collaborative effort, combining high-throughput, system-wide technologies with more focused approaches that integrate traditional disciplines such as cell biology, biochemistry and molecular genetics.

Technological innovation is probably the most important catalyst for progress in any scientific discipline. Yet to date there has been no plant journal specialising on the development and application of new techniques. The result is that technical creativity has not being given the high-profile platform it needs and deserves. Plant Methods aims to redress the balance by promoting and rapidly disseminating technological advances in plant biology. The goals of the journal are to stimulate the development and adoption of new and improved techniques and research tools and, where appropriate, to promote consistency of methodologies for better integration of data from different laboratories.

Open access

All articles published by Plant Methods 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 Plant Methods 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. Plant Methods therefore levies an article-processing charge of £1095/$1765/€1365 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 Plant Methods, 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. Plant Methods 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.

Plant Methods is tracked by Thomson Reuters (ISI) and has an impact factor of 3.28

Publication and peer review process

Criteria for publication

Plant Methods considers the following types of articles:

• Research: reports of data from original research that is principally based on the application of a new experimental method or protocol. The method must be described in detail and must be either completely new or must offer a significant advance on what is currently available.
• Reviews: comprehensive, authoritative, descriptions 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.
• Book reviews: short summaries of the strengths and weaknesses of a book. They should evaluate its overall usefulness to the intended audience.
• Commentaries: short, focused and opinionated articles on any subject within the scope of the journal. These articles are usually related to a contemporary issue, such as recent research findings, and are often written by opinion leaders.
• Database articles: describe a new database or a substantial improvement of an existing database.
• Methodology articles: present a new experimental method, test or procedure. The method described may either be completely new, or may offer a better version of an existing method.
• Software articles: describe the source code for software applications, tools or algorithm implementations. Typically, an archive of the source code of the current version of the software should be included with the submitted manuscript as a supplementary file.

Peer-review policies

Manuscripts will be assigned to a Monitoring Editor, who will appoint at least two referees. On receipt of their reports the Monitoring Editor will make a recommendation to accept, to accept with minor revisions, to request major revisions and resubmission, or to reject. No manuscript will be rejected without being assessed by a member of the Editorial Board and one other expert.

Authors will be able to check the progress of their manuscript through the submission system at any time by logging into My Plant Methods, 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 Plant Methods, 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 Plant Methods 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

Plant Methods 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 Plant Methods is encouraged. A 'post a comment' feature is available on all articles published by Plant Methods. 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 Plant Methods 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.

Plant Methods'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

Plant Methods 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 Plant Methods 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

Plant Methods 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

Plant Methods'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 Plant Methods 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 Plant Methods

Articles in Plant Methods 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. Plant Methods [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. Plant Methods 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Plant Methods?

High visibility

Plant Methods'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

Plant Methods 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 Plant Methods, BioMed Central and PubMed Central and will also be included in PubMed.

Flexibility

Online publication in Plant Methods 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 Plant Methods are included in article alerts and regular email updates. Some may be included in abstract books mailed to academics and are highlighted on Plant Methods's pages and on the BioMed Central homepage.

In addition, articles published in Plant Methods 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 Plant Methods. A list of articles recently press-released by journals published by BioMed Central is available here.

Copyright

Authors of articles published in Plant Methods 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.