Software articles
We encourage authors of software applications, tools or algorithm implementations to publish descriptions of their code using the Software article type.
Availability of software to reviewers and other researchers
The software application/tool described in the manuscript must be available for testing by reviewers in a way that preserves their anonymity. If published, software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement. Because weblinks frequently become broken,
Journal of Cheminformatics
strongly recommends that all software applications/tools are included with the submitted manuscript as additional files to ensure that the software will continue to be available.
Journal of Cheminformatics
recommends, but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so. 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. Since it is likely that the software will continue to be developed following publication, the manuscript should also include a link to the home page for the software project. For open source projects, we recommend that authors host their project with a recognized open-source repository such as bioinformatics.org or sourceforge.net
Should a description of a website be submitted as a Software article or a Database article?
Descriptions of websites and web-based tools should be submitted as Software articles if the intention is that the software that drives the website will be made available to other researchers to extend and use on other websites. On the other hand, if a website's functionality is closely tied to a specific database then the article should instead be submitted as a Database article.
Manuscript sections for Software articles
Manuscripts for Software articles submitted to Journal of Cheminformatics should be divided into the following sections:
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).
Title page
This should list the title of the article. The full names, institutional addresses, and email addresses for all authors must be included on the title page. The corresponding author should also be indicated.
Abstract
This should not exceed 350 words and should be structured into separate sections headed Background, Results, Conclusions. Please do not use abbreviations or references in the abstract.
Background
The background section should be written to be comprehensible to researchers without specialist knowledge in the area concerned. It should clearly described the relevant context and the specific issue which the software described is intended to address.
Implementation
This should include a description of the overall architecture of the software implementation, along with details of any critical issues and how they were addressed.
Results and Discussion
The Results and Discussion may be combined into a single section or presented separately. They may also be broken into subsections with short, informative headings. In any case what should be described is the functionality of the software together with data on how its performance and functionality compare with and improve on functionally similar existing software. There should then be a discussion of the intended use of the software, and the benefits that are envisioned together, if possible, with an outline for the planned future development of new features.
Conclusions
This should state clearly the main conclusions of the article and give a clear explanation of the importance and relevance of the software.
Availability and requirements
Lists the following:
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Project name: e.g. My bioinformatics project
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Project home page: e.g. http://sourceforge.net/projects/mged
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Operating system(s): e.g. Platform independent
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Programming language: e.g. Java
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Other requirements: e.g. Java 1.3.1 or higher, Tomcat 4.0 or higher
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License: e.g. GNU GPL, FreeBSD etc.
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Any restrictions to use by non-academics: e.g. licence needed
List of abbreviations
If abbreviations are used in the text, either they should be defined in the text where first used, or a list of abbreviations can be
provided, which should precede the competing interests and authors' contributions.
Competing interests
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 should disclose any financial competing interests but also 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
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In the past five 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.
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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.
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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 of your co-authors has a competing interest, please discuss it with the editorial office.
Authors' contributions
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.
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; and 3) have given final approval of the version to be published. 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, or a department chair who provided only general support.
Authors' information
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.
Acknowledgements
Please acknowledge anyone who contributed towards the study 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 their source(s) of funding. Please also acknowledge anyone who contributed materials essential for the study.
Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements.
Please list the source(s) of funding for the study, for each author, and for the manuscript preparation in the acknowledgements section. Authors must describe the role of the funding body, if any, in study 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.
References
All references must be numbered consecutively, in the order in which they are cited in the text, followed by any in tables or legends. Reference citations should not appear in titles or headings. Each reference must have an individual reference number. A complete list should then be provided at the end of the article. The references should be presented in a style consistent with the ACS Style Guide and must not contain any form of note or comment. Footnotes may not be included, whether in the reference list or elsewhere. If automatic numbering systems are used, the reference numbers must be finalized and the bibliography must be fully formatted before submission.
Examples of the Journal of Cheminformatics reference style are shown below. Please take care to follow the reference style precisely; references not in the correct style may be retyped, necessitating tedious proofreading.
Links
Web links and URLs should be included in the reference list. They should be provided in full, including both the title of the site and the URL, in the following format:
Molecular Informatics: Confronting Complexity, Proceedings of the Beilstein-Institut Workshop, May 13th-16th, 2002, Bozen, Italy [http://www.beilstein-institut.de/bozen2002/proceedings]
Journal of Cheminformatics reference style
Style files are available for use with popular bibliographic management software:
Article within a journal
1. Koonin EV, Altschul SF, Bork P: BRCA1 protein products: functional motifs. Nat Genet 1996, 13:266-267.
Article within a journal supplement
2. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I: Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999, 43(Suppl 3):149-170.
In press article
3.
Betson MS, Clayden J, Helliwell M, Mitjans D: Org Biomol Chem, in press.
Published abstract
4.
Clayden, J, Collington EW, Warren S: Kinetic resolution of d-hydroxy allylic phosphine oxides: a stereocontrolled route to allylically functionalised systems [abstract]. Phosphorus Sulfur Silicon 1993, 77:187.
Article within conference proceedings
5. Jones X: Zeolites and synthetic mechanisms. In Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Edited by Smith Y. Stoneham: Butterworth-Heinemann; 1996:16-27.
Book chapter, or article within a book
6.
Yus M: Arene-catalyzed lithiation. In The Chemistry of Organolithium Compounds. Edited by Rappoport Z, Marek I. Chichester: Wiley and Sons; 2004:647-748.
Whole issue of journal
7.
O’Brien P (Ed): Recent developments in chiral lithium amide chemistry. In Tetrahedron 2002, 58:4567-4733.
Whole conference proceedings
8. Smith Y (Ed): Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Stoneham: Butterworth-Heinemann; 1996.
Complete book
9.
Gutsche C D: Calixarenes. Cambridge: Royal Society of Chemistry; 1989.
Monograph or book in a series
10.
Goldfuss B: Enantioselective addition of organolithiums to C=O groups. In Organolithiums in Enantioselective Synthesis. Edited by Hodgson DM. Berlin: Springer; 2003:21-36. [Topics in Organometallic Chemistry, vol 5.]
Book with institutional author
11. Advisory Committee on Genetic Modification: Annual Report. London; 1999.
PhD thesis
12.
Westlund N. PhD thesis. University of Manchester 1998.
Link / URL
13.
Molecular Informatics: Confronting Complexity, Proceedings of the Beilstein-Institut Workshop, May 13th-16th, 2002, Bozen, Italy [http://www.beilstein-institut.de/bozen2002/proceedings]
