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Software

Criteria

Journal of Cheminformatics will only publish research or software that is entirely reproducible by third parties. This means that any datasets, software and algorithms that are required to reach the conclusions stated in the paper must be provided as supplemental materials, or be otherwise accessible without the need for registration, login or agreement with license terms other than Creative Commons licenses for data and text and OSI-approved Open Source Licenses for software. For any software, the source code must be provided.

Software articles should describe a tool likely to be of broad utility that represents a significant advance over previously published software (usually demonstrated by direct comparison with available related software).

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 and anonymously available under an open source licence to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement or a registration to access the package. 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 requires 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.

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. 

A graphical abstract can be supplied which, together with the article title, should provide the reader with a visual description of the type of chemistry covered in the article. The graphical abstract should be 920 x 300 pixels and a maximum of 150KB jpeg, png or svg file. Authors are encouraged to make judicious use of colour in graphical abstracts. All graphical abstracts should have a white background and where possible should fill the available width.

Preparing your manuscript

Title page

The title page should:

  • present a title that includes, if appropriate, the research design or for non-research studies: a description of what the article reports
  • list the full names, institutional addresses and email addresses for all authors
    • if a collaboration group should be listed as an author, please list the Group name as an author and include the names of the individual members of the Group in the “Acknowledgements” section in accordance with the instructions below.
  • indicate the corresponding author

Abstract

The abstract should briefly summarize the aim, findings or purpose of the article. Please minimize the use of abbreviations and do not cite references in the abstract.

See the criteria section for this article type (located at the top of this page) for information on abstract and article word limits.

Keywords

Three to ten keywords representing the main content of the article.

Introduction

The Introduction section should explain the relevant context and the specific issue that the software described is intended to address. It should clearly describe 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

This should include the findings of the study including, if appropriate, results of statistical analysis which must be included either in the text or as tables and figures. This section may be combined with the Discussion section for Software articles. They may also be broken into subsections with short, informative headings.

Discussion (if appropriate)

The user interface should be described and a discussion of the intended uses of the software, and the benefits that are envisioned, should be included, together with data on how its performance and functionality compare with, and improve, on functionally similar existing software. A case study of the use of the software may be presented. The planned future development of new features, if any, should be mentioned.

Conclusions

This should state clearly the main conclusions and provide an explanation of the importance and relevance of the case, data, opinion, database or software reported.

Availability and requirements

 

Lists the following:

·       Project name: e.g. My bioinformatics project

·       Project home page: e.g. http://sourceforge.net/projects/mged

·       Operating system(s): e.g. Platform independent

·       Programming language: e.g. Java

·       Other requirements: e.g. Java 1.3.1 or higher, Tomcat 4.0 or higher

·       License: e.g. GNU GPL, FreeBSD etc.

Any restrictions to use by non-academics: e.g. licence needed

Declarations

​​​​​​​All manuscripts must contain the following sections under the heading 'Declarations':

  • Availability of data and material
  • Competing interests
  • Funding
  • Authors' contributions
  • Acknowledgements
  • Authors' information (optional)

Please see below for details on the information to be included in these sections.

If any of the sections are not relevant to your manuscript, please include the heading and write 'Not applicable' for that section.

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 should be provided.

Availability of data and materials

For all journals, BioMed Central strongly encourages all datasets on which the conclusions of the manuscript rely to be either deposited in publicly available repositories (where available and appropriate) or presented in the main paper or additional supporting files, in machine-readable format (such as spreadsheets rather than PDFs) whenever possible. Please see the list of recommended repositories in our editorial policies.

For some journals, deposition of the data on which the conclusions of the manuscript rely is an absolute requirement. Please check the Criteria section for this article type (located at the top of this page) for journal specific policies.

For all journals, authors must include an “Availability of data and materials” section in their article detailing where the data supporting their findings can be found. If you do not wish to share your data, please state that data will not be shared, and state the reason.

For instructions on how to cite your data and format this section see preparation/style and formatting.

Competing interests

All financial and non-financial competing interests must be declared in this section. See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.

Funding

All sources of funding for the research reported should be declared. The role of the funding body in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript should be declared.

Authors' contributions

The individual contributions of authors to the manuscript should be specified in this section.

Acknowledgements

Please acknowledge anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.

See our editorial policies for a full explanation of acknowledgements and authorship criteria.

Group authorship: if you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records (where applicable), 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.

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.

Endnotes

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.

References

Examples of the Basic Springer reference style are shown below. 

See our editorial policies for author guidance on good citation practice.

Web links and URLs: 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.

​​​​​​​Example reference style:

Article within a journal

Smith J, Jones M Jr, Houghton L (1999) Future of health insurance. N Engl J Med 965:325-329.

Article by DOI (with page numbers)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. J Mol Med 78:74-80. doi:10.1007/s001090000086.

Article by DOI (before issue publication and with page numbers)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. J Mol Med. doi:10.1007/s001090000086.

Article in electronic journal by DOI (no paginated version)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. Dig J Mol Med. doi:10.1007/s801090000086.

Journal issue with issue editor

Smith J (ed) (1998) Rodent genes. Mod Genomics J 14(6):126-233.

Journal issue with no issue editor

Mod Genomics J (1998) Rodent genes. Mod Genomics J 14(6):126-233.

Book chapter, or an article within a book

Brown B, Aaron M (2001) The politics of nature. In: Smith J (ed) The rise of modern genomics, 3rd edn. Wiley, New York.

Complete book, authored

South J, Blass B (2001) The future of modern genomics. Blackwell, London.

Complete book, edited

Smith J, Brown B (eds) (2001) The demise of modern genomics. Blackwell, London.

Complete book, also showing a translated edition [Either edition may be listed first.]

Adorno TW (1966) Negative Dialektik. Suhrkamp, Frankfurt. English edition: Adorno TW (1973) Negative Dialectics (trans: Ashton EB). Routledge, London.

Chapter in a book in a series without volume titles

Schmidt H (1989) Testing results. In: Hutzinger O (ed) Handbook of environmental chemistry, vol 2E. Springer, Heidelberg, p 111.

Chapter in a book in a series with volume titles

Smith SE (1976) Neuromuscular blocking drugs in man. In: Zaimis E (ed) Neuromuscular junction. Handbook of experimental pharmacology, vol 42. Springer, Heidelberg, pp 593-660.

OnlineFirst chapter in a series (without a volume designation but with a DOI)

Saito, Yukio, and Hyuga, Hiroyuki. (2007) Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Topics in Current Chemistry. doi:10.1007/128_2006_108.

Proceedings as a book (in a series and subseries)

Zowghi D (1996) A framework for reasoning about requirements in evolution. In: Foo N, Goebel R (eds) PRICAI'96: topics in artificial intelligence. 4th Pacific Rim conference on artificial intelligence, Cairns, August 1996. Lecture notes in computer science (Lecture notes in artificial intelligence), vol 1114. Springer, Heidelberg, p 157.

Article within conference proceedings with an editor (without a publisher)

Aaron M (1999) The future of genomics. In: Williams H (ed) Proceedings of the genomic researchers, Boston, 1999.

Article within conference proceedings without an editor (without a publisher)

Chung S-T, Morris RL (1978) Isolation and characterization of plasmid deoxyribonucleic acid from Streptomyces fradiae. In: Abstracts of the 3rd international symposium on the genetics of industrial microorganisms, University of Wisconsin, Madison, 4-9 June 1978.

Article presented at a conference

Chung S-T, Morris RL (1978) Isolation and characterization of plasmid deoxyribonucleic acid from Streptomyces fradiae. Paper presented at the 3rd international symposium on the genetics of industrial microorganisms, University of Wisconsin, Madison, 4-9 June 1978.

Patent

Norman LO (1998) Lightning rods. US Patent 4,379,752, 9 Sept 1998.

Dissertation

Trent JW (1975) Experimental acute renal failure. Dissertation, University of California.

Book with institutional author

International Anatomical Nomenclature Committee (1966) Nomina anatomica. Excerpta Medica, Amsterdam.

In press article

Major M (2007) Recent developments. In: Jones W (ed) Surgery today. Springer, Dordrecht (in press). 

Online document

Doe J (1999) Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. Available via DIALOG. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.

Online database

Healthwise Knowledgebase (1998) US Pharmacopeia, Rockville. http://www.healthwise.org. Accessed 21 Sept 1998.

Supplementary material/private homepage

Doe J (2000) Title of supplementary material. http://www.privatehomepage.com. Accessed 22 Feb 2000.

University site

Doe J (1999) Title of preprint. http://www.uni-heidelberg.de/mydata.html. Accessed 25 Dec 1999.

FTP site

Doe J (1999) Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt. Accessed 12 Nov 1999.

Organization site

ISSN International Centre (2006) The ISSN register. http://www.issn.org. Accessed 20 Feb 2007.

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