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About Source Code for Biology and Medicine

Aims and scope | Open access | Article-processing charges | Indexing services | Publication and peer review process | Editorial policies | Citing articles in Source Code for Biology and Medicine | Why publish your article in Source Code for Biology and Medicine?

This page includes information about the aims and scope of Source Code for Biology and Medicine, 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

Source Code for Biology and Medicine considers manuscripts on all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining.

The journal's aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.


Fundamentally, the overarching computation-related goals of the journal are to:

  • Increase productivity among source code users working on problems of public and environmental health importance
  • Reduce discovery times in molecular and genomic sciences
  • Reduce search times for source code applied in biological and medical research
  • Provide a historical reflection of source code applied in various fields
  • Serve as a repository for source code

Open access

All articles published by Source Code for Biology and Medicine 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 Source Code for Biology and Medicine 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. Source Code for Biology and Medicine therefore levies an article-processing charge of £1290/$2010/€1515 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

All articles published in Source Code for Biology and Medicine are included in PubMed, the most widely used biomedical bibliographic database service, which is run by the US National Library of Medicine. Other bibliographic databases that index articles published in Source Code for Biology and Medicine include:

  • ACM
  • CAS
  • Citebase
  • Embase
  • EmBiology
  • Google Scholar
  • Index Copernicus
  • OAIster
  • PubMed
  • PubMed Central
  • SCImago
  • Scirus
  • Scopus
  • SOCOLAR
  • Zetoc

The full text of all research articles is deposited in PubMed Central, the US National Library of Medicine's full-text repository of life science literature, and other digital archives including e-Depot (The Netherlands).

BioMed Central is working closely with Thomson Reuters (ISI) to ensure that citation analysis of articles published in Source Code for Biology and Medicine will be available.

Publication and peer review process

Content overview


Source Code for Biology and Medicine considers the following types of articles:

  • Original research: reports of data from original research. Describe novel implementation of source code used for acquiring new results, not previously published elsewhere. Research articles require complete source code files with compiled executables, libraries, or class modules (object-oriented programming with use of class libraries is the recommended programming style).
  • Methodology articles: discuss first-time publication of source code for a commonly used approach, for which code is not widely available in peer-reviewed biomedical literature. Methodology articles require complete source code files with compiled executables, libraries, or class modules (object-oriented programming with use of class libraries is the recommended programming style).
  • Brief reports: short synopsis of applied algorithm without publication of the source code.
  • Software reviews: discuss the application of published workflow or algorithm source code.

Peer-review policies

Source Code for Biology and Medicine uses online peer review to speed up the publication process. The time taken to reach a final decision depends on whether reviewers request revisions, and how quickly authors are able to respond.

Once an article is accepted, it is published in Source Code for Biology and Medicine immediately as a provisional PDF file. The paper will subsequently be published in both fully browseable web form, and as a formatted PDF. The article will then be available through Source Code for Biology and Medicine, BioMed Central and PubMed Central, and will also be included in PubMed.

The ultimate responsibility for any decision lies with the Editor-in-Chief, to whom any appeals against rejection should be addressed.

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

Reprints

High-quality, bound reprints can be purchased for all articles published. Please see our reprints website for further information about ordering reprints.

Supplements

Source Code for Biology and Medicine 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

All manuscripts submitted to Source Code for Biology and Medicine should adhere to BioMed Central's editorial policies.

Citing articles in Source Code for Biology and Medicine

Articles in Source Code for Biology and Medicine 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. Source Code Biol Med [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. Source Code Biol Med 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Source Code for Biology and Medicine?

High visibility

Source Code for Biology and Medicine'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

Source Code for Biology and Medicine 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 Source Code for Biology and Medicine, BioMed Central and PubMed Central and will also be included in PubMed.

Flexibility

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

In addition, articles published in Source Code for Biology and Medicine 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 Source Code for Biology and Medicine. A list of articles recently press-released by journals published by BioMed Central is available here.

Authors of articles published in Source Code for Biology and Medicine 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.