This editorial introduces Source Code for Biology and Medicine, a new journal for publication of programming source code used in biology and medicine. Source Code for Biology and Medicine is an open access independent journal published by BioMed Central. We describe the journal aims, scope, benefits of open access, article processing charges, competing interests, content and article format, peer review policy and publication, and introduce the Editorial Board

Ifeachor, Emmanuel C

Peterson, Leif E

English

PubMed

Springer - Publisher Connector

BioMed Central
Source Code for Biology and 
Medicine
ssOpen AcceEditorial
Welcome to Source Code for Biology and Medicine
Leif E Peterson*1 and Emmanuel C Ifeachor2
Address: 1Department of Medicine; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, US and 2School of 
Computing, University of Plymouth, Plymouth, UK
Email: Leif E Peterson* - peterson.leif@ieee.org; Emmanuel C Ifeachor - E.Ifeachor@plymouth.ac.uk
* Corresponding author    
Abstract
This editorial introduces Source Code for Biology and Medicine, a new journal for publication of
programming source code used in biology and medicine. Source Code for Biology and Medicine is an
open access independent journal published by BioMed Central. We describe the journal aims,
scope, benefits of open access, article processing charges, competing interests, content and article
format, peer review policy and publication, and introduce the Editorial Board.
Aim and scope
Source Code for Biology and Medicine is a peer-reviewed
open access, online journal that publishes articles on
source code employed over a wide range of applications in
biology and medicine. The aim of the journal 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 prob-
lems 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 impor-
tance
• Reduce discovery times in molecular and genomic sci-
ences
• Reduce search times for source code applied in biologi-
cal and medical research
• Provide a historical reflection of source code applied in
various fields
• Serve as a repository for source code
The scope of Source Code for Biology and Medicine includes
workflow and source code for data integration, data
fusion, gene regulatory networks, molecular pathway and
drug discovery, protein structure, biological sequence
analysis, signal processing, geospatial information sys-
tems, patient management systems, decision support sys-
tems, social network systems, environmental risk and
dose modeling, supervised and unsupervised classifica-
tion, text and media mining, and parametric/non-para-
metric numerical methods. Publications in Source Code for
Biology and Medicine may involve the following areas:
• Biometrics
• Biostatistics
• Biopatterns
• Biophysics
Published: 12 October 2006
Source Code for Biology and Medicine 2006, 1:1 doi:10.1186/1751-0473-1-1
Received: 12 October 2006
Accepted: 12 October 2006
This article is available from: http://www.scfbm.org/content/1/1/1
© 2006 Peterson and Ifeachor; licensee BioMed Central Ltd. 
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), 
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Page 1 of 4
(page number not for citation purposes)
Source Code for Biology and Medicine 2006, 1:1 http://www.scfbm.org/content/1/1/1• Bioinformatics
• Ecology
• Environmental health
• Health physics
• Medical physics
• Medical informatics
• Physics in medicine
• Psychometrics
• Toxicology
• Vital statistics
Why an open access journal for Source Code for 
Biology and Medicine is needed
Computer algorithms have been the primary source of
quantitative results in biology and medicine for decades.
Unfortunately, publication of the specific codes used has
never been a major enterprise, so there is not a large body
of information on the implemented codes. Several jour-
nals on computers in biomedicine now exist; however,
they are focused on algorithm design, results, and bench-
marking, and not specifically on publication of the source
code. An online open access journal which requires pub-
lication of the computer source codes used in biomedical
applications meets a great and growing demand, since the
journal would serve as a historical repository for code and
also provide direct access to codes for future use. Direct
access to source code can substantially accelerate scientific
discovery in the biomedical disciplines.
Source Code for Biology and Medicine is an open 
access journal
Under the open access publishing model, all articles
become freely and universally accessible online, which
means that access to articles in Source Code for Biology and
Medicine does not require an annual subscription fee or
online purchase of articles. Open access also guarantees
that authors hold the copyright for their work and grant
anyone the right to reproduce and disseminate the article.
Open access articles are also archived in PubMed Central
[1] as well as repositories at the University of Potsdam [2]
in Germany, INIST [3] in France, and e-Depot [4], the
National Library of the Netherlands' digital archive of all
electronic publications.
There are many benefits of open access publishing. These
include the widest dissemination of published work with
few barriers, which casts a wider net than print and online
subscription-based journals. Recently, Eysenbach [5]
studied open access vs. non-open access articles published
by PNAS from June 8, 2004 to December 20, 2004. Using
a logistic regression model, and controlling for potential
confounders, the odds ratio for citation of open access
PNAS articles 4–10 months after publication compared
with non-Open-Access PNAS articles was 2.1 (95% CI,
1.5–2.9). The odds ratio increased to 2.9 (95% CI, 1.5–
5.5) for 10–16 months after publication. Invariably, open
access results in more downloads and citations, and can
therefore increase Impact Factor [6,7]. Online free access
also enhances literature searching, since direct access to
articles is not constrained by an institutional library's
budget. Open access articles are accessible to all taxpayers,
and not just those with a subscription or those who pur-
chase online. The US National Institutes of Health (NIH)
and the Wellcome Trust in the UK currently have policies
for grant awardees to release their research to the public as
soon as possible after publication [8-10]. Lastly, scientists
in countries with harsh economic environments for which
subscription and online purchase is impossible can access
articles directly.
Article processing charges
An article processing charge (APC) is required for each
article accepted for publication in Source Code for Biology
and Medicine. APCs defray costs for world-wide barrier-
free access to peer-reviewed papers, developing and main-
taining electronic tools for peer review and publication,
preparation of papers in various formats for on-line pub-
lication, securing citation inclusion in PubMed, inclusion
in PubMed Central archives, inclusion into CrossRef for
citations in other electronic journals. APCs also ensure
transparency and allow publishers to compete to provide
the best service at the best price. By coupling the cost of
publication to research budgets, APCs ensure that the
journal publishing system can scale to cope with an ever-
increasing volume of research.
Many institutions [11] and research funders [12] will
cover APCs for their researchers. In addition, in excep-
tional circumstances APCs can be waived for authors who
do not belong to a BioMed Central member institute and
who cannot cover the publishing costs themselves. It war-
rants noting that APCs are required in order to sustain
open access.
Competing interests
The Editors-in-Chief and the majority of Editorial Board
members of Source Code for Biology and Medicine are aca-
demic researchers at non-profit universities mostly sup-
ported by Government research grants. As such, there is
no conflict of interest during the review process or in the
publication of articles appearing in Source Code for BiologyPage 2 of 4
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Source Code for Biology and Medicine 2006, 1:1 http://www.scfbm.org/content/1/1/1and Medicine. Overall, the Editors-In-Chief and Editorial
Board members are genuinely interested in publishing
high-quality articles on computation in the biological and
medical fields for the non-profit reader community.
Content of Source Code for Biology and Medicine
The types of articles published in Source Code for Biology
and Medicine are as follows:
• Research article: describes novel implementation of
source code used for acquiring new results not previously
published. Requires benchmarking with other algorithms
and submission of complete source code files with com-
piled executables, libraries, or class modules (object-ori-
ented programming is the preferred programming style).
• Methodology article: describe first-time publication of
source code for a common application for which code is
not widely available in peer-reviewed biomedical litera-
ture. Requires submission of complete source code files
with compiled executables, libraries, or class modules.
• Brief reports: Provide a synopsis of an applied algo-
rithm without publication of the source code.
• Software reviews: covers the application of a published
workflow or algorithm.
Manuscripts for Research or Methodology articles submit-
ted to Source Code for Biology and Medicine should be for-
matted using the following section headers:
• Title page
• Abstract (350-word limit)
• Introduction/Background
• Methods
• Results and Discussion
• Conclusions
• System and Programming Language Requirements
• Copyright, Trademarks, Licensing, and Registration
Requirements
• Availability
• Competing interests
• Authors' contributions
• Acknowledgements
• References
• Figure legends (if any)
• Tables and captions (if any)
• Description of additional data files
❍ Source Code Listing
❍ Bundled Data Description (if any)
❍ Examples Runs (if any)
These sections may contain subsections. For example:
Methods
❍ Particle energy binning (histograms)
❍ Computation of factorial moments
Peer review policy and publication
Source Code for Biology and Medicine aims at a turnaround
time for manuscript reviews of two weeks. All manuscripts
will be reviewed anonymously by at least two referees.
Review criteria include scope and originality; linguistic
quality; comprehensiveness in background history; review
of previous research with references, completeness in
descriptions of data and samples used and methods
implemented; discussion of results in connection with
data used and results from other studies; benchmarking
with other algorithms using simulated and/or empirical
data sets; comparison with other codes; referencing and
citations; and adequacy of tables and figures. A descrip-
tion of availability is required. Acceptance/rejection crite-
ria are: accept without change, accept with minor
modifications, review after modifications, or reject
(unsuitable for publication).
Once an article is accepted for publication, it will be pub-
lished online immediately in Source Code for Biology and
Medicine, and will be indexed shortly thereafter in
PubMed and PubMed Central.
Editorial board
The membership of the Editorial Board for Source Code for
Biology and Medicine can be viewed online [13].
References
1. PubMed Central   [http://www.pubmedcentral.org]
2. Potsdam   [http://bmc.ub.uni-potsdam.de/cgi-bin/browse.pl]
3. INIST   [http://international.inist.fr/]
4. e-Depot   [http://www.kb.nl/]Page 3 of 4
(page number not for citation purposes)
Source Code for Biology and Medicine 2006, 1:1 http://www.scfbm.org/content/1/1/1Publish with BioMed Central   and  every 
scientist can read your work free of charge
"BioMed Central will be the most significant development for 
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central 
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral
5. Eysenbach G: Citation Advantage of Open Access Articles.
[http://biology.plosjournals.org/perlserv/?request=get-docu
ment&doi=10.1371/journal.pbio.0040157].
6. Hitchcock: The effect of open access and downloads ('hits') on
citation impact: a bibliography of studies.   [http://
opcit.eprints.org/oacitation-biblio.html].
7. Brody T, Harnad S: Earlier Web Usage Statistics as Predictors
of Later Citation Impact.   [http://eprints.ecs.soton.ac.uk/10713/
02/timcorr.htm].
8. Which funding agencies explicitly allow direct use of their
grants to cover article processing charges?   [http:www.human-
resources-health.com/info/faq/apc faq.asp?txt_faq=grants]
9. NIH Calls on Scientists to Speed Public Release of Research
Publications   [http://www.nih.gov/news/pr/feb2005/od-03.htm]
10. Wellcome Trust position statement in support of open and
unrestricted access to published research   [http://www.well
come.ac.uk/node3302.html]
11. BioMed Central Members   [http://www.biomedcentral.com/inst/
]
12. Funding agencies that explicitly allow direct use of their
grantsto cover article-processing charges   [http://
www.biomedcentral.com/info/authors/apcfaq#grants]
13. Source Code for Biology and Medicine – Editorial Board   [http:/
/www.scfbm.org/edboard]Page 4 of 4
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Welcome to 

Leif E Peterson

Emmanuel C Ifeachor

Crossref

Welcome to Source Code for Biology and Medicine

Citation Advantage of Open Access Articles.

Funding agencies that explicitly allow direct use of their grantsto cover article-processing charges [ h t t p : /

Harnad S: Earlier Web Usage Statistics as Predictors of Later Citation Impact.

The effect of open access and downloads ('hits') on citation impact: a bibliography of studies. [ h t t p : / / opcit.eprints.org/oacitation-biblio.html].

Wellcome Trust position statement in support of open and unrestricted access

Which funding agencies explicitly allow direct use of their grants to cover article processing charges? [http:www.humanresources-health.com/info/faq/apc faq.asp?txt_faq=grants]

http://doaj.org/search?source=%7B%22query%22%3A%7B%22bool%22%3A%7B%22must%22%3A%5B%7B%22term%22%3A%7B%22id%22%3A%22ba9c37716b4442239f67544e013498c8%22%7D%7D%5D%7D%7D%7D

Welcome to Source Code for Biology and Medicine

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