bioinformatics editorial news - Oxford Journals

ioinformatics
editorial news
Issue 2 2008
welcome to the annual bioinformatics editorial
newsletter
Welcome to the 2008 edition, including the latest Bioinformatics editorial office news, open access
and software policies, and information about our new automatic PubMed Central deposit service
for NIH-funded authors. We are also pleased to announce that Bioinformatics will shortly become an
official journal of the ISCB – more inside.
Best regards,
Alex Bateman, Alfonso Valencia, and the Bioinformatics Editorial team
Top: Alfonso Valencia, Alex Bateman, Anna Tramontano, David Rocke, and Burkhard Rost.
Middle: Ivo Hofacker, Trey Ideker, Dmitrij Frishman, Joaquin Dopazo, and Limsoon Wong.
Bottom: Thomas Lengauer, Martin Bishop, Olga Troyanskaya, John Quackenbush, and Jonathan Wren.
page 1

ioinformatics
editorial office and
production update
Submissions continue thick and fast. We have
introduced a policy of seeking three high quality peer
review reports wherever possible and appropriate –
we’re pleased to say that this has not impacted on our
fast review times (see below).
Once a manuscript is accepted for publication, it is
usually published online ahead of print within one
week and in an issue within 8 weeks.
2007 2008 projected
Submissions 1890 1950
Acceptance rate 30% 31%
Time from
submission to 31 days 31 days
first decision
Editorial office contact details:
Tracy Knight:
bioinformatics.editorialoffice@oxfordjournals.org
Alison Hutchins:
reviews.bioinformatics.editorialoffice@
oxfordjournals.org
Detailed information about Bioinformatics’ scope and
acceptance criteria is available at:
http://www.oxfordjournals.org/bioinformatics/for_
authors/scope_guidelines.html
calling all authors and
reviewers!
Please update your Manuscript Central user
account with your keywords. This will help us
make the peer review process as fast and smooth
as possible. To update your profile visit: http://
mc.manuscriptcentral.com/bioinformatics and enter
your username and password*. Once you have logged
in, click on the button in the top-right corner of the
screen labelled ‘Edit Account’. On the third screen of
the ‘Edit My Account’ process, you will see there
is a section called ‘Keywords’. Please select between
three and six keywords that best cover your area of
interest and expertise. You can do this by selecting
the appropriate term from the list, and then just click
‘Add’. Once you have selected a minimum of three
keywords, scroll to the bottom of the screen and click
‘Finish’.
*If you are uncertain of your log-in details, you can enter your
email address in the appropriate text field under ‘Password
Help’ and click ‘Go’. You should then receive an email
containing this information.
reviews update from
jonathan wren
Upcoming Bioinformatics reviews to look forward
to regard the prediction of miRNA target genes, a
review on population dynamics and their effect on
genome-wide associations studies, protein multiple
sequence alignment methods, RNA sequence analysis
and secondary structure, identification of eubacterial
sRNAs, integrating heterogeneous networks in
biology and how data compression algorithms can be
used to understand and interpret biological sequence
data.
official journal of the iscb
We are happy to announce that from 2009,
Bioinformatics will be an official journal of the
International Society for Computational Biology
(ISCB). This agreement further cements existing
links between our journal and the ISCB in what we
see as a very natural fit. ISCB members and directors
are of course already well represented among the
Bioinformatics’ editorial team, and we publish the
ISMB Proceedings in the journal each year. Going
forward we see many possibilities for forging stronger
links between Bioinformatics and ISCB, with the aim
of ensuring that the community continues to be well
served by our activities.
page 2

ioinformatics
‘Our organizations have a long history together, and
we are pleased to be re-establishing Bioinformatics as
an official journal of the Society. The ISCB Board of
Directors fully supports this partnership with OUP.’
– Scott Markel, ISCB Board of Directors and
Co-Chair of the ISCB Publications Committee
about iscb
ISCB serves over 2600 members globally by
impacting scientific policies, providing access to
high quality publications, organizing meetings, and
serving as a portal to information about training,
education, employment and news from related
fields. ISCB hosts ISMB annually, the world’s
longest running, largest, bioinformatics conference.
Visit www.iscb.org to join us today!
our software policy
Bioinformatics requires that authors of all manuscripts
that describe software tools and web servers make
them freely available directly via the web without
hindrance of registration or passwords. We won’t
accept manuscripts that require readers to contact
authors for access to the software and these are
returned without review. We encourage authors to
make their source code available and, if possible, to
provide access through an open source license. We
also will only consider software that is available on
a wide range of platforms or browsers so the widest
range of the community can benefit. To help our
readers we are extending the availability section of
our structured abstracts to include implementation
describing the development language and target
platforms of the software.
open access choice for
authors
bioinformatics open
policies
In all our activities we aim to help researchers
disseminate their work easily and widely. For example,
articles are published within days of acceptance
online ahead of print; the journal is accessible to
thousands of institutions around the world including
through the Oxford Journals Developing Countries
initiative; and all articles are made freely available
online after 12 months. This is also why we have an
established software availability policy – encouraging
authors to make their software accessible – and an
option of immediate open access, giving authors
the choice of whether to publish under this model
depending on the funds available to them. You can
read more about these policies below.
Bioinformatics’ policy is to provide a choice for authors
with respect to open access – in 2005 we adopted an
optional open access model (Oxford Open; http://
www.oxfordjournals.org/oxfordopen/) which
means that authors can decide whether or not to
pay for open access publication, depending on the
funds available to them. So far in 2008, ~23% of
Bioinformatics authors have chosen the Oxford Open
option.
Open access charges vary depending on whether
the corresponding author is based at an institution
with an online subscription to Bioinformatics (we
estimate that this applies to over 80% of authors).
The ‘subscriber charges’ are currently set at £900 /
$1800 / €1350 for original papers (£1500 / $3000 /
€2250 for non-subscribers) and £450 / $900 / €675
for application notes (£750 / $1500 / €1125 for
non-subscribers). This compares to charges in the
region of US$2200 for PLoS Computational Biology and
£950/$1395 for BMC Bioinformatics.
page 3

Background
bioinformatics
image--maybe from the journal cover?
journal title placeholder
What Oxford Open means for our authors:
• Publication in Bioinformatics under a Creative
Commons licence which allows anyone to reuse
the article for non-commercial purposes without
needing to seek permission
• Free access to everybody immediately online via
the Bioinformatics web site
• Automatic deposit in PubMed Central (where
the article is also made freely available
immediately)
• Authors are free to deposit their paper
elsewhere, e.g. in an institutional repository,
under the terms of the Creative Commons
licence
• ALL Bioinformatics authors, whether or not they
choose open access, retain copyright in their
work.
automatic pubmed central
deposit – easy compliance
with the nih public access
policy
Oxford Journals is now depositing all NIH-funded
articles and all open access articles published in
Bioinformatics into PubMed Central (PMC). We are
therefore listed as a journal that submits all NIHfunded
articles to PubMed Central without author
involvement at http://publicaccess.nih.gov/submit_
process_journals.htm.
Depositing these articles helps authors to comply
easily with recent mandates by the National Institutes
of Health (NIH) and other funding bodies. The
NIH policy (http://publicaccess.nih.gov/) ‘requires
investigators funded by the NIH to submit to
PubMed Central (PMC) an electronic version of their
final, peer-reviewed manuscript upon acceptance
for publication, to be made publicly available
no later than 12 months after the official date of
publication.’ From 31st July 2008 onwards, all NIHfunded
manuscripts published in Bioinformatics are
being identified and tagged, and the final published
version sent to PMC. We ask authors to indicate their
source of funding in their manuscript so that we can
identify relevant articles. NIH-funded articles which
are published under Bioinformatics’ open access
model (Oxford Open) are then made freely available
immediately in PMC, and those which are not open
access are made available by PMC after 12 months.
This means that NIH-funded authors do not need
to deposit their articles into PMC – we will do this
on their behalf, provided that they have identified
themselves as being NIH-funded. More information
on satisfying funding body requirements can be
found at http://oxfordjournals.org/for_authors/
repositories.html.
citation alerting – did you
know?
You can register for citation alerting to a specific
Bioinformatics article by visiting the article online and
clicking the ‘Alert me when this article is cited’ link
in the ‘This Article’ box (top right). You will need to
register for an Oxford Journals Account to manage
your alerts.
bioinformatics’
2007 impact factor
5.039
advertise jobs with us
Bioinformatics offers print and online advertising
of career opportunities. If you would like more
information about this feature please contact the
Oxford Journals Advertising and Special Sales team
at: http://www.oxfordjournals.org/bioinformatics/
careers_online.html.
page 4

ioinformatics
executive editors
editorial board
Alex Bateman, UK
Alfonso Valencia, ES
associate editors
Martin Bishop, UK
Joaquin Dopazo, Spain
Dmitrij Frishman, GER
Ivo Hofacker, Austria
Trey Ideker, USA
Thomas Lengauer, GER
John Quackenbush, USA
David Rocke, USA
B. Rost, USA
Anna Tramontano, Italy
O. Troyanskaya, USA
L. Wong, Singapore
Jonathan Wren, USA
how editorial board
members can support
bioinformatics
You can help us in a number of ways by:
• acting as reviewers and identifying colleagues
who migh review manuscripts for the journal;
• evaluating manuscripts in difficult cases where
we need an extra solid opinion;
• writing editorials and reviews, or suggesting
review topics and authors;
• contributing advice and ideas on the future
development of the journal;
• helping to raise awareness of the journal.
S. Batzoglou, USA
Alvis Brazma, UK
S. Brunak, Denmark
C.D. Bustamante, USA
K.A. Crandall, USA
M. Gelfand, Russia
J. Heringa, the Netherlands
D. Higgins, Ireland
Charlie Hodgman, UK
L. Holm, Finland
W. Huber, UK
L. Jensen, Germany
P. Karp, USA
Wi Li, USA
R. Matthiesen, Portugal
Satoru Miyano, Japan
A. Navarro, Spain
Christos Ouzounis, UK
D. Posada, Spain
Nikolaus Rajewsky, USA
I. Rigoutsos, USA
G. Sherlock, USA
N. Srinivasan, India
C. Stoeckert, USA
M. Vingron, Germany
G. Yona, Israel
M. Zhang, US
We also see the Editorial Board as a good source of
future Associate Editors, so if you would be
interested in taking on such a role, let us know.
page 5