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BMC Systems Biology Editorial A system for success BMC Systems Biology, a new open access

Bio Med Central BMC Systems Biology

Open Access Editorial

A system for success: BMC Systems Biology, a new open access

journal

Matt J Hodgkinson* and Penelope A Webb

Address: BioMed Central, Middlesex House, 34-42 Cleveland St., London, W1T 4LB, UK

Email: Matt J Hodgkinson*-matt.hodgkinson@https://www.sodocs.net/doc/182899207.html,; Penelope A Webb-penny.webb@https://www.sodocs.net/doc/182899207.html,

* Corresponding author

Abstract

BMC Systems Biology is the first open access journal spanning the growing field of systems biology

from molecules up to ecosystems. The journal has launched as more and more institutes are

founded that are similarly dedicated to this new approach. BMC System s Biology builds on the

ongoing success of the BMC series, providing a venue for all sound research in the systems-level

analysis of biology.

The BMC series – building on success

When the open access publisher BioMed Central launched the BMC series of journals in May 2000, it pro-vided a venue for open access to research covering a wide range of research fields in biology and medicine [1] and the imperative to allow the free flow of scientific ideas [2]. The BMC series was one initiative from BioMed Central in response to recognizing that the quantity of results and data being generated was too much for conventional sys-tems of publication to deal with. We needed a system that was open and allowed data, results, and interpretations to flow freely, be checked and stamped with authority, but also to be freely mined using computational tools.

The aim was to create a resource of scientific research that was freely available online, including for download and reuse – that is, open access. Open Access is more than just being free online – it also means being permanently archived in a public and accessible archive, and being freely distributable and reusable [3].

The BMC series has met that aim, and has proven to be highly successful both when measured by quantity – sub-missions have roughly doubled every 18 months, interest-ingly very much in line with Moore's law for computing [4] – and when measured by quality. The Impact Factor from Thomson Scientific (ISI) [5], although much criti-cised [6,7], is the most widely used metric for the "impor-tance" of the results published in a journal [8]. Judging by the number of journals in the BMC series that have received good Impact Factors, such as BMC Bioinformatics [9], BMC Cancer, BMC Evolutionar y Biology and BMC Genomics [10,11], the research published in these journals is certainly proving to be important and citable. Together with the other journals published by BioMed Central such as Br east Cancer Resear ch, Genome Biology and Jour nal of Biology, the BMC series has proven that open access works. We don't, however, want to rest on our laurels. In the last few years we have launched new BMC journals to address gaps in the series' coverage. BMC Biology and BMC Medi-cine launched at the end of 2003 to provide an outlet for high quality research of broad interest beyond a single dis-cipline [12]. In response to a growing number of enquiries from veterinarians looking for an open access journal in

Published: 4 September 2007

BMC Systems Biology 2007, 1:41doi:10.1186/1752-0509-1-41Received: 16 August 2007 Accepted: 4 September 2007

This article is available from: https://www.sodocs.net/doc/182899207.html,/1752-0509/1/41

? 2007 Hodgkinson and Webb; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://www.sodocs.net/doc/182899207.html,/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

their field, we also launched BMC Veterinary Research in 2005 [13].

BMC Systems Biology – a new journal, in a new field

There has been another gap that has become evident in the biology journals. Studies were beginning to appear that seemed too expansive to fit the scope of our existing journals, encompassing but not contained within bioin-formatics or genomics, nor biochemistry or physiology. That gap was systems biology, and we've now filled it. There has been a rapid growth in the use of the term 'sys-tems biology' in the literature as this new field emerges (see Figure 1). The field is in fact truly 'emergent' (a pop-ular concept in systems biology [14]), arising as it does out of a combination of high-throughput techniques (epitomised by the microarray) along with the mathemat-ical modelling that is made possible by computing power that would once have been housed within aircraft hangers and now sits upon a desktop.

So what is it?

Systems biology has been defined many times [15-17]. However, the essence of systems biology is probably encapsulated within several concepts:

? Viewing biological systems as a whole, rather than solely in terms of their component parts;

? Mathematical modelling;

? Iterative analysis, with experimental data informing models, which in turn refine the experiments;

? Moving between and integrating systems at different scales – from atoms up to ecosystems;

? Interdisciplinary collaboration between researchers from diverse subject areas, both within biology (including physiologists, developmental biologists, evolutionary sci-entists, neuroscientists, cell biologists, genomicists to name but some), and beyond biology (drawing in math-ematicians, physicists, computer scientists, and social sci-entists).

Systems biology is a new way of approaching the investi-gation of biology. Dedicated systems biology institutes have sprung up all over the world: pioneering Japanese and American institutes (The Systems Biology Institute in Tokyo [18], and the Institute for Systems Biology in Seat-tle [19], both founded in 2000), are now being joined by fledging Systems Biology institutes such as the first new department at Harvard for two decades [20], and the new BBSRC-funded centres for integrative systems biology recently established in Edinburgh, London, Manchester, Newcastle, Nottingham and Oxford [21].

The story so far

The first articles published in BMC Systems Biology include work from Editorial Board member Douglas Lauffen-burger concerning the use of decision trees to predict of the behaviour of fibroblasts [22], the identification of functional modules from Ron Shamir [23], and the latest software for analyzing metabolic, regulatory and signal-ling networks from Ernst Gilles [24]. Our international Editorial Board has provided vital support and guidance to ensure the rigorous review of all submitted manuscripts [25]. Between them, the first ten articles were accessed over 7,000 times in the first month of publication, and the ten most viewed articles have together been viewed by more than 20,000 readers [26].

Figure 1

The growth of the use of the term 'systems biology' over the last ten years. (a) Number of references to 'sys-tems biology' in PubMed abstracts per year since 1997. (b) Number of references to 'systems biology' in full text articles

in Google Scholar per year since 1997.

Conclusion

If you are a researcher exploring this new frontier of biol-ogy, we encourage you to consider submitting to BMC Sys-tems Biology, even if you do not think of yourself as a 'system biologist'. You may be a neuroscientist, a physiol-ogist or an ecologist, but if you are applying the key fea-tures of modelling and integration, we want to hear from you. While the focus of the journal is upon original research, we are also keen to publish commentaries that explore the expanding boundaries of the field of systems biology and suggest new opportunities for collaboration between disciplines, such as Nicolas Le Novère's explora-tion of the journey towards a systems biology of neuro-science over the last half century [27].

Nicholas Rajewsky, a member of our Editorial Board, said in summing up the launch of our new journal, "The BMC journals have already proven to be very attractive to many sci-entists and readers. These journals provide open access, do not restrict manuscript length, and do not insist on publishing only 'major' findings, that is, they do not force scientists to strive for 'sensations'. Especially in a new field, such as systems biology, it is necessar y to wor k on solid methodology development. Therefore, BMC Systems Biology seems especially suited to become an impor tant and high impact jour nal" [28]. We couldn't agree more.

Acknowledgements

Our thanks to Elizabeth Moylan and Matt Cockerill for their suggestions for this editorial.

References

1.The BMC series [https://www.sodocs.net/doc/182899207.html,/info/authors/

bmcseries]

2.Fletcher G: Averting the crisis in medical publishing – open

access journals. [https://www.sodocs.net/doc/182899207.html,/html/info/about/ FletcherHOITI.pdf].

3.Suber P: A very brief introduction to open access. [http://

https://www.sodocs.net/doc/182899207.html,/~peters/fos/brief.htm].

4.Moore's Law [https://www.sodocs.net/doc/182899207.html,/technology/mooreslaw/

index.htm]

5.The ISI Impact Factor [https://www.sodocs.net/doc/182899207.html,/free/essays/

journalcitationreports/impactfactor/]

6.Seglen PO: Why the impact factor of journals should not be

used for evaluating research.BMJ 1997, 314:497 [http://bmj.bmj https://www.sodocs.net/doc/182899207.html,/cgi/content/extract/314/7079/497].

7.Monastersky R: The Number That's Devouring Science.Chron-

icle of Higher Education 2005, 52(8A12 [https://www.sodocs.net/doc/182899207.html,/free/v52/ i08/08a01201.htm].

8.Bollen J, Rodriguez MA, Van de Sompel H: Journal status.

ArXiv:cs.DL/0601030 2006 [https://www.sodocs.net/doc/182899207.html,/abs/cs/0601030].

9.Cockerill M: BMC Bioinformatics comes of age.BMC Bioinformat-

ics 2005, 6:140.

10.Impressive new Impact Factors for BioMed Central's open-

access journals [https://www.sodocs.net/doc/182899207.html,/info/about/pr-releases?pr=20060620b]

11.BioMed Central Impact Factor FAQ [http://www.biomedcen

https://www.sodocs.net/doc/182899207.html,/info/about/faq?name=impactfactor]

12.New Open Access choice for authors Open Access Now [http://

https://www.sodocs.net/doc/182899207.html,/openaccess/miscell/?issue=11]. 15th December 2003

https://www.sodocs.net/doc/182899207.html,unch of BMC Veterinary Research [http://www.biomedcen

https://www.sodocs.net/doc/182899207.html,/info/about/pr-releases?pr=20050601]

14.Bhalla US, Iyengar R: Emergent properties of networks of bio-

logical signaling pathways.Science 1999, 283(5400):381-7.15. A glossary for Systems Biology [http://www.sysbio.de/projects/

glossary/Systems_Biology.shtml]

16.Douglas Kell's group at the Manchester Centre for Integra-

tive Systems Biology [https://www.sodocs.net/doc/182899207.html,/sysbio.htm]

17.K itano H: Systems Biology: A Brief Overview.Science 2002,

295(5560):1662-1664.

18.The Systems Biology Institute [http://www.sbi.jp/]

19.Institute for Systems Biology [https://www.sodocs.net/doc/182899207.html,/]

20.Department of Systems Biology, Harvard Medical School

[https://www.sodocs.net/doc/182899207.html,/]

21.BBSRC - The science we support. Systems Biology: Model-

ling, Simulation and Experimental Validation [http:// https://www.sodocs.net/doc/182899207.html,/science/areas/ebs/themes/main_sysbio.html]

22.Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, Wells A:

Decision tree modeling predicts effects of inhibiting contrac-tility signaling on cell motility.BMC Systems Biology 2007, 1:9.

23.Ulitsky I, Shamir R: Identification of functional modules using

network topology and high-throughput data.BMC Systems Biol-ogy 2007, 1:8.

24.K lamt S, Saez-Rodriguez J, Gilles ED: Structural and functional

analysis of cellular networks with CellNetAnalyzer.BMC Sys-tems Biology 2007, 1:2.

25.BMC Systems Biology Editorial Board [http://www.biomedcen

https://www.sodocs.net/doc/182899207.html,/bmcsystbiol/edboard/]

26.BMC Systems Biology most viewed articles[http://

https://www.sodocs.net/doc/182899207.html,/bmcsystbiol/mostviewedalltime/]

27.Le Novère N: The long journey to a Systems Biology of neu-

ronal function.BMC Systems Biology 2007, 1:28.

28.BioMed Central launches BMC Systems Biology, a new open

access journal [https://www.sodocs.net/doc/182899207.html,/info/about/pr-releases?pr=20070108]

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