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Research Article

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

  • Jacob Beal mail,

    jakebeal@bbn.com

    Affiliation: BBN Technologies, Cambridge, Massachusetts, United States of America

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  • Ting Lu,

    Affiliation: Departments of Biological Engineering, Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

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  • Ron Weiss

    Affiliation: Departments of Biological Engineering, Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

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  • Published: August 05, 2011
  • DOI: 10.1371/journal.pone.0022490
  • Published in PLOS ONE

Reader Comments (1)

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Incomplete references

Posted by jpeccoud on 14 Oct 2011 at 18:12 GMT

This article could have done a better job at citing references. There are several issues.
1- Many of the references cited are incomplete. References 14, 22, 23, 24, 25, 26, 28, 29, 32, and others are lacking critical information such as page number or even sources.
2- Other references reporting very similar or complementary work are missing:
Marchisio MA, Stelling J (2011) Automatic Design of Digital Synthetic Gene Circuits. PLoS Comput Biol 7(2): e1001083. doi:10.1371/journal.pcbi.1001083
Francois & Hakim Proc Natl Acad Sci U S A. (2004) Jan 13;101(2):580-5
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Comput Biol 5(10): e1000529. doi:10.1371/journal.pcbi.1000529
3-It is a little surprising that the availability of the compiler is not discussed anywhere in the manuscript.

Note: Two other articles closely related to this one were published in different journals at the same time.
Rodrigo et al. Nucl. Acids Res. (2011), doi: 10.1093/nar/gkr616.
Wu et al Bioinformatics (2011) 27 (19): 2700-2706. doi: 10.1093/bioinformatics/btr465

Competing interests declared: I work in the same space.

RE: Incomplete references

jakebeal replied to jpeccoud on 14 Oct 2011 at 19:37 GMT

The Proto compiler is always available online at http://proto.bbn.com/ and the BioCompiler is available on request.

Re: incomplete references: that's very strange --- the references appear to have been mangled from our preprint, dropping the information you note. I'll see if PLoS ONE is able to correct it. Fortunately, in the era of Google it's easy to find the documents anyway...

A question regarding your 2009 paper that you mention --- is this your preferred citation for GenoCAD rather than the 2009 Nucleic Acids Research paper that we cited?

Competing interests declared: I am an author of the paper.