Problem with PDF anf HTML versions prior to October 20, 2012 (Daniel Kirouac, 14 November 2012)
Note that PDF and HTML versions of this article downloaded prior to October 20, 2012 contained an error: All of the equations presented in the methods section were omitted. Please use current version if you downloaded the article prior to this date.
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Highly Customizable Visualization with Omix (Katharina Noeh, 10 September 2012)
The authors compare different visualization solutions and assess them with respect to their functionalities. One of the software tools is our visualization tool Omix. The authors claim that "the import of external flux data" in Omix is "an absent or inadequately supported feature" (cf. Table...
read full comment
Editor's Note - Error in published abstract (Simon Harold PhD, 13 August 2012)
On 23/7/12 it was brought to our attention that an error had appeared in the published version of the Abstract of this article. The original first line of the Results section read:...
read full comment
At odds with published information (James Burnell, 06 August 2012)
<p>The model of Hart et al., 2011 appears to be at variance with previously published material (see Burnell et al., Australian Journal of Plant Physiology 1986; 13, 203-210) which reports physiological data of PEP and pyruvate concentrations that influence PPDK activity. In addition, the model needs to be addressed in light of recent findings that the site to which ADP (as a substrate) binds and site to which ADP binds to inhibit Pi-dependent activation are the same site Astley et al., 2011 (The Plant Journal doi:10.1111/j.1365-313X.2011.04759.x.</p>
read full comment
Comment on: Hart et al. BMC Systems Biology, 5:171
Error in published abstract (Tim Sands, 23 July 2012)
Thank you for alerting us to this problem. A correction to this abstract has been requested from the authors. The statistical methods used are described in the main article. BioMed Central regrets that this omission was not picked up prior to publication.
read full comment
you will find a properly formatted provisional PDF (with proper equations, accents, and nicely inlined figures). This PDF was built by authors from the original LaTeX sources. The provisional PDF on the journal's site was created from the editors DOC and contains many font-related bugs.
note on a cited web site (Ettore Mosca, 03 November 2011)
I would like to inform the readers that the web site currently available at the URL http://www.breastcancerdatabase.org is radically different from the bioinformatics resource that was available at the time of this publication.
read full comment
Comment on: Mosca et al. BMC Systems Biology, 4:76
Exogenous inhibitors of succinate dehydrogenase (Heikki Savolainen, 25 July 2011)
Dear Editor,
The model on mitochrondrial roles summarizes excellently the metabolic aspects (1). It may be added that inhibitors of succinate dehydrogenase activity can cause direct toxicity to highly oxygen dependent organs. The classical example is 3-niropropanoic acid with cerebral effects.
The alkoxyacetic acids, metabolites of ethylene glycol ethers, are another example. They inhibit in experimental (2) and clinical studies (3) the enzyme activity which should according to the current model contribute to the risk of malignant diseases associated with exposure to them.
1 Smith AC, Robinson AJ. A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. BMC Systems Biol 2011; 5: 102
Comment on: Smith et al. BMC Systems Biology, 5:102
update on results (Steve Horvath, 13 June 2011)
An expanded and updated version of the material can be found in chapters 1-6 of the following book: Horvath S (2011) Weighted Network Analysis. Applications in Genomics and Systems Biology. Springer Book. ISBN: 978-1-4419-8818-8
This paper provides proof that the Hill type equation describes the RNA interfence (Raya Khanin, 25 May 2011)
In this paper, the authors performed in vitro experiments in human and hamster cell lines measuring levels of mRNAs and proteins for a large range of concentrations of siRNA oligomers. They demonstrate the the Hill type equation is the most efficient way to model RNA interference. It would have been a nice study had the authors were not carried away by suddenly referring to the Hill model as theirs. They continue by saying that their "model has a simple mathematical form, amenable to analytical investigations and a small set of parameters with an intuitive physical meaning, that makes it a unique and reliable mathematical tool".
Indeed, the Hill model was introduced by Archibald Hill in 1910, and has since been applied to numerous biological processes, from enzyme reactions to...
read full comment
Buen trabajo (Carlos Manuel Estevez-Breton Riveros, 25 May 2011)
Muy interesante esfuerzo en generar un vector para representar "reacciones" bioquímicas, me deja pensando el asunto de la isomerización... Buscaré un servicio web que permita "convertir" las reacciones en vectores...
read full comment
Comment on affiliations, contact details and acknowledgments (Tatiana T. Marquez-Lago, 28 December 2010)
It has come to our attention an additional principal affiliation should be added to the first two authors of our paper, published in BMC Systems Biology (4:19, 2010).
Tatiana T Marquez-Lago and André Leier: Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia. The current first affiliation should appear as "current address: ETH Zurich, Universitätsstrasse 6, CH-8092 Zurich, Switzerland." -- Ideas were conceived (as well as research and simulations) when the authors were working in Australia but, at the time of submission, the Advanced Computational Modelling Centre no longer existed.
Lastly, we would like to add an additional note in the acknowledgments section: This work was performed under the auspices...
read full comment
Correction: Network properties of human disease genes with pleiotropic effects Sreenivas Chavali*†, Fredrik Barrenas†, Kartiek Kanduri, Mikael Benson The Unit for Clinical Systems Biology, University of Gothenburg, Medicinaregatan 5A, Gothenburg SE405 30, Sweden †Contributed equally Correspondence: sreenivas.chavali@gu.se
Correction After publication, it was observed that a correction is warranted in our article [1]. We regret and apologize for this error. To determine phenotypic divergence we used phenotypic similarity scores as obtained from van Driel et al. 2006 [2] and not CIPHER score [3]. The phenotype similarity scores have been calculated by text mining of OMIM phenotypes using Medical Subject Headings (MeSH) terms. Hence...
read full comment
Modelling of metabolism in cancer and normal cells; relevance of quantum metabolism (Paul Agutter, 09 July 2010)
Vasquez et al. [1] have made a significant contribution to the recent literature arising from renewed interest in the Warburg hypothesis of cancer. The model they develop in their paper is well-articulated and strongly supported. I wonder whether it can be shown to be compatible with the recent publication by Demetrius and colleagues [2], which brings a new theory of allometric scaling, quantum metabolism, to bear on the subject. Mathematical details of quantum metabolism have been published elsewhere [3]. The value of their contribution is that it suggests new non-invasive approaches to cancer treatment, based on metabolic regulation, that could potentially serve as valuable adjuncts to conventional therapeutic measures. If it could be shown to be consistent with and perhaps complementary...
read full comment
This is an interesting paper. I am wondering why equation numbers are missing in the pdf file. Also, there appear to be typos in Eq. 18 and 25. Lastly, Eq. 28 does not seem to list all possible combinations, such as CaM_{01}^{01}, CaM_{01}^{10}. Can these be fixed?
read full comment
While this paper was in revision Goula et al. (PLoS Genet. 2009 December; 5(12): e100074)ublished findings in which they showed that the stoichiometry of base excision repair (BER) roteins differed in striatum compared to cerebellum in an HD fragment mouse odel. It would therefore be of interest to determine whether these findings extend to a roader correlation between tissue instability and BER protein stoichiometry across a wide range of tissues. read full comment
The smallest bistable chemical system and the origin of life (Thomas Wilhelm, 30 November 2009)
The smallest bistable chemical system and the origin of life
Thomas Wilhelm
1971 was a remarkable year. Surely for different reasons (you might have been born then), but one reason is that three people presented the idea of self-organization and autocatalytic cycles as the possible origin of life [1-3]. They did this completely independent of each other, time was simple ripe, it was a nice coincidence. None of them can claim being the first, maybe it was somebody else. Robert Rosen (cited in [1], not in [2,3]) discussed essentially the same idea earlier [4]. Following Rosen’s approach, Letelier et al. presented a “minimal (three-step) autocatalytic set” [5].
However, I would argue that “The smallest chemical reaction system with...
read full comment
Correction from The Authors (Damion Nero, 26 October 2009)
The authors of this work wish to note two corrections to the reference section of our manuscript.
Corrections
Citation 25: A. Tanay, R. Sharan, R. Shamir. Discovering Statistically Significant Biclusters in Gene Expression Data. Bioinformatics 2002, Vol. 18 Suppl. 1 S136-S144.
Citation 31: R. Sharan, A. Maron-Katz and R. Shamir. CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data. Bioinformatics, Vol. 19, No. 14, pp. 1787-1799 (2003). read full comment
What ever happened to single photon scintigraphy? (Lionel Zuckier, 05 February 2009)
Very interesting and comprehensive article. Nonetheless, I was surprised by the complete omission of single-photon imaging, both planar and tomographic. These are powerful techniques with resolution in small animals, such as by microSPECT, superior to that of dual-photon (PET)imaging (though lacking absolute quantification as in PET). These techniques have been used for decades to provide much basic physiologic information by way of imaging and compartmental modeling.
read full comment
Second derivative notation in Equation (13) (Yu Feng Wu, 03 December 2007)
Dear readers,To avoid confusion, according to Leibniz's notation, there should be x square in the bottom of the second derivative term in Equation (13).Sincerely Yu Feng
read full comment
This seems a useful contribution, I like the idea.I wonder if it could be translated into something other than Matlab, that would make it even more useful.
read full comment
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Latest comments
Problem with PDF anf HTML versions prior to October 20, 2012 (Daniel Kirouac, 14 November 2012)
Note that PDF and HTML versions of this article downloaded prior to October 20, 2012 contained an error: All of the equations presented in the methods section were omitted. Please use current version if you downloaded the article prior to this date. read full comment
Comment on: Kirouac et al. BMC Systems Biology, 6:29
"...but what is available for biological researchers?" (Hendrik Rohn, 04 October 2012)
"Dr. Noeh compares OMIX with FluxMap and, indeed, we are impressed... read full comment
Comment on: Rohn et al. BMC Systems Biology, 6:33
Highly Customizable Visualization with Omix (Katharina Noeh, 10 September 2012)
The authors compare different visualization solutions and assess them with respect to their functionalities. One of the software tools is our visualization tool Omix. The authors claim that "the import of external flux data" in Omix is "an absent or inadequately supported feature" (cf. Table... read full comment
Comment on: Rohn et al. BMC Systems Biology, 6:33
Full list of references for edges in the Cellular Stress Network (Jurjen Westra, 13 August 2012)
To view the full reference list, copy and paste the text below into a spreadsheet... read full comment
Comment on: Schlage et al. BMC Systems Biology, 5:168
Editor's Note - Error in published abstract (Simon Harold PhD, 13 August 2012)
On 23/7/12 it was brought to our attention that an error had appeared in the published version of the Abstract of this article. The original first line of the Results section read:... read full comment
Comment on: Xie et al. BMC Systems Biology, 5:S4
At odds with published information (James Burnell, 06 August 2012)
<p>The model of Hart et al., 2011 appears to be at variance with previously published material (see Burnell et al., Australian Journal of Plant Physiology 1986; 13, 203-210) which reports physiological data of PEP and pyruvate concentrations that influence PPDK activity. In addition, the model needs to be addressed in light of recent findings that the site to which ADP (as a substrate) binds and site to which ADP binds to inhibit Pi-dependent activation are the same site Astley et al., 2011 (The Plant Journal doi:10.1111/j.1365-313X.2011.04759.x.</p> read full comment
Comment on: Hart et al. BMC Systems Biology, 5:171
Error in published abstract (Tim Sands, 23 July 2012)
Thank you for alerting us to this problem. A correction to this abstract has been requested from the authors. The statistical methods used are described in the main article. BioMed Central regrets that this omission was not picked up prior to publication. read full comment
Comment on: Xie et al. BMC Systems Biology, 5:S4
(insert statistical method here) (Daniel Mietchen, 23 July 2012)
Why is this phrase in the published abstract? read full comment
Comment on: Xie et al. BMC Systems Biology, 5:S4
Link to a properly formatted provisional PDF (Mikolaj Rybinski, 15 May 2012)
Under this link:
http://www.mimuw.edu.pl/~trybik/sci/tav4sb-preprint.pdf
you will find a properly formatted provisional PDF (with proper equations, accents, and nicely inlined figures). This PDF was built by authors from the original LaTeX sources. The provisional PDF on the journal's site was created from the editors DOC and contains many font-related bugs.
Best regards,
Miko¿aj read full comment
Comment on: Rybiński et al. BMC Systems Biology, 6:25
note on a cited web site (Ettore Mosca, 03 November 2011)
I would like to inform the readers that the web site currently available at the URL http://www.breastcancerdatabase.org is radically different from the bioinformatics resource that was available at the time of this publication. read full comment
Comment on: Mosca et al. BMC Systems Biology, 4:76
Exogenous inhibitors of succinate dehydrogenase (Heikki Savolainen, 25 July 2011)
Dear Editor,
The model on mitochrondrial roles summarizes excellently the metabolic aspects (1). It may be added that inhibitors of succinate dehydrogenase activity can cause direct toxicity to highly oxygen dependent organs. The classical example is 3-niropropanoic acid with cerebral effects.
The alkoxyacetic acids, metabolites of ethylene glycol ethers, are another example. They inhibit in experimental (2) and clinical studies (3) the enzyme activity which should according to the current model contribute to the risk of malignant diseases associated with exposure to them.
1 Smith AC, Robinson AJ. A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. BMC Systems Biol 2011; 5: 102
2 Savolainen H.... read full comment
Comment on: Smith et al. BMC Systems Biology, 5:102
update on results (Steve Horvath, 13 June 2011)
An expanded and updated version of the material can be found in chapters 1-6 of the following book:
Horvath S (2011) Weighted Network Analysis. Applications in Genomics and Systems Biology. Springer Book. ISBN: 978-1-4419-8818-8
The book is also available as an ebook. read full comment
Comment on: Dong et al. BMC Systems Biology, 1:24
This paper provides proof that the Hill type equation describes the RNA interfence (Raya Khanin, 25 May 2011)
In this paper, the authors performed in vitro experiments in human and hamster cell lines measuring levels of mRNAs and proteins for a large range of concentrations of siRNA oligomers. They demonstrate the the Hill type equation is the most efficient way to model RNA interference. It would have been a nice study had the authors were not carried away by suddenly referring to the Hill model as theirs. They continue by saying that their "model has a simple mathematical form, amenable to analytical investigations and a small set of parameters with an intuitive physical meaning, that makes it a unique and reliable mathematical tool".
Indeed, the Hill model was introduced by Archibald Hill in 1910, and has since been applied to numerous biological processes, from enzyme reactions to... read full comment
Comment on: Cuccato et al. BMC Systems Biology, 5:19
Buen trabajo (Carlos Manuel Estevez-Breton Riveros, 25 May 2011)
Muy interesante esfuerzo en generar un vector para representar "reacciones" bioquímicas, me deja pensando el asunto de la isomerización...
Buscaré un servicio web que permita "convertir" las reacciones en vectores... read full comment
Comment on: Triviño et al. BMC Systems Biology, 4:46
Comment on affiliations, contact details and acknowledgments (Tatiana T. Marquez-Lago, 28 December 2010)
It has come to our attention an additional principal affiliation should be added to the first two authors of our paper, published in BMC Systems Biology (4:19, 2010).
Tatiana T Marquez-Lago and André Leier: Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia. The current first affiliation should appear as "current address: ETH Zurich, Universitätsstrasse 6, CH-8092 Zurich, Switzerland." -- Ideas were conceived (as well as research and simulations) when the authors were working in Australia but, at the time of submission, the Advanced Computational Modelling Centre no longer existed.
Lastly, we would like to add an additional note in the acknowledgments section: This work was performed under the auspices... read full comment
Comment on: Marquez-Lago et al. BMC Systems Biology, 4:19
Erratum (Sreenivas Chavali, 12 October 2010)
Correction: Network properties of human disease genes with pleiotropic effects
Sreenivas Chavali*†, Fredrik Barrenas†, Kartiek Kanduri, Mikael Benson
The Unit for Clinical Systems Biology, University of Gothenburg, Medicinaregatan 5A, Gothenburg SE405 30, Sweden
†Contributed equally
Correspondence: sreenivas.chavali@gu.se
Correction
After publication, it was observed that a correction is warranted in our article [1]. We regret and apologize for this error.
To determine phenotypic divergence we used phenotypic similarity scores as obtained from van Driel et al. 2006 [2] and not CIPHER score [3]. The phenotype similarity scores have been calculated by text mining of OMIM phenotypes using Medical Subject Headings (MeSH) terms. Hence... read full comment
Comment on: Chavali et al. BMC Systems Biology, 4:78
Modelling of metabolism in cancer and normal cells; relevance of quantum metabolism (Paul Agutter, 09 July 2010)
Vasquez et al. [1] have made a significant contribution to the recent literature arising from renewed interest in the Warburg hypothesis of cancer. The model they develop in their paper is well-articulated and strongly supported. I wonder whether it can be shown to be compatible with the recent publication by Demetrius and colleagues [2], which brings a new theory of allometric scaling, quantum metabolism, to bear on the subject. Mathematical details of quantum metabolism have been published elsewhere [3]. The value of their contribution is that it suggests new non-invasive approaches to cancer treatment, based on metabolic regulation, that could potentially serve as valuable adjuncts to conventional therapeutic measures. If it could be shown to be consistent with and perhaps complementary... read full comment
Comment on: Vazquez et al. BMC Systems Biology, 4:58
Typos? (David Minh, 19 April 2010)
This is an interesting paper. I am wondering why equation numbers are missing in the pdf file. Also, there appear to be typos in Eq. 18 and 25. Lastly, Eq. 28 does not seem to list all possible combinations, such as CaM_{01}^{01}, CaM_{01}^{10}. Can these be fixed? read full comment
Comment on: Valeyev et al. BMC Systems Biology, 2:48
Note added in proof (JONG-MIN LEE, 15 April 2010)
While this paper was in revision Goula et al. (PLoS Genet. 2009 December; 5(12): e100074)ublished findings in which they showed that the stoichiometry of base excision repair (BER) roteins differed in striatum compared to cerebellum in an HD fragment mouse odel. It would therefore be of interest to determine whether these findings extend to a roader correlation between tissue instability and BER protein stoichiometry across a wide range of tissues.
read full comment
Comment on: Lee et al. BMC Systems Biology, 4:29
The smallest bistable chemical system and the origin of life (Thomas Wilhelm, 30 November 2009)
The smallest bistable chemical system and the origin of life
Thomas Wilhelm
1971 was a remarkable year. Surely for different reasons (you might have been born then), but one reason is that three people presented the idea of self-organization and autocatalytic cycles as the possible origin of life [1-3]. They did this completely independent of each other, time was simple ripe, it was a nice coincidence. None of them can claim being the first, maybe it was somebody else. Robert Rosen (cited in [1], not in [2,3]) discussed essentially the same idea earlier [4]. Following Rosen’s approach, Letelier et al. presented a “minimal (three-step) autocatalytic set” [5].
However, I would argue that “The smallest chemical reaction system with... read full comment
Comment on: Wilhelm BMC Systems Biology, 3:90
Correction from The Authors (Damion Nero, 26 October 2009)
The authors of this work wish to note two corrections to the reference section of our manuscript.
Corrections
Citation 25:
A. Tanay, R. Sharan, R. Shamir. Discovering Statistically Significant Biclusters in Gene Expression Data. Bioinformatics 2002, Vol. 18 Suppl. 1 S136-S144.
Citation 31:
R. Sharan, A. Maron-Katz and R. Shamir. CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data. Bioinformatics, Vol. 19, No. 14, pp. 1787-1799 (2003).
read full comment
Comment on: Nero et al. BMC Systems Biology, 3:59
What ever happened to single photon scintigraphy? (Lionel Zuckier, 05 February 2009)
Very interesting and comprehensive article. Nonetheless, I was surprised by the complete omission of single-photon imaging, both planar and tomographic. These are powerful techniques with resolution in small animals, such as by microSPECT, superior to that of dual-photon (PET)imaging (though lacking absolute quantification as in PET). These techniques have been used for decades to provide much basic physiologic information by way of imaging and compartmental modeling. read full comment
Comment on: Kherlopian et al. BMC Systems Biology, 2:74
Second derivative notation in Equation (13) (Yu Feng Wu, 03 December 2007)
Dear readers,To avoid confusion, according to Leibniz's notation, there should be x square in the bottom of the second derivative term in Equation (13).Sincerely Yu Feng read full comment
Comment on: Wu et al. BMC Systems Biology, 1:52
I like this. (Herbert Sauro, 07 June 2007)
This seems a useful contribution, I like the idea.I wonder if it could be translated into something other than Matlab, that would make it even more useful. read full comment
Comment on: Aho et al. BMC Systems Biology, 1:22