Comment on: Dinov et al. BMC Bioinformatics, 12:304
A slight error in Equation 6 (Hunter Moseley, 26 October 2012)
There is a slight error in Equation 6 in the two summation terms.
The summation should be for y = 0; y ≤ j and x = 0; x ≤ i with the following condition (y ≠ j or x ≠ i) that must be satisfied as well. It is easier to describe this summation with a single summation term which includes the conditional, which I have tried to represent below given the limitations of this editor:
y ≤ j; x ≤ i; y ≠ j or x ≠ i
∑
y = 0; x = 0
read full comment
To avoid any confusion (Sofie Van Landeghem, 06 August 2012)
Please note that the Gent Text Mining system, abbreviated to GETM only within this paper to enable comparison to the TEES software, is not to be confused with the GETM system of Gerner et al., 2010.
read full comment
Introduction of the piRNA cluster - database (David Rosenkranz, 30 May 2012)
For a more comfortable accessibility of the data provided as supplementary material of this paper, all piRNA clusters detected with the proTRAC software are now made available at the piRNA cluster - database.
It appears that the provisional PDF suffers from major formatting problems; as our Latex manuscript was converted to a Word document. We are working with the editor to fix it in the final version.
read full comment
PubChem links ? (Christopher Southan, 06 March 2012)
I'm sure this has been suggested already but having all those structures mapped into PubChem would be very useful. You could instantiate MetRxn as a new source.
read full comment
Errata to section "Matches as Equivalence Classes" (Manuel Holtgrewe, 05 March 2012)
There is an error in the section "Matches as Equivalence Classes". Particularly, the definition of match equivalence is flawed.
This has been fixed in an erratum which is available on Rabema's project website http://www.seqan.de/projects/rabema.html. This page also contains a document with additional material and extended proofs regarding the valid definitions in the original paper and the changed definition.
read full comment
POSTN expression confirmed by Nature paper (Jim Zheng, 14 February 2012)
POSTN is a consistently differentially expressed gene identified by CDEP. Now it has been shown that POSTN is a stromal niche component that is induced on metastasis formation
Malanchi I, Santamaria-MartÃnez A, Susanto E, Peng H, Lehr HA, Delaloye JF, Huelsken J.
Interactions between cancer stem cells and their niche govern metastatic colonization. Nature. 2011 Dec 7;481(7379):85-9.
doi:10.1038/nature10694. PubMed PMID: 22158103.
read full comment
Comment on: Tsoi et al. BMC Bioinformatics, 12:438
This project has been moved to Google Code (Pengyi Yang, 12 January 2012)
The algorithm and software described in this article have been moved to Google Code.
Please refer to:
http://code.google.com/p/genetic-ensemble-snpx/
read full comment
Comment on: Yang et al. BMC Bioinformatics, 11:524
This project has been moved to Google Code (Pengyi Yang, 19 December 2011)
The algorithm and software described in this article have been moved to Google Code.
Please refer to:
http://code.google.com/p/ensemble-of-filters/
read full comment
Comment on: Yang et al. BMC Bioinformatics, 12:S10
Amazingly fast, memory efficient and accurate... in short: very useful! (Julien Dutheil, 06 December 2011)
A very useful piece of software, in an era when more and more genome / transcriptome data are becoming available. We also used it efficiently on a single gene data set displaying high amount of divergence between species, in order to assess its detailed evolutionary history.
read full comment
Comment on: Miele et al. BMC Bioinformatics, 12:116
Dendritic Cell Ontology download (anna maria masci, 28 November 2011)
Dendritic Cell Ontology can be downloaded at http://obofoundry.org/cgi-bin/detail.cgi?id=dendritic_cell
read full comment
Comment on: Masci et al. BMC Bioinformatics, 10:70
local to cloud data transfer, and user data stored on cloud (Konstantinos Krampis, 28 November 2011)
It would be of benefit to the readers if the authors could provide a data point for the time required for data transfer of user input data from the local CLOVR virtual machine to the cloud.
In addition, they could consider in a future version to permanently store the user-uploaded input dataset on the cloud (S3 for example) along with the reference databases. The reason is that users might require to re-run multiple times a pipeline with the same input dataset, but using different parameters (consider days in between runs, so the virtual cluster has to be turned on and off each time). The user input data can be retrieved each time from the cloud storage using the cloud credentials provided by the user through the CLOVR interface. Uploading the same input dataset before each run...
read full comment
Persistent Digital Object Identifiers (DOIs) now available (Gad Abraham, 08 November 2011)
The input data, computational model, and output data from this study have been persistently identified using DOIs (minted using the Australian National Data Service (ANDS) data citation service http://ands.org.au/cite-data/), and each can be re-used and cited independently:
Input Microarray Dataset: Abraham, G; Kowalczyk, A; Loi, S; Haviv, I; Zobel, J. (2011) Five human breast cancer microarray gene expression datasets. Computer Science and Software Engineering, The University of Melbourne. doi:10.4225/02/4E9F695934393
Computational Model: Abraham, G; Kowalczyk, A; Loi, S; Haviv, I; Zobel, J. (2011) Computational Model for Gene Set Analysis to predict breast cancer prognosis based on microarray gene expression data. Computer Science and Software Engineering...
read full comment
Description of Figure 3 (Michal Manas, 06 October 2011)
Figure 3 has description like this:
Formatting nodes and edges of a tree. Dendroscope provides a dialog box for formatting the nodes and edges of a tree; the example shows a tree drawn as an internal circular cladogram.
I think, that the image is more likely rectangular cladogram.
read full comment
Comment on: Huson et al. BMC Bioinformatics, 8:460
my belief (Xu Song, 12 September 2011)
I believe this study can accelerate the development of metabolomics.
read full comment
Comment on: Song et al. BMC Bioinformatics, 12:337
Response to "Seems to not receive data" (Ramon Diaz-Uriarte, 09 September 2011)
Yes, there was a bug in the program, so that missing values in the survival time file were being reported, in the error message, as missing values in the status file. That bug has been fixed now.
As for the example files, they can be downloaded from this page (at the bottom)
Seems to not receive data (laurent tellier, 08 September 2011)
Hello Ramon,
I'm afraid that the webtool may have some kind of issue - it seems that regardless of what data you put into the survival status file, it will always return "file contains missing values", without specifying what is missing. My file is of correct dimensions, a tab delineated text file with line change at the end, and consists of 1's and 0's. If I remove or add a value at the end, the error is in stead that the file is of too great or small a dimension. It has the same dimensions as the time file, which is received without problem.
This is less an issue with your other tools, where one can change to just download an R package and do it yourself on your own computer, and in some cases there is an example file which can be downloaded and used to exemplify...
read full comment
Author edits (Jeanette Eckel-Passow, 05 September 2011)
We would like to thank Henrik Bengtsson for his thorough review of our manuscript. Below we discuss some edits and clarification to our manuscript based on his review.
1. CRMAv2 was the method used in the Aroma.Affymetrix software. Although this can be determined by reading Appendix 2, this was not directly stated in the manuscript. 2. CRMAv2 does not apply an across-array normalization method. Thus, in the Results and Discussion section the following edits should be made: - Under the subsection, “Background correction”, the third sentence should read "Aroma.Affymetrix corrects for allelic crosstalk whereas CRLMM corrects for optical background and non-specific hybridization using a linear model after performing quantile normalization." - The...
read full comment
Survey on the use of the INTERPRET DSS (Margarida Julià-Sapé, 25 July 2011)
We are interested in the use given to the INTERPRET DSS, in order to keep improving it. It is for this reason that we would like to kindly ask for some of your time to fill in a survey. It should take you not more than 10 minutes. Thanks!
The link to the survey is: https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDNaeXd2RHNaTFBaSVp wcDc4aHo4aHc6MQ read full comment
Clarification of Findings (Joyce Davis, 07 July 2011)
Researchers Clarify Outstanding Accuracy of GeneChip® Arrays’ Design and Manufacturing
10 Percent Data Error Attributed to Laboratory Experimental Design Flaws
Researchers studying statistical techniques to reduce data quality variations derived from microarray experiments have clarified that the 10 percent variation they found in data from 809 studies using more than 22,000 Affymetrix GeneChip® Human Genome U133A and Human Genome U133 Plus 2.0 arrays is due to poor quality data, not manufacturing quality.
Speaking on behalf of the scientists involved in the research, Dr. Rafael Irizarry said in this recently published paper it may be mistakenly implied that the cause of the bad data lies in the manufacturing of the arrays and that it...
read full comment
Comment on: McCall et al. BMC Bioinformatics, 12:137
Link to article ref [5] (Joseph Hughes, 13 June 2011)
The link to "Towards a Taxonomically Intelligent Phylogenetic Database" by R. Page is missing. Here it is http://dx.doi.org/10.1038/npre.2007.1028.1
read full comment
RSS
Latest comments
SparSNP is now open source at https://github.com/gabraham/SparSNP (Gad Abraham, 18 January 2013)
SparSNP is now licensed under the GPLv3, and the source code and documentation are available at
https://github.com/gabraham/SparSNP read full comment
Comment on: Abraham et al. BMC Bioinformatics, 13:88
Errors in Table 1. Comparison of common graphical workflow environments (Scott Markel, 11 January 2013)
Thank you for including Pipeline Pilot in your... read full comment
Comment on: Dinov et al. BMC Bioinformatics, 12:304
A slight error in Equation 6 (Hunter Moseley, 26 October 2012)
There is a slight error in Equation 6 in the two summation terms. The summation should be for y = 0; y ≤ j and x = 0; x ≤ i with the following condition (y ≠ j or x ≠ i) that must be satisfied as well. It is easier to describe this summation with a single summation term which includes the conditional, which I have tried to represent below given the limitations of this editor: y ≤ j; x ≤ i; y ≠ j or x ≠ i ∑ y = 0; x = 0 read full comment
Comment on: Moseley BMC Bioinformatics, 11:139
To avoid any confusion (Sofie Van Landeghem, 06 August 2012)
Please note that the Gent Text Mining system, abbreviated to GETM only within this paper to enable comparison to the TEES software, is not to be confused with the GETM system of Gerner et al., 2010. read full comment
Comment on: Van Landeghem et al. BMC Bioinformatics, 13:S6
Introduction of the piRNA cluster - database (David Rosenkranz, 30 May 2012)
For a more comfortable accessibility of the data provided as supplementary material of this paper, all piRNA clusters detected with the proTRAC software are now made available at the piRNA cluster - database.
piRNA cluster - database read full comment
Comment on: Rosenkranz et al. BMC Bioinformatics, 13:5
Formatting problem (Rayan Chikhi, 27 March 2012)
It appears that the provisional PDF suffers from major formatting problems; as our Latex manuscript was converted to a Word document. We are working with the editor to fix it in the final version. read full comment
Comment on: Peterlongo et al. BMC Bioinformatics, 13:48
PubChem links ? (Christopher Southan, 06 March 2012)
I'm sure this has been suggested already but having all those structures mapped into PubChem would be very useful. You could instantiate MetRxn as a new source. read full comment
Comment on: Kumar et al. BMC Bioinformatics, 13:6
Errata to section "Matches as Equivalence Classes" (Manuel Holtgrewe, 05 March 2012)
There is an error in the section "Matches as Equivalence Classes". Particularly, the definition of match equivalence is flawed.
This has been fixed in an erratum which is available on Rabema's project website http://www.seqan.de/projects/rabema.html. This page also contains a document with additional material and extended proofs regarding the valid definitions in the original paper and the changed definition. read full comment
Comment on: Holtgrewe et al. BMC Bioinformatics, 12:210
POSTN expression confirmed by Nature paper (Jim Zheng, 14 February 2012)
POSTN is a consistently differentially expressed gene identified by CDEP. Now it has been shown that POSTN is a stromal niche component that is induced on metastasis formation
Malanchi I, Santamaria-MartÃnez A, Susanto E, Peng H, Lehr HA, Delaloye JF, Huelsken J.
Interactions between cancer stem cells and their niche govern metastatic colonization. Nature. 2011 Dec 7;481(7379):85-9.
doi:10.1038/nature10694. PubMed PMID: 22158103. read full comment
Comment on: Tsoi et al. BMC Bioinformatics, 12:438
This project has been moved to Google Code (Pengyi Yang, 12 January 2012)
The algorithm and software described in this article have been moved to Google Code.
Please refer to:
http://code.google.com/p/genetic-ensemble-snpx/ read full comment
Comment on: Yang et al. BMC Bioinformatics, 11:524
This project has been moved to Google Code (Pengyi Yang, 19 December 2011)
The algorithm and software described in this article have been moved to Google Code.
Please refer to:
http://code.google.com/p/ensemble-of-filters/ read full comment
Comment on: Yang et al. BMC Bioinformatics, 12:S10
Amazingly fast, memory efficient and accurate... in short: very useful! (Julien Dutheil, 06 December 2011)
A very useful piece of software, in an era when more and more genome / transcriptome data are becoming available. We also used it efficiently on a single gene data set displaying high amount of divergence between species, in order to assess its detailed evolutionary history. read full comment
Comment on: Miele et al. BMC Bioinformatics, 12:116
Dendritic Cell Ontology download (anna maria masci, 28 November 2011)
Dendritic Cell Ontology can be downloaded at
http://obofoundry.org/cgi-bin/detail.cgi?id=dendritic_cell read full comment
Comment on: Masci et al. BMC Bioinformatics, 10:70
local to cloud data transfer, and user data stored on cloud (Konstantinos Krampis, 28 November 2011)
It would be of benefit to the readers if the authors could provide a data point for the time required for data transfer of user input data from the local CLOVR virtual machine to the cloud.
In addition, they could consider in a future version to permanently store the user-uploaded input dataset on the cloud (S3 for example) along with the reference databases. The reason is that users might require to re-run multiple times a pipeline with the same input dataset, but using different parameters (consider days in between runs, so the virtual cluster has to be turned on and off each time). The user input data can be retrieved each time from the cloud storage using the cloud credentials provided by the user through the CLOVR interface. Uploading the same input dataset before each run... read full comment
Comment on: Angiuoli et al. BMC Bioinformatics, 12:356
Persistent Digital Object Identifiers (DOIs) now available (Gad Abraham, 08 November 2011)
The input data, computational model, and output data from this study have been persistently identified using DOIs (minted using the Australian National Data Service (ANDS) data citation service http://ands.org.au/cite-data/), and each can be re-used and cited independently:
Input Microarray Dataset:
Abraham, G; Kowalczyk, A; Loi, S; Haviv, I; Zobel, J. (2011) Five human breast cancer microarray gene expression datasets. Computer Science and Software Engineering, The University of Melbourne. doi:10.4225/02/4E9F695934393
Computational Model:
Abraham, G; Kowalczyk, A; Loi, S; Haviv, I; Zobel, J. (2011) Computational Model for Gene Set Analysis to predict breast cancer prognosis based on microarray gene expression data. Computer Science and Software Engineering... read full comment
Comment on: Abraham et al. BMC Bioinformatics, 11:277
Description of Figure 3 (Michal Manas, 06 October 2011)
Figure 3 has description like this:
Formatting nodes and edges of a tree. Dendroscope provides a dialog box for formatting the nodes and edges of a tree; the example shows a tree drawn as an internal circular cladogram.
I think, that the image is more likely rectangular cladogram. read full comment
Comment on: Huson et al. BMC Bioinformatics, 8:460
my belief (Xu Song, 12 September 2011)
I believe this study can accelerate the development of metabolomics. read full comment
Comment on: Song et al. BMC Bioinformatics, 12:337
Response to "Seems to not receive data" (Ramon Diaz-Uriarte, 09 September 2011)
Yes, there was a bug in the program, so that missing values in the survival time file were being reported, in the error message, as missing values in the status file. That bug has been fixed now.
As for the example files, they can be downloaded from this page (at the bottom)
http://signs.bioinfo.cnio.es/Examples/index.html read full comment
Comment on: Diaz-Uriarte BMC Bioinformatics, 9:30
Seems to not receive data (laurent tellier, 08 September 2011)
Hello Ramon,
I'm afraid that the webtool may have some kind of issue - it seems that regardless of what data you put into the survival status file, it will always return "file contains missing values", without specifying what is missing. My file is of correct dimensions, a tab delineated text file with line change at the end, and consists of 1's and 0's. If I remove or add a value at the end, the error is in stead that the file is of too great or small a dimension. It has the same dimensions as the time file, which is received without problem.
This is less an issue with your other tools, where one can change to just download an R package and do it yourself on your own computer, and in some cases there is an example file which can be downloaded and used to exemplify... read full comment
Comment on: Diaz-Uriarte BMC Bioinformatics, 9:30
Author edits (Jeanette Eckel-Passow, 05 September 2011)
We would like to thank Henrik Bengtsson for his thorough review of our manuscript. Below we discuss some edits and clarification to our manuscript based on his review.
1. CRMAv2 was the method used in the Aroma.Affymetrix software. Although this can be determined by reading Appendix 2, this was not directly stated in the manuscript.
2. CRMAv2 does not apply an across-array normalization method. Thus, in the Results and Discussion section the following edits should be made:
- Under the subsection, “Background correction”, the third sentence should read "Aroma.Affymetrix corrects for allelic crosstalk whereas CRLMM corrects for optical background and non-specific hybridization using a linear model after performing quantile normalization."
- The... read full comment
Comment on: Eckel-Passow et al. BMC Bioinformatics, 12:220
Survey on the use of the INTERPRET DSS (Margarida Julià-Sapé, 25 July 2011)
We are interested in the use given to the INTERPRET DSS, in order to keep improving it.
It is for this reason that we would like to kindly ask for some of your time to fill in a survey. It should take you not more than 10 minutes. Thanks!
The link to the survey is:
https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDNaeXd2RHNaTFBaSVp wcDc4aHo4aHc6MQ
read full comment
Comment on: Pérez-Ruiz et al. BMC Bioinformatics, 11:581
Related software (Alfredo Kalaitzis, 25 July 2011)
GPREGE, the R package that implements the methodology described in the paper can be found at
http://staffwww.dcs.shef.ac.uk/people/A.Kalaitzis/
A MATLAB release is to follow.
Please send questions about the software and bug reports at the author's email. read full comment
Comment on: Kalaitzis et al. BMC Bioinformatics, 12:180
Clarification of Findings (Joyce Davis, 07 July 2011)
Researchers Clarify Outstanding Accuracy of GeneChip® Arrays’ Design and Manufacturing
10 Percent Data Error Attributed to Laboratory Experimental Design Flaws
Researchers studying statistical techniques to reduce data quality variations derived from microarray experiments have clarified that the 10 percent variation they found in data from 809 studies using more than 22,000 Affymetrix GeneChip® Human Genome U133A and Human Genome U133 Plus 2.0 arrays is due to poor quality data, not manufacturing quality.
Speaking on behalf of the scientists involved in the research, Dr. Rafael Irizarry said in this recently published paper it may be mistakenly implied that the cause of the bad data lies in the manufacturing of the arrays and that it... read full comment
Comment on: McCall et al. BMC Bioinformatics, 12:137
Link to article ref [5] (Joseph Hughes, 13 June 2011)
The link to "Towards a Taxonomically Intelligent Phylogenetic Database" by R. Page is missing. Here it is http://dx.doi.org/10.1038/npre.2007.1028.1 read full comment
Comment on: Hughes BMC Bioinformatics, 12:178
What about SPR distance? (Ross Mounce, 31 May 2011)
Surprised to see no mention or reference to Subtree, Prune and Regraft (SPR) distance. Is it not relevant?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614206/
http://bioinformatics.oxfordjournals.org/content/25/2/190.abstract read full comment
Comment on: Koperwas et al. BMC Bioinformatics, 12:204