Submit a job

Dense data clustering

To submit a job, upload a data matrix in tab-delimited or CSV format, select objective functions for ordering the rows and columns, and provide an email address to which results should be sent.

Note: For one-dimensional rearrangement, select "none" as the objective function for the dimension not being considered.

Header row   Header column

Monotonic

 

Monotonic

 


Output files

SwappedMatrix.txt
The rearranged matrix, without headers
SwappedRows.txt
A list of the row labels (if provided) or initial indices of the rows in the final rearrangement
SwappedCols.txt
A list of the column labels (if provided) or initial indices of the columns in the final rearrangement

Sparse data clustering

To submit a job for sparse clustering, upload a matrix in tab-delimited or CSV format with missing values left blank. The file should not contain row or column headers.


Output files

ordering.txt
The results of the sparse clustering. This file consists of the following:
  • Line 1  gives the best objective value for the row rearrangement problem.
  • Line 2  lists the rows in the final rearrangement by initial index.
  • Line 3  gives the best objective value for the column rearrangement problem.
  • Line 4  lists the columns in the final rearrangement by initial index.
orderedMatrix.csv
The rearranged matrix, with row and column headers that refer to original ordering.

Citing OREO

If you publish results obtained via the OREO server, please acknowledge its use by citing one of the following articles.

Citing OREO for dense clustering

DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics 2008, 9, 458.
DOI: 10.1186/1471-2105-9-458 | Import citation into BibTeX, EndNote

DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Feng, X. J.; Rabinowitz, J. D.; Rabitz, H. A. Optimal Methods for Re-ordering Data Matrices in Systems Biology and Drug Discovery Applications. Biophys. Rev. Lett. 2008, 3 (1-2), 19-42.
DOI: 10.1142/S1793048008000605 | Import citation into BibTeX

Citing for sparse clustering

McAllister, S. R.; DiMaggio, P. A.; Floudas, C. A. Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. J. Global Optim. 2009, 45, 111-129.
DOI: 10.1007/s10898-008-9393-8