Unit tests for SanXoT - Revision history

Mtrevisan: /* Unit test for Unix/Linux operating systems */

2018-08-17T15:42:57Z

‎Unit test for Unix/Linux operating systems

Mtrevisan: /* Unit test for Unix/Linux operating systems */

2018-08-17T15:16:36Z

‎Unit test for Unix/Linux operating systems

Mtrevisan at 15:14, 17 August 2018

2018-08-17T15:14:25Z

Mtrevisan at 09:20, 17 August 2018

2018-08-17T09:20:35Z

Mtrevisan at 14:33, 16 August 2018

2018-08-16T14:33:49Z

Mtrevisan at 15:02, 14 August 2018

2018-08-14T15:02:28Z

Mtrevisan at 15:01, 14 August 2018

2018-08-14T15:01:30Z

Mtrevisan at 15:00, 14 August 2018

2018-08-14T15:00:56Z

Mtrevisan at 14:56, 14 August 2018

2018-08-14T14:56:23Z

Mtrevisan: /* Test 3: Systems biology */

2018-08-14T14:54:23Z

‎Test 3: Systems biology

@@ Line 29: / Line 29: @@
 # Use the source code from GitHub ('''[https://github.com/CNIC-Proteomics/SanXoT https://github.com/CNIC-Proteomics/SanXoT]'''), rather than the standalone exes provided below.
-This can be done by using the following pip commands:
+Step #2 can be done by using the following pip commands:
   pip install numpy

@@ Line 28: / Line 28: @@
 # Replace the *.bat files within the unit tests by the files contained here: '''[[File:SanXoT commands for Unix shell.zip]]'''.
 # Use the source code from GitHub ('''[https://github.com/CNIC-Proteomics/SanXoT https://github.com/CNIC-Proteomics/SanXoT]'''), rather than the standalone exes provided below.
 ==Test 1: The fundamental workflow==

@@ Line 16: / Line 16: @@
 Links to SanXoT windows standalone executables are provided in this unit test. Additionally, download links to the source code and up-to-date versions of SanXoT are available at: '''[[SanXoT software package]]'''.
 ==Unit test for Unix/Linux operating systems==
@@ Line 26: / Line 28: @@
 # Replace the *.bat files within the unit tests by the files contained here: '''[[File:SanXoT commands for Unix shell.zip]]'''.
 # Use the source code from GitHub ('''[https://github.com/CNIC-Proteomics/SanXoT https://github.com/CNIC-Proteomics/SanXoT]'''), rather than the standalone exes provided below.
 ==Test 1: The fundamental workflow==

@@ Line 13: / Line 13: @@
 For detailed explanations, check: '''[[exploring SanXoT features]]'''.
-==Source code==
+==Unit test for Windows==
-Note that links to SanXoT windows standalone executables are provided in this unit test, but download links to the source code and up-to-date versions of SanXoT are available at: '''[[SanXoT software package]]'''.
+Links to SanXoT windows standalone executables are provided in this unit test. Additionally, download links to the source code and up-to-date versions of SanXoT are available at: '''[[SanXoT software package]]'''.
 ==Unit test for Unix/Linux operating systems==

@@ Line 12: / Line 12: @@
 For detailed explanations, check: '''[[exploring SanXoT features]]'''.
 Note that links to SanXoT windows standalone executables are provided in this unit test, but download links to the source code and up-to-date versions of SanXoT are available at: '''[[SanXoT software package]]'''.
 ==Test 1: The fundamental workflow==

@@ Line 33: / Line 33: @@
 ::* '''''commands_test1.bat''''', a windows batch file with command lines to run this sample analysis.
-::* '''''170415_Marga_GBS_iTRAQ_PSMs.txt''''', a tab-separated-values text file with identifications and quantitative data from a proteomics experiment<ref>Mateos-Hernández, L., et al. (2016) '''Quantitative proteomics reveals Piccolo as a candidate serological correlate of recovery from Guillain-Barré syndrome'''. ''Oncotarget'', 7(46): 74582–74591.</ref>.
+::* '''''170415_Marga_GBS_iTRAQ_PSMs.txt''''', a tab-separated-values text file with identifications and quantitative data from a proteomics experiment<ref>Mateos-Hernández, L., et al. (2016) '''[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5342688/ Quantitative proteomics reveals Piccolo as a candidate serological correlate of recovery from Guillain-Barré syndrome]'''. ''Oncotarget'', 7(46): 74582–74591.</ref>.
 ) get a) the path of your working folder (where you have unzipped the file '''''170415_Marga_GBS_iTRAQ_PSMs.txt'''''), b) the path of the folder where you have unzipped the windows executables, and c) the unit of the latter (C:, D:, etc); modify the following lines in the command_test1.bat file accordingly:

@@ Line 81: / Line 81: @@
 ==Test 3: Systems biology==
-The '''[[SanXoT Sowftware Package]]''' can be used to perform systems biology analises using the SBT (''Systems Biology Triangle'') as described.<ref>García-Marqués, F., Trevisan-Herraz, M., Martínez-Martínez, S., Camafeita, E., Jorge, I., Lopez, J.A., Méndez-Barbero, N., Méndez-Ferrer, S., del Pozo, M.A., Ibáñez, B., Andrés, V., Sánchez-Madrid, F., Redondo, J.M., Bonzon-Kulichenko, E. and Vázquez, J. (2016) '''A novel systems-biology algorithm for the analysis of coordinated protein responses using quantitative proteomics'''. ''Molecular & Cellular Proteomics'', 15(5):1740-60.</ref> In this test we:
+The '''[[SanXoT Sowftware Package]]''' can be used to perform systems biology analises using the SBT (''Systems Biology Triangle'') as described.<ref>García-Marqués, F., Trevisan-Herraz, M., Martínez-Martínez, S., Camafeita, E., Jorge, I., Lopez, J.A., Méndez-Barbero, N., Méndez-Ferrer, S., del Pozo, M.A., Ibáñez, B., Andrés, V., Sánchez-Madrid, F., Redondo, J.M., Bonzon-Kulichenko, E. and Vázquez, J. (2016) '''[http://www.mcponline.org/content/15/5/1740.long A novel systems-biology algorithm for the analysis of coordinated protein responses using quantitative proteomics]'''. ''Molecular & Cellular Proteomics'', 15(5):1740-60.</ref> In this test we:
 * generate a relations file using data from the '''[https://en.wikipedia.org/wiki/DAVID DAVID bioinformatics resource]''' (you can download yourself the data from them, but for your convenience we already included it)

@@ Line 17: / Line 17: @@
 ==Test 1: The fundamental workflow==
-The '''[[fundamental workflow]]''' consists of the steps to quantify proteins using PSMs and quantitative information, based on the WSPP (''Weighted Spectrum, Peptide and Protein'') statistical model, as described<ref>Navarro, P., Trevisan-Herraz, M., Bonzon-Kulichenko, E., Núñez, E., Martínez-Acedo, P., Pérez-Hernández, D., Jorge, I., Mesa, R., Calvo, E., Carrascal, M., Hernáez, M.L., García, F., Bárcena, J.A., Ashman, K., Abian, J., Gil, C., Redondo, J.M. and Vázquez, J. (2014) '''General statistical framework for quantitative proteomics by stable isotope labeling'''. ''Journal of proteome research'', 13, 1234-1247.</ref>, using the following the steps:
+The '''[[fundamental workflow]]''' consists of the steps to quantify proteins using PSMs and quantitative information, based on the WSPP (''Weighted Spectrum, Peptide and Protein'') statistical model, as described<ref>Navarro, P., Trevisan-Herraz, M., Bonzon-Kulichenko, E., Núñez, E., Martínez-Acedo, P., Pérez-Hernández, D., Jorge, I., Mesa, R., Calvo, E., Carrascal, M., Hernáez, M.L., García, F., Bárcena, J.A., Ashman, K., Abian, J., Gil, C., Redondo, J.M. and Vázquez, J. (2014) '''[https://pubs.acs.org/doi/abs/10.1021/pr4006958 General statistical framework for quantitative proteomics by stable isotope labeling]'''. ''Journal of proteome research'', 13, 1234-1247.</ref>., using the following the steps:
 * calibration of spectra

@@ Line 81: / Line 81: @@
 ==Test 3: Systems biology==
-The SanXoT Sowftware Package can be used to perform systems biology analises using the SBT (''Systems Biology Triangle'') as described.<ref>García-Marqués, F., Trevisan-Herraz, M., Martínez-Martínez, S., Camafeita, E., Jorge, I., Lopez, J.A., Méndez-Barbero, N., Méndez-Ferrer, S., del Pozo, M.A., Ibáñez, B., Andrés, V., Sánchez-Madrid, F., Redondo, J.M., Bonzon-Kulichenko, E. and Vázquez, J. (2016) '''A novel systems-biology algorithm for the analysis of coordinated protein responses using quantitative proteomics'''. ''Molecular & Cellular Proteomics''.</ref> In this test we:
+The '''[[SanXoT Sowftware Package]]''' can be used to perform systems biology analises using the SBT (''Systems Biology Triangle'') as described.<ref>García-Marqués, F., Trevisan-Herraz, M., Martínez-Martínez, S., Camafeita, E., Jorge, I., Lopez, J.A., Méndez-Barbero, N., Méndez-Ferrer, S., del Pozo, M.A., Ibáñez, B., Andrés, V., Sánchez-Madrid, F., Redondo, J.M., Bonzon-Kulichenko, E. and Vázquez, J. (2016) '''A novel systems-biology algorithm for the analysis of coordinated protein responses using quantitative proteomics'''. ''Molecular & Cellular Proteomics''.</ref> In this test we:
 * generate a relations file using data from the '''[https://en.wikipedia.org/wiki/DAVID DAVID bioinformatics resource]''' (you can download yourself the data from them, but for your convenience we already included it)
-* use the data from Test 2
+* use the resulting data from Test 2
 * calculate a category-level fold-change
 * make the analysis of the systems biology.
@@ Line 98: / Line 98: @@
 ::* all the files generated in Test 1 and Test 2
 ::* the tab-separated text file '''''SB_Homo_19dic-2017.txt''''' (a set of data downloaded from DAVID)
 ::* the '''''commands_test3.bat'''''.
@@ Line 119: / Line 118: @@
 ) as in Test 1 and Test 2, the only files that are not identical should be the *_logFile.txt from Camacho, SanXoTSqueezer, Sanson, SanXoTGauss and the Coordinometer, as well as the *_infoFile.txt from SanXoT and SanXoTSieve. Additionally, if you use different versions of Graphviz (this test used Graphviz 2.36) you might find differences in the file sanson_simGraph.pdf (which is a pdf containing the final graph with the category clusters).
 ==References==