Basic Tutorial - Revision history

Frodo at 06:46, 13 March 2014

2014-03-13T06:46:14Z

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	[[Category:~~Cheminformatics~~]]		[[Category:SEA]]
	[[Category:Tutorials]]		[[Category:Tutorials]]
	[[Category:Internal]]		[[Category:Internal]]

Frodo at 16:09, 14 February 2014

2014-02-14T16:09:41Z

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	[[Category:Cheminformatics]]		[[Category:Cheminformatics]]
	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]
	[[Category:Internal]]		[[Category:Internal]]

Frodo at 02:55, 14 February 2014

2014-02-14T02:55:50Z

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	> sea-export -t 0.5 -o sea_output 9		> sea-export -t 0.5 -o sea_output 9



			[[Category:Cheminformatics]]
			[[Category:Tutorial]]
			[[Category:Internal]]

TBalius at 20:48, 19 December 2012

2012-12-19T20:48:36Z

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	> sea-run -f model_fit_file model_set_file query_set_file		> sea-run -f model_fit_file model_set_file query_set_file

			Export the results

			> sea-export -t 0.5 -o sea_output 9

Frodo at 23:16, 11 October 2012

2012-10-11T23:16:29Z

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	See [[SEA]]		See [[SEA]]

	To run [[SEA]] we need three ~~query~~ files:		To run [[SEA]] we need, for both the query and the reference, three files with the same basename and different extensions:
	* smiles : The separator between smiles and IDs is a ~~semicolumn~~		* <b>smiles</b> (.smi) : The separator between smiles and IDs is a semicolon. Make sure it has the same characteristics than the reference by running the following command:
	* fingerprints : Separator is also a ~~semicolumn~~. Can be generated by the following command:		> sea-molecule-clean
			* <b>fingerprints</b> (.fp) : Separator is also a semicolon. Can be generated by the following command:
	> sea-molecule-fingerprint		> sea-molecule-fingerprint
	* set ~~file~~ : First element is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a ~~coumn~~.		* <b>sets</b> (.set) : First element (separated by semicolon) is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a colon.


	~~For the reference sets~~ we need ~~the same three files plus~~ the model file, generated from [[SEA]].		Additionally, we will need the model fit file generated from [[SEA]].

	The actual command is:		The actual command to <b>run SEA</b> is:

	> sea-run -f model_fit_file model_set_file query_set_file		> sea-run -f model_fit_file model_set_file query_set_file

Therese: 4 revisions

2012-10-08T18:10:27Z

4 revisions

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Revision as of 18:10, 8 October 2012

Tbalius at 21:11, 1 October 2012

2012-10-01T21:11:49Z

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			See [[SEA]]

	To run [[SEA]] we need three query files:		To run [[SEA]] we need three query files:
	* smiles : The separator between smiles and IDs is a semicolumn		* smiles : The separator between smiles and IDs is a semicolumn

Tbalius at 21:10, 1 October 2012

2012-10-01T21:10:58Z

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	To run SEA we need three query files:		To run [[SEA]] we need three query files:
	* smiles : The separator between smiles and IDs is a semicolumn		* smiles : The separator between smiles and IDs is a semicolumn
	* fingerprints : Separator is also a semicolumn. Can be generated by the following command:		* fingerprints : Separator is also a semicolumn. Can be generated by the following command:

Tbalius at 20:58, 14 September 2012

2012-09-14T20:58:35Z

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	For the reference sets we need the same three files plus the ~~fits~~ file, generated from ~~the~~		For the reference sets we need the same three files plus the model file, generated from [[SEA]].

			The actual command is:

			> sea-run -f model_fit_file model_set_file query_set_file

Tbalius at 20:55, 14 September 2012

2012-09-14T20:55:55Z

New page

To run SEA we need three query files:
* smiles : The separator between smiles and IDs is a semicolumn
* fingerprints : Separator is also a semicolumn. Can be generated by the following command:
> sea-molecule-fingerprint
* set file : First element is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a coumn.

For the reference sets we need the same three files plus the fits file, generated from the