Ridom SeqSphere+ Documentation - Recent changes [en]

Getting Started

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Batch Mode:

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	[[Create_Samples_from_Assembled_Genomes\|Genome sequence data or contig libraries]] that were assembled from NGS reads (e.g., IonTorrent PGM) can be imported to extract the defined targets, including the aligned read data		[[Create_Samples_from_Assembled_Genomes\|Genome sequence data or contig libraries]] that were assembled from NGS reads (e.g., IonTorrent PGM) can be imported to extract the defined targets, including the aligned read data
-	~~(for assembling SeqSphere+ includes the [[Velvet_Assembler\|''de novo'' assembler Velvet]] and the [[BWA_Mapper\|BWA reference mapper]]).~~

	All further processing and analysis is done on target level (i.e., gene-by-gene approach).		All further processing and analysis is done on target level (i.e., gene-by-gene approach).
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	The data can be processed and visualized using phylogenetic trees and minimum spanning trees.		The data can be processed and visualized using phylogenetic trees and minimum spanning trees.

-	==== Batch Mode ====	+	==== Batch Mode and Pipeline Mode ====

	Ridom SeqSphere+ is designed for resequencing projects. Therefore the import and processing steps, once established, are normally started as batch mode. The batch mode allows to choose a Project and a list of input files, to import, check, type and store multiple data entries in one continuous process.		Ridom SeqSphere+ is designed for resequencing projects. Therefore the import and processing steps, once established, are normally started as batch mode. The batch mode allows to choose a Project and a list of input files, to import, check, type and store multiple data entries in one continuous process.
		+
		+	Ridom SeqSphere+ also offers the non-interactive [[Pipeline Mode\|pipeline mode]] to assemble, import, type and analyze hundreds of your NGS sequence data at once automatically.

	=== Data Objects in SeqSphere+ ===		=== Data Objects in SeqSphere+ ===

MLST+ Schema for Neisseria meningitidis

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	== Cluster Type ==		== Cluster Type ==

-	Max. distance: ~~not defined yet~~	+	Max. distance: 60 alleles
-		+
-	~~== Download ==~~	+
-		+
-	~~The N. meningitidis is not yet available in the Task Template Store, because the~~	+
-	~~Cluster Type threshold is not finalized yet.~~	+
-		+
-	~~However, a draft version of the Task Template can be downloaded to perform local allele typing:~~	+
-		+
-	~~[[File:Button16-TaskTemplate.png\|Button16-TaskTemplate.png]]~~	+
-	~~'''[[media:N_meningitidis_DRAFT_MLST+.tasktemplate‎\|N_meningitidis_DRAFT_MLST+.tasktemplate‎]]''' (1241 targets)~~	+

	== MLST+ Target Definition ==		== MLST+ Target Definition ==

Search Similar Samples

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	[[File:searchSimilarSamplesInProject3.png\|thumb\|upright=1.2]]		[[File:searchSimilarSamplesInProject3.png\|thumb\|upright=1.2]]

-	Search for similar Samples, based on the numbers of similar and different allele types. Note: the actual DNA sequence of the allele types is not used for similarity calculation.	+	The menu command [[File:Button16-SearchSamplesLocally.png\|link=]] ''Tools \| Search Similar Samples Locally'' allows to search for Samples that are similar to currently opened Samples, based on the numbers of similar and different allele types. Note: the actual DNA sequence of the allele types is not used for similarity calculation.

	Either all Samples of a Project can be searched, or the Samples defined by a [[Manage_Comparison_Table_Definitions\|Comparison Table Definition]] can be uses for searching.		Either all Samples of a Project can be searched, or the Samples defined by a [[Manage_Comparison_Table_Definitions\|Comparison Table Definition]] can be uses for searching.

User Guide

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	:[[MLST+ Allele Libraries]]		:[[MLST+ Allele Libraries]]
	:[[Comparison Table]]		:[[Comparison Table]]
		+	:[[Search Similar Samples]]
	:[[Sample Analysis Summary]]		:[[Sample Analysis Summary]]
	:[[Position Navigator]]		:[[Position Navigator]]

Phylogenetic tree window

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Distance calculation:

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	Empty values or values that start with a ? are treated as missing values.		Empty values or values that start with a ? are treated as missing values.
-	Depending on the [[Distance Calculation Settings]] these missing values are either treated as an own category or ignored during pairwise comparison. The '''Distance Calculation Settings''' command can be used to change the settings.	+	Depending on the [[Distance Calculation Settings]] these missing values are either treated as an own category or ignored during pairwise comparison. The ''Distance Calculation Settings'' command can be used to change the settings.

-	For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the '''missing values are an own category''' option is recommended. For a larger number of columns (e.g. MLST with hundreds of targets) the '''pairwise ignore missing values''' option is recommended.	+	For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the ''missing values are an own category'' option is recommended. For a larger number of columns (e.g. MLST with hundreds of targets) the ''pairwise ignore missing values'' option is recommended.

	{\|		{\|
	[[File:Dialog-warning.png\|left]]		[[File:Dialog-warning.png\|left]]
-	\|Note that the option '''pairwise ignore missing values''' may result in problems in the tree when a Sample contains many missing values. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating a tree.	+	\|Note that the option ''pairwise ignore missing values'' may result in problems in the tree when a Sample contains many missing values. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating a tree.
	\|}		\|}

Minimum Spanning Tree window

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Distance Calculation:

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	Empty values or values that start with a ? are treated as missing values.		Empty values or values that start with a ? are treated as missing values.
-	Depending on the settings for [[Missing Values in MST]] these missing values are either treated as an own category or ignored during pairwise comparison. The '''Treatment of Missing Data''' command can be used to change the settings.	+	Depending on the settings for [[Missing Values in MST]] these missing values are either treated as an own category or ignored during pairwise comparison. The ''Treatment of Missing Data'' command can be used to change the settings.

-	For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the '''missing values are an own category''' option is recommended. For a larger number of columns (e.g. MLST with hundreds of targets) the '''pairwise ignore missing values''' option is recommended.	+	For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the ''missing values are an own category'' option is recommended. For a larger number of columns (e.g. MLST with hundreds of targets) the ''pairwise ignore missing values'' option is recommended.

	{\|		{\|
	[[File:Dialog-warning.png\|left]]		[[File:Dialog-warning.png\|left]]
-	\|Note that the option '''pairwise ignore missing values''' may result in problems in the MST when a Sample contains many missing values. In this case, many or all of the MST nodes might be merged. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating an MST.	+	\|Note that the option ''pairwise ignore missing values'' may result in problems in the MST when a Sample contains many missing values. In this case, many or all of the MST nodes might be merged. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating an MST.
	\|}		\|}

Comparison Table

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Modifying data:

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	== Modifying data ==		== Modifying data ==
-	Values for multiple Samples can be modified using the menu command '''Set Values for Selected Samples'''. To modify a simple table cell, double-click the cell.	+	Values for multiple Samples can be modified using the menu command ''Set Values for Selected Samples''. To modify a simple table cell, double-click the cell.
	</div>		</div>
	<!-- ================ ========== =========== ================ -->		<!-- ================ ========== =========== ================ -->
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	To edit the available groups, select the command ''Manage Groups'' from the ''Data'' menu. A new window will open that contains a list of groups.		To edit the available groups, select the command ''Manage Groups'' from the ''Data'' menu. A new window will open that contains a list of groups.

-	The menu command '''Set Groups by Value''' can be used to dynamically create groups based on the values of a Sample.	+	The menu command [[File:Button16-GroupByValues.png\|link=]] ''Set Groups by Value'' can be used to dynamically create groups based on the values of a Sample.

	== Distance Calculation==		== Distance Calculation==
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	Some functions, namely the comparison Sample, the phylogenetic trees and the minimum spanning tree require that one or more columns are selected for distance calculation. Columns selected for distance calculation can be recognized by their dark-green column header.		Some functions, namely the comparison Sample, the phylogenetic trees and the minimum spanning tree require that one or more columns are selected for distance calculation. Columns selected for distance calculation can be recognized by their dark-green column header.
	Columns for distance calculation can be chosen in two ways:		Columns for distance calculation can be chosen in two ways:
-	* by using the [[image:modifyColumnSettings.png\|link=]] '''[[Modify Column Settings]]''' (via ''Data'' menu or toolbar button) or	+	* by using the [[image:modifyColumnSettings.png\|link=]] ''[[Modify Column Settings]]'' (via ''Data'' menu or toolbar button) or
	* by clicking the right mouse button on the column header. This opens a context menu that allows choosing the data type for a column and if the column is used for distance calculation.		* by clicking the right mouse button on the column header. This opens a context menu that allows choosing the data type for a column and if the column is used for distance calculation.

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	Each column has a data type. Usually, the predefined data types are adequate. The data types can be changed in two ways:		Each column has a data type. Usually, the predefined data types are adequate. The data types can be changed in two ways:
-	* by using the [[image:modifyColumnSettings.png\|link=]] '''[[Modify Column Settings]]''' (via ''Data'' menu or toolbar button) or	+	* by using the [[image:modifyColumnSettings.png\|link=]] ''[[Modify Column Settings]]'' (via ''Data'' menu or toolbar button) or
	* by clicking the right mouse button on the column header. This opens a context menu, that allows choosing the data type for a column.		* by clicking the right mouse button on the column header. This opens a context menu, that allows choosing the data type for a column.
	</div>		</div>

Server System Administration

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	This window displays the currently active sessions and allows to administrate the server.		This window displays the currently active sessions and allows to administrate the server.

-	* '''Refresh Server Status''': Forces to retrieve the current server status and updates the session list and license state. The status is also refreshed automatically after a period of time.	+	* [[File:Button16-Refresh.gif\|link=]] '''Refresh Server Status''': Forces to retrieve the current server status and updates the session list and license state. The status is also refreshed automatically after a period of time.

-	* '''Server System Info''': Show an overview of the server internals.	+	* [[File:Button16-Information.gif‎\|link=]]'''Server System Info''': Show an overview of the server internals.
-		+
-	* '''Activate Trial License''': ''Only shown if no full license is activated.''<br/>Allows to import a trial license from a file. A trial license can be requested by email from [mailto:support@ridom.de support@ridom.de].	+
-		+
-	* '''Import License Upgrade File''': ''Only shown if a hardware license is found on the server.''<br/>Allows to import a license upgrade file into the hardware license key.	+

		+	* [[File:Button16-Key.png\|link=]] '''Activate Trial License''': ''Only shown if no full license is activated.''<br/>Allows to import a trial license from a file. A trial license can be requested by email from [mailto:support@ridom.de support@ridom.de].
		+	<!--
		+	* '''Import License Upgrade File''': ''Only shown if a hardware license is found on the server.''<br/>Allows to import a license upgrade file into the hardware license key.-->
	* '''Edit Server Backup Settings''': Define the location to store the data backup files, and which day(s) of the week and time of day to perform the backup. The length of time to keep old backup files is an option that can be set by the number of days in age. The backup files are saved in a compressed archive format with extension ''.tgz''. To restore a backup, either		* '''Edit Server Backup Settings''': Define the location to store the data backup files, and which day(s) of the week and time of day to perform the backup. The length of time to keep old backup files is an option that can be set by the number of days in age. The backup files are saved in a compressed archive format with extension ''.tgz''. To restore a backup, either
	** unpack the files into the data directory or		** unpack the files into the data directory or
	** start the server with ''-restoreBackup'' or ''-restoreLastBackup'' parameter (see [[Command Line Parameters\|command line parameters]]).		** start the server with ''-restoreBackup'' or ''-restoreLastBackup'' parameter (see [[Command Line Parameters\|command line parameters]]).

-	* '''Do Server Backup Now''': Immediate backup the server database into the directory that is configured in the backup settings. '''Warning''': While the backup is created, the database will be in a locked state. Therefore all SeqSphere+ users cannot retrieve or store data during this time!	+	* [[File:Button16-Backup.png\|link=]]: '''Do Server Backup Now''': Immediate backup the server database into the directory that is configured in the backup settings. '''Warning''': While the backup is created, the database will be in a locked state. Therefore all SeqSphere+ users cannot retrieve or store data during this time!

	* '''Edit Welcome Message''': Define or modify the welcome message that will be shown to SeqSphere+ user after log in. HTML can be used to add line breaks and text formatting. If no welcome message is defined, a default message is shown.		* '''Edit Welcome Message''': Define or modify the welcome message that will be shown to SeqSphere+ user after log in. HTML can be used to add line breaks and text formatting. If no welcome message is defined, a default message is shown.

-	* '''Close Server''': This will disallow any logins by non-admin users.	+	* [[File:Button16-Lock.png\|link=]]'''Close Server''': This will disallow any logins by non-admin users.
		+
		+	* [[File:Button16-OnlineUpdate.png\|link=]] '''Server Online Update''': Check the Ridom SeqSphere+ site for any updates that your installed server may need.

-	* '''Server ~~Online~~ Update''': ~~Check the Ridom SeqSphere+ site for any updates~~ that ~~your installed~~ server ~~may need~~.	+	* [[File:Button16-Open.gif\|link=]] '''Server Import Update''': Select an update file that will be transferred to the server.

-	* '''Terminate Session''': When a session is selected on the left hand side of the screen, this button can be used to end it.	+	* [[File:Button16-Delete.png\|link=]]'''Terminate Session''': When a session is selected on the left hand side of the screen, this button can be used to end it.

	* '''Shutdown Server''': This will disconnect all sessions and end the running server processes. With large database this shutdown process may take several minutes.		* '''Shutdown Server''': This will disconnect all sessions and end the running server processes. With large database this shutdown process may take several minutes.

-	* '''Send Logs to Ridom Support''': Send the server log files to Ridom SeqSphere+ Support	+	* '''Send Logs to Ridom Support''': Send the server log files to Ridom SeqSphere+ Support.

Administrator Guide

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	<!-- [[Category:Administrator Guide\| ]] -->		<!-- [[Category:Administrator Guide\| ]] -->
	;Administration Menu		;Administration Menu
-	:[[SysAdmin Manager]]	+	:[[SysAdmin Manager\|Server System Administration]]

	;Managing User Access		;Managing User Access

Server Database Backup

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Restoring Database Backups:

Updating

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Updating the Server Software:

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	# Use SeqSphere+ Client to log in as "Administrator"		# Use SeqSphere+ Client to log in as "Administrator"
-	# Open via menu Administration ~~> Show SysAdmin Manager~~	+	# Open via menu [[File:Button16-SysAdminManager.png\|link=]] ''Administration \| Server System Administration''
	# Be sure that no other users are logged in		# Be sure that no other users are logged in
-	# Use "Close Server" to ensure that non-admins may not log in	+	# Use [[File:Button16-Lock.png\|link=]] ''Close Server'' to ensure that non-admins may not log in
-	# Use "Server Online Update" to download and prepare the update	+	# Use [[File:Button16-OnlineUpdate.png\|link=]] ''Server Online Update'' to download and prepare the update
-	# The update will then be automatically installed after the server is shut down.	+	# The update will then be automatically installed after the server is shut down
	# After the update has been installed, the server must started again manually		# After the update has been installed, the server must started again manually

File:Seqsphere choose tasktype.png

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Choose Task Type

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	To separate and simplify the workflows in Ridom SeqSphere+, two different types of Task Templates exist:		To separate and simplify the workflows in Ridom SeqSphere+, two different types of Task Templates exist:
-	* one for '''~~first-gen~~''' ~~sequencing data (also called capillary electrophoresis sequencing data or sanger sequencing data),~~ and	+	* one for '''Sanger sequencing data''' and
-	* one for '''~~next-gen~~''' ~~sequencing data (also called massive parallel sequencing data)~~.	+	* one for '''whole genome sequencing data'''.
		+
	In this first step, you can decide for which data type to create a Task Template.		In this first step, you can decide for which data type to create a Task Template.
	If you want to include both types of sequence data in the same Task, choose ''Create Task Template for Both''.		If you want to include both types of sequence data in the same Task, choose ''Create Task Template for Both''.

	Click on one of the text boxes to proceed to the next step.		Click on one of the text boxes to proceed to the next step.

Managing Projects

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Creating a New Project:

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	Additionally, one or more ''[[Managing Task Templates\|Task Templates]]'' can be used in the Project.		Additionally, one or more ''[[Managing Task Templates\|Task Templates]]'' can be used in the Project.
-	Task Templates define what data may be added to a Sample, and how it can be analyzed. Task Templates can be added from the [[Task Template Store]] using the button [[File:Button16-WebDownload.png\|link=]] '''Add from Store''' or from the list of Task Templates defined on the server using the button [[File:Button16-Plus.gif\|link=]] '''Add Manually'''.	+	Task Templates define what data may be added to a Sample, and how it can be analyzed. Task Templates can be added from the [[Task Template Store]] using the button [[File:Button16-WebDownload.png\|link=]] ''Add from Store'' or from the list of Task Templates defined on the server using the button [[File:Button16-Plus.gif\|link=]] ''Add Manually''.

	The [[Access Control]] can be defined for the Project definition, and for each Sample of this Project the default access can be set.		The [[Access Control]] can be defined for the Project definition, and for each Sample of this Project the default access can be set.

Managing Users

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User Roles:

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	;Scientist		;Scientist
-	:May create and work with all entities in the database (~~samples~~, ~~task entries~~, ~~projects~~, ~~task templates~~, ~~database schemes~~)	+	:May create and work with all entities in the database (Samples, Task Entries, Projects, Task Templates, Database Schemas)

	;Managing Scientist		;Managing Scientist
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	:Has access to low-level administration functions like shutting down the server.		:Has access to low-level administration functions like shutting down the server.

-	The system administrator can also define new roles using the menu item ''Administration \| ~~Manage~~ User Roles''. Each role is defined by the ''privileges'' that are granted to the user. The list of privileges is shown in the first column of the dialog. Move the mouse over a privilege to see a short description in the tooltip.	+	The system administrator can also define new roles using the menu item [[File:Button16-UserRole.png\|link=]] ''Administration \| User Roles''. Each role is defined by the ''privileges'' that are granted to the user. The list of privileges is shown in the first column of the dialog. Move the mouse over a privilege to see a short description in the tooltip.

	=== User Groups ===		=== User Groups ===

Preferences

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	;Online Updates		;Online Updates
	:You can specify if SeqSphere+ should search for updates on every startup.		:You can specify if SeqSphere+ should search for updates on every startup.
		+
		+	== Input Files ==
		+
		+	;SAM/BAM
		+	:Reads with a mapping quality below the given threshold (default 10) are discared when Samples are created from SAM/BAM files using [[Create Samples from Assembled Genomes]] or the [[Pipeline Mode]].

File:Mlstplustargetdefiner.png

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NCBI GenBank Download

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	== NCBI GenBank Bacteria Genoms Browser ==		== NCBI GenBank Bacteria Genoms Browser ==

-	[[File:ncbiGenomeBrowserScreen.png\|thumb]]	+	[[File:ncbiGenomeBrowserScreen.png\|thumb\|upright=1.5]]

	This window allows to browse the finished bacterial genomes from NCBI GenBank. The ''Filter'' textfield allows to show only table rows where the Taxo Name contains the entered text (case-insensitive). The ''Filter by Replicon'' box can be used to show only chromosomes or only plasmids.		This window allows to browse the finished bacterial genomes from NCBI GenBank. The ''Filter'' textfield allows to show only table rows where the Taxo Name contains the entered text (case-insensitive). The ''Filter by Replicon'' box can be used to show only chromosomes or only plasmids.
		+
		+	Select rows in the table and click ''OK'' to use the accession numbers.

File:NcbiGenomeBrowserScreen.png

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NCBI GenBank Download

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NCBI GenBank Bacteria Genoms Browser:

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-	[[File:genbankDownloadScreen.png\|thumb\|~~upscale~~=1.5]]	+	[[File:genbankDownloadScreen.png\|thumb\|upright=1.5]]
-	This window allows to download sequences from NCBI GenBank.	+	This window allows to download sequences from NCBI GenBank. The button [[File:Button16-Paste.gif\|link=]] ''Paste'' can be used to get accession numbers from clipboard or from a text file. The button
		+	[[File:Button16-NCBI.png\|link=]] ''Search'' opens the NCBI GenBank Bacteria Genoms Browser.
		+
		+	== NCBI GenBank Bacteria Genoms Browser ==
		+
		+	[[File:ncbiGenomeBrowserScreen.png\|thumb]]
		+
		+	This window allows to browse the finished bacterial genomes from NCBI GenBank. The ''Filter'' textfield allows to show only table rows where the Taxo Name contains the entered text (case-insensitive). The ''Filter by Replicon'' box can be used to show only chromosomes or only plasmids.

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	The SeqSphere+ server can periodically create database backups.		The SeqSphere+ server can periodically create database backups.
-	By default, the database backups will be created each day at 00:00 in the subdirectory ''backups'' of the [[~~SeqSphere+_Server_Installation~~#Configuration\|working directory]].	+	By default, the database backups will be created each day at 00:00 in the subdirectory ''backups'' of the [[Server_Installation#Configuration\|working directory]].

-	To change this, log in as administrator user, and invoke the menu item [[image:Button16-SysAdminManager.png\|link=]] ''Administration \| ~~Show SysAdmin Manager~~''.	+	To change this, log in as administrator user, and invoke the menu item [[image:Button16-SysAdminManager.png\|link=]] ''Administration \| Server System Administration''.
	Use the button ''Edit Server Backup Settings'' to show and edit the current settings.		Use the button ''Edit Server Backup Settings'' to show and edit the current settings.

-	Additionally, a backup can be directly invoked using the button ''Do Server Backup now''.	+	Additionally, a backup can be directly invoked using the button [[File:Button16-Backup.png\|link=]] ''Do Server Backup now''.

	While the backup is running, users cannot login or work on the server because the database is locked.		While the backup is running, users cannot login or work on the server because the database is locked.
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	:internaldb.properties		:internaldb.properties
	:internaldb.script		:internaldb.script
-	that are located in the database directory (''[[~~SeqSphere+_Server_Installation~~#Configuration\|<working directory>]]/data'').	+	that are located in the database directory (''[[Server_Installation#Configuration\|<working directory>]]/data'').
	The backup is a packed archive file (tgz) that contains these four database files.		The backup is a packed archive file (tgz) that contains these four database files.

	Perform the following steps to restore the most recent backup:		Perform the following steps to restore the most recent backup:
	# Exit the SeqSphere+ server.		# Exit the SeqSphere+ server.
-	# Invoke the SeqSphere+ with command line parameter <code>-restoreLastBackup</code>. The server restores the backup and exits automatically.	+	# Invoke the SeqSphere+ with [[Command_Line_Parameters\|command line parameter]] <code>-restoreLastBackup</code>. The server restores the backup and exits automatically.
	# Start the SeqSphere+ server again (without the command line parameter).		# Start the SeqSphere+ server again (without the command line parameter).

-	Alternatively, you can use the command line parameter	+	Alternatively, you can use the [[Command_Line_Parameters\|command line parameter]]
	<code>-restoreBackup <backup_file></code>		<code>-restoreBackup <backup_file></code>
	to choose a specific backup file.		to choose a specific backup file.