Please be aware that the Seurat (Structure Exploration Utility for Rational Therapeutics) drug discovery and development platform comprises of a Client, Server and Database(s) component. As such to evaluate Seurat you must install or otherwise make available:

At least one but possibly more instances of the Seurat Client. You can install each client instance separately (not recommended with more than one user) or you can use the Java Web Start version of the client to reduce to almost zero the cost of deployment to multiple users.

One instance of the Seurat Server.

At least one database that contains Medicinal Chemistry concepts in either Oracle or PostgreSQL.

You will need to make changes to the configuration files of the Server and preferences of the client through the “Prefs…” button of the Seurat Clients login screen to make Seurat aware of your databases, how to connect to them and where your Seurat license file resides.

If you plan to use the most typical evaluation configuration for Seurat that being:

The Client and Server installed on the same Windows XP Pro, SP2 machine.
Running against the PostgreSQL database installed automatically as part of the Seurat Server installation process
With the cMet test data set loaded into the Synaptic Science native database in a that same PostgreSQL database
And this is the first time you are installing Seurat.

Then we recommend you refer to and follow the instructions in the Seurat Windows Quick Start Guide to get Seurat installed, configured and operational in the shortest possible time.

2 How to use this Manual

There are many configurations under which Seurat can be utilized that range from having Seurat interface to your existing medicinal chemistry database, having it interface with the Synaptic Science native database schema to having Seurat interface with both.

In addition to your primary Medicinal Chemistry database or the one supplied by Synaptic Science Seurat can be configured to interface with partner, CRO and industry standard databases.

As the number of databases to which Seurat is configured to interface increases so too does the number of steps required to configure Seurat.

In order to not repeat the steps required to configure database access to the various combinations of databases and platforms in each installation section a separate section is given toward the end of this manual that goes through each of the currently possible Seurat / Database combinations.

Therefore when using this manual you will need to:

First follow the instructions in the section of the manual that pertain to installing (or upgrading) the Seurat Client and Server to the platform of your choice.

Then proceed to the Create or Update Database sub section of the Post Installation Steps section of this manual and follow the instructions in one of the sub sections that define how to install or upgrade the database of your choice (Oracle or PostgreSQL) on the platform of your choice (Windows or UNIX) with the data of your choice (cMet test data set, exiting data in your own database, start with an empty database and load from SD and CSV files later).

Make configuration file changes to describe these created or update databases to Seurat so that it knows how to retrieve, analyze and report on that data.

Go to the Starting Seurat section of the document for instructions on how to start the Seurat Server and Client after steps 1 through 3 have been completed.

Please keep this overarching sequence of steps in mind as you work on installing and configuring Seurat.

3 Installation Requirements

As SEURAT is a pure Java application it can run on any platform supporting a Java 1.4 or Java 1.5 JVM. Right now we bundle JVM is 1.4.2_12 with the Windows installers and as such we provide a link on our website’s download page to that version for users working under Unix.

This is because our Windows XP installers will install this version for you but on Unix or Mac you will need to download and install this version before trying to install and run Seurat.

The SEURAT Server has been successfully deployed under Windows, AIX and Linux. The SEURAT client has been successfully deployed under Windows, AIX, Linux and Mac OSX.

If your particular platform or configuration does not seem to be supported please contact us at sales@syanpticscience.com and as long as your platform supports a viable 1.4 or 1.5 JVM Seurat will be able to run on your platform.

3.1 Installation Requirements: Unix

Pretty much any flavor of Unix with between 256 and 512 Megabytes of memory for running the server and 256 Megabytes for running the client. The client can run with 128 Megabytes of memory depending on the tasks requested of the platform.
Java 1.4 or 1.5 for your particular platform installed.
Either a PostgreSQL 8.1 or later or Oracle database installed which either holds your existing data or can be used to create the Synaptic Science native database schema.

If you want to map to an existing database you will need to refer to the steps described in the “Map Seurat to Existing Med Chem Database in Oracle” of our Administrators Guide and the “Seurat Database Mapping Guide”. Both guides are available on the documentation page of our website.

The UNIX installer does not come bundled with a particular version of the Java JVM. Synaptic Science currently supports Java 1.4 and Java 1.5 for running the Seurat Server and Client.

This 1.4.2_12 version of the JVM can be downloaded either from the download page of our website or from http://java.sun.com/products/archive/ (sometimes the later may produce faster download speeds). Although version 1.4.2_12 is the version we bundle with the application Seurat also runs under any 1.4 or 1.5 JVM.

At present we provide a jar file based installation of the Seurat Server and Seurat Client for Unix. In the future we plan to provide a more robust and complete installer based experience akin to the one available for Windows XP.

3.2 Installation Requirements: Windows

Windows XP Professional, Service Pack 2 machine (laptop or desktop), Windows Vista or Windows 2000 with at least 512 Megabytes of memory.
You must run the installer as a windows Administrator.

NOTE: For Windows Vista installations you MUST use right mouse click -> run as administrator when running the downloaded installers otherwise the SEURAT installers for the client and server will fail to run.

There is no need to install a version of Java separately as the Seurat installers come bundled with the correct version of Java in order to run the Seurat platform.
The Seurat Server installer will attempt to install PostgreSQL during the installation process. PostgreSQL requires that a windows service account be used to run the PostgreSQL processes for security reasons. The service account must have the following rights:

Log on as a service
Log on locally

You can either create the windows service account before running the Seurat Server installer and supply that username during installation or you can let the installer attempt to create the service account for your.

In the later case you will need to be sure that you run the installer under an account (most likely an Administrator account) that can grant the required privileges to the service account

3.3 PyMol

At present only the Seurat Client Windows XP installer automatically installs PyMol which Seurat uses for the visualization of crystal structures and docking results. In all other cases of a client installation you will need to install PyMol onto your machine as a separate manual step if you wish to view crystal structure information from within Seurat.

The version of PyMol that ships with the Windows XP installer for the Seurat Client includes a PyMol executable that is evaluation only however if you already have a “for-pay” version of PyMol Seruat will not attempt to install the evaluation version and will work with your currently installed version instead.

There is a link to the evaluation version of PyMol available for download from the download page of our website for those users not using the Windows installers (UNIX or MAC users) that do not already have a version of PyMol.

If you wish to use a more recent version of PyMol then see the PyMol home page http://pymol.sourceforge.net/ for details of how to download the correct version for your particular platform.

Note that because PyMol is an open source project to be able to use PyMol without compiling the source yourself you will need to pay a license fee to Delano Scientific LLC for their efforts in producing the executables on your behalf and optionally for support if you elect to use a more recent version of PyMol within Seurat.

If you encounter problems setting up your PyMol installation or just have further questions please contact us at support@synapticscience.com

3.4 Assumptions

It is assumed that if you already have an earlier version of Seurat installed on a UNIX platform then you will be following the instructions in one of the Upgrade sections of this document. These sections take care to detail the steps in such a way that no configuration information will be lost.

In contrast the fresh install sections for a UNIX platform do not take such care and so following the instructions in any of these sections when you have an existing version of Seurat installed may result in the loss of important configuration information.

If you are installing using the Windows XP installers then you do not have to worry about this distinction because the installers are careful not to remove or overwrite any files that could cause you to loose information about your configuration settings.

Please be sure to follow the instructions for the situation that matches your particular installation environment.

4 Recommendations

We recommend that when evaluating Seurat if at all possible you use the following combination of Seurat client and Server when evaluating:

The Seurat Server running on Windows XP Professional against the Synaptic Science native database schema in PostgreSQL and;
The Seurat Client running on the same machine to which the server was installed. This will minimize the number of steps required to get started.
Once a single user is up and running and you want to support more than one remote client then switch to using the Seurat Client deployed via the Java Web Start on the platform of your choice.

We recommend the Windows XP version of the Seurat Server because the installer for that platform is the most complete and automatically installs the PostgreSQL database for you as part of the installation process.

We recommend starting with the native Windows XP installer for the client because it requires no post installation steps to get started.

We recommend moving to the Web Start deployed client installation once you would like to run remote clients and/or more than one client because it makes the second and subsequent “installations” of the Seurat Client almost effortless.

Any of the other combinations (UNIX client or server, non Web Start client) will work they will just take a few more manual configuration steps to get up and running.

5 Downloading Installers

You can download the installers for the client and server via the link sent to you in an email from Synaptic Science (www.synapticscience.com). If you have not yet received an email giving you instructions on how to download the installers go to our website and navigate to the contact us section.

Currently you have six or sometimes seven different download options depending on a combination of the target platform, whether the client is running in Web Start mode and whether you are upgrading from the previous version on installing for the first time.

The titles of each download on the website make it clear which installer you should use. Of course if you still have questions please contact us at support@synapticscience.com.

6 Windows XP Seurat Server Installation

The windows installers are careful not to disturb existing files from earlier installations therefore you can follow the instructions in this section regardless of whether this is your first time installing the Seurat Server on Windows or whether this installation is going to replace an earlier already installed version.

The steps to follow for installation of the Seurat Server for Windows XP Pro are:

1. If you have an earlier version of the Seurat Server installed please uninstall that version by selecting the “Start->All Programs->Seurat Server->Uninstall SEURAT Server” menu option and then click Yes when asked if you really want to uninstall.

2. Start the installation process by double clicking on the installer executable. You will be presented with a screen like the one shown below.

3. After reviewing and accepting the EULA and clicking next and then reading the Remade screen and clicking next you will be asked to either accept the default install location or specify the location to which you want the Seurat Server installed.

4. Once you have selected an install location click the Install button. The Seurat Server installer will now install the Server to the specified location. Once this completes you will be presented with a screen like the one shown below to allow you to specify the format for your corporate and hypothetical compounds as well as a base URL.

5. For the Seurat server to help understand user queries, let it know the prefixes you use for your compounds.

Enter your appropriate prefixes. For example, at Celera we used to call all of our compounds CRA-000001, making the number of digits 6 and the prefix ‘CRA-‘ for all corporate identifiers. We also used a prefix of ‘CRX-‘and again 6 digits for hypothetical compounds. This information gets stored in a file, ‘corporateid.properties’, which you can edit later if you wish (please do not change the order of entries in this file).

NOTE: If you do not see the “Intranet URL” field then you are working with an earlier version of SEURAT. The latest version can be obtained from our website www.synapticscience.com.

The intranet URL field allows you to specify the static portion of the URL that will be constructed when accessing PK reports or other document URL’s that get loaded as assay or property results within SEURAT. SEURAT understands the http, https, ftp and file URL protocols for URL’s

In the screenshot above the evaluation base URL file:///C:/Progra~1/SynapticScience/SeuratClient/pk/ (which allows linking to the test cMet datasets PK reports) has been supplied. If you are just evaluating SEURAT then you can use this value (assuming you installed the Seurat Client to its default location and intend to use the cMet dataset) to link to the example PK reports bundled with the client installer. Otherwise provide a URL that is the base location of where you will be providing access to PK reports and or documents in general.

There are three ways URL’s get used within SEURAT; two of them rely on the specification of the Intranet URL. They are:

<Intranet URL you supply here>/<Content of Assay Result with the string “PK_Protocol” in the name> with the string “PK.doc” added to the end. So for example if the value for a compound of an assay named “PK_IP_MOUSE (PK_Protocol)” was “05-S8040-0211” and you supplied file:///C:/Progra~1/SynapticScience/SeuratClient/pk/ as the Intranet URL protocol then the resulting URL to locate the document would be file:///C:/Progra~1/SynapticScience/SeuratClient/pk/05-S8040-0211PK.doc. You would be able to link to this with a right mouse from the Assay Display view in SEURAT.
<Intranet URL you supply here>/<Content of Assay Result with name “Report_url”. For example, if for a compound an Assay Result or property name with the string “Report_url” in the name existed and had the value “GenericReport.xls” then the complete URL constructed by SEURAT to retrieve the linked document for that compound on right mouse click within the Assay Display would be file:///C:/Progra~1/SynapticScience/SeuratClient/pk/GenericReport.xls.

The third way URL’s are used within SEURAT is by linking to the value(s) within any cell of the AssayDisplay view that contains a complete and valid URL. This mechanism does not rely on the Intranet URL and expects the full and correct URL to be supplied as the value of the Assay Result or property result. For more information regarding use of URL’s to link to external documents within SEURAT please see the “Working with the Assay Display” section of the Users Guide on our website at http://www.synapticscience.com/seurat-users-guide/SeuratUsersGuide.htm.

Finally, don’t worry if you are not sure what to enter for the Intranet URL as it can be easily modified post installation. You do however have to supply a value.

Once you click ‘Next’ if this is the first time you are installing the Seurat server a PostgreSQL installation will start along with a word file with instructions for installing the PostgreSQL database. This is the database that Seurat uses internally for keeping track of information uploaded and the hypothetical compounds.

If you are upgrading to a bug fix or more recent version of the Seurat Server then the PostgreSQL installation steps will be skipped by the installer.

If you intend to run Seurat against an Oracle database then simply skip the PostgreSQL installation by clicking the cancel button. Then after the installation is complete refer to the instructions in the Create or Update Database section of this guide to determine how to configure the database(s) to which Seurat will be communicating

6.1 PostgreSQL Installer

Click on ‘Start’ and go through the installation (some additional screenshots can be found below).

For detailed help on installing postgreSQL you can also go to their web site. For most purposes the instructions below would suffice. http://pginstaller.projects.postgresql.org

6.1.1 Installer walkthrough

The PostgreSQL installer is based on Windows Installer, so it should be familiar to most Windows users. Following is a quick walkthrough of the installer steps.

1. Language selection
Select the language you want to use for the installer. This only sets the language used in the install wizard - the actual installed PostgreSQL can be installed with or without language support and has its own language choice independent from the installer.
You can also select if you want the installer to create a detailed log file of the installation process. Note that this log file will contain both the service user and database super user password if created.

2. Introduction screen
Introduction message. Just click Next to get started.

3. Welcome message and instructions
As always, please read the complete instructions before you continue.

4. Feature selection
Accept at least the defaults from this screen. If you want to install additional features above and beyond the defaults then select what you want to install.

1. The PostgreSQL server bundled with the Seurat Server is compatible only with NT based platforms.

2. Note that the 'Data Directory' option may only be installed on an NTFS partition. If you wish to install the data directory on any other partition type, you will need to run initdb.exe manually after installation.

3. You can change the directory of the entire installation by selecting the feature PostgreSQL and click Browse to pick the new directory.

4. You can also change the directory of an individual feature (such as the server, or pgAdmin) by selecting that feature and clicking Browse.

5. Service installation
Choose whether you want PostgreSQL installed as a service, and if so specify which account should be used. You probably do want to install PostgreSQL as a service as this is the only way to be sure the database will always be running even after server machine reboots.

1. This account will be created and granted the Logon On as a Service right if it does not already have that right. We advise you to retain the ‘Install as service option’ (see next screenshot). The account name is the name of the windows service account under which PostgreSQL will run. This is NOT the database super user account name and password which is specified in a later screen. Please type in a password and retain it for your records.

NOTE: Occasionally the PostgreSQL installer may not be running under a user account that cannot grant the Log on as a Service right to the windows service account named in the screen above. If this happens you will not know until the very end of the installation process when the whole install of PostgreSQL backs itself out. To avoid this issue please be sure to run the Seurat Server installer (and thus PostgreSQL installer) logged into a Windows account that can grant that privilege. Or alternatively have your windows administrator create the windows service account for you *before* running the Seurat Server installer.

6. Accept all the defaults on this screen with the exception of the need to change the port on which PostgreSQL will listen for client connections to 3247. If you do not do this then the Seurat client will not function without some additional configuration changes. Do *NOT* change the super user name otherwise the scripts provided with the Seurat Server to create or update your database to match the latest version will not function. *DO* remember the password you supply for the “postrgres” user as you will need to supply it when you run the Create Database or Update Database options of the Seurat Server installation

1. Specify login details for the database super user “postgres”.

2. Opt to listen for connections on all IP addresses on the system rather than just local host. Note that you will still have to enable access in the host based authentication configuration (pg_hba.conf) and general configuration (postgresql.conf) files to allow remote users to connect to the server.

3. This dialog is only available if you chose to install PostgreSQL as a service.

7. If you do Opt to listen for client connections on all local addresses.. you will be presented with the following screen reminding you of the necessity to make additional configuration changes.

Say OK and then make a note to remind yourself that you will need to go and edit the pg_hba.conf and postgresql.conf files in the <PostgreSQL Installation Dir>/data directory and then stop and restart the postgres service which can be done from the Start->Programs->PostgreSQL 8.1 menu items

8. Procedural languages
Accept the defaults on this screen unless you are familiar with PostgreSQL procedural languages and plan to make use of them as Seurat currently does not rely on any procedural languages.

1. Chose the procedural languages you want activated in template1. All PL files are always installed, this step just activates them by default in all your databases.
This dialog is only available if you chose to install PostgreSQL as a service, and chose to have a database cluster initialized.
Only the languages where the corresponding runtimes were found installed on the system are available for selection.
PL/perl requires ActiveState Perl 5.8 to be installed.
PL/python requires Python 2.3 to be installed
PL/tcl requires ActiveState Tcl 8.4 to be installed.
PL/java requires a valid Sun Java Runtime Environment to be installed.

9. Contrib modules
This dialog is only available if you chose to install PostgreSQL as a service, and chose to have a database cluster initialized.
Note: The Admin81 module is installed by default because pgAdmin will use it to provide enhanced functionality. It may be removed if you do not want it to be installed in all databases; pgAdmin will simply not offer the enhanced functionality it allows.

10. Ready to install
Just click Next to start the actual installation.

11. Installing
A progress bar is shown during the installation.
On some versions of Windows (notably Windows XP before Service Pack 2 and Windows 2003 before Service Pack 1 - see Microsoft Knowledge Base article Q818858) a Command Prompt window will appear during the "Initializing database cluster" step. Don't close this window - it will automatically close once the operation is complete.

Installer screenshot

12. Finished
Installation is complete. You can now go ahead and test your installation and subscribe to the pgsql-announce mailing list to keep up to date.
If you need to add or remove a feature from PostgreSQL, use the Add/remove programs feature in the Control Panel.

13. Now go ahead and click ‘Finish’ on the Seurat Server Installer window.

6.2 Oracle Installer

As mentioned above the installer does not currently come configured to automatically run an installation of Oracle as there are various licensing issue to be considered for Oracle and most people who wish to evaluate using Oracle already have a license for a particular version and have the database installed.

For that reason if you want to use Seurat atop of your existing Oracle installation then just skip the PostgreSQL database installation steps by pressing the “Cancel” button on the first screen and confirming your desire to cancel the PostgreSQL install process.

6.3 Post Installation Steps

In order to avoid overwriting any existing configuration changes you may already have made to the server configuration files the installer creates example files.

The example files in question that should be copied from are given below:

pri_mappings.properties.example
roles.properties.example
corporateid.properties.example will be added soon

If this is your first time installing then create a copy of each file mentioned above and drop the “.example” portion of the name in the copies so the new file names become:

pri_mappings.properties
roles.properties and;
corporateid.properties (again this will be added in versions post 4.2)

If however you have an existing set of these properties files from an earlier installation then you need to:

Copy everything from the pri_mappings.properties.example file starting with the comment “# From here down added since Seurat version x.y” into the end of your existing pri_mappings.properties file.

NOTE: Earlier versions of Seurat called the file syn_mappings.properties. If your file has that name then rename the file to pri_mappings.properties
If you are updating from an earlier version of Seurat than the second to last then copy everything from the comment appropriate for your version onwards from the example file into your configuration file.

Read the roles.properties.example file to see what the appropriate role settings should be for your existing Seurat users and make the appropriate changes in your roles.properties file.

You now need to proceed to the Create or Update Database section of this manual to decide what data if any you will load into the PostgreSQL database just installed as part of the Seurat Server for Windows XP installation and how you will go about loading that data.

7 Windows XP Seurat Client Installation

The windows installers are careful not to disturb existing files from earlier installations therefore you can follow the instructions in this section regardless of whether this is your first time installing the Seurat Client on Windows XP Pro or whether this installation is going to replace an earlier already installed version.

The steps to follow for installation of the Seurat Client for Windows XP Pro are:

1. If you already have an earlier version of the Seurat Client installed then please Select the “Start->All Programs->Seurat Client->Uninstall SEURAT Client” menu option to uninstall the prior version. Click yes when asked if you are sure you want to uninstall.

2. Double-click on the client installer and you will be presented with a screen like the one shown below

4. Clicking Install will then initiate installation of the Seurat Client to the chosen location. After the client installation is done, if you do not already have PyMOL installed the Seurat Client installer will start a PyMOL installation wizard. If you already have PyMOL installed then the installer will skip this part of the installation process.

PyMOL is used by Seurat to visualize PDB files and PSE PyMOL scripts. You should accept all the default options for installation.

5. At the conclusion of the PyMOL installation you will see a screen that give instructions on how to start the SEURAT Client by directing you to the new Start->Programs menu items for the Seurat Client as shown below.

Remember that before you can successfully start the client and log into Seurat you must have already installed the Server component and configured it to access your medicinal chemistry database.

7.1 Troubleshooting

Under a Web Start deployment the Seurat Client log file will be written to C:\Documents and Settings\<your windows username>\Desktop\logs on a windows XP. This is the first place you should look if you suspect something is wrong. If you find exceptions in this file then please send them, along with a description of the task you were performing within the Seurat client at that time the exception occurred to support@synapticscience.com

8 Seurat Web Start Client Installation

NOTE: As the Seurat Web Start Client version serves up the Seurat Client jar files using the pure Java jetty Web Server the Seurat Web Start Client can be installed equally well on a UNIX or Windows machine. We assume a UNIX machine in the instructions here just because that is the more typical scenario.

It is possible to deploy the Seurat Client to your users via the Java Web Start mechanism. This mechanism allows the client to be retrieved from your corporate intranet and allows Seurat Client updates and bug fixes to be picked up by all users without the need for a manual re-installation.

This means that the Seurat Client can be installed once to a central machine and then distributed, on-demand, to each user who requires it via a link on an intranet web page.

The Seurat Web Start client installation is downloaded from the Synaptic Science website as a zip file that contains the Seurat Client bundled inside of the Jetty pure java web server application.

8.1 Requirements

Java Web Start comes bundled with the Java JDK or JRE in versions 1.4 or greater of java. Therefore in order to be able to deploy the Seurat Client though Java Web Start you need to install an appropriate version of Java.

Currently we support Java 1.4 or 1.5.

Once you have downloaded the JRE run the JRE installer and accept all of its defaults.

8.2 Deploying Seurat Client within Jetty

Once you have the Java JRE installed then all you need to do to make a Java Web Start version of the Seurat Client available to your users is (Using version 4.1 as an example):

Unjar the SeuratClientWebstart_V4.1.jar file downloaded from the Synaptic Science website. Note that a seurat-jetty directory will be created in whichever destination directory you choose to unjar the jar file

Change directory to the seurat-jetty/seurat sub-directory of the directory in which you chose to extract the jar file.

Edit the chemwb.jnlp file and change all references to an IP address like 192.168.1.xxx (where xxx is something like 101) to either the hostname or IP address on the machine to which you unjared the jar file.

Change directory to the seurat-jetty sub-directory of the directory in which you chose to extract the jar file and issue the command “java -jar start.jar”. This will start the Jetty web server on port 9080 on the local machine.

If you wish to run jetty on a port other than 9080 then edit the jetty.xml file in the etc sub-directory of the seurat-jetty directory.

To test that the Web Start version of the Seurat Client is available through the Jetty Webserver open a internet browser and point it to http://localhost:9080/seurat/chemwb.jnlp This will kick off Web Start and will install the Seurat Client in Web Start configuration to the local machine.

If everything is configured correctly you should receive the following sequence of screens:

This screen will cycle through a download of the components that make up the Seurat Client. The first time you run the Web Start client it may take a few minutes to download. Every time after that when you run the Seurat client through Java Web Start there will be no download time (unless a new release has been made in which case the download time will be minimal in comparison).

Next you will be presented with a security warning indicating that the code you are downloading has not been signed by a verifiable source. As the Web Start configuration is intended for internal use through an intranet Synaptic Science does not sign the jars that make up the Seurat client with a registered certificate. It is safe to choose “Start” from the options shown in the screenshot below.

The final question you will be asked is whether you want to install a desktop icon to run the Web Start version of the Seurat client in the future (see screenshot below).

This is entirely up to you. If you do not elect to install a desktop icon then you will have to continue to launch the Web Start version of the Seurat client from the same link on your intranet as was used to initiate the first download.

If you click “Yes” an icon will be placed on your desktop and in your start menu that can be used to launch Seurat from now on. If you choose “No” you will not get an icon and Web Start will not ask you this question again.

If you are unsure then it is probably best to choose the “Ask Later” option until you have a chance to consult with your colleagues.

NOTE: The screenshots above represent those that would be seen for a Java 1.4 installation. The screens you see the first time you run Seurat under a 1.5 JVM may be slightly different but the intent of the screens will be almost the same.

9 Upgrade: Seurat Web Start Client

A Seurat Web Start client upgrade is performed using a jar file that extracts the upgraded Seurat Client files into your existing Web Start client directory on your Unix (or Windows) web server machine. To upgrade your Web Start Seurat Client to a new version you need to (using an upgrade from 4.1.1 to 4.1 as an example):

Click the Download link next to the title “SEURAT Web Start Client Upgrade to Version 4.1.1 from Version 4.1 (any platform)” on the download link of our website www.synapticscience.com

When prompted select “Save File” and choose the location to which you want the SeuratClientWebstartUpgrade_V4.2.jar to be placed into

If possible stop the existing web server that is serving up the Seurat Client through the Web Start mechanism.

Make a backup of the seurat sub directory of the seurat-jetty directory (or the top level of the Web Server directory from which you are serving up the Seurat Client if you are not using the Jetty Web Server as configured and delivered by Synaptic Science). A suggested way of doing this would be:

jar cvf seurat_webstart_client.jar seurat

Copy the SeuratClientWebstartUpgrade_V4.2.jar file to the directory just above the seurat directory of your Web Server

Then issue the command:

jar xvf SeuratClientWebstartUpgrade_V4.2.jar

Re-start your web server if you were in fact able to stop it for this upgrade.

The next time any of your clients access the Web Start version of the Seurat Client through a web browser this new version of the client will be downloaded and installed onto their machine.

10 Upgrade: UNIX SEURAT Server

10.1 From Version 4.1.x to Version 4.2 or Later

You should only be following the steps in this section if you are upgrading from an earlier version of the Seurat Server installed on a Unix platform to Version 4.2 or later.

A Unix Seurat Server upgrade is performed using a jar file that extracts the upgraded Seurat Server files into your existing SeuratServer directory on your Unix box. Click the Download link next to the title “SEURAT Server Upgrade to Version 4.2 from Version 4.1.2 for UNIX” to download the appropriate jar file for a server upgrade.

NOTE: We are using 4.1.2 and 4.2 as examples of a progression of versions, replace with the version applicable to your situation throughout if you are upgrading to a version later than Version 4.2.

Make sure you stop the server and jar up the whole SeuratServer directory into something like SeuratServer_V4.1.2 before you start the upgrade to make sure you have a way to rollback if a problem is found.

You need to create this jar as a backup mechanism as the upgrade jar file will overwrite some files and may introduce some new server directories needed for the new version.

The steps to follow in order to upgrade using the downloaded jar file are:

Change directory to the SeuratServer directory of your installation, place the downloaded jar file either in this same directory (or somewhere on the Unix machine and then specify the path to the file) and then issue the command following command from within that directory:

jar xvf SeuratServer_V4.2_UnixUpgrade.jar

NOTE : the jar utility is just a java version of tar.

If your existing mapping file connects Seurat to your own or a third parties database then:

Rename your syn_mappings.properties configuration file to pri_mappings.properties.
Copy everything in the pri_mappings.properties.example file that came as part of the upgrade jar from the comment “From here down added since Seurat version 4.2” and paste these values into the end of your newly renamed pri_mappings.properties file

i. If you are upgrading from a version earlier than 4.1.2 then copy everything from the version number one greater than your current version instead of from version 4.2

Set the new property is_writeback_db to true
Modify the new properties pri.driver, pri.host, pri.port, pri.url and pri.sid properties to the appropriate settings for connecting to your database

IF on the other hand you are interfacing with the Synaptic Science native database schema then you need to be aware that significant changed were made to the Synaptic Science database schema between version 4.1.2 and version 4.2 of Seurat. In order to bring your server and database schema up to date you will need to:

Make a copy of the pri_mappings.properties.example file and rename it to pri_mappings.properties.
Then take any changes you have made in your syn_mappings.properties file and move them into your pri_mappings.properties file.
Ensure the new property is_auth_db is set to true
Ensure the new property is_writeback_db is set to true
Modify the new properties pri.driver, pri.host, pri.port, pri.url and pri.sid properties to the appropriate settings for connecting to your database
Take a backup of your entire database.
Log into sqlplus or psql (Oracle or PostgreSQL) or otherwise connect to your database as the database user who owns the tables in the Synaptic Science Schema
Run the script updateSchema_Oracle_XE.sql in the SeuratServer/oracle or updateSchema.sql in the SeuratServer/postgresql directory depending on the type of database to which you interface. Once complete your database schema will have been updated to be compatible with version 4.2

The way that users roles are handled for authorization has been changed in Version 4.2 such that you must now provide an entry in the roles.properties file for every Seurat user otherwise by default a user will not be able to:

Initiate a load of file data into a database
See crystal structure data
View PK reports
See other users folders and jobs
NOTE: The provided roles.properties.example file explains what the new roles are. Use the example entries in that file as a guide as to how to change your own roles.properties file

As part of the version 4.2 upgrade any JChem Base structure tables need to be updated to match the version of JChem Base bundled within Seurat. To perform this update:

Change directory into the SeuratServer/bin directory
Issue the following command

java –cp seurat-server.jar chemaxon.jchem.JChemManager.

This will start the JChem Manager GUI and present the database connection dialog as shown below.

Enter the appropriate connection parameters for your database.

i. The correct values for Oracle XE are shown above (your login name might be different).

ii. For Oracle 9 you need to format the URL of database entry as shown below as well as providing the login name and password again in the Login name and password fields.

jdbc:oracle:thin:user/password@host:port:sid

iii. For PostgreSQL enter

JDBC Driver: org.postgresql.Driver

URL of Database: jdbc:postgresql://host:port/sid

Property table: JChemProperties

Password: password of owner of structure tables

iv. Click OK and then JChem Manager will detect a version difference in your tables and ask if you want to update them to match the latest version of JChem Base. Choose OK and then after a short pause you will receive a message saying the update has completed.

v. Exit the JChem Manager GUI

If you experience any difficulties upgrading to the latest version of Seurat please send a report to support@synapticscience.com or post a question on our forum which can be accessed from our website www.synapticscience.com.

10.2 From Version 4.x to Version 4.1.2 or Earlier

A Unix Seurat Server upgrade is performed using a jar file that extracts the upgraded Seurat Server files into your existing SeuratServer directory on your unix box. Click the Download link next to the title “SEURAT Server Upgrade to Version 4.1.1 from Version 4.1 for UNIX” to download the appropriate jar file for a server upgrade. We are using 4.1.1 and 4.1 as examples of a progression of versions , replace with the version applicable to your situation throughout.

Make sure you stop the server and jar up the whole SeuratServer directory into something like SeuratServer_V4.1 before you start the upgrade to make sure you have a way to rollback if a problem is found.

The upgrade jar file will overwrite some files and may introduce some new server directories needed for the new version.

It may also place an updated version of the syn_mappings.properties file called syn_mappings.properties.X.X.X in the top level directory of the Seurat Server. The files is named with a version specific extension so that it does not overwrite your existing syn_mappings.properties file which contains important information Seurat is using to understand how to communicate with your particular database schema.

To extract the new server components into the existing Seurat Server directories you need to change directory to the SeuratServer directory, place the downloaded jar file either in this same directory (or somewhere on the unix machine and then specify the path to the file) and then issue the command:

jar xvf SeuratServer_V4.1.1_UnixUpgrade.jar

NOTE : the jar utility is just a java version of tar.

Once all the files have been extracted you will need to take all the entries in the syn_mappings.properties.V4.1.1 file from the comment in the file “From here down added since Seurat version 4.1.1” down and paste it into the end of your existing syn_mappings.properties file so that your mapping file has the new properties supported in Version 4.1.1 that were not present in Version 4.1

11 UNIX Seurat Server

11.1 Download, Extract and Configure Files

The instructions in this section assume that you DO NOT have an existing installation of an earlier version of the Seurat Server. If you do have an earlier version installed and want to keep any configuration changes you might have made then please follow the instructions in the Upgrade: UNIX SEURAT Server section of this guide.

A Unix Seurat Server installation is performed using a jar file that extracts all the files necessary for the Seurat Server into a directory named SeuratServer (relative to the location from which you extract the files) on your unix box.

NOTE: We are using 4.2 as an example version, replace with the version applicable to your situation throughout.

To install the Seurat Server onto a Unix platform perform the following steps:

Go to the download link of the Synaptic Science website and click the Download link next to the title “Linux self extracting Java 1.4.2_12 JVM” or “Linux RPM self extracting Java 1.4.2_12 JVM”.

If you are installing on a platform other than Linux then please go to the sun website http://java.sun.com/products/archive/ to obtain a 1.4.2_12 JVM appropriate for your platform.

Run the downloaded installer and accept all the defaults.

Configure the UNIX user account under which the Seurat Server is to be run to have the newly installed Java 1.4.2_12 in its PATH. If you do not do this then you will need to provide an absolute path to the java executable in all places where java is invoked.

Go to the download link of the Synaptic Science website and click the Download link next to the title “SEURAT Server Version 4.2 for UNIX” to download a jar file applicable for a fresh Seurat Server installation on UNIX.

Change directory into the parent directory where you want the SeuratServer directory created and issue the following command:

jar xvf SeuratServer_V4.2_Unix.jar

or if you don’t have a JDK installed;

unzip SeuratServe_V4.2_Unix.jar

NOTE: The JDK (Java Development Kit) is different to the JRE (Java Runtime Environment) and only the JDK (which is larger) contains the jar command.

Change directory into the newly created SeuratServer directory and then:

Make a copy of the pri_mappings.properties.example file and rename that copy to pri_mappings.properties
Make a copy of the roles.properties.example file and rename that copy to roles.properties

Decide whether you will be using the Synaptic Science native database or your own database and follow the instructions appropriate for that choice in the next section of this guide.

11.2 Create Necessary Database Tables and Users

Before you can start the Seurat Server you will need to decide which type of database configuration you will be using. The options are:

Create a complete Synaptic Science database schema containing the cMet test data set in either Oracle or PostgreSQL.

Create the minimal set of support tables required by Seurat when configured to interface with a third party medicinal chemistry database (like ISIS Base, Activity Base, Accord, RS3, Chem Office or your companies own proprietary databases) again in Oracle or PostgreSQL.

Create a complete but empty Synaptic Science database schema in either Oracle or PostgreSQL

In the second scenario the vast majority of chemical and biological data is retrieved and analyzed directly from the third party database via changes to Seurat’s database mapping configuration file(s).

Step by step instructions are given to achieve the database configuration of your choice in the Create or Update Database section of this guide.

12 UNIX Seurat Client Installation

A Unix Seurat Client installation is performed using a jar file that extracts all the files necessary for the Seurat Client into a directory named SeuratClient (relative to the location from which you extract the files) on your unix box. To install the Seurat Client for UNIX:

We are using 4.1.2 and 4.2 as examples of a progression of versions, replace with the version applicable to your situation throughout.

Click the Download link next to the title “SEURAT Client Version 4.2 for UNIX” to download a jar file applicable for a fresh Seurat Client installation on UNIX.

To extract the client you need to change directory to the directory into which you want the SeuratClient directory to be created and then issue the command:

jar xvf SeuratClient_V4.1.1_Unix.jar

NOTE : the jar utility is just a java version of tar.

Once the files are un-jarred you can then start the client by changing directory to SeuratClient directory and issuing the command ./run.sh. This script assumes that the correct version of Java is you’re the PATH of the unix user executing the command. If it is not simply edit the run.sh script to use an absolute path to the correct Java version.

13 Post Installation Steps

13.1 Create or Update Database

13.1.1 Unix

13.1.1.1 Create cMet Test Data in Oracle

If you intend to load the cMet test data into the Synaptic Science database schema in an Oracle database then follow the steps in this section of the guide.

You will need to have installed Oracle separately as Seurat does not currently come bundled with an installation script for Oracle. Either go to the Oracle website and download and install Oracle Express Edition or install your companies licensed version of Oracle.

Once Oracle has been installed the steps to create the Synaptic Science schema and load the cMet test data set into it are:

Create a user account in oracle named seurat with a password of seurat (the password can be changed at a later point)

Change directory into the data sub directory of the Seurat Server. So if for example you had installed the Seurat Server into /opt/seurat then the directory to cd into would be /opt/seurat/SeuratServer/data.

The CMET_STARTER_ORACLEXE.DMP file in this directory was created with Oracle data pump and as such uses an Oracle directory object to specify the location of the files with which data pump will work. Therefore to be able to use impdb to load the data into Oracle you need to:

Create a database directory object using a command like (NOTE: You must name the directory seurat_dumpdir if you want to use the command as provided in the example script):

SQL> CREATE DIRECTORY seurat_dumpdir AS ‘/opt/seurat/SeuratServer/data’;

You then need to grant the appropriate privileges to the seurat user who will be doing the import using data pump with a command like the one shown below:

SQL> grant read, write on seurat_dumpdir to seurat;

Adapt the installCmetSampleDataToOracle.bat windows batch file to an equivalent Unix script in the scripting language of your choice. Alternatively if data pump is in your path you can cut and past the command from the batch file, remove the path information for invoking impdp and execute the command directly.

Run the adapted script or command to load the cMet test data set

Upon completion the impdp command the seurat schema of your Oracle database will contain all the tables of the Synaptic Science schema loaded with the cMet test data set.

13.1.1.2 Create cMet Test Data in PostgreSQL

If you intend to load the cMet test data into the Synaptic Science database schema in a PostgreSQL database then follow the steps in this section of the guide.

You will need to have installed PostgreSQL separately as Seurat does not currently come bundled with an installation script for PostgreSQL on Unix. Either go to the PostgreSQL website location http://www.postgresql.org/ftp/binary/v8.2.3/linux/ and download and install PostgreSQL for your version of Linux

NOTE: You will need to supply the postgres super user database account password during the creation of the Synaptic Science database schema and loading of test data so please make sure you note it down.

Once PostgreSQL has been installed the steps to create the Synaptic Science schema and load the cMet test data set into are:

Unzip the script used to create the schema and test data in PostgreSQL from the file cMet_project_starter.sql.zip which can be found in the data sub directory of the SeuratServer directory. So if you installed the Seurat server into /opt/seurat the path would be /opt/seurat/SeuratServer/data. Use the unzip command as follows:

unzip -j cMet_project_starter.sql.zip

Please then ensure that the resulting cMet_project_starter.sql file is sitting in the /opt/seurat/SeuratServer/data directory

Adapt the installCmetSampleData.bat windows batch file to produce a Unix script in the scripting language of your choice to initiate a load of the cMet_project_starter.sql file into PostgreSQL. If you have psql in your path then you can simply cut and paste the single command out of the installCmetSampleData.bat remove the windows specific path and execute the command directly.

Supply the postgres super user password when prompted. You will then see several screens of output as the database is create and loaded with test data. You can safely ignore any messages you see about duplicate objects.

Once the script completes you are ready to move to the instructions on how to start the Seurat Server, install the Seurat Client and login to Seurat in order to start working with the cMet test data.

13.1.1.3 Map Seurat to Existing Med Chem Database in Oracle

If you intend to use Seurat in conjunction with an existing medicinal chemistry database (for example ActivityBase from IDBS, ISIS/Base from MDL, ChemOffice from Cambridgesoft or Accord/RS3 from Accelrys databases) then follow the instructions in this section.

Even if you plan to use your existing medicinal chemistry database from another vendor there are still a few bookkeeping tables that Seurat requires to function. In order to create those bookkeeping tables Seurat provides a script.

The steps to follow to create the tables from the script are:

Create a user named “seurat” in your Oracle database with a password of seurat (NOTE: The password can be changed at a later date through changes to the seurat.ini configuration file but for now use seurat as the password)

Log into sqlplus as the newly created seurat user and at the sqlplus prompt enter @ synsci_orace_xe_schema_minimal.ddl

Check the output to ensure that no errors occur. You can safely ignore any messages about duplicate object definitions.

Once the script has completed the seurat schema of your Oracle database will contain the minimal set of table definitions for Seurat to function alongside your existing database.

Grant all privileges to each intended user of Seurat using the standard Oracle mechanisms for user schema creation, creation of public synonyms and granting of access to tables and sequences through those synonyms.

Next you will need to configure Seurat through the pri_mappings.properties configuration file located in the top level directory of the SeuratServer (C:\Program Files\SynapticScience\SeuratServer on Windows by default) by modifying at least the following properties in that file:

syn_properties – This property describes to Seurat how each logical concept like Compound Structure, Lot, Protocol, Assay Result etc maps to a table name / column name combination
syn_tables – This property describes to Seurat how to navigate between tables
syn_fake_table_names – Gives “fake” names to tables that can be navigated to through orthogonal paths from other tables
syn_primary – Describes the main paths from which a query in Seurat should start.
syn_long_subs – What column can substitute for long (and blob) column when being used in a “select distinct”
Several other properties that are used to populate controlled vocabularies.
A complete description of each of the properties in the pri_mappings.properties file and how to modify them is given in the Seurat Database Mapping Guide on our website at www.synapticscience.com

We also need to configure the Seurat Server to have the correct property settings to be able to connect to your existing medicinal chemistry database. To do this edit the pri_mappings.properties file in the SeuratServer directory of your installation and change the properties below as shown:

pri.driver=oracle.jdbc.driver.OracleDriver
pri.host=(DNS name of machine hosting the database)
pri.port=(the port for your instance of Oracle)
pri.url=jdbc:oracle:thin
pri.sid= (the database SID for your database)

For details on the contents of the pri_mappings.properties file and how to modify it to suit your database please refer to the Seurat Database Mapping Configuration Guide on our website under the Documentation link.

NOTE: If your existing database is RS3 then you can download an appropriate pri_mappings.properties file from the Synaptic Science website on the download link next to the title “RS3” with sub title “Database Mapping Configuration File”.

13.1.1.4 Create Empty Synaptic Science Seurat Database in Oracle

If you intend to use the Synaptic Science native database schema in an Oracle database as your primary database schema for storage of compounds and their chemical and biological data then follow the instructions in this section.

Once Oracle has been installed the steps to create the Synaptic Science schema are:

Create a user account in oracle named seurat with a password of seurat (the password can be changed at a later point)

Change directory into the oracle sub directory of your Seurat Server installation. So if for example you installed the server in /opt/seurat then you would need to go to the /opt/seurat/SeuratServer/oracle directory.

Log into sqlplus as the seurat user created in earlier and then run the synsci_oracle_xe_schema.ddl script in the current directory by issuing the commands:

SQL> spool synsci_oracle_xe_schema .log
SQL> @synsci_oracle_xe_schema.ddl
SQL> spool off
SQL> exit

Now we need to configure the Seurat Server to have the correct property settings to be able to connect to the database you just created. To do this edit the pri_mappings.properties file in the SeuratServer directory of your installation and change the properties below as shown:

pri.driver=oracle.jdbc.driver.OracleDriver
pri.host=localhost (or your hosts DNS name)
pri.port=1521 (or the port for your instance of Oracle)
pri.url=jdbc:oracle:thin
pri.sid=xe (or the database SID for your database)

You can either decide to use the seurat user account that owns the Synaptic Science database schema tables for testing purposes or create additional users before proceeding to run the server, install the client and log into Seurat.

The synsci_oracle_xe_schema.ddl creates public synonyms for all the database objects (tables and sequences) that Seurat needs to function. Therefore to create additional users create a role that has select, insert, update and delete privileges to all the synonyms created in the synsci_oracle_xe_schema.ddl script.

Usernames in Seurat are converted to lower case in order to avoid the confusion associated with two names with the same spelling and different case. To that end you should create your usernames in lower case.

After completing these steps your Oracle database will contain all the table definitions required for the Seurat Server to run and your users will have the appropriate privileges to connect to the Seurat Server from the client.

The database at this stage however does not contain any data and so you will need to load some of your own from an SD or CSV file through the File->“Load into database” menu option of the List Manager window of the Seurat client.

Please refer to the Seurat Users Guide for details on how to load data into the Synaptic Science database from the Seurat Client.

13.1.1.5 Create Empty Synaptic Science Seurat Database in PostgreSQL

If you intend to use the Synaptic Science native database schema in a PostgreSQL database as your primary database schema for storage of compounds and their chemical and biological data then follow the instructions in this section.

You will need to have installed PostgreSQL separately as Seurat does not currently come bundled with an installation script for PostgreSQL on Unix. You can either go to the PostgreSQL website location http://www.postgresql.org/ftp/binary/v8.2.3/linux/ and download and install PostgreSQL for your version of Linux

Once PostgreSQL has been installed the steps to create the Synaptic Science schema and load the cMet test data set into are:

Change directory into the postgresql sub directory of your Seurat Server installation. So if for example you installed the server in /opt/seurat then you would need to go to the /opt/seurat/SeuratServer/postgresql directory.
Issue the following command to create the Synaptic Science native database schema in PosrgreSQL using the synsci_postgreSQL_schema.ddl file:

psql -h localhost -p 3247 -U postgres -f synsci_postgreSQL_schema.ddl

You will be prompted for the postgres super user database accounts password. Enter it when prompted and monitor the script for errors. Errors relating to duplicate objects not being able to be created or object already exist messages can be ignored. You may want to redirect the output of the execution of the script above to a file for convenience of review.

Now we need to configure the Seurat Server to have the correct property settings to be able to connect to the database you just created. To do this edit the pri_mappings.properties file in the SeuratServer directory of your installation and change the properties below as shown:

pri.driver=org.postgresql.Driver
pri.host=localhost
pri.port=3247
pri.url=jdbc:postgresql
pri.sid=synaptic

The script to create the Synaptic Science native schema creates a default user account called demo with a password of demo. It also creates a user named seurat with a password of seurat. You can use one of these accounts to login and do minimal testing of Seurat through the Seurat Client.

Usernames in Seurat are converted to lower case in order to avoid the confusion associated with two names with the same spelling and different case. To that end you should create your usernames in lower case.

Ultimately you must give each user of seurat a unique account in the PostgreSQL database as that is the mechanism that authenticates the user and it ensures that their seurat jobs (saved work) do not get overwritten by another user logging into Seurat with the same user name.

After completing these steps your PostgreSQL database will contain all the table definitions required for the Seurat Server to run and your users will have the appropriate privileges to connect to the Seurat Server from the client.

Please refer to the Seurat Users Guide for details on how to load data into the Synaptic Science database from the Seurat Client.

13.1.2 Windows

13.1.2.1 Create cMet Test Data in Oracle

If you intend to load the cMet test data into the Synaptic Science database schema in an Oracle database then follow the steps in this section of the guide.

Once Oracle has been installed the steps to create the Synaptic Science schema and load the cMet test data set into it are:

Create a user account in oracle named seurat with a password of seurat (the password can be changed at a later point)

Change directory into the data sub directory of the Seurat Server. So if for example you had installed the Seurat Server into /opt/seurat then the directory to cd into would be /opt/seurat/SeuratServer/data.

The CMET_STARTER_ORACLEXE.DMP file in this directory was created with Oracle data pump and as such uses an Oracle directory object to specify the location of the files with which data pump will work. Therefore to be able to use impdb to load the data into Oracle you need to:

Create a database directory object using a command like (NOTE: You must name the directory seurat_dumpdir if you want to use the command as provided in the example script):

SQL> CREATE DIRECTORY seurat_dumpdir AS ‘/opt/seurat/SeuratServer/data’;

You then need to grant the appropriate privileges to the seurat user who will be doing the import using data pump with a command like the one shown below:

SQL> grant read, write on seurat_dumpdir to seurat;

Run the installCmetSampleDataToOracle.bat windows batch file by double clicking on it or changing directory to the directory that holds the script in a command file and issuing the command .\installCMetSampleDataToOracle.bat

Upon completion the impdp command the seurat schema of your Oracle database will contain all the tables of the Synaptic Science schema loaded with the cMet test data set.

13.1.2.2 Create cMet Test Data in PostgreSQL

If you intend to load the cMet test data into the Synaptic Science database schema in a PostgreSQL database then follow the steps in this section of the guide.

After installation on a Windows platform the PostgreSQL database will have been automatically installed.

Once PostgreSQL has been installed the steps to create the Synaptic Science schema and load the cMet test data set into are:

Unzip the script used to create the schema and test data in PostgreSQL from the file cMet_project_starter.sql.zip which can be found in the data sub directory of the SeuratServer directory (which is C:\Program Files\SynapticScience\SeuratServer by default).

Do this by opening the zip file in WinZip or using the windows XP built-in unzip utility

WARNING: If you use the built-in Windows XP zip extraction utility rather than another program like WinZip the extraction process will create a folder named cMet_project_starter.sql under C:\Program Files\SynapticScience\SeuratServer\data which will contain the actual file cMet_project_starter.sql.

If this happens you need to rename the folder, copy the cMet_project_starter.sql file inside the folder into the C:\Program Files\SynapticScience\SeuratServer\data directory and then remove the renamed folder.

Run the installCmetSampleData.bat windows batch file by double clicking on the file.

Supply the postgres super user password when prompted. You will then see several screens of output as the database is create and loaded with test data. You can safely ignore any messages you see about duplicate objects.

Once the script completes you are ready to move to the instructions in the Starting Seurat section of the document describing how to start the Seurat Server, the Seurat Client and login to Seurat in order to start working with the cMet test data.

13.1.2.3 Map Seurat to Existing Med Chem Database in Oracle

The steps for mapping Seurat to an Existing Med Chem Database in Oracle are exactly the same (except for the steps to install Oracle which are outside of the scope of this manual anyway) as those found in the Map Seurat to Existing Med Chem Database in Oracle section for Unix. Please refer to those instructions.

13.1.2.4 Create Empty Synaptic Science Seurat Database in Oracle

Once Oracle has been installed the steps to create the Synaptic Science schema are:

Create a user account in oracle named seurat with a password of seurat (the password can be changed at a later point)

Change directory into the oracle sub directory of your Seurat Server installation. So if for example you installed the server in /opt/seurat then you would need to go to the /opt/seurat/SeuratServer/oracle directory.

Log into sqlplus as the seurat user created in earlier and then run the synsci_oracle_xe_schema.ddl script in the current directory by issuing the commands:

SQL> spool synsci_oracle_xe_schema .log
SQL> @synsci_oracle_xe_schema.ddl
SQL> spool off
SQL> exit

Now we need to configure the Seurat Server to have the correct property settings to be able to connect to the database you just created. To do this edit the pri_mappings.properties file in the SeuratServer directory of your installation and change the properties below as shown:

pri.driver=oracle.jdbc.driver.OracleDriver
pri.host=localhost (or your hosts DNS name)
pri.port=1521 (or the port for your instance of Oracle)
pri.url=jdbc:oracle:thin
pri.sid=xe (or the database SID for your database)

You can either decide to use the seurat user account that owns the Synaptic Science database schema tables for testing purposes or create additional users before proceeding to run the server, install the client and log into Seurat.

The synsci_oracle_xe_schema.ddl creates public synonyms for all the database objects (tables and sequences) that Seurat needs to function. Therefore to create additional users create a role that has select, insert, update and delete privileges to all the synonyms created in the synsci_oracle_xe_schema.ddl script.

Usernames in Seurat are converted to lower case in order to avoid the confusion associated with two names with the same spelling and different case. To that end you should create your usernames in lower case.

Please refer to the Seurat Users Guide for details on how to load data into the Synaptic Science database from the Seurat Client.

13.1.2.5 Create Empty Synaptic Science Seurat Database in PostgreSQL

The installer for Windows XP creates a menu item that can be used to launch the script required to create an empty Synaptic Science native database in PostgreSQL.

Therefore to create an empty Synaptic Science database schema in PostgreSQL you should:

Select the “Start->All Programs->Seurat Server->Create Database Schema menu item

Enter the postgres super user database accounts password when prompted

Note that you can ignore any error message about not being able to create duplicate objects or a language already existing.

13.2 Add SEURAT Users

The SEURAT administrator will need to supply each user that will be logging into SEURAT with a database login (as SEURAT uses the underlying databases authentication mechanism to authenticate SEURAT users).

Detailed instructions on how to add SEURAT users to the system can be found in the Seurat Administrators Guide which is available from the “Start->All Programs->Seurat Server->Administrators Guide” menu item.

Note that for initial tests to ascertain installation success you can log into Seurat using the username of seurat and a password of seurat. In the case of the use of a PostgreSQL database there is also a username of demo with a password of demo available.

13.3 Provide Clients with License File (Version 4.3 or earlier)

With all versions of SEURAT prior to 4.3 license management was performed in the SEURAT client. As such each client will need to configure the SEURAT Client with a license file that validates their right to use the SEURAT platform. The SEURAT Administrator should have received the license file from Synaptic Science when they purchased licenses or downloaded an evaluation version of SEURAT. If you did not receive a license file then please visit www.synapticscience.com and go to the “Contact Us” link or send an email to sales@synapticscience.com

Detailed information plus screenshots on how to point the SEURAT Client to an appropriate license file can be found in the Seurat Administrators Guide which is available from the “Start->All Programs->Seurat Server->Administrators Guide” menu item.

14 Starting Seurat

Once you have completed the steps in the sections described above to:

Install the Server and Client
Copy and modify the appropriate configuration files for your preferred method of use.
Create or update a database and load it with the data of your choice
Grant permissions on the database objects if necessary.

You can then start the Seurat Server and Client as follows

14.1 Seurat Server

Please note that starting with version 4.4 of Seurat license management was moved to the SEURAT Server. As such this means that a valid SEURAT license file must be supplied to the Seurat Server in order for the Server to run.

By default the license file is expected to reside in the SeuratServer/bin directory and to be called seurat.lic. Therefore if you have received your license file (evaluation or production) from Synaptic Science go ahead and save it into the SeuratServer/bin directory and name it seurat.lic. If you do not yet have a license file then please contact Synaptic Science sales on sales@synapticscience.com or call our offices on 301 915 0274.

14.1.1 Windows XP

You can start the Seurat Server by selecting the Start->All Programs->Seurat Server->Interactive Seurat Server menu item. This will produce a window that looks similar to the one shown below:

This indicates that the Seurat Server is now ready to accept connections from clients. To stop the server close the window or enter Ctrl-C in the window.

If you want to install and run Seruat as a Windows service then please refer to the Seurat Administrators Guide on our website for details of the steps you need to follow to install and run the Seurat Server as a service.

14.1.2 Unix

Change directory to the SeuratServer/bin directory and issue the command ./runServer.sh. Note that this script assumes that the correct version of Java is in the path of the UNIX user’s account executing the command. If it is not simply edit the runServer.sh script to use an absolute path to the correct Java version.

14.2 Seurat Client

14.2.1 Windows XP

You can start the client by selecting the Start->All Programs->Seurat Client->Seurat Client menu option. After the presentation of a splash screen a few moments you will be presented with the Seurat Login Screen as shown below.

For versions of SEURAT prior to and including 4.3 each client will need to configure the SEURAT Client with a license file that validates their right to use the SEURAT platform. Versions 4.4 or later can skip this step.

The SEURAT Administrator should have received the license file from Synaptic Science when they purchased licenses or downloaded an evaluation version of SEURAT. If you did not receive a license file then please visit www.synapticscience.com and go to the “Contact Us” link or send an email to sales@synapticscience.com

If you do have a license file then click on the Prefs… button and navigate to the License tab as shown below:

Use the Browse… button to locate the Seurat license file on your file system and then select the file and press OK. This will return you to the login screen.

To get started you can enter a username of demo and a password of demo if your database is PostgreSQL as this user is created by default. If your database is Oracle then please use a username of seurat and a password of seurat.

We strongly encourage you to switch away from the use of these default usernames by creating your own Seurat users.

14.2.2 Unix

Change directory to the SeuratClient directory and issue the command ./run.sh. Note that this script assumes that the correct version of Java is in the path of the UNIX user’s account executing the command. If it is not simply edit the run.sh script to use an absolute path to the correct Java version.

After the presentation of a splash screen a few moments you will be presented with the Seurat Login Screen as can be seen below:

Each client will need to configure the SEURAT Client with a license file that validates their right to use the SEURAT platform. The SEURAT Administrator should have received the license file from Synaptic Science when they purchased licenses or downloaded an evaluation version of SEURAT. If you did not receive a license file then please visit www.synapticscience.com and go to the “Contact Us” link or send an email to sales@synapticscience.com

If you do have a license file then click on the Prefs… button and navigate to the License tab as shown below:

We strongly encourage you to switch away from the use of these default usernames by creating your own Seurat users.

15 Troubleshooting

This trouble shooting section only documents problems that may be encountered during the installation process.

For troubleshooting tips on administering the SEURAT platform see the Troubleshooting section of the Seurat Administrators Guide which is available from the “Start->All Programs->Seurat Server->Administrators Guide” menu item.

For troubleshooting tips on using SEURAT in general see the Troubleshooting section of the Seurat Users Guide which is available from the “Start->All Programs->Seurat Client->Users Guide menu item.

15.1 Seurat Server Installation

15.1.1 PostgreSQL Installation Automatically Uninstalls Itself

15.1.1.1 Description

At the very end of the PostgreSQL installation wizard the PostgreSQL installer issues an error and automatically uninstalls itself.

15.1.1.2 Cause

You are attempting to install the Seurat Server from a non windows administrator account or an account that cannot grant the “Log on as a service” and “Log on locally” rights to the windows service account the PostgreSQL installer tried to create during installation (or the account you created before installation and specified to the installer did not have these rights).

15.1.1.3 Solution

Please log into the machine as a windows administrator and re-run the installer.