Mascot Insight Installation and setup guide

System requirements

These are the system requirements for a Mascot Insight server. On the client side, Mascot Insight

can be accessed from most web browsers. See Web browsers for additional information and known

issues.

The operating system must be 64-bit Windows, XP service pack 2 or later. Access to an in-house

Mascot Server, version 2.4.2 or later, is required. Response time will depend on processor speed, the

total number of cores, adequate RAM, and disk speed. It is more useful to suggest suitable and ideal

hardware specifications than any kind of minimum.

Suitable:

Intel Core processor

8 GB RAM

500 GB SATA or SAS disk

1000 Base-T network adapter

64-bit Windows, XP SP2 or Server 2003 SP2, or later

Ideal:

Intel Core i7 or multiple Xeon processors

24 GB RAM

2 TB SATA or SAS RAID

1000 Base-T network adapter

64-bit Windows, XP SP2 or Server 2003 SP 2 or later

Mascot Insight runs on the Apache Tomcat 7 application server. You can choose whether to

configure it to use HTTP or HTTPS, and this port is the only one that needs to be open through any

firewall.

If the Mascot Server is Windows, and the hardware has significantly more capacity than is required

for searches, particularly if it is the non-searching head node of a cluster, there are some advantages

to using the same computer for both Mascot Server and Mascot Insight - for example, there is no

need to copy search result and quantitation XML files between the two machines

Web browsers

Client access to Mascot Insight can be from any computer with access to the server using a web

browser. Any recent web browser on any operating system should be suitable as long as Java and

Javascript are enabled. For graphical reports, you need a web browser with native SVG support. This

rules out Microsoft Internet Explorer version 8 and earlier. The majority of development and testing

has used

Microsoft Internet Explorer versions 9, 10

Opera versions 10 and up

Firefox versions 18 and up

Chrome versions 27.0.1453.94 and up

Java 7 is recommended, Java 6 is supported. The browser may require its Java plugin to be updated

or enabled. If you are using a recent Oracle Java7 release (1.7.0_13 and up), then the default security

settings have been raised so that you have to give permission to an applet to run. The pop-up dialog

for this often appears behind another window (especially if you've move away from the browser),

and it always appears in the primary display (so if you're using two monitors and you open the

browser on the secondary monitor the permissions window will open on the 'wrong' screen).

The majority of web browsers on Windows are 32-bit, even when Windows is 64-bit. With a 32-bit

browser, you may need to increase the memory available to Java. In the Java control panel, choose

the Java tab and View. Select the correct version of Java (you may have several installed, but only

the most recent should be being used by the browser) and enter a new memory 'Runtime

Parameter'. The parameter to set the maximum memory Java can use is -Xmx and you enter it in the

format -Xmx<Amount>M e.g. -Xmx1024M for 1GB (which seems to be the maximum you can give

Java7 on Windows 32-bit, although Java6 allowed you to grant up to 1.5Gb). For 64-bit operating

systems, the default memory settings for Java are based on a percentage of the available system

memory, so if you have a reasonable amount of memory on your system, you're unlikely to need to

change the settings.

Before starting

Mascot security must be enabled on the Mascot Server because this is used to identify which results

belong to which user and determine each user's level of access. If both Mascot Server and Mascot

Insight are essentially single user systems, and there is no requirement for separate log-ins, you can

enable the guest account and make it a member of the MIAdmininistrators and MIPower users

groups, so that there is never a need to enter a user name and password.

Mascot Insight requires that the associated in-house Mascot Server is version 2.4.2 or later. If you

have not already updated to Mascot Server 2.4.2, you must do so before installing Mascot Insight.

Your Mascot server must have a valid license for Mascot Insight, and you should replace any existing

license with the Mascot Insight enabled license before installing Mascot Insight. If you do not have a

valid license for Mascot Insight, the software will go into a 'read only' mode and will not allow you to

import any new data into the system.

You should also update all client installations of Mascot Daemon to the latest version from your

Mascot server. Mascot Daemon 2.4.1 includes additional integration features for use with Mascot

Insight. Once you have updated a Mascot Daemon client installation, start the Mascot Daemon GUI,

and navigate to the Preferences dialog window (Edit->Preferences), select the 'Data import filters'

tab, check the checkbox labelled 'Mascot Insight integration' and then click 'Save'.

This will enable Mascot Daemon to automatically upload Distiller quantitation data to the Mascot

Server, and Mascot Insight will then automatically import the quantitation data from the Mascot

Server.

If Apache Tomcat is already installed and the version is earlier than release 7.0.42, you must either

uninstall it or specify a different path and a different HTTP port number for the Apache Tomcat

installed with Mascot Insight.

Mascot Insight Installation

If you are installing Mascot Insight from the Mascot Insight CD, From ‘My Computer’ or Windows

Explorer, select the Mascot CD and double click on setup64.exe. If you are installing from the

downloaded installer, navigate to the downloaded file and double click on

insight_2_5_x86_win64.exe.

Before the installation of Mascot Insight begins, required Microsoft Visual C++ libraries, Postgresql,

Java 7 Runtime and Apache Tomcat 7 will be installed if they are not already installed on the system:

If required, the Postgresql database will be installed by the Mascot Insight installer. There are no

user options for this, please allow the installer to complete.

If required, Java 7 Runtime and Apache Tomcat 7 will launch their own installers as part of this

progress. You must complete these installers in order for Mascot Insight installation to continue. We

recommend leaving all installer options as the defaults on the Java 7 installer. On the Apache Tomcat

7 setup and installation Wizard, you can change any of the options if you wish.

Java 7 Runtime installation

If Java 7 is already installed on your server, you can skip this section and go to Apache Tomcat 7

installation.

The following window will open. You should install Java to the default location.

Installing Java will only take a few of minutes.

Click close to return to the Mascot Insight installer and initiate Apache Tomcat 7 installation if

required.

Apache Tomcat 7 installation

If Apache Tomcat 7.0.42 or later is already installed on your server, you can skip this section and go

to Mascot Insight installation.

If Apache Tomcat is already installed and the version is earlier than release 7.0.42, you must either

uninstall it or specify a different path and a different HTTP port number for the Apache Tomcat

installed with Mascot Insight.

The Tomcat installation wizard will open with this screen

You will need to agree to the Apache license before you can carry on. Click on the 'I Agree' button to

continue.

We would again recommend using the default values and you should always include the 'Start menu

items' and the 'Choose Components' page.

On the 'Configuration' page, you may change any of the settings if you wish. However, we would

again suggest leaving these as the default values as changing the Port numbers could lead to clashes

with other software.

On the 'Java Virtual Machine' page, the Java 7 installation should already be selected. You should not

have to change the default value, but make sure that the 64-bit version of Java has been selected

and not the 32-bit version if both are installed as the Tomcat installer can incorrectly select the 32-

bit installation. The 64-bit version of Java will be installed to C:\Program Files\Java\jre7 by default,

where as the 32-bit version will be installed to C:\Program Files (x86)\Java\jre7.

You may change the Apache Tomcat installation location if you wish (for example if you have more

space available on a different drive).

Once Apache Tomcat has installed, you can uncheck the 'Run Apache Tomcat' checkbox if you wish,

as the Mascot Insight installer will stop and then restart the Apache Tomcat Windows service as part

of the installation process. Click 'Finish' to close the Apache Tomcat installation wizard and return to

the Mascot Insight installer.

Mascot Insight installation

Once all the prerequisites are installed the following window will be displayed:

If the installation cannot proceed, a message box will be displayed. Typical problems include:

You do not have Administrator privileges: Log out and log in as a user with local

Administrator rights

Unsupported Windows platform: Refer to the system requirements at the beginning of this

page

Any problem(s) must be fixed before the installer will proceed. Pressing Next displays the Mascot

Insight End-User Licence Agreement:

If you do not consent, you cannot proceed with the installation.

If you have more than one instance of Apache Tomcat installed on the server, you can change the

instance you want Mascot Insight to use. The Mascot Insight web application will be installed under

the selected Tomcat instance. However, the majority of the Mascot Insight configuration and

database files will be created in the selected 'Data directory'. You may change the location of the

data directory if you wish - for example, if you have more free space available on a different drive.

The next step is you last chance to cancel the installation!

Copying the program files takes only a few minutes

Once installation has completed, there are some initial setup steps that must be completed before

Mascot Insight is ready to use. Do not uncheck the 'Open configuration wizard' checkbox. Click

'Finish' - The configuration wizard will open.

Configuration wizard

The configuration wizard will open in your default browser. If you unchecked the checkbox, this can

be found at http://SERVER_NAME:8080/mascot_insight/installation.htm, where SERVER_NAME is

the name of the server you have installed Mascot Insight onto. If the Tomcat HTTP port is something

other than 8080, this will also need to be changed. You can also find a link to the configuration

wizard from the Start menu under Mascot->Mascot Insight. Before proceeding with the

configuration wizard, please ensure that your browser has javascript enabled.

If there is more than one version of Postgresql installed on the system, the following page will open

allowing you to choose which instance of Postgresql to install the Mascot Insight database on. You

will not see this page if there is only one instance of Postgresql installed

If you select an instance of Postgresql other than the one installed by Mascot Insight, you will also be

prompted to enter the Postgresql superuser password before you can continue. You will not see this

page if you are using a Postgresql instance installed by the Mascot Insight installer.

If the only instance of Postgresql installed on the system was the one installed by the Mascot Insight

installer, the following page will be the first page of the setup wizard. Enter the URL of your Mascot

server into the input box. If you have not updated your Mascot server to version 2.4.2 or later, or if

Mascot security is not enabled on the Mascot Server, the setup wizard will not be able to continue

until you update your Mascot server or enable Mascot security.

On the next page, enter the username and password for your Mascot server admin user.

Next enter a username and password you wish to use for the Mascot Insight administrator user. This

can be an existing Mascot security user if you wish - the required security groups will automatically

be added to the user. This user will be used by the Mascot Insight server to run its various

background tasks and monitor the search import job queues. We therefore recommend that you use

a separate admin account for this, rather than a day-to-day user account.

On the next page, you have the opportunity to grant existing Mascot security users access to Mascot

Insight. You can also do this via the security admin pages on your Mascot server. If you use Mascot

Daemon then you must grant the user(s) used to run searches from Mascot Daemon access to

Mascot Insight otherwise searches submitted from Mascot Daemon will not be automatically

imported into Mascot Insight.

Enter or confirm the email address of the system administrator and the location of the Mascot result

file archive.

If you are installing Mascot Insight onto the same computer as your Mascot Server, the default

location will be the existing Mascot Server data directory. This saves Mascot Insight having to copy

the Mascot result files and also saves disk space. If you are installing Mascot Insight onto a separate

computer, this is the location in which local copies of the Mascot result files will be stored. Click

'Finish' to complete the configuration wizard.

The configuration will run. If there is a problem, an error message will be displayed. If this happens,

please contact Matrix Science support. If configuration completes correctly, the log on page for

Mascot Insight will open with the details of the Mascot Insight administrator user filled in. Mascot

Insight is now ready to use. Any searches submitted to the Mascot server by a user with Mascot

Insight access will automatically be imported into the system, please see the 'Tutorial' and

'Populating the Mascot Insight results database' sections in the online help text for further details

and help getting started. You may also wish to set up Gene Ontology (GO), UniProt? accession and

interactions database in the system. Because of size restrictions, these files are not shipped as part

of the Mascot Insight installation. However, you can initiate automatic download and update tasks

to handle the required files. You may also wish to set up the details of your email server so that the

system can send the administrator automatic emails if there is a problem. Please see

'CongurationGuide.pdf’ on the 'Installation' page of the online help.