Installation Instructions for TRIM
Total Risk Integrated Methodology (TRIM)
1. Installation of third party software
1.1 Install the Java Runtime Environment (JRE) 1.5
1.2 Install MySQL Version 4.1
1.3 Install R version 2 or later.
2. Installation of TRIM
2.1 Installing TRIM for the First Time
2.2 Updating Your TRIM Installation
TRIM needs the following third party software to run: Java (1.5), MySQL (4.1), and R (2.x).
If you do not already have the specified versions of Java, MySQL, and R installed, please install the current versions of these products before proceeding with the TRIM specific installation instructions in Section 2.
Note: if you are not comfortable with software installations, you may want to have an IT support person perform the steps in this section.
Java 1.4.x or 1.5.x is required to run TRIM.Prior to installing Java, you should determine
if you already have a sufficient version of Java on your computer.You
can do this one of two ways:
- From the start menu, open a Command Prompt window. Then type the
If the information that is printed starts with the words java version "1.5, then your version is sufficient and you do not need to install Java.
- From the start menu, open the Control Panel, and then open Add
or Remove Programs. Scroll down through the alphabetical listing to the 'Js'.
If Java 1.5 is installed, it is listed as
J2SE Runtime Environment 5.0 Update N, where N is the number of the update.
If Java 1.4 is installed, you would see Java 2 Runtime Environment, SE v1.4.2_N,
where N is the revision of Java 1.4.2 that you have installed. The latest version
available at the time this document was written is 1.4.2._09.
- If you have Java 1.5 installed you do not need to install Java, so skip to Section
1.2. If you need to install Java, continue with the instructions in this
- From the start menu, open a Command Prompt window. Then type the command:
- Go to http://java.sun.com/j2se/1.5.0/download.jsp to
prepare to download the Java runtime environment.
- Scroll down and click on the link named "Download
JRE 5.0 Update N". You will be taken
to a page with a license agreement. Examine
the agreement and if you agree to the terms,
- click the Accept License Agreement option,
- then go to the section with the heading "Windows
Platform - J2SE(TM) Runtime Environment 5.0 Update 5".
- Now, click the link that corresponds to your operating system, e.g., "Windows
Offline Installation, Multi-language".
- click the Accept License Agreement option,
- You will be prompted to save the installation package on your computer.
Choose a location in which to save the installation package and save the file.
Note that you will be able to delete this file after you are finished installing
- Execute the Java installation package by
using My Computer or Windows Explorer to go to the folder in which you saved
the installation package and by double clicking on its icon. The
file should be named something similar to jre-1_5_0_05-windows-i586-p.exe.
- After you double click on the installation package, an installer will start.
Follow the prompts of the installer to accept
the license agreement and perform a Typical installation. Click Finish when
it is done.
- Note that on Windows, the Java runtime environment is typically installed into
a directory similar to C:\Program Files\Java\j2re1.5.0_05.
- If the above instructions were not sufficient to obtain a successful installation, more detailed information is available at http://java.sun.com/j2se/1.5.0/jre/install-windows.html.
TRIM requires MySQL Version 4.1 to run. Note: MySQL Version 5.0 is not supported for use with TRIM, therefore you will need to install version 4.1 even if you already have Version 5.0 installed. Instructions for installing MySQL are provided here.
- If you have a version of MySQL prior to Version 4.1 installed,
follow the steps in this section, otherwise proceed to Step 2.
- If you have previously installed MySQL 4.0 or earlier, you must
uninstall that version before proceeding with the upgrade.
- To begin the uninstallation, first stop the service,
by typing the following command at the command prompt: NET STOP MySQL.
(If your service is registered under a different name than MySQL,
please use that name).
- Next, remove the service by executing the following command: C:\mysql\bin\mysqld -remove
(If MySQL was installed in a different directory,
please use the appropriate path e.g. D:\mysql\bin\mysqld
- Next, go to Windows Start Menu —> Control Panel —> Add or
- Look for MySQL Servers and Clients
xxx and click on Change/Remove.
- It will ask you Are you are sure you
want to remove MySQL Servers and Clients and all
its components? Say Yes. Your previous version MySQL will then be uninstalled.
- If you have previously installed MySQL 4.0 or earlier, you must uninstall that version before proceeding with the upgrade.
- Perform the following steps to download the MySQL Version 4.1 installation
- Go to http://dev.mysql.com/downloads/mysql/4.1.html.
- Scroll down on this page until you see the section Windows Downloads.
- In the line that starts with Windows Essentials, Click on Pick
- The next page gives you a chance to enter some information about yourself
and how you're using MySQL. You may answer these questions if you wish,
or you may click on No thanks, just
take me to the downloads.
- In either case, you should come to a section titled Mirrors in the United
on HTTP next
to one of the mirror sites. You may
find that choosing a mirror close to you geographically gives you a faster
download, but you can click on any one.
- You will be prompted to save the MySQL Version 4.1
installation package to your computer. Choose a folder and Save the installation
package to the folder on your computer.
- Use My Computer or Windows Explorer to go to the folder in which you saved
the installation package. The file should be named something similar
- Go to http://dev.mysql.com/downloads/mysql/4.1.html.
- Execute the MySQL Version 4.1 installation package
(e.g. mysql-4.1.14-essential-win.msi) by double
clicking on its icon.
- Once the installation package has started, click Next and
follow the prompts
to perform a Typical installation.
- When prompted with setting up an account, you may fill in the information
it asks or you may choose to Skip Sign-Up.
- On the last screen of the installation wizard, there is a checkbox for Configure
the MySQL server now. Make
sure this is checked before you click Finish. Clicking Finish will
start the MySQL Server Instance Configuration Wizard.
- Once the installation package has started, click Next and follow the prompts to perform a Typical installation.
- Make a note of the directory into which MySQL was
installed (e.g. C:\Program Files\MySQL\MySQL Server 4.1).
- On the MySQL Server Instance
Configuration Wizard click Next,
choose Detailed Configuration for
the configuration type and then click Next. When prompted,
choose the following options in the wizard:
- Server Machine, since it would be
advisable not to use your computer for other things while TRIM is running.
This setting will help MySQL operations (and therefore
TRIM) to execute faster.
- Next, choose the Non-Transactional Database
Only option, since TRIM currently does not use transactions. This will
avoid requiring MySQL to perform additional operations
to ensure transaction compliance.
- Next, select the Manual Setting option
and set the number of concurrent connections to be 15.
- Next, select the Enable TCP/IP Networking checkbox,
and select the default port setting (3306).
- Select Standard Character Set.
- Make sure the Install as Windows Service and
the Launch the MySQL Server
automatically checkboxes are checked and select MySQL as
the Service Name. It is suggested
that you also choose to Include Bin
Directory in Windows PATH.
- On the following page that starts with Please set the security options, check
the Modify Security Settings checkbox, enter a New
root password and Confirm. Do not check 'Enable root access from remote
machines' (this is a security risk). Write
down the new password you have set for future reference. Leave the Create an
Anonymous Account option unchecked. Be sure to make
a note of the root password as you will need this later in the installation
- Once all settings have been selected, you will see a Ready to
Execute page with an Execute button
at the bottom.If you are satisfied
with the selections you made, click Execute.Otherwise, you can
use the Back or Cancel buttons and change your selections or start
- Server Machine, since it would be advisable not to use your computer for other things while TRIM is running. This setting will help MySQL operations (and therefore TRIM) to execute faster.
- Using MySQL from a command prompt: To access the MySQL server
directly (this is not a requirement), from a
command prompt window you can
log into the MySQL database by typing this:
mysql -u root -p
and then entering the MySQL root password at the prompt.
Once you are logged in, you should see a message that says "Welcome to MySQL Monitor..." You may issue commands like show databases; and create database dbname from here if you need to. However, most users will not need to interact with the database this way.
- To obtain the R installation package,
do the following:
- Go to http://cran.us.r-project.org/.
On this page you should see a section labeled Precompiled
Binary Distributions. Click on Windows (95 and later).
- On the R for Windows page, click on the link
- On the R-2.1.1 for Windows page (Note: there may be a version later
than 2.1.1. by the time you read this, proceed with that version), click on rw2011.exe (note:
the 2011 here is the file name for version 2.1.1 only - if the version you
are downloading is different, this file name should be adjusted accordingly).
- After clicking on rw2011.exe you
will be prompted to save the installation package to your local disk. Click Save then
choose a folder to place it in.
- Once it is finished saving, click Close,
- Go to http://cran.us.r-project.org/. On this page you should see a section labeled Precompiled Binary Distributions. Click on Windows (95 and later).
- Once you have an installation package
(e.g. rw2011.exe), use My Computer or Windows Explorer to go to the folder
in which you saved the R installation package.Start the installation process
by double clicking on the icon that corresponds to the installation package.
- In the Setup - R for Windows Wizard, select
the Setup Language and click OK,
then click Next.
- Review the license agreement and
if you accept it, select the I accept the agreement option and then click Next.
- Select the location in which you
want R installed, and then click Next.
- On the Select Components page, click Next to accept
the default settings.
- On the Select Start Menu Folder page, set the
name you want to use for the folder that will be created on your start menu
then click Next.
- On the Select Additional Tasks page,
accept the default settings then click Next. R will then be installed.
- Make a note of the directory into which R was installed (e.g. C:\Program
Files\R\rw2011). You will need this information later in your installation
process. When the installation
is complete, click Finish.
- Click Finish when the installation
is complete. If you wish to make sure
the installation worked, find the R submenu on your Start Menu and choose R
2.1.1. If the application RGui comes
up, it is working properly. Close the RGui application - TRIM
does not use the RGui, instead it calls R "behind the scenes".
- Review the license agreement and if you accept it, select the I accept the agreement option and then click Next.
An installer has been developed for TRIM to streamline the download and installation process.The installer will download all needed TRIM files and set up the bat files to run TRIM for you automatically. It also supports updating TRIM as new versions become available.
It is recommended that you create a MySQL username for use with TRIM. To do this:
- From your list of programs, choose MySQL —> My SQL Server 4.1 —> MySQL
Command Line Client
- Enter your MySQL root password when prompted (which you specified when you
- Once you are logged in, you should see a message that says “Welcome
to MySQL Monitor…..”.
- At the mysql prompt (i.e., mysql > ), type the following command (replacing
USERNAME and PASSWORD with your choices, e.g., "trim" and "trim"):
GRANT ALL PRIVILEGES ON *.* TO 'USERNAME'@'%' IDENTIFIED BY 'PASSWORD';
If entered correctly, MySQL will respond with something like "Query OK, 0 rows affected (0.02 sec)".
- Type Exit to exit MySQL, and then close Command prompt window.
- If you specify the same username and password on Page 1 of the TRIM installer
(shown below), the installer will enter these values as values for the parameters “MYSQL
User Name” and “MySQL Password” in each of the TRIM Scenarios.
- Download the TRIM installation program and save it
to your computer. Note that the installer program is available from the Software Available for Download section
- Once you have downloaded the installer, double click
on it to run it. When the installer starts, you will see a screen labeled TRIM Installer
Extractor.Follow these steps to extract the installer:
- Click on the Next button. You will
see a page that allows you to specify a location for the installer (default
is C:\triminst).The installer itself
is only 62 Kb.If you wish to specify
a different location, you may type into the field or use the Browse button.
- Once you are satisfied with the location of the installer, click the Next button.
- After the installer has been extracted, a Windows explorer window will
appear showing you where the installer has been installed and the installer
within a few seconds.In addition, an icon called TRIM Installer
will have been placed on your desktop.You
may run the installer in the future to download TRIM updates by double clicking
on the TRIM Installer icon.
- If the installer does not work, make sure that you can type "java -version" at
a command prompt and that it this returns the version of Java you are using.If
this does not work, follow the steps appropriate to your operating system to
make sure that Java is on your path. But,
the Windows installer for Java should have taken care of this for you.
- On the first page of the installer, you select the
directories that TRIM needs to know about.These
- The TRIM Download URL, which specifies
where to download TRIM from.Typically you will not need to change this
- The TRIM Home Directory is the directory
into which you want to install TRIM. A common location to select is C:\models\TRIM.
If the directory you select does not exist, it will be created for you.
- The R Bin Directory is the bin directory
for the R software package, which should already be installed. You may use
the Browse button to find the directory. On Windows this is typically a directory
like C:\Program Files\R\rw2011\bin.
- The MySQL Bin Directory is the bin directory for the MySQL
software, which should already be installed. You may use the Browse button
to find the directory.
On Windows, this is typically a directory like C:\Program Files\MySQL\MySQL
- The MySQL Username is a
valid username for the MySQL software package.If you have not created a special
username for use with TRIM, enter root, otherwise
use the username you created for TRIM (e.g. In section 2 above).
- The MySQL Password is
the password that corresponds to the selected MySQL username.
If you created a MySQL username and password to use with TRIM (e.g., in section
2 above), enter the new password here. Otherwise, enter the password you selected
the MySQL server (e.g., step 5.g. of section 1.2). If you are unsure of the
password, you can try some entries that you think are correct by typing the
following from a command prompt window: mysql -u
root -p [Return].You
will then be prompted for the password
and will be informed of whether you can successfully access MySQL.
- When you are finished filling in the information, the installer should
look something like Figure 1. Once you are satisfied with all the entries,
- On the second page of the installer, you specify information
about the activities you expect to perform with TRIM. Activate the checkboxes
next to the activities you think you will perform.If you are unsure of the activities you
plan to perform, click the Select
All button at the top of the page. A picture of Page 2 of the installer
is shown in Figure 2.If you plan
to perform risk or exposure assessments with TRIM.Expo or
HAPEM, it is recommended that you install the corresponding software and
databases prior to proceeding with the TRIM installation.
- On the third page of the installer, you specify information about the
directories that contain programs and data that are related to TRIM. The user-specifications
made here are to facilitate use of the TRIM scenarios by populating some of
their input fields. A picture of Page 3 is shown in Figure 3.
- For the APEX Directory, enter the name for the directory
to contain output subdirectories for TRIM.Expo-Inhalation (i.e.,
For example, c:\trimdirectory\APEX. You may use the Browse button to help specify
the directory, or type it in directly. The APEX executable program is downloaded
automatically by the installer and does not need to be found under the APEX
directory. If desired, this name can be subsequently changed by the user within
any of the TRIM scenarios.
- For the HAPEM Directory, enter the name of the directory that contains
the input and output subdirectories that will be used for HAPEM, along with
the HAPEM executable. For example, c:\HAPEM5. You may use the Browse button
to select the directory, or type it in directly. Typically the input directory
underneath the HAPEM Directory will contain subdirectories such as Activity
Pattern, Add, airqual, Commute, factor, and Population.
- For the FaTE Data Directory,
enter the name of the directory that will contain the data and project files
for TRIM.FaTE. Typically this will be something like C:\models\trim\data\fate.
You may use the Browse button to help specify the directory, or type it in
directly. If you are uncertain of what to put, you may leave it blank and fill
this in later when using a TRIM scenario to perform your ecological risk assessment.
- Once you are satisfied with your selections, click the Install button.
The installer will proceed with downloading the files into
the TRIM Home Directory, loading the TRIM projects and scenarios, and configuring
those scenarios to use the directories you have selected. When completed, the
screen will show a message “Installation complete”. Click “Exit” to
close the window, and a pop-up window will indicate that the installation has
completed successfully. Click “OK” to close that window, and you
will be back at your desktop.
- You may now access TRIM via your Start menu. By selecting Programs
and TRIM, you will see the four main programs that come with TRIM (TRIM, DAVE,
FaTE, and the Analysis Engine Table). The TRIM entry will include generic projects
for the uses specified on page 2 of the installer (e.g., ecological and/or
human health inhalation risk assessment, and/or exposure assessment). The FaTE
entry is to access the stand alone TRIM.FaTE program. For detailed information
on running the TRIM programs see the TRIM.Risk or TRIM.FaTE User’s
Figure 1. Page 1 of the TRIM Installer
Figure 2. Page 2 of the TRIM Installer
Figure 3. Page 3 of the TRIM Installer
- To update your TRIM installation, run the installer by double
clicking on the TRIM Installer shortcut from your desktop.The installer will come up using the settings
from the previous run of the installer.
- On the first page of the installer, if you select a new TRIM Home Directory, a new installation
of TRIM will be created.If you select the
same TRIM Home Directory as you did the first time, the installer will
prompt you whether to Reinstall or Update your installation.If you select Reinstall, the installer
will download a whole new set of files and will overwrite your current installation.For
this case, the same steps will follow as did for the first time installation.
- If you select Update,
the install will download only the files that have been updated since your
last TRIM update or installation. Once you click Update, a fourth page of
the installer will appear and will show you which files will be updated.You may cancel the update by clicking
Cancel, or proceed by clicking OK.Once
the update is complete, click Exit to exit the installer.
- Note that when you Update your installation, if any TRIM
projects have been updated the existing projects will be moved to a new name
with "Backup" appended to it, and the newly downloaded project will be loaded
using the default name.