Beginner’s Tutorial for Pipeline Pilot

Welcome to the Beginner’s Tutorial for Pipeline Pilot. Contents

These introductory lessons are intended to help you
get the most out of using Pipeline Pilot in the least Lesson 1
amount of time. In less than an hour, you should be Getting Familiar with Pipeline Pilot Client ...... 2
able to get familiar with the basics of Pipeline Pilot, Lesson 2
including how to create and save a new protocol, run a Creating and Saving a New Protocol ............. 10
protocol and view the job results, customize a protocol Lesson 3
in different ways, and export it as a standalone file. Finding and Opening a Protocol ..................... 12

All example protocols used in these lessons are part of Lesson 4

the generic protocols included with Pipeline Pilot (no Running a Protocol and Viewing Results ....... 15
separately purchased component collections are Lesson 5
required). For instructions on using components and Customizing an Existing Protocol .................. 16
protocols that ship with a separately purchased
Lesson 6
package, see the Pipeline Pilot Help Center.
Exporting a Protocol....................................... 21
Your Notes ........................................................... 22
Accelrys Technical Support ................................ 22

Copyright © 2007, Accelrys Soft ware Inc. All rights reserved.

Lesson 1 Components
Getting Familiar with Pipeline Pilot Components are the basic building blocks of a data pipeline. They
Client process data as it flows throughout a protocol. Components perform
specific functions on data including:
Objective: The first beginner’s lesson is intended to help you get  Reading data from external files and bringing it into a pipeline
familiar with the Pipeline Pilot work environment.
 Supplying data to downstream components
Pipeline Pilot is based on a technology known as data pipelining,
which makes it possible to connect different data sources with
 Manipulating and filtering data
applications and rapidly process data through a branching network of  Calculating data properties
computational steps. Points of data are processed independently via  Writing data to an external source and displaying it in an
components, and multiple data points can be processed
application
simultaneously via protocols. Visualization exposes the key data
processing steps, making it straightforward to work with data
Component Types
pipelines.
Components are organized into several broad categories, each
Pipeline Pilot is a Windows-based application that runs on your client
represented by a top-level folder, arranged in alphabetical order in
computer. It provides a graphical environment for viewing and
the Components tab. These top-level folders relate to the type of
editing protocols and for sending data to the server for processing.
operation performed by the components it contains (reading, viewing,
filtering, manipulating, and so on). Pipeline Pilot includes a collection
Basic Concepts of generic components designed to perform tasks such as reading
To effectively use Pipeline Pilot, it is important to understand the incoming data, filtering, sorting, merging, and sending processed data
following basic concepts: to output files and viewers. You can customize these generic
components and design new ones to suit your particular needs.
 Components  Ports
Customization includes changing what the component does, its label,
 Component types  Pipelines and its icon.
 Component collections  Accessibility to files and data
 Component reference help  Data sources and destinations Component Collections
 Parameters  PilotScript In addition to the generic components, Pipeline Pilot offers a variety
 Protocols  Subprotocols of component collections that you can separately purchase and install
on your server. These collections are intended for more specific tasks,
such as working with chemistry data, producing reports, partitioning
data, and performing text analytics.

Beginner's Tutori al for Pipeline Pilot  2 

Component Reference Help Parameters
Help is available for every component in Pipeline Pilot. It is Most components are equipped with parameters and corresponding
commonly referred to as ―component reference help‖ and is intended values. These parameters control how a component processes data
to provide very specific and detailed information about a component. records for handling downstream in a protocol. The Parameters
Reference help describes its purpose, parameter values, and more. window (lower-right) exposes all the parameters for a selected
When you select a component icon in your pipeline, its reference help component. Some parameters are preset and do not need to be
is displayed in the Help window (lower-left): changed unless you want a different output. Parameters that require
values at run time are displayed in red (and so is the component icon
before its required parameters are set).

Component reference help for File Reader component

Parameters for Join Data from File component

Beginner's Tutori al for Pipeline Pilot  3 

Protocols Ports
A protocol is a collection of components, that are connected by pipes, Data flows in and out of components via the data ports. A component
to create one or more pipelines, each designed to perform a specific can have any combination of ports including one input port and one
task. A protocol begins with input and ends with output (generated or two output ports (a green Pass and a red Fail port). Data enters a
after the protocol job successfully runs). component through the input port and exits a Pass or Fail port. The
The first component is some type of reader that specifies the data number of data records that pass through a port are tracked via
source used as input. The middle components are designed to handle numbers of the same color.
your data in one or more ways. Protocols always end with an output
component that writes data to an external source that you may view
online or use in another application.
The following shows an example of a protocol that checks whether a
file exists before reading it and displaying the results in an HTML
Table Viewer.
Component with Input (left), Pass (green) and Fail (red) ports

The types of ports required for a given component depend on the

type of component you need to use in your protocol. You can connect
ports to other components for processing somewhere else in the
pipeline, turn them on and off, and even define what types of data to
use with them if necessary.
Protocol designed to sort data and display output in Excel

You can view, create modify and run protocols. When you run Pipelines
protocols, you may need to fix errors (debug), especially if you When constructing a protocol, you place components in the order that
change parameter values at run time. The results are usually available they need to process your data. Each component needs to be
for you to view after the protocol execution is complete. connected to the next one with one or more pipes. Data moves from
one component to the next through a series of pipes in left-to-right
Note: As an end user, you can create, run, and save your own
order. Collectively, the series of pipes is known as a pipeline. The
personal protocols to your ―User Name‖ tab. You can also access
pipes connect components via their data ports.
shared protocols and change parameter values at run time. Protocol
designers can customize components and protocols, and then publish A protocol can include one or more pipelines. Each pipeline can be
them on your server for use by end users. simple or complex, is numbered sequentially, and is executed from
top-to-bottom order (the next pipeline starts when the previous one is
complete). You can drag and drop components into the workspace
and move them around by adding new pipes and branching data in
different directions.

Beginner's Tutori al for Pipeline Pilot  4 

 Accessibility to Files and Data
The Explorer window (upper-left) serves as your starting point for
working in Pipeline Pilot. It displays different tabs for accessing
components and protocols, plus a ―User Name‖ tab for files that you
create for your own personal use.
The Explorer window has different modes for accessing files. In flat
mode, files are displayed in a sortable list.

Example of a protocol with two pipelines that

get progressively more complex with the addition of components

Explorer window in Flat mode

Tip: In hierarchical mode, folders are displayed in an

expandable/collapsible hierarchy of folders and subfolders.

Beginner's Tutori al for Pipeline Pilot  5 

A search bar is available above the folder list to make searching for You can drag and drop components and protocols from the Explorer
and opening files as convenient as possible. When you enter text in window into the workspace on the right side of the program window.
the search bar, the Explorer starts searching for components and When a component is open in the workspace, it is displayed as an
protocols that have similar names. When it finds the first item that icon. It looks something like this:
matches what you type (partial or whole words), the file is
highlighted.
To keep searching on the same string of text, press F3. (When the
search bar turns a bright orange color, it cannot find a file that
matches your search string.)

Icon for a viewer component

Data Sources and Destinations

Many tasks you perform in Pipeline Pilot involve defining data
sources and destinations. You can do this when setting parameters for
components such as readers and writers. File browsers are available
for helping you perform these tasks.
Reader components require sources. You can select files on the
server, another server on your network, or on your client system. On
the server, data sources are located in a root folder called ―public‖.
You can also specify which data record properties in a data source
you want to use. Any properties you choose to exclude are not read
by the component or streamed into the pipeline.
Writer components require destinations as parameter settings. You
can only select destinations on the server. By default, the output files
are written to your ―User Name‖ tab on the server, so you can easily
access the files at a later time.
Explorer window in Hierarchical mode

Note: If you connect to more than one protocol database, a Network

tab is also displayed in your Explorer window.

Beginner's Tutori al for Pipeline Pilot  6 

Subprotocols Starting Pipeline Pilot
Subprotocols encapsulate a number of components into a single top- When Pipeline Pilot is installed on your system, an icon is available
level component that hides the individual components from view at on your Windows desktop for starting the application. It looks like
runtime. This is useful for protocol designers who want to hide the this:
complexity from end users. If you are an end user, you may only see
the subprotocol icon and not any of the components it contains.

To start Pipeline Pilot:

1. Double-click the icon. When the Pipeline Pilot opens, the work
environment is displayed in the main program window.
2. Take a moment to get familiar with all the parts of the window,
illustrated below.

Protocol with three subprotocols

Beginner's Tutori al for Pipeline Pilot  7 

Pipeline Pilot client program window

Beginner's Tutorial for Pipeline Pilot 8

Program Window Description [ 9 ] Favorites Bar: For components and protocols you open
frequently, provides a place to both find and open them in a single
[ 1 ] Menu Bar: Select commands and perform tasks, such as opening
step to save time.
and saving files and customizing the work environment.
[ 10 ] Workspace: Your work area for creating, viewing, running, and
[ 2 ] Toolbar: Click shortcut buttons for commonly used functions,
modifying protocols. Drag and drop files from the Explorer window
such as running a protocol or zooming in and out of the workspace.
into the workspace to build new protocols.
[ 3 ] Search Bar: Quickly find and open components and protocols
[ 11 ] Status Bar: Displays information about the progress of your
based on the text you enter. Click the button (left-side) to switch
running protocols.
between flat and hierarchical modes.
[ 12 ] Protocol Task Bar: Navigate your open protocols and
[ 4 ] Explorer Window: Displays all available components and
subprotocols in the workspace by clicking the item displayed in the
protocols that you can open.
taskbar.
[ 5 ] Explorer Tabs: Decide what you want to display in Explorer
[ 13 ] Parameter Window: One of the most commonly used features
window—files in the shared tabs (Protocols, Components) or files
at protocol run time, this window exposes all parameters and their
from your personal ―User Name‖ tab.
corresponding values. From here, you can set new values and
[ 6 ] Network Tab: If you are connected to more than one protocol reconfigure existing ones. Required parameters are displayed in red.
database, use the Network tab to switch between active servers and
[ 14 ] Right Windows: The windows in the lower right are provided
change connections.
to help you perform specific tasks. Parameters is the default window,
[ 7 ] Component Reference Help: Depending on what is selected in which displays the parameters for a component selected in the
the workspace (upper-right) or Parameters window (lower-right), the workspace. If you click a blank area of the workspace, the Parameters
Help window displays help about the selected item (protocol-level window displays the protocol-level parameters (if there are any).
help, component-level help, or parameter help). Other windows are available for implementation parameters,
[ 8 ] Left Windows: The windows in the lower left are provided to background information about a protocol or component, error
help you perform specific tasks. Help is the default window, which handling information, and debugging parameters. Web Service
displays component reference help (described above). Jobs displays protocols also have a window for viewing parameters and results.
information about the protocols that you ran (from here, you can re- [ 15 ] Active Server Bar: Reveals the name of the active protocol
open protocol results for previously run jobs). If you work with database for running your protocols. To change servers, double-click
checkpoints, you can view information about them in a Checkpoint and select a different server name from the dialog that opens.
Data window. If you are debugging or validating a protocol, a Debug
Messages window or Validation window is displayed to provide you
with the necessary information.
Next Lesson: Creating and Saving a New Protocol

Beginner's Tutori al for Pipeline Pilot  9 

Lesson 2 Tip: Remember how to use this Search feature. You will need it
Creating and Saving a New Protocol again for the remaining lessons.
3. Drag and drop the Delimited Text Reader into the workspace. Since
Objective: This lesson is intended to help you add new components
this component needs parameter values set before it can run in a
to a blank workspace to create and save a new protocol. It assumes
protocol, the icon is displayed in red.
you already read the first lesson and are familiar with the Pipeline
Pilot work environment and the basic concepts of protocol building.
This lesson walks you through the steps of creating a very simple
protocol that includes an input and output component.
To start creating a new protocol:
1. Click New Protocol . A new blank workspace opens on the right Delimited Text Reader icon displayed in red,
side of the program window. to indicate that it requires parameter values

2. From the Components tab in the Explorer window, type ―del‖ in 4. Select the red icon and look in the Parameters window (lower-
the Search bar. The ―Readers‖ folder opens and highlights the first right). The Source parameter tells the component what data to use
component that matches the search criteria —Delimited Text and where it is located. It is displayed in red to alert you that it
Reader. This component reads tab-, space-, and comma-delimited needs a value.
text files.

Delimited Text Reader parameters

Delimited Text Reader component

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5. Select the Source parameter by clicking (right side of parameter Note that the parameter name is now displayed in black, and the icon
name). The Select Sources dialog opens. From here, you can select in the workspace is displayed in blue, since the required value is now
the data source to use with the reader. defined for this component.
6. There is a quick way to find files that work with this reader. Select
the Shortcuts icon on left side of the dialog. The main folders of
files you can select on the server are listed.
7. Open the ―Generic Data‖ folder and ―Tables‖ subfolder, choose
the ―Selwood.tab‖ file from the list of files, and then click Select.

Source parameters (configured)

The protocol needs a component to receive and do something with

the data read by the first component. For this lesson, you can add a
simple viewer to the pipeline.
To add a data viewer component:
1. Type ―ecel‖ in the Search bar (note the deliberate typo). The
Search bar is unable to find any components that include the
phrase ―ecel‖. The text appears against an orange background as a
visual clue that you may have entered the wrong spelling.

Select Sources dialog

The Parameters window is updated and reveals the file you selected
to use for the Source parameter.
Search bar is displayed in orange when it cannot locate a search term
(possibly due to a typo)

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2. Change the search text to ―excel‖ and press F3 repeatedly until the 5. In Name, type ―Lesson1‖ and click OK. (By default, the new
Excel Viewer component is highlighted. protocol is saved to your ―User Name‖ tab.)
3. Drag and drop the Excel Viewer into the workspace so it is
connected to the reader component in the pipeline. Next Lesson: Finding and Opening a Protocol

Lesson 3
Finding and Opening a Protocol
Objective: The previous lesson showed you how to use the Search bar
in the Explorer window to quickly locate components. This lesson
shows you how to use the Search bar in different ways to find and
open a protocol.
The protocol you need to open is stored in a subfolder. The quickest
way to find it is to search for it.
To search for and open the sample protocol:
1. From the Explorer window, select the Protocols tab.
New protocol with Delimited Text Reader and Excel Viewer components 2. Look for the folder ―SciTegic Examples‖. This is where all the
example protocols you can run are located.
4. Click Save Protocol . The Save Protocol dialog opens.

Save Protocol dialog

“SciTegic Examples” folder

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3. In the Search bar, type ―sort‖. The Explorer highlights the first item
that matches the search criteria.

Flat mode search results list all files without folder hierarchy

Tip: To sort components by collection, click the Author column.

6. Open Sort Data Example. The protocol opens in the workspace.

Results highlighting first example protocol that matches search term

4. Press F3. The Search feature finds the next file that matches your
search string. In this example, it highlights the next example
protocol directly below the one found in the initial search.

Search results highlighting next protocol example matching search criteria

5. Switch to Flat mode by clicking on the left side of the Search

Sort Data protocol open in workspace
bar. Flat mode displays a list of files that match your search
criteria without the folder hierarchy. In some cases, it might be
quicker to locate files in this mode.

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7. The yellow box displayed underneath the pipeline is a sticky note.
In addition to what the protocol reference help provides (Help
window in lower-left), the sticky note provides extra information
to help you better work with the protocol. Take a moment to read
the sticky note and get familiar with the protocol details.
8. Click in the blank area of the workspace and then select the Help
window (lower-left). This window displays reference help about
the protocol. Take a moment to read the help and get more
familiar with the protocol.

Help for Read Auto Data component

10. To get an idea of what the other components in this example

protocol are configured to do, review the reference help for each
remaining component.
After you get familiar with the protocol and all of its components, you
can run it and view the results. The next lesson shows you how.

Next Lesson: Running a Protocol and Viewing Results

Help for the Sort Data example protocol

9. Select the Read auto data icon in the workspace and then click the
Help window. Help about the selected data reader component is
displayed. Take a moment to read this information.

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Lesson 4 After the protocol runs, HTML reports are generated your browser.
The output should look something like this:
Running a Protocol and Viewing
Results
Objective: This lesson is intended to help you run a sample protocol
and view the resulting data. Once open, the protocol Sort Data
Example is ready to run.
To run the protocol:
1. Click Run Protocol . The protocol job is sent to your server for
processing. The workspace indicates the number of records
processed as the data flows throughout the pipeline. It should
look something like this:

Sort Data example protocol running in the workspace. Data counters indicate
number of records leaving Pass and Fail ports (enclosed in red boxes for this tutorial
illustration).

Sort Data example output

Note: There are two reports in the output because there were two
pipes for output in the protocol. One report sorts the data by
horsepower, and the other by price.

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Whenever you run a protocol, your client issues a ―job‖ to the server. Lesson 5
Pipeline Pilot includes a Jobs window (lower-left) that tracks the
protocols that you run and provides job details, including the results Customizing an Existing Protocol
of a job (even after it is completed). You can easily retrieve the results
Objective: This lesson shows you how to customize an existing
of jobs you ran previously from this window, without having to
protocol by getting familiar with the data properties used with a data
re-run the job. This is especially useful if you run any protocols that
source, changing parameter settings that manipulate the data, and
take considerable time to process. Having a quick and easy way to
finally, replacing the components that generate the output for the
access the results saves you time.
protocol.
To view protocol job results:
To select data properties for a source file:
1. Click the Jobs window.
1. Open the protocol Sort Data Example. If you just completed the
2. Expand the job listing by clicking . The result files are displayed previous lesson, this protocol should be open in the workspace.
as links. Clicking a link opens the result file, in this case, it opens
the .htm report files in a browser. The ―Finished‖ status indicates 2. Select the first component icon, Read auto data.
that the job was successful. 3. From the Parameters tab, open the Source parameter group by
clicking . The parameters contained in this group are exposed
(Maximum, SourceTag, Keep Properties, and HasColumnNames).

Source parameter group for Read auto data component

4. Make a note of the file used as the data source,

―data\Tables\imports-85.txt‖. This is a simple text file that
Jobs tab
contains one record per line with numerous data properties for
Next Lesson: Customizing an Existing Protocol various automobiles.

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 When selecting data sources for reader components, you can find 8. Scroll across the source properties and make a note of all the ones
out which data properties the records contain to get an idea of that are available for this data source (―imports-85.txt‖). There are
what you can do with the data in downstream components. You numerous properties. When specifying the properties to use in
can also include and exclude data properties. Excluded properties your data records, you can discard any unnecessary ones from
are not used by the component when it reads the data source. being read into the pipeline from this dialog.
5. Select the Keep Properties parameter by clicking . The Source 9. Select the column headers for ―losses‖ then click (Discard). The
Preview dialog opens. By default, this dialog shows properties dialog is updated and the losses properties are moved to the
only for the first five data records. Discarded list on the right side.
6. Change the number of data records to preview to ―100‖, and then 10. Discard the ―fuel‖ property. The dialog should look something
click Reload. The preview list is updated to display 100 records. like this, with the two discarded data properties:

Data properties available in the data source “imports-85.txt”

Excluded data properties “losses” and “fuel”
7. Scroll down the list and note all the makes of automobiles listed 11. Click OK to close the dialog. The Parameters tab is updated to
for 100 data records. (Expand the width of the ―make‖ column by show the properties that are included for the Keep Properties
dragging the cell border to the right.) parameter. (When all properties are included, the field is blank.)

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 Keep Properties exposes the data properties that are used for “imports-85.txt”

Now that you’ve had a chance to get familiar with the data properties
available in the data source, you can get a better idea of how they are
used by other components in a protocol.
To select data properties in a downstream component:
1. From the workspace, select the second component in the pipeline,
Keep only a few properties. It keeps only those properties you
specify for each incoming data record, which is another way to
include or exclude properties after the data is read into the
String that specifies the properties to keep
pipeline.
2. From the Parameters tab, select the Expression parameter for this 4. For this lesson, you can leave the PilotScript expression intact, but
component by clicking . An expression editor opens. keep in mind how you access the expression editor. (In later
lessons, you can learn more about how to edit expressions and
3. Make a note of all the property names that are used in the string.
work with PilotScript functions.)
They match the names displayed in the Source Preview dialog.
This expression tells the component which properties to keep and 5. Click Cancel to close the editor.
which ones to exclude. The existing protocol sorts data by horsepower and by price. For this
lesson, you can change this sort criteria.

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To change parameter values for sorting: Your protocol should look something like this:
1. Select the component Sort Data by horsepower and change the
following parameters:
Parameter Value
Property 1 ―Make‖
Sort Order ―Ascending‖
Sort As ―Text‖

The Parameters window should look something like this when the
parameter values are updated:
Excel Viewers attached to Sort Data components

6. For the top Excel Viewer component, set the WorkSheetName value
to ―Sorted by Make‖. In the Excel output, the worksheet tab will
display this label.

Parameters for Sort Data component

2. Click the label for this component in the workspace and change
the text to ―Sort Data by Make.‖ (What you type should replace
what is highlighted in the label.)
3. Customize the Sort Data by price component in the lower branch so
it sorts data by ―numdoors‖ in ascending order, as text. Rename
the label ―Sort Data by NumDoors‖.
4. Remove both Table components, Tile Horizontal, and the HTML
Report Viewer components from the pipeline. (Press and hold
CTRL as you click each icon and then press DELETE.)
5. Attach Excel Viewer components to the end of each Sort Data Parameters for Excel Viewer component
component.
Tip: Click Show/Hide Sticky Notes to hide the sticky note (so
you can more easily view all the component icons and their labels).

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7. Customize the bottom Excel Viewer component so it generates a 9. Run the protocol to view the results. The output for the first
worksheet named ―Sorted by Number of Doors‖. worksheet ―Sorted by Number of Doors‖ should look something
like this:

Parameters for Sort Data component in second branch

Note: When the data records exit the second component in the
pipeline, these sort components sort the data by make and number of
doors, rather than by horsepower and price. The viewers will reflect
this when the output is generated.
8. Save this protocol to your ―UserName‖ tab as ―CustomProtocol‖
(so you can use it again in the next lesson).
Protocol output for customized Sort Data example

Next Lesson: Exporting a Protocol

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Lesson 6 3. The Export dialog opens. In Save In, navigate to the drive and
folder where you want to save the XML file.
Exporting a Protocol
Tip: Click Create New Folder to export the XML file in a new
Objective: This lesson shows you how to save a protocol in a different directory.
way by exporting it as an XML file. You can export the protocol you
created in the previous lesson (―CustomProtocol‖). This is useful for
creating extra copies of your files, so you can access them from
different client systems, such as your laptop computer.

Note: The files you export are saved in XML format. To open an
exported file, you need to import it to your ―User Name‖ tab on the
client where you are doing your work.
When you save a protocol to your ―UserName‖ tab, the file is saved in
the protocol database where all other components and protocols
reside. This database is located on your server.
You can also save copies of the protocol to other locations such as
your local hard drive or a CD, by exporting the protocol.
To export a protocol:
1. From your ―User Name‖ tab in the Explorer window, search for
―CustomProtocol‖.
2. Right-click the file and select Export.
Exporting a protocol as an XML file to a local drive

4. By default, the XML file is saved with the same name as the
original file, in this case, ―CustomProtocol‖. Feel free to change
the name or save it as is.
5. Click Save. Your protocol is saved to the target location as an XML
file.

Exporting a protocol in the Explorer window

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 Tip: This lesson demonstrates how to export a single file, but Accelrys Technical Support
you can also export multiple files and even entire folders. When
exporting multiple files, press and hold CTRL and click each If you have any problems or questions, contact Accelrys Technical
filename, then right-click and select Export to Folder. When Support:
exporting an entire folder, right-click the folder and then select
Export Folder. Pipeline Pilot Enterprise Server and Professional Client
EMAIL: [email protected]
If you’ve made it this far, you have completed all the lessons in the
Beginner’s Tutorial. You now may have a basic understanding of how ONLINE SUPPORT: http://accelrys.com/services/support.html
Pipeline Pilot works. Congratulations!

Next Lesson: Advanced Tutorial Phone Support

To learn more tasks and get familiar with PilotScript, continue with AMERICAS: M–F 6:00 AM – 5:30 PM (PST)
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