Pipeline Pilot

Rapidly create, test and publish science-based services
that automate the ability to access, analyze, report and
share scientific data


January 2009

Accelrys Pipeline Pilot Newsletter

News and Events
Training, Short Courses and Webinars
Pipeline Pilot Tips and Tricks
Protocol of the Month
Accelrys Community Forums
An Update from Our Partners

News and Info

Pipeline Pilot 7.5 Now Available

Pipeline Pilot 7.5 was released in December and it is now available for downloading by registered customers. Release highlights include:

  • Platform and User Interface
    • Pipeline highlighting for cut-and-paste and auto-expand when navigating the explorer window
    • Protocol queuing, job distribution, and coarse grain parallelization with SGE, PBS/Pro, or Platform/LSF
    • Proxy server authentication for file readers
    • Administrative report indicating usage of clients and collections
  • Reporting
    • Protocol deployment with Pipeline Pilot SharePoint Bridge
    • RSS feeds for report deployment
    • Report hierarchical, multi-dimensional data using the new Cross Tab component
  • Collections
    • Manage, manipulate and process spectral data using the Analytical Instrumentation Collection
    • Prototype component integrating MATLAB
    • GFA method and model selection in the Advanced Data Modeling Collection


Accelrys 2009 User Group Meeting

The 2009 Accelrys User Group Meeting (UGM) will take place February 18–20, 2009, at the Dana Hotel on Mission Bay, in beautiful San Diego, CA. The meeting will be preceded by optional training sessions, which will take place February 16–18.

The User Group Meeting will offer the opportunity to see innovative ways your colleagues are applying Accelrys solutions to solve real world problems, and will feature presentations and optional training courses for Pipeline Pilot and Accord, and also Discovery Studio and Materials Studio in the new Modeling and Simulation tracks. The UGM will also demonstrate innovative applications and techniques for informatics, drug discovery, and materials research.
Details and Registration >>>

Recap of Accelrys 2008 European User Group Meeting

Over 70 users gathered in a snowy Divonne-Les-Bains, France in December for the 2008 European Platform and Informatics User Group meeting. In a wide ranging agenda, attendees heard from 10 users on their application of Pipeline Pilot for cheminformatics, bioinformatics and imaging applications. One particular area of application this year was the exploration and analysis of high throughput screening data for which a number of users presented. Others discussed developing and validating predictive models, the application of Pipeline Pilot to systems biology, and even on the use of NASA's WorldWind Earth Mapping application to the presentation of chemical clustering results.

Accelrys provided updates on the new Pipeline Pilot 7.5 release and previewed future developments in a variety of areas including the scientific enablement of Microsoft SharePoint, a new cheminformatics component collection, and new advances in imaging and bioinformatics. A series of rapid-fire talks and exhibits provided a spotlight for our ISV partners — Sophia Search, HP, DiscNgine, BioFocus, Tibco/Spotfire, ChemAxon and Microsoft — who showcased how their products integrate with the platform. The meeting concluded with our traditional "pet-peeves" session run by Ian Stott from Unilever, which gave customers the opportunity to express their wishes for future product enhancements and offerings. The meeting was sponsored by IBM and HP, and we thank them for their generous support.

As usual, the final discussion focused on the location for next year's European User Group Meeting. Most attendees enjoyed the snow and December holiday atmosphere close to Geneva, but the unanimous verdict was to find a warmer location in southern Europe for the next gathering!

Accelrys Hardware and Software Platform Survey - Take Some Time to Offer Your Feedback

We appreciate your input in our hardware and software survey that covers the Pipeline Pilot, Accord, Materials Studio, and Discovery Studio applications. Please take this chance to tell us about what hardware and software platforms you use to run these applications.
More information and start this survey >>>

Short Courses and Webinars

Pipeline Pilot Short Courses:

Accelrys is offering a series of free Web-based short courses covering basic uses of Pipeline Pilot

  • Advanced PilotScript, January 14th, 2009: This course is geared toward users who already have a good handle on the basics of PilotScript and would like to take their expertise to the next level. It covers deep properties (XPath), n-dimensional arrays, global scoping, string token replacement, and more. Register here >>>
  • What's New in 7.5, February 18, 2009: This course covers a sample of the new features in Pipeline Pilot Version 7.5. Register here >>>

Recordings of Recent Webinars and Short Courses

Recordings of past Accelrys Webinars are available in Windows Media Video format upon request. Recent recordings related to Pipeline Pilot include:

  • Increase Research Productivity in Gene Expression Data Mining. Learn how to increase research productivity by using powerful, yet easy-to-use computational tools. These tools help bench scientists and informatics specialists reduce the bottleneck of information flow between experimental results and informatics analysis. Request the Recording >>>
  • Medicinal Chemist's Workbench: A Computational Toolset for the Medicinal Chemist. Learn how you can increase research efficiency with powerful Web-based analysis and data mining tools designed specifically for the Medicinal Chemist. Request the Recording >>>

    Sign up for upcoming Accelrys Webinars and download recent recordings here>>>

Recordings of past Short Courses are available to customers through Accelrys Advantage, which requires a separate login from the Accelrys Community Forums pages. If you do not yet have an Accelrys Advantage ID, Register here >>>

Recent Pipeline Pilot Short Courses include:

Ongoing Training Opportunities

Accelrys offers ongoing training in Pipeline Pilot, Cheminformatics, Life Science, and Materials Science. Training courses help you to:

  • Minimize the time it takes to get up and running with your software purchase
  • Become an expert user of your Accelrys product
  • Start using your new software tools immediately and effectively

We offer a range of training workshop and delivery methods so you can choose what works for you.

Pipeline Pilot course offering details here >>>

Pipeline Pilot Tips and Tricks

Using the Network Tab to Test and Move Protocols

Are you migrating protocols from a development server to a production server? Did your site recently install a software update, making it necessary for you to now migrate your protocols from the older version?

The Network tab (introduced in Pipeline Pilot Client Version 7) supports connecting to multiple protocol databases. Once connected you can:

  • Deploy protocols from test to production servers
  • Conveniently copy files from one server to another by dragging and dropping items between folders
  • Efficiently search across servers. When you enter text in the Search bar at the top of the Explorer window, the databases on all connected servers are included in the search for fast and powerful information retrieval (if the Network tab is the active tab when you enter your search query).
  • Copy files from a 6.x to a 7.x protocol database. (You cannot copy 7.x files to a 6.x server.)
  • Copy files between 7.x protocol databases
  • Designated Client administrators have additional functionality available (consult your system administrator for details)

To view the Network tab in Pipeline Pilot 7.x: Select View > Explorer Windows > Network.

Enable Network Tab

Once the Network tab is active, right-click and select Add Protocol Database. A dialog opens for specifying the server name. (You can also access this dialog from the Tools menu.) In Pipeline Pilot protocol database to add, enter the server name and port, in the format "servername:9944", where "servername" is the name of the Pipeline Pilot server that hosts the protocol database. If you previously connected to the protocol database, the server name should be available from the drop-down list, so you don't have to retype the information.

Once the protocol database is added to your Network tab, its protocols can be read, updated, and saved to the desired location.

When you connect to multiple protocol databases, the Network tab displays all server connections in a folder hierarchy. Each folder label indicates the server name, port, server version, and your current login user name for the connection (you can change server logins at any time). The active server — your default server for saving files — is always displayed at the top of the list.

When opened, a server folder shows the hierarchy of the protocol database on each server ("User Name", Protocols, and Components folders). You can conveniently copy files from one server to another by dragging and dropping items between folders. You can also load and test protocols from other protocol databases on your active server and ensure they work before migration.

Network tab

For further details, go to the SciTegic Help Center on your Pipeline Pilot Client, and from the Users section, open Pipeline Pilot > Protocol Database Management. 

If you have a favorite short tip or trick that you would like to share with others, please post them to our Community Forums site or email Lynn Miller, and they could be featured in a future newsletter.

Protocol of the Month

Looping Example

Here is an example that shows how you can loop a pre-determined number of times over the functionality in a given subprotocol. PilotScript includes FOR and WHILE loops for operating on variables and record properties, but sometimes you need to loop through components and subprotocols.

A subprotocol, named Looper, at the top level of the protocol shown below has a parameter that determines the number of times the loop will be executed. The heart of this example is contained in a Run-To-Completion subprotocol that is called repeatedly until the specified Loop Limit is reached:

RTC loop protocol

Opening the Do the looping subprotocol exposes the core of the example:

Put your function here

After being ungrouped, the data records pass through the components you include here. The Loop Index is incremented; the data records are then regrouped and passed back to the calling subprotocol where the looping continues until the specified number of iterations is reached.

This example, contributed by Noj Malcolm of Accelrys, provides a nice starting point for your looping protocols. The protocol is posted to the Accelrys Community Forums Web site and can be downloaded here >>>

Accelrys Community Forums

Highlights from the Protocol Download Library

The Pipeline Pilot discussion forums and protocol download library are available on the Accelrys Community Web site, where you can share Pipeline Pilot protocols and components. Discussion forums let users communicate about scientific and technical topics with one another, and share your findings with Accelrys scientists. (To view details and download the components and scripts, be sure to first register and become a member.)

Click here to find out how to get automatically notified when new posts are made into the forums. Here are some recent highlights:

An Update from Our Partners

Molecular Discovery Pipeline Pilot Components

By Simon Cross, Molecular Discovery

Building on the success of the GRID software, in recent years Molecular Discovery expanded the application of GRID Molecular Interaction Fields to physicochemical property prediction with MoKa, virtual screening with FLAP, scaffold hopping with SHOP, 3D QSAR with ALMOND, ADME prediction with VolSurf, and Metabolism prediction with MetaSite.

Now, through an interactive partnership with Accelrys, Molecular Discovery is making components available for Pipeline Pilot that enable increased integration between our scientific methods as described on our Web page:


Several components are now available for physicochemical property prediction and compound preparation, ADME profiling and descriptor calculation, as well as site of metabolism prediction and metabolite enumeration. The components currently available are:

  • Calculate pKa (MoKa)
  • Ionize Molecule at pH (MoKa)
  • Enumerate Ionization States  (MoKa)
  • Enumerate Tautomers (MoKa)
  • Predict Site of Metabolism (MetaSite)
  • Enumerate Metabolites (MetaSite)
  • Calculate VolSurf+ Descriptors (VolSurf+)

Example protocols for each component are provided, and these are also documented in our technical notes, covering more complex tasks such as generating an ADME report using the VolSurf+ descriptors and visualizing the site of metabolism for drug-like molecules as predicted by MetaSite, for a wide range of Cytochromes.

Protocol with Results
The example protocol shows how you can use the MetaSite Site of Metabolism Prediction component to highlight the three most likely sites of metabolism with CYP2C9, for the molecule Celecoxib. The benzylic methyl is correctly identified as the most likely site. For further information, contact sales@moldiscovery.com.

If you are an Accelrys ISV partner and would like to be featured in a future newsletter, please contact us.

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Pipeline Pilot 9.0 Webinar Series - Register Today!