September 2008
Accelrys Pipeline Pilot Newsletter
| News and Info | |
| Training and Webinars | |
| Pipeline Pilot Tips and Tricks | |
| Protocol of the Month | |
| Accelrys Community Forums | |
| An Update from Our Partners |
News and Info
SciTegic Enterprise Server 7.5: Call for Beta Testers
As announced on our Community Forum, we are gearing up for the beta release of PPES 7.5. Feature highlights include:
- SharePoint integration
- Grid integration for queuing and load balancing (SGE, PBS/Pro, LSF)
- Proxy server authentication for file readers
- Support for non-specific features in the PPES data model
- New collection: List management and querying
- New collection: Analytical instrumentation
- Updates to existing collections including advanced modeling and plate data analytics
We are looking for customers who can commit to spending at least two days testing the above functionality and offering their feedback. We also need Web Port customers who are able to test and verify their protocols with the 7.5 enhancements.
If you are interested, email Ton van Daelen.
Accelrys European User Group Meeting: Call for Abstracts
The 2008 Accelrys European User Group Meeting will take place on December 9–12 at the Domaine de Divonne Hotel in Divonne, France. The meeting will cover applications of SciTegic Enterprise Server, Pipeline Pilot, and Accord. The hotel is only minutes away from Geneva, Switzerland.
User presentations are an essential part of the success of the User Group Meeting. We invite you to submit a presentation describing your application of SciTegic Enterprise Server, Pipeline Pilot and/or Accord in any of the following areas:
- Cheminformatics applications
- Biological sciences: gene expression, sequence analysis, BioMarker identification, etc
- Screening applications: HTS, HCA
- Image analysis
- Text analytics, including chemical text mining with ChemMining
- Data mining and analysis
- Modeling and simulations
- Reporting and dashboarding
- Web application development and portal deployment (including SharePoint integration)
- Application or data integration
- Enterprise deployment, administration and security
Preliminary title and a short abstract are due by October 1st.
Further details are available here >>>
Training and Webinars
SciTegic Enterprise Server Short Course: RunToCompletion Subprotocols
Accelrys is offering a series of free Web-based short courses covering basic uses of the PPES platform and Pipeline Pilot client.
Please participate in our session on RunToCompletion (RTC) subprotocols on on Oct. 22. RTC subprotocols are an important concept in protocol design and are particularly useful for performing operations on subsets of your data independently. This course explains how and when to use RTC subprotocols, particularly for grouped data, and demonstrates how to use RTC subprotocols in string token replacement for dynamically setting parameter values.
Future sessions will discuss basic protocol building, PilotScript, and reporting. These sessions are open to all Pipeline Pilot users.
Where: Web-based
When: Wednesday October 22, 11:00 AM — Noon PDT. Others to be announced.
Cost: Free
Reserve your Webinar seat here >>>
Imaging Webinar Series Recordings
In September, we hosted a successful series of webinars that showcased our Imaging collection. If you were unable to attend, recordings are available.
Recordings and details on the series are available here >>>
Ongoing Training Opportunities
Accelrys offers ongoing training in Pipeline Pilot, Cheminformatics, Life Science, and Materials Science.
Training courses help you:
- 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
- To quickly access an overview page that summarizes the help text for a component and all parameters, select a component in your protocol and then go to "Help->Help Center" from the main menu (or use the shortcut F1).
- How to add a date to a filename using string replacement tokens:
Setting the Destination parameter for a Delimited Text Writer to include the current date in the filename is simple with string replacement tokens. First set up your date in the desired format, for example, in a Custom Manipulator (PilotScript):
format := DateProposeFormat('2008-01-01');
@todays_date := datecurrent();
DateSetFormat(@todays_date, format);In the Destination parameter for the Delimited Text Writer, use the value of "@todays_date" by entering:
$(UserDir)\your_file_name_$(todays_date).csv
The string replacement token syntax "$(variablename)" is used to substitute in-place for both the default global property @UserDir and the newly defined global property @todays_date. - When do you use a string replacement token "$(variablename)" and when do you use expression syntax?
If you are setting a value for a String Type parameter, type in your desired variable as a string replacement token using the $(variablename) syntax (without extra quoting or punctuation).
If you are setting an Expression Type parameter, or editing an expression in a Custom Manipulator (PilotScript) or Custom Filter (PilotScript) component, refer to the variable as "@variablename" and use all necessary quoting and expression syntax as described in the PilotScript documentation.
Note: String token replacement occurs when the component is first initialized. To have the parameter value change as the protocol executes, place the component inside a RunToCompletion subprotocol to ensure the parameter is updated for each data record or group that enters the subprotocol.
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
Accord Structure Checker Filter
The Accord Structure Checker Filter protocol integrates the Web service provided by Accord Structure Checker to filter your molecules in Pipeline Pilot according to your corporate 2D structure rules.
Accord Structure Checker lets you define a customizable set of cheminformatics rules to check and correct chemical structures based on a set of corporate business rules, attain control over the consistency and quality of your chemical data, and check structures prior to their registration in your corporate database.
The Accord Structure Filter component, which integrates Accord Structure Checker, allows you to test new compounds against your business rules or test old ones against new rules. New properties are added on the fly to show any automated correction performed by Structure Checker, or provide reasons of any check failure.
Molecule |
failure |
correction |
warning |
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Charge separated nitro groups |
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Hidden Stereocentres from CIP calculations |
Convert enol to keto form |
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Hidden Stereocentres from CIP calculations |
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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, making it possible for users to share Pipeline Pilot protocols and components written by both users and Accelrys scientists. Discussion forums let customers communicate about scientific and technical topics with one another and share their findings with Accelrys scientists. To view details and download the components and scripts, you must first register to 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:
- HTML Table Reader Download here >>>
- Equation Plot Download here >>>
- Sudoku collection – R Integration example Download here >>>
- Generate 2D and 3D Histogram components Download it here >>>
- Accord for Excel Writer – updated Download it here >>>
- Tabbed Panel component Download it here >>>
An Update from Our Partners
Here we provide our partners with an opportunity to highlight their products in their own words.
BioSolveIT Announces New Components for FlexX, FTrees, and FlexS
By Dr. Christian Lemmen; CEO, BioSolveIT GmbH
BioSolveIT just released a completely reworked set of modules for access of our technology within the Pipeline Pilot framework. The software is available for Windows and Linux platforms, and other UNIX platforms on request. It does not matter whether you have licenses to run our tools on Windows or Linux, or on which platform your Pipeline Pilot is installed, you will be able to work with our unique solutions. Also, if you have licensed our software for a Linux cluster to enable parallel calculations, you will still be able to take full advantage of this with the new component.
FlexX – Dock Fast, Find Leads
For over a decade satisfied customers have made FlexX their premier choice in structure-based drug design software. Its ability to accurately predict the binding mode of a potential drug c
andidate with a receptor in seconds makes it a must-have if you want to reliably perform ultra-high throughput docking and screening. FlexX is one of the most established protein-ligand docking tools in the literature. Cited hundreds of times, it has proved to be highly successful in numerous drug discovery applications. Several sub-nanomolar inhibitors have been discovered with FlexX and are on the market after having proved their potential as a drug. FlexX poses are scored based on a variety of different scoring functions, and all possible data, incl. details about interactions made available for analysis by the user. Our novel GUI permits the user to setup the protein target for docking in a most user-friendly way. The Pipeline Pilot component, including the target and all settings can be exported from the GUI and by drag & drop imported in Pipeline Pilot to become part of a workflow.
FTrees – Search Fast, Bridge Scaffolds
Feature Trees
(FTrees) is a highly efficient software tool for fuzzy similarity searching facilitating virtual HTS. The ability to detect novel molec
ular scaffolds is one of several features special to FTrees. Its underlying topological descriptor captures connectivity and physico-chemical properties of functional groups. The optimum similarity of two descriptors is defined by an alignment, so an SAR may be readily detected. FTrees have been reported to be highly successful in numerous projects by various customers in (a) lead finding, (b) HTS analysis, and (c) general virtual screening applications. The new components for calculating Feature Tree similarity now maximize the speed of your FTrees workflows by giving you the chance to separate the calculation of descriptors from the similarity and molecular comparison step. The FTrees Fragment Space component is the first and only external interface to the unique FTrees Fragment Space search. The user may input a query file and a target similarity – FTrees-FS then uses the query to search in a Fragment Space and construct new molecules according to similarity with the query. The Pipeline Pilot component is available complete with a pre-defined example Fragment Space comprising 1018 virtual products.
FlexS – Align Compounds, Explore Similarity
FlexS is a world leading technology for shape-based screening of drug-like m
olecules. It provides the prerequisite for 3D QSAR studies and further helps detecting bioactive molecules where the receptor structure is missing. FlexS has proved to be successful in numerous cases. Detect novel active candidates with different scaffolds that exhibit improved properties: FlexS accurately superposes query molecules with potential drug candidates. A reference compound serves as a negative imprint of the active site, with e.g. hydrophilic or hydrophobic regions, hydrogen bond donors, or acceptors, partial charges etc. Like the other BioSolveIT-components for Pipeline Pilot, FlexS seamlessly integrates into the workflow software. 3D-conformations of the aligned compounds as well as similarity scores are added as data fields for further exploitation in subsequent steps.
For more information
and to download the Pipeline Pilot components,
visit the
BioSolveIT Web site.
If you are an Accelrys ISV partner and would like to be featured in future newsletters, please contact us.
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