The document discusses new features in Pipeline Pilot 8.5 Collection Update 1. It introduces protocol comparison capabilities, updates to the documents and text collection including new visualization and search components. The Accelrys Query Service allows unified searching across data sources. Imaging components now include curvature analysis and color deconvolution. The NGS collection includes performance updates and new viewers. Additional resources and services are available to assist with the upgrade.

1. Pipeline Pilot 8.5
Collection Update 1
Andrew LeBeau
Tim Moran

2. Agenda
• Pro Client: Protocol Comparison Demo
• Documents and Text Collection
Documents and Text Collection
• Accelrys Query Service
• Imaging
• NGS
• Wrap‐up

3. Pro Client: Protocol Comparison
• Allows protocol authors to compare two
p
versions of a protocol
• Use Protocol Comparison to...
– review current changes as you edit a protocol
review current changes as you edit a protocol
– check changes against a previous protocol version
– compare protocols across databases
compare protocols across databases
– compare protocol files

4. Protocol Comparison Demo
• Demo movie available
• Note: Pro Client 8.5 will work with CU1‐
upgraded server (Pro Client does not need to be
upgraded server (Pro Client does not need to be
upgraded)

5. Documents and Text Collection
• Documents and Text Collection combines:
– Text Analytics Collection
Text Analytics Collection
– ChemMining Collection

6. Documents and Text Collection
• OpenEye Name‐to‐Structure converter is now
included in the collection automatically
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– Converts chemical names to structures

7. Documents and Text Collection
• New detailed “example” protocols, covering
– website crawling
– integrated structure search of documents
– PubMed document analysis (aka Biblio Platform)
See webinar from June 2011
• A new Tag Cloud visualization component
• A new Search Bing component
– Replaces Yahoo Search
• A new component for extracting content from
tables in html documents ‐ E t t T bl D t f
t bl i ht l d t Extract Table Data from
HTML
• ChemMining components updated to use the latest
version of Accelrys Direct
version of Accelrys Direct
– Simplifies building chemically‐intelligent document
searching

8. Accelrys Query Services (Prototypes)
• Components for searching across disparate data
sources
• Leverages Isentris IDS technology
• Benefits
– Unified query engine for Accelrys platform
– Rapid application building
d l b ld
– Data federation
– Data abstraction

9. Use Cases
• Notebook project lead wants to create report
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by querying across Notebook documents and
chemistry and biology databases
• Notebook administrator wants to report on
Notebook administrator wants to report on
Notebook usage patterns and post on
SharePoint
• Query available chemicals in corporate DB and
ACD; deploy through Notebook, DS, and PP
ACD; deploy through Notebook DS and PP

10. Substructure Search over ACD

11. AQS Components

12. Status and Next Steps
• Released as prototype in CU1
– Allow user input before finalizing “production”
Allow user input before finalizing production
versions
• Most useful to users with data integration
Most useful to users with data integration
needs (Notebook and/or PP)

13. Imaging

14. Imaging (8.5 CU1)
• Find Curvature component calculates the curvature of all pixels on
lines or region boundaries. The output image at each location
contains the curvature value of the corresponding pixel in the input
contains the curvature value of the corresponding pixel in the input
image. This component has a great deal of utility across domains and
crystal detection, material science and life science applications.
• C l D
Color Deconvolution component separates a color image into a set of
l ti t t l i i t t f
monochromatic images. For histological images like H&E stained
tissue, it can be helpful to use these separated images as input for
segmentation or learning component.
i l i

15. Next Generation
Sequencing
S i

16. NGS (8.5 CU1)
• Updates and enhancements to numerous third party tools used in
the collection (too numerous to list) (8.5 CU1)
• New third party viewers have been added including the Integrative
New third party viewers have been added including the Integrative
Genomics Viewer (IGV) and Tablet components
• Numerous performance improvements
– Repository‐based components now share an in‐memory copy of
the repository.xml contents, greatly improving performance for
repositories with large numbers of entities.
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– Improved Add Features to Repository and Region Generator
component performance when there are thousands of contigs ‐
Depth calculations can now go over 8000x.
Depth calculations can now go over 8000x
– FASTQ Splitter and FASTQ Splitter for Parallel Processing
components were included. These components assist with load‐
balancing unmapped data files when using compute node clusters
b l i d d t fil h i t d l t

17. NGS (8.5 CU1)
• Numerous enhancements in
support of repository enterprise
readiness.
readiness
– Use Existing Files component
to use existing reference
sequence, mapping indices,
i i di
mapped read, and feature
files can be used to create or
modify a repository,
dif i
– The repository XML file now uses relative paths for files that are in
the repository directory, which allows for easy relocation of
th it di t hi h ll f l ti f
repository directories .
– The initial display names of the reference sequences are now
being used as internal reference IDs so that repository files can be
b i d i t l f ID th t it fil b
used directly by third‐party programs .

18. NGS (8.5 CU1)
• Protocol Example Updates
– Contrast Two Mapping Programs: Added histogram of Bowtie and
BWA mismatches.
BWA mismatches
– Strand‐specific Sequencing: Added strand‐specific RNA‐Seq
examples.
– List NGS Third‐party Software Tools: Provides a summary table of
third‐party tools used in the collection, including version numbers
and release dates. demo
– Viral Population Analysis: Added Viral Population Analysis
example demo
– Trim reads based on quality score
– Calculate the frequency of each base across reads
– Correlate ≥2 mutations on a single read
Correlate ≥2 mutations on a single read

19. Additional Resources & Next Steps
Learn more about the latest release:
• Jan 10: What’s New in the NGS Collection for Pipeline Pilot?
• Jan 24: Best Practices in Pipeline Pilot Protocol Development & Deployment
Jan 24: Best Practices in Pipeline Pilot Protocol Development & Deployment
• Datasheet: What’s New in Pipeline Pilot 8.5 (CU1)
• Video: Protocol Comparison
Accelrys Services can help with the upgrade:
• Datasheet: Pipeline Pilot Upgrade Assessment Service
Datasheet: Pipeline Pilot Upgrade Assessment Service
• Contact: consulting@accelrys.com
Questions?
Andrew.LeBeau@Accelrys.com Tim.Moran@Accelrys.com