Webinar: What's New in Pipeline Pilot 8.5 Collection Update 1?

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Collection Update 1 for Pipeline Pilot 8.5 includes key new features for the Pipeline Pilot Client, as well as the Imaging, Next Gen Sequencing, Chemistry, Documents and Text, and Statistics and Modeling collections. An exciting new feature for the Pipeline Pilot Client is Protocol Comparison – the ability to compare protocols, or versions of protocols, allowing you to see and resolve differences between them.

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Webinar: What's New in Pipeline Pilot 8.5 Collection Update 1?

  1. 1. Pipeline Pilot 8.5Collection Update 1Andrew LeBeauTim Moran
  2. 2. Agenda• Pro Client: Protocol Comparison Demo• Documents and Text Collection Documents and Text Collection• Accelrys Query Service• Imaging• NGS• Wrap‐up
  3. 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. 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. 5. Documents and Text Collection• Documents and Text Collection combines: – Text Analytics Collection Text Analytics Collection – ChemMining Collection
  6. 6. Documents and Text Collection• OpenEye Name‐to‐Structure converter is now  included in the collection automatically y – Converts chemical names to structures
  7. 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. 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. 9. Use Cases• Notebook project lead wants to create report  yq y g 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. 10. Substructure Search over ACD
  11. 11. AQS Components
  12. 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. 13. Imaging
  14. 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. 15. Next Generation  Sequencing S i
  16. 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. p g – 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. 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. 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. 19. Additional Resources & Next StepsLearn 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 ComparisonAccelrys Services can help with the upgrade:• Datasheet: Pipeline Pilot Upgrade Assessment Service Datasheet: Pipeline Pilot Upgrade Assessment Service • Contact: consulting@accelrys.comQuestions?Andrew.LeBeau@Accelrys.com Tim.Moran@Accelrys.com

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