Pipeline Pilot

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Pipeline Pilot
Developer(s) Accelrys
Initial release 1999 (1999)
Stable release
8.5 CU3 / May 2012 (2012-05)
Written in C++
Operating system Windows and Linux
Type Visual and dataflow programming language
License Proprietary
Website accelrys.com/products/collaborative-science/biovia-pipeline-pilot/

Pipeline Pilot is the authoring tool for the Accelrys Enterprise Platform. It is a scientific visual and dataflow programming language, used in various scientific domains, such as cheminformatics and QSAR,[1][2][3] Next Generation Sequencing,[4] image analysis,[5][6] text analytics.[7]


Originally created in 1999 by SciTegic, Pipeline Pilot is now developed by BIOVIA.

Pipeline Pilot was used at first in the pharmaceutical and biotechnology industries and by academics and government agencies. Then other industries started to adopt it, but always in science driven sectors such as Chemicals, Energy, Consumer Packaged Goods, Aerospace, Automotive, Electronics.

Basic introduction[edit]

Pipeline Pilot includes contextual help that is searchable and interactive; users should refer to it. Reviewing the examples and the documentation is the best place to start.

Components, pipelines, protocols and data records[edit]

The graphical user interface, called the Pipeline Pilot Professional Client, allows users to drag and drop components, connect them together in pipelines, and save the application developed as a protocol.

Think of the components as nodes of a directed graph: each one has a specific task on the data. Users have the choice to use predefined components, or to develop their own: components can be chosen from the library, configured, redesigned, or even created from scratch and documented at will. When a new component is made by collapsing a few components together, it is called a subprotocol.

In a typical protocol, the reading components (on the left) send the data records through the pipelines (to the right) for further process, analysis, and reporting.

Component Collections[edit]

The components are organised by science in collections.[8]

Group Domain Component Collection
Science specific Chemistry Chemistry
Biology Gene Expression
Sequence Analysis
Mass Spectrometry for Proteomics
Next Generation Sequencing
Materials Modeling & Simulation Materials Studio
Polymer Properties (Synthia)
Generic Reporting & Visualization Reporting
Database & Application Integration Integration
Imaging Imaging
Analysis & Statistics Data Modeling
Advanced Data Modeling
R Statistics
Document Search & Analysis Chemical Text Mining
Text Analytics
Laboratory Plate Data Analytics
Analytical Instrumentation

The most interesting protocols are often those mixing collections:


Many custom script components are available in Pipeline Pilot, allowing experts to include their code directly into the pipelines and maintain a library of components based on their preferred language, such as Perl, Java, VBScript, .NET, JavaScript, Python, Matlab, etc.[9]

Another option is to use PilotScript, the internal scripting language of Pipeline Pilot, which syntax is based on PLSQL. It can be used in components such as the Custom Manipulator (PilotScript) or the Custom Filter (PilotScript).

Hello := "Hello World!";

This script above will add, to each data record passing through its component, a property named Hello containing the string "Hello World!".


The community forum allows users to share ideas, components, and protocols.

Companies such as ACD/Labs,[10] BioSolveIT,[11] ChemAxon,[12] Cosmologic,[13] Cresset,[14] Linguamatics,[15] Molecular Discovery,[16] and Molecular Networks,[17] partner with Accelrys[18] to develop and provide component collections to interface with their technologies, allowing automation from within Pipeline Pilot.

Oxford Nanopore Technologies offers Pipeline Pilot NGS collection as the preferred and supported solution for secondary and higher level data analysis in their GridION system.[19][20]

Scitegrity produces Controlled Substances SquaredTM, an application built on Pipeline Pilot for the detection and management of controlled substances.


  1. ^ Hassan, Moises; Brown, Robert D.; Varma-O'Brien, Shikha; Rogers, David (2007). "Cheminformatics Analysis and Learning in a Data Pipelining Environment". ChemInform. 38 (12). doi:10.1002/chin.200712278. ISSN 0931-7597. 
  2. ^ Hu, Ye; Lounkine, Eugen; Bajorath, Jürgen (2009). "Improving the Search Performance of Extended Connectivity Fingerprints through Activity-Oriented Feature Filtering and Application of a Bit-Density-Dependent Similarity Function". ChemMedChem. 4 (4): 540–548. doi:10.1002/cmdc.200800408. ISSN 1860-7179. 
  3. ^ Warr, Wendy A. (2012). "Scientific workflow systems: Pipeline Pilot and KNIME". Journal of Computer-Aided Molecular Design. 26 (7): 801–804. doi:10.1007/s10822-012-9577-7. ISSN 0920-654X. PMC 3414708Freely accessible. PMID 22644661. 
  4. ^ "Accelrys Enters Next Generation Sequencing Market with NGS Collection for Pipeline Pilot". Business Wire. Retrieved 15 February 2013. 
  5. ^ Rabal, Obdulia; Link, Wolfgang; G. Serelde, Beatriz; Bischoff, James R.; Oyarzabal, Julen (2010). "An integrated one-step system to extract, analyze and annotate all relevant information from image-based cell screening of chemical libraries". Molecular BioSystems. 6 (4): 711–20. doi:10.1039/b919830j. ISSN 1742-206X. PMID 20237649. 
  6. ^ Paveley, Ross A.; Mansour, Nuha R.; Hallyburton, Irene; Bleicher, Leo S.; Benn, Alex E.; Mikic, Ivana; Guidi, Alessandra; Gilbert, Ian H.; Hopkins, Andrew L.; Bickle, Quentin D. (2012). "Whole Organism High-Content Screening by Label-Free, Image-Based Bayesian Classification for Parasitic Diseases". PLoS Neglected Tropical Diseases. 6 (7): e1762. doi:10.1371/journal.pntd.0001762. ISSN 1935-2735. 
  7. ^ Vellay, SG; Latimer, NE; Paillard, G (2009). "Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed". Infectious disorders drug targets. 9 (3): 366–74. doi:10.2174/1871526510909030366. PMID 19519489. 
  8. ^ "Pipeline Pilot Component Collections". Accelrys. Archived from the original on January 15, 2013. Retrieved 26 January 2013. 
  9. ^ "Pipeline Pilot Integration Component Collection Datasheet" (PDF). Accelrys. Retrieved 8 February 2013. 
  10. ^ "ACD/Labs Component Collection for Accelrys Pipeline Pilot". ACD/Labs. Retrieved 26 January 2013. 
  11. ^ "Pipeline Pilot Interfaces". BioSolveIT. Retrieved 26 January 2013. 
  12. ^ "Pipeline Pilot Components". ChemAxon. Retrieved 26 January 2013. 
  13. ^ "Integration of COSMOfrag and COSMOsim in Pipeline Pilot". Cosmologic. Retrieved 26 January 2013. [dead link]
  14. ^ "Pipeline Pilot Protocols". Cresset. Archived from the original on May 21, 2012. Retrieved 12 February 2013. 
  15. ^ "I2E Pipeline Pilot Integration". Linguamatics. Retrieved 26 January 2013. 
  16. ^ Cross, Simon; Sforna, Gianluca; Vianello, Riccardo. "Technical Note: Integration of MoKa, VolSurf+, and MetaSite into Pipeline Pilot" (PDF). Molecular Discovery. Retrieved 26 January 2013. 
  17. ^ "Components for Pipeline Pilot". Molecular Networks. Retrieved 26 January 2013. 
  18. ^ "Accelrys Partners". Accelrys. Retrieved 26 January 2013. 
  19. ^ "Oxford Nanopore selects Accelrys Pipeline Pilot NGS Collection as preferred analysis platform". News-Medical.net. 16 March 2011. Retrieved 15 February 2013. 
  20. ^ "DNA sequencing informatics, GridION™ Nodes". Oxford Nanopore Technologies. Retrieved 26 January 2013.