(ATS4-DEV10) Creating Pipeline Pilot Components by Wrapping Third-Party Tools

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Although we’d like Pipeline Pilot to be your Enterprise’s complete solution, there are many tools out there that offer functionality not currently available. Sometimes all you need is a one-off call to the tool, but other times it may make sense to “componentize” the tool for your users. This session will demonstrate different methods for wrapping up this functionality into an easy-to-deploy component that your users can then integrate into their protocols. Because different types of tools require different types of wrapping, we will cover different methods, possibly to include wrapping on-server tools, remotely deployed tools, and web service-based tools.

(ATS4-DEV10) Creating Pipeline Pilot
Components by Wrapping Third-
Party Tools
Ian Kerman
Support Scientist, Platform Support
Ian.Kerman@accelrys.com

Agenda

The information on the roadmap and future software development efforts are
intended to outline general product direction and should not be relied on in making
a purchasing decision.

Agenda

• Why you should build a component
• Command Line Interface
• Handling Input and Output Files
• Web Services

Pop Quiz

How do you enable the display of the runtime statistics in the Pro Client?

Ctrl + T (twice)

What is a Component?

• See ATS3-DEV05 for full overview of components
• Encapsulated functionality
• Input and Output ports
• Reusable

Reasons for Building a Component

• Favorite application / script
• Functionality not in Pipeline Pilot
• In-house application

Pipeline Pilot Integration Points
Client Integration
Build clients that connect to Pipeline Pilot
and run protocol services.
Web Browser
Run Protocol .NET Client Java Client
Professional JavaScript Client
Command Line Web Port SOAP Client HTTP Client
Client
Client
.NET Client
JavaScript Client SDK Java Client SDK
SDK
Pipeline Pilot Enterprise Server

Web Apps Web Services API Admin Portal Help Portal
Protocol Runtime Environment

VB Script VB Script
Run SOAP & Telnet / ODBC /
(On (On Java Perl Python .NET SSH / SCP
Program HTTP FTP JDBC
Client) Server)

Java Perl .NET
VB Script Cmd Line
Classes Scripts Classes

Server Integration REST SOAP
Cmd Line
Extend pipelines with new Service Service DBs

components that integrate
your code, data and services.

Running from the Command Line

• Components to use
– Run Program (on server)
– Run Program (on grid)
– Run Command on Remote Host (SSH) / (Telnet)
• Set command line options
• What to do with the results?

Working with Input and Output Files

• Components to use
– Create Tempfiles
– Copy File to Remote Host (SCP) / (FTP)
– Copy File from Remote Host (SCP) / (FTP)
– Various File Readers and Writers

Demo
• Wrapping a Program with Input and
Output Files

Wrapping a Web Service

• Components to use
– HTTP Connector
– SOAP Connector
• Not that different than command line

Summary

• Add additional functionality to Pipeline Pilot by wrapping
a third-party program / service
• Take advantage of functionality already built-in to
Pipeline Pilot
• Other Related Tech Summit Sessions:
– ATS3-DEV04 / ATS2-15 (Introduction to Pipeline Pilot Protocol Development
for Developers)
– ATS3-DEV05 / ATS2-16 (Coding up Pipeline Pilot Components)
• When in doubt, call Support!

An overview of techniques for building Pipeline Pilot protocols, using the languages and paradigms familiar to software developers. Sound engineering principles should be applied to the development of protocols, so this session will discuss concepts like modularity and re-use, minimizing side effects, clarity of interfaces, multi-threading, version control. We will also cover the data pipelining architecture of Pipeline Pilot and how that affects the approach to protocol authoring.

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Pipeline Pilot Chemistry 9.0 is inheriting many new chemical representations from the Accelrys Direct data model. These include the support of the Self Contained Sequence Representation (SCSR) biologics, enhanced Markush structure representations, Markush homology groups, and Non Specific Structures (NONS). Also significantly enhanced is the support for Sgroups, in particular for polymers, mixtures, and formulations. Further, Pipeline Pilot depiction has been upgraded to support these enhancements and the stereochemical perception and ring perception capabilities were improved based on Direct. The major benefit of these changes is that Direct and Pipeline Pilot now use the same data model. Searches carried out in Direct or in Pipeline Pilot will return identical results and both products will deliver identical structural perceptions. This session will give guidance on how these changes will impact your calculators and models and how you can plan for a smooth upgrade.

(ATS6-GS04) Performance Analysis of Accelrys Enterprise Platform 9.0 on IBM’s...

BIOVIA

IBM recently completed a benchmarking study of several key modules of the Accelrys Enterprise Platform (AEP) 9.0, using IBM’s iDataPlex and General Parallel File System (GPFS). The results show that the performance of IO intensive workloads, such as Next Generation Sequencing (NGS), can be improved significantly by using GPFS. NGS workloads can also benefit from better load balancing implemented on AEP 9.0. Best practices for scalable IT solutions will also be discussed.

(ATS6-GS02) Integrating Contur and HEOS

BIOVIA

This document outlines an integration between the Contur and HEOS software. The integration is focused on allowing scientists to record experimental data in Contur and register compounds to HEOS as part of their workflow. It describes the Contur REST API and protocol execution framework that can extract and create Contur content. It also describes the HEOS SOAP API that can extract and create content in HEOS, including registering compounds. Components and protocols are provided that use these APIs to facilitate transferring data directly from Contur experiments to HEOS compound registration, without needing to re-enter information, in order to save time and reduce errors.

(ATS6-GS01) Welcome

BIOVIA

This document contains an agenda for a two-day Accelrys software development event with over 50 registered attendees from partner companies like BT, Discngine, and IBM. On day one, there are sessions on new features and improvements to various Accelrys products, like Direct and PPChem. There are also sessions on deploying products like Discoverant and using collections. Day two focuses on roadmaps for products like LIMS and ELN. Additional sessions discuss maximizing performance, deployment strategies, and integration. The event aims to provide information to help attendees improve their ability to use Accelrys products.

(ATS6-DEV08) Integrating Contur ELN with other systems using a RESTful API

BIOVIA

In order to enable easy integration between Contur ELN and other informatics systems a RESTful API has been developed. Data may be extracted from ELN experiments using GET calls, but external applications can also insert results directly into the ELN record. In particular the API can be used with Accelrys Enterprise Platform to create complex flows for resolving scientific problems. Such protocols may be launched from within the ELN client.

(ATS6-DEV07) Building widgets for ELN home page

BIOVIA

From a developer’s perspective, the Accelrys ELN Home Page is a container of widgets. It manages the layout of widgets, and handles the persistence of their settings. Several widgets are provided with the application: one for creating new experiments, another for tracking work in progress, and an inbox widget for messages sent through the notebook. This out-of-the-box set can be supplemented by building custom widgets. This session will show several custom widgets examples to demonstrate the basic concepts of widget development and the API they implement. We will also discuss best practices, and how to make your widget a good citizen of the Home Page.

(ATS6-DEV06) Using Packages for Protocol, Component, and Application Delivery

BIOVIA

Delivering protocols, components, and applications to users and other developers on an AEP server can be very challenging. Accelrys delivers the majority of its AEP services in the form of packages. This talk will discuss the methods that anyone can use to deliver bundled applications in the form of packages and the benefits of doing so. The discussion will include how to create packages, modifying existing packages, deploying packages to servers, and tools that can be used for ensuring the quality of the packages.

(ATS6-DEV05) Building Interactive Web Applications with the Reporting Collection

BIOVIA

The document discusses building interactive web applications using the Reporting Collection. It describes components like forms, data connectors, interactive elements and AJAX capabilities that allow adding interactivity. The reporting components generate reports in formats like HTML, PDF from data and layouts. Interactive components allow generating full web applications without additional coding. Forms capture user input. The data connector synchronizes selections across visualizations. Protocol links and functions enable drill-down and AJAX functionality. JavaScript attributes and components add custom scripting.

(ATS6-DEV04) Building Web MashUp applications that include Accelrys Applicati...

BIOVIA

One of the biggest challenges in most corporate environments is providing a way for users to access all the data they need, usually stored in multiple disparate locations, from one interface that they are comfortable with. As web applications have become more popular, RESTful APIs have emerged as the preffered web service format in recent years. Many Accelrys applications now provide RESTful APIs that allow developers to build mashup applications. This session will explore some of these APIs and how to use them to build a simple application.

(ATS6-DEV03) Building an Enterprise Web Solution with AEP

BIOVIA

(ATS6-DEV02) Web Application Strategies

BIOVIA

This document discusses different strategies for building web applications using the Accelrys Enterprise Platform (AEP). It outlines three main strategies: Form & Result, Dashboard, and Enterprise Application. Form & Result is best for simple applications that focus on running protocols and displaying results. Dashboard adds interactivity with JavaScript and the Data Connector. Enterprise Application employs a third-party JavaScript library to build a fully customized user interface, separate from AEP. The document provides examples and discusses the technologies involved in each approach. It recommends choosing based on requirements complexity, development time, and skill sets, noting that Form & Result is fastest but least customizable, while Enterprise Application is most complex but powerful.

(ATS6-DEV01) What’s new for Protocol and Component Developers in AEP 9.0

BIOVIA

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(ATS6-GS02) Integrating Contur and HEOS

(ATS6-GS01) Welcome

(ATS6-DEV08) Integrating Contur ELN with other systems using a RESTful API

(ATS6-DEV07) Building widgets for ELN home page

(ATS6-DEV06) Using Packages for Protocol, Component, and Application Delivery

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(ATS6-DEV01) What’s new for Protocol and Component Developers in AEP 9.0

(ATS4-DEV10) Creating Pipeline Pilot Components by Wrapping Third-Party Tools

1. (ATS4-DEV10) Creating Pipeline Pilot Components by Wrapping Third- Party Tools Ian Kerman Support Scientist, Platform Support Ian.Kerman@accelrys.com

2. Agenda The information on the roadmap and future software development efforts are intended to outline general product direction and should not be relied on in making a purchasing decision.

3. Agenda • Why you should build a component • Command Line Interface • Handling Input and Output Files • Web Services

4. Pop Quiz How do you enable the display of the runtime statistics in the Pro Client? Ctrl + T (twice)

5. What is a Component? • See ATS3-DEV05 for full overview of components • Encapsulated functionality • Input and Output ports • Reusable

6. Reasons for Building a Component • Favorite application / script • Functionality not in Pipeline Pilot • In-house application

7. Pipeline Pilot Integration Points Client Integration Build clients that connect to Pipeline Pilot and run protocol services. Web Browser Run Protocol .NET Client Java Client Professional JavaScript Client Command Line Web Port SOAP Client HTTP Client Client Client .NET Client JavaScript Client SDK Java Client SDK SDK Pipeline Pilot Enterprise Server Web Apps Web Services API Admin Portal Help Portal Protocol Runtime Environment VB Script VB Script Run SOAP & Telnet / ODBC / (On (On Java Perl Python .NET SSH / SCP Program HTTP FTP JDBC Client) Server) Java Perl .NET VB Script Cmd Line Classes Scripts Classes Server Integration REST SOAP Cmd Line Extend pipelines with new Service Service DBs components that integrate your code, data and services.

8. Running from the Command Line • Components to use – Run Program (on server) – Run Program (on grid) – Run Command on Remote Host (SSH) / (Telnet) • Set command line options • What to do with the results?

9. Demo • Simple Command Line Example

10. Working with Input and Output Files • Components to use – Create Tempfiles – Copy File to Remote Host (SCP) / (FTP) – Copy File from Remote Host (SCP) / (FTP) – Various File Readers and Writers

11. Demo • Wrapping a Program with Input and Output Files

12. Wrapping a Web Service • Components to use – HTTP Connector – SOAP Connector • Not that different than command line

13. Demo • Integrating with a Web Service

14. Summary • Add additional functionality to Pipeline Pilot by wrapping a third-party program / service • Take advantage of functionality already built-in to Pipeline Pilot • Other Related Tech Summit Sessions: – ATS3-DEV04 / ATS2-15 (Introduction to Pipeline Pilot Protocol Development for Developers) – ATS3-DEV05 / ATS2-16 (Coding up Pipeline Pilot Components) • When in doubt, call Support!

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