Components, pipelines, protocols and data records

The graphical user interface, called the Pipeline Pilot Professional Client, allows users to drag and drop discrete data processing units called "components". Components can load, filter, join or manipulate data. Components can also perform much more advanced data manipulations, such as building regression models, training neural networks or processing datasets into PDF reports.

Pipeline Pilot implements a Components paradigm. Components are represented as nodes in a workflow. In a mathematical sense, components are modeled as nodes in a directed graph: "pipes" (graph edges) connect components and move data along the from node to node where operations are performed on the data. To help in industry-specific applications, such as Next Generation Sequencing (see High-throughput sequencing (HTS) methods), BIOVIA has developed components that greatly reduce the amount of time users need to do common industry-specific tasks.

Users can choose from components that come pre-installed or create their own components in workflows called "protocols". Protocols are sets of linked components. Protocols can be saved, reused and shared. Users can mix and match components that are provided with the software from BIOVIA with their own custom components. Connections between two components are called "pipes", and are visualized in the software as two components connected by a pipe. End users design their workflows/protocols, then execute them by running the protocol. Data flows from left to right along the pipes.

Modern data analysis and processing can involve a very large number of manipulations and transformations. Pipeline Pilot has the ability to visually condense a lengthy series of data manipulations that involve many components. A workflow of any length can be visually condensed into a component that is used in a high level workflow. This means that a protocol can be saved and used as a component in another protocol. In the terminology used in Pipeline Pilot, protocols that are used as components in other protocols are called "subprotocols". This allows users to add layers of complexity to their data processing and manipulation workflows, then hide that complexity so they can design the workflow at a higher level of abstraction.

Component collections

Pipeline Pilot features a number of add-ons called "collections". Collections are groups of specialized functions like processing genetic information or analyzing polymers offered to end users for an additional licensing fee. Currently, there are a number of these collections.^[8]

Given the number of different add-ons now offered by BIOVIA, Pipeline Pilot's use cases are very broad and difficult to summarize succinctly. The product has been used in:

• Predictive maintenance
• Image analysis, for example the determination of the inhibitory action of a substance on biological processes (IC50) by calculating the dose–response relationship directly from information extracted from high-content screening assay images, associated with dilution in the plate layout and chemistry information about the tested compounds (Imaging, Chemistry, Plate Data Analytics)
• A recommender system for scientific literature based on a Bayesian model built using fingerprint and user's reading list or papers ranking
• Access to experiment methods and results from electronic laboratory notebook or laboratory information management system, with resulting reports for resource capacity planning

PilotScript and custom scripts

As with other ETL and analytics solutions, Pipeline Pilot is often used when one or more large (1TB+) and/or complex datasets are processed. In these situations, end users may want to utilize programming scripts that they have written. Early in its development, Pipeline Pilot created a scripting language called PilotScript that enabled end users to write basic programming scripts that could be incorporated into a Pipeline Pilot protocol. Later releases extended support for a variety of programming languages, including Python, .NET, Matlab, Perl, SQL, Java, VBScript and R.^[9]

The syntax for PilotScript is based on PLSQL. It can be used in components such as the Custom Manipulator (PilotScript) or the Custom Filter (PilotScript). As an example, the following script can be used to add a property named "Hello" to each record passing through a custom scripting component in a Pipeline Pilot protocol. The value of the property is the string "Hello World!".

Hello := "Hello World!";

Currently, the product supports a number of APIs for different programming languages that can be executed without the program's graphical user interface.