Pipette Analysis - Pipelining

Last Updated: Oct 10, 2015 04:48PM PDT

Summary: Pipette Analysis makes it possible to augment, manipulate, merge, filter, and sort data by combining a range of services. The services and features that are available with Pipette Analysis are described below.

Covered Topics

Clicking a link will scroll the page to the relevant section.

Getting Started

ScienceCloud Analysis includes the following features:

  • My Data – A place for saving data to use later. Data is stored on the server so it can be accessed by different computers and devices.
  • Input Data ("The Pipeline") – Data flows from the top-down through a series of services that are designed to generate and manipulate data.
  • Outputs – Provides a way to transfer data into different forms, including reports, files, and other systems.


Pipette Analysis: Pipelining

In the Pipelining section, data flows from the top-down through a series of services. Each service can augment, manipulate, merge, filter, and sort data.

A pipeline can be started in the following ways:

Drag and drop data from My Data into the Input Data area at the top of the pipeline. The data is produced and displayed in the Preview Data pane as illustrated below.


Add a service that generates data by clicking Add a Service and making a selection from the dialog.


If a service requires more than a default configuration to run the first time, you are prompted to provide the additional required settings before it can initialize.


After a service or data is added, a step is displayed in the Pipelining section that reveals the name of the service, the data it produced, and other pertinent information.


The Steps

All steps includes the information described below:

  • Name of the service
  • Number of data records that passed the service
  • Number of data records that failed the service
  • Data properties on the data record



The following features are available to use with each step:

Feature Icon(s) Description
Settings ppt_settings_24.png Change the settings for a service
Toggle Visibility Show Preview Data Pane for a service in the pipeline. (Only visible when pane is collapsed.)  
Remove ppt_delete_24.png Remove the service
Show Passed Data, Show Rejected Data ppt_passed_24.png  ppt_rejected_24.png

Paging controls to navigate the data produced

Left/right arrow buttons ppt_arrow_24_buttons.png
Green grab handle ppt_grab_handle.png Reorder and insert services
Thumbnail of compound or image on the data record (expands when clicked) ppt_thumbnail.png View molecular image in more detail


  • To save the data in any step, click and drag from the data area in the step to My Data.
  • To send the data in any step to an output, click and drag from the data area to the desired Output option.

Built-in Services

The following services are available from the service bar:

Service Icon Description
Add a Service ppt_add_service_button_24.png Adds a new service to the pipeline.
Rename ppt_rename_24.png Renames or removes properties on the data.
Filter ppt_filter_24.png Filters the data based on one or more criteria.
Sort ppt_sort_24.png Sorts the data based on selected properties.


Features that are available for filtering a service are illustrated below.


Features that are available for sorting the data are illustrated below.


Reordering Services

To Do This
Reorder a service Click the green grab handle on the left side of the services bar and move it up and down.
Insert a service between an existing service Click the green grab handle on the left side of the services bar and move it to the desired location.

Clearing the Pipeline

To clear the pipeline and start over, click Clear Pipeline.

Saving the Pipeline

The services in the pipeline and its settings are serialized to a web page URL that you can save as a template and return to later.

  1. Click Save Pipeline.
  2. In the Save Pipeline as a Template dialog, enter the following information:
  • Visibility: Specify who can access your pipeline to share it with other colleagues. The default is Only Me.
  • Name:
  • Help Summary
  • Help Description
  1. Click Save.

My Data

My Data shows data that is uploaded or saved from the steps in the Pipelining section. Data is saved on the server, so it is available on other computers and devices. The data is only visible to the logged in user.


Uploading Data

To upload data, drag and drop files from your computer into the Drop Files area.


Supported file types include:

  • Sketcher – Sends the current data store into the Pipette Sketcher application so structures can be added or updated.
  • Charting – Sends the current data store into the Pipette Analysis Charting application for visual exploration.
  • Pipelining – Sends the current data to Pipette Analysis Pipelining application for modification or saving.
  • Hit List – Saves the data as a hit list for later use in ScienceCloud.
  • 3D Structure View – Displays the current data in a 3D viewer for chemical and biological entities.
  • Compound Profile – Saves the data as a compound profile.
  • Save to Experiment - Saves the current data store into a Contur ELN experiment. 
  • Write to Excel – Write data records to an Excel workbook. Each data record will appear in its own row.
  • Write to PDF – Saves the current data records in a simple tabular PDF file.
  • Write to SD – Writes data to an SD file describing both the chemical structure and properties.


  • For tabular formats such as Excel and PDF, the first row in the document must contain the names of the properties in subsequent rows.
  • Multiple files can be uploaded simultaneously with a separate data store created for each. The default data store names correspond to the file names.
  • Internet Explorer version 9 browsers display the traditional file section dialog (drag and drop is not supported).

Working with Pipelines and Outputs

The Pass or Fail data for any step can be dragged into the My Data section. Each data step includes a "Current" drag icon on the right side for moving the current data record (not all data records) to My Data.

Data can be dragged from My Data to the input data area where it can flow into the first service or into individual outputs.

Managing Data Stores

To Do This Field/Icon
Rename a data store Click on the name of the data store and enter a new name. ppt_new_data_store_24.png
Remove a data store Click Remove, or press DELETE while hovering over a data store. ppt_delete_24.png

Combining and Appending to Data Stores

When data is dragged onto an existing data store, it is added to that data store. This allows data from the Pipelining section to be appended to a data store. It also provides a way to combine two data stores from My Data.


Data can be dragged from steps or My Data into the various outputs. The outputs can send data to other systems and generate files and Pipeline Pilot reports.


Keyboard Shortcuts for Pipette Analysis

Available Chart Types for Pipeline Analysis

Creating Haptic Bonds with Pipette Sketcher

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