ChemAxon Tools for Workflow, Visualization and Analysis

Visual Workflow Creation
Wokflow management frameworks provide an easy-to-use solution to work with work phases in a drag and drop manner.
Chemical Discovery
ChemAxon’s extension nodes offer a rich collection of discovery features for the chemical and pharamceutical industries.
3rd Party Integration
Solutions of the external partners of workflow management frameworks can be easily integrated with the JChem technology.
Powerful visualization
The integrated solution of IJC & Spotfire provides easy data visualization, analysis and exploration.
KNIME, Pipeline Pilot, InforSense and Spotfire
Workflow management systems were designed to easily compose and execute complex computational tasks, such as data mining, data processing or statistical analysis. In order to handle the more specific needs of chemistry informatics within this clean and straightforward framework, ChemAxon technology has been implemented into three major scientific workflow management systems: KNIME, Pipeline Pilot and Inforsense. Thanks for the partnership of TIBCO Spotfire and ChemAxon, new levels of visualization, analysis and exploration tools are available for chemists and for the life science community. The full integration of TIBCO Spotfire’s Analytical Platform with ChemAxon’s Instant JChem allows our users to spot trends in complex datasets through the use of multiple linking visualizations and chemical structure viewing.
Workflow tools: KNIME, Pipeline Pilot, InforSense Visualization and Analysis tool: Spotfire

ChemAxon tools in KNIME Workflow

Infocom’s JChem Extension nodes enable researchers to use ChemAxon tools within KNIME

What is KNIME?

KNIME is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME has been designed for general purposes, thus the basic setup contains features that are common in numerous fields. Moreover, there are plenty of cheminformatics and bioinformatics extensions which are useful especially in early phase drug discovery but can be applied anywhere chemical structure management or analysis is needed.
KNIME Workflow

KNIME portfolio

The base product is KNIME Analytics Platform which is an open-source and free platform for integrated data access, data mining, statistics, visualization, and reporting. KNIME Productivity Extensions provide enhanced workflow and node organizing features . For corporate environments, KNIME Collaborative Extensions come with all KNIME Productivity features plus shared workflow store, shared data space and shared metanodes. Further server-side capabilities are scheduled execution, user access rights, SOA integration, configurable web portal access to workflows and reports through a web browser. For details, check out KNIME Product Matrix. Additionally, with KNIME Big Data Extension or KNIME Cluster Execution one can leverage the advantages of submitting workflows to a compute cluster, distribution of single nodes, splitting of large data sets, and remote execution.

ChemAxon in KNIME

Create your own application

ChemAxon tools can be modularized and have been integrated into various software. However, if a feature is missing or a specific process is needed, generally you need to do programming. KNIME overcomes this by allowing you to use these modules as building blocks for your workflow. Basically you can create your own ChemAxon application.

Combine tools of different vendors easily

KNIME is an open platform, hence there are numerous open-source and commercial extensions provided by different vendors. This variety allows scientist to combine not just our modules but also others’. For example, in a virtual library enumeration, after characterizing structure using ChemAxon tools, you could pipe your selected structures into a docking tool from our partner.

Publish workflows to your colleagues

A commercial addition to KNIME Desktop is KNIME Server where workflows can be centrally accessed even via KNIME Web Portal. It allows you to easily set up an interface for a web browser to input necessary data and then receive the output in the desired format. This is enhanced with our structure sketchers Marvin Applet and Marvin for JavaScript.

ChemAxon tools integrated into Pipeline Pilot Workflow

The free Component Collection provides access to most ChemAxon tools, toolkits and functionalities

What is Pipeline Pilot?

Pipeline Pilot, Accelrys’ scientific informatics platform, was designed by scientists for scientists. It aggregates and provides immediate access to the volumes of disparate research data locked in silos, automates the scientific analysis of that data and enables researchers to rapidly explore, visualize and report research results. Pipeline Pilot and its integrated set of applications address the modeling and simulation, informatics and scientific businesses intelligence needs of research and development organizations. A key strength of the platform is the ability to manage and synthesize scientific information in a way that allows you to rapidly adjust workflows, optimize research cycles and respond to changing market conditions. ChemAxon is an Independent Software Vendor (ISV) Partner of Accelrys. The Component Collection provides access to a number of ChemAxon tools from Pipeline Pilot. The collection is free of charge and it is fully developed and supported by ChemAxon.

Available functionalities

Most ChemAxon tools are available in Pipeline Pilot. Some of the most important integrated functionalities:
  • MarvinSketch Applet and Marvin JS chemical editors
  • Standardizer, a canonicalization tool
  • Reactor, a chemically intelligent virtual reaction tool
  • JChem Base, chemical database manager and searcher
  • JChem Oracle Cartridge search, JChem PostgreSQL Cartridge search
  • JChem for Excel: import and export of “live” structures
  • Structure Checker, a batch toll for checking and fixing structures
  • Markush enumeration
  • Name to Structure and Structure to Name conversions
  • Document to Structure, extracting chemical information from documents
  • and a number of property predictor and calculator tools like logP, logD, pKa, tautomerization and conformer generation tools.

ChemAxon integrated into InforSense Workflow

IDBS’ InforSense provides sophisticated analytics solutions for life science, healthcare and even finance

What is InforSense?

The InforSense Suite is a next generation, Business Intelligence (BI) solution that enables organizations to create analytical applications based on any data source, in any format, however complex. With the InforSense Suite, you can understand and navigate through large amounts of data quickly and combine data from any source inside or outside an organization. Analysts can build visual applications by combining data from data warehouses, marts, Excel© and web services, applying predictive and statistical modelling techniques and deploying to end users via VisualSense interactive web pages.

ChemAxon integrated in InforSense

ChemAxon provides the rich chemistry functionality in InforSense to integrate it with other data, to perform rich analytics and to provide a web based application platform. Among others, InforSense uses JChem Cartride, ChemAxon’s Oracle integration, and structure rendering and sketching tools. For the workflow integration a whole host of nodes are exposing the numerous chemical capabilities offered by ChemAxon. Among others the Markush enumeration, the reaction based enumeration, the fragmentation and several property prediction tools can be used by building a workflow in InforSense.

Spotfire Professional integration with Instant JChem

Integration with Spotfire offers powerful data visualization and statistical analysis

Spotfire and Instant JChem

The integration of Instant JChem with TIBCO’s Spotfire Professional results in a powerful combination of the two software allowing researchers to speed up the analysis of large chemical libraries. With Instant JChem one can create and manage large amounts of chemical and non-chemical data, which then can be visualized in Spotfire while building high quality reports.

Personal Server

Instant JChem’s key new feature, the personal server, plays a important role in setting up an interactive communication route between clients using open data communication protocol (OData). The personal server can be started from Instant JChem directly, and as an active interface it manages the data transfer in an interactive fashion. This process makes sharing structural and non-structural information with Spotfire seamless.
Once the personal server has been started, the selected data tree, including all the information from the fields displayed in Instant JChem, can be imported into Spotfire’s initial visualization page using the import wizard.

Spotfire tools

For data analysis Spotfire offers an arsenal of visualization tools (e.g. table, scatter plots, 3D scatter plots, pie chart, combination chart, heat map, etc.), quick and flexible filtering options as well as statistical analysis tools (e.g. K-means clustering, hierarchical clustering, data relationship, etc.). With the help of these functions large chemical libraries, managed by Instant JChem, can quickly be analyzed, reduced and fed back to Instant JChem for further chemical processing and storing. Furthermore, the analysis results can be exported into Microsoft PowerPoint as well as into pdf.

Articles in the library

Farewell, PipelinePilot : Migrating the Exquiron cheminformatics platform to…

May 21, 2014 - Presentation
As a service provider for hit identification, Exquiron needs to offer a state-of-the-art cheminformatics, data analysis and reporting platform to their clients. For historical reasons, th…

Using Knime to provide desktop tools to chemists

May 18, 2011 - Presentation
This presentation will show how at Evotec we are using Knime as a desktop tool to help chemists process their data. The talk will provide illustrations of extracting reports and data from…
Author: ()

A Chemical Library Design Tool

Sep 25, 2013 - Presentation
As the usage of parallel synthesis in early stage drug discovery has evolved, medicinal chemists have demanded ever more sophisticated tools for the design and virtual screening of potent…

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