ChemAxon workflow tools
KNIME, Pipeline Pilot and InforSense nodes
Workflow tools: KNIME, Pipeline Pilot, InforSense
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.
ChemAxon tools in KNIME Workflow
Infocom’s JChem Extension nodes enable researchers to use ChemAxon tools within KNIME
What is KNIME?
KNIME GmbH provides commercial enterprise solutions and services around the open-source platform KNIME. The modular data exploration platform enables the user to visually create data flows or pipelines, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for ChemAxon’s tools too due to its open and modular API.
Related links
Where ChemAxon and KNIME meet
JChem Extensions
The Japanese Infocom Corporation released its JChem Extensions nodes in 2008. This is a package program for the KNIME platform, which covers over 90% of ChemAxon’s cheminformatics functionality, from basic processes such as managing and searching chemical structures to special functions such as chemical canonicalization, clustering and enumeration.
Free Marvin nodes in KNIME
By using JChem Extensions users can easily build their own workflows and data mining applications to work with chemical data. In accordance with ChemAxon’s practice Infocom offers the Marvin Suite nodes for free.
KNIME Enterprise Server
KNIME Enterprise Server provides all the functionality needed to deploy KNIME in a corporate environment. In addition to workflow sharing through a central workflow repository, it delivers full user access control as well as manual and scheduled workflow execution. The server can also be integrated into an existing SOA architecture by providing access to workflows via web services.
KNIME Cluster Execution
KNIME Cluster Execution allows using KNIME nodes or complete workflows in a compute cluster environment. This solution is ideal to parallelize calculation intensive workflows. All KNIME Partner Extensions including the ChemAxon / Infocom extensions are supported and can now be used in a cluster environment.
KNIME Report Designer
The goal of this tool is to provide advanced reporting functionality for KNIME. It allows KNIME workflows to be used in reports. Templates can be designed within a dedicated KNIME perspective.
KNIME Report Server
This is an extension to KNIME Report Designer and KNIME Server products. Templates created with the free designer can be uploaded to a central server. You can access and execute these templates via your browser.
KNIME Support and Maintenance Subscriptions
KNIME.com offers a support and maintenance subscription for reliable, stable and well-tested KNIME versions of KNIME Desktop and KNIME Report Designer.
ChemAxon tools integrated into Pipeline Pilot Workflow
The free Component Collection provides access to 16 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
Currently around 16 different ChemAxon tools, toolkits and functionalities are available in Pipeline Pilot. Among the most important components the following functionalities can be listed:
- Marvin Suite, ChemAxon’s chemical drawing and visualization tools
- Standardizer, a canonicalization tool
- Reactor, a chemically intelligent virtual reaction tool
- JChem Base, chemical database manager and searcher
- Markush enumeration
- Name to Structure and Structure to Name, ChemAxon’s naming tools
- and a number of property predictor and calculator tools like logP, logD, pKa, tautomerization and conformer generation tools.
Related links
- Pipeline Pilot webpage
- Download Pipeline Pilot Components
- Pipeline Pilot integration presentation (2010 Dec)
- Pipeline Pilot forum topic
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.
