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HCBI - High Content Bioinfromatics
HCPD - High Content Public Database
HCDB OpenBIS - Laboratory Information Management System
HCDC - High Content Data Chain
HITS nodes- Hi gh T hroughput S creening nodes
HCIP - High Content Image Processing
3Imax - Interactive Visualization
Interested in professional support for HCDC, HCDB, OpenBIS, HCPD, Image Processing packages?
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HCPD -HCPD is open source web-based biological database for visualisation, management and publication of biological results from experiments including microscope images. Project webpage
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HCDB OpenBis -HCDB in connection with OpenBIS provide an open source web-based LIMS system for experiment tracking, visualisation, image based management of High Content Screening data. Project webpage
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HCDC is a data management, data processing and data visualization software designed for biologists working in the High Content Screening (HCS) / High Throughput Screening (HTS) field. HCDC is an open source platform for a workflow environment of HCS/HTS for data exploration. HCDC is based on and uses many features of the popular KNIME (Konstanz information miner) platform (http://www.knime.org).
Features:
- Management of large scale biological data
- Oriented towards multi-well plates
- Handling of high content screening library
- Investigation of an incoming library
- Supports image based experiments
- Handling of results
- Data mining: statistics, machine learning and statistical pattern recognition
- Data visualization
- Data flow is handled in one comprehensive workflow system
HCDC Introduction
Screening for biological or chemical compounds with a favourable biological effect is at the core of the modern drug discovery process. HCS/HTS is increasingly used for the automated evaluation of spatio-temporally resolved experiments with multiple biochemical and morphological parameters within a cellular system. HCS data include comprehensive information about the bioactive molecules, the targeted genes and images, as well as their extracted data matrices after acquisition. The architecture of HCDC was based mostly on the eclipse plugin framework and Eclipse-KNIME data workflow system. HCDC is a functional node set and works together with the KNIME package and ImageJ. A plug-in for opening and processing proprietary HCS files (library data, numeric results and images) was developed within the KNIME environment. All these open source components (Eclipse environment, KNIME, R-Project, Weka and ImageJ) were chosen for their platform-independence, openness, simplicity, and portability. They are also the fastest pure Java image and data-processing programs currently available. The programs have a built-in command recorder, editor, and Java compiler; therefore, they are easily extensible through custom plug-ins. The pipeline model of HCDC describes the exact behaviour of the workflow when it is executed.
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HITS nodes- Hi gh T hroughput S creening nodes
At current stage the plugin is able to import data (the summary by wells data) from IN Cell Analyser 1000 Excel output, analyse it using CellHTS2, and use KNIME plugins to further analyse the results of the output of the CellHTS2 node. Also created some nodes to visualise the data in a plate-based form heatmaps, denrogram with heatmap, or just a heatmap.
Project (Nodes) webpage |
