OSE

Open Screening Environment is a open source system for management of High Throughput Screening related experiments. OSE stands also for Open Source Environment and will be released under a GNU LGPL licence. 

The project idea is to combine different research tools to enhance significantly management and analysis of data generated during biological experiments. The focus is to incorporate independent, complementary modules from different research fields into a one dynamic, interoperable, practical application to be used by different research actors.

A number of modules have already been implemented but further research is required to combine them into a one system. 

Prof. Werner Dubitzky's group from University of Ulster has joined the consortium. A new partner is offering data management, integration and warehousing, development of distributed data management and computing aspects, and bioinformatics.

Fondazione Politecnico in Milan will be the project coordinator, responsible for preparing a grant proposal. Our target call will be FP7-ICT-5.3 (Virtual Physiology Human).

BioImageXD developers from University of Turku and Jyväskylä in Finland have joined the consortium. They offer their free, open source software for analysis, processing and 3D rendering of multi dimensional microscopy images.

Dynomica Ltd. has joined the consortium. The company has offered an antigenic determinant (epitope) prediction software system to purposes of the OSE. Dynomica delivers technology transfer consultancy services in the field of systems biology, medicine, pharmacy, cybernetics and robotics. The company developed integrated software solutions for pharmaceutical industry (Altana Pharma, Boehringer, Merck, Serono and BASF) in terms of drug design, knowledge-based data storage, and algorithmic solution for automated high-throughput screening of biological data.

Wroclaw Technology Park is willing to offer the laboratory equipment for pursposes of the OSE project. It would be possible to take the advantage of facilities equipped with modern research and scientific equipment: 

• liquid chromatograph HPLC 
• gas chromatograph combined with mass spectrometer 
• spectrophotometer UV-VIS 
• processor tensiometer 
• apparatus for measurements of wetting angle 
• pressure laboratory reactor 
• cooling equipment 
• sterilizing equipment
• other laboratory equipment that is indispensable to run research and development programs in the field of biotechnology, such as an apparatus for polyacrylamide electrophoresis, homogenizer, electronic pH-meter, mini-shaker, magnetic stirrer (mixer), water bath, vacuum concentrator, desktop liofilizer, centrifugal machine, biological incubator, laboratory scales, fraction corrector, equipment for production of ultra-pure water, laboratory glass.

Wroclaw University of Technology will adopt FPGA (Field-Programmable Gate Array) to speed up the image analysis in HCS. There are a number of algorithms, such as image filtering, auto-focus or image segmentation, that can be executed 100x faster when performed on hardware.  

A modular and interactive data analysis framework called KNIME has joined the OSE project. The application was developed by the Chair for Bioinformatics and Information Mining at the University of Konstanz.

Press Release: Start-Up Vratis Seeks Partners to Develop
Open Image-Analysis Screening Platform (Cell-Based Assay News, March 2007)

Following software modules from Max Planck Institute of Cell Biology and Genetics and BIOTEC have joined OSE:

• BioImage.
• TracePilot.
• Cell Detective.