Scientific computing specialists at Genedata and ChemAxon have successfully integrated the chemical intelligence functionality of MarvinView with Hit Profiler, Genedata’s newly-released software solution for the prioritisation of hits to leads.
MarvinView is a platform-independent interactive visualisation tool for viewing and managing chemical structure information and is aimed at chemists or other scientists who want to draw or view chemical structures.
It can display a 2D or 3D molecule, or many molecules in a table. A molecule table may also contain GUI components such as text labels, buttons and checkboxes. Checkboxes and buttons can trigger JavaScript calls from the Java applet, buttons may also trigger CGI script loading. The applet has a pop-up menu, but the user can also view a molecule in a separate window that has an ordinary menu bar. A viewer window can be easily transformed into a MarvinSketch window, so the user can even edit the molecule(s).
Marvin can be equipped with custom chemical calculation tools by the integrated plugin services. Plugins are loaded dynamically upon request, saving download time and system resources. ChemAxon also offers a range of calculator plugins for MarvinView.
For its part, created in collaboration with industry and in particular with the screening expertise at Altana Pharma, Hit Profiler facilitates the structured compilation of biological and chemical data on hit compounds. The system features compound visualisation, annotation, filtering and reporting, for the benefit of efficient lead identification in drug discovery projects.
Hit Profiler displays HTS and HCS data in a compound-centric, interactive table environment. Semantic integration technologies are exploited, for example in rendering SMILES information as 2D structures, or in depicting multiple concentration data as dose response curves. Other advantages include the comparison across assays and the integration of annotations and compound properties.
Utilising databases and other available sources within the company, Hit Profiler provides an easily accessible, yet customised corporate information platform. As data are seamlessly transferred and can be stored back in corporate systems, no information gets lost in the process.
The success of the integration rests on the fact that both companies use the same advanced software technologies, including Java 5’s generics and concurrency APIs. Proven technology standards such as these have been designed and developed to make integration between systems as seamless as possible.
Seamless integration ultimately brings benefit to the scientific end-user. It means that Genedata and ChemAxon can evolve their solutions independently, yet maintain interoperability that is robust and intuitive.
Other collaborators
Swizerland-based Genedata was founded in 1997, while Hungary-based ChemAxon was founded a year later. Now among the longest-standing bioinformatics providers in the world, this is new announcement is the closest collaboration so far between the two companies. However, they continue with their separate business collaborations too.
For example, ChemAxon has just announced that it is to enter into partnership with US company Core Informatics to provide its state-of-the-art chemo informatics capabilities within the CoreLIMS solution.
Core Informatics is a Connecticut-based software company focused on delivering state-of-the-art, fully customised laboratory information management systems (LIMS) to customers in a variety of industries. Its signature product, Core LIMS, is a web-based LIMS that features a component-based architecture, which provides its clients the freedom to pick and choose only the functionality relevant to their specific research.
Core LIMS is a highly configurable LIMS that enables scientists to track any aspect of a drug candidate’s life from sample registration to IND filing. Each installation is customised to reflect the unique needs and requirements of the client, offering rich opportunities for integration.
The addition of the ChemAxon toolkits brings chemical awareness to the Core LIMS suite and powers chemistry functionalities such as chemical registration, chemical inventory, substructure and similarity searches, SAR table generation and calculated properties.
Genedata has also announced a new collaboration, with Wyeth Pharma, to support the computational requirements of the company’s drug discovery efforts in Cambridge, Massachusetts, US.
Wyeth’s installation of Genedata Expressionist and Phylosopher will provide a highly automated processing and annotation platform capable of analysing tens of thousands of microarrays per month.
Genedata’s solution has been integrated with Wyeth’s existing informatics infrastructure, including databases of experimental protocol information, to create powerful new analysis portals for complex omics data. These portals enable researchers to navigate large result repositories and drill down to obtain data quality and experimental design information – which is valuable when information must be shared among researchers with different areas of technical expertise.
Wyeth’s scientific business rules have also been integrated with Genedata’s automated workflows for processing and analysing gene expression data. So far, many such business rules have been incorporated into Expressionist’s workflow environment.
These rules are applied in the context of data quality issues. They extend to statistical criteria applied to results, such as the statistical significance level used to define biomarkers. This increases the repeatability of research findings obtained in a high-throughput context.
In addition, Genedata has also just announced its participation in BaSysBio, an integrated systems biology project involving 15 research organisations from nine European countries.
BaSysBio (Bacillus Systems Biology) will study the global regulation of gene transcription in the model bacterium Bacillus subtilis. This bacterium has significant economic potential as a producer of enzymes and metabolites, and is used in a wide range of industries, from pharmaceutical and chemical manufacturers to the agro and food sectors. Two disease-causing bacteria, Bacillus anthracis, responsible for anthrax, and Staphylococcus aureus, responsible for secondary infections, are objects of research as well.
The project will provide new insight into the fundamental principles that control cellular processes. Subsequently, the initiative will contribute to the identification of new biomarkers, and innovative therapeutic targets for anti-bacterial drugs.
Genedata Phylosopher has been chosen as the central management and infrastructure solution for sharing and interpreting the experimental data generated within BaSysBio (Fig.1).
The project will adapt an array of
high-throughput genomics technologies, including transcriptomics, proteomics, metabolomics, fluxomics and cell reporter assays. As quantitative molecular profiling information is key for the development of predictive mathematical models, the Genedata Phylosopher tools will be used for integrating the BaSysBio data and interpreting it in its pathway context.
“Thanks to Genedata we are able to pool the various partners’ genomics and systems biology expertise across the entire network,” BaSysBio project coordinator Philippe Noirot said.
