Title: ChemAxon and an Electronic Research Habitat at the Biopolis Experimental Research Centre
Presenter: Peter Condron
Abstract: The Experimental Therapeutics Centre, the newest A*STAR Research Institute is located at the Biopolis, Singapore’s bio-medical research campus. ETC was formed to 'mine the gap' between basic and applied biomedical research, enhancing high potential projects in order to move them towards commercial development. To manage the various high through-put technology platforms that have been assembled at ETC in support of our mission, we have constructed an 'Electronic Research Habitat', a comprehensive hardware and software infrastructure designed to effectively manage terabyte dataflows in the context of ETC’s knowledge based workplace. We implemented ChemAxon as the Habitat's cheminformatics platform and describe here our on-going development and integration of ChemAxon into our electronic environment.
Post subject: Successful Implementation of the ChemAxon Chemistry Cartridg
Posted: Mon Aug 25, 2008 1:32 pm
Title: Successful Implementation of the ChemAxon Chemistry Cartridge in a Custom Built Screening Management Application: A case Study.
Presenter: Yao Liu
Abstract: To facilitate and manage the growth of our high throughput screening activities at Memorial Sloan Kettering Cancer Center, we have developed and deployed a web based application to register chemical structures for ChemScan or nucleotide sequences for GeneScan, to manage compound plating, to acquire and manage instrument output data, and to summarize and export screening campaigns results in a desired format ready for further evaluation. We will present and discuss the overall flow of our application, in particular functional and robust aspects of the Marvin tools in chemical registration.
Abstract: Palatin has implemented a robust cheminformatics solution based on DeltaSoft’s web applications and ChemAxon’s chemistry tools. Our ChemCart Registration, BioAssay, and Structure-Activity applications are powered by the JChem Cartridge chemistry engine and Marvin tools. With this implementation, researchers can update, search, browse, and share both chemical structures and related test result data (including files and images). This system allows for seamless communication across the scientific groups at Palatin, and will be described in detail during this talk.
Title: Large-Scale Annotation of Small-Molecule Libraries Using Public Databases.
Presenter: Kaisheng Chen
Abstract: The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological data-bases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. We will demonstrate an annotation pipeline based on integrating multiple databases. We will also discuss how annotations can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest and expediting the assay validation process. The automated an-notation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.
Post subject: PubChem data extraction and integration using Instant JChem
Posted: Mon Aug 25, 2008 1:48 pm
Title: PubChem data extraction and integration using Instant JChem
Presenter: Oleg Ursu
Abstract: PubChem is the largest known public repository of biological and chemical data. One of the goals of PubChem is to archive and make the structure-bioactivity data available. The use of various data mining and machine learning tools such as SVMs, Decision Trees, Bayesian models, etc., or advanced searching tools like Markush, custom fingerprints, 2D and 3D similarity, is essential during the post-HTS analyses process. Intellectual property monitoring is another key aspect of PubChem data-mining. Thus, the process of extracting chemical and associated bioassay data from PubChem, processing, arching and storing it in an in-house compatible system is an important task, which can result in increased speed and processing ability, with respect to the above tasks. Once PubChem data is available off-line, data integration with existing in-house HTS or other bioactivity databases becomes an equally important task; the resulting integrated system would enable researchers to query, investigate and profile compounds in a much broader context. We used Instant JChem to create and populate a database containing the MLSMR library and associated bioactivity data from PubChem; further integration with WOMBAT was also performed. The resulting database can also be accessed using the standard JDBC interface with JChem API, and is also amenable to custom data mining tools or search algorithms. Lessons learned from PubChem data mining will be discussed.
Post subject: Developing a Compound Registration System utilizing ChemAxon
Posted: Mon Aug 25, 2008 1:52 pm
Title: Developing a Compound Registration System utilizing ChemAxon's Oracle Cartridge and incorporating Web 2.0 concepts into research informatics
Presenter: Matthew Pustelnik
Abstract: We have committed to web-based technologies to deliver research information systems to scientists. This talk will highlight the journey of developing a compound registration system that includes the following components: single compound registration, importing, compound correction /administration, and simple query tools. In addition, key integration points for compound registration will be presented for streamlined research operations. Finally, in recent years we have seen the development of next generation internet applications and technologies, Web 2.0 i.e. Google maps, AJAX, etc. What can the life science research Informatics community glean from this new trend in high technology?
Post subject: Very large databases and 2D- and 3D-Similarity Searching
Posted: Mon Aug 25, 2008 1:59 pm
Title: Very large databases and 2D- and 3D-Similarity Searching
Presenter: Lutz Weber
Abstract: Using different hardware platforms / operating systems we have explored different possibilities to build and implement JChem based chemical-biological databases with more than 100 million chemical compounds. These datasets are then subject to various 2D and 3D similarity searching methods to provide ideas for novel molecules of biological interest. We will show examples for using these integrated technologies for lead finding.
Post subject: The Pistoia Alliance: An Emerging Cross-pharma Collaboration
Posted: Mon Aug 25, 2008 2:08 pm
Title: The Pistoia Alliance: An Emerging Cross-pharma Collaboration
Presenter: Kevin Hebbel & Matthias Nolte
Abstract: An Open Source initiative known as the Pistoia Partnership has been established to streamline non-competitive elements of the pharmaceutical drug discovery workflow by the specification of common business terms, relationships and processes. Initial focus has been on chemistry, biological screening and sample logistics.
Every pharma company & software vendor is challenged by the technical interconversion, collation and interpretation of drug/agrochemical discovery data, and as such, there is a vast amount of duplication, conversion and testing that could be reduced if a common foundation of data standards, ontologies and web-services could be established within a nonproprietary and non-competitive framework. Such would allow interoperability between a traditionally diverse set of technologies to benefit the healthcare sector.
Through global collaboration, this pragmatic community will derive, instantiate and make available web-services for consumption by Academic institutions, Vendors and Companies under an Open Source framework.
We will describe current progress, learnings and how companies, academics and others can participate in this approach.
Post subject: Toward the Development of an Open Source Cheminformatics Pla
Posted: Mon Aug 25, 2008 2:41 pm
Friday August 8th
Title: Toward the Development of an Open Source Cheminformatics Platform for HTS Data Analysis and Visualization
Presenter: Trung Nguyen
Abstract: The identification of promising chemical series from high through-put screening (HTS) data is an integral part of a therapeutic project, one which ultimately can determine whether the project will be successful. Despite its importance in deciding how to invest resources during the discovery process, analyzing HTS data is often performed in an ad-hoc manner using various combination of commercial and in-house tools. Furthermore, with the proliferation of available HTS data in the public domain (e.g., PubChem), the need for a widely available, easy-to-use tool to analyze and visualize HTS data has never been greater. To this end, we describe NCGC's on-going effort to develop an open cheminformatics platform to address this need. The current platform embodies our collective experience in analyzing and visualizing HTS data across a large number of assays (>200) over the years. The JChem library, known for its maturity and robustness, has been instrumental in allowing us to develop a fairly feature-complete prototype within a short period of time. In this talk, we highlight some key features (e.g., standardization, data visualization, fragment-based automated analysis) of the platform and discuss its future directions.
Post subject: Clustering for the Masses: Pairing JKlustor with Seurat
Posted: Mon Aug 25, 2008 2:52 pm
Title: Clustering for the Masses: Pairing JKlustor with Seurat
Presenter: Derek A. Debe
Abstract: This presentation will discuss the integration of ChemAxon's JKlustor with Synaptic Science's Seurat to provide easy-to-use substructure clustering capabilities to biologists and chemists across a Global Discovery organization. Data formatting, presentation, and analysis examples will be discussed.
Post subject: Instant JChem - latest developments and future plans
Posted: Mon Aug 25, 2008 2:55 pm
Title: Instant JChem - latest developments and future plans
Presenter: Tim Dudgeon
Abstract: Instant JChem is ChemAxon's desktop solution for chemistry. We will present the recent developments which have been primarily in improving the ability to deploy Instant JChem to a large community of users, and for those users to share information. We will also describe the functionality that is currently under development.
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