EUGM 2013 - Eufrozina Hoffmann (ChemAxon): Marvin extending the scope of usability
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The Marvin package consists of applications for drawing and visualization of chemical structures and reactions. We will focus on the main features of MarvinSketch version 6.0 giving special attention to structure drawing, displaying and usability improvements. To finish we will be looking at the new member of the package: Marvin for JavaScript, which we will introduce as an easily integrable web component for 2D sketching and basic rendering.
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EUGM 2013 - Sergio H. Rotstein (Pfizer): What about the “big guys”? The emerg...
The recent increase in utilization of complex macromolecules such as Antibody-Drug Conjugates (ADCs) as therapeutic agents has revealed a substantial gap in the biopharmaceutical industry’s portfolio of informatics tools and methods, most of which were designed to work primarily with either small molecules or unmodified and unconjugated amino acid and nucleotide sequences. The Hierarchical Editing Language for Macromolecules (HELM), along with a software toolkit that leverages that language was developed by Pfizer researchers to address this gap (see J. Chem. Inf. Model 2012, 52, 2796-2806). HELM and related technologies such as SCSR (Self-Contained Sequence Representation, see: JChem Inf Model. 2011 51, 2186-208.), enable the representation of unnatural, conjugated or otherwise modified building blocks in biopolymers such as oligonucleotides, peptides, proteins and ADCs. HELM is being released into the Open Source and the Pistoia Alliance has initiated a project that has the goals of (1) facilitating this release, (2) adopting HELM as an industry standard for the manipulation and exchange of complex biomolecule data, and (3) setting up the organizational infrastructure to govern the future development of the standard. Given the recent FDA approval of the Antibody Drug Conjugate Kadcyla (Ado-Trastuzumab Emtansine) for Her2-Positive Metastatic Breast Cancer, one can reasonably assume that standards such as HELM and associated software tools will play an increasingly prominent role as part of the modern drug discovery informatics arsenal.
EUGM 2013 - Steve Hajkowski (Thomson Reuters): Patent analytics - what can Ma...
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EUGM 2013 - Peter Englert, Peter Kovacs (ChemAxon) - The Next Generation of M...
This document summarizes improvements to ChemAxon's Maximum Common Substructure (MCS) search module. The new module has improved accuracy and run time, reduced memory usage, and reduced fragmentation compared to previous versions. Extensive tests show major improvements in these areas, including faster running times (e.g. from 20 minutes to 2.5 seconds on difficult structures), fewer fragments identified, and identification of more common bonds. Examples are provided to illustrate the improvements.
EUGM 2013 - Michael Dippolito (Deltasoft): Great Migrations! – Approaches to ...
Many research teams are facing chemistry data migrations in the coming months due to legacy system retirements and/or the opportunity to move to new informatics platforms. Some approaches, case studies, and experiences will be shared on migrating chemistry data between vendor technologies, with a focus on moving to ChemAxon cartridge technology.
EUGM 2013 - Christopher Southan (TW2Informatics): Chemicalize.org, SureChemOp...
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EUGM 2013 - Björn Windshügel (European ScreeningPort): Chemoinformatic tools ...
In the drug discovery process high-throughput screening is often applied as initial procedure for the identification of hit molecules against a certain target, e.g. an enzyme or G protein-coupled receptor. In addition, virtual screening campaigns utilizing commercially available compound libraries are often performed that allow the search for potential hit molecules within a much larger chemical space as usually accessible within the in-house compound libraries. Chemoinformatic tools provide the opportunity to assist in the setup of experimental and virtual screening campaigns (e.g. assembly of compound libraries) as well as the analysis of screening results and structures of hit compounds. In this presentation the implementation of ChemAxon tools into the European ScreeningPort workflow will be presented using selected examples from previous and ongoing experimental and virtual screening campaigns.
EUGM 2013 - Gyorgy Pirok (ChemAxon) - Prediction of Xenobiotic Metabolism
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EUGM 2013 - Ian Berry, Bob Marmon (Evotec): Classification and analysis of 21...
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EUGM 2013 - Bernd Rupp (FMP) Chemical Information systems: From compound coll...
The FMP has developed a database of commercially available compounds which is used to design our in-house HTS collection and is additionally applied to create focused libraries. But the dramatically increase of unique compounds of one order of magnitude from less than 10 to around 30 to 40 million compounds currently and approximately hundred million compounds in the next years requires a reorganization and redevelopment of our storage and searching strategy. To manage such a massive amount of data we developed a Registration Database for registration and normalisation of vendor catalogues. This database contains the highly redundant data of the vendor catalogues and is converted in a second step into the non-redundant Unique Structure Database which represents a data warehouse combining vendor data, structural descriptors and in-house classification tools including our earlier developed ADMET- and reactivity filters as well as our in-house fragment-based fingerprints used for library design tasks. The management of both database systems is part of a new developed Java application, which handles the user management for the data upload in the Registration Database and the conversion into the Unique Structure Database. Further a first version of a Web service is in preparation. This service allows the scientist not only to search for compounds and fragments in the Unique Structure Database but also to combine such a search with the FMP tools to classify compounds for their usability in biological assays.
EUGM 2013 - Jon Patterson (ChemAxon) ChemAxon Platform for Scientists
As scientists we need to deal with inordinate amounts of data every day: we generate, retrieve and manipulate new data as part of our job. Simple excel worksheets are not the solution in the modern era of drug discovery, development and beyond. In this session learn how you can use and integrate ChemAxon’s tools to solve your day-by-day tasks more quickly and efficiently. Whether you prefer a desktop, web-based or touch screen application, we have a solution. Learn how to manipulate your data using Instant JChem (on your desktop or via Web layer) or draw sophisticated queries using Marvin or our new addition Marvin for Java Script (Marvin JS) to reduce the search times, visualize your data in 3D using Marvin Space, export and explore chemistry with the Ubiquitous Excel using the JChem for Excel plugin and share ideas and data with you colleagues and/or collaborators using Crais Board. Integrate our tools in Pipeline Pilot and Knime protocols and generate new data to expedite your processes. Analyze your data using Spotfire through Instant JChem. Also learn how our newest addition, Plexus, will help you do you tasks on desktop using web technology.
EUGM 2013 - Anna Tomin (ChemAxon) - Reaction Library Design
ChemAxon’s Reaction Library provides a full spectrum of organic chemical reactions used in synthetic routes from recent chemical literature. It incorporates both experimental and in-silico transformation rules to help chemists explore chemical space. Reactor provides a wizard-like interface to generate products without minimal manual interference. However, users are also provided with full control over the reaction rules, and they are able to implement their own reactions easily. The presentation will highlight chemical features as well as design and application of our diverse reaction collection in Reactor.
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This document outlines the steps for migrating from the JChem Oracle Cartridge (JOC) to the JChem PostgreSQL Cartridge (JPC) or Choral. It discusses the reasons for migration, strategies for large ecosystems, non-cartridge migration steps, and cartridge-specific data and code migration steps. Key points include moving to new features, performance gains, compatibility with PostgreSQL and Amazon RDS, and references for more information.
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Monitoring and Managing Anomaly Detection on OpenShift.pdf
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
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4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
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6. Viewing Kafka Messages in the Data Lake
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7. What is Prometheus?
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10. Configuring Camel K Integrations for Data Pipelines
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11. What is a Jupyter Notebook?
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12. Jupyter Notebooks with Code Examples
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EUGM 2013 - Eufrozina Hoffmann (ChemAxon): Marvin extending the scope of usability
- 1. Marvin: extending the scope of usability Efi Hoffmann
- 2. • Sketching structures/queries • Smart (2D clean, 3D clean, mapping) • Displaying thousands of structures (MView) • Built in calculations/naming • Customization • Integration • No publication quality drawing • Image handling • Textbox • It uses Java • Applet loading is slow
- 3. What is new in Marvin?
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- 14. Marvin for JS ˗ Future Plans Reaction Reaction query Lone pair Radical Electron flow R-group Query features Server side customization Custom templates Display options 3D Support for Touch Devices 2014v6.0 v6.1 v6.2
- 15. What is new in MarvinSketch?
- 18. Bond Scaling
- 19. Unlimited number of S-group attachment points
- 20. Server Side Image import
- 21. 6.0 GUI is refreshed
- 22. MSketch - Future plans Publication Quality Drawing
- 25. Thank you for your attention!