PRESENTATION SLIDES & VIDEOS
Right at the beginning we would like to give our audience a general understanding of ChemAxon’s future development plans and business directions.
Based on our future vision, we already started to develop products that will help us move forward on this path. During the meeting there will be more detailed presentations about our newest hits. Though we will quickly talk about the MadFast Similarity Search, the BioEddie, the new Compliance Checker, the revamped Chemicalize, the ChemLocator and the Plexus Analysis. Just to give you the opportunity to explore these applications from the very beginning of the meeting.
After talking about the corporate wide goals and plans, our senior application scientist will briefly introduce all of our available software – including the new ones as well, and she will put them into context through short use-cases and workflows. This way we will demonstrate how our tools connect to each other offering a solution for a number of problems.
MadFast is an ongoing development effort to provide useful tools for similarity based search, overlap analysis and clustering. I would like to give a short introduction on the current state of the development and future plans.
An update of MVL will be given with some observations obtained from its one-year long cloud deployment in terms of performance, robustness, cost, and admin effort required. An overview of MVL application in discovery projects will be given, followed by more discussions on two use cases (fragment hit follow-up and support for de novo compound design). Two major enhancements requested by discovery project teams will be discussed at the end.
Compliance Checker is a combined software system and content package providing a way to check whether your compounds are controlled according to the relevant laws of the countries of interest. A completely redesigned version of the Compliance Checker software has been released this year, providing a significantly increased performance and a complete redesign of the user interface. This combined presentation will give an overview about Novartis’ controlled substances program and how they use Compliance Checker for this purpose. The Novartis presentation will be followed by an overview of the revamped version of Compliance Checker.
ChemAxon’s Biomolecule Toolkit – now extended with an editor, called BioEddie – is a webservice-based toolkit to bridge the gap between biology and chemistry for complex biomolecular entities. It provides unambiguous representation at sequence and atomic level for a diverse set of biomolecules such as peptides, oligonucleotides, proteins, antibody drug conjugates, including those containing unnatural and chemically-modified components, thereby allowing their storage, indexing and search within a database. The toolkit can be applied to extend existing biologics management platforms or to form the basis of a biomolecule registration system. It is capable of mapping your specific workflows and business logic for canonicalization, registration and querying.
ChemAxon’s Compound Registration is a system built on a set of web services, aiding users to register molecular structures into a compound database. The registration process spots unique compounds among a set of structures already contained within the database. The configurability of the registration’s business rules enables flexible definition of uniqueness in accordance with enterprise level requirements. Incoming compound submissions are processed by these business rules, and fully audited registration data is stored for all unique compounds while minimizing the amount of manual curation. In this presentation a typical implementation process will be described.
Compound Registration is a crucial component of small molecule research application platforms. The system needs to follow complex workflows in order to validate and standardize chemical structures. It must also be able to integrate with related systems including the ELN, LIMS and data warehouse. Using Amazon Web Services, we have implemented a cloud-hosted solution of ChemAxon’s Compound Registration application. Our architecture and experiences will be presented.
IDBS are strategically migrating the E-WorkBook electronic laboratory notebook (ELN) to a modern web-enabled architecture and interface. As part of the re-development of the chemistry ELN, IDBS chose to partner with ChemAxon, given their expertise in chemical and biological molecule representation.
Marvin JS and JChem was implemented in E-WorkBook v10.0 in December 2015, and IDBS released the first version of the stoichiometry component in June 2016, to support discovery chemists. In addition to molecule handling and naming, IDBS have developed direct integrations to ChemAxon’s Compound Registration. IDBS have also worked with ChemAxon to develop proof-of-concept integrations to other modules, to harmonise chemists’ workflows and to facilitate the simple exchange of data.
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The Schürer research group at The University of Miami is one of three sites for the Big Data to Knowledge (BD2K) Data Coordination Integration Center (DCIC) of the Library of Integrated Network-based Cellular Signatures (LINCS) program. BD2K and LINCS are NIH Common Fund projects with the goal to accelerate data science approaches in biomedical research. The LINCS project generates large datasets of cellular response signatures for small molecule, genetic or environmental perturbations. Signatures include transcriptional, proteomics, cell phenotype, and biochemical profiles in various cell model systems. The BD2K-LINCS DCIC encompasses operational and discovery components; major tasks include to process these diverse datasets, integrate them, make them accessible in a variety of ways, and develop data analytics tools and pipelines. One of the tools developed at the DCIC is the LINCS Data-Portal (LDP). LDP provides integrated access to all LINCS datasets, metadata, aggregate information and links to data analysis tools. To populate information into LDP, we developed several data processing pipelines and registration functionality.
Registration and integration of small molecule chemical structure information required a strict standardization protocol. These include automated and manual curation steps to correct or clean-up chemical structures including FDA approved drugs and clinical compounds. In both steps, we have made use of ChemAxon tools, such as standardizer, calculator plugins, Instant JChem, and Reactor, while also leveraging Pipeline Pilot integration. The subsequent chemical structures are stored in JChem. In LDP we recently added a chemical structure search allowing the user to find compound activity based on structure and common substructure. This is implemented using Marvin for Java Script. In summary we have implemented an end-to-end data processing pipeline including chemical structure registration and a chemically aware Data Portal powered by ChemAxon.
Marvin JS is ChemAxon’s chemical editor web component designed for the wider community. It provides a clean, smart user-oriented interface for quick and convenient drawing of chemical structures and reactions/reaction mechanisms in web pages. In this presentation we will focus on integration use cases and show several examples of it.
This presentation talks about a real world use case where Marvin JS embedded chemical drawing abilities into a new, global Business Process Management (BPM) platform at Sanofi R&D and enabled functionalities critical to success and adoption of the solution by key stakeholders.
Quality in molecule design needs to be ensured from the get go to avoid unnecessary late-stage project setbacks. There’s data and tools to guide ideas, but the volume is staggering and it keep growing every day. There are experts for each area, more and more specialized, but often they’re at collaborating partners. Finding potentially useful bits is not an easy task by any measure. How does your team manage this? How does your team exploit the possibilities here? Quality and collaboration are the primary focus of Marvin Live.
We will describe briefly how Marvin Live is used at Vertex Pharmaceuticals Incorporated. We will share our involvement in the early development of Marvin Live.
Questel starts what we expect to be a long time collaboration with ChemAxon, leader in Chemical Structure detection. We present you the first implementation of chemical features in Questel products, starting with INTELLIXIR and continuing with Orbit Intelligence early next year.
We will show you how INTELLIXIR will allow you to detect chemical structures and sub-structures in documents submitted to it, including articles and patents from any sources. Structure visualization will be available on the fly, along with a structure drawing tool for finding and labeling unnamed molecules. You will also see how the INTELLIXIR categorization features will allow you to deeply and accurately analyze your content enriched by this chemical structure information, including the ability to create custom fields for categorization. We expect this implementation to be released on September 26, 2016 in INTELLIXIR followed by integration into Orbit Intelligence full text patent information early next year.
Chemicalize was created as a free, online demonstration and advertising application of ChemAxon’s naming and calculation technologies eight years ago. Currently this is one of the most well-known and popular cheminformatics service on the web.
This talk will introduce the renewed Chemicalize platform and cover our future development plans.
This presentation will focus on several, smaller user stories where the core problem is to find relevant chemical data in various internal and external document repositories. The problem gets even more complicated by the different environments our users have to handle. Some of the data sits on local machines’ drives, but many colleagues used Dropbox or Google folders to store data. Our new ChemLocator tool will be of a great help in these cases.
Instant JChem is a desktop application designed for researchers. With Instant JChem you can create, explore and share chemical and non-chemical data in local and remote databases without additional administration. Instant JChem has a wide and growing range of functionality including customizable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions.
Plexus Suite is a web-based software package to access, display, search and analyze scientific data. A number of ChemAxon tools are integrated into the software suite and more will come, combining our strong chemistry knowledge with all the technical benefits of a browser-based environment. Plexus Suite consists of various tools. Each of them adds specific knowledge to the major display and query tool, Plexus Connect. Currently four tools are released: Plexus Connect, Plexus Design, Plexus Mining and Plexus Analysis.
ChemAxon has been a strategic partner with GSK for many years now and has allowed for GSK to envision a comprehensive Chemistry Desktop that works seamlessly from molecule design to all the related lead optimization tools and given us the infrastructure and tools to afford advanced, consistent search capabilities. Efforts to keep the systems consistent and up-to-date have been challenging in recent years due to inconsistent upgrade strategies at GSK and ChemAxon and diverse use cases at GSK but a concerted effort has allowed GSK to work toward that goal. This topic will cover what progress and challenges still await us as we move toward consistency and stability on our chemistry desktop.
AMRI recently launched a Compound Library Consortium (CLC), to deliver 70,000 compounds within 2.5 years for three different partners. AMRI selected Instant JChem (IJC) from ChemAxon to manage the data associated with preparation and deliverables for the CLC. In library preparation there exists two cycles. Firstly is the development of which compounds should be prepared to make up the library. This cycle is predominantly a virtual/paper process. Only limited laboratory chemistry has been completed to support the Scaffold/Template/Compound selection. Once the virtual library has been accepted, physical process starts and the preparation begins. Based on this flow, the security of IJC is organized into groups with specific permissions leveraging LDAP authentication. Form controls have been incorporated to prevent users from inadvertently changing or viewing content. As an additional control, IJC uses several temporary or staging tables before committing the data to the overall database. AMRI has been able to successfully utilize this application to deliver >10,000 compounds to each of the CLC partners’ to date.
Plexus Analysis, just like other tools in the Plexus product family, is a web-based software for data visualization and analytics. It can fetch data from Plexus Connect tables, but through its web service interface it can be called from other external applications as well.
Since Plexus Analysis has been released recently, currently it supports scatter plots and histograms. Also linear and non-linear curve fitting was added to Plexus Analysis’ features.
The largest benefit of the new Plexus tool is that it is already able to handle very large datasets dynamically. It is also capable of visualizing even millions of data points while keeping the granularity in data.