Annual Meeting Budapest 2016 Archive


PRESENTATION SLIDES & VIDEOS

Tuesday 24th

Starts at
9:15 am
ChemAxon portfolio walk through

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Right at the beginning we would like to give our audience a general understanding of ChemAxon’s available solutions and tools. Our application scientists will briefly introduce all our available software, and they will put them in 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.

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10:00 am
Plexus Suite

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Plexus Suite delivers intuitive and easy-to-use cheminformatics solutions to life sciences team members, specially focusing on chemists and biologists for pharmaceutical research. A single, easy to use and very intuitive user interface, with easy access to data and analysis techniques, enabling scientists to access data from a variety of disparate sources and generate, share reports. Plexus Suite is a web-based software package and well suited for remote collaboration. This talk will shortly sum up what Plexus Suite is, and what our plans are in the near future in its development.

Tools covered by Plexus Suite:

Instant JChem – an easy-to-use chemistry Swiss Army knife for chem/biological data management, search, analysis and reporting, supporting common workflows
Plexus Connect – key reporting and query user interface of Plexus Suite to access, display and query scientific data supporting grid and form based views
Plexus Analysis – generic, web-based, integratable data viz & analysis tool
Compound Registration – register chemical entities as concepts into a database
Plexus Inventory – register batches and samples together with their relevant info
Plexus Mining – data mining solution supporting chemically intelligent search
Plexus Design – virtual library design via scaffold & reaction based enumeration
Plexus Assay – a new user interface for capturing processed assay data

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11:00 am
Macromolecule registration and analysis

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Learn how Biochemfusion’s Proteax software suite makes it easy to work with macromolecules; in databases, in Excel and in custom applications. Macromolecule data is easily transferred from literature thanks to notations that closely resemble peptide and protein nomenclature as recommended by IUPAC. Existing chemistry databases can be extended to handle macromolecule registration thanks to Proteax’s easy integration with existing tools, e.g. ChemAxon’s JChem cartridge and MarvinSketch.

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11:12 am
D360 - The Pharmaceutical Industry’s Data Analytics and Scientific Informatics Platform

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Certara biosimulation (model based drug development and informatics) software portfolio is the most wide-ranging in the industry. Combining legacy brands including Pharsight, Simcyp, Tripos and Certara, these technologies are used across the drug development life cycle. Pharmacologists, toxicologists, biostatisticians, pre-clinical scientists, chemists, geneticists, and other scientists use Certara software to inform key safety and efficacy decisions, including target identification and optimization, dosing, trial design, target validation, compound triaging, comparison with competitor compounds, and mechanistic drug performance. Certara’s D360 R&D data platform solves data challenges faced by scientists and IT staff throughout biopharmaceutical organizations by integrating and leveraging the large amount of diverse scientific data generated by sponsor companies and their outsourced partners to optimize crucial decisions.

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11:18 am
IDBS & ChemAxon

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As part of IDBS’ web-enabled strategy, new technology was required for the representation of chemical structures, and IDBS considered a build, buy or partnership approach. Given that ChemAxon are considered the world leaders in chemical and biological molecule representation, their technology was an excellent fit, which allowed for rapid implementation of a cheminformatics platform. IDBS view ChemAxon as a strategic partner in development, as we re-design the E-Workbook Chemistry product to support comprehensive synthetic workflows for discovery & development chemists.

1:00 pm
Questel partners with ChemAxon

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A partnership was recently signed between ChemAxon and Questel. The outcome of such partnership has already lead to a new product released this month on the Intellixir platform. With further developments in the pipe, we will explore what such partnership consists on and what chemists can expect to see and use in the near future.

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1:20 pm
ChemCurator

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ChemCurator is a desktop application to extract chemical information including compounds, Markush structures and related assay data from English, Chinese and Japanese patents, journal articles, and other documents. Combining ChemAxon’s text mining, structure handling and Markush technology, this application can extract and highlight structures within documents, allowing users to interactively extract chemical information or assemble the Markush structures in a semi-automated way.

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1:30 pm
Development of ChemAnalyser - a novel, large scale patent search engine

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Together with infoapps GmbH in Munich, Germany, OntoChem has developed a chemistry search engine for patent full text documents. Thus, about 90 million patent documents are annotated using OntoChem’s UIMA based annotators, ranging from chemistry up to material sciences, from diseases up to cosmetic and nutraceutical terms. In the backend, we are using JChem Base and in the front-end Marvin JS.
We will compare the recall and precision of this new search engine with SciFinder, describing the advantages of using ontology based “cognitive search” and searching knowledge N-tuples in non relational databases.

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1:55 pm
Leveraging the value of documents content - Plexus for agile dissemination of text/datamining results

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Most of the information “produced and consumed” (by the industry) is packed into documents either structured, e.g. as tables, or as free text. This heterogeneity and the constant increase in the data makes it very challenging to search for specific, simple or rather complex information. A, nowadays, feasible way to extract and structure this information is using a pipelining tool (e.g. KNIME) to combine several applications in the fields of cheminformatics, OCR, OSR, text-/datamining and semantics: it allows extracting “single-entity” terms, complex linguistic pattern, numerics, units, chemistry, etc.

Ideally, the results of such (complex) workflows should then be exposed to the users. As the process to reach a “satisfying” user-friendliness usually includes several iterative and interactive steps, agile and flexible solutions for search and visualization are demanded, essential to adapt to the various content. In this talk some use cases of how to leverage information from internal and external documents using Plexus, in combination with Instant JChem, will be shown, highlighting possibilities as well as the difficulties encountered.

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2:50 pm
Chemical search and database technologies

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ChemAxon’s search and database technology includes our JChem Base tool and two cartridges: One running on Oracle, the other one on PostgreSQL. We usually refer to these products as the heart of ChemAxon, since all the search capabilities derive from these tools throughout our software portfolio.
This talk will focus on the latest and newest changes in this technology, highlighting the youngest member of this product family, the JChem PostgreSQL Cartridge.

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3:00 pm
Handling large volumes of chemical data in a scalable way and on a tight budget with the PostgreSQL database and the JChem PostgreSQL Cartridge

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Background
We ran a pilot on the idea of pushing a very large amount of chemicals through reactor. That is a challenge in itself, not just performance-wise because of the amount of data, but also keeping the results structured, clean and correct. Coming from a data-processing background the approach was obvious: use a database! More specifically we chose for the PostgreSQL database in combination with the new JChem PostgreSQL Cartridge.

Approach
Rather then simply pumping millions of compounds into reactor, a route through a tool that can make smart selections makes it possible to scale the whole process up. Thus, after compiling a large library of compounds, we had to pre-filter the data before pumping it into reactor. This means substructure and feature searches, and optimizing those can be very tricky.

Findings
In the presentation I will elaborate on the various hurdles that had to be taken, and the ways those can be avoided.

Conclusion
We now know that Postgres and the JChem cartridge can be excellent performers, if handled with care. The huge operation that we plan on undertaking is probably possible with these very cost effective tools. Though not fully mature yet, the combination of an opensource database with a chemistry-aware backend does have the potential to be a game-changer.

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3:25 pm
ChemAxon's MadFast Search

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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.

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3:35 pm
Fast similarity searching – making the virtual real

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Similarity searching is a key component of many chemoinformatic processes including compound collection design, compound clustering and lead hopping. We have command-line tools for bespoke analysis and Cartridge based systems for similarity searching standard compound sets. However, we would like to use these applications in a more interactive manner whilst compounds are being designed: “who else is working on something similar?”, “can we buy this compound?”, “is in our virtual set?”. Several years ago ChemAxon approached us about the MadFast prototype and we have been collaborating to develop the application. In this talk I will give some benchmark statistics against existing in-house command-line tools and describe how MadFast is being deployed to provide interactive searching as part of LiveDesign.

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4:25 pm
Compound Registration & Plexus Inventory

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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.

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4:35 pm
Compliance Checker

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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 last month, providing a significantly increased performance and a complete redesign of the user interface. This presentation will give an introduction to this new version.

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4:45 pm
Plexus Assay

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The biological effects of entities are interrogated in a wide variety of (bio)assays. As ChemAxon is moving to the cloud-hosted solution space, we are aiming at providing a fully web-based, easy-to configure solution for capturing processed assay data. Furthermore, viewing assay data in the context of other types of data will enable better Structure-Activity Relationship studies within the Plexus Suite.

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4:55 pm
Biomolecule Toolkit

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ChemAxon’s Biomolecule Toolkit 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.

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5:10 pm
BioScity - Interfacing Biomolecule Toolkit with lab reality

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How getting the best of the Biomolecule Toolkit in the daily activity of a laboratory? Texelia is proposing a flexible and intuitive interface to facilitate sample management, inventory of small and medium size working environment. BioScity is integrating the strength of Biomolecule Toolkit platform with internally developed data structure and interfaces allowing the quick setup of an evolutive and customizable database. From small to macro molecules, BioScity is the solution to regroup bio and chemical information with project results and information.

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Wednesday 25th

Starts at
9:00 am
Marvin JS

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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 the features which help seamlessly integrate Marvin JS into your web application.

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9:08 am
Development of a chemical drawing program that provides scientifically correct and engaging first impression for students

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The ever-expanding internet access and the mass availability of affordable computers for students provide a new and exciting opportunity for academia. The online education enables scaling of the class size and allows students to attend sessions remotely, even if they cannot be physically present on campus. Emerging technologies bear the promise of a more engaging experience for online education, but they have to meet the same high standards as the ones used in the classroom: a chemically-correct representation is at least as important as an attractive and intuitive user interface. Customization also needs to fit simultaneously the course type (organic, inorganic, biochemistry, etc), the skill level of the student and the control needs of the instructor.

In this presentation we will look at a few case studies of novel, visual and interactive solutions developed in Marvin JS for handling various chemical structure representations, such as lone electron pairs, electron flow arrows, organic and generic reaction mechanisms, systematic naming or isomer visualization. Given the widespread adoption of Marvin JS across different chemical industries, students have the added benefit of learning and honing their skills on the same tools they are likely to use when they will enter the work force, after graduation.

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9:33 am
IDBS & ChemAxon - a 1:1 Stoichiometry

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As part of IDBS’ web-enabled strategy, new technology was required for the representation of chemical structures, and IDBS considered a build, buy or partnership approach. Given that ChemAxon are considered the world leaders in chemical and biological molecule representation, their technology was an excellent fit, which allowed for rapid implementation of a web-enabled cheminformatics platform in E-WorkBook. IDBS view ChemAxon as a strategic partner in the development of our next-generation chemistry ELN, to provide data management support for organic chemists in discovery chemistry, process chemistry and industrial research.
View more at: https://www.idbs.com/en/platform-products/e-workbook/e-workbook-for-chemistry/

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9:58 am
Calculations & Predictors in ChemAxon's Discovery Tools

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ChemAxon’s Discovery Toolkit is a software suite, which implements expert knowledge, and provides robust, class-leading performance to computational and medicinal chemists, aiding the in silico drug discovery process. It covers aspects of design, assessment and analysis of custom virtual screening libraries, and will thus leverage well-founded decisions in lead identification and optimization.

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10:08 am
Chemicalize

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is a public web resource developed by ChemAxon which currently uses our Name to Structure parsing to identify chemical structures on webpages and other text. Related to each structure, structure based predictions are available, as well a search interface is provided to discovery substructures or similar structures.

This talk will cover our future development plans of chemicalize.org.

11:03 am
Roaming through natural products space with JChem & KNIME

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Following our quest to reveal and demonstrate the link between nutrition and health at the molecular level we are looking for chemical substances occurring in nature that are pharmacologically active, i.e. natural bioactives. With that goal in mind, we are establishing a screening library based on natural products. Here we discuss how chemical space of natural products differs from that of typical drug-like molecules and different strategies to select natural products subsets for screening on biochemical assays. Along we demonstrate the powerful combination of JChem and KNIME when it comes to manipulations and analysis of molecular libraries.

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11:28 am
MarvinSketch in publication

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MarvinSketch allows users to quickly draw molecules through basic functions on the GUI to advanced functionalities. This talk will focus to the many useful features added to help the chemists to report and publish their research according to the highest standards.

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11:35 am
Marvin Live

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Drug discovery teams are increasingly spread out over the world and involve CROs or consultants. Circulating ideas within such a team is cumbersome with regular tools. Marvin Live is designed for them and enables real time collaboration from any location and any device with productivity features for automatically characterizing and searching molecules on the canvas, generating actions and capturing meetings in a searchable format.

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11:45 am
Marvin Live to facilitate structure-based drug design

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How to make better molecules faster is a key challenge in preclinical drug discovery. At Sprint Bioscience we use fragment-based techniques to quickly find high-quality chemical starting points for our small molecule drug discovery projects. Then, we use structure-based drug design to optimize the compounds towards clinical testing.

In this talk, we will illustrate how Marvin Live is used to streamline our collaborative workflow in the medicinal chemistry team – from a design idea to a target molecule ready to be synthesized in the lab.

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12:10 pm
ChemAxon tools at Gedeon Richter

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Headquartered in Hungary, Gedeon Richter Plc. (GR) is an innovation-driven specialty pharmaceutical company. Vertically integrated, the company is engaged in pharmaceutical manufacturing, research and development, sales and marketing. The Company has around 11000 employees worldwide, more than 500 of whom work in R&D. The original research portfolio of GR focuses on central nervous system diseases.

Parallel with the fascinating worldwide development of cheminformatics tools, in the last 20 years GR placed effort into building up a modern in-house cheminformatics system facilitating the research projects. This system includes a proprietary compound library, effective molecular modeling software tools, physchem prediction and database packages, and lately solutions for handling large datasets.

The aim of this presentation is to show how ChemAxon tools have been built up within the cheminformatics system used at GR. After this, our recent experiences on the installation and usage of a new ChemAxon software package, Marvin Live, are presented in some detail. Marvin Live was accepted for testing and was found to be a great platform for facile idea sharing in a collaborative research project between chemists working at different locations (GR and Orion Pharma). Finally, a case study is presented where JChem tools are used within Instant JChem and from command line. This study focuses on an everyday question in the early phase of pharmaceutical research projects: how to prepare and filter a vendor database using public data from multiple vendors in order to choose a set of diverse molecules as a starting point in drug development.

1:35 pm
JChem for SharePoint & ChemLocator

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This presentation will focus on a user story where the core problem is to find relevant chemical data in different company databases and inventories. The problem gets even more complicated by the different environments our user has to handle. One one hand the company has a massive amount of information on the corporate SharePoint. JChem for SharePoint adds chemical intelligence to text and image search, we will cover quickly how.
However, life is never that simple. 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.

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1:55 pm
Using Plexus Design to create chemical space for structure-based drug design

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How to make better molecules faster is a key challenge in preclinical drug discovery. At Sprint Bioscience we use fragment-based techniques to quickly find high-quality chemical starting points for our small molecule drug discovery projects. Then, we use structure-based drug design to optimize the compounds towards clinical testing.

In this talk, we will illustrate how Plexus Design is used in our drug design process. With Plexus Design we can efficiently expand and evaluate chemical space, which facilitates the generation of new design ideas.

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3:00 pm
Instant JChem & Plexus Connect

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Instant JChem is a desktop application designed for the chemist. 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 customisable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions.

As part of the Plexus Suite, Plexus Connect provides the backbone, connecting to research data and enabling powerful search, browsing and list management in a simple, intuitive user interface. It incorporates ChemAxon’s industry-leading chemistry capabilities and provides a central user interface for gathering information from the integrated database of Plexus Suite.

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3:10 pm
Instant JChem as a basis to construct a customized database to store biological activity data

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Instant JChem was customized to create a simple, versatile and efficient database to store biological activity data associated to small molecules for Drug Discovery projects. The database has both a single-compound view as well as a list view, is fully searchable (both by chemical structure as well as by any kind of data) and each view can be easily adapted to show the data that is necessary. Data aggregation (for example, averaging of data from the same experiment) is automatically performed according to predetermined rules for each type of biological data (for example, IC50s are averaged, but PK results are not). For loading the data we used simple Excel (biological data) or sd (loading of compounds) files. Because of its simplicity, versatility and easy adaptability to different needs, the system is very well suited for smaller biotech companies such as iTeos.

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3:35 pm
Instant JChem in virtual high throughput screening and commercial compounds selection

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Search for potential hit compounds using commercially available compound libraries is an important step in the early stage of drug discovery process. An in-house database of commercial compounds can be used for streamlining virtual screening campaigns including filtering for drug-like compounds, ordering compounds from different vendors, and storing the history of small molecules purchased during project development. We developed an in-house database that contains nearly 7m commercially available compounds that are used at various steps of the screening process. For this purpose Instant JChem and ChemAxon plugins are extensively used. During the presentation details of the database set up, in-house scripts and workflows will be presented.

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4:00 pm
Rollout of Plexus Connect at GSK, a brief history and update

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The Instant JChem (IJC) application is a thick client that has been delivered via a desktop application at GSK. The client uses direct connections to the GSK database infrastructure to provide access to registration, biological data and structure searches. Complex data joins and access from sites remote to the data made the connection and query slow for many users. GSK have worked closely with ChemAxon scientists to develop their Plexus Connect tool, as a performant web interface for this client and we are in the process of delivering this new client across GSK. This presentation will reflect on the setup we are changing from, the status of the rollout of the new product, current issues and future challenges.

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4:25 pm
Plexus Analysis

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Plexus Analysis is a web-based data visualization and analytics software for all industries. It can receive data from Plexus Connect tables, from files and through its web service interface it can be called from other external applications as well.
Plexus Analysis supports the most popular chart types: scatter plots and histograms at the moment. The charts are interactive and the visualization is fully synchronized with the data. A special, distinguishing feature of the new Plexus tool is that it is already able to handle very large data sets dynamically in a web browser. It is also capable of visualizing even millions of data points while keeping the granularity of data.

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4:35 pm
JChem for Office

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JChem for Office integrates chemical structure handling and visualizing capabilities within a Microsoft Office environment. This presentation will show how JChem for Office enhances the analysis, reporting and communication in a typical discovery cycle in a centralized enterprise environment.

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