Instant JChemPresentation by Tim Dudgeon · March 2009
Instant JChem is ChemAxon’s desktop chemistry solution, allowing scientists to manage and search chemical structures and related information. This presentation gives an overview about the most important features of the Instant JChem, it describes the typical users of the tool and gives an idea about the upcoming developments for short and medium terms.
Full abstract The description of the Instant JChem is built around ten bullet points:
- Simple and flexible deployment
- Create and manage structure databases
- Import/export/merge/edit data
- Build tabular and form based reports
- Run combined structure and data searches
- Structure based predictions
- Manage relational data
- Access sophisticated chemistry features
- Collaborate with other users
- Extensible
Among the most typical usage scenarios of the Instant JChem the building of the database is fundamental. Afterwards customers usually use the Instant JChem to create reports from the existing database, share data and customize the tool to fulfill their own needs. The future development of the product contains mostly the synchronization with other JChem releases. It means that the next release of the Instant JChem will improve the database’s server, the schema editor, the handling of the URL fields and probably the Reactor will be integrated to it.
2009 Instant JChem Seminar Series · Feb-March 2009
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Structural Search Using ChemAxon ToolsJanuary 2009
Structural searching techniques are invaluable tools in all cheminformatics systems including but not limited to rational drug design, compound registration systems and laboratory information management systems.
Full abstractJChem, one of ChemAxon’s major suites of programs, provides a very rich set of features related to structural searches. These features are demonstrated by examples. Covered topics are: substructure, exact, superstructure, MCS (maximum common substructure) and similarity searching. Reaction and R-group searches (including R-logic) are also available, which are complemented by a rich set of query features. SMARTS and query features of the MDL formats are supported.
The database components of JChem are also described: JChem Base and JChem Cartridge for Oracle. An example of a fast MCS-based clustering is also presented.
Finally the recently developed descriptive Chemical Terms Language is demonstrated by powerful structural searches.
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Pipelining ChemAxonPresentation by et al, Szilárd Dóránt · December 2008
This presentation gives a thorough overview about the component collection that allows you to get access to all ChemAxon tools from Pipeline Pilot. In the introduction part the basic quick facts are provided about the collection.
Full abstractThe major part of the presentation shows the development of the pipeline functionalities within ChemAxon that starts with the description of the available features. Among the most important functionalities the Standardizer, the Reactor, the Marvin applets, the MCS based clustering, the microspecies distribution, the IUPAC name and molecule converter or the burden eigenvalue descriptor are worth to mention. However the presentation puts the focus on the 2008 improvements, on the changes that happened in the versions from 1.2 to 1.4. The features that are emphasized in the presentation are as follows:
- Chemical Terms Calculator
- Canonicalization with Standardizer
- IUPAC naming components
- Changes in Reactor
- Clustering with LibMCS
- JChem Base insert
- JChem Database search
- Improved error reporting
On the closing slides of the presentation the planned components are discussed.
2008 Accelrys European User Group Meeting · 9-12 December 2008.
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Migration from ISIS environmentsPresentation by et al, Szabolcs Csepregi · November 2008
The presentation focuses on the differences, similarities, pros and contras of migration from an ISIS environment to a related ChemAxon product. It gives a proper overview about the features of several ChemAxon products, it describes the functionalities of the ISIS tools, you can find independent comparisons, migration case studies and feedback from users and an appendix about the technical resources of ChemAxon products.
Full abstractThe presentation starts with a brief overview of ChemAxon tools like the Marvin family, the Calculator plugins, the Chemical naming, the JChem family, the Markush features, the Standardizer, the drug discovery tools and even the embedded ChemAxon tools.
The first product that is discussed in this presentation is JChem Cartridge. This part starts with the thorough overview of the software’s purpose, features, operators and functions. Afterwards the migration from MDL/Direct cartridge and from ISIS/Host is described through independent comparison and from technical point of view. On the end of this section an overview of a migration questionnaire takes place.
In the next section the ChemAxon’s Standardizer goes through a comparison against the Cheshire including such topics like counting groups, adding explicit hydrogens, group conversion and structure checker.
In the following slides the Instant JChem is compared to the ISIS/Base with special focus on architecture, databases, forms and security. Within the topic of the migration the presentations gives an overview about the comparison of the JChem’s Data Tree and the ISIS Hview and the migration options are explained here thoroughly.
Afterwards comes the brief description of the JChem for Excel and its short comparison to ISIS for Excel. It is followed by the migration of the custom applications including Java applications, .NET applications, web based applications and SOAP.
Finally among the ChemAxon products the migration of the Web Services is discussed.
The presentation closes with the review of the developers’ resources emphasizing the Java API, the Marvin Applets for web applications, the .NET API and native .NET solutions, SOAP interface, AJAX GUI and the integration of ChemAxon components to vendors’ softwares.
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ChemAxon for DevelopersPresentation by Ferenc Csizmadia · November 2008
The presentation aims to give an overall understanding of the ChemAxon’s application programming interfaces, graphical user interfaces, additional development informations mostly about Instant JChem and the company’s softwares’ integration.
Full abstractThe main topics of the presentation are as follows:
- Java API
- Marvin Applets for web applications
- .NET API over JNBridge
- Native .NET solution
- JChem Cartridge for Oracle
- SOAP interface
- AJAX GUI
The final slide of the presentation gives an overview about the software vendors that integrated ChemAxon softwares. For example the Pipeline Pilot, KNIME, Spotfire, Aureus and Integrity are mentioned among the most important vendors.
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Alternatives to MDL® CheshirePresentation by György Pirok · November 2008
The presentation gives a thorough comparison of MDL’s Cheshire and ChemAxon’s tools. Among the alternatives of the Cheshire the presentation lists three ChemAxon functionalities: the Java API, the Chemical Terms and the Standardizer.
Full abstractIn the first few slides the three previously mentioned tools are described. Afterwards the Cheshire, the Java API and the Standardizer is compared to each other from three different point of view:
- Counting Groups
- Adding explicit hydrogens
- Group conversion
In the end of the presentation stands as a summary of the comparison that Java API provides similar flexibility for programmers as Cheshire, though it is a widely used language. The Chemical Terms feature can handle Cheshire codes in the same complexity level but the Chemical Terms expressions can be used in other cheminformatics applications. The Standardizer enables chemists to create conversion rules without encoding.
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What's new for Pipeline PilotPresentation by Larry Norder, Szilárd Dóránt · March 2008
Pipeline Pilot solutions are based around a powerful client-server platform that lets you construct workflows by graphically combining components for data retrieval, filtering, analysis, and reporting. ChemAxon implemented these functionalities to a number of its products that are described in this presentation as for 2008.
Full abstractAfter the introduction of the ChemAxon’s product line the presentation starts to give an overview about the products that implemented Pipeline Pilot: Marvin Sketch, Marvin View, the Calculator Plug-ins or Chemical Terms. Among the ChemAxon tools the JChem Base is emphasized as several features and interfaces were added to that. Most of the innovations improved the searching facility of the database manager through concentrated functionality. The next important development the presentation talks about is the canonicalization functionality of the Standardizer that is simple to use but it can handle complex tasks too. The virtual synthesis of the ChemAxon’s Reactor was updated with Pipeline Pilot solutions as well to make the tool more effective, flexible, smart and compatible. The Pipeline Pilot was implemented to the Instant JChem as well to create and update databases that can be intuitively searched and analyzed. On the last few slides there’s an overview about the plan of the current and future developments, the list of the available components and the ones that are planned to become a component.
2008 SciTegic Pipeline Pilot User Group Meeting, March 5-7, 2008
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Chemical Terms, a Language for CheminformaticsPresentation by György Pirok, Attila Szabó, Ferenc Csizmadia, István Cseh, József Szegezdi, Miklós Vargyas, Nóra Máté, Szabolcs Csepregi, Zsolt Mohácsi · March 2007
This presentation gives an overall understanding about ChemAxon’s Chemical Terms which is a simple but extensible language, a general interface to combine chemical functions for various cheminformatics purposes. Briefly the Chemical Terms enables the software programs to extend their “chemical intelligence”.
Full abstractOn the first slides of the presentation you can read about the problems that belong to the topic of the Chemical Terms. The related questions are listed within four categories: virtual reactions, filtering, pharmacophore mapping and random evolutionary de Novo drug design. The following slides give the answers for these questions presenting the development of the Chemical Terms functionality to solve the above mentioned chemical problems. Afterwards you can read about the Chemical Terms’ function examples including substructure matching, chemical calculations, the calculation of returning molecules and combining functions in the tools. In the end of this part of the presentation the Chemical Terms Editor is introduced in a few words.
The major part of the presentation focuses on the ChemAxon applications that the Chemical Terms functionality is built in. The Instant JChem, the filters of the Pipeline Pilot, the Reactor, the Metabolizer are mentioned in this section. Finally an overview of the upcoming Chemical Terms features is discussed in three major groups: simplified syntax, simplified editing and new functionalities.
American Chemical Society Spring meeting, March 25-29th, 2007
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Standardizer - Molecular Cosmetics for ChemoinformaticsPresentation by György Pirok, Alex Allardyce, Ferenc Csizmadia, István Cseh, Nóra Máté, Péter Kovács, Szabó Attila, Szabolcs Csepregi, Szilárd Dóránt · August 2006
The Standardizer is a customizable chemical structure conversion tool that was developed by the ChemAxon. This presentation gives a thorough overview about this tool. The introduction of the Standardizer starts with the explanation of the goals of the tool that are discussed in three large topics: canonicalization, beautification and modification.
Full abstractThe first part of the presentation focuses on the canonicalization: it describes the solutions of the Standardizer through examples of handling the tautomers, hydrogens, resonant structures, mesomers, fragments and removing the solvents and the specific counterions. The next slides of the presentation describe the fundamental problems that are related to the beautification with a special focus on the cleaning methods of the Standardizer. This section includes a description of the database usage of the tool.
After the short overview of the modification the presentation focuses on the appearance and applications of the Standardizer: it introduces the tool’s GUI, the Virtual Synthesis and the structure databases as applications.
Workshop Chemoinformatics in Europe: Research and Teaching, May 29-June 01, 2006
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Standardizer - Molecular Cosmetics for ChemoinformaticsPresentation by György Pirok, Nóra Máté, István Cseh, Attila Szabó, Szilárd Dóránt, Zsolt Mohácsi, Péter Kovács, Szabolcs Csepregi, Alex Allardyce, Ferenc Csizmadia · July 2006
A chemical compound can appear in various forms and its graphical representation often depends on the taste of the chemist. These variants are usually represented with different graphs in chemical software programs making the structural identification difficult.
Full abstractApart from the naturally occurring mesomeric and tautomeric issues, chemical compounds are rarely neutral and pure, thus counterions and solvents might appear in the chemical structure files making the identification even more problematic.
ChemAxon1 developed Standardizer, a Java-based software tool for the batch conversion of chemical structures according to a standard defined by the chemical database administrator.
25th Chinese Chemical Society Congress, 11-15, July 2006
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Standardizer - Molecular Cosmetics for ChemoinformaticsPresentation by György Pirok, Alex Allardyce, Ferenc Csizmadia, István Cseh, Nóra Máté, Péter Kovács, Szabó Attila, Szabolcs Csepregi, Szilárd Dóránt · June 2006
The Standardizer is a customizable chemical structure conversion tool that was developed by the ChemAxon. This presentation gives a thorough overview about this tool. The introduction of the Standardizer starts with the explanation of the goals of the tool that are discussed in three large topics: canonicalization, beautification and modification.
Full abstractThe first part of the presentation focuses on the canonicalization: it describes the solutions of the Standardizer through examples of handling the tautomers, hydrogens, resonant structures, mesomers, fragments and removing the solvents and the specific counterions. The next slides of the presentation describe the fundamental problems that are related to the beautification with a special focus on the cleaning methods of the Standardizer. This section includes a description of the database usage of the tool.
After the short overview of the modification the presentation focuses on the appearance and applications of the Standardizer: it introduces the tool’s GUI, the Virtual Synthesis and the structure databases as applications.
Workshop Chemoinformatics in Europe: Research and Teaching, May 29-June 01, 2006
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