Where and when? - ChemAxon's 4th US User Group Meeting (UGM San Diego) will be held on Tuesday and Wednesday, September 27-28th, at the Catamaran San Diego Hotel, Spa and Beach Resort.

Monday, 26th Sept afternoon - Markush Forum, a meeting for those who are interested in the development of ChemAxon’s Markush structure enumeration and search tools and the available content.

Tuesday & Wednesday, 27th-28th Sept - The UGM will include presentations from ChemAxon users, partners and developers with opportunity to network with peers and meet with developers.

Thursday, 29th Sept - Following the UGM program we host the training day that consists of two parallel tracks. The developers' training deals with technical questions, the Application focus training introduces ChemAxon products to end users.

Networking opportunities at the UGM

Plenty of opportunities for networking

Speaking to peers and colleagues in addition to the lunches and breaks we have organized social programs to keep the ideas flowing.

Sunday: informal gathering in the bar of the event hotel from 7 pm.
Monday: chat and dinner in The BeachWood
Tuesday: Gala Dinner in San Diego downtown, in the Stingaree
Wednesday: chat and dinner in the Pacific Beach Bar & Grill

Markush Forum

Monday September 26th afternoon, preceding the UGM San Diego. The Markush Forum provides an opportunity for interested organizations to participate in the further development of ChemAxon’s Markush tools for IP search.

More about the Markush Forum

Developer training

Thursday September 29th, the UGM will be followed by a dedicated Training day with two parallel tracks: one for developers and one for end users. The main goal of our technical training is to introduce the new product features and give answers to the questions of how ChemAxon tools can be best integrated in various cheminformatics applications.

More about the developer training

Application focus training

Thursday September 29th, the UGM will be followed by a dedicated Training day with two parallel tracks: one for end users and one for developers. The aim of our Application focus training is to give end users and those new to ChemAxon a handle on basic ChemAxon functionality and how you can interact with it.

More about the application focus training

One to one session

In the first break of the UGM we will host our traditional one-to-one session, where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group will have a discussion table in the break room.

For more details on the topics of the 1-2-1 session visit this link.

ChemAxon Partner participation

Partners' lightning round presentations On Tuesday, 27th of September, from 2 pm a one and a half hour session will be dedicated for ChemAxon Partners who will give brief overviews of how ChemAxon works within their products and services.

Partners' table-top exhibition Throughout Tuesday and Wednesday, partners will be available at exhibition sessions where attendees can meet and find out more about partner products and services.

For more details on partners' participation please contact Nóra Lapusnyik.

Contact us

If you have any questions, comments or requirements about the ChemAxon UGM feel free to contact János Fejérvári.


The cost of the 2 day User Group Meeting is $400 for corporate attendees and $200 for academics.

For the training day (either/both tracks) the costs are $550 for corporate attendees and $275 for academics. Training attendees can attend either track. The fee for the training day does not include the user group meeting fee.

The cost includes all breaks, lunches and the social programs and all attendees will receive upon payment an evaluation license for all products valid for one month after the event.

We look forward to welcoming you in September.


The Catamaran San Diego Hotel, Spa and Resort will host our UGM in San Diego. Note that the hotel tends to be full soon, so please proceed with your room reservation.

Getting there

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Tuesday 27th

Starts at
9:00 am
9:20 am
9:50 am
10:20 am
11:35 am
12:05 pm
12:20 pm
12:50 pm
4:10 pm
4:40 pm
5:05 pm

Wednesday 28th

Starts at
9:00 am
9:30 am
10:00 am
11:10 am
11:40 am
12:10 pm
12:25 pm
1:40 pm
2:10 pm
2:30 pm
3:00 pm
3:20 pm
4:05 pm
4:20 pm
4:50 pm
5:05 pm
5:15 pm

Markush Forum

September 26th, informal lunch at 12:30 pm, session between 1:30 pm - 5:30 pm.

ChemAxon and Thomson Reuters have formed a partnership to enable storage, search and enumeration of Markush DARC format (VMN), which is used in Thomson Reuters’ Merged Markush Service database - interlinked with DWPI (Derwent World Patent Index) and DCR (Derwent Chemistry Resource).

The Markush Forum provides an opportunity for members of ChemAxon's Markush forum to meet and discuss developments and future directions with ChemAxon Markush search and enumeration technology working on Thomson Reuters MMS content.

Agenda of the Forum:

  • Intro from Thomson Reuters and ChemAxon
  • Review & discussion of user needs
  • Instant JChem Product demo
  • Thomson Reuters update on Markush data availability
  • How Thomson Reuters extract & create the Markush data
  • Overview of recent ChemAxon developments & roadmap
  • Discussion on future developments/priorities

Who should attend?

Information Managers, Patent information Specialists, Research Managers concerned with investigation of patent space, Patent Attorneys, Business Intelligence Analysts.


Developer training

September 29th, approximately between 9:00 am - 4:15 pm. Runs concurrently with the Application Focus training day track.

The main goal of our technical training is to introduce the new product features and give answers to the questions of how ChemAxon tools can be best integrated in various cheminformatics applications

The sessions will be based around Marvin, JChem Base, JChem Cartridge and JChem Web Services.

The training program will involve common problems, different concepts, the ChemAxon's Application Programming Interface (API) and examples to understand how to integrate ChemAxon’s components in discovery pipelines and custom applications. Common problems ranging from basic to more complex scenarios will be explored and solved by Marvin/JChem developers with interactive demonstrations.

Morning session

appr. 9:00 am - 12:15 pm - Introduction into ChemAxon's Marvin Suite

  • Structure representation, structure i/o, building molecules
  • Break
  • Marvin, basic and advanced programming, using applets and beans
  • Lunch

Afternoon session

appr. 1:00 pm - 4:15 pm - JChem solutions

  • Chemical database concepts, an introduction to JChem Base
  • Chemical database programming, examples of JChem Base API and JChem Oracle Cartridge usage
  • Break
  • JChem Web Services, introduction, concepts, live demo of worked examples
  • Closing remarks

101 FAQ's to be answered:

  1. How are molecular structures represented with focus on implicit and explicit hydrogen atoms and stereo-chemistry?
  2. How to build molecule from API?
  3. What are the constituting components of a molecule, reaction?
  4. How to read and write molecules in various file formats (SDF, Marvin document file)?
  5. How MarvinView and MarvinSketch can be embedded in an HTML page?
  6. How to embed Marvin in Swing components (JTable, JFileChooser)?
  7. How Marvin can be customized in client applications: how to enable/disable tool bars, menu items; how to show/hide hydrogen atoms, labels?
  8. How to generate images with Marvin?
  9. How to add custom event handlers to Marvin applications?
  10. How to add custom templates to the Template Library, or to Advanced Template Toolbar?
  11. How to create editable molecular tables with MarvinView and MarvinSketch?
  12. How to change the structure while transfering between the viewer and editor?
  13. What tools does the Marvin library provide for other specific tasks?
  14. How are structures stored in the JChem database?
  15. How to search for molecular structures in chemical databases and how to sort hit lists?
  16. What are the best approaches to visualize search hits?
  17. How substructure search is sped up with the use of hashed chemical fingerprints?
  18. How to fine tune and optimize structural searches?
  19. How to standardize structures during compound registration and in hit visualization?
  20. How to write web service clients in PHP, JavaScript, and Python to access JChem Web Services?
  21. How JChem Web Services provides access to the JChem suite of tools? OR ... to your web applications?
  22. How JChem Web Services uses SOAP to provide access to the JChem Suite of tools?

Application focus training

September 29th, approximately 9:00 am - 5:30 pm: Runs concurrently with Developer Training Day track

Application focus training is designed mainly for end users (chemists and biologists) and those new to ChemAxon, to get a handle on basic functionality and how you can interact with it. The morning session introduces key technologies and features, it introduces ChemAxon technology in general. The entire afternoon session is dedicated for hands-on training and workshops for advanced and new users too. For more details see the agenda below.

Since the training will have hands-on part you will need to bring your own laptop or let us know if you want to get a loaner for the training day. Also you will need to download and install the recommended software and licenses to your desktop (for the exact details please re-visit this page later). All attendees will get a free license valid for all ChemAxon products following payment until one month post event. To finish with registration and downloads in time we recommend to arrive at 8:00 am to the training.

Introduction to ChemAxon technologies

This lecture session is designed to introduce beginners or new users to the general capabilities of ChemAxon technologies, focusing on the most commonly used visualization techniques, chemical representations, property predictions, chemical databases and chemical database clients. It is also useful for current users who have not had the advantage of a structured introduction to the general functional expectations of ChemAxon technologies.

9:00 am - 10:30 am
Desktop technology
This lecture explains the usage of the technology built-in Marvin Suite. Sketching, visualization of molecules and reactions will be demonstrated. It will detail the concept and usability of some property calculations (e.g.: pKa calculations, conformation generation) demonstrating the Calculator plugin technology, moreover will discuss a new plugin technology that will enable users to integrate their own existing calculators easier.
10:45 am - 12:00 pm
Enterprise technology
This lecture covers the basic concepts and use cases for JChem Base/JChem Cartridge and will also detail the latest improvements. Usage of interacting or built-in technologies will also be discussed such as JChem for Sharepoint and Chemical name recognition and search in document repositories.

Advanced usage of ChemAxon technology

This workshop session is designed to elaborate the morning session and provides hands-on experience for not only advanced users but beginners. Moreover, the workshops allow attendees to discuss and find solutions for their specific problems. The session is run in two tracks for desktop and enterprise solutions.

1:00 pm - 2:15 pm
Structure visualization and characterization
Basic, advanced features and latest improvements of Marvin are covered. Combining JChem for Excel functions and fine tuning visualization is discussed during this session.
2:30 pm - 4:30 pm
Enumeration technologies
Enumeration technologies enable users to generate virtual libraries based on generic reaction rules by Reactor or from Markush structures after drawing a generic reaction and a Markush structure using Instant JChem.
1:00 pm - 2:15 pm
Pipelining ChemAxon
This session covers the use of ChemAxon technology in Pipeline Pilot and Knime. Database management, property calculation, structure searching, similarity searching, reaction enumeration are covered.
2:30 pm - 4:30 pm
Instant JChem
Topics such as database management, hierarchical tables, form view design, standardization, structure checking, structure searching, Markush structure searching, Groovy scripting are covered.