Where and when? - ChemAxon's 6th US User Group Meeting will be held on Tuesday and Wednesday, September 24-25th, at the Catamaran Resort Hotel & Spa.

Monday, 23rd Sept. - 3 all-day Satellite Sessions:

Tuesday & Wednesday, 24th-25th Sept. - 31 presentations, plus posters, from ChemAxon and ChemAxon users covering solutions for bench scientists, building platforms for discovery and the science of ChemAxon. Our partners showcase their ChemAxon integrated solutions during the exhibition and Partner Lightning Session.

Networking opportunities at the UGM

Plenty of opportunities for networking

We know speaking to catching up with peers and colleagues is a major part of the user meeting so we have many opportunities to keep the ideas flowing.

Sunday: Warm things up gently with an informal gathering in Catamaran Bar from 7 pm.
Monday: In the end of the day we'll walk to the Nick's at the Beach bar to watch the sunset, and have a dinner and few drinks during an informal chat.
Tuesday: Every year we try to bring our attendees to a special local venue for our Gala Dinner. This year the oldest active sailing ship,the Star of India, will host us.
Wednesday: If you are still around, we will close the UGM with an informal chat and dinner in a bar close to the Catamaran, called Moondoggies.

Satellite Sessions - Monday Sept 23rd

Integration Workshop

For senior developers and IT managers, the overarching story of the integration workshop will be creating a chemical registration system. This workshop will run concurrently with the Markush Forum and the KNIME Workshop.

More about the Integration Workshop

KNIME Workshop

Relevant to anyone using workflow tools we overview KNIME, the ChemAxon functionality available using chemistry centric workflows and then explore downstream processes such as data mining, data transformation and reporting. This workshop will run concurrently with the Markush Forum and the Integration Workshop.

More about the KNIME Workshop

Markush Open Day

For IP searchers and patent professionals working with chemical structures we overview a new service to search and analyse Thomson Reuters Markush content. This workshop will run concurrently with the Integration Workshop and the KNIME Workshop.

More about the Markush Open Day

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 separate discussion area where ChemAxon experts will be on call.

More about the One-to-One Session

ChemAxon Partner participation

ChemAxon technology isn't just available from ChemAxon. On Tuesday 24th September we hold a Partners' lightning round session highlighting how our technologies compliment the products and services of our Partners.

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 $500 for corporate attendees and $250 for academics.

The Satellite Sessions - are free of charge to all UGM attendees.

Costs include all breaks, lunches and social programs.

We look forward to welcoming you in September.


Catamaran Resort Hotel & Spa will host our UGM in San Diego. The event hotel tends to book out early in September, so do not forget to book your room in time. We can guarantee rooms available in the Catamaran Resort & Spa until 22nd of August.

Book your room here!

Getting there

Read the directions on Catamaran's website!

View Larger Map


Tuesday 24th

Starts at
9:00 am
9:30 am
9:40 am
9:55 am
10:10 am
10:25 am
11:10 am
2:10 pm
2:30 pm
2:45 pm
3:00 pm
3:20 pm
3:50 pm
4:25 pm
4:40 pm

Wednesday 25th

Starts at
9:00 am
9:10 am
9:40 am
9:55 am
10:55 am
11:25 am
11:55 am
12:10 pm
1:30 pm
2:00 pm
2:30 pm
2:45 pm
3:40 pm
4:00 pm
4:20 pm
4:40 pm
5:00 pm

Download Program Table of Satellite Meetings

Integration Workshop

Integration Workshop

Intended for senior developers and IT managers, the overarching story of the integration workshop will be creating a chemical registration system. Through this example we will show ChemAxon’s Java and web toolkits and how they work together. In the afternoon session, we will present analysis and reporting solutions as well as describe common customization issues.

Presentations will focus on an overview of functionality and available features, integrating toolkits into existing systems, but of course we will use code examples as well.

For those who previously attended a ChemAxon developer workshop, significant new content is added:

  • the introduction and usage of Marvin for JavaScript
  • the introduction and usage of JChem Web Services’ new REST API
  • the introduction and high level overview of ChemAxon’s .NET API
  • database management and querying using JChem Cartridge for Oracle
  • introduction and usage of the new Screen and JKlustor API

Attending this day should help both beginner and intermediate users with ChemAxon’s developer toolkits and give an insight into integrating cheminformatics systems.

Agenda of Integration Workshop

9:00 am - 9:15 am Introduction

9:15 am - 9:50 am Structure import and drawing

  • import/export system and file format handling
  • choosing between MarvinSketch and Marvin for JavaScript

9:50 am - 10:25 am Canonicalization and structure checking

  • automatic structure canonicalization with Standardizer
  • using Structure Checker for structure revision
  • implementing custom checkers and fixers

10:25 am - 11:00 am Database handling and querying

  • structure searching and database handling with JChem Base
  • using JChem search and standardization
  • search result visualization

11:00 am - 11:20 am BREAK

11:20 am - 12:00 pm Database handling and querying continues

  • accessing search features through JChem Cartridge and JChem Web Services
  • advanced search features
  • database migration

12:00 pm - 1:00 pm LUNCH

1:00 pm - 1:30 pm Property calculation

  • phys-chem property prediction and calculation using Calculator Plugins
  • implementing custom calculators with Marvin Services
  • using built-in and custom calculators from desktop apps, API, command line and through Chemical Terms

1:40 pm - 2:00 pm Structure analysis

  • Virtual screening and similarity searching compounds using descriptors
  • Single level and hierarchical clustering
  • R-group decomposition of structures

2:00 pm - 2:30 pm Reporting

  • accessing the ChemAxon toolkit through KNIME nodes and Pipeline Pilot components
  • generating reports and Office documents in Instant JChem

2:30 pm - 2:40 pm BREAK

2:40 pm - 3:00 pm .NET API

  • available features of the .NET API
  • overview of visual controls
  • using the ChemAxon .NET API from ASP/.NET environment

3:00 pm - 3:40 pm Instant JChem platform apps

  • extending Instant JChem using Groovy scripts
  • overview of several scripted apps: next query button, a simple registration system, creating GUI panels

3:40 pm - 4:00 pm JChem Web Services

  • introduction to JChem Web Services’s REST API
  • overview of utility functions of the server
  • showcase of JavaScript based web applications

KNIME Workshop

Integration Workshop

Similar in function to Pipeline Pilot and the InforSense platform, KNIME is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, predictive analytics, visualisation and reporting. The open integration platform includes over 1,000 modules (nodes), which integrate third party functionality, like ChemAxon's.ChemAxon partnered with the Infocom five years ago to build nodes for KNIME to make our cheminformatics functionality available from within the KNIME platform.

The full day session will overview KNIME, the ChemAxon functionality available and will then explore some more chemistry centric workflows and follow up with downstream processes such as data mining, analysis and reporting which can be useful to chemists and life science researchers.

Agenda of KNIME Workshop

Program might change

9:00 am - 9:40 am KNIME introduction and overview

9:40 am - 10:00 am Infocom/ChemAxon nodes in KNIME

10:00 am - 10:40 am Managing JChem structure databases

10:40 am - 11:00 am BREAK

11:00 am - 12:00 pm Exploring drug discovery workflows

12:00 pm - 1:00 pm LUNCH

1:00 pm - 2:30 pm Other aspects of KNIME: data mining, analytics and reporting

Markush Open Day

Integration Workshop

In collaboration with Thomson Reuters we introduce a major new Markush evaluation platform and outline a new offering to simplify and accelerate chemical IP consideration. The all day session for content users, will be of interest to content IP searchers and patent professionals working with chemistry within research and legal environments.

ChemAxon’s Markush technology is a major step forward in simplifying common workflows which consider chemical IP processes involving Markush structures. By supporting Thomson Reuters Markush structures and other IP content, users can; create sub-structure and full structure queries which can also include Markush features; perform partial and random enumeration of Markush hits and queries; avoid assembling or disassembling scaffolds/fragments and; query and review other relevant data available from within Thomson Reuters content.

Agenda of Markush Forum

Program might change

9:00 am - 9:10 am Executive introduction

9:10 am - 9:40 am Thomson Reuters: Derwent and Markush

9:40 am - 10:10 am ChemAxon structure search, enumeration and Markush

10:10 am - 10:25 am Introducing a new service to explore Thomson Reuters Derwent Chemistry Resource (DCR), Derwent World Patents Index (DWPI) in one place

10:25 am - 10:40 am Evaluation group feedback

10:40 am - 11:00 am BREAK

11:00 am - 11:15 am Hands on with the Evaluation

11:15 am - 11:50 am Introduction to Instant JChem Markush functionality

11:50 am - 1:00 pm LUNCH

1:00 pm - 2:30 pm Hands on training with the Service evaluation

One to One Session

Right after the workshops, preceding our Monday evening social event we will have a One to One session, where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group, decision area will have a discussion table where ChemAxon experts will be on call.

We plan to start the one hour long session at 4.20 pm in the Sessions rooms.

List of Topics

Each topic will have a table

  • JChem Base, JChem Cartridge, Markush technologies
  • Marvin, Marvin for JavaScript and Structure I/O
  • Reactor, Fragmenter, Metabolizer, Structure Checker and Standardizer
  • Screen, JKlustor, MarvinSpace, Screen 3D, Generate 3D, LibMCS and Calculator Plugins
  • Instant JChem
  • JChem for Office, JChem for SharePoint, .NET
  • JChem Web Services, Plexus
  • Compound Registration
  • Naming: Name to Structure, Structure to Name, Document to Structure, Document to Database and Chinese Name to Structure
  • Biologics registration
  • Business