HELM Web-editor

The HELM web-editor is the opensource tool to create and edit HELM molecules.

The webeditor fully supports HELM2 as well as the more basic HELM1 features. It also includes a monomer manager which allows you to manage your monomer library and a rule manager that allows you to create and apply your own custom changes to HELM molecules. 

Trial version

A demo version is available for you to try the functionality. Please note that this is for trial use only, if you want to use it in a production environment please take the code and deploy it on your own servers.


The demo web-editor uses the monomer set supplied with the old HELM editor. However, the code includes both this and an alternative set curated by Ionis with a larger range of nucleotide monomers.

The demo monomer manager allows user to add, delete and edit monomers, something you will want to restrict inside an organisation! Public use means the original set is likely to change over time. We will keep an eye on this and reset back to the original monomers every now and then. Please be aware when using!

User guide

A user guide is available



The project has taken a modular approach to the architecture. The diagram below shows the components, each of which can be found in their own repository.
You can use either CDK or Marvin, but do not need both.

Source Code

All HELM code is published in GitHub.

The web-editor code is at: https://github.com/PistoiaHELM/HELMWebEditor.

The webeditor Javascript code will be available in NPM soon.


An installation guide is available in the readme file at https://github.com/PistoiaHELM/HELMWebEditor

Compiled code for the Java components is available in Nexus https://oss.sonatype.org/#nexus-search;quick~org.pistoiaalliance.helm which provides an easy way to manage the dependencies.

Licenses and restrictions

HELM is an open source project and all components are released under the MIT license

The HELM web-editor has some dependencies on third party tools, all of which are open-source. Details of their licences are below:


dojo toolkit