NOTE
From September 2018 new changes to the HELM code will start to use Java 8 and may include some features not supported by Java 7. Please take this into account in your HELM plans. Specific details will be available in the repository release notes.
HELM (hierarchical editing language for macromolecules) is both a notation, and a set of tools and applications that implement the notation. It allows (among other things) the compact representation of complex biomolecules, includes the ability to use non-natural monomers, enables you to create conjugates of different types of polymers or small molecules and describe ambiguity.
Our wiki is the best place to start if you have a general interest in HELM. You can get easy access to compiled versions of the tools, links to the documentation including slide sets, videos and information about the community and project.
Developers will find all the open source code under this PistoiaHELM organisation.
We have an active group which meets regularly and works on extending the tools and supporting HELM. We love it when new people want to get involved, so please do get in touch.
Email us at info@openHELM.org
There are two major versions of HELM:
- HELM1 - (the original)
- HELM2 which added the ability to define ambiguous components, connections and compositions as well as more complex annotations and groups.
Some tools support HELM1 only and some also include HELM2 support:
The original HELM Editor - a Java thick client
The HELM Antibody Editor - a Java thick client, kindly donated by Roche.
There is also a toolkit to play with.
HELM WebEditor - a Javascript editor
- The webeditor depends on a a set of services which have been split into modules for easier maintenance. The diagram below shows the relationship between the components.
The HELM Antibody Editor 2 - a Java thick client containing many improvements over the first version. Also kindly donated by Roche.
Installation packs for many components are available in Maven repositories within Nexus Repository Manager, so you won't find all the binaries in GitHub.
The exceptions are:
- HELM Editor
- HELM Antibody Editor (V1 & V2)
- HELM Webeditor Javascript code
Where releases are available in the GitHub release folder.
See the individual repositories for full details.
Alternatively you can use the Docker image available in https://github.com/PistoiaHELM/pistoiahelm.github.com/tree/master/docker Full instructions are available in this folder.
Please use the issue list in this repository to post general HELM questions (and feel free to add answers to other peoples!).
Code defects should be discussed in the respective repository.
All code is released under the permissive MIT licence.