HELM Resources
- Claire Bellamy (Unlicensed)
This is the old HELM Wiki Space.
Please go to http://wiki.openhelm.org/ for the latest information
- HELM Notation
- HELM Web-editor
- HELM Antibody Editor (HAbE)
- HELM Toolkit
- About the HELM Project
- HELM Editor
- HELM Best Practices
- Peptide and Nucleotide Ambiguous Monomers
- Blobs and CHEM{*}
- Monomers in mixtures or alternative lists
- Polymer mixtures and alternatives
- Ambiguous bonds
- Annotations and how to use them
- Monomer numbering and hydrogen bonds
- Oligo backbones - phosphate and sugar quirks
- Complex monomer connections
- Changing the direction of backbone connections
- HELM in Online Databases
- HELM Parsers and Writers
- HELM Challenges
- Search
- Monomer Discussion
HELM is both a notation, and a set of tools and applications that implement the notation. The tools are available as open source software released under the permissive MIT licence.
All the HELM code is on GitHub.
Move to Java 8
From September 2018 new changes to the HELM code have used 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.
This wiki is the main source for information about HELM and its tools. Please have a look around and get in touch if you can’t find what you need, or want to connect with other HELM enthusiasts.
Try out our free open-source web-editor
HELM has a wide and growing ecosystem and can be used at various levels: from facilitating information exchange between organisations to forming the foundation of your biologics infrastructure.
External information on HELM
BioIT World article - Universal language: The Pistoia Alliance Takes on Indescribable Biology
GSK use of HELM for registration Pistoia-Alliance-HELM-GSK-BIOVIA-Case-Study.pdf
Printable Leaflet
A history and overview of the HELM project is described in this leaflet.
Forum
Please use the issue list in GitHub to post general HELM questions (and feel free to add answers to other peoples!).
Code defects should be discussed in the respective repository.
Code Orientation
If you want to get started with the code, and need a general overview please look through the code orientation video below. The slides are included for completeness, but much of the information was a live demo, so please note that they do not contain everything.
More detail is available in the application specific pages.
Wikipedia
We are even on Wikipedia! Not sure who added us, but many thanks to whoever it was.
https://en.wikipedia.org/wiki/Hierarchical_Editing_Language_for_Macromolecules
FAIR
HELM has an entry on the FAIR resource https://fairsharing.org/bsg-s001222/ and is pleased to support the initiative to make information Findable, Accessible, Interoperable and Reusable.