HELM Community

HELM is an open source project with an active volunteer community. Anyone is welcome to join and contribute to making HELM even better. You can do this at several levels:

  • Propose minor revisions to the code, highlight defects or make suggestions for smaller changes via our issues log on GitHub
  • Contribute your own code to expand the functionality of HELM
  • Join the project team and influence the direction of development

Joining is simple, just email us on info@openhelm.org and we will get you set up!

Currently the following companies are involved in the active project team:

But we also have a wide community of HELM adopters and contributors, all of whom are highly valued.

Current work

Ambiguity

The increasing focus of the biopharmaceutical industry on biotherapeutics R&D, has led to an increase in the preparation of complex biomolecules, including oligonucleotides (such as antisense and siRNA), peptides, proteins, antibodies, and bioconjugates. The processes employed, although sophisticated, include variability which cannot be fully controlled, thus structure of the biomolecule produced may not be fully specifiable. Ambiguous HELM has been designed to capture fully specified structural information alongside any ambiguity in the components, connection and composition, of the molecule, in a single notation, thus making the maximum information available to the researcher.

The HELM toolkit will be updated to include this functionality and made available under the permissive MIT licence. Work has started to commission a partner to develop the code.

HELM Challenges

HELM has a number of self-contained challenges that we would like to make available to developers and informatics specialists. We hope these are conceptually interesting challenges that will be fun to solve. Please get in touch if you want to take one on, as we can provide much more detail and background on ideas explored in our discussions.

Full details of the current challenges can be found on the HELM wiki resources page.

Canonicalization

Specific purposes, e.g. the registration of biomolecules, require the ability to identify and filter for distinct biomolecules to create a database without redundancies. There is some canonicalization functionality in the toolkit, but it is limited in scope and needs to be extended to include ambiguous structures.

Fragmentation

The migration of legacy molecules, many of which are stored in a chemical file format is a common challenge faced by the community. HELM represents biomolecules as polymeric structures composed of monomeric building blocks, so the first step in converting structure is to fragment the molecules into such blocks.

Searching

There is a growing need for HELM users to search the molecules being stored in corporate repositories. Although there is a limited proof of concept which allows exact match and substructure searching at an atom/bond and sequence level, there is much more that should be done. Ambiguity creates an added level of complexity that is not currently supported.

Technical information and help

The resources pages have been developed to help new users get started, but the project team also acts as an active source of technical expertise on HELM. If you have HELM-related questions or are starting to use HELM and would like an overview of the code to help get started, please get in touch and we will see what we can do to help.