KNIME Cheminformatics Workshop September 2014

The 2nd KNIME Cheminformatics Workshop was hosted by Vernalis in Cambridge on September 29th 2014. Thanks to Steve R and James L for taking notes.

Topics

Dave Morley brought this up, and most other users agreed, that a "real" versioning mechanism (GitHub, Mercurial, SVN etc) was needed

Various users reported having investigated using SVN or Mercurial in KNIME
Thorsten explained that the KNIME explorer view does not show the Eclipse Project explorer "add-ons" – e.g. commit status
Need an Import from … repository option under import workflows

Lilly and Vernalis have independently implemented generic frameworks to access their internal webservices
Different companies have different architectures, so probably these will remain bespoke
James L / Steve R may be able to liaise around shared issues

Identified as important in April meeting
Both Vernalis and Lilly working on new MMP nodes, with a view to release. Complementarity between functionality of the nodes (Vernalis – multi-cut, no data columns, split fragmentation and MMP generation)
Lilly nodes currently in legal approval
Vernalis in advanced development, and nearly release-ready, but again require approval
Steve R / James L should liaise to ensure overlap is avoided

See Steve's presentation
See Matched Pairs
Timed loops (run for / to)
Pause nodes (wait for / to)
Interest in Vernalis Timed loop / delay nodes – We will seek permission to release asap
Ertl Scaffold keys (in RDKit)
Co-ordinate manipulations in RDKit (Rotate about axes, align to principal axes etc)
Read/Write Variables nodes

Sam W described some of the internal Lhassa Limited nodes, and interest in a number of them was expressed.

Lot of interest in this, either for small or macro-molecules
Richard S been using GLMol
Richard S / James L / Dave M (& others?) to share experiences with various viewers
Maybe easier with the new JS-based views and quickforms
James L showed the multi-molecule sketcher from Lilly. Everyone else wants it too!

Nodes needed – SDR to investigate which nodes where in development at Vernalis, as we already have 1 fingerprint node released – these are relatively easy pickings to add to our contribution!
Lhassa have these nodes for BitSets, but BitVector column implementations would be useful
Are there BitVector aggregators in the GroupBy node? SDR Will look into adding aggregators for them too.

Vernalis looking at DNA / RNA / Protein Sequences based on corresponding BioJava sequence objects – still a work-in-progress
James L suggested possible Lilly contacts
Ultimately, depends on use-case
Some discussion around a HELM or xHELM datatype
- Would need careful definition of what is required for the types
- Utility?
- Viewer?
Possible topic for KNIME partner meeting?

Lilly have implemented extensive logging of node configure /execution events – might be able to share stats, or implementation details?

Easier node creation for developers
- a graphical interface for drag-and-drop dialog creation, which also handled settings models in NodeDialog and NodeModel classes
- Alternatively, an Add SettingsModel... menu option, which deals with the creation / load/save/validate methods automatically to reduce typing?
- Wizard for column rearranger or full-blown execute methods
- Enhancement to current wizard, which asks for number of ports, number of views, port types, and provides appropriately ‘adjusted’ code in the node model / node factory classes
Workflow preferences
- E.g. default settings for automatic chemistry type conversions
Fulltext search in node repository
Integration of GLMol in WebPortal
More than one report per workflow
Reports distributable in meta/subnodes
Easier molecule input quickform (currently needs at least two nodes)
"Linked" workflows in local workspace that can be synchronized with server
Select all nodes between two selected nodes in workflow editor