Software automation – What STAB sees as key aims? 1.Brief review of activities and recommendations (so far) 2.Reality checks 3. Things to do…

March first meeting Suggested strategy:  review suite capabilities  set up test suite – initially to be used for calibrating CHART  build up from small isolated scripts Requirements:  modular design  command line and GUI interface  database and information transfer files requirements  information retrieval from legacy code for the machine (mark-up vs. parsing)  information retrieval for users (sensible summary information) Suggested first task: Phasing from coordinates – MR pathway Data preparation (symmetry etc) SSM (Aligned models – PHASER can take ensembles/weighted transform of PDBs to SF) PHASER (refined MR models) PIRATE (bias removal/solvent flattening) Refmac-arp/warp

Meeting in Manchester on 30 September 2004 Key outcomes: STAB remit agreed: scope – all CCP4 activities related to automation, including BioXHit and eHTPX role – set targets, provide advice, monitor progress Charles Ballard – contact person for CCP4 (working closely with Peter Briggs), Tadeusz Skarzynski - contact for STAB preferred model: a bottom-up, evolutionary approach, where easy meta-tasks are first automated and they progressively joined with more and more sophisticated decision making. identified the need for a CCP4 standard for information transfer between crystallographic programs, similar to the CCP4 standards on X-ray data and map file formats (XML - the most obvious candidate for this) PYTHON framework and objects developed for DNA – to be explored as a starting point for CCP4 task automation (MR – a pilot project)

Reality checks… everything takes longer than we think… bursts of activity followed by not much going on. staffing problems – of course… fragmented nature of CCP4 – good for individual creativity (refmac, ccp4i, coot) but not suitable for large, integrated projects (?). - people funded from a variety of sources, personal career needs… - lack of true line management. joint effort only successful in well-defined projects with clearly-specified requirements (e.g.. establishing standards: mtz, map format, program input format) no clear strategy in automation – short-term goals for different projects

Things to do: snapshot of where we are in automation, who does what, what are people’s current remits, experience… what has been achieved so far (CHART?, MR) other automation efforts – which concepts worked and which did not (e.g. agent or workflow?) what tasks need automation? (data processing and analysis, phasing from coordinates and experiment, model rebuilding and refinement, ligand fitting, others?) review of CCP4i – a key element of the automation project – do we need to change it (language, information tracking, etc?) firm decisions on key standards: language (Python?), tools, information flow (databases, XML files?) within the constraints of the existing CCP4 infrastructure timely implementation and release of automated tasks

Summary… automation is not just another project within CCP4… it involves review of existing standards and project tracking. agreeing standards and means of information transfer is critical. need for getting key programmers on board (a “task force meeting”) need for clear goals with timelines