Worldwide Protein Data Bank wwPDB Common D&A Project Full Project Team Meeting Rutgers March 16-19, 2010

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Attendees:

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Review of Deliverable Objectives 1Q2010 Deliver production functionality that will provide a significant impact on the annotation workflow. –Implement the chemical and model coordinate sequences issue resolution and integration using the Master Format. –Graphical User Interface for the annotators  Sequence Editor –Build the “GO BACK” functionality architecture  Session management and Tracking infrastructure  WFE/API  WFM

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Deliverable Details Master Format. Finalization of Physical Data Exchange Annotator graphical interface for sequence functionality  Extended API Tracking DB creation/support  Extended Work Flow Engine (WFE)  Work Flow Manager (WFM)  Work Flow Manager User Interface (WFM UI)  Integration of this “module” of new functionalities into the existing workflows.

Worldwide Protein Data Bank wwPDB Common Tool Annotation Progress PDBe Sequence Processing Ligand Processing Ligand Processing Release Processing Geometry CK Validation Geometry CK Validation Calculated annotations (Bio Assem) Calculated annotations (Bio Assem) Corrections (water trans, pro- chiral ck) User Interface WFE/API Requirements Design Progress Tracking/ Status wwPDB Common Tool Sequence Processing Ligand Processing Ligand Processing Integration & Release Processing Geometry CK Validation Geometry CK Validation Calculated annotations (Bio Assem) Calculated annotations (Bio Assem) Corrections (water trans, pro- chiral ck) ADIT RCSB Autodep Release Processing Seq. Editor Ligand Processing Ligand Processing Geometry CK Validation Geometry CK Validation Calculated annotations (Bio Assem) Calculated annotations (Bio Assem) Corrections (water trans, pro- chiral ck) CIF - PDB PDB - CIF 4.1, , ,

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Goals for this meeting  Take advantage of face to face project team opportunities –Some current Data content/policy issues –Critical path development issues  Complete the design and development plan for the full sequence processing module  Complete the documentation of the Ligand processing module functional and technical requirements and design.  Take the opportunity for Course Correction –Adjust requirements, design and development strategies as needed. –Document lessons learned and adjust plan accordingly  Refine our design and development documentation strategy.

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Sequence Processing Current Task List April Objectives  Complete development and testing of Sequence Editor unit – near completion  Complete integration of Sequence Editor unit with existing pipelines – March 31  WFE/APIs instantiated for the full Sequence Processing module against the existing functionality, with preliminary WFM functionality in test, independent of current pipeline. End of April

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Functional Requirements: Process Overview With GO BACK functionality Graphical User Interface WFE, WFM

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Sequence Processing – the whole megillah  Annotator Team and Tech Team to review the remaining process steps for Sequence Processing –Elaborate on existing process maps – ID process order flexibility –WFM Discussion –Map existing functional software components to workflow components  Identify and resolve software choice issues FASTA vs BLAST  Tech Team – review API and WF implications, granularity?  Tech Team – Design and development plan

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Next Target – Ligand Processing With GO BACK functionality

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Ligand Processing – Functional Requirements Annotator exchange – experience with and analysis of existing work flows Draft of new TO BE process – Level 1  Annotator Team to elaborate and drill down - Level 2,3  Annotator Team to create decision trees and SIPOCS for all process steps.  Annotators to begin Use Case documentation  Annotator Team to map existing functional software components to the proposed workflow components.  Annotator Team to mock up interfaces for process interactive components

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Ligand Processing – Technical Requirements and Design  Tech Team to review the requirements  Review Functional software components  Capture technical requirements  Complete the draft design for the Ligand processing module  Create and initial plan.

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Rules of Engagement  Meetings will start at 8:45 AM each day  We will all work to gain the best advantage of our time together – during breaks only.  All discussions will be documented – process maps, tech requirements, design, glossary additions, use cases, CONCERNS.  All documentation will be a Team effort.  Decisions will be made as much as possible by consensus.  If a vote is necessary we agree to adopt the group majority vote.

Worldwide Protein Data Bank Common D&A Project March 2010 Project Team Meeting Next Steps  Complete meeting reports – –Appropriate functional, technical and design documentation –Implement development documentation strategy –Sequence processing delivery plan –Initial Ligand processing development plan  Schedule PI update/review of the project plans – Second week of April target