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Marking the Completion of One Phase, Pivoting to the Next

Over 120 people from over 50 organizations connected at Amgen in Cambridge for Allotrope™ Connect in November. The public session featured presentations from Member companies and vendors in the Allotrope™ Partner Network (APN) describing the latest work on implementing the Allotrope™ Framework and data standards in products and IT solutions. Allotrope Foundation® and Partner Network Members continued working Wed. and Thurs. in three parallel technical and strategic tracks.

Three major themes emerged over the course of the week:

1. First Allotrope™ Data Model (ADM) ready for release! The work of the technical community (several Working Groups, contributions of some member projects, and our partners at OSTHUS) have delivered the data model to complete the Chromatography use cases (LC-UV), as well as developing a scalable, modular approach to model development as a whole. This will be a subject of a future article, but in summary, the meeting featured a preview of a ‘catalog’ of reusable data model patterns- small subgraphs that make building models for new techniques more efficient, and ensure consistency across different data sets and domains. This constitutes the completion of the first ADM release, the final of the three phased releases, following the Allotrope™ Data Format (ADF) and Allotrope Foundation® Ontologies (AFO) releases in 2017.

Further, different levels of depth and complexity in data models can be leveraged according the needs of the use-case. The current pipeline includes models in various stages of development for a broad range of techniques (some nearly complete) including extensions to LC-UV and Gas Chromatography, LC-MS (single quadrupole), as well as instruments like Cell Counter, Blood Gas Analyzer, pH Meter, Conductivity, Osmolality, RAMAN, NMR, Balance and Differential Scanning Calorimetry.

2. The technical community continues to grow and has matured to a diverse, highly collaborative and productive ecosystem. Technical tracks on Wednesday and Thursday were the most broadly attended and most successful yet, including participants from 20 organizations. In addition to deeper dives on the modelling approaches led by Helge Krieg and Thomas Weber (OSTHUS), there were hackathons on modelling for Mass Spectrometry led by Michael Athanas (ThermoFisher) and Chromatography led by Wes Schaefer (Merck & Co.), and sessions on reducing the effort for on-boarding new developers and tooling led by Don Rolph (Amgen). The community left the meeting with shared understanding and a lot of momentum going into 2019 to rapidly expand the portfolio of instruments, techniques, and most importantly- data- enabled by the Allotrope Framework and standards.

3. The pivot from single techniques or local workflows to fully realizing the vision of the digital lab. Presentations in the public forum featured companies staking out strategic ground in the digital transformation of the lab and data flow.

  • Amgen & Biovia described the realization of “The Holistic Lab Ecosystem – A Single Pharmaceutical Development Solution Modular Architecture with Data Integrity by Design” and the vision for “Semantically Driven Data Aggregation and Reporting to Industrialize the Assembly of CMC data for the eCTD.”

  • Merck provided a reflection on recovering from a cyber-event, and what it can teach us about the next generation architecture of the lab. Their roadmap for the Digital Lab will pay dividends in: end to end data capture, integration, and analysis; Io(L)T for lab instrument command and control, inventory, utilization and data collection; secure operating system and infrastructure, automated workflows, and human-machine interfaces- as well as the security to maintain business continuity in the face of an ‘event’.

  • Finally, Agilent and GlaxoSmithKline described the launch of an initiative to “Fight Entropy with Informatics” and develop a fully digital set of capabilities for the release of material for First Time in Human studies. This includes new informatics capabilities leveraging Allotrope ontologies and data models throughout.

Other presentations included updates on several other collaborations: Allotrope™ Members working with TetraScience (as a “Community Project”) to build an ADF adaptor for Empower; and the joint Allotrope – Pistoia Alliance project to build a proof-of-concept database for analytical methods, leveraging methods built using the AFO and ADM, stored in an ADF. Bristol-Myers Squibb described a functional proof-of-concept developed with Agilent and Zifo to use the Framework for Intact Mass Determination by walk-up LC/Time-of-Flight MS and the data integration in BioBook. The most novel application of the Framework to date came from the work of Dennis Della Corte at Brigham Young University to use the ADF for Protein Structure & MD Simulation results to enable the reuse of the results of computationally expensive simulations and improve the capture of parameters and setup.

We introduced a “lightning round” session into the agenda, which included brief but highly engaging talks from Elemental Machines, TetraScience, Lablicate, and Paradigm4 about their platforms, strategy, use of the Framework, and in the case of Paradigm4, even a quick demo. This was followed by an extended network session that allowed for more detailed discussions and brainstorming. Be sure to check out the presentations posted here.

As you can see, it was a very busy week.

We’re grateful for the support of this year’s sponsors TetraScience & Elemental Machines, and want to acknowledge our media partnership with IQPC SmartLab 2019. We want to again thank our hosts at Amgen, for excellent arrangements and a space highly conducive to collaborative and creative interaction.

Mark your calendar for the Spring 2019 Allotrope Connect, April 8-12, 2019, hosted by Biovia in Vélizy-Villacoublay, France at Dassault Systèmes 3DS Paris Headquarters! Stay tuned for more details and agenda.

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