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May 2020 Allotrope™ Connect

Allotrope Connect

May 2020 Allotrope Connect

Public Session Day 2, May 11th: Abstracts

10:00am - Zifo  RnD Solutions: Efficiently and effectively integrate and on-board your applications and instruments through a configurable ADF generator solution.


Bagavathi "Buggs"Rajan Kathiresan, Zifo RnD Solutions

Paul Denny Gouldson, Founder and Lead Consultant, Avidity Partners Ltd.

Abstract: Several organizations have been undertaking their journey to adopt Allotrope standards. This can take quite a lot of effort considering the typical lab landscape with a large number and diversity of applications and instruments that need to be integrated and managed. There are a number of well-documented challenges with the sheer number of instrument models and their native formats that need to be aligned with the Allotrope standards. To accelerate this process, Zifo offers a solution that can be configured with relative ease along with the support services to build connector libraries, manage ongoing integrations and provide a systematic process and methodology to deliver the business value and support down stream usage of the data.

10:30am - ZONTAL: Bringing Allotrope to the people. Enterprise ready ingestion, conversion, & management of ADF files


Dennis Della Corte, VP Marketing & Sales, ZONTAL

Abstract: Together with leading Pharma companies and as a member of the Allotrope Partner Network, ZONTAL developed a highly scalable digital integration hub. The integration hub is able to ingest a variety of source data files and convert these into Allotrope Data Files (ADF). Further,  a holistic information life cycle management of ADF files from creation - over preservation - to reuse is now available to members of Allotrope Foundation. Here, we will showcase how raw data is transformed to ADFs that can be used to streamline audits and power data science.

11:00am - Biogen & TetraScience: Harnessing the Power of Allotrope: From Data Models to Data Analytics


George Van Den Driessche, Informatics Lab Specialist, Biogen

Evan Anderson, Delivery Engineer, TetraScience

Siping "Spin" Wang, CEO and Co-Founder, TetraScience

Len Blackwell, Associate Director, Analytical Development & Strategic Analytics, Biogen

Abstract: Collectively, pharmaceutical companies recognize the value of creating and implementing instrument data standards, like those created by Allotrope Foundation. However, the limitations faced for adopting these standards are two-fold. First, the creation of standardized files, in the case of ADFs, are technically challenging and require specialized IT resources. Second, accessing these files programmatically using common data science tools (e.g. python and R) is challenging. One solution that overcomes these hurdles combines the efforts of the Allotrope Modeling Working Group with the TetraScience File Converter. The Allotrope Modeling Working Group has adopted a crowdsourcing approach that leads to fast development of leaf node data models. These data models are then applied using the TetraScience File Converter. File conversion is performed by fitting raw instrument files into an Intermediate Data Schema JSON (IDS-JSON); the IDS-JSON is then mapped to the Allotrope leaf node model and the ADF file framework to generate an ADF file. These combined resources provide an avenue for companies to quickly and efficiently generate ADF files. It also enables data scientists to access the information stored in ADF files with common tools, like Python, by utilizing the underlying HDF5 file framework of an ADF. During this talk, Biogen will highlight how our partnerships with TetraScience and the Modeling Working Group were applied to the Beckman Coulter Vi-CELL Cell Counter instrument.

11:30am - Sartorius: Sample Preparation Working Group Progress


Reinhard Baumfalk, Head of Product Development, Sartorius

Thomas Schink, Head of Embedded Computing, Sartorius

Abstract: Every analytical process contains usually also a precedent sample processing step.  While this step so far is only seldom documented in the analytical results itself it´s common sense that a deviation during the sample preparation can have a serious impact on the data quality, reproducibility and integrity of the results.


The Sample Prep Working Group proposes a modular data model to manage the high variety of sample prep processes, with focus on documentation of all quality critical information. The concept covers not instrument results only, but also the documentation of manual (in this sense “analog”) steps as well.

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