Track 3: Software Applications and Services

As data generation increases, there is a need for workflows that are reproducible across infrastructures, able to empower scientists and researchers to apply cutting-edge analysis methods. A main challenge is scientific data is not centralized or standardized and is fragmented – from instrumentation to clinical research to legacy software. The Software Applications & Services track explores how biopharma companies are utilizing software tools to leverage data platforms to advance data strategies. Themes of case studies that will be presented will focus on data analytics approaches, data methods and standards approaches, transparency, efficiency, security, and cost-effective solutions.

Final Agenda

Tuesday, April 16

7:00 am Workshop Registration Open and Morning Coffee

8:0011:30 Recommended Morning Pre-Conference Workshops*

W1. Data Management for Biologics: Registration and Beyond

12:304:00 pm Recommended Afternoon Pre-Conference Workshops*

W9. Research Project Management

* Separate registration required.

2:006:30 Main Conference Registration Open


5:007:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, April 17

7:30 am Registration Open and Morning Coffee


9:45 Coffee Break in the Exhibit Hall with Poster Viewing

beacon Hill

10:50 Chairperson’s Remarks

Robert Zeigler, PhD, Director, Customer Solutions, L7 Informatics, Inc.

11:00 Making Clinical Data Available to Researchers at the Princess Máxima Center for Pediatric Oncology with tranSMART and cBioPortal

Patrick Kemmeren, PhD, Principal Investigator, Princess Máxima Center for Pediatric Oncology

The Princess Máxima Center for Pediatric Oncology ( is the centralized pediatric oncology center for all children with cancer in the Netherlands since 2018. As a new institute, the Princess Máxima Center has had the opportunity to set up their research IT infrastructure right from the start, with limited legacy software to take into account. By building a Central Subject Registry (CSR), the center’s researchers have full access to pseudonymized data from all relevant hospital data sources in a timely manner. At regular intervals the data from all hospital data sources are exported, transformed and pseudonymized, to be loaded in both the tranSMART and cBioPortal data warehouses, where the center's researchers can easily create their 'shopping list’ for patients and samples of interest. The oncology center even extended the Glowing Bear user interface to notify researchers by email when new patients of interest are available, to ensure no time is lost waiting for research data and samples.

11:30 CO-PRESENTATION: Building a Standards-Based Clinical Data Resource for Cancer: Challenges, Goals, and Progress

Eva Lepisto, Data Services Team Lead, Dana-Farber Cancer Institute

Oncology’s pioneering role in precision medicine has led to routine tumor sequencing; Dana-Farber has clinically sequenced more than 30,000 tumors. However, the incompleteness and inconsistency of clinical data from EHRs and other sources present significant challenges to building the patient-specific diagnosis, treatment and outcome data that are required to discover correlates to genomic data that inform diagnosis, prognosis, and personalized treatment. At DFCI, we are striving to improve the quality and coverage of clinical data for translational research and clinical decision support. In this presentation, we will describe the standards-based data model we have created for representing cancer patient phenotypes, along with a curation software platform we have developed to streamline abstraction of unstructured data into the standard data model and NLP approaches to populating the same model from clinical text.

Discngine 12:00 pm CO-PRESENTATION: Discngine presents 3decision, a Collaborative Platform for Structural Knowledge Management

Eric Le Roux, CEO, Discngine

Peter Schmidtke, Scientific Project Manager, Discngine

Discngine develops innovative IT solutions for Life Science research. In 2018, It launched 3decision, a web application that combines a fully annotated & searchable protein structure database and a web-based user interface with state of-the-art structural analytical tools. The user interface is designed to give molecular modelers, medicinal chemists and structural biologists a common ground for structure-based drug discovery.


12:15 CASE STUDY: How a Top Pharmaceutical Company Supports Scientific Discovery with Contextualized Information Retrieval

Michael Iarrobino, Senior Product Manager, Copyright Clearance Center

A pharmaceutical company needed a better way to support scientific discovery and realize the value of its information assets. But, with siloed data, a lack of awareness of available licensed resources, and multiple discovery workflows it was taking researchers too long to find information and synthesize data to advance research. In this session, learn how the organization tackled these challenges.

12:30 Session Break

IDBS12:40 Luncheon Presentation I : Keys to Success in Preclinical Informatics Development; All About That Data

Graeme Dennis, Commercial Director, Pre-Clinical Pharma IDBS

In the R&D industry today, beleaguered system implementations are more common than anyone would prefer to admit.  Data harmonization tasks, expectation management, and risk mitigation opportunities can pass before their urgency is even fully appreciated. This 30-minute talk will explore the keys to success for developing a data-centric approach to R&D, which acknowledges the breadth of project workstreams.


1:10 Luncheon Presentation II: Certara Integral: Next Generation Data Repository

Kevin Trimm, Senior Director, Product Strategy & Services, Software, Certara

A successful drug development program relies on data being centralized in an accessible, understandable, mineable, traceable, and secure location for analysis and interpretation.  Provisioning data to scientists in an organized manner with high performance can be a challenge.  Certara Integral is a validated and 21 CFR Part 11 compliant software as a service data and model repository utilizing the CDISC data model and Amazon Web Services Infrastructure, providing an intuitive solution to this problem.

1:40 Session Break

Beacon Hill

1:50 Chairperson’s Remarks

Susan A. Roberts, Senior Director, Scientific Computing, Vertex Pharmaceuticals

1:55 Turning WGS Genetic Testing into a Dialogue between Physicians and Labs with GenomeDiver

Christian Stolte, Data Visualization Designer, Informatics Research Innovation, New York Genome Center

Developed as part of the NYCKidSeq project, GenomeDiver fosters a dialogue between the clinician and genetic testing lab. The software leverages the physician’s knowledge of their patient by asking them to provide additional information to the lab, which then forms the basis for reanalysis. It delivers understandable information about mutations in the entire genome, using knowledge about functional variants coming from an increasing number of public sources, in particular the GTEx project.

2:25 Crowdsourcing Network Biology

William Hayes, PhD, CTO, BioDati, Inc.

Through the use of a publicly available application, BioDati Studio, and an open standards-based language, BEL, we provide an application and platform to allow users to take standard, shareable notes as BEL Nanopubs. These Nanopubs are processed into Edges, which are stored in a database and used to create networks for any biological context, drive insights, and power analytics. BioDati Studio powers network biology by providing the capability to host biological knowledge from a variety of sources and provide powerful knowledge sharing/collaboration for the life sciences.

2:55 Scientific Information Management (SIM) – Elevating the Health and Science Process to the Next Level

Robert Zeigler, PhD, Director, Customer Solutions, L7 Informatics, Inc.

Precision medicine and new classes of treatments, including gene and cell therapies, require a new category of companion informatics platforms that automate and synchronize complex drug discovery and therapeutic processes. This talk will discuss how to enable SIM from bench to bedside in life sciences and healthcare organizations with real-world case studies.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing, Meet the Experts: Bio-IT World Editorial Team, and Book Signing with Joseph Kvedar, MD, Author, The Internet of Healthy Things℠ (Book will be available for purchase onsite) 

Beacon Hill

4:00 beRi Suite of Tools for Managing the R Language

Robert Gilmore, Researcher II, Psychiatry and Human Behavior, University of Mississippi Medical Center

beRi “beri environments for R installations” is an R environment, R installation, and R package management system for the R programming language. beRi is a suite of Python packages composed of the following components: (1) renv, a virtual environment manager for R; (2) rinse, an R version manager; and (3) rut, an R utility tool for installing packages. These CLIs were originally developed at Hackseq 2018 at which the project won by popular vote.

4:30 Design Ops in Life Science UX

Kirk Brote, Owner & Founder, Kirk Brote Consulting; Former Director, Communications Team, UX Working Group, The Pistoia Alliance

Software end users in life science deserve easy to use, intuitive software that allows them to focus on science and push forward the boundaries of human knowledge. Unfortunately, because the problems they work on are by definition new and the workflows they follow complex, that is often not the case. Tools and systems that are hard to use and difficult to onboard new users to restrict discovery. More challenging still, every individual scientist that creates their own tools, and tools for others, brings into the process their own personal bias about how the system should work. Design Ops for life science allows for the creation of pattern libraries, interaction systems, and other common UX elements to ensure those making tools follow a standard and consistent set of rules, making software much easier to use and opening up discovery. Last year the Pistoia Alliance introduced a UX toolkit specific to Life Science to address the lack of design methodology in the biopharmaceutical industry. With the introduction of Design Ops for Life Science UX, it is now possible to show concrete steps for how to take those tools and workflows and distribute them across all of your working teams. By adopting a standardized design practice based in both human cognition and perception as well as human centered design leads to usable, efficient tools for scientists, which can accelerate innovation, a critical goal in the bio-IT space, where stakes are high and patients are in need.

Dassault-Systems 5:00 Data Integration and Analytics Strategies for Pharma

John McCarthy, Pre Sales Director, Global Life Sciences, Dassault Systemes

Automated lab procedures, sensor technologies and digitalization has increased the amount of available data. Companies need flexible workflows that enable ad hoc analytics, fast indexing/ontology building and a way to manage best practices within their organization, and need to be able to integrate their own data/data collected from the public domain, and productize the resulting models generated by their teams.

5:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

Thursday, April 18

7:30 am Registration Open and Morning Coffee


9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

Beacon Hill

10:30 Chairperson’s Remarks

Gurpreet Kanwar, MBA, PMP, Senior Project Manager, NAV CANADA

10:40 CO-PRESENTATION: Implementation of Complex Innovative Designs (CID) at Janssen

Raj Malathker, Manager, Quantitative Sciences IT, Johnson & Johnson Pharmaceutical R&D

Vlad Dragalin, PhD, Vice President & Scientific Fellow, Global Quantitative Sciences, Janssen Pharmaceuticals R&D

Both the 21st Century Cures Act and the PDUFA VI legislations call for wider use and acceptance of complex innovative clinical trial designs with the goal of streamlining drug development and bringing needed new medicines to patients in a more timely and efficient manner. Importantly, adaptive designs will provide ethical advantages and make clinical trials more attractive for patients, allowing a larger number of participants to receive the most promising treatment regimen in a shorter timeframe. We are the first PhRMA company to build an in-house platform, aptly named ACTIVE (Adaptive Clinical Trial’s Interactive Virtual Environment), for efficient implementation of such complex innovative designs.

11:10 Effectively Complete Your Projects

Gurpreet Kanwar, MBA, PMP, Senior Project Manager, NAV CANADA

Most organizations say they have too many projects on the go and are not able to manage with backlog still growing. They want to achieve a high throughput of successful projects, however many are unable or unwilling to allocate an appropriate level of resourcing to approved initiatives. Methodologies to execute projects are not consistent and lacking standard processes. There is a need to manage project delivery expectations, satisfaction of business stakeholders and balance the demand to help them achieve their strategic goal.

11:40 Increasing the Velocity of Team Data Science

Gregg TeHennepe, Program Manager, Computational Scientist, The Jackson Laboratory
Beena Kadakkuzha, PhD, Research Project Manager, The Jackson Laboratory

Learn how the Jackson Laboratory has leveraged concepts and processes from Agile and Scrum to significantly increase the effectiveness and pace of teams focusing on data science.

12:10 pm  Enjoy Lunch on Your Own (Lunch Available for Purchase in the Exhibit  Hall)

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing


1:55 Chairperson’s Remarks

Chris Dwan, Senior Technologist and Independent Life Sciences Consultant

2:00 PANEL DISCUSSION: High Performance Consultancies


Chris Dwan, Senior Technologist and Independent Life Sciences Consultant


Tanya Cashorali, CEO, Founder, TCB Analytics

Aaron Gardner, Director of Technology, BioTeam, Inc.

Eleanor Howe, PhD, Founder and CEO, Diamond Age Data Science

An organization must learn and understand the value of why, when and how to use a consultancy. Highly trained and skilled professional experts gather to discuss their role in leading and managing projects for organizations to help them achieve goals. They will discuss a variety of themes including the best kinds of projects to hire a consultancy for, the timeline of when an organization should hire a consultant vs. full time staff, and big challenges on the horizon. The session will feature short podium presentations, followed by a moderated Q&A panel with attendees. The topic of hiring a consulting company came up in the data science plenary keynote at Bio-IT 2018. We want to spend time at Bio-IT 2019 exploring this topic in finer detail.

3:20 KEYNOTE PRESENTATION: Trends from the Trenches 2019

Chris Dagdigian, Co-Founder and Senior Director, Infrastructure, BioTeam, Inc.

The “Trends from the Trenches” in its original “state of the state address” returns to Bio-IT! Since 2010, the “Trends from the Trenches” presentation, given by Chris Dagdigian, has been one of the most popular annual traditions on the Bio-IT Program. The intent of the talk is to deliver a candid (and occasionally blunt) assessment of the best, the worthwhile, and the most overhyped information technologies (IT) for life sciences. The presentation has helped scientists, leadership, and IT professionals understand the basic topics related to computing, storage, data transfer, networks, and cloud that are involved in supporting data intensive science.

4:00 Conference Adjourns

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