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BioIT 2019: The New “Official” Future Involves Data Sharing, Artificial Intelligence, Open Source, and More

The 18th installment of Boston’s Bio-IT World Conference was attended by over 3,400 participants and featured more than 185 exhibiting companies, both established and startups. The conference program kicked off with a great presentation by John Wilbanks, Chief Commons Officer at Sage Bionetworks, who focused in his discussion on Open Science – From Ideology to Methodology.

In his provocative presentation – with Sage Bionetworks ten years in the making – Wilbanks examined that research has seen a massive incrementalism which translates into “good in the micro, but not in the macro” or in other words we do know a lot of details about certain diseases (e.g. Alzheimer’s disease) but we still do not understand how to treat them. Wilbanks emphasized that radical changes are required which the pharma industry is longing for.  While there is a long list of “magic bullets” – e.g. microarrays, RNAi, NGS – we do appear with those to only achieve incremental changes. And with the current open science approach not much is changing, especially when it comes to impacts for the patient at the center. Some of the challenges observed are analytical challenges: we think of open science as a suite of shared methods. The field needs to think beyond that, as the crowd collectively is smarter than individual experts, and this requires the adoption of open standards. Ideally, we connect little networks to create a big network that brings together an entire suite of data (e.g. genomics, proteomics, clinical data, etc.), ontologies, data standards, tools, trials, data mining approaches, etc. At Sage open science is Just (for justification) and means:

  • Transparency increase is justification
  • Replication increases justification, but expensive
  • Registration increases justification
  • Triangulation increases justification

Wilbanks mentioned the All of Us Research Program which is trying to achieve just that – open science which enables trust via a distributed network of communities – with Sage awarded to provide the protocol (but think of the protocol as a plugin, a piece of software).

Interesting quotes from Wilbanks’ talk:

  •  “Open science is a series of patterns, such as better leveraging data commons, benchmarking, bringing analysis to the data, leveraging developer culture, and open source.”
  • “Open science is not a magic bullet – we learned some important things like the wisdom of the crowd isn’t actually that much better, most bioinformaticians do a decent job of analyzing their data”
  • We need open science to address the danger that science becomes just another sector that is consumed by a stack.”
  • “Massive incrementalism means you get grants based on papers, not fishing expeditions. So we build information in tiny little steps. Really good in the micro, but not the macro.”
  • “Open Data is one of the only ways to ensure justice in AI and algorithms.”
  • “We train our algorithms with our own data and there is bias there.”
  • “The importance of creating adequate consent trail is a central theme of open science.”
  • Vannevar Bush had a vision of collaborative science, going beyond the single investigator producing ‘paper models’ already in the 50s. Today, we are living it, for example with Sage Bionetworks.”

Quotes from various other Bio-IT talks:

  • Vijay Bulusu (Pfizer):
    • “Converting data to insights — while there has been an explosion in machine learning and big data, there has been a fundamental lack of progress and investment in improving the “quality” of data. We need to focus on the right thing, converting data to insights.”
    • “In the life sciences, we don’t have a big data problem. We have the “lots of small data” problem.”
    • Asked the audience: “If they had $1M would they improve the quality of the data or buy a machine learning platform. Nearly everyone would improve the quality of data.”
  • Chris Dagdigian (BioTeam): “We’re still bad at helping intermediate users advance to become experts. Again: mentor ship problem!”
  • Anthony Philippakis (Broad Institute): “Genomics is at risk of becoming the sport of kings, where only the wealthy can play.”
  • Kees van Bochove (The Hyve): “The biggest challenge we have for AI is getting clean data.”
  • Sandy Aronson (Partners Healthcare): “AI and Apps are not the solution in hospitals — it’s the more effective care workflows hat the apps and algorithms enable.”
  • Susie Stephens (Pfizer): “Lots of AI pilot programs. There is much more work to be done to begin to operationalize AI and automate the use of AI and related insights throughout the business.”
  • Dana Vanderwall (BMS): To successfully achieve digital transformation of the lab, it needs to be automated, self-documenting, and interoperable.”
  • Anne Carpenter (Broad Institute): “We need more user friendly interfaces for AI to allow average biologists to use the tools.”

Coinciding with Bio-IT were a number of major announcements as listed below:

Best of Show Award

Five commercial products were selected and honored among the 31 originally considered new products or product updates with 12 finalists. Winners were selected across four product categories:

  • “No BS AI” Award: Genedata AG for Genedata Imagence 1.0 – a deep learning-based solution for phenotypic imaging and corresponding workflows based on convolutional neural networks.
  • “Patient-Focused Software” Award: Kanda Software for Trapelo & LifePod Virtual Caregiver – enables alignment of decision making and reimbursement policies with most current clinical evidence in molecular biology
  •  “Nailed It” Award: PetaGene for PetaSuite Protect v1.0 – enables organizations to manage access to their genomic data by internal and external teams, secured with fine grain regional encryption and deep auditing of data usage.
  • And the “People’s Choice Award” went to the faceted browsing and visual analytics ‘2019 Linked Data Ingestion Engine’ created by ONTOFORCE.

Innovative Practices Award

New this year was the Innovative Practices Award which highlights outstanding examples of how technology innovations and strategic initiatives can be powerful forces for change in the life sciences, from basic biomedical research to drug development and beyond. Winning entries included:

Following is a review of different announcements timed for release with Bio-IT 2019 and spanning commercial product launches, new partnerships and collaborations, product integrations, and other interesting and relevant topics.

Strategic partnerships and collaborations

New product announcements

  • 1Cellbio announces custom targeted bead program to accelerate next phase in single-cell analysis The new program will supply select customers with its proprietary inDrop™ hydrogel beads synthesized with custom primers that target user-specified transcripts. These are synthesized with custom primers that target transcripts selected by the client which supports focus on sequencing depth on specific genes of interest.
  • Seven Bridges Launches Automation Tools and Services which enables biotechnology and biopharmaceutical companies to increase productivity by bringing a diverse set of users into one environment. Scripts written with the Python Automation Development Kit (ADK) automatically gain concurrency, dependency management, memorization, retries, and execution logs, enabling developers to focus on business logic and ultimately, reduce their lines of code by up to 80%.
  • Zifo RnD Solutions Announces Launch of Sci-Desk an on-demand, cloud based, Scientific Application Support-in-a-box. Sci-Desk offers comprehensive managed services for Scientific & lab computing systems spanning Discovery, R&D and manufacturing industries.

Other Announcements

Brigitte Ganter

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