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IBM’s Watson Health division – How will the Future look like?

Reporter: Aviva Lev-Ari, PhD, RN

 

Comment regarding Technology companies:

On April 18, 2019, IBM halting sales of Watson AI tool for drug discovery – STAT

https://www.statnews.com/2019/04/18/ibm-halting-sales-of-watson-for-drug-discovery/?utm_source=STAT+Newsletters

 

LPBI Group’s view on this news from IBM has few parts:

  • We believe that IBM needed to reorganize its application development efforts using AI in the Watson Business Unit. Drug discovery was targeted for downsizing. Watson will continue development of applications for Diagnosis applications. The realignment at IBM Watson is related to performance in the last three quarters when revenues decrease was recorded.
  • IBM will focus on other health units to compete with Oracle’s venturez in Health.
  • Watson requires high performance most sophisticated hardware and software. This was IBM focus on the high end computing machines since mid 70s with Series 360. They will not abandon that mission to be #1 in the World in high end market.
  • LPBI Group’s IP is most suited for IBM Watson for Diagnosis. Therefore we as a Team decided not to remove IBM Watson from our Opportunities Map.
  • We will prioritize among the players in the IT Sector and IBM will be the second tier for 2019-2020.

 

STAT News: The past year has been a tumultuous one for IBM’s Watson Health division.

In June, the team that manages the supercomputer once touted as a revolution in cancer care started to scale back its hospital business, citing weak demand. In July, internal IBM documents revealed that the supercomputer often delivered cancer treatment advice that was not only incorrect, but unsafe for patients as well. In November, a mass exodus began to erode the elite team of medical specialists and engineers tasked with fixing the artificial intelligence software. And in December, Watson Health’s fallback strategy — expanding operations in China — began to unravel.

In spite of all of this, IBM CEO Ginni Rometty kicked off 2019 with a bold statement — that IBM would not roll back its use of Watson in health care. But as STAT national technology correspondent Casey Ross reported last week, IBM is now halting its development and sales of a drug discovery and development product that uses Watson artificial intelligence software.

For more stories like this from health tech industry giants like IBM, Amazon, Google, and Apple, subscribe to STAT Plus today. Members enjoy unlimited access to STAT Plus stories, subscriber-only networking events across the country, and intelligence reports on key industry trends.

SOURCE

From: STAT Plus <marketing@statnews.com>

Reply-To: STAT Plus <marketing@statnews.com>

Date: Wednesday, April 24, 2019 at 3:15 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: The latest from IBM Watson

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Reporter: Gail S. Thornton

This report is entitled, “REDEFINING YOUR VALUE TO WIN THE EMPOWERED PATIENT. Six Steps for Life Sciences Firms to Stay Relevant in the New Healthcare Ecosystem,” which was published by Strativity Group, LLC in 2019. Please find an excerpt below.

Patients have taken charge of their lives, and they are empowered by increasingly more sophisticated and accessible tools. They still require physicians, hospitals, insurance companies, and life sciences companies to support them, but the dialogue, expectations, and engagement are changing radically as patients approach their healthcare with confidence and knowledge rather than fear and submission.

Today’s Patient Is the New Industry Authority Changing consumer expectations and behaviors have brought just about every industry to a tipping point, where consumers – not traditional experts, companies, or brands – have appointed themselves as the new authority. While the trend may have started in less expert-dependent industries like travel and banking, it’s now also penetrating areas where consumers have historically had much less power and influence, including healthcare. The healthcare industry itself also emboldened patients to redefine their roles in response to rising healthcare costs, shrinking provider availability, and increased skepticism of the medical insurance and life sciences industries. Macro- and micro-trends have come together to create a perfect storm in healthcare, and that means life sciences firms need to seriously rethink their roles and value in the new patient centered landscape. To get a deeper understanding of the new environment, consider the following trends that are putting patients in the driver’s seat: • Knowledge abundance The wealth of knowledge available online has made health information both broadly accessible and much more understandable. Hospitals, nonprofit associations, and bloggers transformed professional jargon and made it accessible to billions of consumers who are now turning to the web before they turn to traditional experts, such as physicians. In fact, a dotHealth Consumer Health Online 2017 Research Report that found 57% of consumers consult the internet for information before visiting a doctor and only 32% consult with their doctor first. iv • Evolution of peer groups Patients are establishing local and global support groups of peers in similar situations. They find this authentic support system trumps traditional knowledge sources such as physicians and pharmaceutical companies. Patients find more strength and support in those groups and amplify their roles in the overall ecosystem.

About Strativity Strativity is a strategy activation firm that partners with organizations that want to differentiate through consistently exceptional customer and employee experiences during a time of ever-evolving expectations and digital disruption. With a deep understanding of human motivation and a proven methodology, we engage the hearts, heads, and hands of executives, employees, and customers to deliver rapid and lasting change. Our philosophy, approach, and results have inspired industry leaders like BMW, FedEx, GSK, Honeywell, Johnson & Johnson, MasterCard, Mazda, Mercedes-Benz, The New York Times, Royal Caribbean Cruise Line, Teleflex, and Walmart to rely on Strativity to transform their organizations and enhance their performance.

Source:

https://pages.questexweb.com/rs/294-MQF-056/images/Strativity%20-%20Redefining%20Your%20Value%20to%20Win%20the%20Empowered%20Patient_revised_to%20Fierce_041519.pdf?aliId=eyJpIjoiWU1NdHFMbzJONkd1VldLMCIsInQiOiJaM2NUdUY3eVJKalhxdERtWElBMUlRPT0ifQ%253D%253D




Lesson 10 on Cancer, Oncogenes, and Aberrant Cell Signal Termination in Disease for #TUBiol3373

Curator: Stephen J. Williams

Please click on the following file to get the Powerpoint Presentation for this lecture

cell signaling 10 lesson_SJW 2019

There is a good reference to read on The Hallmarks of Cancer published first in 2000 and then updated with 2 new hallmarks in 2011 (namely the ability of cancer cells to reprogram their metabolism and 2. the ability of cancer cells to evade the immune system)

a link to the PDF is given here:

hallmarks2000

hallmarks2011

Please also go to other articles on this site which are relevant to this lecture.  You can use the search box in the upper right hand corner of the Home Page or these are few links you might find interesting

Development of Chemoresistance to Targeted Therapies: Alterations of Cell Signaling & the Kinome

Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation: a Compilation of Articles in the Journal http://pharmaceuticalintelligence.com

Feeling the Heat – the Link between Inflammation and Cancer

Lesson 4 Cell Signaling And Motility: G Proteins, Signal Transduction: Curations and Articles of reference as supplemental information: #TUBiol3373

Immunotherapy Resistance Rears Its Ugly Head: PD-1 Resistant Metastatic Melanoma and More

Novel Mechanisms of Resistance to Novel Agents

 


18th Annual 2019 BioIT, Conference & Expo, April 16-18, 2019, Boston, Seaport World Trade Center, Track 5 Next-Gen Sequencing Informatics – Advances in Large-Scale Computing

 

https://www.bio-itworldexpo.com/programs

https://www.bio-itworldexpo.com/next-gen-sequencing-informatics

 

 

Leaders in Pharmaceutical Business Intelligence (LPBI) Group

represented by Founder & Director, Aviva Lev-Ari, PhD, RN will cover this event in REAL TIME using Social Media

@pharma_BI

@AVIVA1950

@evanKristel 

TUESDAY, APRIL 16

2:00 – 6:30 Main Conference Registration Open

 

4:00 PLENARY KEYNOTE SESSION
Amphitheater

5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

 

WEDNESDAY, APRIL 17

7:30 am Registration Open and Morning Coffee

8:00 PLENARY KEYNOTE SESSION
Amphitheater

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

 

CURRENT AND EMERGING TECHNOLOGIES
Waterfront 3

10:50 Chairperson’s Remarks

David LaBrosse, Director, Genomics, Research, Life Sciences & Healthcare, NetApp

11:00 Long Read Sequencing

Justin Zook, PhD, Researcher, National Institute of Standards and Technology

11:20 NovoGraph: Loading 7 Human Genomes into Graphs

Evan Biederstedt, Computational Biologist, Memorial Sloan Kettering Cancer Center

11:40 Building a Usable Human Pangenome: A Human Pangenomics Hackathon Run by NCBI at UCSC

Ben Busby, PhD, Scientific Lead, NCBI Hackathons Group, National Center for Biotechnology Information (NCBI)

netapp12:00 pm Co-Presentation: Faster Genomic Data

Michael Hultner, PhD, Senior Vice President, Strategy; General Manager, US Operations, PetaGene

David LaBrosse, Director, Genomics, Research, Life Sciences & Healthcare, NetApp

Genetic testing demand is driving up the volume of genomic data that must be processed, analyzed, and stored. Gigabyte-scale genome sample files and terabyte- to petabyte-scale cohort data sets must be moved from data generation to processing to analysis sites, historically a slow, arduous process. NetApp and PetaGene will describe compression and data transfer technologies that overcome I/O bottlenecks to accelerate the movement of genomic data and reduce the time to process and analyze it.

12:30 Session Break

12:40 Luncheon Presentation I: Deep Phenotypic and Genomic Analysis of UK Biobank Data on the WuXi NextCODE Platform

Saliha Yilmaz, PhD, Research Geneticist, WuXi NextCODE

The increasing size and complexity of genetic and phenotypic data to include hundreds of thousands of participants poses a significant challenge for data storage and analysis. We demonstrate use of the GOR database and query language underlying our platform to mine UK Biobank and other datasets for efficient phenotype selection, GWAS and PheWAS, and to archive and query the results.

Seven-Bridges-rectangular1:10 NEW: Luncheon Co-Presentation II: Optimizing Drug Discovery and Development with Data-Driven Insights

Christian Frech, PhD, Associate Director, Scientific Operations, Seven Bridges

Serhat Tetikol, Research & Development Engineer, Seven Bridges

1:40 Session Break

DATA VISUALIZATION, EXPLORATION & ANALYSIS
Waterfront 3

1:50 Chairperson’s Remarks

Jeffrey Rosenfeld, PhD, Manager of the Biomedical Informatics Shared Resource and Assistant Professor of Pathology, Rutgers Cancer Institute of NJ

1:55 AbbVie’s Target and Genomics Compilation (ATGC): A Target Knowledge Platform

Rishi Gupta, PhD, Senior Research Scientist, Information Research, AbbVie, Inc.

Author: Anne-Sophie Barthelet, Scientific Developer, Discngine

ATGC is a web-based platform that allows AbbVie scientists to gather relevant information to make accurate decisions on target ID, target validation, biomarker selection and drug discovery. This platform provides in-depth information on several key pieces of information such as gene expression, RNA expression, protein expression, mouse knockout studies, etc. for each target. This talk focuses on key aspects of this application including application architecture, currently available tool sets and how various pieces of information are provided to the user.

2:25 Self Service Data Visualization and Exploration at Genentech Research

Kiran Mukhyala, Senior Software Engineer, Bioinformatics and Computational Biology, Genentech Research and Early Development

Genomic data requires specialized infrastructure to enable data exploration and analysis at scale. We built an integrated, modular, end-to-end gene expression analysis platform implementing data import, storage, processing, analysis and visualization. The multi-layered architecture of the platform supports general, high-level applications for self-service analytics, as well as infrastructure for prototyping, incubating and integrating scientist-driven innovations. The platform coexists with other in-house and commercial software to provide a wide range of genomic data analysis and visualization options for Research scientists.

2:55 Exploring and Visualizing Single-cell RNA Sequencing Data

Michael DeRan, PhD, Scientific Consultant, Diamond Age Data Science

Recent advances in single-cell RNA sequencing (scRNA-seq) technology have made this powerful method accessible to many researchers, but have not brought with them a clear, simple workflow for data analysis. As the number of scRNA-seq datasets has increased, so too has the number of analysis tools available; for those looking to perform their first scRNA-seq analysis the range of options can seem daunting. In working with our clients, I have had the opportunity to apply many different tools to scRNA-seq data from a variety of tissues and organisms. I have used this experience to select a set of tools that are flexible and suitable to many common scRNA-seq analysis tasks. In this talk I will introduce popular tools and methods for identifying cell populations, assessing differential expression and visualizing biological processes. I will discuss common pitfalls encountered in analyzing this data and make recommendations that anyone can use in their own analysis.

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)

NGS APPROACHES FOR CANCER
Waterfront 3

4:00 Comparison of Different Approaches for Clinical Cancer Sequencing

Jeffrey Rosenfeld, PhD, Manager of the Biomedical Informatics Shared Resource and Assistant Professor of Pathology, Rutgers Cancer Institute of NJ

The sequencing of tumors is important for guiding the treatment of cancer patients. While it is agreed that there is a need to perform sequencing of the tumor, there are a wide variety of approaches ranging from paired whole genome tumor-normal sequencing to tumor-only small panel sequencing with many intermediate possibilities. Each of the approaches has a different cost and associated benefit. I will present a comparison of different methods and their efficacy for guiding cancer treatment.

4:30 Integrated NGS Analysis to Accelerate Disease Understanding for Drug Discovery

Helen Li, Director- Research IT – Biologics & Informatics, Eli Lilly and Company

5:00 Identification of Cancer Biomarker Genes

Maryam Nazarieh, PhD, Postdoctoral Researcher, Center for Bioinformatics, Universität des Saarlandes, Saarbrücken, Germany

Identification of biomarker genes plays a crucial role in disease detection and treatment. Computational approaches enhance the insights derived from experiments and reduce the efforts of biologists and experimentalists to identify biomarker genes which play key roles in complex diseases. This is essentially achieved through prioritizing a set of genes with certain attributes (1). Here, I propose a set of transcription factors that make the largest strongly connected component of the pluripotency network in embryonic stem cells as the global regulators that control differentiation process determining cell fate. This component can be controlled by a set of master regulatory genes.  The regulatory mechanisms underlying stem cells inspired us to formulate the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. The developed methods were applied to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma.  As not all the nodes in the solutions are critical, a prioritization method was developed named TopControl to rank a set of candidate genes which relate to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. To this purpose, the NGS data were utilized taken from The Cancer Genome Atlas for matched tumor and normal samples of liver hepatocellular carcinoma (LIHC) and breast invasive carcinoma (BRCA) datasets. Moreover, the topological features were demonstrated in regulatory networks surrounding differentially expressed genes that were highly consistent in terms of using the output of several analysis tools. We present several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human. 1) Maryam Nazarieh, Understanding regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. Ph.D. thesis, Saarland University, Saarbrücken, Germany (2018).

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


Bio-IT World Announces 2019 Best Of Show Award Winners

UPDATED on 4/22/2019

Genomenon Wins Best of Show at Bio-IT 2019

Mastermind Genomic Search Engine Recognized for Proactively Solving Genomics Problems

Genomenon Inc., the leading genomic search company, today announced that Bio-IT World has awarded them Best of Show for the Mastermind Genomic Search Engine. Mastermind was one of 31 products considered for this prestigious award at last week’s Bio-IT World Conference & Expo in Boston.

Bio-IT World’s Best of Show Awards Program recognizes the best of the innovative product solutions for the life sciences industry, as judged by a panel of experts from academia, industry, pharma and biotech. Winners are judged based on the products’ technical merit, functionality, innovation, and in-person presentations to the judges at the show. During the April 18th awards ceremony, Mastermind was applauded as a product that was unique, important to the industry, and offered a compelling return on investment.

“The judges believe Mastermind and the team behind it are addressing not only really interesting problems in genomics, but are anticipating customer needs and solving problems proactively.” Said Bio-IT World Editor Allison Proffitt at the presentation of the award to Mark Kiel, founder and CSO, Genomenon.

“It’s quite an honor to be recognized as Best of Show at Bio-IT this year”, said Mike Klein, CEO of Genomenon. “This recognition belongs to our entire team, dedicated to putting the genomics information needed to diagnose & cure patients with cancer and rare diseases at the fingertips of doctors and researchers.”

The Mastermind Genomic Search Engine is part of the suite of genomic data services Genomenon provides to pharma, clinical, and life sciences companies. Genomenon specializes in delivering the most comprehensive collection of genomic data from the medical literature in any format needed to address any business challenge.

About Genomenon

Genomenon powers evidence-based genomics for faster; more comprehensive diagnosis and treatment decisions. Their flagship product, the Mastermind Genomic Search Engine provides immediate insight into the published genomic research for every disease, gene, and variant found in the literature.

Used by hundreds of diagnostic labs around the world, Mastermind accelerates genomic interpretation by providing unique insight into genomic relationships found in the full text of millions of scientific articles.

Pharmaceutical researchers license the Mastermind database for a comprehensive genomic landscape associated with any given disease – to identify and prioritize genomic biomarkers for drug discovery and clinical trial targets.

SOURCE

https://www.genomenon.com/genomenon-wins-best-of-show-bio-it-2019/?utm_source=press

 

Bio-IT World | Today Bio-IT World announced the 2019 winners of the Best of Show Awards Program to a packed audience at the Bio-IT World Conference & Expo. ONTOFORCE, Genomenon, Genedata, Kanda Software, and PetaGene were honored.

April 17, 2019 | BOSTON—Today Bio-IT World announced the 2019 winners of the Best of Show Awards Program to a packed audience at the Bio-IT World Conference & Expo. The awards program recognizes the best of the innovative product solutions for the life sciences industry on display at the Bio-IT World Conference & Expo in Boston.

“The innovation on display by Bio-IT World exhibitors never disappoints,” said Bio-IT World Editor Allison Proffitt. “It’s always a treat to see the work and dedication from companies firsthand, and we are excited to shine a spotlight on the best life sciences has to offer.”

The Best of Show program relies on a panel of expert judges from academia and industry who screen eligible new products and hear presentations from finalists on site. This year our judges considered 31 new products and viewed presentations on site from 12 finalists.

The judges chose five winners this year. The Bio-IT community also voted on the People’s Choice Award, selecting products that they believe measurably improve workflow or capacity, enabling better research.

The 2019 judging panel included Richard Holland, New Forest Ventures; Eleanor Howe, Diamond Age Data Science; Phillips Kuhl, Cambridge Healthtech Institute; Steve Marshall, Marshall Data Solutions; Nanguneri Nirmala, Tufts University School of Medicine; Alexander Sherman, Massachusetts General Hospital; Subi Subramanian, Vertex Pharmaceuticals; Bill Van Etten, BioTeam; Anthony Dibiase, a consultant, Shikha O’Brien, Illumina and Proffitt.

 

2019 Bio-IT World Best of Show Winners

People’s Choice

ONTOFORCE

Product Name: 2019 Linked Data Ingestion Engine

The new Data Ingestion Engine added to the existing faceted browsing and visual analytics engine in the DISQOVER platform contains the following:

– A performant and scalable Extract, Transform, Link, Infer & Load (ETLIL) engine, capable of creating massive amounts of links & performing inferencing.

– Using semantic concepts (RDF triples and ontologies) as a data reasoning model.

– Capable of performing ETLIL actions on massively linked data using commodity hardware (e.g. ~10 billion triples on single machine with 6 cores / 64Gb RAM).

– Managed by a graphical, component-based pipeline via a user-friendly frontend.

-Incremental updating of the pipeline when a data source gets updated

– Including full data transformation inspection capacities (both upstream & downstream).

– All combined with tolerance-based, process-oriented Quality Control (QC), usable for real-world data.

> Tolerance-based: no rigid schema is required

> Process oriented:

– incoming QC (verifying source data)

– within-process QC (verifying intermediate results) and

– outgoing QC (verifying end result data) can be specified.

 

“Where the Puck is Going” Award

Genomenon

Product Name: Mastermind Reporter

Genomenon uses Artificial Intelligence (AI) and Machine Learning (ML) to accelerate the literature curation process. The result is Mastermind, the most comprehensive database of genomic information in the world.

Mastermind automatically reads the titles and abstracts of every scientific medical paper published, over 30 million! The full text of papers with genomic information is then indexed to develop the most comprehensive view of the genomic landscape. To date, Mastermind has indexed the text of over 6.2 million genetic publications and covers over 4.1 million variants.

The genomic data found in the publications is processed through Genomenon’s patented Genomic Language Processing (GLP). More sophisticated than Natural Language Processing, GLP identifies every way that an author can describe a gene or variant and filters out erroneous information that can be mistaken for genomic data.

The data is then presented in a multi-faceted web interface, utilizing sophisticated algorithms designed to show the most relevant results first. Advanced filtering options allow the user to search broadly for maximal sensitivity or narrowly for optimal specificity.

The latest version of Mastermind includes Mastermind Reporter, a visualization tool that enables researchers to view, search, and filter large collections of curated data such as complete functional variant landscapes for solid tumor and heme oncology.

The Mastermind Genomic Search Engine, together with Mastermind Reporter, gives pharma and bio-pharma researchers the most comprehensive genomic landscape for any disease assembled from the published research for applications in drug discovery and clinical trial target identification.

 

“No BS AI” Award

Genedata AG

Product Name: Genedata Imagence 1.0

The new product presents a new deep learning based solution for phenotypic imaging and corresponding workflows based on convolutional neural networks. It yields improvements in automated image analysis for high content screens (HCS) including the ability to:

  • rapidly detect and define all cellular phenotypes in an HCS;
  • efficiently generate training data and on these train Deep Learning networks for subsequent classification of HCS image sets in production assays; and
  • precisely quantify the relevant pharmacology.

The solution reduces time and costs required for phenotypic image analysis by generalization of expert input, producing quality results from a new experiment takes just seconds vs. weeks typically required by manual optimization with existing legacy systems.

The solution seamlessly integrates with Genedata Screener for detailed pharmacological assessment and profiling.

 

Patient-Focused Software Award

Kanda Software

Product Names: Trapelo & LifePod Virtual Caregiver

Trapelo is the only real-time precision medicine platform that enables everyone involved in cancer care to align their decision making and reimbursement policies with the most current clinical evidence in molecular oncology.

The platform features configurable practice, lab and payor modules that facilitate real-time, evidence-based decision support that lets oncologists know what to tests to order for which patients and from which labs, and then helps them interpret the results for more informed treatment decisions – all of this in the context of the patient’s insurance policies. This optimizes efficiency while giving oncologists confidence they’ve ordered the most relevant tests based on their patient’s disease and clinical stage.

Kanda’s second application, LifePod’s Virtual Caregiver service, expands the capabilities of popular smart speakers (e.g., Amazon’s Echo) with patent-pending innovations that make LifePod an easy-to-use, 2-way voice service for seniors or chronically-ill patients living at home and their caregivers. Unlike traditional voice assistants, LifePod can be set up and controlled by a remote caregiver using LifePod’s online Portal and Dialog Management System. In addition, LifePod’s unique “initiation” capability – enabling LifePod to speak to a senior without first being “woken” by the user – means the senior doesn’t have to remember a “wake word” or how to phrase commands in order to feel more connected and supported. Instead, LifePod provides proactive, voice-first check-ins and reminders each day, and encourages senior users to access voice services (e.g., music, weather, etc.) to enhance their day, based on routines configured online by their caregivers.

 

“Nailed It” Award

PetaGene

Product Name: PetaSuite Protect v1.0

PetaSuite Protect 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. Moreover, this is done in a manner transparent to existing tools and pipelines and integrates with existing on-premises and cloud storage infrastructure.

The state-of-the-art prior to PetaSuite Protect is to grant access to users of genomic data on a whole-file or whole-object basis, which means the person it belongs to might be identifiable. While some file-systems support auditing of accesses by internal users, there is very little visibility into what users are doing with this data. And when granting access to external users, there is typically no visibility at all once the data have been transferred to them.

With PetaSuite Protect, users see regular genomic files. When they access these files, they only see the specific regions that they have permissions to view. PetaSuite Protect gives live information on the use of genomic data by those parties, and the ability to immediately grant or revoke access privileges.

Organizations can allocate GA4GH-defined data management roles. Every user access is logged in a tamper-resistant and easily searchable cryptographic ledger. Not only is user and file information recorded but also details of what application was used for access, and what genomic regions were read. Furthermore, decryption and decompression are performed on the client with a transparent high-performance library, rather than by the server. This ensures high scalability across multiple users.

 

 

SOURCE

https://www.bio-itworldexpo.com/next-gen-sequencing-informatics


2019 Bio-IT World Announces Inaugural Innovative Practices Awards Winners

Bio-IT World | Bio-IT World has announced the winners of the 2019 Innovative Practices Awards. The winners were announced live at the Bio-IT World Conference & Expo. Entries from Abbvie, Novo Nordisk, and Sentieon were honored.

April 18, 2019 | BOSTON—Bio-IT World has announced the winners of the 2019 Innovative Practices Awards. The winners were announced live at the Bio-IT World Conference & Expo. Entries from Abbvie, Novo Nordisk, and Sentieon were honored.

Since 2003, Bio-IT World has hosted an elite awards program, highlighting 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. This year we rechristened the awards the Innovative Practices Awards, recognizing partnerships and projects pushing our industry forward.

“These awards celebrate the dedication and innovation in the life sciences, and the winners chosen highlight the inspiring work being done in our industry,” said Allison Proffitt, Editorial Director of Bio-IT World. “The Bio-IT World Community is increasingly open, and the partnerships and projects showcased in this year’s award program prove our dedication to collaborative excellence.”

This year, a panel of expert judges joined the Bio-IT World editors in reviewing detailed submissions from pharmaceutical companies, academic centers, government agencies, and technology providers.

The awards ceremony was held at the Seaport World Trade Center in Boston, where the winning teams received their prizes from Proffitt and Philips Kuhl, president of conference organizer Cambridge Healthtech Institute.

2019 Bio-IT World Innovative Practices Awards

Winning Entries:

Abbvie nominated by Discngine

3decision – next generation structural knowledge management solution

Although wildly used, rational structure-based drug design (SBDD) techniques are far from being applied to their fullest potential. The major hurdles lie in the inconsistent data persistence and the complexity of analyzing structural data. Moreover, the structural data is often analyzed by domain experts only and their knowledge and experience are not well shared and exposed to other communities. Abbvie has addressed these pitfalls by co-developing a web-based structural knowledge management solution called 3decision. It allows Abbvie to transform a massive amount of data coming from in-house and public 3D structures and sequences, into applicable knowledge for drug discovery projects. The collaborative aspects within SBDD projects are in focus and the user interface allows all types of users to easily generate, test and connect their ideas with each other. The development of 3decision allowed Abbvie to dramatically increases the ROI of SBDD work and protein structure production.

Novo Nordisk nominated by Linguamatics

Integrating NLP to generate actionable insights from real world data

Novo Nordisk wanted to extract more value from the real-world data (RWD) being collected about the use of its products, so that commercial teams could better understand what patients and healthcare professionals were saying, and take appropriate action. Novo Nordisk used Linguamatics I2E to analyze three key RWD sources and extract well-structured data. The resulting information was then presented to the business users via Tableau-based self-serve dashboards, for exploration and insight generation. In addition, Novo Nordisk migrated I2E and Tableau to its AWS cloud-based global big data and analytics platform. This now provides business users and product teams with enhanced access to real world data around Novo Nordisk products for better derivation of actionable insights. With the new system, Novo Nordisk have reduced manual work by FTEs, reduced vendor spend, automated the process of generating insights, and significantly broadened access to these insights across a global team.

Sentieon

Sentieon DNAseq and TNseq software tools for NGS data processing-BWA/GATK drop-in- replacements

To aid the genomics industry without adding “yet another variant caller,” Sentieon identified BWA/GATK as high-quality tools because of the rigor of their mathematical models and resulting accuracy. Sentieon has improved on this foundation using redesigned computational algorithms with high efficiency, better usability, and 100% consistency. Sentieon’s software package realizes the same math as in BWA-MEM, GATK, MuTect, MuTect2 based pipelines, while using 3-10x fewer core hours, lower memory requirements, and achieving 100% consistency by removing downsampling and thread dependency. Sentieon software automatically scales to efficiently use all available CPU cores. Further, improved computational algorithms enable Sentieon software to joint-call large cohorts of tens of thousands of genomes without intermediate steps. As a result of these improvements, the Sentieon tools have been used to win PrecisionFDA Consistency Challenge and Truth Challenge awards and are currently used by customers around the world.

Honorable Mention:

Regeneron Pharmaceuticals and the RGC UK Biobank Consortium nominated by DNAnexus

The RGC UK Biobank Consortium Data Delivery and Cohort Browser

The UK Biobank (UKB) has collected and developed a biospecimen and data resource on over 500,000 individuals. The resource is of strategic importance to pharmaceutical companies, as it serves to understand how different factors influence disease. In collaboration with a consortium of pharma companies, The Regeneron Genetics Center has undertaken the exome sequencing and analysis of all 500,000 samples, using the DNAnexus Platform to host the dataset and run Regeneron’s software pipeline. To increase the value to the RGC UKB consortium, Regeneron and DNAnexus partnered to construct a combined database of the UKB genomic and phenotypic data to explore through an innovative “geno/pheno cohort browser” user interface. The cohort browser was designed to democratize data access, giving diverse teams the ability to browse through 3,000 phenotypic fields and 15,000,000 genomic variants across 100,000 samples and build cohorts.

SOURCE

https://www.bio-itworldexpo.com/programs


42.5K impressions over this 28 day period, 1.7K impressions per day, March 17, 2019 – April 11, 2019

 

Your Tweets earned 42.5K impressions over this 28 day period

2.0K4.0K6.0K8.0K50 Mar 17Mar 24Mar 31Apr 7
YOUR TWEETS
During this 28 day period, you earned 1.7K impressions per day.
Engagements
Showing 28 days with daily frequency
Engagement rate
1.9%
Apr 11
0.3% engagement rate
Link clicks
19
Apr 11
1 link click
On average, you earned 1 link clicks per day
Retweets
95
Apr 11
5 Retweets
On average, you earned 3 Retweets per day
Likes
173
Apr 11
5 likes
On average, you earned 6 likes per day
Replies
0
Apr 11
0 replies
On average, you earned 0 replies per day
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