The 15th annual Bio-IT conference – with the theme “Building a global network for precision medicine by uniting the Bio-IT community” – clearly had as its underlying theme the many different aspects of data that need to be addressed to make precision medicine a true reality, as echoed throughout the many talks and discussions. This was reflected in both the keynotes, as well as the panel discussions that focused on data regulations, security, and getting patients to feel good about sharing their data. The first hackathon launched by Bio-IT World had the focus on FAIR [findable, accessible, interoperable, and reproducible] data. Many commercial announcements or recent advancements in artificial intelligence revolved around new and improved data analysis solutions. This year’s Best in Show award selections featured Starfish Storage’s Starfish V4, SciBite LaunchPad, SolveBio’s Operating System for Molecular Information, Dana Farber Cancer Institute / The Hyve’s MatchMiner v1.0, and Seven Bridges’ CAVATICA.
Coinciding with Bio-IT were a number of major announcements as listed below:
Benjamin Franklin Award
- This year’s Benjamin Franklin Award – an award presented annually by bioinformatics.org to an individual who has, in her or his practice, promoted free and open access to the materials and methods used in the life sciences – was awarded to Rafael Irizarry, Professor of Biostatistics at Harvard and the Dana-Farber Cancer Institute, who has dedicated his career to developing statistical methods and open source software for helping researchers analyze genomics data.
Best Practices Award
- As every year the commercial sector is actively following the Best Practices awards leading up to this event (check out the pre-conference finalists). This year’s Best Practices award winners included the Maccabi Healthcare System “Clinical IT & Precision Medicine” for the implementation of an advanced AI and machine learning algorithms to identify high-risk, under-the-radar patients, Rady Children’s Institute for Genomic Medicine in “Informatics” for improved and expedited precision medicine for newborns by 26-hour whole genome sequencing, Allotrope Foundation in “Knowledge Management” for developing a holistic set of capabilities to improve data access, interoperability, and integrity through standardization, and the Earlham Institute in “IT infrastructure/HPC” by applying high-performance computing to improve global food security, Biomedical Imaging Research Services Section (BIRSS) as the Judges’ Choice Award, and last but not least Alexion Pharmaceuticals as the Editors’ Choice Award.
- Six new products were selected and honored among the 47 originally considered new products or product updates. Winners were selected across four categories:
- Storage Infrastructure & Hardware – Starfish Storage, Starfish V4
- Analysis & Data Computing – SciBite, SciBite LaunchPad
- Genomic Data Services – SolveBio, SolveBio Operating System for Molecular Information
- Data Visualization and Exploration – Dana Farber Cancer Institute / The Hyve, MatchMiner v1.0
- With the “People’s Choice Award” going to the data analysis and sharing platform CAVATICA by Seven Bridges.
Data management and analysis
- Bioinformatics is sorted, whereas the pain is in data management – an interview with Genestack’s CEO Mischa Kapushesky.
- Illumina announced that a European instance of BaseSpace Sequence Hub is now available in addition to receiving ISO 27001 Certification on its Information security management system supporting BaseSpace Sequence Hub and BaseSpace Variant Interpreter (Beta), hosted in Amazon Web Services (AWS), in both the US and EMEA.
- Edico Genome’s DRAGEN Added to Illumina’s BaseSpace Sequence Hub. Edico’s FPGA-centric DRAGEN enables whole human genome analysis in under 10 minutes, featuring algorithms for mapping, alignment, sorting, variant calling, and real-time compression of data files.
- Qiagen announced the launch of the CLC Genomics Cloud Engine, the newest addition to their bioinformatics portfolio which supports the analysis of NGS data.
- Broad Institute to release Genome Analysis Toolkit 4 (GATK4) under an open source software license. The software package, designated GATK4, contains new tools and a rebuilt architecture. It is available currently as an alpha preview on the Broad Institute’s GATK website, with a beta release expected in mid-June.
- Intel Collaborates with Broad Institute on Enhanced Genomics Research Solution. Intel and Broad have developed the Broad-Intel Genomics Stack (BIGstack) architecture, which currently delivers a 5x improvement to Broad’s genomics analytics pipeline using Intel’s CPUs, Omni-Path Fabric and SSDs.
- Wolfram Research, creator of Mathematica, Wolfram|Alpha, and the Wolfram Language, announced the integration of its Wolfram technology with SolveBio. The integration uses the natural language processing capabilities of the Wolfram Language which allows doctors and scientists to intuitively query complex biomedical data in plain language for reliably actionable insights.
- SolveBio and Elsevier announced a collaboration to integrate the use of Pathway Studio, Elsevier’s database of biological molecular interactions and curated pathways, with the SolveBio platform. This new integration is providing all SolveBio customers free access to Pathway Studio’s Pathway Viewer software for functional relationship analysis for genes of interest.
- Eagle Genomics launched automated eaglecurate, a data curation platform. eaglecurate addresses data curation challenges through automation of the data curation process and the automated semantic enrichment of curated data sets.
Informed drug discovery
- AstraZeneca selected DNAnexus to develop its secure genomics informatics environment for AstraZeneca’s Centre for Genomics Research (CGR) initiative to analyze two million genomes in the next 10 years to inform drug discovery and development. Financial terms of the collaboration were not disclosed.
- Biomatters announced the launch of Geneious Biologics software platform which will allow biopharma and biotechnology enterprises to create highly annotated antibody databases, significantly improving their ability to leverage accumulated knowledge and gain insights into trends and relationships that may otherwise have been missed.
- Judge rules in favor of Oxford Nanopore in patent dispute with PacBio. ‘Single molecule sequencing (process)’, was resolved with the judgment favoring Oxford Nanopore. PacBio had argued that at the time of writing the patent, the meaning was plain and ordinary, thus requiring no further clarification.
- Ovation Receives $1.5M in funding and launches collaboration with iGeneTRAiN. The company will use the funds to continue the development of its next-generation scientific data-layer-as-a-service platforms. Ovation also announced a partnership with iGeneTRAiN to use Ovation Research to maximize collaboration capabilities across iGeneTRAiN’s transplant consortium.