Bio-IT World Announces 2018 Best Of Show People’s Choice Aw…


May 3, 2018 | Bio-IT World is pleased to announce the 2018 Best of Show competition with the Bio-IT World People’s Choice award.

The Best of Show Awards offers exhibitors at the Bio-IT World Conference & Expo an opportunity to showcase their new products. A team of expert judges views entries on site and chooses winners in four categories based on the product’s technical merit, functionality, innovation, and in-person presentations. The judges’ finalists are highlighted in the list of contenders.

In addition to the judges’ prizes, Bio-IT World presents a People’s Choice Award as well, which is chosen by votes from the Bio-IT World community. All of the Best of Show entries are eligible for the People’s Choice Award. Voting will open at 5:00 pm ET on Tuesday, May 15, and will remain open until 1:00 pm ET on Wednesday, May 16.

The four awards named by the judges and the People’s Choice Award will be announced at a live event on the Bio-IT World Expo floor at 5:30 pm on Wednesday, May 16.

We are excited to have the community’s input again this year on the best new products on display at Bio-IT World. Watch the Bio-IT World Twitter account @BioITWorld and #BestofShow18 for the voting link on Tuesday, May 15, at 5:00 ET.

 

2018 Bio-IT World Best of Show Contenders

 

ACD/Labs | Booth 523
Product Name: Luminata v2017.1
acdlabs.com/luminata
Luminata is a scientific software application designed to enable organizations to establish effective impurity control strategies based on assembled analytical and chemical information, in a single environment.

Built on the multi-technique, vendor-agnostic ACD/Spectrus Platform, Luminata offers comprehensive data standardization of analytical data from multiple instrument vendors and analytical techniques in a single application that is designed to process, analyze and store the data in a searchable and easily accessible manner. Furthermore, chemical reaction information and the associated formation and fate of impurities are also aggregated with chromatographic and spectral data offering unprecedented line-of-sight through a development project. Luminata facilitates efficient organization of, the typically overwhelming quantity of, analytical knowledge for processes and associated impurities, at every stage.

Luminata’s unique assembly of searchable knowledge provides unprecedented visualization, decision-support, and reporting capabilities; and facilitates collaboration between process chemistry and analytical research and development groups.

Luminata is an enterprise system with standard three-tier architecture designed to run on Windows with either an Oracle or PostgreSQL database.

 

Atgenomix | Booth 637
Product Name: Atgenomix SeqsLab v2
atgenomix.com
Enterprise-grade NGS analysis platform software that accelerates your existing whole genome and exome best practices with accuracy, scalability and reliability, powered by Apache Spark/Hadoop.

Easy to use and ready to run in your labs or in the cloud, including the full-spectrum of germline and somatic SNP/INDEL/SV analysis.

  • 10x FASTQ to VCF acceleration
  • 50% Lower computing cost
  • 4hrs BWA/GATK whole genome turnaround

 

Avere Systems – A Microsoft® Company | Booth 327
Product Name: Avere FXT Edge filer 5850
averesystems.com

The Avere FXT 5850 Edge filer is a scale-out network attached storage (NAS) solution that empowers enterprises to deploy and scale compute in the cloud, using both on-premises and cloud-based resources. FXT 5850 enables customers to speed time-to-market, produce higher quality output, and modernize IT infrastructure with both cloud and advanced networking technologies. Enterprises can integrate the public cloud, private object storage solutions, and existing NAS systems into a single, easy-to-manage infrastructure. With a complete NAS feature set, including network file system (NFSv3) and server message block (SMB2) protocols, businesses can seamlessly store data and run applications on premises or in the cloud with minimal latency.

Compared to previous generations of FXT Edge filers, the FXT 5850 provides:

  • More than double the performance with improvement from 4 gigabytes per second (GB/s) to 9 GB/s aggregate read throughput
  • Double the capacity with twice as much dynamic random-access memory (DRAM) from 384GB to 768GB and solid-state drive (SSD) from 9.6TB to 19.2TB
  • Two and a half times higher network bandwidth with an increase from four 10 gigabit ethernet (GbE) ports to four 25 GbE ports

 

BC Platforms | Booth 506
Product Name: BC GeneVision
bcplatforms.com/news/bc-platforms-launches-end-end-solution-precision-medicine-powered-microsoft-genomics-service/
In March 2018, BC Platforms released GeneVision, a genomic data platform offering end-to-end solution from raw genome data to patient reports. Platform is available in public or private cloud or on-premise data center, as Software-as-a-Service solution, or license based terms.

BC GeneVision enables hospitals to expand the role of genomics beyond individual genomic tests, towards producing genome data at large scale and expanding its applications for healthcare and research use. GeneVision implements scalable, automated secondary analysis workflows for both genotyping and next-generation sequencing, quality monitoring and approval, as well as production of different patient reports for clinical genomics. The use of genotyping technology facilitates preventive medicine using genomic risk scores, and allows hospitals to optimize genome resource or lab utilization by focusing more expensive NGS technology efforts to patients that benefit the most. In addition, the solution provides a secure genome data warehouse, and easy access via open API for accessing genome data from other applications and research.

GeneVision is comprised of multiple interlinked and interacting modules, each dedicated to performing part of the whole functioning workflow:

  • Fully automated genotyping workflow from Illumina iScan binary files, quality control and approval and imputation
  • Fully automated NGS data secondary analysis workflow with quality control and approvals
  • Secure, compliant genome data warehouse scalable to population scale projects
  • Genome variant interpretation and reporting, including pharmacogenomic reports (PGx), genomic risk scores for preventive medicine (GRS) and well-being reports
  • API’s for new clinical reports and accessing data
  • Two-way communication with EHR systems using HL7 messages

 

Finalist: BC Platforms | Booth 506
Product Name: BC|RQUEST
bcplatforms.com/news/bc-platforms-launches-end-end-solution-precision-medicine-powered-microsoft-genomics-service/

Launched Sept 2017, BC|RQUEST is a service platform for pharmaceutical research teams, and biobanks to communicate with each other. The platform provides data discovery users (research teams) with tools to browse and analyse the summary level information from data providers (collections), who have connected to the platform. Collection administrators connect their data collections to the service via a secure BC|LINK software module that collects summaries of query results, never exposing the actual content. This feature allows data administrators to overcome contractual issues in data sharing, and to ensure that varying consent types are honored.

BC|RQUEST is a data broker coordinating data queries from a cloud, or similar available service location. Each participating collection connects to the service using local BC|LINK module, which acts as a secure client for relaying research queries to the collection hosts, and responses to queries back to the BC|RQUEST researchers.

The platform provides meta-analysis capabilities relying on genomic individual-level data, if it is made available, and provides consent and sample availability information. Researchers are able to contact the data collection administrators via the platform to request more details, samples, or for other purposes of communication.

BC|RQUEST is a safe and confidential environment for pharmaceutical researchers to seek suitable patient cohorts within validated data cloud of multiple biobanks and collections world-wide. The ability to perform controlled meta-analysis on genomic data provides researchers with necessary tools to run feasibility studies, and to investigate the safety of specific pathway targets utilizing naturally occurring mutations in the cohorts. As the platform is highly flexible in its data model and access control, it’s utility in the most complex data environments is unique.

 

Benchling | Booth 341
Product Name: Benchling
benchling.com/enterprise

Benchling is the first and only modern informatics platform for biologics R&D. It gives companies complete context on the samples and results in their organizations and how they were generated and accomplishes this by capturing the full context of biologics as they move from early discovery to late-stage development.

To do so, Benchling — cloud hosted on AWS — provides an integrated platform that involves an application layer, data layer, and developer platform. The application layer features Lab Notebook, Molecular Biology Suite, Bioregistry, Sample Tracking, Workflow Management, and Request Management functionality. These products connect end-to-end needs of biologics R&D and talk and function seamlessly with one another, ensuring context always gets transferred as candidates move downstream. Once data is inputted through Benchling’s application layer, all data is consequently centralized into a data layer that stores both unstructured data (e.g. user files, images) and structured data (e.g. biological samples, entities, physical containers, and results), the latter which can then be mined or queried by anyone in the organization through the search interface or a SQL warehouse. With this information, organizations can easily ask questions pertaining to the lineage, location, or result associated with a sample, while R&D managers can quickly troubleshoot and optimize their work in real-time. Lastly, IT organizations can use tools that sit in the developer layer — including REST APIs and the data warehouse — to easily connect Benchling to instruments and other software; these features make the system easy to customize, integrate, and extend.

CherryCircle Software, Inc. | Booth 124
Product Name: QbDVision v1.0
cherrycirclesoftware.com

QbDVision™ is a cloud-based software solution (SaaS) allowing for the iterative, risk-based management of your drug manufacturing process over the life cycle of development.  Start with your Target Product Profile and then build your Quality Target Product Profile defining the quality attributes of the final product.  Define your manufacturing process right in our software and identify critical material attributes and process parameters.  Then link these to the product final quality attributes and assign risks based on the current knowledge of the process and the impact of these variables on patient safety and efficacy.  As your program evolves and your process knowledge increases, the specifications and risks can be revisited and revised using science-based justifications supported by data with revisions tracked in accordance with 21 CFR Part 11.  In addition to standard risk tables and reporting, utilize our novel graphical tools to visualize traceability of requirements and quickly assess your risks. QbDVision takes you through this journey designing quality into your product and arriving at a robust, well-controlled manufacturing process. 

The value propositions for QbDVision are clear and compelling:

  • Track the evolution of your drug manufacturing process and acceptance criteria from pilot batches to PPQ batches; 
  • Identify critical variables, track risk mitigation activities, and control risk in complex manufacturing processes;
  • Ensure data integrity with requirements traceability and version control;
  • Develop a robust manufacturing process using data-based, scientific principles for process validation;
  • Streamline pre-approval inspections by FDA;
  • Significantly reduce risk of batch failure at commercial scale.

 

ClusterOne | Booth 124
Product Name: ClusterOne
clusterone.com

ClusterOne is a machine learning platform that provides scalable compute, flexible workflows and total infrastructure freedom with Zero DevOps. It enables machine learning teams to spend time on the models, not on the setup. Teams can use its SaaS platform, or install in any cloud or on-premise thanks to ClusterOne’s proprietary infrastructure technology.

 

Congencia Ltd | Booth 311
Product Name: Sapientia 1.7
congenica.com

Sapientia integrates a suite of powerful analytical tools, enabling rapid, accurate and scalable interpretation of a patient’s whole genome, whole exome or gene panel data facilitating a swift, actionable and comprehensive diagnosis.

Central to Sapientia is the fully integrated Genome Browser, which allows customers to thoroughly interrogate and visualize the patient’s variants. It includes a karyogram display to navigate chromosomes, alongside SNPs, small insertions and deletions, CNVs and larger structural variants.

The system integrates leading tools such as Exomiser, which allows users to prioritise variants according to their relevance to patients’ phenotypes whilst filtering out common and synonymous variants. It leverages reference databases including ClinVAR and DECIPHER, unified alongside Congenica’s own internal knowledgebase of HPO annotated variants curated by clinical experts through routine use of the platform, and users’ own databases.

Powerful bioinformatics pipelines underpin these systems and are developed by Congenica’s world-class bioinformaticians. Clinical diagnoses and reports are signed-off by a team of leading registered clinical scientists. The easily scalable, secure and ISO certified cloud based platform of Sapientia allows for effortless asynchronous multi-disciplinary meetings with complete confidence.

Sapientia is easy to adapt and consolidate into a wide range of instantly scalable workflows; from a lab deeply interrogating an individual sample or labs processing population wide studies. Congenica has proven this through our role as an official interpretation partner for the UK 100K Genomes Project.

Sapientia enables clinicians to interpret a patient’s genome in as little as 30 minutes, empowering doctors and clinicians to diagnose the previously undiagnosable.

 

Finalist: Diploid | Booth 638
Product Name: Moon 1.0
diploid.com/moon

Moon is the first software to autonomously diagnose rare diseases from WES/WGS data. By applying AI to the domain of rare disease diagnostics, Moon brings speed and scalability to the genome interpretation process.

The software only requires the patient’s gender, age of onset and his/her symptoms – in addition to the genetic data. Moon then goes from whole genome variant data (VCF) to pinpointing the causal variant in less than 5 minutes.

The software highlights one or a few variants that could explain the patient’s phenotype. For every variant, Moon displays an extensive list of annotations that it mined from the literature, allowing geneticists to easily verify decisions from the AI algorithms. Moon’s speed does not only save a lot of time and money, it also saves lives: Moon has already proven its utility in the NICU at Rady Children’s Hospital (San Diego): https://goo.gl/7TDrQD.

Unfortunately, about 50% of rare disease patients remain undiagnosed, even after whole genome sequencing and expert interpretation. Most hospitals don’t have the resources to keep analyzing negative cases even though new correlations between genes and disorders are published every day. Moon changes all this: as the software autonomously mines the literature and analyses samples, it can reanalyze older, negative cases in the background. Only when new information that might lead to a diagnosis becomes available, the assigned geneticist is notified. That way, hospitals can frequently reanalyze thousands of cases with minimal labor, providing a perspective to undiagnosed patients.

 

Finalist: DNAnexus | Booth 310
Product Name: Clinical Trials Solution
dnanexus.com/clinicaltrials

Promoting a drug from the laboratory and preclinical testing arena into first-in-human studies and later phase clinical trials represents the largest, most costly gamble in the drug discovery pipeline. DNAnexus de-risks this process by enabling companies to transition validated next-generation sequencing pipelines from translational research into clinical development and, for approved drugs and devices, into clinical and companion diagnostics, all in compliance with HIPAA, CAP/CLIA, and GxP regulations.  This framework has been designed to complement CTMS vendors of choice.

The DNAnexus Clinical Trials Solution (CTS) facilitates association of participants’ genomic profiles with their clinical results. Insights are used to refine participant selection criteria for subsequent phases to increase the likelihood of a successful efficacy and safety outcome. This ability to support adaptive trial design is critical in the era of NGS-driven basket and umbrella trials.  DNAnexus hosts the CTS, and provides scientific expertise in human and microbiome genome analysis, translational informatics, and clinical data integration.

A flagship pharmaceutical customer uses the CTS to integrate multi-site sequencing data from patient and microbiome genomes using validated bioinformatic pipelines:

  •   Bioinformaticians deploy, test, and validate their pipelines and reports
  • Sequencing partners process participants’ DNA samples and results are uploaded to the CTS for validated analysis and reporting
  • Sequencing partners track the status of data and analyses using the CTS service provider interface
  • Trial clinicians run additional validated analysis pipelines using the CTS clinician interface

Genomic analysis results and reports are sent to study physicians, and deposited into the electronic data capture system

 

Edico Genome | Booth 305
Product Name: DRAGEN and Dell EMC Compute + Storage Bundle
edicogenome.com/dragen-bioit-platform/dell-emc/

The DRAGEN and Dell EMC Isilon Compute + Storage Bundle offers a pre-configured, out-of-the-box solution for ultra-rapid analysis and hyper-efficient storage of NGS data.

DRAGEN is built on a Xilinx Field Programmable Gate Array (FPGA), and provides a comprehensive, ultra-rapid secondary analysis solution. DRAGEN leverages FPGAs to provide hardware-accelerated implementations of secondary analysis pipeline algorithms, such as BCL conversion, compression, mapping, alignment, duplicate marking, and haplotype variant calling. FPGAs implement algorithms as logic circuits, providing an output almost instantaneously. As a result, DRAGEN can process a genome at 30x coverage in ~20 minutes, compared to 20-30 hours using CPU-based systems. The flexibility of FPGAs also allows Edico Genome to seamlessly update DRAGEN with new pipelines and performance upgrades. Thanks to this technology, 1 DRAGEN platform can replace up to 80 compute instances, drastically reducing compute, maintenance, and storage costs.

DRAGEN comes preinstalled in a Dell EMC 2U R730 Server with integrated Dell EMC’s Isilon Scale-Out-Network. The R730 is a dense rack server designed to accelerate a range of demanding workloads , including genomics analysis. The R730 delivers outstanding performance, flexibility, and efficiency while reducing space and cost. The Isilon storage architecture automatically aligns application needs with performance, capacity, and economics. As performance and capacity demands increase, both can be scaled simply and non-disruptively, allowing sequencing applications and users to continue working. An Isilon storage cluster consolidates large, unstructured file-based data such as FASTQ, BAM and VCF files into a single system that simplifies solution integration, and is transparent to users.

 

Edico Genome | Booth 305
Product Name: DRAGEN VLRD Pipeline
edicogenome.com/pipelines/dragen-vlrd/

The DRAGEN Virtual Long-Read Detection (VLRD) Pipeline is an advanced algorithm that calls variants in segmental duplications from short-read sequence data. During mapping and alignment, DRAGEN generates a BED file that identifies highly similar genomic regions in the reference genome over a 1 kb sliding window. Users can set the similarity threshold for the BED file; we have found that traditional variant callers perform equally to VLRD below 97% similarity. In addition to using the reference genome, VLRD also comes with a pre-built BED file of ~600 segmental duplications in the human genome. To call variants, VLRD finds sequence reads that map to the duplications annotated in the BED file and performs alignment to the two regions jointly. MAPQ scores are not considered because they would result in filtering of reads. The reads corresponding to each region are piled up and VLRD uses maximum likelihood estimates to solve for the four most likely haplotypes, and then calls variants based on those haplotypes. VLRD takes advantage of small differences between the duplications to assign reads to a location. When regions are 99.5% identical, VLRD still performs with >95% accuracy for 100 bp paired-end reads, compared to only 40% accuracy for a traditional variant caller. VLRD outputs data as a VCF file and can produce a BAM file with alignments for users to evaluate the underlying data. VLRD only requires about 25 minutes to run when similarity is set to 97%, making it a quick addition to an NGS analysis workflow.

 

Finalist: Elastifile | Booth 618
Product Name: Elastifile Cross-Cloud Data Fabric, v2.5
elastifile.com

Elastifile’s cross-cloud data fabric enables scientific computing workflows to efficiently integrate with the public cloud, with no application refactoring required.  Our solution delivers scalable, enterprise-grade, high-performance file services…in the cloud, on-premises, or spanning both.  Elastifile supports a full suite of enterprise storage features (including snapshots, asynchronous replication, compression, and deduplication) and scales performance linearly as additional capacity is added.

The two key components of the Elastifile solution are the Elastifile Cloud File System (ECFS) and CloudConnect object tiering, as described below:

ECFS key attributes:

  1. High-Performance, Enterprise-Grade File Services: Distributed, flash-native architecture delivers high IOPS and throughput while maintaining consistent, low latency
  2. Software-only, Hardware and Environment Agnostic: Frees admins from vendor lock-in, enabling flexible use of any hardware, cloud, or on-premises environment
  3. Unlimited Scalability: Supports on-demand, granular expansion to any capacity or performance level
  4. Data and Application Mobility: Presents strictly-consistent POSIX interface, enabling existing apps to run in-cloud without refactoring

CloudConnect key attributes:

  1. Efficient Hybrid Cloud Data Sync: Delivers efficient, policy-based sync between any on-premises file system and cloud object storage, while retaining file hierarchy and versioning information.
  2. Active and Inactive Data Management in the Cloud: Supports on-demand, granular data “check in” and “check out” between an Elastifile file system and cloud-based object storage, allowing data to reside in the most appropriate (i.e. considering cost, performance requirements, etc.) data tier at all times
  3. Multi-Cloud Connectivity: Unifies any number of private and public clouds, enabling dynamic workload migration and eliminating cloud vendor lock-in

 

Elemental Machines | Booth 622
Product Name: Elemental Machines IOT Smart Lab System
elementalmachines.io

Elemental Machines harnesses the power of IOT and a Cloud Based Dashboard to provide users with full stack solution.  Whether you want to monitor laboratory freezers, refrigerators, ovens, incubators, liquid nitrogen tanks or other equipment, or understand the ambient temperature and humidity in the lab itself, Elements are the answer. Easy to install and battery-powered, they stream high-resolution data to the Elemental Insights dashboard for easy access to visualizations and a lab-wide view of equipment performance. NIST-traceable devices available.  The rich, web-based dashboard gives teams on-site and remote access to all data from the Elements. Track performance of critical equipment to understand usage patterns and identify potential maintenance issues. Manage notifications and alerts. Generate monthly performance for reports for compliance requirements. Anytime. Anywhere. Data Science has never been easier.

 

Genestack | Booth 436
Product Name: Genestack Platform
genestack.com

Genestack is a software solution for biologists and bioinformaticians. It can be used in the cloud or deployed remotely and integrates into a users existing omics data workflows. It is modular with applications for data and metadata management, data visualisations and data analysis. Customers are not required to take all modules nor required to completely replace all their existing software and tools. Instead customers can create their own perfect ecosystem by taking which modules they require and integrate them within their existing workflows and analysis pipelines. With built in metadata templates, popular algorithms, ontologies, custom vocabularies and on-team support customers can take control of there data management and better extract knowledge from the wealth of omics data they produce.

 

Finalist: The Hyve BV | Booth  418
Product Name: RADAR-base
radar-cns.org

Developed in the framework of the IMI RADAR-CNS project, RADAR-base is an open source platform designed to securely collect, store and share readings from wearable devices and smartphone sensors to enable remote monitoring. The RADAR-base platform consists of three major categories of components:

Data ingestion: Recognizing and registering data-sources (including smartphones and wearable devices), collecting the data via a direct Bluetooth connection or through a 3rd party API and streaming in near real time to the server (green box in the figure). Using Apache Kafka, the collected data is streamed to dedicated topics in real-time where the data is optimally schematized using Apache Avro;

Data storage and management: Consists of two centralized storage systems behind an authorized security layer. A cold-storage based on HDFS that is scalable and fault-tolerant focusing on storing large volumes of high frequency raw-data, and a hot-storage based on MongoDB storing aggregated data to provide a near real-time overview of the raw-data. (blue box in the figure);

Data sharing: Visualizing aggregated data in a live dashboard and exporting raw data for further analyses in various formats including AVRO, JSON and CSV (yellow box in the figure).

The platform is highly secured by a centralized management system of users and their authorities, participants, allowed devices and their specifications. RADAR-Base platform is distributed as Docker containers with associated scripts and configuration files to enable easy installation.

 

iRODS Consortium | Booth 316
Product Name: iRODS Storage Tiering Framework v1
irods.org

The newly available packaged iRODS Storage Tiering Framework allows iRODS to automatically move data between any number of identified tiers of storage within a configured tiering group.

A tiering group is an abstraction in the iRODS Catalog that defines which storage resources are in the group, how long data should reside in each tier within the group, and other policy configurations.

Any number of tiering groups can be configured, and the customizable tiering policies can vary based on any information in the Catalog (including ownership, physical location, filename, or any other user-curated metadata).

Metadata-driven orchestration and tiering of managed storage is here.  And it’s open source.

 

Finalist: Linguamatics | Booth 549
Product Name: iScite 2.0
iscite.com

Linguamatics iScite, a Software-as-a-Service search application, puts the power of text analytics directly into scientists’ hands.

Award-winning Natural Language Processing
Researchers can extract and analyze relevant data to rapidly answer business-critical questions. iScite utilizes Linguamatics’ award-winning Natural Language Processing (NLP) based blend of analytical methods. By understanding the semantics and structure of text, iScite handles the variety of ways people express the same information, ensuring searches are comprehensive and accurate.

Easy to use on any device
iScite’s intuitive HTML interface includes a simple search box and auto-complete suggestions. The innovative answer-routing engine lets users answer simple or complex questions using puzzle-piece building blocks – simplifying access to powerful queries that extract concepts, relationships, numerical data such as drug dosages, mutations and more.

Get answers to questions, not just documents
Data sources include Linguamatics’ cloud-hosted content. MEDLINE, Clinical Trials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts are annotated with curated terminologies for diseases, drugs, genes and organizations. Scientists can answer questions such as:

  • What genes are involved in breast cancer?
  • What protocol designs have been used for immuno-oncology trials?
  • What are the adverse events for kinase inhibitors?

Actionable results
Results are presented in structured form, with bar chart facets for dynamic, visual results-filtering, a document viewer that highlights key terms and relationships, and relevant link-outs. Users can curate, save, and export their results.

iScite allows users across drug discovery and development to cut through the vast information landscape and discover the most valuable insights.

 

Finalist: MediSapiens Inc. | Booth 716
Product Name: MediSapiens Accurate, Version 1.0
medisapiens.com

Curated and ontologized data is the foundation of discovery and reliable data use. However, the process of curation and ontologizing has been a tedious, manual, time-consuming affair so far.

Accurate™ is a browser-based solution that combines data curation and automated ontology mapping functions to efficiently curate clinical and phenotype data sets and ontologies. Using artificial intelligence and machine learning-based proprietary algorithms it automatically maps clinical terms to selected ontologies or controlled vocabularies.

Accurate™ is an intuitive, easy-to-use application that can be hosted on any preferred server. It allows you to map with any ontology of choice. It provides a framework for organizational curation rules and workflows, ensuring standard practices in the curation process across teams in different locations, and providing a complete audit trail of all actions performed.

No matter how large or small your data set, with Accurate™ you save time and resources in the curation and ontology mapping processes, with reductions of up to 75% in time spent on curation and ontologizing work from day one.

 

Finalist: Mind the Byte | Booth 617
Product Name: MtB SaaS Platform
mindthebyte.com

Mind the Byte offers a pay-per-use SaaS platform with the latest generation software. We provide a versatile set of applications using cloud computing which lowers the entry barrier to the technology. 

Our virtual profiling methods can facilitate target identification and elucidate the mechanisms of action (MoA) of phenotypic screening hits or natural products with reported activity. Additionally, our virtual screening methods let our clients identify compounds acting on a specific target by mining internal or commercial compound libraries, expand hit or lead series and conduct repurposing of known drugs.

Users do not require extensive training because the platform is really intuitive. They have a manual at their disposal and in case additional support is needed, we also have technical and scientific teams to assist them.

There is no need to purchase licenses and the platform runs on the cloud. Thanks to this, our clients save up to 67% on investments in technology and can scale resources up or down to meet their computer power needs at any given time. Also, we are constantly upgrading our platform, improving both functionality and usability as well as launching new computational tools and models to meet researchers’ scientific needs.

Our SaaS platform for drug discovery is supported by the certified infrastructure of Amazon Web Services (AWS). These environments are continuously audited, with certifications from accreditation bodies across the globe.  We guarantee a safe working environment by encrypting all data transfers, by strictly safeguarding services and by conducting system audits with penetration testing.

 

Finalist: Nanome | Booth 711
Product Name: NanoPro
nanome.ai/

Nanome is helping to improve the drug discovery process through intuitive virtual reality interfaces. They developed applications for experimentation, collaboration, and learning at the nano-scale leveraging leading VR hardware like the Oculus Rift and HTC Vive to create immersive virtual workspaces wherein users can visualize, design, and simulate molecules, proteins, and more. To try the next generation of tools for small molecule design and macromolecular exploration, stop by the Nanome Booth: #711.

There you’ll have the ability to:

  • Import molecular structures from a local machine or an online database such as RCSB or DrugBank.
  • – Manipulate molecular structures by literally grabbing, rotating, or enlarging the area of interest with their hands.
  • – Apply different representations to their selection of Atoms, Residues, Chains, or Proteins such as Stick, Wire, Ball & Stick, or Van der Waals.
  • – Measure distances and angles between atoms.
  • – Mutate amino acids and cycle through rotamer libraries.
  • – Design small molecules by building with any element from the periodic table.
  • – Minimize manipulated molecules to prevent clashes and provide a local energy minimum conformation.
  • – Duplicate or Split any selected area of your structure to modify or export independently.
  • – Export your molecular structures to PDB.
  • – Join a virtual reality session as a guest with or without virtual reality hardware.
  • – Present and collaborate in the same virtual environment with colleagues to demonstrate proposals or compare before and after results.

 

OnRamp BioInformatics, Inc. | Booth 539
Product Name: ROSALIND
onramp.bio/meet-rosalind

OnRamp BioInformatics provides ROSALIND™, the first-ever genomics analysis platform specifically designed for life science researchers to analyze and interpret datasets, while freeing up more time for bioinformaticians. Named in honor of pioneering researcher Rosalind Franklin, who made a major contribution to the discovery of the double-helix structure of DNA with her famous photograph 51, OnRamp’s ROSALIND platform aims to simplify the practice of genomic data interpretation.

ROSALIND puts the researcher into the driver’s seat of data analysis and democratizes bioinformatics by broadly expanding access to genomic and proteomic technologies for cancer research, precision medicine and sustainable agriculture.

While many open-source tools remain the lifeline of genomic analysis, a simplified and innovative user experience for the biologist can empower them to run their own analyses, while utilizing these tools without the need for typing any command-line instructions.

ROSALIND is powered in partnership with Google Cloud and features scalable compute power and economical cloud-based storage. ROSALIND is a swarming docker-based genomic analysis solution incorporating the industry’s most trusted open-source tools and algorithms, with an angular front-end and secure RESTful API. ROSALIND is also deployable on-premise.

We believe that by empowering biologists with an intuitive and comprehensive platform to explore their data and collaborate with colleagues and bioinformaticians, we can help accelerate our industry and the widespread adoption of genomic technologies by dramatically lowering costs, taking out complexity and, ultimately, putting more focus back on what to do with results, not how to get to them.

Finalist: ONTOFORCE | Booth 425
Product Name: DISQOVER v4.0
ontoforce.com

DISQOVER’s newly released visual analytics capability enables discovery of insights from massively complex data sets, in situations where even the questions are often not clear, by strengthening the synergy between two fantastic tools: computers and the human brain.

The main challenge is integrating conflicting requirements of massively linked data, extended text full search capabilities and quantitative analytics in a single, fully interactive environment.

DISQOVER allows you to create custom dashboards over vast amounts of heterogeneous data via one consistent and easy to use interface with an extremely simple to use faceted search but also uses a wide variety of chart types, ranging from simple ones such as bar charts, focusing on a single aspect of the data, to more complex charts such as heat maps or bubble charts, visualizing interactions between two or more data aspects.

All charts are fully interactive and dynamically linked through brushing and linking: if you select data on one chart (e.g. dragging a rectangular area on a scatter plot), the selected data becomes automatically highlighted on all other charts. This happens with near-real time speed, even in the case of tens of millions of data points.

In DISQOVER, you can start with a semantic search, seamlessly switch to a visual analytics dashboard to spot trends and drill down data, and subsequently follow links to related data using semantic search again. At any time you stay in a single, coherent UI, without the need to transfer data from one environment to another.

 

Finalist: PerkinElmer Informatics Inc. | Booth 340
Product Name: PerkinElmer Signals™ Medical Review
perkinelmer.com/product/signals-medical-review-smr

PerkinElmer Signals™ Medical Review empowers medical monitors to detect safety signals faster and reduce overall time to submission by combining innovative medical review workflow with advanced analytics. The key to getting submission ready faster is speeding the time to review, collaborate, and make decisions on data. Signals Medical Review allows you to cut through the noise and go straight to the subjects of interest, and analyze data for those subjects with exactly the visual analytics you need. And, with a secure cloud infrastructure, users conveniently access their set modules while their organization gains huge IT cost efficiencies. From data unification and standardization, advanced statistics and predictive modeling, Signals Medical Review sets the standard for illuminating big and disparate data, reducing clinical risks, and increasing the speed to submission.

 

PerkinElmer Informatics Inc. | Booth 340
Product Name: PerkinElmer Signals™ Notebook
perkinelmer.com/product/signals-notebook-signalsn

PerkinElmer Signals™ Notebook is the next generation cloud-native electronic lab notebook (ELN) and scientific collaboration platform for today’s scientists. With embedded ChemDraw to support synthetic chemistry workflows, drag and drop capture of a wide variety of electronic data files, lightning fast structure search, and a modern, highly responsive design, Signals Notebook is quickly becoming the preferred cloud -based ELN for discerning chemists and researchers alike. Collaboration is supported with social media-like commenting and notifications and creating contextual relationships between experiments. Integration with the ChemACX database gives scientists immediate access to pertinent data around commercial availability of materials. Signals Notebook employs modern, cloud-based micro-service architecture with advanced data lake storage technologies for document storage and indexing. PerkinElmer has architected Signals Notebook to grow with organization’s needs and is horizontally scalable.

Updates with new functionality and bug-fixes are automatic and occur roughly every 3 to 6 weeks. Signals Notebook can be validated and deployed in a multitenant (Standard Edition) or private tenant environment (Private Cloud) depending on customer needs. While data is secure and separate in both instances, some customers may prefer the control a private tenant environment provides over the timing of updates. Security settings and permissions are achieved with a combination of user roles, groups, attributes and experimental states and are effortless for administrators to modify with changing needs (e.g. upon employment of more CROs or addition of projects).

Signals Notebook is the intuitive, searchable, scalable and secure platform designed to increase productivity, enhance collaboration and reduce risk.

 

PerkinElmer Informatics Inc. | Booth 340
Product Name: PerkinElmer SIGNALS SCREENING
perkinelmer.com/product/signals-screening-signalss

PerkinElmer Signals™ Screening adds an intuitive, configurable, and flexible screening workflow engine on top of the unparalleled data visualization and analysis capabilities that come with TIBCO Spotfire®.  In this tool, a screening scientist can compose a stepwise data analysis process assay development data and build a data processing protocol to parallel the wet-lab protocol. 

PerkinElmer Signals™ Signals Screening includes all the standard components for basic screening operations to help a new user get started, but also includes cutting edge capabilities for high-content screening, image processing, high-dimensionality data reduction, SPR (surface plasmon resonance), etc.  Once the scientist is satisfied with the assay and data processing, she can save that as a re-useable protocol to allow for consistent and efficient processing of subsequent experiments.  Finally, PerkinElmer Signals™ Screening integrates elegantly with PerkinElmer Signals™ Lead Discovery to allow result to be published for those newly generated data to be interleaved with previously generated data at the click of a button.

PerkinElmer Signals™ Screening extends TIBCO Spotfire® more deeply into the scientific workflows and offers scientists the opportunity to perform the full screening, data processing, SAR analysis, and lead optimization workflows all in one package.  It is built on a framework and with API’s that enable new screening technologies to be added quickly and even for customers to extend the palette of tools themselves.

 

PerkinElmer Informatics Inc. | Booth 340
Product Name: Signals Lead Discovery
perkinelmer.com/product/signals-lead-discovery-sld

PerkinElmer Signals™ Lead Discovery enables instant access to the scientific data, so scientists can discover better drugs faster. Powered by Attivio and TIBCO Spotfire®, structured and unstructured scientific data is normalized and contextualized such that it can be discovered by Lead Discovery scientists in an intuitive and efficient workflow. Those data sets are then automatically presented in a well-organized SAR workflow that encourages data exploration and drug candidate assessment.

PerkinElmer Signals™ Lead Discovery functionality drives the full life-cycle of data.  Data Generators (assay and analytical scientists) can more easily publish their data with the confidence that data will be discovered and re-used by the project teams.  Data consumers (Lead Discovery project team members) can dedicate their time to understanding the science rather than painstakingly assembling data.  PerkinElmer Signals™ Lead Discovery includes a patent-pending technology to enable structure searching on arbitrarily large small molecule dataset, bringing search speeds to mere seconds.

For Data Generators PerkinElmer Signals™ Lead Discovery enables:

  • Definition of how their data should be captured and represented.
  • Upload data from flat files and Spotfire, or integrate data from existing data sources.
  • Definition of reusable data mappings such that data from regular protocols upload easily.

For Data Consumers S PerkinElmer Signals™ Lead Discovery enables:

  • Point-and-click data discovery.
  • Integrated search over structures, key structure attributes, and all assay or analytical results.
  • Real-time feedback of what structures and data matches the defined query criteria.

 

Finalist: PetaGene | Booth 320
Product Name: PetaSuite Cloud Edition – Version 1.2
petagene.com

Launching at Bio-IT World 2018, PetaSuite Cloud Edition (CE) combines two innovations: (i) the ability for a user’s software tools and pipelines to seamlessly integrate with a wide variety of cloud platforms without modification, and (ii) significantly improved, high-performance, scalable PetaSuite genomic compression technology.

For example, users can now directly run, without modification, their custom BWA-mem, GATK, Python, Java, shell scripts, and other POSIX-based software/pipelines streaming directly to/from AWS, Google Cloud, Azure, and private cloud storage, as though they were local filestores. PetaSuite CE supports each platform’s object encryption during transfer and at rest. User applications can connect to multiple cloud platforms, buckets and regions as desired, transparently, and on demand, in user-mode, without needing to modify their pipelines, setup mounts, or have administrator privileges.

Whether running on bare-metal, in VMs, or within Docker containers, for public, private or hybrid cloud, PetaSuite CE enables organizations to unlock the power of distributed object storage seamlessly from their POSIX-compliant tools and pipelines.

PetaSuite CE is built from the ground-up for the extremely high performance streaming and random-access workloads demanded by genomics applications. The integrated, transparent PetaGene compression has been significantly improved to deliver even faster compression and greater reductions of up to 6x of both BAM and FASTQ.GZ files, enabling large costs savings in cloud storage and data transfer times. Moreover, PetaGene compression can also preserve the MD5 checksum of the original BAM or FASTQ.GZ file and not just the internal raw SAM/FASTQ data.

 

Quantum | Booth 518
Product Name: Quantum Xcellis Scale-out NAS
http://www.quantum.com/en/products/scale-out-storage/xcellis-scale-out-nas/

Leveraging Quantum’s high performance StorNext® parallel file system and data management platform, Xcellis® Scale-out NAS is the life science industry’s first workflow storage appliance to provide the management capabilities and robust features of enterprise scale-out NAS with the cost-effective scaling organizations need to address modern data growth. It delivers greater than 3X the performance of competitive enterprise NAS offerings and, with integrated storage tiering, an end-to-end solution can cost as little as 1/10 that of alternative enterprise NAS solutions with the same capacity and performance. This combination makes Xcellis Scale-out NAS unique in comprehensively addressing the needs of high-value data environments where the organization’s research and development are all built around data.

Flexible Scaling With Maximum Performance – Scale up or out to maximize performance, capacity, and cost.

  • 3x to 10x faster performance than enterprise NAS
  • Up to 12 GB/sec per client
  • Up to 1 million IOPS per node
  • Unified Access and Management
  • Converged block and file
  • Unified data view for access, multi-site, and multi-cloud
  • All NAS administration and data management policy functions accessible via intuitive UI

Add Performance and Capacity Independently

  • Add drives or arrays to scale out capacity
  • Add nodes to scale out client access
  • Add active object storage archive
  • Add deep tape archive
  • Add public cloud

Enterprise-Class Capabilities

  • Automated tiering
  • Hybrid cloud
  • Data protection
  • AI data enhancement Extensive Ecosystem
  • Certified with all major backup packages

Tier to Quantum, commodity, or heterogeneous hardware

 

Finalist: Qumulo | Booth 306
Product Name: Qumulo File Fabric (QF2)
qumulo.com

QF2 is a modern, highly scalable file storage system that runs in the data center and the public cloud. QF2’s scalability, performance and multi-protocol support make it ideally suited to the growing storage demands of next-generation sequencing (NGS). Even if an organization’s sequencers use SMB and its researchers use NFS, a QF2 cluster can span the entire workflow. QF2 eliminates data silos and simplifies workflows. Researchers can do analysis in place because of QF2’s low access times.

NGS workflows can generate a billion or more files a year. QF2 easily scales to keep pace with an ever-growing data footprint. Simply add another node to the cluster to add capacity and increase performance. QF2’s efficiency at storing small files makes 100% of provisioned capacity available for data. Organizations save not just on the storage itself but on infrastructure costs such as rack space, power and cooling.

Cloud-based and collaborative workflows are becoming increasingly common in NGS applications. QF2 has the highest performance of any cloud-based file system. In QF2, cloud instances and computing nodes with standard hardware work together to form a cluster that has scalable performance and a single, unified file system. QF2 has the highest performance of any cloud-based file system. 

QF2 provides a level of real-time visibility and control that no other storage vendor offers. You can instantly identify hot spots, apply quotas, and get detailed information on how your storage is being used.  Use the web GUI or create custom reports with the QF2 API.

 

Finalist: Riffyn, Inc. | Booth 447
Product Name: SDE (Scientific Development Environment) v2.0
riffyn.com/

As scientific R&D grows more data intensive and more global, scientists’ ideas and efforts are often impeded by uninterpretable spreadsheets, inaccessible data, or excessive experimental noise. It’s costing billions of dollars in lost opportunities for discovery. The traditional data management approaches of Laboratory Information Management Systems (LIMS), Electronic Laboratory Notebooks (ELNs), and spreadsheet archives have failed to address these problems.

The cloud-based Riffyn SDE is a SaaS offering which structures and links experimental designs and data across R&D teams for real-time analytics. It is for global R&D organizations who need more productive, more reliable science.

The Riffyn SDE takes you from laboratory data collection to machine learning in 30 seconds, so you will…Never Miss a Discovery®

 

RockStep Solutions, Inc. | Booth 624
Product Name: Climb 1.0
rockstepsolutions.com/

Climb™ is a pure-cloud animal lab informatics system, architected to scale, in the global Microsoft Azure™ cloud. Climb is a modularized application that cover all aspects of an animal research program, including: animal breeding and vivarium management, lab and facility operations, experimental design and data collection, and sample production and storage.  From the technician to the scientist, Climb has features that ease the burden of paperwork and increases efficiency for every role in the research lab.

Because each research lab is unique, workgroups can configure their Climb environment to suit their particular research needs, while still retaining data and operational standards across all labs and partners sites.

Based on Angular 2, Breeze, and Bootstrap, Climb’s web application runs on Azure App Services and is compatible with all major operating systems, browsers, and mobile devices. On the back-end Climb uses advanced cloud systems including elastic database pools, mobile services, machine learning, blob storage, and IoT hubs. With Azure, Climb provides near limitless compute and storage capacity for the most demanding research programs.

Delivered as a SaaS solution with annual subscription licenses, Climb can be deployed to a research site in minutes and organizations can be up and running quickly with minimal training required.

Climb includes an IoT Smart Lab module where devices monitoring time-series parameters, such as environmental conditions, can be connected to anomaly detection algorithms and alerts. IoT data streams can also be associated with objects in the database providing high resolution data for managing operations and/or scientific data analysis.

 

Rudraya Corporation | Booth 437
Product Name: Sonic Platform 4.0
rudraya.com

Sonic Platform is an enterprise level secure software solution for management of computational clusters (local, cloud or hybrid) along with regulatory compliant version-controlled data repository with capability to manage seamless handling of data between clusters and analysts desktop. Sonic also provides an integrated environment to host third party analysis and visualization tools. The platform is comprised of four components; Sonic Cluster, Sonic Project, Sonic Apps and Sonic Visual.   Sonic Cluster component of the platform makes it easy to deploy and manage cloud resources. Users can use Sonic Cluster to launch a regulatory compliant burst or elastic cloud computing cluster in the Amazon AWS environment for on demand computing needs.  Sonic Project will store and manage data, workflow, analysis scenarios and reports supporting drug development programs in a highly secure and controlled environment with full regulatory compliance. Project is built on the SVN version control repository but extends the tool to work with the more demanding regulatory data management needs.   Sonic Apps provides a complete virtual app solution to meet all your needs from a single, easy-to-deploy platform for all windows based PK/PD modeling and simulation tools with integrated secure regulatory compliant data repository. Sonic Visual is a data browsing, filtering, and analytics platform with built in visualizations libraries and integrated R Shiny server.

 

Finalist: Saphetor S.A. | Booth 626
Product Name: VarSome – The Human Genomic Variant Search Engine
varsome.com

VarSome is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants. VarSome renders and displays a detailed annotation of the queried variant, including multiple notations, predicted pathogenicity status from a variety of tools, genomic context, as well as information from 37 databases. Where applicable, also displays all possible equivalent variants that result in the same final genotype. It allows users to mark the pathogenicity of variants and to link variants to specific phenotypes, diseases, and publications. Finally, it provides an automated pathogenicity assessment consistent with the widely accepted ACMG guidelines. It, therefore, provides a powerful analysis resource as well as a repository for the accumulated knowledge of the genomics community and offers a convenient way for this knowledge to be shared globally.

Appearing as the first search engine of-its-kind (the “Google” for geneticists), has seen its numbers of active users rise at a fast-organic rate, gaining popularity and interest among its users since the first beta version launched in spring 2016 at the conference of the European Society of Human Genetics in Barcelona. With a library of over 50 million genomic variants, the website has already 5.000 monthly active users in the community of clinicians, laboratory specialists and researchers in genetics.

 

Finalist: Seven Bridges Genomics | Booth 426
Product Name: Spatial Transcriptomics on Seven Bridges
sevenbridges.com

Seven Bridges and Spatial Transcriptomics present a sample-to-interpretation workflow that combines cutting edge bench techniques, with automated data analysis in the cloud, and data visualization via a local desktop application.

Briefly, the Spatial Transcriptomics kit provides glass slides with printed arrays of DNA capture spots. Each spot contains hundreds of millions of capture probes with unique barcodes to identify the location of each spot in the array. Fresh frozen histological tissue sections are imaged, applied to the slides, and the sections then permeabilized to release cellular RNA, which is captured in situ, and then prepared as a RNAseq library. In addition, the slide is imaged with a fluorescent label to record the location of the arrayed spots.

After sequencing, the RNAseq data and imaging data are uploaded to the Seven Bridges Platform. The RNAseq data are then demultiplexed and transcripts identified using Spatial Transcriptomics bioinformatics workflow, which is described in Common Workflow Language to optimize portability and reproducibility. The histological images and fluorescent images are processed by “Spotty” an automated image recognition algorithm that registers both images together and allows association of the RNAseq results with each spot. Lastly, the processed data, which are located in the cloud, can be mounted locally for visualization by the Spatial Transcriptomics data viewer using Seven Bridges File System (SBFS) technology.

Our combined solution provides researchers facile access to this novel, yet complex, data type backed by the power of cloud bioinformatics, as well as a responsive user experience through local data visualization.

 

Finalist: Sinequa | Booth 525
Product Name: Sinequa ES v10
sinequa.com

The Sinequa Cognitive Search and Analytics platform handles all structured and unstructured data sources and uses Natural Language Processing (NLP), statistical analysis and Machine Learning (ML) in order to create an enriched “”Logical Data Warehouse”” (LDW). This LDW is optimized for performance in delivering rapid responses to users’ information needs. Users can ask questions in their native language or ask that relevant information be “”pushed”” to them in a timely fashion when it emerges.

More than 180 connectors ready for use “”out of the box”” make the process of connecting multiple data sources fast and seamless. Company and industry-specific dictionaries and ontologies can be easily integrated, putting specific knowledge “”under the hood”” of the Sinequa platform, making it an intelligent partner for anyone in search of relevant subject information.

 

Smart IOPS | Booth 239
Product Name: Data Engine T2 HP – High Performance Edition
smartiops.com

Smart IOPS Data Engine solid state drives (SSDs) are the new category of enterprise PCIe NVMe SSDs that offer supercharged performance engineered to remove the storage bottleneck in High Performance (HPC) and high -end enterprise datacenters. With its unprecedented 1.7M IOPS, Data Engine SSDs deliver 4X the I/O processing bandwidth of competing high -end PCIe NVMe enterprise SSDs with ultra-low latency, eliminating performance bottle necks and significantly improving QoS.  Smart IOPS offers three new and distinctive product categories targeting multiple market segments for our data-centers, enterprise, and High–Performance Computing (HPC) customers.

1. Data Engine T2HP High-Performance: The fastest and highest performing PCIe NVMe SSD available in the market today. Offered in 3.2 and 6.4TB user capacities, Data Engine T2HP is in a class of its own, surpassing 1.7 million IOPS and 6.8GB/s in bandwidth per SSD.  The lowest $/IOPS total cost of ownership with unmatched QoS and bandwidth.

2. Data Engine T2LL Low Latency: Smart IOPS has combined the superior performance that it has come to be known for with best-in-class NAND technology to rival the latest non-volatile memory products. Data Engine T2LL offers QoS latency and response time that is on par and at a small fraction of the cost of new trendy non-volatile memory solutions.

3. Data Engine T2HC High Capacity: One of the largest user capacity in a HHHL add-in card form factor with up to 25.6TB. Unlike other larger SSDs, the performance in this product continues to far exceed other SSD in its class.

 

SnapGene | Booth 416
Product Name: SnapGene Server 2.0
snapgene.com

SnapGene Server is a server-based software solution that allows organizations to share richly annotated, beautiful, interactive plasmid maps created on the fly from a multitude of file formats. With SnapGene Server powering your website, ELN, or other web-based molecular biology platform, users can:

  • View interactive or static maps
  • View a scrollable interactive nucleotide visualization
  • Convert between common file formats*,**
  • Detect common genes, regulatory regions, and other features
  •                Identify primer binding sites
  • Generate a summary of restriction sites
  • Generate a summary of annotated features
  • Generate a summary of hybridizing primers
  • Generate a summary of open reading frames

An example of SnapGene Server in action can be found on the Addgene plasmid pages (addgene.com).

File Format Conversion
No matter what program scientists use to plan experiments, they should be able to see their data in an easy-to-read map, so we ensure that you can import* and export** common file formats.

* ApE, CLC Bio, Clone Manager, DNAssist, DNADynamo, DNASTAR Lasergene®, DNA Strider, DS Gene, EMBL (ENA), EnzymeX, GenBank / DDBJ, Gene Construction Kit®, Geneious, GeneTool, Jellyfish, MacVector, pDRAW32, Serial Cloner, Swiss-Prot, Vector NTI®, Visual Cloning
** FASTA, GenBank, EMBL

System Requirements

Ubuntu Linux 14 or 16, or Fedora Linux 23
Memory: 1 GB RAM
Hard Drive: 25 MB available disk space

 

Starfish Storage | Booth 332
Product Name: File Translation Gateway
starfishstorage.com

The Starfish FTG (File Translation Gateway) is a unique file sharing solution that allows files from a variety of disparate storage devices to be presented as a single mountable file system. The backend volumes can serve files via NFS, SMB, or S3, and they can be hosted locally, in the cloud, or even at another institution.  The user accesses the virtual file system via SMB or NFS after authenticating with their institution’s LDAP or Active Directory.

The contents of the virtual file system can be renamed and reorganized, and permissions can be altered without affecting the backend namespaces. The FTG can be used to enforce unusual access control logic such as that which might be required by an IRB for human subject data.   

Virtual file systems are compromised only of metadata, and thus practical to make them as large or small as desired and to have as many of them as necessary. When files reside in the cloud or at another institution, the FTG can optionally cache file contents locally, with or without encryption.

The FTG can work like a bi-directional file to object gateway, where data can be written as a file and read as an object in the cloud, or written as an object and read as a file. This model extends across institutional boundaries, such that users in different institutions can collaborate on the same file collections as if they were accessing a conventional local file server or NAS (network attached storage) device.             

 

Symmetric Computing, Inc | Booth 728
Product Name: 4 Node GPU Cluster
symmetriccomputing.com

At Bio-IT 2018, Symmetric Computing is demonstrating the ability for researchers and scientists to model and analyze millions of biomolecular compounds both economically and quickly. We are showing popular open-source biomolecular modeling programs running on our affordable 4-node GPU Cluster.

Symmetric Computing’s 4-node GPU Cluster is running AutoDock Vina, NAMD and VMD. AutoDock Vina is an open-source molecular docking program. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems and uses the VMD molecular graphics program for simulation setup and trajectory analysis.

Symmetric Computing’s GPU Cluster is state-of-the art. It is powered by the most powerful off-the-shelf processors available today: two AMD EPYC™ processors and twelve AMD Radeon Instinct™ MI25 GPUs (each with 12.3 TFLOPS FP32 performances). The four nodes share 2 TB of memory with Symmetric Computing’s patented Distributed Symmetric Multi-Processing (DSMP™) Linux kernel extension.

Using Symmetric Computing’s powerful 4-node GPU cluster (priced well below $200K), researchers and scientists can analyze almost 1 million molecular compounds in a 24-hour period.

 

Univa | Booth 309
Product Name: Navops Launch
univa.com

Univa is the leading independent provider of software-defined computing infrastructure and workload orchestration solutions. Univa’s intelligent cluster management software increases efficiency while accelerating enterprise migration to hybrid clouds.

Univa® Grid Engine® accelerates the processing of massive amounts of data and sophisticated analyses to increase productivity in life sciences. It manages workloads automatically, maximizes shared resources and accelerates the execution of any container, application or service. The solution can be deployed in any technology environment: on-premise, cloud, hybrid cloud or Cloud-native HPC. By using Univa Grid Engine, life science organizations can deliver products and results faster, more efficiently, and with lower overall costs.

Coupled with Navops Launch, Grid Engine can dynamically schedule workload to a hybrid cloud while Navops Command enables HPC workloads and microservices to run on a shared Kubernetes cluster. The solution also monitors any resource or software license and schedules applications ensuring they are automatically matched to the appropriate licenses and machines.

 

Univa | Booth 309
Product Name: Navops Command
univa.com

Univa is the leading independent provider of software-defined computing infrastructure and workload orchestration solutions. Univa’s intelligent cluster management software increases efficiency while accelerating enterprise migration to hybrid clouds.

Univa® Grid Engine® accelerates the processing of massive amounts of data and sophisticated analyses to increase productivity in life sciences. It manages workloads automatically, maximizes shared resources and accelerates the execution of any container, application or service. The solution can be deployed in any technology environment: on-premise, cloud, hybrid cloud or Cloud-native HPC. By using Univa Grid Engine, life science organizations can deliver products and results faster, more efficiently, and with lower overall costs.

Coupled with Navops Launch, Grid Engine can dynamically schedule workload to a hybrid cloud while Navops Command enables HPC workloads and microservices to run on a shared Kubernetes cluster. The solution also monitors any resource or software license and schedules applications ensuring they are automatically matched to the appropriate licenses and machines.

 

Finalist: Wasabi Technologis Inc. | Booth 718
Product Name: Wasabi Hot Cloud Storage, Version 2.0
wasabi.com

Wasabi is a public cloud object storage service that can be used for a wide range of research and other Bio-IT use cases that require cost-effective, high-performing, and secure cloud storage.  It is ideal for storing and retaining electronic healthcare records, medical imaging files, and healthcare IoT data, as well as big data for life sciences research and development initiatives. With Wasabi, you can maintain massive volumes of structured or unstructured data in the cloud, at radically low cost, while satisfying stringent security, durability and compliance requirements. Wasabi hot cloud storage is 6x faster than the leading cloud storage platform (Amazon S3) making the retrieval of critical healthcare, medical and research data nearly instantaneous from the cloud. Wasabi’s groundbreaking technology includes an innovative data protection feature known as ‘immutability’ which protects storage against accidental or malicious deletion. Healthcare providers, insures and clearinghouses can use Wasabi hot cloud storage for a variety of purposes including primary storage for application data and content, secondary storage for backup or disaster recovery, and archival storage for long-term data and record retention. Wasabi stores and maintains electronic health records (EHRs) in accordance with the HIPAA and HITECH regulations.

 

WekaIO | Booth 519
Product Name: WekaIO Matrix v3.1
weka.io/

WekaIO’s Matrix shared, accelerated software-based scale-out storage solution is optimized to leverage the performance of flash technology to support both large and small file access, either randomly or sequentially, which is a ideal for life science and precision medicine workflows. It can be deployed natively in the cloud with compute and storage integrated into the application cluster or as a dedicated storage server (appliance model), eliminating infrastructure cost and complexity. With the WekaIO Matrix software, performance and scalability is defined by the user, not by predetermined capabilities of the NAS appliance—dynamic performance and capacity tuning is an inherent product feature. Each WekaIO core can deliver more than 30,000 I/O’s per second and more than 400MB per second throughput—all at less than 500 microseconds of latency—a cluster of 100 cores will deliver 3 million IOPS and 40GB of bandwidth to the research application. WekaIO eliminates the storage siloes and underutilized capacity that frequently results from legacy storage platforms by creating a distributed, single namespace file system capable of scaling to thousands of compute nodes and petabytes of storage. One user can manage Petabytes of data by simply installing Matrix FS on any Intel-based server and dedicate an SSD to WekaIO. Users have instant access to and complete visibility to all of the data managed by MatrixFS.Our patented data protection scheme distributes data across the entire file system ensuring the highest level of protection. A cluster can survive up to four concurrent failures without loss of service.

 

Finalist: WuXi NextCODE | Booth 602
Product Name: face2gene integration version 1
wuxinextcode.com

Our new platform can greatly accelerate diagnosis of rare diseases by bringing together cutting edge facial recognition based on artificial intelligence with big omics. WuXi NextCODE has the world’s largest knowledge base for diagnosing rare genetic diseases.  We have now integrated our Clinical Sequence Analyzer (CSA) tool with FDNA’s Face2Gene phenotyping software, which is based on facial recognition and artificial intelligence.  FDNA has built up a massive database of phenotypes that are derived from clinical cases.  WuXi NextCODE’s CSA, meanwhile, allows researchers and clinicians to query massive datasets on-the-fly and visualize raw sequence instantly.  No other system in the world manages, mines and interprets more genomes than WuXi NextCODE’s platform. Now that these two systems operate together, physicians can much more easily go from a software-derived phenotype determination to the appropriate genetic testing for any patient. This saves time, money and lives.

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