By Bio-IT World Staff
April 26, 2012 | Bio-IT World announced the winners of the Best of Show competition yesterday evening at the 2012 Bio-IT World Conference & Expo in Boston. Recentris, Opscode, Clear Trial, and Cambridge Semantics were honored.
The Best of Show competition recognizes new products available at the Bio-IT World Conference & Expo. Of the 34 new products that were considered by a panel of expert, industry judges, twelve finalists were named in four categories, and the judges viewed their products and demonstrations at the event. This year’s winners and finalists are:
IT Hardware & Infrastructure Category
WINNER: Opscode Chef
Chef is an open-source systems integration framework built specifically for automating IT infrastructure in the era of the cloud. No matter how complex your IT infrastructure is, Chef makes it easy to deploy servers and scale applications throughout your entire infrastructure. Because Chef combines the fundamental elements of configuration management and service oriented architectures with the full power of Ruby, Chef makes it easy to create an elegant, fully automated infrastructure. Available as either a hosted software service or an enterprise-grade software solution installed behind your firewall, Opscode Chef enables users to create highly available, dynamically scalable, fully managed and supported automation environments.
Red Hat Storage Software Appliance
Red Hat Storage Software Appliance is built upon GlusterFS 3.2 and Red Hat Enterprise Linux 6.1. This software-only appliance enables enterprises to treat physical storage as a virtualized, standardized and scale-on-demand pool while continuing to provide the flexibility, performance and enterprise-class quality required for successful open source enterprise environments across physical and cloud deployments. The Virtual Appliances install in minutes, are deployed as user space applications and require no changes or modifications to the operating environment. Gluster Virtual Appliances are fully-POSIX compatible and enable a choice for private cloud users to deploy and manage storage with the superior economics of commodity hardware.
TeraServer is an extraordinarily capable single server providing the same computing power as a department sized GPU-enabled compute cluster. It combines over 10 TFLOPS performance with the simple ease of use and management of operating one node: complicated cluster coding is no longer required. A single TeraServer delivers 80 x86 CPU cores from 8 Intel Xeon E7 series CPUs, 2TB of DDR3 memory, and 8 NVIDIA Tesla GPUs with a total of 4096 GPU cores. TeraServer not only outperforms multi-node GPU clusters, it allows researchers to tackle previously unsolvable problems. Sequencing applications will benefit from loading an unheard of 2TB of data into memory at once and from GPU-enabled BLAST-P support; molecular dynamics applications like AMBER, NAMD, and GROMACS leverage 80 CPU cores and 10-100x speedups on GPUs; capability for InfiniBand, SAS, or FC connections to high-performance storage ensure customers can feed terabytes of data to TeraServer for computation.
Informatics Tools & Data Category
WINNER: Anzo Competitive Intelligence Solution by Cambridge Semantics
The Anzo Competitive Intelligence Solution makes it easy to route targeted information to the right people at the right time from the right sources. Anzo combines data from company databases, spreadsheets, news sources on the web, scientific journals, and curated sources like Thomson Reuters Life Sciences into a single view. Anzo Unstructured enables Anzo to process unstructured data—such as news stories, press releases, blogs, and scientific journals—so that facts from those documents can augment information coming from more curated sources. Anzo is an OSGI platform that implements Semantic Web standards from its very core. RDF, the data model of the Semantic Web, provides an incredibly flexible data model, while OSGI and an internal ESB enable Anzo server components to be loosely coupled. Said another way, the system was built from the ground up to be flexible and to adjust to changing situations.
Biomolecular Hub v1.0 by IDBS
The Biomolecular Hub is a breakthrough product that provides comprehensive data management for NGS, GWAS, gene expression, proteomics and other molecular meta-data and results. It contains the explosion in omics data with full security, audit and search capabilities. Analysis results are stored and associated with their source files to ensure traceability and reproducibility of results, providing a single source of truth around any omics run. The Biomolecular Hub is a file-based repository with a fully associated relational metadata registry. It is lightweight, flexible and highly scalable with a low administration and maintenance overhead. It enables researchers to store internal and external data files from any molecular technique including gene expression, arrayCGH, proteomics, and NGS; leave large datasets where they are, Biomolecular Hub will index those files for rapid access; provide secure access to data files and results either hosted off site or installed on your site for additional control; share results and annotations from current and previous experiments with colleagues; organize molecular research activities into studies, projects, experiments and analyses; trace the origin of selected features, down to source files; and easily associate clinical data for translational studies.
Omixon Target v.1.0
Omixon Target is designed to meet the requirements of diagnostics research and biomarker discovery. It is based on accurate read mapping, alignment and variant calling algorithms. Simulated reads can be generated for the particular target, the sequencer and sequencing protocol. This can help design experiments as well as finding any artifacts introduced by analysis errors. The simulated dataset gives an indication of false positive and negative rates. The simulation can be used to verify variants in the experimental data and to separate analysis artifacts from PCR artifacts such as PCR stutter or off-target effects. Omixon Target interface was designed to meet the requirements of targeted sequencing analysis including pre-configured targets and target definition wizards, multi-sample or family trio comparison, workflows for automated and manual approval of variants, multi-sequencer support including Illumina, Ion Torrent, Roche 454 and SOLiD sequencers. Its accelerated graphics capabilities used for visualizing tracks provides fast interface for convenient work with multiple tracks.
Web-based Services & Software Category
WINNER: CERF 5 by ELN Technologies
ELN Technologies' (formerly Rescentris) CERF is award-winning ELN software for life sciences research organizations of any type (commercial, government, academic/nonprofit) and size. It provides the expected ELN functions—including data entry/visualization, 21CFR11 compliant recordkeeping and intellectual property protection—and adds enterprise document and scientific data management. CERF is the only enterprise ELN providing native Windows and Mac OSX clients to support scientists that need the power and flexibility of an integrated desktop environment for authoring and batch operations. CERF 5 supports mobility with a new native iPad client, web client, and ‘Email-to-CERF’ function. CERF is uniquely built on semantic technologies—for data/metadata models and also for business logic. This makes the data smart and semantically linked and also allows the modular system to be extensible and easily updated. SDIMS module adds structured (semantic) and validated data entry for LIMS-like functions such as experiments, samples, and tasks, as well as idea management. CERF is hosted on customer’s servers or “in the Cloud” to centralize data and enables role- and workgroup-based access to notebooks, records, datasets, and search results. CERF 5 offers new social networking features and architecture to better support collaboration the way people work. New features include sending invitations to partners to join projects (or CERF) with admin approvals, granular sharing of notebook subsections, ability to subscribe to content and people and be notified of updates, discussion forums linked to projects and content, social tagging and folksonomies, and message dashboards. CERF is highly flexible including workflows, databases, and large data management.
Ingenuity Variant Analysis
Ingenuity Variant Analysis helps researchers quickly go from millions of variants down to a prioritized list of the most compelling variants without making “cuts” to the dataset. Many current next-gen sequencing solutions are focused on streamlining the ability to get to called variants. Ingenuity Variant Analysis picks up at the called variant stage, supporting VCF, GVF, and Complete Genomics data. It is unique relative to other analysis approaches because it leverages hundreds of thousands of human mutation findings as well as gene findings in the Ingenuity Knowledge Base, predicted and established transcription factor, microRNA, and enhancer regulatory sites, functional impact inference algorithms, and integrated OMIM, COSMIC, and pharmacogenetic content for the interpretation of variants. It is this knowledge-driven approach that facilitates a faster identification of variants for follow-on study.
The Igor Platform by Seven Bridges Genomics
The Igor platform by Seven Bridges Genomics brings the AppStore concept to genomics. Igor is a scalable cloud platform that enables researchers from any technical background to design, execute, and share NGS analysis workflows using the leading open-source tools. Igor features fine-grained data privacy controls, instant data transfer within the cloud, and workflows that can be shared between collaborators. Teams can collaborate in real-time. With leading tools wrapped into our system and an intuitive workflow designer to build custom pipelines, we require no particular IT skills. SBG also publishes complete workflows as Public Resources; they can tweaked and customized, or they can be deployed just as they are. We give researchers complete control over their analysis pipelines, but our interaction design requires scientists to deal only with the complexity they want to handle. Every analysis task executed on Igor can be replicated with one click; our workflows are complete computational representations of everything that happens to the results that are produced. SBG is also developing smart metadata tools that remember when and how files were updated.
Clinical Trials & Research Category
ClearTrial 4.5 is Clinical Trial Operations (CTO) software, purpose-built for clinical planning, forecasting, outsourcing, and project tracking. A cloud-based application incorporating clinical analytics and delivered as Software-as-a-Service (SaaS), the application stores operational study data in a secure database, accessible at any time from any location via a secure web connection. The ClearTrial software architecture follows a project management methodology that includes activity-based costing, which predicts the level of effort for a specific resource (person) to perform a given task (activity). The level of effort is calculated based on an algorithm that has been derived from analysis of the cost and time drivers that affect each task. The ClearTrial Work Breakdown Structure defines and groups the tasks and subtasks that comprise a clinical trial in a way that organizes and defines the total work scope of the clinical project. Utilizing up to 140 documented clinical input assumptions (e.g., number of sites, number of patients, type of data collection, monitoring frequency, etc.) users can generate clinical trial operational plans, RFP documentation, and budgets encompassing 200 therapeutic indications, with internal as well as CRO labor rates for work performed in 90 countries—specific to each indication and country.
Vendor Integration Manager by ePharmaSolutions
Vendor Integration Manager (VIM) streamlines the user provisioning process through a single application that programmatically completes account activation forms for every clinical system on a given study. A site, CRO or sponsor user is added to the VIM, and every vendor account activation form is completed in the exact format and data structure the vendor requires. VIM functions much like an automated currency exchange system for identities. User and site profiles are entered in a standardized format in User Management Application (UMA) and changed in real time into user and site profiles required by each vendor. VIM enables UMA to be the single system of record where user, site and role information is managed for each study. Alternatively, VIM can be integrated with a CTMS and used to augment user, site and role information not supported in that CTMS. VIM is a SharePoint 2010 application with custom ASP.NET mapping algorithms that transform data into the unique formats used by each vendor, respecting both different username, name, address, date and time conventions, and the different metadata, relationships and roles needed by each vendor application.
Wingspan eTMF v. 1.0
The Wingspan eTMF (electronic Trial Master File) features customizable dashboards, zero folder navigation and a robust metrics system, giving pharmaceutical companies and their study partners an unprecedented solution that supports their changing business models and avoids the problems of former electronic trial master files. Wingspan eTMF helps study owners to ensure their trials are complete, consistent and compliant at all times. Study owners can anticipate and track all the documents that are expected for a study across five levels: Enterprise, Program, Study, County and Site. Wingspan’s use of Question and Answer wizards ensure that study owners generate a consistent set of artifacts required for each and every study. Quality Control Workflow ensures that documents submitted by document contributors are accurately matched to their corresponding study placeholders, which are tied back to the TMF Reference Model. Most importantly, Wingspan eTMF provides tools for the monitoring and tracking of document timeliness to ensure that they are submitted punctually with respect to key milestones and generates multiple reports so study owners can instantly know what documents are missing, which are late and which are coming due.
Congratulations to all the winners and finalists. Bio-IT World is especially thankful to our team of judges who volunteer their time and expertise to the program:
- Michael Barmada, University of Pittsburgh
- Joseph Cerro, The Schooner Group
- Kevin Davies, Bio-IT World
- Ming Guo, Cambridge Healthtech Institute
- Jon Haddad, Sirtris, a GSK Company
- Richard Holland, Eagle Genomics
- Phillips Kuhl, Cambridge Healthtech Institute
- Bill van Etten, BioTeam
- Susan Ward, Consultant