News Article | May 25, 2017
Eagle Genomics, the smart data management company for life sciences, is today announcing the commercial launch of eaglecurate, a product set to revolutionize the time and resource intensive process of data curation. The platform has been named a Best of Show Finalist at BioIT World, the third year in a row the company has achieved such an award, winning last year’s Best of Show with eaglediscover. Data curation is the single most significant bottleneck impeding progress towards data driven innovation at scale in Life Sciences R&D today. As scientific data generation accelerates and as data volumes increase, the current industry approach, employing costly armies of expert human biocurators, will present an ever more significant challenge. eaglecurate addresses this challenge through automation of the data curation process and the automated semantic enrichment of curated data sets. This will drive dramatic productivity improvements in the innovation process and the targeted use of data assets for relevant analysis. eaglecurate is the latest addition to the company’s award winning “Automated Data Scientist” smart data management platform, putting data science at the fingertips of life sciences researchers and bridging the divide between data and new scientific insight. Building on the foundations of the Best of Show award-winning eaglediscover product, eaglecurate enables value-driven data curation. It’s launch represents the maturation of many years of experience and thorough ethnographic observations of how biocurators actually work. When biocuration is focused on semantic enrichment, it is mainly a contextual activity that consists in constructing an “entailment mesh” of data sources, context and underlying entities of interest, rather than merely structural or syntaxical transformation. “Context” is often tacit and implicit in the mind of the biocurator and in the case of life sciences data it consists often in the experimental and design studies used to generate data. By combining advanced machine learning and data measurement capabilities, eaglecurate allows for reverse-engineering of data into a graphical representation of the context, in the form of a process-oriented graph. The graph represents the experimental processes, study designs, observational studies and assays, etc., employed to generate the data. eaglecurate delivers a self-service platform to biocurators, bioinformaticians and scientists for curating their datasets by exploiting this sophisticated graph structure connecting process-elements and artefacts that, at the same time, provides executive management with an advanced dashboard for oversight enabling data governance by design. According to Abel Ureta-Vidal, CEO of Eagle Genomics “eaglecurate is a truly innovative milestone towards automated data curation. It is the latest module of our smart data management platform bringing us closer to our vision and providing a conversational interface allowing the scientists to “talk” with their data.”
News Article | July 7, 2017
CAMBRIDGE, England & CAMBRIDGE, Mass.--(BUSINESS WIRE)--Smart data management company, Eagle Genomics, is pleased to announce the formation of an Advisory Board comprised of some of the world’s thought leaders in data and life sciences. Members of the board are all exceptional individuals representing enterprise, academia, investment and education. The purpose of the Advisory Board is to further the Company’s mission to enable insight through data driven discovery, with members offering specialised scientific expertise to the executive management team. Founding members of the Advisory Board include Nessa Carey, Douglas Kell CBE, Researcher and Systems Biologist at the University of Manchester, Cliff Meltzer, CEO at Excellcare, David Cleevely CBE, Chairman at Raspberry Pi Foundation and Paul Flicek, Head of Genes, Genomes and Variation Resources at European Bioinformatics Institute. “Each advisor brings a wealth of knowledge, experience, and a valuable external perspective to ensure Eagle Genomics remains at the forefront of scientific innovation,” said Executive Chairman Anthony Finbow. Providing a combination of software and bioinformatics expertise, the Eagle Genomics platform acts as the “Automated Data Scientist”, qualifying and collating the relevant data from which faster and more accurate insight can be achieved. The company also announce the retirement of Alan Barrell as Non-Executive Director. Chairman Anthony Finbow commented: “I would personally like to thank Alan for his years of service and the valuable contribution he has made to Eagle, and wish him a healthy, happy retirement.” Further details of the Advisory Board members are given on the Eagle Genomics website. Eagle Genomics is a smart data management software company helping life sciences companies conducting data intensive research to bring new candidate medicines, therapies and products to patients and customers more quickly. Its Automated Data Scientist software platform exploits state of the industry data science to radically reduce time to cost of research, thus enabling customers to achieve drastic productivity improvements and true data driven discovery. For more information on Eagle Genomics, please visit the company’s website, follow Eagle Genomics on Twitter (@Eaglegen) or call Eagle Genomics at +44 (0)1223 654481.
News Article | August 8, 2017
CAMBRIDGE, England--(BUSINESS WIRE)--Smart data management for life sciences company, Eagle Genomics, has today announced it has been awarded a close to £600,000 grant from Innovate UK, the UK’s innovation agency, to support the company’s ongoing commitment to radically reduce time to insight through data science. The project which has received the grant, under the banner; ‘Increase your data's value: A value-driven semantic enrichment system to speed up scientific insight’ – will further develop the pioneering e[curate] data curation module. Using a unique combination of conversational and statistical learning, decision theory and semantic enrichment, e[curate] will enable scientists to question data with context, significantly improving relevancy and, therefore, speed to insight. Integrated as part of Eagle’s ‘e[automateddatascientist]’ platform, e[curate] will solve the constraints scientists currently experience in being able to weave and store data consistently. In support of the project Eagle Genomics will receive a share of the £197m to be invested in healthcare and medicine through the Industrial Strategy Challenge Fund, introduced by the UK Government to help meet the ‘major industrial and societal challenges of our time’. The impact of the e[curate] platform on life sciences research will be significant, not only in addressing the challenge of speeding up patient access to new drugs and treatments, but also in reducing the cost of bringing drugs to market. Executive Chairman at Eagle Genomics, Anthony Finbow commented - “We are delighted to have received this Innovate UK award, in recognition of the potential of our platform to radically reduce the time and cost involved in achieving scientific insight. We’re excited about the impact this will have on drug discovery and innovation, resulting in better tailored therapeutics (precision medicines) and safer consumer products.” The Chief Executive of the UK’s innovation agency, Innovate UK, Dr Ruth McKernan commented: “Innovate UK is proud to support Eagle Genomics in the development of the e[curate] platform which has the potential to accelerate scientific discovery, through intelligent data storage and analysis. This will speed the creation of new medicines, increasing productivity in the health and life sciences, a key aim of the Industrial Strategy Challenge Fund.” Eagle Genomics is a smart data management software company helping life sciences companies conducting data intensive research to bring new candidate medicines, therapies and products to patients and customers more quickly. Its e[automateddatascientist] platform puts state of the industry data science at the fingertips of biologists to radically reduce time to cost of research, thus enabling customers to achieve drastic productivity improvements and true data driven discovery. For more information on Eagle Genomics, please visit the company’s website, follow Eagle Genomics on Twitter (@Eaglegen) or call Eagle Genomics at +44 (0)1223 654481 Innovate UK is the UK's innovation agency. It works with people, companies and partner organizations to find and drive the science and technology innovations that will grow the UK economy.
Prlic A.,University of California at San Diego |
Yates A.,European Bioinformatics Institute |
Bliven S.E.,University of California at San Diego |
Rose P.W.,University of California at San Diego |
And 12 more authors.
Bioinformatics | Year: 2012
Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model. © The Author 2012. Published by Oxford University Press. All rights reserved.
News Article | November 23, 2016
MarketStudyReport.com adds “Precision Medicine Market Size By Technology (Big Data Analytics, Gene Sequencing, Drug Discovery, Bioinformatics, Companion Diagnostics), By Application (Oncology, CNS, Immunology, Respiratory), Industry Analysis Report, Regional Outlook (U.S., Canada, Germany, UK, France, Scandinavia, Italy, Japan, China, India, Singapore, Mexico, Brazil, South Africa, UAE, Qatar, Saudi Arabia), Application Potential, Price Trends, Competitive Market Share & Forecast, 2016-2023” new report to its research database. The report spread across 94 pages with table and figures in it. Global Precision Medicine Market size was more than $39.1 billion for 2015 and is predicted to register 10.51% of CAGR during forecast timeframe. It is innovative procedure for treating and preventing chronic ailments depending upon changes in individual genes and other lifestyle features. New approach helps doctors properly assess ailment risk and predict optimal treatment. Growing occurrence of cancer and increase in cancer prone geriatric population all across the globe is predicted to boost industry expansion. Threats related with sharing of patients genetic information can hinder industry growth. Insurance firms can use patient data and raise their premium for people who are at a risk of acquiring inherited diseases. Further, decline in rate of FDA (U.S. Food and Drug Administration) drug approval has minimized the rate of production of new medicines in spite of heavy investments. This aspect can hinder global precision medicine market expansion. Technology Trends The industry is segmented into different technologies like gene sequencing, companion diagnostics, big data analytics, bioinformatics and drug discovery. Gene sequencing segment size was more than $8.1 billion for 2015. Current FDA guidelines on next -generation sequencing dependent tests takes into consideration individual differences in genes of various persons, environments and life patterns while creating new type of healthcare. Companion diagnostics segment has acquired importance owing to rising concerns about rates of drug failures. Further, the segment is expanding at rapid pace owing to rise in financial support and approvals by government. Heavy throughput omics techniques applied in biological and basic research are predicted to propel bioinformatics segment growth. Out of all omics techniques next-generation technique is predicted to create key impact on the segment growth. Drug discovery technique contributed more than $9 billion for 2015 and is predicted to register CAGR of 8.31% during forecast timeframe. Further, biomarker directed treatments with medicine targeting epidermal growth factor receptor (EGFR),c-ros oncogene 1 receptor tyrosine kinase (ROS1) and anaplastic lymphoma kinase (ALK) have speeded up the production of new medicines. Precision Medicine Market Application Trends Global industry is segmented into various applications like respiratory application, oncology application, Immunology application and central nervous system (CNS) application. Oncology application contributed more than 30.1% of precision medicine market share for 2015 and is predicted to record CAGR of 10.91% during forecast timeframe. CNS application contributed more than $9.1 billion for 2015. Neuroscience therapeutics has been utilizing the approach for long duration. Regional Trends Global industry was segmented into key geographical regions like North America, MEA, Europe, APAC and Latin America. U.S. precision medicine market share was about 65.1% of revenue of North America. Factors like large allocation of budget by U.S. president to agencies like FDA( U.S. food and drug administration) , NIH (National Institute of Health) and NCI (National Cancer Institute) along with favorable government rules have contributed to the regional industry growth. Germany precision medicine market share was more than $2.5 billion for 2015 and is predicted to contribute significantly to the growth of European industry. Reason for industry growth in the region can be credited to the fact that many institutions have acquired biomarker analysis certification required for colorectal cancer detection tests. Further, medicine producing and diagnostic firms are making tremendous efforts for enhancing industry growth in Europe. Favorable compensation policies are predicted to promote industry growth in France. China contributed more than 25.1% to APAC precision medicine market share for 2015 and is predicted to remain key region in future. Favorable government initiatives and high contributions from academic labs has assisted in the regional industry growth. Competitive Trends Key industry players profiled in the report include Roche Holdings AG, Qiagen, Pfizer, Medtronic, Source Precision Medicine Incorporation, Silicon Biosystems, Tepnel Pharma Services, Covance, Biocrates Life Sciences AG, Novartis, Nanostring Technologies, Laboratory Corporation of America Holdings, Quest Diagnostics, Teva Pharmaceuticals, Intomics, Ferrer InCode, Eagle Genomics Limited and Quest Diagnostics. To receive personalized assistance, write to us @ [email protected] with the report title in the subject line along with your questions or call us at +1 866-764-2150
Chen C.,Cornell University |
DeClerck G.,Cornell University |
Tian F.,China Agricultural University |
Spooner W.,Eagle Genomics |
And 3 more authors.
PLoS ONE | Year: 2012
PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.4.2-1 | Award Amount: 8.33M | Year: 2014
Asymptomatic vascular damage accumulates for years before patients are identified and subjected to therapeutic measures. The limited knowledge on early vascular disease pathophysiology is reflected in the lack of therapeutic options. SysVasc aims to overcome this limitation by mounting a comprehensive systems medicine approach to elucidate pathological mechanisms, which will yield molecular targets for therapeutic intervention. The consortium is based on established multidisciplinary European research networks, including specialists in pre-clinical and clinical research, omics technologies, and systems biology from research intensive SMEs and academia; partners synergistically provide access to an extensive number of selected population-based cohorts and associated datasets, cutting edge modeling and simulation methods, and established cardiovascular disease (CVD) animal models and patient cohorts. The coordinated application of these tools and know-how will identify pathophysiological mechanisms and key molecules responsible for onset and progression of CVD and validate their potential to serve as molecular targets for therapeutic intervention. To this end, the consortium will also use unique resources to evaluate molecular homology between the available model systems and human disease, which will yield reliable essential preclinical research tools to explore proof of concepts for therapeutic intervention studies and ultimately translate relevant results into novel therapeutic approaches. Collectively, SysVasc will identify and validate novel biology-driven key molecular targets for CVD treatment. Major scientific, societal and economic impact is expected including, but not limited to, providing a valuable resource to further CVD research, and enhance competitiveness of participating SMEs and European health industry in general by translating knowledge into innovative services in therapeutic target and drug research.
Agency: GTR | Branch: Innovate UK | Program: | Phase: Collaborative Research & Development | Award Amount: 266.18K | Year: 2011
High-throughput technologies, such as microarrays or Next Generation Sequencing (NGS), are revolutionising life science research. These technologies are already having an impact on plant and animal breeding, research into crop protection and more importantly in human health. The cost of generating these data is falling, but the ongoing cost of supplying locally the substantial compute and associated resources required for their analysis remains high. As an efficient and scalable alternative to local provision, this proposal will develop infrastructure that will harness the power of cloud computing and UK e-research expertise in scientific workflows to provide an on-line analytics service, in the first instance, for DNA analysis. It is an innovative use of existing commercial Amazon EC2 cloud computing technologies to deliver computationally intensive analyses without the financial overhead of local computational infrastructure. It is also innovative in the analysis pipelines it will offer, providing new, leading-edge scientific methods. We will operate an analysis on-demand service via a web portal. Customers will be charged for their compute time on the cloud and for the maintenance of the service. Bespoke solutions for individual clients can be developed and deployed in consultation.
Agency: GTR | Branch: Innovate UK | Program: | Phase: Innovation Voucher | Award Amount: 5.00K | Year: 2012
In this project the performance of a bioinformatics tool kit will be evaluated within an oil seed rape breeding programme. We will test the tool kit on large data sets to identify molecular genetic markers associated with oil content. The project will help Eagle Genomics to access new markets in crop breeding.