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    November 11, 2018
    Dallas, TX
    works.cs.cardiff.ac.uk
    Held in conjunction with SC18, sc18.supercomputing.org
    Paper submission deadline: July 30, 2018

    CALL FOR PAPERS

    Data-intensive workflows (a.k.a. scientific workflows) are routinely used in most scientific disciplines today, especially in the context of high-performance, parallel and distributed computing. They provide a systematic way of describing a complex scientific process and rely on sophisticated workflow management systems to execute on a variety of parallel and distributed resources. With the dramatic increase of raw data volume in every domain, they play an even more critical role to assist scientists in organizing and processing their data and to leverage HPC or HTC resources, being at the interface between end-users and computing infrastructures.

    This workshop focuses on the many facets of data-intensive workflow management systems, ranging from actual execution to service management and the coordination and optimization of data, service and job dependencies. The workshop covers a broad range of issues in the scientific workflow lifecycle that include: data-intensive workflows representation and enactment; designing workflow composition interfaces; workflow mapping techniques to optimize the execution of the workflow for different infrastructures; workflow enactment engines that need to deal with failures in the application and execution environment; and a number of computer science problems related to scientific workflows such as semantic technologies, compiler methods, scheduling and fault detection and tolerance.

    The topics of the workshop include but are not limited to:
    • Big Data analytics workflows
    • Data-driven workflow processing (including stream-based workflows)
    • Workflow composition, tools, and languages
    • Workflow execution in distributed environments (including HPC, clouds, and grids)
    • Reproducible computational research using workflows
    • Dynamic data dependent workflow systems solutions
    • Exascale computing with workflows
    • In Situ Data Analytics Workflows
    • Interactive workflows (including workflow steering)
    • Workflow fault-tolerance and recovery techniques
    • Workflow user environments, including portals
    • Workflow applications and their requirements
    • Adaptive workflows
    • Workflow optimizations (including scheduling and energy efficiency)
    • Performance analysis of workflows
    • Workflow debugging
    • Workflow provenance
    • Workflows in constrained environments e.g. IoT, Edge computing, etc.

    IMPORTANT DATES

    Papers due: July 30, 2018
    Paper acceptance notification: September 9, 2018
    E-copyright registration completed by authors: October 1, 2018
    Camera-ready deadline: October 1, 2018

    PAPER SUBMISSION

    Submitted papers must be at most 10 pages long. The proceedings should be formatted according to the IEEE format (see www.ieee.org/conf[...].html). The 10-page limit includes figures, tables, and appendices, but does not include references, for which there is no page limit. WORKS papers will be published in cooperation with TCHPC and will be available from IEEE digital repository.

    Monday, August 13 – Friday, August 17, 2018
    University of Washington Campus, Seattle, WA, USA
    bit.ly/uwcmgworkshop

    We still have a few slots open for our 6th annual Mendelian Analysis Workshop.

    If you want to learn how to use bioinformatic tools to analyze exome and whole genome sequence data for the diagnosis and study of rare genetic diseases, check out the schedule and share with anyone you think might be interested!

    BACKGROUND

    The University of Washington Center for Mendelian Genomics (UW-CMG) is offering a weeklong course on the analysis of next generation sequence data that will focus on strategies and tools for solving Mendelian disorders. The course is intended for data analysts/researchers who analyze next generation sequence data. Application available here: uwcmg.org/#analysisWorkshop

    This is our 6th consecutive year running this workshop!

    COURSE OUTLINE

    The course will consist of lectures and hands-on exercises designed to help reinforce the lecture content.

    Monday: IT infrastructure; pipeline overview, CMG data, VCF files and Unix basics
    Tuesday: Sample/project level QC, study design & modes of analysis
    Wednesday: Annotation, interpreting CNV results, introduction to Gemini, and analysis using Gemini for autosomal recessive and de novo models
    Thursday: Analysis using Gemini for autosomal dominant models, candidate genes and variants, data sharing, and hands-on exercises
    Friday: Team projects, presentations, wrap up, additional questions, and feedback

    NOTE

    Space is limited and applications will be accepted until all spaces are filled. The cost to attend the Workshop is $300 (US). Attendees are responsible for costs associated with attending the workshop (i.e., airfare, housing, and incidentals).

    Lunch and snacks provided each day. Campus housing is available. A laptop and specific software are required for participation.

    Submitter

    EXCERPT

    Scientists seeking new ways to fight drug-resistant superbugs have mapped the genomes of more than 3,000 bacteria, including samples of a bug taken from Alexander Fleming's nose and a dysentery-causing strain from a World War One soldier.

    The DNA of deadly strains of plague, dysentery and cholera were also decoded in what the researchers said was an effort to better understand some of the world's most dangerous diseases and develop new ways to fight them.
    Source: www.yahoo.com/news[...].html
    Education: LBRN Summer Bioinformatics Training Program
    Submitted by Elia Brodsky; posted on Tuesday, June 05, 2018

    Submitter

    June 6 through July-August, 2018
    LSU Baton Rouge, Louisiana
    edu.t-bio.info/summer-program/

    Pine Biotech and the Louisiana Biomedical Research Network (LBRN) are announcing registration for the upcoming Louisiana Biomedical Research Network Summer Bioinformatics Training Program. The program is starting June 6, 2018 and will last through August, providing students and faculty access to online resources and practical experiences analyzing large high-throughput biomedical datasets.

    For the duration of the Summer Bioinformatics Training Program, participants from all major Louisiana Universities will attend interactive sessions and on-site workshops, joining over 100 students online in a 3-month long learning program. This innovative program consists of several online courses and hands-on sessions and will cover major types of Next Generation Sequencing data types (i.e. genomics, transcriptomics and metagenomics), analysis methods (i.e. pre-processing, mapping of reads, quantification and annotation), machine learning concepts (dimension reduction, classification, feature selection, etc.) and applications to biomedical research.

    The registration is open for on-site and online participation and will last until June 20, when the first hands-on workshop will be conducted at the LSU Center for Computation and Technology in Baton Rouge. Online workshops are extended to USA and international students interested in bioinformatics, biomedicine and data science. While the program is supported by the Louisiana Biomedical Research Network, applications will be reviewed on a competitive basis and additional payment will be required to access all of the features of the program, especially for students outside of Louisiana.

    Submitter

    EXCERPT

    The roundup is mostly led by LunaDNA of Solana Beach and Nebula Genomics of San Francisco, startups that are still figuring out how much a person would be paid for their contribution.

    It's part of the booming bio-economy, where so-called "sequencing subsidies" are starting to emerge.

    Scientists say they need enormous amounts of genetic data from across different ethnic, racial and age groups, and different genders, to develop diagnostics and drugs.
    Source: www.sandiegouniontribune.com/news[...].html

    CloudLIMS, a leading laboratory data management informatics provider, announces the release of a web-based client portal for its Laboratory Information Management System (LIMS), CloudLIMS. The client portal is designed for biorepositories and testing laboratories – such as clinical, cannabis, and environmental- facilitating quick and easy online access to sample purchase, sample storage, testing services, etc. Additionally, it provides self-service facility to customers enabling seamless access to sample data, test results, test reports, and invoices. The testing laboratories and biorepositories can configure the client portal to grant controlled access to their customers.

    With laboratories striving to enrich customer satisfaction and reduce operational costs, the client portal enables the staff to concentrate on laboratory tasks rather than on responding to routine customer service requests. With CloudLIMS' client portal, the customers are able to access requisite information in real-time. They can place service requests, check their status, view test results, and download invoices instantly. Biorepositories and testing laboratories can add unlimited numbers of client portal users, each having unique login credentials. The client portal keeps a track on all transactions between the laboratory and their customers. All the communication and data sharing is encrypted, and therefore, secure. Key benefits of the client portal include:
    • Place purchase order for samples, storage, and tests
    • View the status of samples sent for testing in real-time
    • View and download sample test results
    • Download invoices

    AVAILABILITY

    For more information, please visit: cloudlims.com
    Events: Integrative Bioinformatics 2018
    Submitted by Keywan Hassani-Pak; posted on Tuesday, May 22, 2018

    13-15 June 2018
    Rothamsted Research, Harpenden, UK
    tinyurl.com/y7b4sc32

    We have invited the "crème de la crème" in post-genomics Bioinformatics to present their exciting work at the 14th Integrative Bioinformatics Symposium at Rothamsted. IB2018 will be an excellent opportunity for keeping abreast with the latest in bioinformatics R&D and for establishing collaborations in new areas such as protein structure prediction, systems biology, statistical genomics and biological knowledge management. No matter if you are working on humans, plants, animals, insects, fungi or microbes; in industry or academia, Integrative Bioinformatics provides the key science and technology platforms to generate meaningful insights from big data and from complex biological systems. The invited speakers are experts in their field and will be covering a range of topics including but not limited to:
    • Bioinformatics resources for gene discovery
    • Multi-omics and systems biology
    • From FAIR data to knowledge graphs to AI
    • Better software, better research
    Register here: ib2018.eventzilla.net

    Hope to see you this summer in the beautiful UK-town Harpenden (25-min by train from London).

    October 10-11, 2018
    Richo Arena, Coventry, UK
    www.hsi2018.com

    On behalf of the Hyperspectral Imaging Centre at the University of Strathclyde in Glasgow, we invite you to participate in HSI 2018, the 7th international conference on Hyperspectral Imaging.

    This cross-disciplinary conference will bring together high profile companies and leaders in hyperspectral technologies, participants from all fields of hyperspectral imaging, application engineers, manufacturers, researchers and users in industry with the aims of exchanging knowledge and investigating the latest techniques & developments in this exciting technology.

    Original contributions are welcomed on all aspects of hyperspectral imaging – we particularly invite contributions in the following, though not exclusive areas:Antiquity Analysis, Biology, Chemical Analysis, Defence, Food Technology, Geographical Information Services, Industrial Vision, Medicine, Microscopy, Environmental Modelling, Product identification, Remote Sensing, Surveillance.

    Please visit the website for further details.
    Education: Training in Metagenomics Data Analysis @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Monday, May 21, 2018

    June 12-15, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]85aba

    OBJECTIVES

    Metagenomics is gaining importance due to low cost next generation sequencing technologies.This training will introduce participants to the end-to-endsolutions for analyzing metagenomicdata, starting from data quality analysis, alignment, community profiling, taxonomic comparison and novel taxa discovery.

    Hands-on Skills/Tools Taught:
    • Processing and Analysis mothur, FLASh
    • Analysis Permanova
    • Analysis ANOSIM
    • Marker analysis LEfSe
    • Marker analysis QIIME
    • Functional analysis PICRUSt
    • Metagenomics analysis A5miseq
    • Contig annotation MEGAN
    • Functional analysis bioBakery
    • Advanced visualizations phyloseq
    • Network analysis Cytoscape

    Submitter

    EXCERPT

    The Nuffield Council on Bioethics has released a briefing note asking what it sees as the big ethical questions on the use of artificial intelligence in healthcare. The note acknowledges the huge potential of AI in making healthcare more efficient and friendly, as well as making faster and more accurate diagnoses, but its focus is on the serious questions about the use of AI that the healthcare industry needs to tackle head on if public trust in AI in healthcare is to be gained.
    Source: newatlas.com/heal[...]4636/
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