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    Submitter

    Scientists argue that there is a need to have strong standards for p-value statistics to claim new discoveries.

    EXCERPT

    So, in a provocative manuscript posted on the PsyArXiv preprint server on 22 July, researchers argue that P-value thresholds should be lowered to 0.005 for the social and biomedical sciences (D. Benjamin et al. Preprint on PsyArXiv osf.io/prep[...]mky9j; 2017). The final paper is set to be published in Nature Human Behaviour.
    Source: www.nature.com/arti[...]190-5
    Software: LizardFS Software Defined Storage
    Submitted by Mark Mulrainey; posted on Wednesday, August 09, 2017

    Open Source solutions can provide a greater return on your storage investment by opening the path to competitive technology procurement. Automated data management unifies the end-to-end storage footprint and enables our users to spend a far greater proportion of their time and budgets on accelerating science and research (changing the world).

    LizardFS is an example of Open Source Software-Defined Storage. It provides enterprise-class storage using commodity hardware and specialized software to deliver storage services, advanced features, and management capabilities. Compared to traditional enterprise storage that requires proprietary or custom storage systems, open source software-defined storage platforms such as LizardFS have much lower up-front and ongoing operational costs.

    This solution removes the complexity that historically has burdened organizations who struggle to keep up with massive data growth, and simplifies the storage processes for IT professionals in all types of industries. LizardFS increases IT agility by enabling organizations to leverage hardware from any vendor, as well as the option to use existing IT infrastructure to create a custom storage solution to any storage need. It adjusts well to new technologies giving the opportunity to tune and increase performance by integrating SSD, Flash, NvME, etc. Organizations can achieve massive scale by increasing storage capacity and performance as needed, up to 8192 chunkservers and 1 Exabyte of data.

    In one use case, Vang Qu Le, the bioinformatician in charge of the storage facility was tasked with finding a replacement for the the existing NFS setup. They are bound with the same budget restrictions like most of the scientific and research community, so the replacement had to be scalable but cheap . "We have existing workstations, with internal 10TB storage, and other hardware, we need to make use of them, for cost effectiveness." Since installation and familiarization with the system he has had no issues with projects or meeting deadlines.

    Some examples of our latest innovations that are being tested and about to be launched for LizardFS, are a Hadoop plugin to allow you to connect your LizardFS storage to a Hadoop cluster and NFS 4.1 giving you native support for NFS.

    AVAILABILITY

    lizardfs.com

    Submitter

    August 15-24, 2017
    Two evenings per week – two hour sessions – Tuesday and Thursday – two weeks only!
    Stanford University, Stanford, CA, USA
    www.hpcadvisorycouncil.com/even[...]ries/

    OVERVIEW

    Stanford University's High Performance Computing Center, in collaboration with fellow members of the HPC Advisory Council and the OpenPOWER Foundation, invite you to the 2nd Annual Stanford Summer Series.

    Register today! This summer's syllabus, comprised of four individual Industry Leadership Sessions, focuses instruction on 'State of the Art Architectures for HPC'.
    • Courses offered August 15th, 17th, 22nd and 24th on the university's main campus.
    • Tuesday Thursday Twilight Tutorials begin at 4:00 p.m.
    • Industry Expert Instructors
    • Syllabus includes a introductory tutorial and immersive hands-on labs.
    • Limited only by room capacity 24hr advanced registration is required to attend.
    Attendees will learn parallel programming and architecture basics and graduate skilled in code optimization and porting to advanced accelerator-based platforms.

    Students can select specific courses or attend the entire series. The two hour sessions are open to all – from learning something new or more about a given topic, as an extension of summer school or continuing education – as stepping stones towards building foundations of expertise ~ Join us!

    Submitter

    EXCERPT

    In one of the largest efforts to build a comprehensive catalog of genetic vulnerabilities in cancer, researchers from the Broad Institute of MIT and Harvard and Dana-Farber Cancer Institute have identified more than 760 genes upon which multiple types of cancer cells are strongly dependent for their growth and survival.
    Source: news.harvard.edu/gaze[...]ased/

    Submitter

    EXCERPT

    Just a few weeks after DARPA announced a major investment in developing brain-computer interface technology, the US government department has revealed another major project. The Safe Genes program is set to invest US$65 million over four years in seven teams that will investigate ways to make gene editing technologies safer, more targeted and potentially even reversible.
    Source: newatlas.com/darp[...]0612/

    November 13-16, 2017
    Kansas City, MO, USA
    staff.icar.cnr.it/cannataro/hibb2017/
    Held in conjunction with BIBM 2017 (muii.missouri.edu/bibm2017/)

    CALL FOR PAPERS

    High-throughput technologies (e.g. microarray, mass spectrometry, NGS) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large-scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine.

    High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data.

    At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patient's clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so-called collaboratories where remote scientists may conduct experimental research in a collaborative way.

    The goal of HiBB is to bring together scientists in the fields of bioinformatics, biomedicine, medical informatics, high performance computing, as well as scientists working in biology and medicine, to discuss, among the others, the challenges and the requirements posed by novel data analysis pipelines for the management and analysis of omics data, that are more and more produced by high-throughput experimental platforms as well as diagnostic tools. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed.

    TOPICS OF INTEREST

    The workshop is seeking original research papers presenting applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to:
    • High performance data mining for bioinformatics and biomedicine
    • Large scale biological and biomedical databases
    • Data integration and ontologies in biology and medicine
    • Parallel bioinformatics algorithms
    • Parallel visualization and exploration of biomedical data
    • Parallel visualization and analysis of biomedical images
    • Computing environments for large scale collaboration
    • Scientific workflows in bioinformatics and biomedicine
    • Services for bioinformatics and biomedicine
    • Cloud Computing for bioinformatics and biomedicine
    • Peer-To-Peer Computing for bioinformatics and biomedicine
    • Emerging architectures and programming models for bioinformatics and biomedicine
    • Parallel processing of bio-signals
    • Modeling and simulation of complex biological processes

    PROGRAM

    The workshop will take place on November 13-16, 2017 (To Be Announced). It is scheduled as half-day. The program is not available yet.

    PAPER SUBMISSION, REGISTRATION AND PUBLICATION

    Please submit a full-length paper (up to 8 page IEEE 2-column format) through the BIBM-2017 Workshops submission system: wi-lab.com/cybe[...]t.php

    You can download the format instruction here: www.ieee.org/conf[...].html

    Electronic submissions (in PDF or Postscript format) are required. Selected participants will be asked to submit their revised papers in a format to be specified at the time of acceptance.

    IMPORTANT DATES

    Due date for full workshop papers submission: Sept 20, 2017
    Notification of paper acceptance to authors: Oct 10, 2017
    Camera-ready of accepted papers: Oct 25, 2017
    Workshop: Nov 13-16, 2017

    JOURNAL SPECIAL ISSUE

    After of the workshop, we plan to invite the best papers of the workshop for a special issue of an international journal.

    Submitter

    March 22-23, 2018
    Florence, Italy
    conference.pixel-online.net/NPSE

    OBJECTIVES

    The objective of the New Perspectives in Science Education Conference is to promote transnational cooperation and share good practice in the field of innovation for science education. The New Perspectives in Science Education Conference is also an excellent opportunity for the presentation of previous and current projects in the science field.

    CALL FOR PAPERS

    The Call for Papers, within the New Perspective in Science Education Conference, is addressed to teachers, researchers and experts in the field of science education as well as to coordinators of science and training projects.

    Experts in the field of science teaching and learning are therefore invited to submit an abstract of a paper to be presented during the New Perspective in Science Education international conference. The abstract should be written in English and submitted no later than 22 November 2017. In order to submit an abstract please visit our website: conference.pixel-online.net/NPSE[...]n.php.

    There will be three presentation modalities: oral, poster and virtual presentations.

    All accepted papers will be included in the Conference Proceedings published by LibreriaUniversitaria with ISBN and ISSN codes. This publication will be sent to be reviewed for inclusion in SCOPUS (www.elsevier.com/solutions/scopus). Papers will also be included in ACADEMIA.EDU (www.academia.edu) and Google Scholar.

    IMPORTANT DATES

    Deadline for submitting abstracts: November 22, 2017
    Notification of Acceptance / Rejection for Abstracts: December 13, 2017
    Deadline for final submission of papers: January 22, 2018
    Dates of the conference: March 22-23, 2018

    FOR MORE INFORMATION

    For further information, please contact us at the following address: science[at]pixel-online.net or visit the New Perspectives in Science Education conference website linked above.

    Submitter

    EXCERPT

    IBM is busy applying its Watson AI to as many health arenas as possible and it looks like cancer genomic sequencing could be its next big market.

    In a new proof-of-concept study testing a beta version of its genomic sequencing-specific version of Watson, Watson for Genomics, IBM's AI has once again shown potential.
    Source: pharmaphorum.com/news[...]mour/

    Full article: ng.neurology.org/cont[...].full

    Submitter

    EXCERPT

    The malaria parasite's success is owed to the stripping down of its genome to the bare essential genes, scientists at the Wellcome Trust Sanger Institute and their collaborators have found. In the first ever large-scale study of malaria gene function, scientists analysed more than half of the genes in the parasite's genome and found that two thirds of these genes were essential for survival – the largest proportion of essential genes found in any organism studied to date.
    Source: phys.org/news[...].html

    Full article: www.cell.com/cell[...]714-6
    Events: NGS Data Analysis -- 1 day hands-on training
    Submitted by Vijayaraj Nagarajan; posted on Wednesday, July 12, 2017

    July 30, 2017
    Coimbatore, Tamil Nadu, India
    americanbiomedicalinformatics.org/india.php
    www.eventbrite.com/e/ng[...]40702

    BACKGROUND

    This course will introduce students/faculty to bioinformatic analysis of next generation sequencing data, particularly for DNA-seq (variant analysis), RNA-seq and CHIP-seq. The course will be comprised of short lectures and mostly hands-on sessions.

    HIGHLIGHTS

    • Free lunch, NGS analysis book, cloud server
    • Training certificate issued by American Academy for Biomedical Informatics, USA
    • Free Linux desktop Amazon machine image with all required software

    REQUIREMENTS

    • Basic computer skills and basic biology knowledge
    • Only 35 participants per class (both teachers and students can participate)
    • Bring your own laptop (a basic laptop that you can install software and could connect to wireless internet)

    FOR MORE INFORMATION

    Got questions or need more information? Email us at contact[at]aabi.us OR call us at Phone: +91 97919 85129.
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    Acknowledgments

    We wish to thank the following for their support:

    [St. Jude]
    [OMICtools]
    [Bio-IT World]
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