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    Submitter

    April 22-24, 2020
    Brno, Czech Republic
    www.seqme.eu/en/c[...]nners

    Nowadays, Next-Generation sequencing technologies form an essential part of almost all disciplines of biological sciences in research and diagnostics. Due to their quantity and namely complexity, NGS data are typically processed by qualified bioinformaticians or computational biologists. This presents a serious issue even for experienced researchers who have never studied this field of science simply because it has emerged just recently and suddenly there is a need to adapt to completely new tools, workflows and scientific terminology not to perform this sequencing data analysis process – after all, this is why we employ bioinformaticians, but to understand it properly.

    Our workshop gives you the opportunity to understand basics of NGS data processing. The aim of the workshop is to teach you to perform basic steps of NGS data analysis including but not limited to raw data manipulations, quality control, removal of low-quality sequences, sequencing adapters, artifacts, or other contaminations, and especially preparation of a high-quality data set that can be used for downstream analysis.

    You will get to know various NGS data formats, learn about specific problems of sequencing technologies used and how to handle them, and understand the background of individual processes in NGS data editing. You will not become a bioinformatician after this 3-day workshop, but you will set off for becoming a qualified partner for bioinformaticians in your team.

    Please note: If you are not familiar with Next-Generation sequencing technologies, we do encourage you to take part also at our 2-day Introduction to Next-Generation Sequencing Course, which is just preceding this workshop.

    Who should attend?
    This workshop is designed for biologists or beginners in bioinformatics who perform or plan to perform Next-Generation sequencing data analysis. No prior knowledge of sequence data analysis or specific programming skills are required.

    You will learn to:
    • Work in a command line in Ubuntu Unix operating system environment
    • Evaluate quality of raw NGS data
    • Perform basic operations with NGS data
    • Remove low-quality reads, sequencing artifacts, duplications and contaminations
    • Visualize results
    • You will have the option of networking with experienced team of speakers and other participants
    Overall, you will learn all essential steps how to prepare NGS data for advanced downstream analysis (application-specific).

    Submitter

    EXCERPT

    Researchers at the Crick, UCLA Jonsson Comprehensive Cancer Center, Oregon Health & Science University, the Oxford Big Data Institute, and the University of Toronto have created new open-source software which determines the accuracy of computer predictions of genetic variation within tumour samples.
    Source: www.crick.ac.uk/news[...]etics

    ARTICLE

    dx.doi.org/10.1[...]364-z

    Submitter

    EXCERPT

    Online services that allow users to upload their genetic information, research genealogy and find lost relatives may be vulnerable to a sort of genetic hacking, according to two geneticists at the University of California, Davis. A paper describing the work is published Jan. 7 in the journal eLife.
    Source: medicalxpress.com/news[...].html

    ARTICLE

    dx.doi.org/10.7554/eLife.51810
    Education: Physalia courses in 2020
    Submitted by Carlo Pecoraro; posted on Tuesday, December 31, 2019

    Submitter

    See you in Berlin with a mix of "old" and "new" courses and an amazing lineup of instructors: physalia-courses.org/courses-workshops/
    • Advanced Programming in R
    • Bayesian data analysis
    • Bioinformatics Workflows with Nextflow
    • DataViz in R with ggplot2
    • Ecological niche models in R
    • Eukaryotic Metabarcoding
    • Genome Assembly Using Oxford Nanopore Sequencing
    • Geometric Morphometrics
    • Introduction to GWAS
    • Introduction to statistics in R
    • Landscape Genomics
    • Mapping and spatial analysis (GIS) with R
    • Metabarcoding in Spanish
    • Metabarcoding of microbial communities
    • Metagenomics, metatranscriptomics, and multi'omics for microbial community studies
    • Phylogenomics
    • Population Genomics
    • Proteomics using R/Bioconductor
    • RADseq data analysis
    • Single Cell RNAseq
    • Speciation Genomics

    I wanted to introduce a new open access platform for the analysis and visualisation of transcriptomics and proteomics data that we recently published in NAR Genomics and Bioinformatics (academic.oup.com/narg[...]61104). The platform is designed for ease of use once installed and requires users to input four flat text files (including a raw read counts file) as input. Examples of the format are provided in the documentation.

    The platform can be installed locally on various operating systems (including Windows) via a docker file, while the source code is available on github:

    Docker: hub.docker.com/r/bi[...]round
    Github: github.com/bigo[...]round
    Documentation: omicsplayground.readthedocs.io/en/l[...].html

    The platform supports both bulk and single cell RNA-seq data. It can perform a wide range of analyses, including statistical comparison with Connectivity Map expression profiles. It can also intersect different algorithms to provide more stringent and reliable hits (for example, at the gene expression level it can intersect the results of up to 8 different methodologies used in EdgeR, Deseq2 and limma) . A more exhaustive list of functions is described in the documentation.

    We also have a google group where you can contact us with questions: Google Group: groups.google.com/foru[...]round. We would appreciate your feedback on the platform.

    We are planning to develop an open access web-based version in the near future as well, to make the platform more accessible.
    Education: RNA-Seq Data Analysis Workshop
    Submitted by Dr. David Langenberger; posted on Friday, December 20, 2019

    Submitter

    March 2-5, 2020
    Berlin, Germany
    www.ecseq.com/work[...]lysis

    Advance your research. Understand RNA-Seq analyses challenges and solve them yourself.

    IN A NUTSHELL

    • Learn the essential computing skills for NGS bioinformatics
    • Understand NGS analysis algorithms (e.g. read alignment) and data formats
    • Use bioinformatics tools for handling RNA-Seq data
    • Create diagnostic graphics and statistics
    • Compare different approaches for differential expression analysis

    SCOPE & TOPICS

    The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the course we will use a real-life RNA-seq dataset from the current market leader illumina.

    All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.
    Software: New software for multi-omic and evolutionary analysis
    Submitted by Dalang Yu; posted on Tuesday, December 17, 2019

    We have developed a comprehensive software for multi-omic and evolutionary analyses!

    For full view of the published article, please refer to academic.oup.com/nsr/[...]19874

    As a new and comprehensive piece of software, eGPS contains more than 20 popular methods and 20 data visualization tools that cover genomics, population genetics, evolutionary biology, differential gene expression and network data analyses. Users can consult the eGPS website and the user manual for further information.

    The eGPS combines the power of cloud computing and the advantage of desktop application, has a user-friendly graphic interface and is highly interactive. Moreover, third-party plug-ins are supported and their developers can take the credit for contributing the plug-ins.

    For full view of the function,please refer to the user manual www.egps-software.org/egps[...].html

    We will have long-term support for this software, and we will update every 1-2 months! Please feel free to send feedback to us!

    January 25-26, 2020
    Zurich, Switzerland
    cosit2020.org

    SCOPE & TOPICS

    7th International Conference on Computer Science and Information Technology (CoSIT 2020) will provide an excellent international forum for sharing knowledge and results in theory, methodology and applications of Computer Science, Engineering and Information Technology. The Conference looks for significant contributions to all major fields of the Computer Science and Information Technology in theoretical and practical aspects. The aim of the conference is to provide a platform to the researchers and practitioners from both academia as well as industry to meet and share cutting-edge development in the field.

    Authors are solicited to contribute to the conference by submitting articles that illustrate research results, projects, surveying works and industrial experiences that describe significant advances in the following areas, but are not limited to:
    • Algorithms and Bioinformatics
    • Computer Architecture and Real Time Systems
    • Database and Data Mining
    • Dependable, Reliable and Autonomic Computing
    • Distributed and Parallel Systems & Algorithms
    • DSP/Image Processing/Pattern Recognition/Multimedia
    • Embedded System and Software
    • Game and Software Engineering
    • Geographical Information Systems/ Global Navigation Satellite Systems (GIS/GNSS)
    • Grid and Scalable Computing
    • Intelligent Information & Database Systems
    • Sociocybernetics
    • Transportation Systems
    • Power Systems
    • Manufacturing Systems
    • Neural Networks & Fuzzy System
    • Image Signal Processing
    • Computer Vision
    • Soft Computing
    • Genetic Algorithm
    • Database & Information Retrieval
    • Decision Support System
    • Risk Management

    PAPER SUBMISSION

    Authors are invited to submit papers through the conference submission system: cosit2020.org/subm[...]x.php.

    CONTACT US

    Here's where you can reach us: cosit[at]cosit2020.org or Cosit23_conf[at]yahoo.com

    Sunday, November 17, 2019, 9 a.m. - 5:30 p.m.
    Denver, CO, USA
    Held in conjunction with SC19 (sc19.supercomputing.org)
    works.cs.cardiff.ac.uk

    The program of the 14th Workflows in Support of Large-Scale Science (WORKS) Workshop is now available at works.cs.cardiff.ac.uk/program.php.

    Submitter

    June 18-19, 2020
    Florence, Italy
    conference.pixel-online.net/FOE/

    OBJECTIVE

    The objective of the Conference is to promote transnational cooperation and share good practice in the field of education. The Conference is also an excellent opportunity for the presentation of previous and current education projects and initiatives.

    CALL FOR PAPERS

    The Call for Papers is addressed to teachers, researchers and experts in the field of education as well as to coordinators of teaching and training projects. Experts in the field of education are therefore invited to submit an abstract of a paper to be presented in the conference.

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

    All accepted papers will be included in the Conference Proceedings published by Filodiritto Editore with ISBN, ISSN, DOI and ISPN codes. This publication will be sent to be reviewed for inclusion in Conference Proceedings Citation Index by Thomson Reuters (ISI-Clarivate). The publication will also be included in Academia.edu and indexed in Google Scholar.

    For further information, please contact us at the following address: foe[at]pixel-online.net or visit the Future of Education conference website.

    IMPORTANT DATES

    Deadline for submitting Abstracts: February 27, 2020
    Notification of Acceptance / Rejection for Abstracts: March 12, 2020
    Deadline for final submission of Papers: April 24, 2020
    Conference days: June 18-19, 2020
    Submit Archive Subscribe

     

    Acknowledgments

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