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    Education: Prague Summer School -- Next-Gen Seq Data Analysis
    Submitted by Stepan Stoces; posted on Friday, July 01, 2016

    Submitter

    Sept. 5-9, 2016
    Institute of Molecular Genetics, Prague, Czech Republic
    www.seqme.eu/en/c[...]chool

    SCOPE

    The goal of this workshop is to give you a deeper understanding of the Next-Generation Sequencing technology with a special focus on bioinformatics issues. All workshop participants will perform important steps of NGS data analysis tasks themselves!

    The course will be done using a bootable USB stick containing a Linux environment with all needed NGS tools already installed! After the course you will get the stick with all exercises and results you created during the week. Thus, you can immediately apply what you have learned with your own data by just booting your machine from the stick!

    TARGET AUDIENCE

    Molecular biologists or data analysts with an interest in Next-Generation Sequencing (NGS) data analysis. You should be computer literate and have a basic understanding of molecular biology (DNA, RNA, gene expression, PCR).

    The course language is English. Registration fee includes: Workshop materials, Lunches/Coffee breaks, Workshop dinner. Please kindly notice that lodging, travel and other incidental expenses are the responsibility of the attendee. Please kindly notice no labwork is to be performed during the course.

    Last five seats!!

    Submitter

    September 21-23, 2016
    Berlin, Germany
    ecseq.com/work[...]ncing

    Understand small RNA sequencing analysis issues and solve them yourself.
    • Learn the basics of different small non-coding RNAs and their characteristics
    • Understand the method of small RNA sequencing
    • Find differentially expressed small RNAs
    • Perform microRNA gene prediction
    • Analyze your small RNAs (microRNA target prediction, functional analysis, etc.)
    • Execute popular open-source microRNA tools (miRanallyzer, miRDeep, etc.) on a Windows machine (using a Linux VM)

    SCOPE

    The purpose of this workshop is to obtain a thorough understanding on the expression profiling of known microRNAs and the prediction of novel microRNA genes using next-generation sequencing technologies (NGS). The participants will be trained to understand both the data analysis aspects of NGS technologies and the functional implications of small RNAs. Downstream analysis to infer the functional implication of the detected microRNAs will be discussed including target prediction/detection and functional analysis. After this workshop, the participants will be able to perform their own microRNA analysis using up-to-date methods and extract scientific valuable findings.

    REQUIREMENTS

    Basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)

    TARGET AUDIENCE

    Biologists or data analysts with no or little experience in analyzing small RNA-Seq data.

    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.

    Submitter

    ABSTRACT

    Recent technological innovations have ignited an explosion in microbial genome sequencing that has fundamentally changed our understanding of biology of microbes and profoundly impacted public health policy. This huge increase in DNA sequence data presents new challenges for the annotation, analysis, and visualization bioinformatics tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data. Genomes are organized in a hierarchical distance tree using single-copy ribosomal protein marker distances for distance calculation. Protein distance measures dissimilarity between markers of the same type and the subsequent genomic distance averages over the majority of marker-distances, ignoring the outliers. More than 30,000 genomes from public archives have been organized in a marker distance tree resulting in 6,438 species-level clades representing 7,597 taxonomic species. This computational infrastructure provides a foundation for prokaryotic gene and genome analysis, allowing easy access to pre-calculated genome groups at various distance levels. One of the most challenging problems in the current data deluge is the presentation of the relevant data at an appropriate resolution for each application, eliminating data redundancy but keeping biologically interesting variations.

    ARTICLE

    Leonid Zaslavsky, Stacy Ciufo, Boris Fedorov, Boris Kiryutin, Igor Tolstoy and Tatiana Tatusova. 2016. Dealing with the Data Deluge – New Strategies in Prokaryotic Genome Analysis. Next Generation Sequencing – Advances, Applications and Challenges, Dr. Jerzy Kulski (Ed.), InTech (doi: 10.5772/62125). www.intechopen.com/book[...]lysis
    Software: NCBI prokaryotic genome annotation pipeline
    Submitted by Dr. Leonid Zaslavsky; posted on Friday, July 01, 2016

    Submitter

    ABSTRACT

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see www.ncbi.nlm.nih.gov/geno[...]prok/ and the NCBI Handbook, www.ncbi.nlm.nih.gov/books/NBK174280/.

    ARTICLE

    Tatiana Tatusova, Michael DiCuccio1, Azat Badretdin, Vyacheslav Chetvernin, Eric P. Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D. Pruitt, Mark Borodovsky and James Ostell. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research (Advance Access doi: 10.1093/nar/gkw569). nar.oxfordjournals.org/cont[...].full
    Events: Invitation to 2016 NGBT International Conference
    Submitted by Srijith V M; posted on Wednesday, June 29, 2016

    October 3-5, 2016
    Cochin, India
    www.sgrfconferences.org/2016/NGBT/

    The meeting is organized by SciGenom Research Foundation (SGRF), Chennai, India and is jointly hosted with the Centre for the Commercialization of Antibodies and Biologics (CCAB), Toronto, Canada; Tata Institute of Fundamental Research (TIFR Biology Department), Mumbai, India; and Institute of Bioinformatics (IOB), Bengaluru, India. This is the sixth international conference that is hosted by SGRF Conferences, the educational outreach arm of SciGenom Research Foundation (SGRF), setup to promote science research and education in India/Asia Pacific region. You can find additional information about the meeting at the 2016 conference website over the next few weeks.

    The 2016 conference will showcase and promote application of next-gen sequencing and genomics technologies for basic and translational science in all areas of biology including human genetics, drug discovery, clinical medicine, biomarkers, diagnostics, animal, plant and agricultural sciences. The 2016 meeting will feature drug discovery as a major meeting theme. We expect over 500 delegates. The conference, as in the past, is designed to provide a forum for scientists and students to share their work, build new connections and explore collaborations.

    We are glad to announce that 2016 NGBT Conference provides the opportunity to apply for Travel Awards, Meeting Scholarship and Genomics Project Grant.

    CSBB (Computational Suite for Bioinformaticians and Biologists) is a command-line based bioinformatics suite for analyzing biological data acquired through varied avenues of biological experiments. The major focus is to allow users to perform down-stream analysis tasks while eliminating the need to write programming code.

    CSBB is currently available on Linux, UNIX, MAC OS and Windows platforms. It provides 13 modules focused on analytical tasks like performing upper-quantile normalization on expression data or converting genome-wide gene expression to z-scores when comparing expression data from different platforms, etc.

    AVAILABILITY

    Please check the tool out and provide your valuable feedback to help us improve it with time.

    github.com/skyg[...]-v1.0
    Research: Bio-IT World: NCI Launches GDC
    Submitted by J.W. Bizzaro; posted on Thursday, June 16, 2016

    Submitter

    EXCERPT

    The push to cure cancer has, to paraphrase Neil Armstrong, taken one giant leap forward with the launch of the National Cancer Institute's (NCI) Genomic Data Commons (GDC), which was officially unveiled June 6 at the American Society of Clinical Oncology (ASCO) Annual Meeting.

    Part of the National Cancer Moonshot Initiative, the data sharing platform will support precision medicine efforts by enabling the access, standardization, analysis, and submission of cancer genomic data.
    Source: www.bio-itworld.com/2016[...].aspx

    February 21-23, 2017
    Porto, Portugal
    www.biodevices.biostec.org

    SCOPE

    The purpose of the International Conference on Bio-Devices is to bring together researchers and practitioners from electronics, mechanical engineering, physics and related areas who are interested in developing, studying and using innovative materials, devices and systems inspired by biological systems and/or addressing biomedical requirements. Monitoring and diagnostics devices, sensors and instrumentation systems, biorobotics and prosthetics, micro-nanotechnologies including microfluidics systems and biomaterials are some of the technologies addressed at this conference. The fabrication and evaluation of biodevices, including wearable and implantable devices is also addressed.

    BIODEVICES is part of BIOSTEC, the 10th International Joint Conference on Biomedical Engineering Systems and Technologies.
    Resources: IPC: Isoelectric Point Calculator
    Submitted by Lukasz Pawel Kozlowski; posted on Sunday, June 12, 2016

    The estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many biochemistry and proteomics techniques such as 2D-PAGE, IEF or mass spectrometry.

    Isoelectric Point Calculator allows for prediction of pI using different algorithms (17 algorithms implemented including two new ones).

    IPC outperform previous algorithms by at least 14.9% for proteins and 0.9% for peptides (on average, 22.1% and 59.6%, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively.

    AVAILABILITY

    The IPC can be accessed freely at isoelectric.ovh.org as a web service or standalone program.

    ARTICLE

    doi: dx.doi.org/10.1101/049841

    Submitter

    The Global Alliance for Genomics and Health has come up with a policy on training and infrastructure needs related to data storage, management and security pertaining to genomic and clinical data.

    EXCERPT

    Early data-sharing efforts have led to improved variant interpretation and development of treatments for rare diseases and some cancer types. However, such benefits will only be available to the general population if researchers and clinicians can access and make comparisons across data from millions of individuals.

    Despite much progress, genomic and clinical data are still generally collected and studied in silos: by disease, by institution, and by country. Regulatory data-privacy requirements do not seamlessly lend themselves to the secure sharing of data within and across institutions and countries. Current practices in research and medicine hinder the sharing of data in ways that tangibly recognize an individual's contributions. Tools and analytical methods are nonstandardized and incompatible, and the data are often stored in incompatible file formats. If we stay this course, the likely outcome will be an assortment of balkanized systems akin to those developed for U.S. electronic health records, which, although designed to advance human health by sharing clinical data across institutions, have by all measures fallen short of that goal because of a lack of interoperability.
    Source: science.sciencemag.org/cont[...].full
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    Acknowledgments

    We wish to thank the following for their support:

    [NEU MS in Health Informatics]
    [Bio-IT World]
    [Become a sponsor]

     

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