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    Submitter

    EXCERPT

    On Wednesday, in what many experts are calling a milestone in neuroscience, researchers published a spectacular new map of the brain, detailing nearly 100 previously unknown regions – an unprecedented glimpse into the machinery of the human mind.
    [...]
    Scientists created the map with advanced scanners and computers running artificial intelligence programs that "learned" to identify the brain's hidden regions from vast amounts of data collected from hundreds of test subjects, a far more sophisticated and broader effort than had been previously attempted.
    Source: www.nytimes.com/2016[...].html

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

    SCOPE

    The purpose of the International Conference on Health Informatics is to bring together researchers and practitioners interested in the application of information and communication technologies (ICT) to healthcare and medicine in general and to the support of persons with special needs in particular.

    Databases, networking, graphical interfaces, data mining, machine learning, intelligent decision support systems and specialized programming languages are just a few of the technologies and research areas currently contributing to medical informatics. Mobility and ubiquity in healthcare systems, physiological and behavioral modeling, standardization of technologies and procedures, certification, privacy and security are some of the issues that medical informatics professionals and the ICT industry and research community in general are addressing in order to further promote ICT in healthcare. In the case of medical rehabilitation and assistive technology, research in and applications of ICT have contributed greatly to the enhancement of quality of life and full integration of all citizens into society.

    IMPORTANT DATES

    Regular Papers:
    Paper Submission: September 29, 2016
    Authors Notification: November 23, 2016
    Camera Ready and Registration: December 9, 2016

    Position Papers:
    Paper Submission: November 8, 2016
    Authors Notification: December 14, 2016
    Camera Ready and Registration: December 27, 2016

    Workshops:
    Workshop Proposal: November 3, 2016

    Doctoral Consortium:
    Paper Submission: December 29, 2016
    Authors Notification: January 11, 2017
    Camera Ready and Registration: January 23, 2017

    Special Sessions:
    Special Session Proposal: November 21, 2016
    Paper Submission: December 6, 2016
    Authors Notification: December 21, 2016
    Camera Ready and Registration: December 29, 2016

    Tutorials, Demos and Panels Proposals: December 27, 2016

    Submitter

    EXCERPT

    "Like all law enforcement technologies, once agencies have already invested money, they will try to use that technology in as many contexts as they can – in the case of Rapid DNA, there is nothing in the bill to stop agencies from using it to collect DNA from people stopped on the street," [Jennifer Lynch, senior staff attorney at the Electronic Frontier Foundation] said. "The technology is portable, and, apparently not difficult to use, so there's nothing to prevent an officer from using the machine right out of the trunk of a squad car."

    Responding to civil liberties concerns, the Judiciary aide pointed to a 2013 Supreme Court decision that ruled the warrantless collection of DNA from those arrested for a serious crime does not violate the Fourth Amendment prohibition against unreasonable search and seizure.
    Source: www.nextgov.com/defe[...]9735/
    Events: NETTAB 2016 Call for Abstracts and CHARME support information
    Submitted by Paolo Romano; posted on Wednesday, July 06, 2016

    Submitter

    Reproducibility, standards and SOP in Bioinformatics
    A combined CHARME, EMBnet and NETTAB 2016 Workshop
    October 25-26, 2016
    Rome, Italy
    www.igst.it/nettab/2016/

    The deadline for the submission of abstracts for oral communications has been extended until next July 15, 2016.

    NB! If you plan to apply for CHARME support (travel and daily budget), you must submit your abstract within the above deadline even if it is a poster abstract.

    ANNOUNCEMENT & CALL FOR ABSTRACTS

    The Workshop "Reproducibility, standards and SOP in Bioinformatics" is co-organised by the EU COST Action CHARME, EMBnet (The Global Bioinformatics Network) and NETTAB (International Workshop Series on Network Tools and Applications for Biology). It is hosted by the ELIXIR-ITA Node and will be held at the Italian CNR (National Research Council) head quarter, in Rome.

    The workshop will be preceded by a GOBLET/ELIXIR-ITA Tutorial and an ELIXIR Hackathon on Monday 24th.

    Topics of interest:
    Reproducibility, standards and SOPs in bioinformatics, including:
    Trends in open science, Open access journals, Open source practices; Good programming practices for reproducibility; The role of cloud computing in reproducible research; Computational tools, such as Sweave, knitr, supporting automatic production of research papers; Standard operating procedures (SOP) in bioinformatics; Tools, practices, and dissemination platforms for ensuring reproducibility; Role of workflow management systems and ontologies in reproducible research; Automatic tools for tracking the provenance of data, analyses, and results; Data FAIR-ness; Bioinformatics standards for models and data.

    Bioinformatics Education and Training:
    Special Session held in collaboration with GOBLET and ELIXIR-ITA.

    NETTAB Workshop topics, including:
    On-line databases, software tools, user interfaces; Data integration and data fusion platforms, integrated bio-search; Grid and clouds applications and platforms; APIs and Web Services, workflow management platforms; Semantic tools, biomedical ontologies; Semantic Web tools, Linked Open Data, SPARQL endpoints; Biological Wikis, social applications for life sciences; Tools for collaborative development of software, databases and documents; Mobile bioinformatics apps

    Instructions for abstract submission:
    Authors are invited to submit abstracts dealing with the topics of the workshop through EasyChair at the following address: www.easychair.org/conf[...]b2016 . The instructions for authors can be found at: www.igst.it/nett[...]hors/.

    Works presented at the workshop will be invited to a Call for Papers in a special issue of a peer-reviewed journal of International level, indexed by Pubmed and ISI.

    REGISTRATION

    Registration fees and CHARME support:
    Early registrations fees are: 130.00€ for students, 200.00 € for researchers from academia / no-profit Institutes, 300.00 € for researchers from for-profit companies.

    A discount of 30.00 € is granted to members of various Societies and Institutes. Check the web site for a full list.

    CHARME COST Action will reimburse travel and stay costs to presenting authors of works selected by a purpose review group. Standard COST reimbursement rules apply.

    IMPORTANT DATES

    Submission of abstracts for oral communications: July 15, 2016 (max four pages)
    Submission of abstracts for posters: September 19, 2016 (max two pages)
    Early registration deadline: September 26, 2016

    FOR MORE INFORMATION

    Email: nettab.workshops[at]gmail.com
    Mailing list: nettab-announce[at]googlegroups.com
    Twitter: @NETTABWorkshops
    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
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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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