Bioinformatics.org
[OMICtools]
[Repositive.io]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (40316+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • Latest announcements
    Submit Archive Subscribe

    Submitter

    EXCERPT

    Far from just being the product of our parents, University of Adelaide scientists have shown that widespread transfer of genes between species has radically changed the genomes of today's mammals, and been an important driver of evolution.

    In the world's largest study of so-called "jumping genes", the researchers have traced two particular jumping genes across 759 species of plants, animals and fungi. These jumping genes are actually small pieces of DNA that can copy themselves throughout a genome and are known as transposable elements.

    They have found that cross-species transfers, even between plants and animals, have occurred frequently throughout evolution.
    Source: phys.org/news[...].html

    Article: doi.org/10.1[...]456-7
    Education: Course on the analysis of single cell RNA-seq data
    Submitted by Carlo Pecoraro; posted on Wednesday, July 11, 2018

    February 25 – March 1, 2019
    FU University in Berlin
    www.physalia-courses.org/cour[...]se18/

    OVERVIEW

    In recent years single-cell RNA-seq (scRNA-seq) has become widely used for transcriptome analysis in many areas of biology. In contrast to bulk RNA-seq, scRNA-seq provides quantitative measurements of the expression of every gene in a single cell. However, to analyze scRNA-seq data, novel methods are required and some of the underlying assumptions for the methods developed for bulk RNA-seq experiments are no longer valid. In this course we will cover all steps of the scRNA-seq processing, starting from the raw reads coming off the sequencer. The course includes common analysis strategies, using state-of-the-art methods and we also discuss the central biological questions that can be addressed using scRNA-seq.

    FORMAT

    The course will be delivered over the course of five days. Each day will include a lecture and laboratory component. The lecture will introduce the topics of discussion and the laboratory sessions will be focused on practical hands-on analysis of scRNA-seq data. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group. Computing will be done using a combination of tools installed on the attendees laptop computer and web resources accessed via web browser.

    TARGETED AUDIENCE & ASSUMED BACKGROUND

    This course is aimed at researchers and technical workers who are or will be analyzing scRNA-seq data. The material is suitable both for experimentalists who want to learn more about data-analysis as well as computational biologists who want to learn about scRNASeq methods. Examples demonstrated in this course can be applied to any experimental protocol or biological system.

    REQUIREMENTS

    • Working knowledge of unix (managing files, running programs)
    • Programming experience in R (writing a function, basic I/O operations, variable types, using packages)
    • Bioconductor experience is a plus.
    • Familiarity with NGS data and its analyses (using alignment and quantification tools for bulk sequencing data)

    INSTRUCTORS

    Dr. Ayshwarya Subramanian (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)
    Dr. Dana Silverbush (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)
    Dr. Ehsan Habibi (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)

    Submitter

    To encourage bioinformaticists in India who have had made outstanding contributions in the area of Bioinformatics and Functional Genomics, we have initiated the Bioclues Innovation, Research and Development (BIRD) awards in 2011.

    Nominations are invited for outstanding contributions in the area of Functional Genomics and Bioinformatics. This award is meant not just for academicians but also for scientists who have shown exemplary excellence in the field of Bioinformatics. While scientists who have been working for not-for-profit organizations will be given importance, the ones who are working for commercial organisations are no less exception if the research they have carried out has been widely honoured and if they have made longstanding contributions. The awardee would receive a plaque and a citation with certificate. The awardee would further be invited to join the core/rep team of Bioclues society.

    ​More at ​http://bioclues.org/bird-awards/​
    Education: Course on Comparative Genomics
    Submitted by Carlo Pecoraro; posted on Monday, July 09, 2018 (1 comment)

    October 1-5, 2018
    Berlin, Germany
    www.physalia-courses.org/cour[...]se34/

    We still have a few places available for our course on "Comparative Genomics", which will take place this October (1-5) in Berlin.

    This course will introduce biologists and bioinformaticians into the field of comparative genomics. Different techniques will be introduced to identify single nucleotide polymorphism (SNP) and structural variations (SVs) as well as the annotation of these variations and the assessment for their functional impact.

    Our instructors are:
    Dr. Fritz J. Sedlazeck (Assistant Professor at the Human Genome Sequencing Center at Baylor College of Medicine, USA).
    Prof. Ingo Ebersberger (Professor for Applied Bioinformatics, Goethe University Frankfurt, Germany)

    Should you have any questions, please feel free to write to: info[at]physalia-courses.org.

    Submitter

    We are happy to announce a new web server, VaxinPAD, developed in our group and published in the Journal of Translational Medicine. This is a unique server which allows the user to design peptide-based vaccine adjuvants, and it is based on "A-cell epitope," a new term coined by the group. We hope this server will improve the speed of vaccine discovery drastically.

    AVAILABILITY

    Web server: webs.iiitd.edu.in/raghava/vaxinpad/
    Full paper: rdcu.be/2uJ6

    Submitter

    EXCERPT

    The new study, which is the first of its kind, has helped scientists identify key differences in cell-pathway activity in the blood of septic adults and children. Establishing the pathways that help prevent sepsis is a powerful new way to discover drugs for intervention against sepsis and provides direct insight into potential cures for the disease.

    Winston Hide, Professor of Computational Biology at the University of Sheffield's Institute of Translational Neuroscience (SITraN), is an author of the pioneering study published in the journal Molecular Systems Biology.
    Source: medicalxpress.com/news[...].html
    Article: doi.org/10.1[...]77998

    Submitter

    June 14 through July-August, 2018
    Jaipur, India
    edu.t-bio.info/amit[...]tics/

    Pine Biotech and Amity University announce the registration for its upcoming Amity University Summer Bioinformatics Training Program which starts June 14 and continues through August 15, 2018. This training program will provide students and faculty access to online resources and practical exercises in analyzing high-throughput biomedical datasets.

    Are you interested in gaining practical bioinformatics skills to be able to analyze large collection of biomedical datasets? The upcoming summer program organized by the Amity University this summer is your chance to acquire such skills in its bioinformatics training program.

    Bioinformatics is a blend of molecular biology and data science and deals with the application of computational methods to analyze large collections of biological data, such as genetic sequences, cell populations or protein samples.

    For today's world biologists, scientists, engineers, students and educators bioinformatics provides an opportunity to enhance their understanding of biology using public domain datasets accumulated in such repositories NCBI, TCGA and many others. Amity University is collaborating with Pine Biotech to prepare online educational modules that provide curated projects and guided tutorials on how to apply algorithms and visualization tools through the user-friendly visual interface platform T-BioInfo (t-bio.info). This platform allows scientists and students from all backgrounds to use computational approaches to explore large biomedical data.

    The innovative program will address the major skills gap in processing and analysis of high-throughput biomedical data. This will be achieved by participants applying algorithms to quantify gene expression and detect statistically significant variation from RNA-seq projects in oncology.

    The summer program will see the use of a "deep dive" project based approach that reduces time spent on theoretical introductions to quickly introduce the students to the real issues and challenges one faces in a research project. This milestone achievement is possible due to utilization of the popular T-BioInfo platform that provides an intuitive and educational interface for the complex processing and analysis tools.

    About Amity University & Pine Biotech:
    Amity University, Jaipur established by the Govt. Act of 2008 of Government of Rajasthan. Its goal is to increase student interest in biomedical research careers throughout the world by providing summer research opportunities and programs to all Indian institutions.

    Pine Biotech is biomedical data analytics company that is commercializing a SaaS informatics platform for commercial researchers in need of a reliable and flexible solution to analyze large volumes of multi omics data. It's mission is to bring exiting new capabilities of big omics data analysis and integration using a simple and intuitive interface, innovative algorithms, integration and visualization.

    For more information and course registration visit the website or send an email to info[at]pine-biotech.com

    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
    Submit Archive Subscribe

     

    Acknowledgments

    We wish to thank the following for their support:

    [OMICtools]
    [Repositive.io]
    [Bio-IT World]
    [Become a sponsor]
    Copyright © 2018 · Scilico, LLC