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    Two microbiome challenges launched this week with a common goal: evaluate and advance the ability of computational methods to accurately detect known microbial strains in metagenomic samples.

    Both Challenges are great opportunities for the community to come together to advance research and for members in this group to test out their microbiome tools.

    The CFSAN Pathogen Detection Challenge, hosted by precisionFDA, asks participants to develop and use bioinformatics pipelines to identify the types and distribution of Salmonella strains in each of several metagenomics samples. This type of technology will expedite determining the source of foodborne illness. As the food safety community moves to metagenomic sequencing, bioinformatics algorithms must be developed to detect pathogens amongst a mix of organisms sequenced directly from a sample. This Challenge was designed as the first step towards this goal.

    The Mosaic Community Challenge: Strains #2, hosted by Janssen Research & Development, LLC, aims to speed the translation of microbiome science into novel products by tracking the presence of certain known strains in a sample. It is critical to accurately determine the type and quantity of microbes in a sample at the strain-level in order to bring safe and effective products to market, and to precisely monitor their status within the human body. Insights from the Challenge will provide an objective comparison of the performance of different tools. Participants can submit multiple entries and see immediate results of their performance throughout the Challenge using the Mosaic Platform.

    Join us today to get started! Access both Challenges at

    March 13-16, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA[...]c3073


    Predicting the effect of a mutation on the structure and function of a protein is not just for researchers with super-computer facilities. Thanks to public cloud computing options, anyone with basic molecular biology background can setup and run compute intensive computational modeling and dynamics experiments.


    Participants will use popular open source tools and techniques necessary for conducting successful molecular modeling and dynamics experiments in the cloud.

    Hands-on Skills/Tools Taught:
    • Ab initio protein structure modeling: QUARK / Rosetta
    • Remote homology detection: HHpred
    • Fragment-based protein structure modeling: Phyre2
    • Homology-based protein structure modeling: I-TASSER, MODELLER
    • Protein structure quality analysis: PROCHECK, WHAT_IF, Verify3D, PDB-REDO
    • Protein structure refinement: ModRefiner, ModLoop, Ramachandran plot
    • Macromolecular visualization: VMD, USCF Chimera
    • Molecular dynamics: NAMD
    Education: Training in Creating Plots, Graphs and Maps using R at NIH
    Submitted by Vijayaraj Nagarajan; posted on Wednesday, February 14, 2018

    March 6-9, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD, USA[...]1eb6b


    R is the industry standard for creating scientific graphs and plots. There are several different R packages available for creating impressive plots, graphs and maps including plotly, ggplot2, ggvis, diagrammer – for diagrams, dygraphs – for time series data, leaflet – for plotting maps, graphviz – for graphs. This training will walk through participants in creating awesome, interactive, static, shareable plots using the popular R packages.


    Participants will get a brief hands-on introduction to the R platform, followed by hands-on walkthrough for creating several different popular plots, graphs and maps like scatter plots, density plots, correlation plots, pca plots, surface plots, dot plots, star plots, circular plots, trees, heatmaps, panel graphs, 3D graphs, network graphs. We will start from formatting data and go all the way to loading data, setting parameters, creating the images and saving the outputs.


    Participants will work with RStudio. A copy of all the scripts used in the class to create plots, graphs and maps would be provided to the participants at the end of the training. Participants will also receive a cookbook style manual for all the hands-on exercises. After training support is also provided through exclusive members only forum.
    Resources: A database of topically delivered peptides
    Submitted by Gajendra Raghava; posted on Tuesday, February 13, 2018


    We are pleased to announce a new database from our group, called TopicalPdb (a database of topically delivered peptides).


    It is available from following URLs:
    Web Site:



    Cryptocurrency in exchange for your genetic data! Sounds a bit like a scam, but it's the premise behind a new company founded by a leading geneticist. Nebula Genomics says it plans to sequence your genome for under $1,000, give you insights about it, secure it using a blockchain, and allow you to do whatever you want with the data.

    Nebula is the brainchild of geneticist George Church, PhD student Dennis Grishin, and graduate Kamal Obbad, all from Harvard. Mirza Cifric, CEO of Veritas Genetics, which offers a genome-sequencing service for $999, is a founding advisor.
    Resources: World Community Grid
    Submitted by Tony Travis; posted on Thursday, February 08, 2018


    World Community Grid is a simple way to support cutting-edge research into important global humanitarian causes. Your computer or mobile device could be powering scientific research on health, poverty and sustainability:

    If you're running Bio-Linux, please consider joining the Bio-Linux team on WCG (World Community Grid):[...]ND692

    April 18, 2018
    UCL, London, UK[...]e.php

    Significant advances in photonics are leading to an ever increasing role in the biomedical, chemical and life sciences, in medicine, clinical sciences, neurophysiology, etc. In particular there is increasing awareness of the potential for solving health challenges in Africa and other low income countries.

    The conference aim is to fire your imagination. Whilst it will address advances in imaging, biomedical spectroscopy, quantitative imaging, super resolution microscopy and other topical subjects, the conference will also examine the application of biophotonic devices for global health. It will look at real-world clinical applications and new diagnostic uses, the deployment and the translation of optical sciences and light based technologies.

    This is the ninth conference which changes venue from year to year and will be held at University College London this year on Wednesday 18th April 2018.

    The conference programme comprises presentations by invited speakers from academia and selected professional updates from industry. There will be a poster session of contributed papers from early career scientists who are researching novel and exciting new techniques or unique applications.

    What else is going on:
    There is an exhibition of 25 companies dedicated to optical components instruments, imaging, lasers, optoelectronics, sensing technologies, tools and techniques. You can view latest photonics applications and solutions.

    Photonics is an enabling technology – exhibitors develop solutions to satisfy your applications and it is only face-to-face that you can really find out how a company can help you in your work. For further details, please visit our website.
    Research: GEN: First nanopore sequencing of human genome
    Submitted by J.W. Bizzaro; posted on Monday, January 29, 2018



    For the first time, researchers using a nanopore sequencer have assembled a human genome using ultra long reads. This achievement, described today in Nature Biotechnology, marks a milestone for the technology, as well as a considerable step toward eventually completing the human genome.

    "The ability to do this is significant," Matthew Loose, Ph.D., associate professor of medicine at the University of Nottingham and one of the lead authors on the paper, tells GEN. "This is the first time it's been possible to generate enough data on a nanopore sequencer to perform a de novo assembly of the human genome." Using the Oxford Nanopore Technologies (ONT) MinION sequencer, the team generated over 91.2 Gb of sequence data, or 30x coverage of the genome. They achieved single reads of up to 882 kb, with over half the reads coming in at more than 100 kb.

    Paper: (open)
    Education: Book and online course: Biostar Handbook
    Submitted by Steven Allford; posted on Wednesday, January 17, 2018



    The answers to some of the greatest questions of life lie within ourselves. Bioinformatics is the new science created by fusing Biology and Data Science.

    Since its release at the end of 2016, the Biostar Handbook has been continuously expanded, improved, and enriched to become one of the most comprehensive and systematic presentations of Bioinformatics from a Data Science perspective:

    Since its release, the book has been adopted across the globe in several universities and research centers. In addition, over the course of the last year, the Biostar Handbook has been expanded with several new chapters covering Metagenomics and ChIP-Seq analysis.

    With the help of the e-book, readers are able to reproduce analytics results from realistic, and cutting-edge data analysis scenarios such as genome variation, SNP calling, genome assembly and RNA-Seq based gene expression studies:

    In the Fall of 2017 an online Bioinformatics Course titled "Learn Bioinformatics in 100 hours" has been added to the book and made available to the readers free of charge:

    The online course provides a structured path through the book and includes assignments and thorough tests and evaluations.

    The Biostar Handbook is the most affordable, low-cost option to get introduced to this new scientific domain. Join the thousands of readers, hundreds of enrolled students that are currently progressing through the book. With the help of the Biostar Handbook, you too can connect to the new generation of scientists that are well prepared to handle the challenges of the data-centric life sciences.
    Education: Variant Analysis at NIH
    Submitted by Vijayaraj Nagarajan; posted on Wednesday, January 10, 2018

    February 27 - March 2, 2018
    National Institutes of Health
    9000 Rockville Pike
    Bethesda, MD, USA


    Next generation sequencing technologies have made genotyping a day to day research and diagnostic tool. Genotyping has come all the way from bench-to-bedside. Genetic variants are being used in personalized medicine to identify susceptibility genes, common disease variants and mutations relevant for diagnosis and therapy.


    Participants will use popular open source tools and techniques necessary for analysing variants starting from raw data quality control. Apart from the regular analysis like alignment, variant calling and annotation, this training will walk through participants in several advanced variant analysis methods and techniques.

    • NGS Basics, experimental design, data format
    • Data quality control, preprocessing and alignment
    • Germline variant calling
    • Somatic variant calling
    • Variant score recalibration and filtering
    • Variant calling best practices
    • Indels, structural and copy-number variation
    • Cohort and population scale analysis
    • Recombination, linkage, LOH, haplotype, allelic imbalance
    • Variant annotation and association analysis
    • Co-variation, causal variation, network analysis
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