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  • News & Commentary - Summary

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    Project admins: [Photo] Gary Van Domselaar
    [Photo] J.W. Bizzaro
    John S. J. Anderson

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    Submitter

    The Repositive platform is an online portal indexing multiple human genomic databases, and currently the largest portal of its kind in the world. By indexing the metadata from 50+ global data sources, Repositive enables almost 2 million human genomic datasets to be browsed, and using its powerful query engine, Boolean predicates and predefined filters can help connect the research community with the genomic data they need.

    Repositive is more than just a listing of data, it is also a community-driven platform with 2,000+ global users. Repositive advocates open collaboration, open access and open science and rewards users for contributing to the resource with "reputation" points and aims to show to the world just how impactful data, collaboration and further data annotation can be. Giving visibility to how your contributions are being used is an excellent way for researchers to secure grants, where traditional citations of dataset contributors are failing.

    At the center of Repositive is a belief that a collaborative community and better discoverability and accessibility of data can power research and support better diagnosis of diseases and development of treatments. It is their mission to "help researchers to help patients, faster". With most researchers only knowing of 4-5 sources of human genomic data, indexing the hundreds of data sources globally and making them cross comparable can help researchers utilize all the data which is already out there.

    The core Repositive platform is free to join, with non-users able to browse the data currently indexed here: discover.repositive.io. Repositive also offers several services (repositive.io/services/) like data scouting, help guiding difficult access applications and creating bespoke data catalogues, such as their recent PDX model platform (repositive.io/pdx/) with AstraZeneca, Boehringer Ingelheim and Horizon Discovery.

    AVAILABILITY

    Please visit repositive.io/?bioinformaticsorg

    Submitter

    Over 1,000 private beta registrations in August for our online courses resulted in a lot of feedback. Taking it all in (both positive and negative), we've updated the first two courses – Introduction and Transcriptomics part 1. Transcriptomics part 2 is almost done, we are just finalizing the practical exercises. Next up is Metagenomics – the materials are ready to post, provided by our research partners at the Tauber Bioinformatics Research Center. If you are interested in bioinformatics, please try out the courses and let us know if you have any suggestions! edu.t-bio.info/gett[...]-seq/

    If you have access to students and professors that would like to contribute by testing, developing projects and courses, please let us know! The courses provide a broad overview of main topics related to data types (such as Next Generation Sequencing or Mass-Spec) and a variety of projects that allow students to study the data in detail. Our vision is to develop a comprehensive platform for all types of data and various applications in ecology, agriculture, clinical research and pharma.

    We are still in beta, so if you find anything that needs to be corrected or improved, please let us know! info[at]pine-biotech.com
    Software: Bio-Linux 8.0.8
    Submitted by Tony Travis; posted on Friday, September 08, 2017

    Submitter

    We are pleased to announce a point release of Bio-Linux 8.0.8 that can be downloaded from: www.bioinformatics.org/grou[...]d=341

    This release is based on the work done by Will McCaffery to update and improve Tim Booth's "build-bio-linux" scripts during a summer internship with me at the University of Aberdeen, and I want to thank Will for his valuable contribution to Bio-Linux.

    RELEASE NOTES

    The Bio-Linux 8.0.8 point release contains an updated Linux kernel to improve support for modern WiFi chipsets in particular, and all the packages have been updated. This release is mainly intended to improve the use of Bio-Linux on a USB-stick or DVD. However, the 8.0.8 release also has "mdadm" pre-installed to make installation and rescue of Bio-Linux instances on "md" RAID simpler.

    PLEASE NOTE: Bio-Linux 8.0.7 instances installed to hard disk do NOT need to be updated using the Bio-Linux 8.0.8 point release. Bio-Linux is normally configured for unattended upgrades of core packages and will be upgraded automatically in situ. A manual update will be necessary to upgrade ALL packages installed:
    sudo apt update
    sudo apt full-upgrade

    CHANGELOG

    The Bio-Linux 8.0.8 point release was created using Tim Booth's "build-bio-linux" scripts, updated and modified by Will McCaffery and Tony Travis: github.com/Bio-Linux/
    Research: BMC Biology: Where did the Neanderthals go?
    Submitted by Prashanth Suravajhala; posted on Thursday, September 07, 2017

    Submitter

    Genomic evidence has recently been found for humans and Neanderthals interbreeding. In the following Q&A, the authors discuss the data!

    bmcbiol.biomedcentral.com/arti[...]414-2

    Submitter

    EXCERPT

    A few years ago, a team of researchers at Stanford University launched a video game called Eterna. The game was designed to harness the brain power of thousands of gamers, challenging them to design new chemical sequences of RNA. A new follow-up game has just been launched, and this time players are challenged to create a new RNA molecule that can essentially function as an on/off switch for the CRISPR/Cas9 gene editing process.
    Source: newatlas.com/eter[...]1160/

    Eterna website: www.eternagame.org/web/

    We've just released data from Iso-Seq interrogations of brain tissue from two avian models of vocal learning, Anna's hummingbird (Calypte anna) and zebra finch (Taeniopygia guttata), sequenced in collaboration with the Erich Jarvis and Olivier Fedrigo labs at the Rockefeller University.

    For this data set, we used the Iso-Seq method to characterize the transcriptomes of two birds, with brain total RNA. The two species' brain samples were barcoded, pooled, and sequenced using 4 SMRT Cells on the Sequel System. An average of ~460,000 reads was generated per SMRT Cell; total sequencing data yields ranged from 6.1 to 7.7 Gb per SMRT Cell. More than 15,000 isoforms were identified in each species, including thousands that had not been previously annotated in each bird and 400 to 500 new genes.

    FOR MORE INFORMATION

    Please visit www.pacb.com/blog[...]ssue/

    We are looking for developers in for a preview testing phase who can create or port their tools (or even pipelines) in Databiology Lab using our CIAO (Continuous Integration Application Onboarding) framework. CIAO allows developers:
    • Integrates with your own source or binaries using container technologies
    • Simple configuration to create application specifications
    • Stack independence – middleware are packaged with the application
    • Quick and easy to adapt existing applications – minimal to no refactoring required
    • Common biomedical datasets readily available (1000 Genomes, GIAB, NCBI SRA, ...)
    • Scale applications to production grade environments with free storage and compute capacity to test and optimize applications for all platform configuration
    • Real-time inspection capabilities for each container
    • Reach users of dozens of organizations in the DBE Application Store
    Databiology CIAO is free to use for open source developers and includes compute and storage capacity (usage restrictions may apply).

    If you are interested in trying out CIAO on Databiology Lab, you can sign up here: www.databiology.com/inde[...]eview

    To learn more about the platform: www.databiology.com

    If you have any questions please reply to this post or email us at webcontacts[at]databiology.com

    Submitter

    EXCERPT

    A new survey of DNA fragments circulating in human blood suggests our bodies contain vastly more diverse microbes than anyone previously understood. What's more, the overwhelming majority of those microbes have never been seen before, let alone classified and named, Stanford researchers report August 22 in the Proceedings of the National Academy of Sciences.
    Source: news.stanford.edu/2017[...]ence/

    Article: www.pnas.org/cont[...].full

    Submitter

    Scientists argue that there is a need to have strong standards for p-value statistics to claim new discoveries.

    EXCERPT

    So, in a provocative manuscript posted on the PsyArXiv preprint server on 22 July, researchers argue that P-value thresholds should be lowered to 0.005 for the social and biomedical sciences (D. Benjamin et al. Preprint on PsyArXiv osf.io/prep[...]mky9j; 2017). The final paper is set to be published in Nature Human Behaviour.
    Source: www.nature.com/arti[...]190-5
    Software: LizardFS Software Defined Storage
    Submitted by Mark Mulrainey; posted on Wednesday, August 09, 2017

    Open Source solutions can provide a greater return on your storage investment by opening the path to competitive technology procurement. Automated data management unifies the end-to-end storage footprint and enables our users to spend a far greater proportion of their time and budgets on accelerating science and research (changing the world).

    LizardFS is an example of Open Source Software-Defined Storage. It provides enterprise-class storage using commodity hardware and specialized software to deliver storage services, advanced features, and management capabilities. Compared to traditional enterprise storage that requires proprietary or custom storage systems, open source software-defined storage platforms such as LizardFS have much lower up-front and ongoing operational costs.

    This solution removes the complexity that historically has burdened organizations who struggle to keep up with massive data growth, and simplifies the storage processes for IT professionals in all types of industries. LizardFS increases IT agility by enabling organizations to leverage hardware from any vendor, as well as the option to use existing IT infrastructure to create a custom storage solution to any storage need. It adjusts well to new technologies giving the opportunity to tune and increase performance by integrating SSD, Flash, NvME, etc. Organizations can achieve massive scale by increasing storage capacity and performance as needed, up to 8192 chunkservers and 1 Exabyte of data.

    In one use case, Vang Qu Le, the bioinformatician in charge of the storage facility was tasked with finding a replacement for the the existing NFS setup. They are bound with the same budget restrictions like most of the scientific and research community, so the replacement had to be scalable but cheap . "We have existing workstations, with internal 10TB storage, and other hardware, we need to make use of them, for cost effectiveness." Since installation and familiarization with the system he has had no issues with projects or meeting deadlines.

    Some examples of our latest innovations that are being tested and about to be launched for LizardFS, are a Hadoop plugin to allow you to connect your LizardFS storage to a Hadoop cluster and NFS 4.1 giving you native support for NFS.

    AVAILABILITY

    lizardfs.com
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