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    Events: Integrative Bioinformatics 2018
    Submitted by Keywan Hassani-Pak; posted on Tuesday, May 22, 2018

    13-15 June 2018
    Rothamsted Research, Harpenden, UK
    tinyurl.com/y7b4sc32

    We have invited the "crème de la crème" in post-genomics Bioinformatics to present their exciting work at the 14th Integrative Bioinformatics Symposium at Rothamsted. IB2018 will be an excellent opportunity for keeping abreast with the latest in bioinformatics R&D and for establishing collaborations in new areas such as protein structure prediction, systems biology, statistical genomics and biological knowledge management. No matter if you are working on humans, plants, animals, insects, fungi or microbes; in industry or academia, Integrative Bioinformatics provides the key science and technology platforms to generate meaningful insights from big data and from complex biological systems. The invited speakers are experts in their field and will be covering a range of topics including but not limited to:
    • Bioinformatics resources for gene discovery
    • Multi-omics and systems biology
    • From FAIR data to knowledge graphs to AI
    • Better software, better research
    Register here: ib2018.eventzilla.net

    Hope to see you this summer in the beautiful UK-town Harpenden (25-min by train from London).

    October 10-11, 2018
    Richo Arena, Coventry, UK
    www.hsi2018.com

    On behalf of the Hyperspectral Imaging Centre at the University of Strathclyde in Glasgow, we invite you to participate in HSI 2018, the 7th international conference on Hyperspectral Imaging.

    This cross-disciplinary conference will bring together high profile companies and leaders in hyperspectral technologies, participants from all fields of hyperspectral imaging, application engineers, manufacturers, researchers and users in industry with the aims of exchanging knowledge and investigating the latest techniques & developments in this exciting technology.

    Original contributions are welcomed on all aspects of hyperspectral imaging – we particularly invite contributions in the following, though not exclusive areas:Antiquity Analysis, Biology, Chemical Analysis, Defence, Food Technology, Geographical Information Services, Industrial Vision, Medicine, Microscopy, Environmental Modelling, Product identification, Remote Sensing, Surveillance.

    Please visit the website for further details.
    Education: Training in Metagenomics Data Analysis @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Monday, May 21, 2018

    June 12-15, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]85aba

    OBJECTIVES

    Metagenomics is gaining importance due to low cost next generation sequencing technologies.This training will introduce participants to the end-to-endsolutions for analyzing metagenomicdata, starting from data quality analysis, alignment, community profiling, taxonomic comparison and novel taxa discovery.

    Hands-on Skills/Tools Taught:
    • Processing and Analysis mothur, FLASh
    • Analysis Permanova
    • Analysis ANOSIM
    • Marker analysis LEfSe
    • Marker analysis QIIME
    • Functional analysis PICRUSt
    • Metagenomics analysis A5miseq
    • Contig annotation MEGAN
    • Functional analysis bioBakery
    • Advanced visualizations phyloseq
    • Network analysis Cytoscape

    Submitter

    EXCERPT

    The Nuffield Council on Bioethics has released a briefing note asking what it sees as the big ethical questions on the use of artificial intelligence in healthcare. The note acknowledges the huge potential of AI in making healthcare more efficient and friendly, as well as making faster and more accurate diagnoses, but its focus is on the serious questions about the use of AI that the healthcare industry needs to tackle head on if public trust in AI in healthcare is to be gained.
    Source: newatlas.com/heal[...]4636/
    Software: New Atlas: Web tool squeezes more info out of DNA samples
    Submitted by J.W. Bizzaro; posted on Wednesday, May 16, 2018

    Submitter

    EXCERPT

    When it comes to determining a person's eye, hair and skin color based on a DNA sample, scientists typically need to compare that evidence sample to an existing reference sample. That's reportedly no longer the case, however, if they're using the new HIrisPlex-S DNA test system.
    Source: newatlas.com/hiri[...]4607/

    AVAILABILITY

    hirisplex.erasmusmc.nl

    Monday, August 13 – Friday, August 17, 2018
    University of Washington Campus, Seattle, WA, USA
    uwcmg.org/#analysisWorkshop

    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.

    Frustrated that their discovery scientists spend more time looking for and preparing relevant omics data than analysing it, Genestack's pharmaceutical clients challenged the company to solve this industry problem. The result is two new modules for its biodata platform, which will both be previewed at Bio-IT World Conference 2018. The omics data manager module allows biologists to interrogate and visualise transcriptomics data at scale, and the expression data miner module supports users to collaborate on omics studies to speed up research and enable data re-use and meta-analysis.

    The expression data miner module accelerates not only the workflow, but also new target discovery, by enabling biologists to look across multiple sources of transcriptomic data to better understand gene function. A custom interface enables biologists to interrogate and visualise data without support of a bioinformatician, for example viewing the highest expressed gene or most specific gene for any organ or organ system. The module also makes it easier to work with multiple genes and tissues/cell lines/cell types in one flexible, super-fast interface.

    The omics data manager module provides a collaborative environment for capturing and organising study and sample-level metadata along with required sequencing procedures, produced raw data and secondary analyses. The result is a single point of truth for all omics metadata, including sequencing and analysis requirements. Metadata is cleaned up with validation rules and ontologies. Results are easy to find and use in meta-analyses.

    Genestack CEO, Dr Misha Kapushesky, will be discussing how creating a collaborative ecosystem of multi-vendor systems can offer the best solution for discovery science, in the Pharmaceutical R&D Informatics Track of the Bio-IT World Conference and Expo 2018 on Wednesday 16 May at 2.55pm.

    Genestack is also at booth 436, and the new modules will be available to trial in Summer 2018.

    More information about the two modules is available here:
    Omics Data Manager: genestack.com/plat[...]ager/
    Expression Data Manager: genestack.com/plat[...]iner/

    June 5-8, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]6b852

    BACKGROUND

    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.

    OBJECTIVES

    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.

    HIGHLIGHTS

    • 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

    Submitter

    EXCERPT

    A University of Kansas anthropological geneticist is part of an international research team working to shed light upon one of the unanswered questions concerning the peopling of the New World: Namely, what was the size of the original founding population of the Americas?

    Despite numerous genetic studies that have helped contribute to knowledge about how ancient groups populated the Americas, scientists have not reached a consensus about how many Native Americans made up the original population. This analysis of DNA sequences suggests the Native American founding population that migrated from Siberia consisted of approximately 250 people.
    Source: phys.org/news[...].html

    Submitter

    EXCERPT

    Previous research on lifeforms that are closely related to animals – single-celled organisms such as choanoflagellates, filastereans and ichthyosporeans – has shown they share many genes with their animal cousins. This means that these genes are older than animals themselves and date back to some common ancestor of all these creatures. So the recycling of old genes into new functions, a kind of genome tinkering, must have been an important force in the origin of animals.

    But Professor Peter Holland and I wanted to find out which new genes emerged when animals evolved. We used sophisticated computer programs to compare 1.5m proteins (the molecules that genes contain the instructions for) across 62 living genomes, making a total of 2.25 trillion comparisons to find out which genes are shared between different organisms today.
    Source: theconversation.com/we-r[...]95900

    ARTICLE

    J. Paps and P.W.H. Holland. 2018. Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nature Communications 9: 1730. doi.org/10.1[...]136-5
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    Acknowledgments

    We wish to thank the following for their support:

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