<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41956? https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics Thu, 18 Dec 2014 11:05:42 -0600 https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics <![CDATA[Google Genomics]]>

  • Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

  • Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.

  • Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.

  • Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

    • Address of the bookmark: https://cloud.google.com/genomics/

    ]]>     Tenzin Paul     https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links Thu, 13 Feb 2020 00:20:00 -0600 https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links <![CDATA[genomics public data links !]]> List of publically available databases on google server.

    More at https://software.broadinstitute.org/gatk/download/bundle

    ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

    ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

    Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

    ]]>     Jit     https://bioinformaticsonline.com/videolist/watch/16685/webinar-blast-in-the-cloud Mon, 15 Sep 2014 17:29:32 -0500 https://bioinformaticsonline.com/videolist/watch/16685/webinar-blast-in-the-cloud <![CDATA[Webinar: BLAST in the Cloud]]> Presented July 30, 2014 and covering: an NCBI BLAST AMI at Amazon Web Services; introduction to AWS and setting up an instance; running command line BLAST and using the BLAST URL API via the AMI; and answers to attendee questions.]]> https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics Fri, 17 Oct 2014 02:14:14 -0500 https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics <![CDATA[Google Genomics]]> Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.

    • Store alignments and variant calls for one genome or a million.
    • Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
    • Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
    • Share genomic data with your research group, collaborators, the broader community, or the public. You decide.

    Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

    Address of the bookmark: https://cloud.google.com/genomics/

    ]]>     Reshma Khatun     https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform Fri, 17 Oct 2014 02:16:00 -0500 https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform <![CDATA[Big genomic data on Google Cloud Platform]]> As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.]]> https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu Fri, 31 Jan 2020 01:31:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu <![CDATA[Google Colab : Google Colab is a free cloud service and now it supports free GPU!]]> You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV. 

    If you have just a single notebook to submit, use the website https://google-colab.com/, it is really easy, on the top right corner click 'submit +'. The earlier you post the more visibility you will get over time

    Address of the bookmark: http://colab.research.google.com

    ]]>     Jit     https://bioinformaticsonline.com/news/view/22770/blast-updated Tue, 16 Jun 2015 16:55:24 -0500 https://bioinformaticsonline.com/news/view/22770/blast-updated <![CDATA[BLAST+ updated !!!]]> A new version (2.2.31) of the stand-alone BLAST executables (Linux, Windows and MacOSX on FTP) is now available. New features include support for BLAST-XML2 specification (information here) and JSON BLAST output format, as well as several bug fixes and improvements. The BLAST AMI at AWS will also be updated to 2.2.31 (see this BLAST Help page for more information). For a full list of improvements, see the release notes.

    More at http://www.ncbi.nlm.nih.gov/news/06-16-2015-blast-plus-update/?

    ]]>     Jit     https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files Sat, 08 Feb 2020 04:44:55 -0600 https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files <![CDATA[Explore taxdump files !]]> This is an extract of taxdump-readme.txt to be found at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ The content of the archive -------------------------- It may look like this: delnodes.dmp division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp readme.txt The readme.txt file gives a brief description of *.dmp files. These files contain taxonomic information and are briefly described below. Each of the files store one record in the single line that are delimited by "\t|\n" (tab, vertical bar, and newline) characters. Each record consists of one or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters. The brief description of field position and meaning for each file follows. nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxonomy database parent tax_id -- parent node id in GenBank taxonomy database rank -- rank of this node (superkingdom, kingdom, ...) embl code -- locus-name prefix; not unique division id -- see division.dmp file inherited div flag (1 or 0) -- 1 if node inherits division from parent genetic code id -- see gencode.dmp file inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent mitochondrial genetic code id -- see gencode.dmp file inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet comments -- free-text comments and citations names.dmp --------- Taxonomy names file has these fields: tax_id -- the id of node associated with this name name_txt -- name itself unique name -- the unique variant of this name if name not unique name class -- (synonym, common name, ...) division.dmp ------------ Divisions file has these fields: division id -- taxonomy database division id division cde -- GenBank division code (three characters) division name -- e.g. BCT, PLN, VRT, MAM, PRI... comments gencode.dmp ----------- Genetic codes file: genetic code id -- GenBank genetic code id abbreviation -- genetic code name abbreviation name -- genetic code name cde -- translation table for this genetic code starts -- start codons for this genetic code delnodes.dmp ------------ Deleted nodes (nodes that existed but were deleted) file field: tax_id -- deleted node id merged.dmp ---------- Merged nodes file fields: old_tax_id -- id of nodes which has been merged new_tax_id -- id of nodes which is result of merging ]]> Jit https://bioinformaticsonline.com/news/view/5887/pubmed-opens-for-comment Thu, 24 Oct 2013 12:40:17 -0500 https://bioinformaticsonline.com/news/view/5887/pubmed-opens-for-comment <![CDATA[PubMed opens for comment]]> The informal conversations that researchers have at scientific meetings look set to move online, if a new initiative by the US National Center for Biotechnology Information (NCBI) has its way. On 22 October, the NCBI of Bethesda, Maryland, launched the pilot phase of a programme called PubMed Commons. This will allow users to comment on published abstracts on the PubMed website, which indexes some 22 million papers.

    For now, only a select group of researchers and their invited guests can use the system. But the NCBI's director David Lipman, who helped to develop the programme, says that soon any PubMed author will be allowed to comment under his or her real name and anyone will be able to read the comments.

    More @ http://www.nature.com/news/pubmed-opens-for-comment-1.14023

    News source Nature.

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/videolist/watch/16686/sequence-viewer-download-transcripts-exons-and-proteins Mon, 15 Sep 2014 17:30:36 -0500 https://bioinformaticsonline.com/videolist/watch/16686/sequence-viewer-download-transcripts-exons-and-proteins <![CDATA[Sequence Viewer: Download Transcripts, Exons and Proteins]]> How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3]]>