74 Matching Annotations
  1. Last 7 days
  2. Aug 2020
    1. Consortia Advancing Standards in Research Administration Information (CASRAI) contributorship taxonomy

      Which has now become NISO CRediT (Contributor Roles Taxonomy), see http://credit.niso.org/

  3. Jul 2020
    1. All supporting data and materials are available in the GigaScience database, GigaDB [48].

      Sequencing data is also in NCBI via BioProject: PRJNA576514 and proteomics data is in PRIDE: PXD018943

  4. Jun 2020
    1. The annual Parasite Awards

      See Parasite Award website here: https://researchparasite.com/

    2. SRA and Gene Expression Omnibus (GEO)

      See the NCBI short read archive (SRA) and Gene Expression Omnibus (GEO) databases here:

      https://www.ncbi.nlm.nih.gov/sra/ https://www.ncbi.nlm.nih.gov/geo/

      Other centralized data repositories are available.

    3. In 2018, eLife published a demonstration
    4. VMs

      We wrote about our first experiences publishing virtual machines back in 2014 http://gigasciencejournal.com/blog/publishing-our-first-virtual-box-of-delights-to-aid-the-fight-against-heart-disease/

    5. Hypothes.is

      GigaScience has hypothes.is integration, and you can read more about how we are using it to add value to papers in this GigaBlog posting http://gigasciencejournal.com/blog/hypothes-is-integration/

    1. teaching hands-on genome assembly courses

      Another example is the Bauhinia Genome project that has used the crowdfunded genomics data to educated the public and teach MSc students at the Chinese University of Hong Kong genome assembly http://bauhiniagenome.hk/2018/03/crowdfunded-genomes-and-the-plant-genome-big-bang/

    2. even small research groups

      There have even been community funded genome projects such as the "peoples parrot" and Azolla genome project, with strong education components such as this one (although using short reads to make an initial draft genome) http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/

  5. May 2020
  6. rvhost-alpha.rivervalleytechnologies.com rvhost-alpha.rivervalleytechnologies.com
    1. Members of the Free State Society for the Blind putting the 3D models through a trial run at a recent visit to the Museum
    2. National Museum in Bloemfontein

      See museum website here https://nasmus.co.za/

    1. accumulate potent phytotoxins

      Inspiring the film "The Birds", which you can read more in the Sanger Institute blog https://sangerinstitute.blog/2020/05/04/prising-open-the-scallop-genome/

    2. Katherine James Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK Search for other works by this author on: Oxford Academic Google Scholar Katherine James, Emma Betteridge Wellcome Sanger Institute, Cambridge CB10 1SA, UK Search for other works by this author on: Oxford Academic Google Scholar

      This Q&A features some discussion of her contribution to this project

  7. Apr 2020
    1. Wellcome Sanger 25 Genomes Project

      This project's goal is to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute's wider 25th Anniversary celebrations. See https://www.sanger.ac.uk/science/collaboration/25-genomes-25-years

    1. interspecies F1 hybrid of yak (Bos grunniens, NCBI:txid30521) and cattle (Bos taurus, NCBI:txid9913)

      In Tibet this type of yak-cow hybrid is know as a "dzo" (མཛོ)་ https://en.wikipedia.org/wiki/Dzo

    2. Timothy P L Smith US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA Correspondence address. Timothy P. L. Smith, US Meat Animal Research Center, US Department of Agriculture, Clay Center, NE 68933, USA. E-mail: tim.smith2@usda.gov   http://orcid.org/0000-0003-1611-6828 Search for other works by this author on: Oxford Academic Google Scholar Timothy P L Smith

      See the Q&A with Benjamin Rosen and Timothy Smith in GigaBlog for more insight http://gigasciencejournal.com/blog/dna-day-2020-cattle-reference-genome/

    1. progression of respiratory diseases

      Including COVID-19, as it is estimated 50% of patients with COVID-19 who have died had secondary bacterial infections. Watch the COSMIC project looking at metagenomics of respiratory samples to identify the bacteria, fungi, and viral co-infections present in patients with COVID-19 https://www.covid-coinfections.org/t/cosmic-co-infections-and-secondary-microbial-infections-in-covid-19/17

    1. Supplemental File 1: Extended Chinese language (中文版) version on the editorial.

      See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

    2. A version of the editorial translated into Chinese is included as a Supplementary File

      See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

    3. Here, we help clarify this and also provide a clear statement of our expectations around how authors are assigned to manuscripts submitted to GigaScience.

      A more detailed version of this clarification and background is available via our blog: http://gigasciencejournal.com/blog/appropriate-authorship/

    4. Laurie Goodman

      ‡ Senior author

  8. Mar 2020
    1. which is the basis of our planned second release (PLINK 2.0).

      See the homepage for updates taking it towards PLINO 2.0 alpha https://www.cog-genomics.org/plink/2.0/

      We also have phased and annotated data for use in plink2.0 worked examples in GigaDB http://dx.doi.org/10.5524/100516

    1. 3.Li Z, Barker MS. Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: Access to gene family phylogenies and age distributions. bioRxiv. 2019:735076. https://www.biorxiv.org/content/10.1101/735076v1.

      A peer reviewed and updated version of this has now been published in GigaScience https://doi.org/10.1093/gigascience/giaa004

    2. chlorophyte green algae

      Some of the authors have recorded a podcast discussing the implications for algae research from this data https://podcasts.apple.com/us/podcast/gane-ka-shu-wong-michael-melkonian-on-if-algae-can/id1420197433?i=1000458893924

    1. hypothes.is (use the hashtag/tag #chromosomenomenclature)

      Please add comments directly on the key parts of the commentary you would like to raise any issues with.

    1. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.

      Using hypothes.is this information can also be updated via annotations here. e.g. adding mention of Twist biosciences, whose Oligo pools are utilized in many CRISPR applications including generation of CRISPR guide RNA (sgRNA) libraries. See https://www.twistbioscience.com/products/oligopools

    2. Table S1. Online tools for TALEN and CRISPR/Cas9. Collected online tools for TALEN and CRISPR/Cas9 are presented in this table. Updates can be accessed in GitHub [107]. Table S2. Commercial service for TALEN and CRISPR/Cas9. Collected commercial service for TALEN and CRISPR/Cas9 are presented in this table. Updates could can accessed in GitHub [107]. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.

      Given that new methods, kits, and services continue to be rapidly developed and updated, an editable version we set up on Github wiki, and readers encourage to update it. See https://github.com/gigascience/paper-chen2014/wiki

    1. This must be achieved by sequencing and archiving huge numbers of microbial genomes, both from clinical cases and known environmental reservoirs, on a continual basis.

      Even without reference genomes, mining metagenomes for coronavirus sequences has become particularly topical in 2020. See the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660

    2. swine flu

      Jennifer Gardy discusses the groundbreaking H1N1 crowdsourcing efforts in her TEDx talk here (with lots of lessons for the coronavirus outbreak a decade later) https://www.youtube.com/watch?v=LmAugMSJ1-Y

    3. Escherichia coli O104: H4

      See more in GigaBlog about the novel "tweenome" method of datasharing for this project http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/

    1. MERS coronavirus

      Mining metagenomes for coronavirus sequences has become particularly topical in 2020 (see the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660)

    2. RNA viruses

      As this works with RNA viruses it has been made part of the "Free access to OUP resources on coronavirus and related topics" collection on the Oxford University Press website https://academic.oup.com/journals/pages/coronavirus

    1. direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date.

      This approach of using Oxford Nanopore direct-RNA sequencing for viruses has now been carried out on the SARSCov2/COVID19 causing coronavirus. See https://doi.org/10.1101/2020.03.05.976167

  9. Feb 2020
  10. Oct 2019
    1. African eggplant

      Also know as the scarlet eggplant or bitter tomato.

    2. “orphan crop”

      The African eggplant is a good example of the work of the Africa Orphan Crop consortium and many of the authors are consortium members. You can read more on the first genomes released in GigaBlog here: http://gigasciencejournal.com/blog/democratising-data-aocc/