EGAarchive<p>Finding genomic and clinical information can be challenging in a world full of data 🔎🧬 What if there was a tool to help?</p><p>Check this video about <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> Beacon, the API that works as a search engine for specific queries on genomic and biomedical data ▶️↘️</p><p><a href="https://youtu.be/Z13sklz9Ylk" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">youtu.be/Z13sklz9Ylk</span><span class="invisible"></span></a></p>
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#GA4GH
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Pierre Lindenbaum<p>Using htsget-rs GA4GH's public endpoint <a href="https://umccr.org/blog/htsget-rs-crypt4gh/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">umccr.org/blog/htsget-rs-crypt</span><span class="invisible">4gh/</span></a> <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a></p>
Michael Baudis<p>Working on <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> projects under VRSed conditions. </p><p><span class="h-card" translate="no"><a href="https://genomic.social/@a" class="u-url mention">@<span>a</span></a></span> ¯\_(ツ)_/¯</p>
progenetix<p>Congratulations to Rahel Paloots for passing her defence for a PhD with the topic “Molecular Heterogeneity among Cancer Cell Lines and their Correspondence to Primary Neoplasias”! Rahel has been a contributor to progenetix.org and the main developer behind cancercelllines.org (a resource for, well, <a href="https://genomic.social/tags/cancer" class="mention hashtag" rel="tag">#<span>cancer</span></a> <a href="https://genomic.social/tags/celllines" class="mention hashtag" rel="tag">#<span>celllines</span></a>…) - but also to the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> & <a href="https://genomic.social/tags/ELIXIR" class="mention hashtag" rel="tag">#<span>ELIXIR</span></a> Becaon project.</p>
Michael Baudis<p>As one of the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> Beacon leads I’m happy about seeing the increasing uptake of this genomic data discovery protocol - and we try to help with our own “bycon” implementation (github.com/progenetix/bycon/; the one running progenetix.org). But increasing uptake => more requests for help & support ¯\_(ツ)_/¯ </p><p>From: <span class="h-card" translate="no"><a href="https://mstdn.science/@elixir_europe" class="u-url mention">@<span>elixir_europe</span></a></span><br /><a href="https://mstdn.science/@elixir_europe/112060077147997049" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">mstdn.science/@elixir_europe/1</span><span class="invisible">12060077147997049</span></a></p>
progenetix<p>… and we’re back at <a href="https://progenetix.org" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">progenetix.org</span><span class="invisible"></span></a> , including the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> Beacon API <a href="https://progenetix.org/beacon/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">progenetix.org/beacon/</span><span class="invisible"></span></a></p><p>From: <span class="h-card" translate="no"><a href="https://genomic.social/@progenetix" class="u-url mention">@<span>progenetix</span></a></span><br /><a href="https://genomic.social/@progenetix/111124639419697135" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">genomic.social/@progenetix/111</span><span class="invisible">124639419697135</span></a></p>
Michael Baudis<p>On my way to the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> plenary in San Francisco. I hope this train in <a href="https://genomic.social/tags/zurich" class="mention hashtag" rel="tag">#<span>zurich</span></a> will bring me there…</p>
Alex H. Wagner 💫<p>Having a blast at the <a href="https://genomic.social/tags/VICC" class="mention hashtag" rel="tag">#<span>VICC</span></a> <a href="https://genomic.social/tags/CIViC" class="mention hashtag" rel="tag">#<span>CIViC</span></a> <a href="https://genomic.social/tags/ClinGen" class="mention hashtag" rel="tag">#<span>ClinGen</span></a> hackathon reception at <a href="https://genomic.social/tags/CGC2023" class="mention hashtag" rel="tag">#<span>CGC2023</span></a>, sponsored by the Global Alliance for Genomics and Health <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a></p>
Michael Baudis<p>Current <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> <a href="https://genomic.social/tags/ELIXIREurope" class="mention hashtag" rel="tag">#<span>ELIXIREurope</span></a> <a href="https://genomic.social/tags/Beacon" class="mention hashtag" rel="tag">#<span>Beacon</span></a> protocol work mode: Tuscan.</p>
Michael Baudis<p>A warm welcome to Nara Sobreira as my new co-lead in the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> Discovery work stream! Let’s work on making genomic data sharing for rare diseases and cancer a bit easier :-) <a href="https://www.ga4gh.org/news_item/ga4gh-discovery-work-stream-welcomes-new-co-lead-nara-sobreira-of-johns-hopkins-medicine/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">ga4gh.org/news_item/ga4gh-disc</span><span class="invisible">overy-work-stream-welcomes-new-co-lead-nara-sobreira-of-johns-hopkins-medicine/</span></a></p>
Michael Baudis<p><span class="h-card" translate="no"><a href="https://mastodon.social/@brembs" class="u-url mention">@<span>brembs</span></a></span> Sure; trying; also <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a>, <a href="https://genomic.social/tags/ELIXIREurope" class="mention hashtag" rel="tag">#<span>ELIXIREurope</span></a> … either “our communications team will look into this” or (for smaller projects) even a pre-bird site status quo.</p>
mbaudis<p><span class="h-card"><a href="https://genomic.social/@fiamh" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>fiamh</span></a></span> … too late for <a href="https://mas.to/tags/GA4GH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GA4GH</span></a> Connect where at least somebody may have recognized it (but probably fewer my “first time I heard of Theranos I said ‘only idiots and/or ppl. w/o any medical lab knowledge; or investors looking into a covering-the-market scheme will fall for it’” gloating).</p><p><a href="https://mas.to/tags/theranos" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>theranos</span></a></p>
mbaudis<p>I forgot about that - sometimes a leaky memory is a blessing… Now let’s talk about date/time representation to get me worked up a bit (I once wrote a page for <a href="https://mas.to/tags/ga4gh" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ga4gh</span></a> … <a href="https://schemablocks.org/standards-recommendations/#dates-times" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">schemablocks.org/standards-rec</span><span class="invisible">ommendations/#dates-times</span></a> to settle this for <a href="https://mas.to/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genomics</span></a> but obviously <a href="https://mas.to/tags/xkcd" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>xkcd</span></a> had been there before…).</p><p>From: <span class="h-card"><a href="https://chaos.social/@tba" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>tba</span></a></span><br><a href="https://chaos.social/@tba/110096186773837597" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chaos.social/@tba/110096186773</span><span class="invisible">837597</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>snakemake</span></a> 7.25.0 has been released. Our awesome community has added an authentication layer for <a href="https://fosstodon.org/tags/GA4GH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GA4GH</span></a> TES and massively improved <a href="https://fosstodon.org/tags/slrum" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slrum</span></a> job status checking. <a href="https://snakemake.github.io" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Ben Berman<p>If we can achieve 30% reduction in adverse drug outcomes using a 12-gene panel, isn't it the time for forward thinking health-care systems/countries to have databases in place to store every genetic variant for every patient? (ala <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> toolsets <span class="h-card" translate="no"><a href="https://genomic.social/@ewanbirney" class="u-url mention">@<span>ewanbirney</span></a></span> )</p><p><a href="https://www.sciencedirect.com/science/article/abs/pii/S0140673622018414" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">sciencedirect.com/science/arti</span><span class="invisible">cle/abs/pii/S0140673622018414</span></a></p>
Alex H. Wagner 💫<p><span class="h-card" translate="no"><a href="https://mstdn.science/@wes_goar" class="u-url mention">@<span>wes_goar</span></a></span> presenting on the <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> <a href="https://genomic.social/tags/VRS" class="mention hashtag" rel="tag">#<span>VRS</span></a> standard at <a href="https://genomic.social/tags/PSB23" class="mention hashtag" rel="tag">#<span>PSB23</span></a>, and illustrating the challenges of standardizing concepts across genomics communities (i.e. VCF, HGVS, PGx, etc.)</p><p>Check out the associated publication: <a href="http://psb.stanford.edu/psb-online/proceedings/psb23/goar.pdf" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">http://</span><span class="ellipsis">psb.stanford.edu/psb-online/pr</span><span class="invisible">oceedings/psb23/goar.pdf</span></a></p>
Alexander (Sasha) Wait Zaranek<p><span class="h-card"><a href="https://genomic.social/@ewanbirney" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>ewanbirney</span></a></span> <span class="h-card"><a href="https://mstdn.social/@andganna" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>andganna</span></a></span> we created <a href="https://scholar.social/tags/arvados" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>arvados</span></a> to help orgs with biomedical data-management and analyses as well as avoid bespoke toolsets / infrastructure.♥️</p><p>Arvados is 100% Free and Open Source Software with commercial support subscriptions available from my employer.</p><p>Ideally several orgs -- all interoperating around <a href="https://scholar.social/tags/GA4GH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GA4GH</span></a> standards -- could collaborate on a meaningful project.</p><p>Would love to see Arvados move out of pharma to broader adoption.</p><p><a href="https://arvados.org" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">arvados.org</span><span class="invisible"></span></a></p>
Alex H. Wagner 💫<p>Hi everyone, here’s my go at an <a href="https://genomic.social/tags/introduction" class="mention hashtag" rel="tag">#<span>introduction</span></a>. I’m Alex, a Principal Investigator at the Institute for Genomic Medicine at Nationwide Children’s Hospital.</p><p>My lab works on models and tools for standardizing the representation and interpretation of genomic variants in cancer, with a focus on improving knowledge computability.</p><p>I spend a lot of time working in consortia settings on things like <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> VRS (“verse”) and the <a href="https://genomic.social/tags/HGVS" class="mention hashtag" rel="tag">#<span>HGVS</span></a> nomenclature.</p><p>I’m excited to be on Mastodon and genomic.social!</p>
Shannon McWeeney<p>Nice overview of EU <a href="https://dair-community.social/tags/Data" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Data</span></a> <a href="https://dair-community.social/tags/Governance" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Governance</span></a> Act from <a href="https://dair-community.social/tags/GA4GH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GA4GH</span></a> - DGA will pave way for European "data spaces" + hopefully make information ‘as open as possible, as closed as necessary’ w/ key <a href="https://dair-community.social/tags/DataSharing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DataSharing</span></a> infrastructure as well as a key bridge w/ <a href="https://dair-community.social/tags/GDPR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GDPR</span></a> by requiring practical tools for individuals (and companies) to exercise their rights Link: <a href="https://www.ga4gh.org/news/ga4gh-gdpr-briefs-the-eu-data-governance-act-new-pathways-for-consented-re-use-of-information/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">ga4gh.org/news/ga4gh-gdpr-brie</span><span class="invisible">fs-the-eu-data-governance-act-new-pathways-for-consented-re-use-of-information/</span></a></p>
Oliver Hofmann<p><test, <a href="https://genomic.social/tags/introduction" class="mention hashtag" rel="tag">#<span>introduction</span></a>, two-three> </p><p>Same username, same profile, still same job - computational biologist in Melbourne working on (clinical) cancer <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="tag">#<span>genomics</span></a>, standards via <a href="https://genomic.social/tags/GA4GH" class="mention hashtag" rel="tag">#<span>GA4GH</span></a> and national infrastructure as part of <a href="https://genomic.social/tags/AustralianGenomics" class="mention hashtag" rel="tag">#<span>AustralianGenomics</span></a></p>
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