Finlay Maguire
@finlaym.bsky.social
Ast Prof CS+Epi at Dalhousie/Pathogenomics Bioinformatics Lead at Shared Hospital Lab (Sunnybrook): infectious disease genomic epidemiology (AMR/SC2/Zoonoses) & socially-focused collab data science (he/him)
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
September 14, 2025 at 1:37 PM
Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.
It may not be worth much right now but this campaign still holds true.
April 1, 2025 at 5:47 PM
It may not be worth much right now but this campaign still holds true.
Final talk in our harmonizing pathogen data collection from Zetty Jamaluddin (UKM) on hAMRonized (github.com/pha4ge/hAMRo...) AMRfinderplus analysis via Google Colab
zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!
zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!
October 31, 2023 at 11:00 AM
Final talk in our harmonizing pathogen data collection from Zetty Jamaluddin (UKM) on hAMRonized (github.com/pha4ge/hAMRo...) AMRfinderplus analysis via Google Colab
zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!
zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!
Jillian Paull (Broad) on PHA4GE's wastewater contextual data specification. Making sure investment in WW capacity is not wasted by bad data. Machine readability, interoperability to other specs, reuse of terms from pubmed.ncbi.nlm.nih.gov/35169842/, & input from HIC/LMIC folks across disciplines.
October 31, 2023 at 10:14 AM
Jillian Paull (Broad) on PHA4GE's wastewater contextual data specification. Making sure investment in WW capacity is not wasted by bad data. Machine readability, interoperability to other specs, reuse of terms from pubmed.ncbi.nlm.nih.gov/35169842/, & input from HIC/LMIC folks across disciplines.
Gerald Mboowa (AfricaCDC): 10 genomics centers for excellence coming w/ ACEGID/SANBI/KRISP bioinf support. 2019-2023: only 7 countries with WGS to only 7 without. ONT&Ill diversify the risk of reagent access issues. Federated African Pathogen Data Sharing & Archive to try and solve data challenges.
October 31, 2023 at 8:59 AM
Gerald Mboowa (AfricaCDC): 10 genomics centers for excellence coming w/ ACEGID/SANBI/KRISP bioinf support. 2019-2023: only 7 countries with WGS to only 7 without. ONT&Ill diversify the risk of reagent access issues. Federated African Pathogen Data Sharing & Archive to try and solve data challenges.
Kim Ng (SSI) on IT challenges scaling infrastructure and new MicrobeSeq initiative
microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!
microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!
October 31, 2023 at 8:20 AM
Kim Ng (SSI) on IT challenges scaling infrastructure and new MicrobeSeq initiative
microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!
microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!
Katrina Kalantar (CZID) on their cloud metagenomics workflows characterising the taxonomy, AMR (w/ RGI), & consensus sequences (github.com/chanzuckerbe...). Takeaways: Inference of abundance and significance (v water control), RNA more sensitive than DNA, Sneathia as possible undernoticed pathogen.
October 30, 2023 at 12:15 PM
Katrina Kalantar (CZID) on their cloud metagenomics workflows characterising the taxonomy, AMR (w/ RGI), & consensus sequences (github.com/chanzuckerbe...). Takeaways: Inference of abundance and significance (v water control), RNA more sensitive than DNA, Sneathia as possible undernoticed pathogen.
First up in Computational Tools for Pathogen Surveillance we have Jen Guthrie highlighting the undersampling and sequencing of non-tuberculosis mycobacterium, needs for genepi doi.org/10.1111/nyas... and a new abscessus workflow incorporating improved pangenome phylogenetics: github.com/waglecn/mabs
October 30, 2023 at 11:39 AM
First up in Computational Tools for Pathogen Surveillance we have Jen Guthrie highlighting the undersampling and sequencing of non-tuberculosis mycobacterium, needs for genepi doi.org/10.1111/nyas... and a new abscessus workflow incorporating improved pangenome phylogenetics: github.com/waglecn/mabs
A great sets of talks on QA to kick off #pha4gecon sessions: Josephina Campos (IPSN), Karen Osman (UKHSA), Constantina Laou (UKHSA@AfricaCDC), and Sarah Mwangi (AfricaCDC) about the challenges of external quality assurance programs for pathogen genomics at a national, regional, and global level.
October 30, 2023 at 11:30 AM
A great sets of talks on QA to kick off #pha4gecon sessions: Josephina Campos (IPSN), Karen Osman (UKHSA), Constantina Laou (UKHSA@AfricaCDC), and Sarah Mwangi (AfricaCDC) about the challenges of external quality assurance programs for pathogen genomics at a national, regional, and global level.
Conference organiser Emma Griffiths kicking us off with a great introduction to the purpose of #GMI13 and the (still) open and growing challenges in global microbial genomics data sharing and harmonisation.
September 13, 2023 at 4:23 PM
Conference organiser Emma Griffiths kicking us off with a great introduction to the purpose of #GMI13 and the (still) open and growing challenges in global microbial genomics data sharing and harmonisation.