james hadfield

@BillHanage Completely upside down. But that's because I'm now back in New Zealand ;)

@hamesjadfield nice to hear from you james. Bet your life is totes normal

Ok. Here's a little insight into the life of an infectious disease epidemiologist trying to handle uncertainty and report responsibly. Warning - the coming thread will contain many "i'm not exactly sure" statements. Also shout out to @nataliexdean who made me notice this 1/n

@ogrecio @NetworkArtic regarding accessing rampart using a given IP, I _think_ you're wanting a reverse proxy or something more temporary like chenhuijing.com/blog/tunnellin… (aside: you can easily change the ports, see `rampart --help`). 2/2

@ogrecio @NetworkArtic Hi Oscar -- for the protocol, see github.com/artic-network/… 1/2

Hi .@NetworkArtic ! When running the rampart standalone prtocol, is it possible to point the output to a given ip, instead of the localhost:3000? So output is in http://ip:3000. Thanks!

@BillHanage All good points Bill. In terms of the stats used in the paper I found Andrew Gelman's run-through really helpful statmodeling.stat.columbia.edu/2020/04/19/fat…

coda: uncertainties include how well the various tests work, how much immunity they generate and exactly where everywhere is on its epidemic curve. Other than that, peachy

@GageKMoreno @nextstrain @KATarinambraun @dho_lab @tcfriedrich Congrats on getting this local build set up & running auspice yourself 💯. Let us know if you're interested in having your own nextstrain group (e.g. nextstrain.org/groups/blab/) which you could upload datasets & narratives to

Check out our WI-only #SARSCoV2 / #HCoV19 @nextstrain build! @KATarinambraun and I are so lucky to have contributed 83 genomes so far and to be able to continue adding to the ever growing tree. go.wisc.edu/pxq2b5 @dho_lab @tcfriedrich

@arambaut @nextstrain Frustrating & unsurprising. Hopefully when all is said and done the insights made possible by data sharing, virological, nextstrain etc will be seen as the way forward.

@B_Gutierrez_G @firefoxx66 @nextstrain @richardneher @trvrb Yeah this is a great example Bernado (and to think how many analogous situations exist due to incomplete sampling!). We're working on improving this, esp for singletons/cherries etc as Emma said. Ideas welcome from the ox crew BTW!

@firefoxx66 @nextstrain @hamesjadfield @richardneher @trvrb I'm sure it'll be fine-tuned in time, thanks for the amazing work @firefoxx66! This particular case is just an interesting example given the previous knowledge of the sample origin, with this degree of global sequence representation things like this are bound to happen.

As part of the last push, you might notice things looking a bit different on our website! As the number of available sequences has grown, we've looked for ways to better display them - so they can be useful within the context that matters, while still giving a global view. 1/7

@mattloose @bioinfomatt @nanopore @scastesparraka @samstudio8 rampart is becoming a bit rampant, but in a good way I hope 😉

@bioinfomatt @nanopore @hamesjadfield @scastesparraka @samstudio8 Latest rampant works without any issues

Successful run of the sequencing pipeline for COVID-19 at UCL, from extraction to Nanopore genome. Thanks to Rachel Williams, Mark Kristiansen, Paola Resende, Tony Brooks, Sunando Roy, Paola Niola and others. This is led by Judith Breuer. Sequencing in earnest starting now!

@Psy_Fer_ @NetworkArtic Yes 🎉 but read this first re double barcoding: community.artic.network/t/ont-enabling…. We'll try to get the artic-ncov2019 env updated too.

@hamesjadfield @NetworkArtic Nice! Well done! So does this mean we can use live demuxing during a run? Can we port this into the artic-ncov2019 conda environment? Great job!

. @NetworkArtic RAMPART v1.1.0 released, w support for guppy-demuxed fastqs, fixes out-of-memory bugs + bunch of other improvements. More frequent releases on the way 🤞. More details: community.artic.network/t/rampart-v1-1… It's been great to see this being used -- keep up the good work!

12 covid-19 samples on to contribute to the work of the COG-UK consortium. Thanks to team and all at @UoNLifeSci @UniofNottingham #WeareUoN

@NetworkArtic V3 #SARSCoV2 / #HCoV19 primers on 15 samples. 5 minutes in. I’d say it’s a success! @nanopore @KATarinambraun

The #genomics of #COVID19 from the scientists who 1st sequenced it, its origin, and how it relates to the previous coronavirus epidemics cell.com/action/showPdf… @CellPressNews @CellCellPress

65 genomes added to @nextstrain (nextstrain.org/ncov) **today**

@nextstrain @ESRNewZealand @MathStorey @Joepdl @sciolato @MathStorey @Joepdl was the NZ genome (20VR0206) an independent travel history to Iran, or linked to NZ01?

nextstrain.org/ncov updated with 3 more genomes: 2 from Saitama, Japan separated by 1 SNP (C29743T) & 1 genome from NZ which groups with sequences w. travel history to Iran cc. @ESRNewZealand @MathStorey @Joepdl @sciolato

@klevy_emory @nextstrain Hey Karen, these are still accessible but we haven't got a list of URLs up. If you load the current sit-rep (nextstrain.org/narratives/nco…) then change the date ("2020-03-20") in the URL to "2020-01-23", "2020-01-25", "2020-01-30", "2020-03-04", "2020-03-05", "2020-03-13"

@nextstrain how can we access older situation reports? is there an archive? using this in my teaching this week, thx

@Joepdl @phydyn @hendysh @Bureauchem @nextstrain Doing a great job Joep, Matt, Una et al. Is there a (public) way to link health.govt.nz/our-work/disea… to the genome names (20VR0189, 20VR019 etc).

Two new SARS-CoV-2 sequences from NZ up on @nextstrain nextstrain.org/ncov?c=recency…

Sunday's update 👇 The fact we are picking up so many cases is a credit to NZ testing capacity, with ~6k tests done now (still working on incorporating test numbers & rate of +ves here)

Today's update: 11 +ve out of ~1000 tests. Amazing job to get this much testing capacity. I'll try to get those data to plot in the coming days, that's the success story here.

Update: now 28 NZ cases, all linked to overseas travel. (Cases now scaled to pop size.) Priority is avoiding community spread & widespread testing will be crucial for this. More testing=more knowledge. We're in a relatively strong position at this stage but we have to act fast.