Devin Leopold

@JosiahParry datathief.org

@mixotrophe patchwork.data-imaginist.com

Still basically the only thing I make using ggplot. Paying for it because I cannot for the life of me figure out how to place it side-by-side with another figure. Maybe I'll export & then import as an image file. 😅 #figaday 2.223/n #year2

What the heck, let's start all this again. (I read somewhere that threads > 400 tweets get downgraded in visibility.) It's a revisions day. Help us out by letting me know if you prefer the left or right versions. #figaday 2.1/n #year2

@pseudotsugonoid fwiw - I never heard about the GG issue you mentioned. I just spot checked some samples from a novaseq 2x250 single 12bp indexed run and there were plenty of reads for samples with GG on either end of the index.

Speaking with various sequencing core folks, it seems that having equal base diversity is sufficient. Illumina examples probably need to be more clear, but I think this message still comes through, more or less...

Hi folks--I'd appreciate some wisdom in the area of Illumina 2-channel SBS. My SEQanswers post has it all: seqanswers.com/forum/sequenci… Basically, are leading-GG indices unusable? Illumina examples seem to suggest that just having equal base diversity at each position is sufficient...

@pseudotsugonoid Is it that the examples in your post are acceptable because the i7 index is always read in reverse?

@biogeocycle I'll take one.

@chesscom_in Qh8 is the only guarantee of mate in 2. Other solutions don't account for black moving Kf1

Can you checkmate in TWO as White? Composed by Vladimir Viktorovich Sokolov, 1993

#phish They only scanned one of our tickets on the way into Dicks tonight. Respond if you are outside and need a ticket.

@mixotrophe Maybe you could modify the one on the left so the values are shown by the proportion of the box filled in as opposed to the hue/shade. That way you can keep the color scheme but the values would be easier to compare (and interpret).

OK sci-twitter, please help again! Which of these 3 do you prefer? Trying to show pathway completeness (rows) for 4 species of #Mesodinium (columns). Box saturation = completeness. (Lead author doesn't think left works b/c hard to compare across colors). #figaday 2.7/n #year2

@schloerke @SaveToNotion #shiny

📢 {shinytest2} v0.2.0 is on CRAN! #rstats 🕸️ rstudio.github.io/shinytest2/new… Breaking: * Downloaded file names * Default `load_timeout`: 15s * Remaining default `timeout`s: 4s Features: * Fuzzy screenshot comparison * Seamless `test_app()` reporter * Skip test if {chromote} can't start

@e_hannula @ldereske @MAnthony02 @PacBio ITSx extracts the synthetic sequences from the amptk paper just fine in my experience. The ITSx model only searches for the conserved regions flanking ITS which are based on real fungal sequences in the amptk synmock seqs.

@ldereske @MAnthony02 @PacBio Indeed, you should loose the synthetic sequences if using ITSx (which is a sign it works 😉). I don't use spike in mock but rather selfmade mock community (made of variety of cultures) - and it performs well with ITSx. I can live with relative abundances...

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@colinaverill @JonahVentures provides these services.

Anyone work with a fee for service soil DNA extraction, library prep and DNA sequencing lab? Have a project where it makes sense to send this out rather than doing it in house, but not sure where to start looking.

@BentonRochester @drewmck The relative abundances we recover from eDNA sequencing are subject to multiple sources of bias, and should be interpreted with that in mind. But your bees were most definitely consuming everything we detected.

@drewmck I don’t unfortunately. It’s hard to believe cucumber was a primary flower that they pollinated but we do have a farm a half mile from us and bees go up to three miles to forage.

My neighbor profiled the honey my bees produced. These are the plants he found. Science is cool! #beekeeping

@jdierks @BentonRochester This was done by sequencing plant DNA present in the honey, which is one of the eDNA sequencing services we offer @JonahVentures.

@BentonRochester How is this done? Mass spectrometry of some sort, maybe?

In this paper, Leopold et al. show that the diversity of putative #ericoid #mycorrhizal #fungi increases with soil age and progressive #phosphorus limitation across a 4.1-million-year #chronosequence @DevinLeopold #FEMSMicrobiolEcol #pedogenesis academic.oup.com/femsec/article…

Devin Leopold is our bioinformatician. All the data you get back from us, whether in files or on the data portal goes through him first. Welcome to @JonahVentures, Devin!

HIPR-FISH: Highly multiplexed spatial mapping of microbial communities. Visualize microbes in the gut with high taxonomic resolution! It was super fun to collaborate with @DeVlaminckLab and @haoiseetheworld on this! @nature @CornellBME

I’m excited to invite applications for two PhD positions in my lab at UT Arlington! Love insects? Love the microbiome? Check it out and spread the word: wfscjobs.tamu.edu/jobs/phd-posit…

hi all! Im looking for a new postdoc on an NSF funded fungal endosymbiont interaction genomics project, see more detail at gradschool.oregonstate.edu/sites/gradscho… please RT