Pat Schloss @PatSchloss
Papa to 9 microbes, mackerel snapper, farmer, master of sucking. I want to help you learn the skills you'll need to succeed in science riffomonas.org University of Michigan Joined September 2010-
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I got some great feedback and questions on my previous Code Club where I discussed vectors. Today I incorporate those questions into my benchmarking. I also take a closer look at how things scale with vector size youtu.be/fxk2xocatL4
Society: People have no common sense these days, no problem solving skills. Society: AI!AI!AI!AI!AI!AI!AI!AI!AI!AI!AI!AI!AI!AI!AI! Me: You do know what that "A" stand for, right?
If you had a community of 10^5 individuals, how would you know who the most important individual was to the health of the community? Thankfully the UM is so well resourced that we have just the laboratory to test these types of questions. youtu.be/6bt7mM-_ovk
I held out on giving a departmental seminar in my home department for more than a decade. Last Thursday, I gave a very UM-themed talk: The Team, The Team, The Team. Basically why scientists should fight the urge to be reductionists youtu.be/6bt7mM-_ovk
Do you use c() to grow vectors in R? Do you think for loops are the worst thing since that brogrammer told you to code in Python instead of R? Check out yesterday's Code Club to see some of the experiments I ran with {microbenchmark} youtu.be/MpenxnZAw6o
Do you know the most efficient way to create a vector in #Rstats? How about the best way to access values from a vector? Check out today's Code Club where I use {microbenchmark} to help with some experiments youtu.be/MpenxnZAw6o
Check out the latest episode of Code Club where I am developing an R package to implement the RDP's naive Bayesian classifier. Today I try out some of my tested code with real data 💣 youtu.be/HhjrETgFS70
This is from my backyard - my kids know me so well that when I sent screengrab to the family group text without comment, they asked if I was making a data viz critique 🤣 Fascinated by the multi-hour loss of production and gain around the eclipse
Today I continue my development of phylotyper - an R package that will implement the naive Bayesian classifier for 16S sequences. Today I try to build the database with real data. What could go wrong? youtu.be/HhjrETgFS70
Using testthat to do test driven development is helping me to write better functions and have a better handle on what each step is doing. Check out how I use TDD with testthat in today's episode as I march forward in developing my new R package youtu.be/qUkyQjF1k3o
Have you used testthat to do test driven development in R? Check out today's episode where I use TDD to generate and test functions for calculating probabilities for my naive Bayesian classifier R package youtu.be/qUkyQjF1k3o
So the good old 10 joke isn't very funny after all🤣 Check out today's episode if you ever wanted to count in base4 or any other base using R youtu.be/rnV2aPGBmhs
Did you know there are 10 different DNA nucleotides? Sounds weird, but I explain in today's episode of Code Club! youtu.be/rnV2aPGBmhs
What's the best way to make sure you write a test for your code? Write the test before you write the code! In the most recent Code Club, I describe and demonstrate test driven development using the R testthat package youtu.be/VbXkK_nsmu4
As I build out my phylotyper R package, my plan is to use test driven development (TDD) with the help of testthat. Curious what TDD is and why it's such a powerful technique? Check out today's Code Club youtu.be/VbXkK_nsmu4
Ever wonder what a kmer is or how they're used to classify DNA sequences? Check out the most recent episode of Code Club as I break down the RDP's Naive Bayesian 16S rRNA gene sequence classifier youtu.be/VbXkK_nsmu4
One of the more popular tools in microbial ecology over the past 17 years has been the Naive Bayesian Classifier that was published and hosted by the RDP. In today's episode, I'll step through the results of their benchmarking and breakdown the algorithm youtu.be/VbXkK_nsmu4
Naming things is hard. I'm creating a new R package to classify DNA amplicon sequences. What do you think I should name it? Check out this episode to learn what I came up with and why. Let me know if you have a better idea! youtu.be/N1yn2716Hng
I'm going to be creating a new R package that implements the RDP's Naive Bayesian classifier along with some other approaches. What should I name it? Check out this episode to learn my candidate name - let me know if you have any better ideas! youtu.be/N1yn2716Hng
With the help of the R Packages book, in the coming episodes of Code Club, I'll be building a R package - something I've never done before. Join me on this first episode as I learn by doing and teaching. youtu.be/XjolVT16YNw
Cameron Thrash @jcamthrash
17K Followers 503 Following Associate Professor @USC_MEB, microbe hunter. he/him. Not a bot. @[email protected] @jcamthrash.bsky.socialMichael Baym @baym
22K Followers 2K Following Microbiology, evolution, applied math, molecular biotech. Associate Professor @HarvardDBMI. “The scholarship… is nearly non-existent.” -Reviewer 3Akos T. Kovacs @EvolvedBiofilm
20K Followers 2K Following Professor of Microbiome Ecology at Leiden University🇳🇱 (part time at DTU 🇩🇰): Biofilms, Experimental Evolution, Sociomicrobiology, Plant microbiomeTorsten Seemann @torstenseemann
16K Followers 2K Following Microbial genomics, bioinformatics software, training. A/Prof ORCID: 0000-0001-6046-610X Retro 8-bit computers; VIC=20, C=64, C=128.Dr. Elinne Becket - @.. @bielleogy
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10K Followers 517 Following Husband, father, educator, researcher, moderate libertarian, and always a microbial centrist!Jonathan Jacobs 🧬�.. @bioinformer
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5K Followers 2K Following microbiome science | associate professor @isbsci | affiliate prof @UWBioE & @uwgenome | @uwescience & @AMIposts fellow | systems bio of 💩 🦠 | 🏳️🌈 he/himDave “slowly leavin.. @surt_lab
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62 Followers 304 FollowingBritt Abrahamson @BrittAbrahamson
164 Followers 410 Following Graduate Student @UW | Microbial Ecophysiology (Nitrification & Methanogenesis) | Surf, hike, readRain Haworth @RainHaworth
28 Followers 147 Following Comp sci PhD student @UofMaryland. Interested in applying deep learning to climate science and metagenomics. she/they.Chris Powers @CC_Powers
538 Followers 485 Following PhD student at the University of Rhode Island studying metabolism of foraminifera // Master's of Marine Science // he/him/they/themRichard Sever @cshperspectives
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1 Followers 7 FollowingTakuro Nunoura @Takuro_Nunoura
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1 Followers 38 FollowingJason E. Osborne @PaleoExplorer
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79 Followers 214 FollowingJasmine Rajai @jasmine_rajai
44 Followers 1K FollowingFlora @FloraPhageMKT
13 Followers 143 FollowingEYNK @EYNK261294
0 Followers 175 FollowingNajmuj Sakib @nsakib11235
46 Followers 281 Following #Microbiology student @ISU_Micrograd ERasmus+scholar #univTours #UABBarcelona #EdinburghUni #FU_Berlin #Bangladeshi |Portraits capturer|Sabrin_Bashar @SabrinBashar
83 Followers 339 Following PhD candidate @SyMBIOTA @UAlberta graduate awardee @WCHRIUofAFAHIM Khaniii Marwat @Fahimkhaniii
1K Followers 5K Following Proud to be a MUSLIM and Beloved Pakistani. A Chemist 🕵Mitra Ghotbi @GhotbiMitra
728 Followers 2K Following Soil-Plant-Microbe interactions | ❤️ & 🙏 creatures, 🗽🕊️✊🏿🔬🌍🦠👩🎓💚🌱DoloresYale @0APkL125hH9wHg
9 Followers 578 FollowingVernaWarner @vl2cyuC9782wq
23 Followers 566 FollowingPlasma-PEPSC - EuroHP.. @Plasma_PEPSC_EU
155 Followers 1K Following💥 Matthew MacLenna.. @matthwmaclennan
885 Followers 3K Following PhD, Environmental Analytical Chemist with https://t.co/DBNkswYkEb Electrophoresis/Chromatography/Mass spectrometry/Data analysisthomas laura @thomaslaura451
15 Followers 145 Following if you believe in things you do,all will very be possible,just believe 😵sintinben @sintinben99849
38 Followers 101 FollowingEmmanuel Chijindu ALL.. @ChijinduAl98799
28 Followers 246 Following Ph.D Candidate @UTKMicrobiology| Phage Engineering | Host-microbe interaction | Synthetic Biology| Molecular Biology #BlackExcellence #AMillionDreamsChen YANG @CafferyYang
101 Followers 371 Following Incoming Statistics PhD Student @TAMUstats | Microbiome & Multi-Omics Enthusiast | Developer of ggpicrust2 & MicrobiomeStatYunjeong @yunjeong_k_so
9 Followers 53 Following PhD student @DTUbioengineer studying infant gut microbiome maturation during weaning with culturomics&metagenomics, focusing on HMO utilising CAZymes.AC @AberhamAbere
35 Followers 124 FollowingAsha @Asha2080087
4 Followers 112 FollowingCarrie @carrgomoo
183 Followers 835 Following Carrie 💫 PhD student in bioinformatics and waste water surveillance with @Lackner_TUDa | she/her | married to @willowcabinsUndine Mies @Undine_M
5 Followers 21 FollowingArne Weinhold 🐧 @pundemics
369 Followers 791 Following Microbial Molecular Ecologist 🧫 | Butterfly Microbiota 🦋 | Microbial Community Assembly 🦠| @LMU_Muenchen ex @MPI_CE @fubcp 👉 https://t.co/Zx7kLaGKXDLuciano @lucianopb2000
43 Followers 238 FollowingMohamad Sater @msater15
70 Followers 409 FollowingMJ Bugay @majbugay
87 Followers 221 Following A constant work in progress ❋ EEPB PhD candidate @WUSTL ❋ @AgnesScott '19 ❋ she/her/hers ❋ 🇵🇭Nabeeha Kashfi @Kashfi81115
3 Followers 127 FollowingKenny Shin @Kenny000431
9 Followers 50 Following MSc student @University of Ottawa/ Microbiology and Immunology + bioinformatics/ Lab of Dr. Alain StintziBouilloud Marie @BouilloudM
123 Followers 368 Following Post-doc @Cornell - Transmission of microbiome between Seabirds-Rodents. PhD @CBGPMontpellier - Anthropisation, Biodiversity, Rodent,Microbiome, PathogensLuca Tonietti @Antiprotony
1K Followers 3K Following -Astrobio PhD Stud. @uniparthenope, Geobiology at #GiovannelliLab. Collab. @unimib, @UninaIT, @CometIntercept, @oacn_inaf, @mindat. Visit. at @UKAstrobiologyTara Wade @wadein4u
69 Followers 299 Following All work is play when you like the sandbox in which you play.Usman Asghar @Usman93949118
54 Followers 352 Following Working on aquatic microbial ecology and aquatic microbial food web at Institute of hydrobiology, Biology center, Czech Academy of Science.Urvish Trivedi @txurv
1K Followers 1K Following Asst. Prof. @uni_copenhagen & @COPSAC_com | PhD @microUCPH | Previously @TTUHSCSurgery | Microbial interactions, Biofilms, Polymicrobial infections, MicrobiomeAna Sofia Carranco @microbiana_
52 Followers 197 Following PhD candidate @SSommerLab @uni_ulm researching freshwater turtle egg micro and mycobiome interactions with the fungal disease fusariosis. Funded by @dfg_publicPiotr @Piotr_Rozwalak
55 Followers 170 Following PhD candidate in bioinformatics | Metagenomics and Ancient DNA | Viral Ecology and Omics group in Jena Microverse ClusterCameron Thrash @jcamthrash
17K Followers 503 Following Associate Professor @USC_MEB, microbe hunter. he/him. Not a bot. @[email protected] @jcamthrash.bsky.socialMichael Baym @baym
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15K Followers 5K Following Associate Prof at UArizona interested in genome rummaging and farm animals post = @surt_lab 🐘= @[email protected] “I’m something of a scientist myself”Jen Biddle @DrJenBiddle
8K Followers 2K Following Mostly migrated to the blue place. Don't consider this a surefire way to contact me!Trina McMahon 🌪 @quendi
3K Followers 1K Following Loving microbes, water, genomes, computers, and Wisconsin. @quendi.bsky.socialRan Blekhman @blekhman
7K Followers 538 Following Assoc Professor at @UChicago / Human genomics & microbiome research / Opinions my own (he/him) / https://t.co/v7TIGaAfYubioRxiv Microbiology @biorxiv_micrbio
19K Followers 0 FollowingGeorge O'Toole (he/hi.. @GeiselBiofilm
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3K Followers 692 Following ID doc/microbiologist, lucky dad, PI and wannabe musician.Irene Newton @chicaScientific
7K Followers 3K Following Environmental functional genomics PI interested in all things microbial symbiosis. Prof at IUBloomington she/her @[email protected]Brett Baker @archaeal
6K Followers 4K Following Marine microbiologist - studying the ecology and evolution of new branches on the tree of life. Professor @UTAustin @UTMSI @texas_IB Stay metal.The ISME Journal @ISMEJournal
12K Followers 381 Following Journal of the International Society for Microbial EcologyPeter Girguis @pgirguis
5K Followers 2K Following A father, a son, and a wholly owned subsidiary of the Girguis Flying Circus. Occasional talking head. Here to fight entropy, and you know how that’s going.Joe Zackular @joeyzacks
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2K Followers 1K Following Microbial ecologist, biogeochemist, mom, & crazy cat lady. Vice Chair of @ASMicrobiology COMS & the 2023 Appl Env Micro @ GordonConf.Julie Huber, PhD @JulesDeep
7K Followers 2K Following I watch volcanoes explode in the deep sea and wonder how life continues to survive such drama. Scientist, Ocean Explorer, & Storyteller (she/her)Dept of Microbiology .. @UMMicroImmuno
2K Followers 37 Following We are the department of Microbiology and Immunology at the University of Michigan.Sr. Miriam James @onegroovynun
65K Followers 428 Following Lover of Jesus, sports, reading, beauty and coffee. Author of Restore: A Guided Lent Journal and Loved As I Am. Podcaster at https://t.co/O6GN1ttYHLBrady Spencer @BradySpencer12
895 Followers 1K Following Postdoc in @Kdoranlab at CU-Anschutz studying host-strep interactions | she/her 🏔🦮🔬🎼☕️Sherrone Moore @Coach_SMoore
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45K Followers 5K Following Wife to Tom. Mom to🌹& 🐻 @siriusxm host of The Katie McGrady Show on @CatholicChannel 🎙️on @avemariapress @hallowapp & @osv 📝 @lacroixint. sometimes on @cnnFr. Harrison Ayre @FrHarrison
28K Followers 712 Following Pastor of St Peter's in Nanaimo, BC. Doctoral Candidate @MaryvaleInst. Amazon Wishlist for Doctoral Studies in the link. Co-host of Clerically SpeakingJessica Hooten Wilson @HootenWilson
10K Followers 1K Following I worship Jesus Christ. I want to be a saint. Fletcher Jones Chair of Great Books @Pepperdine @CLT_Exam @liberating_arts Senior Fellow @trinityforumDeClue's Views @DeclueViews
534 Followers 145 Following Dr. DeClue (STB, STL, & SThD, CUA) is Professor of Theology at the Word on Fire Institute and specializes in Systematic Theology.Fr. Andrew Younan @younan3000
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12K Followers 23 Following @[email protected] #rstats Weekly Updates from the R Community. Real-time updates @rweekly_live , submit with https://t.co/25qcZXqSTq https://t.co/jHBfFTpHuOKristin M. Collier, M.. @HSRdirector
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60K Followers 2K Following editor and cofounder at @pillarcatholic. Canon lawyer, husband, dad.Archbishop Sheen @FultonSheen
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28 Followers 41 Following Nature-Loving Illustrator Jesus-Following Michigander Ad Maiorem Dei Gloriam @jpcatholic ‘24 Portfolio 👇🏻New Polity @PostliberalTho1
4K Followers 275 Following ...until all unrighteousness pass away, and all principality and every human power be brought to nothing, and God be all in all.sam @MazzarelliSam
6 Followers 89 FollowingStacey Schultz-Cherry @SSCLabQuips
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171 Followers 137 Following University of Michigan ADVANCE Program promoting diversity by improving campus environments for faculty recruitment, retention, climate, and leadership.Jacob Cram @JacobACram
496 Followers 1K Following Assistant professor at Horn Point Laboratory. Interested especially in microbial community ecology.Zineb Bazza @zinebbazza
627 Followers 3K Following PhD student @McGillU studying cyanobacteria | Former @FAO Global Soil Partnership | @UBC alumnus | Views are my own (She/her)Kyle Gontjes @KyleGontjes
171 Followers 246 Following PhD Candidate @UMMicroImmuno. Microbial Epidemiologist in @SnitkinLabWGS. GSTP T32 Trainee & CRIISP Mentee (PI=@LonaMody). MPH @umichsph. BSc @Calvin_Uni.FOCUS @FOCUScatholic
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6K Followers 6K Following gut microbiome scientist | artist | postdoc @Harvard @wyssinstitute | Microbiome Digest contributor | opinions minechartr 📊 @chartrdaily
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643 Followers 613 Following Postdoctoral Researcher @imperialcollege | Computational Biology + Maternal and Newborn Health | 👩🏻💻👩🏻🔬👩🏻🎨👩🏻🍳 | She/HerMicrobiology Spectrum @JournalSpectrum
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3K Followers 125 Following Fan of bugs, resistance genes and salsa dancing Editor in Chief, Antimicrobial Agents and Chemotherapy;Levi Waldron @LeviWaldron1
2K Followers 445 Following Professor of Biostatistics at CUNY SPH, #rstat / @Bioconductor enthusiast, cancer genomics/metagenomics, proud #HPV #OSCC cancer survivor. @lwaldron@fosstodonKatherine Gallagher @BTBKGMD
2K Followers 743 Following Vascular surgeon, mom, scientist, immunology enthusiast, former college athlete, sports mom for Eian and Riley GallagherSzerlip. https://t.co/0uMKV8PTrBHeather Reed @hreedmicro
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140 Followers 306 Following Pediatric pulmonologist, cystic fibrosis researcher, mom of 3.Science Around Michig.. @sciencemi
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95 Followers 24 Following Data Analysis Networking Group (DANG) at UMich is a trainee-led forum for grad students/postdocs/faculty to discuss all things data analysis/visualizationBroderickFlyLab @BroderickFlyLab
353 Followers 162 Following Twitter account for @nabroderick lab. Flies. Microbes.Dr.T 💉🧫🦠 @DrAlfredoTorre1
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779 Followers 0 Following A Podcast with an unconventional view of the business of farmingElissa Slotkin @ElissaSlotkin
60K Followers 530 Following Congresswoman, dog mom, Michigander. Fighting for better jobs, lower health care costs, and cleaner politics. Running to be Michigan’s next U.S. Senator.Grateful for this national award from @AACOMmunities @ACOMEDU. Blessed to be able to start medical school with a PhD and continually excited to play even a small role in other student doctor's growth as researchers. #physicianscientist @A_P_S_A
Sarah J. Adkins, OMSIII from @ACOMEDU is National Student Researcher of the Year.
Saw this beautiful field of Texas wildflowers on our drive to see some friends today. Too beautiful not to share...unfortunately the two cute donkeys that were standing in the field had disappeared by the time we got back to take the picture. 🥰
Date night with @swirlgirl31415 makes things better.
Pia was in a play tonight about the American Revolution. She delivered her line: “Down with the British!” with conviction and aplomb.
That’s my boy!
Fran Love ‘25 with the big 10th inning double to give Greenhills a lead from last Friday’s marathon game against Roeper
@PatSchloss This is awesome! I’m definitely going to be sharing this with my students! By the way, I’m totally enjoying your Riffomonas / code club videos!
@biologistimo Since we’re sharing colonoscopy stories, at my first screening (last year) apparently I yelled out “I WANT A PRISON TATTOO!”, then I told the Dr. that he was oh so gentle that I wanted him to do this every year. He laughed and said “Maybe I’ll see you in ten years but there’s…
Amazing views from @Baylor on #Eclipse2024
Congratulations to amazing Zackular lab @CAMBUpenn @pennbgs graduate student, Ashley Weiss, for being awarded the NSF GRFP!! We are so proud!! @PennMicro @CHOP_Research
beautiful words on this plaque that was in the old children’s hospital at @umichmedicine which speaks to the care of children “They are the most wholesome part of the human race, for they are the freshest from the hand of God.”
Today would have been my late mother's 91st birthday. She passed away from ovarian cancer in 2012. She was a complicated person who did her best to deal with her two challenging sons. 1/2
A happy memory of my late brother Jack Martin and my sons from years ago.
These guys are weird and i love em.
An excellent meditation on the difficulties in naming packages. Many commonly used bioinformatics packages (I often think snippy, shovil, roary etc) often have meaningful and catchy names...but this is challenging to do well.
I'm going to be creating a new R package that implements the RDP's Naive Bayesian classifier along with some other approaches. What should I name it? Check out this episode to learn my candidate name - let me know if you have any better ideas! youtu.be/N1yn2716Hng