Nikos Papadopoulos

staff scientist @univienna / #bioinformatics #evodevo / previously @embl @mpi_nat / Occasionally sports and esports

[Nikos Papadopoulos @galicae]

It took...
📆15 months
⚡️lots of computational time (and electricity😓)
🧐2.5 rounds of review
💾92 code commits
📝260 manuscript commits
🪧3 new DOIs
🧔153 new white hairs on my beard

but MorF is now accepted at Genome Biology!
https://t.co/Spom1qEMyO

what's new? ⏬ 1/

[Bobby Hollingsworth @BobbyHollings]

You might ask: why not submit to a journal? We have too many talented scientists, and too precious little funding, to tolerate the current academic standard of publish-or-perish. We should build an impact-centric nonprofit research culture where we instead publish-and-persist.

[Nikos Papadopoulos @galicae]

@ilyakorsunsky trying to figure out the calculation of E_kb for Harmony - could it be that for Pr(k) I'm supposed to scale R_ki by N rather than N_b? The final formula and python code suggest so. Apologies if you've clarified elsewhere and I missed it!

[Nikos Papadopoulos @galicae]

@thibaut_brunet @zolotarg @epcrocha @mkrupovic @QuintanaMurci @R3RT0 @BIUPasteur @AudeBer @NRascovan @CamLBerthelot @institutpasteur absolutely blew my mind hahaha

[Nikos Papadopoulos @galicae]

@darencard just wanted to say thanks for the extract-fastq-from-bam tutorial. It really saved my mental state this week, and I learned something new as well!

[B. Duygu Özpolat, Ph.D. @biyolokum]

We are very excited to announce the Platynereis Satellite Meeting at the EuroEvoDevo in Finland. Abstracts can be submitted via the meeting registration. We will prioritize Platynereis abstracts but other annelid friends are welcome to submit and attend. @EED2024 #WormWednesday

[Nikos Papadopoulos @galicae]

@YuyaoSong123 @NatureComms Congrats Yuyao! Very needed contribution as cross-species comparisons become more and more accessible 📈

[Wanninger Lab @WanningerLab]

Thanks to funding by @FWF_at we will put worm snails in the limelight of evodevo and omics research! 2 fully funded PhD positions being announced soon. Feel free to spread the word and send inquiries directly to me if interested. 🐌🪱

[Nikos Papadopoulos @galicae]

@NicolasSMRober1 where would we be without conda envs :O

[Nikos Papadopoulos @galicae]

every once in a while I try to create another conda environment that has python/R interoperability and I am reminded again that we don't live in the nice timeline

[Nikos Papadopoulos @galicae]

@NicolasSMRober1 I need rpy2 to work, and that is somehow always finicky from inside conda envs D: Maybe trying the R -> python direction works better? I've heard good things about the new Rstudio...

[Nikos Papadopoulos @galicae]

@vitaliikl @tangming2005 Yep, that is what I'm suggesting, more or less

[Nikos Papadopoulos @galicae]

@tangming2005 @vitaliikl Wouldn't you be better off mapping the spatial data to normal scRNA and then seeing what expression looks like there?

[Nikos Papadopoulos @galicae]

today I learned that if

1) a gene is expressed a little bit all over the place
2) I am writing a paper/want to sound pompous

the correct phrasing is "it is expressed in a punctate pattern" #sciencespeak

[Julian Bibermair @bibermair]

May I present to the world: Hirosella fruticosa. A #Bryozoa once known as Plumatella fruticosa has long been ambiguously discussed. We confirm recent phylogen. considerations by #ahmedjoudahnass and erect a new family for this species https://t.co/lQMy4xgrJM #phdlife #morphology

[Nikos Papadopoulos @galicae]

@bibermair Finally out! Good job, Julian!

[Nikos Papadopoulos @galicae]

@Jeff_Mold Preach 🙏🙏

[Nikos Papadopoulos @galicae]

I need to preface this by saying the data seems sound and this had no real implications on the science described in the paper, but I still had to chuckle at this figure (anonymised slightly)

[Nikos Papadopoulos @galicae]

Are you interested in...
- winding scientific journeys🤷‍♀️
- revisiting conventional wisdom🧙‍♂️
- cutting-edge experiments🪚
- combining multiple data modalities🧬🔬⚡️🎥
- a result that can be summarised in one sentence?

...well then, @FabianRuperti has just the thing for you!

[Arendt Lab @wormduty]

https://t.co/23ujvW2OjO

Did you know that sponges can move? @FabianRuperti with @savitski_lab and @Prevedel_lab studied sponge movement and found an evolutionary ancient mechanism controlling cellular tension and defense which is also present in our vasculature! A thread 🧵:

[Nikos Papadopoulos @galicae]

this is the equivalent of assembling a genome and then only uploading the raw fastq with instructions on how to assemble🤷‍♀️ Like, sure, that is *technically* reproducible, yay us

[Nikos Papadopoulos @galicae]

this, again🥲Digging through notebooks to piece together the cluster assignments or figure out which cells made it through filtering is not my idea of "reproducible". For the love of God, please upload your final .h5ad/.RDS somewhere🙏

[Nikos Papadopoulos @galicae]

It is the year of our Lord 2023 and people still can't find it in them to actually share .RDS/.h5ad objects? Applause for uploading the raw .mtx on GEO, but ✨I don't want to re-do literally all the steps of your analysis✨, I just wanna look at something real quick #singlecell