Lucas Czech

95 posts

Lucas Czech

@LucCzech

Postdoc in bioinformatics 🌱 and computer scientist 🤖 working on interdisciplinary ways to save the planet 🌍

Copenhagen, Denmark Katılım Temmuz 2015

267 Takip Edilen227 Takipçiler

Lucas Czech retweetledi

Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso·30 May

Excited to release a huge evolution project on the works for many years: An experimental evolution project across climates to understand rapid adaptation Preprint: doi.org/10.1101/2025.0… All data available: grene-net.org/data #MOILAB @UCBerkeley @HHMINEWS 🧵👇

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Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso·29 Ağu

New paper from our #MOILAB at @OUPBioinfo from @LucCzech w/ long term collab @spence_jeffrey_ Lucas created a ⚡️speed C++ code for popgen analysis using Pool sequencing! github.com/lczech/greneda… @UCBerkeley @HHMINEWS @Stanford @carnegiescience doi.org/10.1093/bioinf…

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Climate Change AI@ClimateChangeAI·1 Ara

New @ClimateChangeAI blog post by @LucCzech, @bjornlutjens & @dwddao presenting ForestBench and talking about their efforts in technological innovation and community engagement for carbon data collection in the Global South. Read more: climatechange.ai/blog/2023-11-2…

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Lucas Czech@LucCzech·22 Haz

@MartynaZwoinska @MExpositoAlonso @spence_jeffrey_ Thank you 😊 - happy to get you insights on which new features to prioritize!

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Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso·21 Haz

Another episode of "have you ever fought with software X?" Current tools for pool-seq in Evolve+Reseq data are too slow or have other problems (🧵) @LucCzech wrote from scratch an easy to use C++ tool for pool-seq + comp popgen stats w @Spence_Jeffrey_ arxiv.org/abs/2306.11622

Moi Expósito-Alonso (#MOILAB) tweet media

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Lucas Czech@LucCzech·22 Haz

@IanDworkin @MExpositoAlonso @github happy to hear, and happy to get feedback on it! there is much to be done still, with much room for improvement - let me know what urgent features are missing!

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Lucas Czech@LucCzech·22 Haz

@ChrisWWheat @MExpositoAlonso @github Grenedalf is under active development, and we value constructive feedback and feature requests. It is indeed hard to guess which functionality is most needed in practice. If you have suggestions, feel free to open a GitHub issue.

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Christopher Wheat@ChrisWWheat·21 Haz

@LucCzech @MExpositoAlonso @github Well, no. This recurring lack of depth commonly accompanies improvements for fast analysis, at the price of solid PopGen for the coding level. It’s hard to do what I’m asking. If you “see” the problem, you won’t forget it. Few informaticians appreciate the biology enough to care

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Lucas Czech@LucCzech·21 Haz

@MExpositoAlonso @GonzalezLab_BCN @MikeWhitlock63 @DarrenObbard @PetrovADmitri @SethRudman @jrossibarra @PlantEvolution @evo_gen @grg_perry @capoony @TomBooker12 @SallyNAitken @_johntlovell And to add to that, we are also working on Python bindings for the library at the moment, to make it more accessible 😁

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Lucas Czech@LucCzech·21 Haz

@MExpositoAlonso @GonzalezLab_BCN @MikeWhitlock63 @DarrenObbard @PetrovADmitri @SethRudman @jrossibarra @PlantEvolution @evo_gen @grg_perry @capoony @TomBooker12 @SallyNAitken @_johntlovell If I may chime in here: We do have a pretty solid software backend for a lot of pop gen and pool seq formats and functionality now (github.com/lczech/genesis). If you have ideas for new tools to solve interesting problems on large datasets, let's chat!

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Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso·21 Haz

CCing some colleagues that may be interested ;) @GonzalezLab_BCN @MikeWhitlock63 @DarrenObbard @PetrovADmitri @SethRudman @jrossibarra @PlantEvolution @evo_gen @grg_perry @capoony @TomBooker12 @SallyNAitken @_johntlovell

Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso

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Lucas Czech@LucCzech·21 Haz

@ChrisWWheat @MExpositoAlonso @github Yeah, you'd currently have to split the positions yourself first by S/NS. Can you open an issue on GitHub about this please, so that we can consider it for the future?

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Christopher Wheat@ChrisWWheat·21 Haz

@MExpositoAlonso @LucCzech @github Bummer. This is exactly what I find lacking in tools, as window approaches can’t know NS vs SS. I can give it positions 1+2, or 3, but those != NS or SS, and if I can only get results per exon, this is not similar to Popoolation PopGen (eg piNS or piSS per gene). 😢

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Lucas Czech@LucCzech·21 Haz

@IanDworkin @MExpositoAlonso @spence_jeffrey_ I think email gives you more space to elaborate, but as you prefer. We even accept GitHub issues :-) Thanks, looking forward to it!

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Lucas Czech@LucCzech·21 Haz

@ChrisWWheat @MExpositoAlonso @github Grenedalf treats every line in the gff as a region window, and computes the statistic in each of those windows. So you can add or filter regions in the gff beforehand as needed. Or do you have a more convenient way in mind?

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Christopher Wheat@ChrisWWheat·21 Haz

@LucCzech @MExpositoAlonso @github Great. So with this option stats would be generated for CDS of a gene, or only per exon?

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Lucas Czech@LucCzech·21 Haz

@ChrisWWheat @MExpositoAlonso @github Thanks for the suggestions! To compute stats in regions (instead of fixed sized intervals), see `--window-type`, and `--window-region-gff` to provide a GFF file. SS/NS is not implemented yet, I've put it on the list ;-) Feel free to suggest more: github.com/lczech/greneda…

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Christopher Wheat@ChrisWWheat·21 Haz

@MExpositoAlonso @LucCzech @github Great stuff. One thing kinda unique that I really liked in popoolation1 was the ability to calculate SS and NS, as well as window based, stats via a GFF file. I didn’t see that on GitHub. Hopefully I didn’t dig enough?

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Lucas Czech@LucCzech·21 Haz

@IanDworkin @MExpositoAlonso @github Thanks @IanDworkin, happy to hear that you like the cathedral plot idea (see picture)! Also thanks for spotting the typo - if that's the only mistake we made in close to 50 pages, I'm happy! 😂

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Lucas Czech@LucCzech·21 Haz

Our new preprint is out! grenedalf: population genetic statistics for the next generation of pool sequencing Preprint: arxiv.org/abs/2306.11622 GitHub: github.com/lczech/greneda… with @spence_jeffrey_ and @MExpositoAlonso also to be presented at #evolution2023

Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso

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Lucas Czech@LucCzech·21 Haz

Getting ready for #evolution2023 #evol2023 - come find my talk, Friday 23rd, 4:30pm, Brazos/115: "Population genetic statistics for the next generation of pool sequencing" Also don't miss out on the other #moilab talks: @BellagioTatiana @ksmualim @leg2015 @LauraCLeventhal

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Lucas Czech@LucCzech·16 Haz

Come join us at #evolution2023, with several hot topics from the #moilab

Moi Expósito-Alonso (#MOILAB)@MExpositoAlonso

The #MOILAB will be at #evolution2023 presenting in diverse topics: experimental evolution and popgen, ecology and local adaptation, to conservation biology, and biogeography! evolutionmeetings.org @CarnegiePlants @CarnegieEcolo @Stanford @HHMINEWS moilab.science/team

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Gavin Sherlock@gsherloc·12 Nis

me: makes all figure in pdf form, so they are infinitely scaleable without loss of resolution journal: please convert to tiff or eps, both of which look like garbage at the maximum allowed file size. Thanks! me:

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David Dao@dwddao·3 Şub

So together with @eth @medialab @filecoingreen @bjornlutjens @LucCzech @WWF @fsc_if @SimplexDNA @GainForestNow @CeloOrg @frcamillerivera @DavaExplorer and many more, we build a system to reward local communities for data. End-to-end. And tested it out in Cagwait, Philippines 🇵🇭

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Lucas Czech@LucCzech·1 Şub

@DanielBolnick Do you know which those tools were, and what they compute? In existing implementations, Tajima's D has been bugged, and Fst had biases in pool-seq analysis. @MExpositoAlonso, @spence_jeffrey_ , and I are working on fixing this. Would like to compare ours to the tools you mention!

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Lucas Czech@LucCzech·11 Ara

@HITStudies not quite, the picture was taken by the fabulous @PierreBarbera :-)

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HITS@HITStudies·7 Ara

Three and a half weeks left until 2023, and we are fully prepared thanks to our new HITS #Calendar ! In this edition, the overall theme is #scales - tangible scales in our garden, abstract ones in our research (title image by HITS Alumnus @LucCzech )

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Keşfet

@UCBerkeley @Stanford @carnegiescience @ClimateChangeAI @bjornlutjens @dwddao @MExpositoAlonso @github