Andrew Severin @isugif
Andrew Severin Bioinformatician and Team Manager AI enthusiast Author of ChatGPT 4 Professors (https://t.co/0puLGwRVth ) tweets are my own bioinformaticsworkbook.org Iowa State University Joined October 2011-
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3. Visualize with Markmap - Visit Markmap - Paste your markdown content into the editor. Watch your ideas grow into a colorful mind map as if by magic. After finishing, download it as an interactive HTML for online use or as an SVG for pictures.
Good to see this published. HPAI viruses from Uruaguay suggest pinnipeds ancestral to birds. Viruses in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route. Big implications! 👉academic.oup.com/ve/advance-art…
All the prompts and more are here: oneusefulthing.org/p/innovation-t…
While you are waiting for the next model, it is worth noting that GPT-4 class LLMs can do a lot more than you think. This long prompt works well in all three major frontier models, for example, and has the AI work as a pretty solid tutor.
I made a custom GPT that helps with NIH grant writing. "Write a proposal revamping a graduate curriculum that incorporates scientific computing from the outset" chat.openai.com/g/g-aHWmqCQHp-… ...I haven't been on a study section in ages. What's it like out there these days?
8/ Spreadsheets are just the start. If we can master extracting any data we need with a click, we can spend more time on hypotheses and less in sheets. Check out our open-source demo and code: github.com/sphinxbio/slic…
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs bmcbioinformatics.biomedcentral.com/articles/10.11…
Great to see a California Conservation Genomics Project paper out, led by Brock Wooldridge & Chloe Orland !👇Love talking about this story bc we thought the PCA signal was some kind of batch effect; turns out it was a huge inversion & the only notable variation in the species!
Great to see a California Conservation Genomics Project paper out, led by Brock Wooldridge & Chloe Orland !👇Love talking about this story bc we thought the PCA signal was some kind of batch effect; turns out it was a huge inversion & the only notable variation in the species! https://t.co/IWqct3cTKu
Fantastic review of #metagenomics with long read sequencing, including @PacBio HiFi; many advances covered. Strong conclusion: "long-read sequencing has firmly established its position and is poised to revolutionize another frontier in life sciences with unwavering potential" 🎉
Fantastic review of #metagenomics with long read sequencing, including @PacBio HiFi; many advances covered. Strong conclusion: "long-read sequencing has firmly established its position and is poised to revolutionize another frontier in life sciences with unwavering potential" 🎉
Super nice when people asked me if they can use my repository for teaching. I always say yes. Friends don’t let friends make bad graphs repository: github.com/cxli233/Friend…
Wooo! Check out Liz's monumental effort to improve heterotrophic dinoflagellate representation in phylogenomic analyses! 🤩 sciencedirect.com/science/articl…
Wooo! Check out Liz's monumental effort to improve heterotrophic dinoflagellate representation in phylogenomic analyses! 🤩 sciencedirect.com/science/articl… https://t.co/mx97gHEJqw
📘 An Introduction to R, April 9, 2024 (open access) "This book will be a useful introduction for anyone who wants to learn how to use R" 👉intro2r.com #Statistics #Datavisualization #MachineLearning #DataScience #Python #rstudio #bioinformatics #postdoc #neuroscience
A painless way to customize #Circos plot: From data preparation to visualization using #TBtools onlinelibrary.wiley.com/doi/10.1002/im… Available at: github.com/CJ-Chen/TBtool… #Bioinformatics #visualization #pipeline
So apparently if someone knows / guesses the name of your S3 bucket - even if it's private (!) - they can just bankrupt you by sending infinite PUT requests and there is nothing you can do about it. > requests get rejected > but AWS still counts it as a write operation against…
The new #ZooTraits R Shiny app explore animal trait data for ecological and evolutionary studies. Dive into a universe of over 23,000 species traits across multiple ecosystems and taxonomic groups, now more accessible than ever. (1/7) #Ecology #Evolution #OpenScience
I think there is a huge benefit to standardizing a chunked on-disk binary typed arrays (e.g. Zarr) to store VCF data. Then, build bioinformatics and population genomics software on top of this format. bio2zarr is alpha but I'm very excited: github.com/sgkit-dev/bio2…
A multi-million-year natural experiment. Comparative genomics on a massive scale and its implications for human health academic.oup.com/emph/article/1…
getting-started-with-genomics-tools-and-resources with over 1000 stars now! github.com/crazyhottommy/…
Does anyone know tutorials for mass spec proteomics data analysis from raw data to quantification?
Michael Love @mikelove
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112K Followers 31K Following Developer Advocate @Streamlit (acq. @SnowflakeDB) | prev. Samsung • 𝕏 about LLMs, AI, Data Science, Web Apps and SEO • My heart is open source • Views mine!While you are waiting for the next model, it is worth noting that GPT-4 class LLMs can do a lot more than you think. This long prompt works well in all three major frontier models, for example, and has the AI work as a pretty solid tutor.
I made a custom GPT that helps with NIH grant writing. "Write a proposal revamping a graduate curriculum that incorporates scientific computing from the outset" chat.openai.com/g/g-aHWmqCQHp-… ...I haven't been on a study section in ages. What's it like out there these days?
Fantastic review of #metagenomics with long read sequencing, including @PacBio HiFi; many advances covered. Strong conclusion: "long-read sequencing has firmly established its position and is poised to revolutionize another frontier in life sciences with unwavering potential" 🎉
Review paper out today @naturemethods on long-read #sequencing for #metagenomic: rdcu.be/dGeIj Great advancements on utility of @nanopore @PacBio forming novel insights in diversity and resolution. Great work by @D_Agustinho @fuyvei96 @traingene @BCM_HGSC @RiceCompSci
Super nice when people asked me if they can use my repository for teaching. I always say yes. Friends don’t let friends make bad graphs repository: github.com/cxli233/Friend…
Scientists often bemoan society's inability to take collective action to solve climate change. But our problems with academic publishing are far easier and comparatively inconsequential, yet we cannot collectively solve them because of reshaping incentive structures is hard.
getting-started-with-genomics-tools-and-resources with over 1000 stars now! github.com/crazyhottommy/…
Does anyone know tutorials for mass spec proteomics data analysis from raw data to quantification?
Apparently I need to download everything in XML format and then parse it into something tab delimited? WHY
LLM benchmark question: benchmarks like MMLU do a lot of testing for knowledge - what are the most interesting benchmarks for if I don't care as much about what the model "knows" but more about how good it is at tasks like summarization, data extraction and RAG Q&A against input?
And - because with zoom all things are possible - I was able to (remotely) give a talk and engage in really exciting discussion at the Second Annual Sex Differences in Cancer workshop in Lausanne Switzerland this morning!
I don’t know about overall use, but when you go to conferences you can see the sad decline of Twitter’s relevance to the professional world. People used to talk about who they learned from & their interactions on this platform, now it is all private chat groups & (yikes) LinkedIn
@saronyitbarek Best trick I've learned here is to book follow-up zoom calls with people during at the conference itself - get out a phone and say "let's set something up right now" Most effective possible way to guarantee a follow-up doesn't fall through the cracks
I have gained lots of experience and skills from this long-term project, on how to make bioinformatic tools user-friendly, robust, and fast. I also continue to apply them in my new projects. Here is some advice useful for developers, reviewers, and users. github.com/shenwei356/per…
We just published a short paper on @iMetaScience to introduce SeqKit's new functionality, performance optimizations, and improved user-friendliness, since the initial publication 7 years ago. onlinelibrary.wiley.com/doi/10.1002/im…
Another shocking case of scientific fraud and plagiarism. I bet in 1-2 years, AI will be able to quickly comb through past papers and find suspicious analyses. I imagine outright fraud is relatively rare, but finding it helps science a lot.
NEW: We have the University of Rochester's 124-page investigation report. A committee of external reviewers made an unequivocal finding: Dias falsified and fabricated data, and he committed serial plagiarism—including in his 2020 NSF proposal. nature.com/articles/d4158…
Due to family history, this year I just completed: ✅ Mammogram ✅ Bilateral breast ultrasound ✅ Colonoscopy Each has taken part or a complete day. I'm thankful for the privilege of being able to take the time to check up on myself. If you can, please check up on yourself.
Had such a great virtual visit presenting my recent background selection work at the University of Edinburgh today! Fantastic post-talk discussion too.