Laura Luebbert @NeuroLuebbert Twitter profile

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Laura Luebbert

2 years

A thread of #gget threads - all gget updates in chronological order I will continue to add to this threadception as we post more updates. 🧵🧵

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Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold: Predict the 3D structure of a protein from its amino acid sequence using @DeepMind ’s AlphaFold v2.0 from a Python or command-line environment in 3 lines of code. Runs on any laptop and requires only ~4 GB of disk space. Simply ‘pip install gget’ and:

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Laura Luebbert

@NeuroLuebbert

5 years

”Imagine that DNA had a diameter of 1 m. Then the complex that copies the DNA would be the size of a @FedEx truck. It would be traveling at a speed of 500 km/h. It would be making a delivery on both sides of the street every ~10 cm. It would finish its journey in 40 min... 1/2

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Laura Luebbert

@NeuroLuebbert

1 year

I created a Colab tutorial that checks if a gene/transcript ID has an associated crystal structure, checks if related proteins with associated crystal structures are available, and then compares those to a de novo structure prediction:

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Laura Luebbert

@NeuroLuebbert

2 years

Come find me and my giant poster at #ASHG2022 poster board 3211 tomorrow 3-5 pm! Let’s talk genomic reference databases and how to access them quickly and effortlessly. @GeneticsSociety

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Laura Luebbert

@NeuroLuebbert

29 days

Lior and I wrote a blog post about what it was like for me to find occurrences of duplicated (and seemingly manipulated) data as a first-year graduate student at @Caltech . I am speaking openly because I believe that we, as the scientific community, can do better.

Lior Pachter

@lpachter

29 days

In a blog post, she tells the story of the reaction she received when she pointed this out to her (tenured) professor at the time, and to others. She was basically told not to waste her time: "a lot of the scientific literature has problems". 7/

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Laura Luebbert

@NeuroLuebbert

8 months

Can you spot the difference between these two BRCA2 protein sequences? They are 3,418 amino acids in length and only differ in a single amino acid. Yet, women expressing the mutant BRCA2 protein have a high likelihood of developing breast cancer. Why is that?

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Laura Luebbert

@NeuroLuebbert

8 months

We expanded kallisto to translated alignment (nucleotides <-> amino acids), and used it to detect novel viruses in RNA seq data. The single-cell resolution allowed us to determine whether the presence of these viruses affected host gene expression. 🧵

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Laura Luebbert

@NeuroLuebbert

1 year

@JeremiahDJohns That highway would be considered walkable in California

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Laura Luebbert

@NeuroLuebbert

2 months

Honored to be featured in @CaltechMagazine with my story about switching fields during my PhD, from wet lab neuroscience to computational genetics. TLDR: Follow your passion; sometimes, being a beginner in a new field can be your greatest advantage.

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Laura Luebbert

@NeuroLuebbert

2 years

We just released #gget version 0.2.0! 🎉 Thanks to your feedback, we were able to further improve its ease of use. In addition to Ensembl IDs, gget now also supports WormBase 🪱 and FlyBase 🪰 IDs. All new features are listed here:

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Laura Luebbert

@NeuroLuebbert

5 years

It would make a mistake once every three years. THAT is DNA replication fidelity.” And that is why it's cool to think about Biology in numbers. Check out this fantastic talk by Prof. Rob Phillips: Analogy by Tania Baker and Stephen Bell. 2/2

Molecular Vitalism: Energy for Fun and Profit ▸ Blackboard Talk by...

Learn more at: https://www.kitp.ucsb.eduBe a part of emerging ideas in science about our universe in a variety of events and talks at: https://www.kitp.ucsb....

www.youtube.com

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Laura Luebbert

@NeuroLuebbert

4 years

I found two papers from the same author reporting identical data with different numbers of replicates and experimental conditions (on more than one occasion). The papers are 20 years old, mostly cited by the author himself and the scientific topic quite niche. 1/3

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Laura Luebbert

@NeuroLuebbert

21 days

A few updates on the data duplications and irregularities in the honeybee papers 🧵

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Laura Luebbert

@NeuroLuebbert

5 months

The best thesis defense is a good thesis offense

Thomas Henning

@15thenning

5 months

Laura @NeuroLuebbert @lpachter passed her defense, but at what cost? Congratulations Dr. Luebbert!!

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Laura Luebbert

@NeuroLuebbert

1 year

Congratulations to me 🎉🎉🎉 I am officially NOT the owner of a car anymore. Here’s to biking everywhere! 🚴‍♀️🚴‍♀️🚴‍♀️ (Please vote for bike lanes so I don’t die.)

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Laura Luebbert

@NeuroLuebbert

4 years

This is a golden silk spider, or “banana spider” (Trichonephila clavipes). A single thread of their anchor silk has a tensile strength of 4×10^9 N/m^2, which exceeds that of steel by a factor of eight - the strongest material known to humans. But it gets better! 1/2

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Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold is a Python and command-line implementation of a simplified version of @DeepMind ’s AlphaFold2 () originally released and benchmarked for AlphaFold Colab ().

GitHub - pachterlab/gget: 🧬 gget enables efficient querying of genomic reference databases

🧬 gget enables efficient querying of genomic reference databases - pachterlab/gget

github.com

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Laura Luebbert

@NeuroLuebbert

3 months

I'm saddened to hear @GoogleDeepMind won’t release the code for this new model. To add to the list, gget alphafold, which brought Alphafold2 to the fingertips of 100k users without requiring any fancy computing resources, would not have been possible without the source code.

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social

@RolandDunbrack

3 months

In my review, I made a list of much science that happened bc AlphaFold2 code was released. I suggested that so much science will not happen if AlphaFold3 code is not released (or not with AF3 itself). We've made ~100k models with AF2 code. How could we use a server for all that?

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Laura Luebbert

@NeuroLuebbert

2 years

Excited and proud that #gget is finally out! :)

Efficient querying of genomic databases for single-cell RNA-seq with gget

Motivation A recurring challenge in interpreting single-cell RNA-seq data is the assessment of results in the context of existing genomic databases. Currently, there is no tool implementing automat...

www.biorxiv.org

Lior Pachter

@lpachter

2 years

Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from @ensembl et al., @NeuroLuebbert developed gget: (code @ ). gget has many uses; a 🧵on the its amazing versatility: 1/

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Laura Luebbert

@NeuroLuebbert

5 months

Who is at @Winter_QBio in Hawaii this year? Come talk to me about our most recent preprint! (poster #37 ) Link to preprint:

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Laura Luebbert

@NeuroLuebbert

1 year

Check out the Interactive Mutation Browser by @ElliotHershberg (and this article about it featuring gget). This browser lets you mutate amino acid seqs and immediately generates comparative interactive structure predictions using ESM.

Interactive Mutation Browser

Prototyping a new way to interact with Protein Language Models

centuryofbio.com

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Laura Luebbert

@NeuroLuebbert

4 years

Gotta love linear algebra

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Laura Luebbert

@NeuroLuebbert

2 years

I know I'm REALLY late to the game, but just in case anybody here is not aware of the @3blue1brown videos, they are the best, fun, accessible, pleasant resource on linear algebra (amongst others) I have encountered so far:

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Laura Luebbert

@NeuroLuebbert

13 days

Srinivasan called @lpachter and me “unprofessional” for carefully documenting instances of manipulated data in his work. You can read about my thoughts regarding this response and my hope for the future in this Q&A by @Sara_Talpos for MIT’s @undarkmag

Interview: Should There Be Peer Review After Publication?

After Laura Luebbert uncovered problems with a body of research, she struggled to get journals to engage with her work.

undark.org

Sara Talpos

@Sara_Talpos

13 days

Thanks to @NeuroLuebbert for talking with me about honeybees, scientific publishing, and her years’ long effort to correct what she characterizes as flaws in the scientific literature.

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Laura Luebbert

@NeuroLuebbert

2 years

scRNAseq analysis? pip install ffq scanpy gget and you're ready to go!

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Laura Luebbert

@NeuroLuebbert

2 years

Nobody: Me: I ADDED A NEW MODULE TO GGET!! To complete the series on protein structure modeling, I added 'gget pdb', which can fetch the structure and metadata of a protein stored in the RCSB Protein Data Bank @buildmodels . 🧵

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Laura Luebbert

@NeuroLuebbert

1 year

@DrAnneCarpenter I expect this poll is going to be biased towards researchers who had a “smoother” time during their PhD/PostDoc since that makes them much more likely to stay in academia

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Laura Luebbert

@NeuroLuebbert

4 years

However, this situation has left me quite frustrated. How often do you encounter fraud? Is this how these things are usually handled for old papers? Can we establish a “fraud-police” for academia that treats fraud as fraud no matter who committed it and when? 3/3

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Laura Luebbert

@NeuroLuebbert

8 months

Want to quickly check what your proteins are up to or predict the effect of mutations on protein-protein interactions? gget elm can efficiently analyze thousands of sequences or UniProt IDs. gget elm preprint:

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Laura Luebbert

@NeuroLuebbert

3 years

I would like to present grubClub (“grub” for larva, and “club” for… well, you will see). I built off of the ethoscope by @qgeissmann and @giorgiogilestro to enable automated long-term optogenetic stimulation of Drosophila larvae. Here is my Halloween release (turn up your 🔊):

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Laura Luebbert

@NeuroLuebbert

2 years

No need for a thread with #gget Links & metadata from release 103? $ gget ref homo_sapiens -r 103 Just annotation & DNA? $ gget ref homo_sapiens -w gtf,dna Just links? $ gget ref homo_sapiens -ftp Just download it! $ gget ref homo_sapiens -w gtf,dna -d

GitHub - pachterlab/gget: 🧬 gget enables efficient querying of genomic reference databases

🧬 gget enables efficient querying of genomic reference databases - pachterlab/gget

github.com

Ensembl

@ensembl

2 years

1/ Do you need reference sequence files from #Ensembl ? All of the different files available can be confusing. Here’s a thread to help you decide which files you need…🧵 #genomics #bioinformatics #tweetorial #Ensembltraining 🧬

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Laura Luebbert

@NeuroLuebbert

1 year

#BoG23 #ScientistsWhoSelfie

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Laura Luebbert

@NeuroLuebbert

5 years

@overheardsfn (Very drunk researcher) “I will illustrate random walks now!” #SfN19

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Laura Luebbert

@NeuroLuebbert

2 years

$ gget pub —journal bioinformatics 🎉

Efficient querying of genomic reference databases with gget

AbstractMotivation. A recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. With th

academic.oup.com

Lior Pachter

@lpachter

2 years

Two of our recently developed tools to simplify bioinformatics are now published ffq for metadata retrieval from sequence databases ( @agalvezmerchan , @lioscro , @sinabooeshaghi ): gget for querying genomic databases ( @NeuroLuebbert )

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Laura Luebbert

@NeuroLuebbert

4 years

The author is a practicing professor at a renowned university today. I was advised that any debating/contacting the author or editorial board is not worth my time. Especially since I am only at the beginning of my career. 2/3

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Laura Luebbert

@NeuroLuebbert

28 days

I received countless messages with stories like mine. I am very grateful to have been given a platform to share my experience, but this is the exception to the norm. Junior scientists are ignored when they bring forward problems with existing literature, and it is unacceptable.

Rosewind

@Rosewind2007

28 days

@NeuroLuebbert @tyto96 @lpachter Go you! As an undergraduate I was assigned a project looking at damsel fly larvae behaviour and could only conclude the paper I was supposed to be basing my work on was…well, I couldn’t see how they possibly got the results they claimed… XNo one wanted to know

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Laura Luebbert

@NeuroLuebbert

1 year

Thanks to @ChiHoangCaltech and @AviMaayan , gget enrichr finally allows the specification of a background gene list! 🧬🧬🧬 P.S. Check out our renewed website! ¡Ahora también en español!

Chi Hoang

@ChiHoangCaltech

1 year

gget enrichr now supports enrichment analysis with a user-provided list of background genes! Why should you care about background genes? A 🧵

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Laura Luebbert

@NeuroLuebbert

8 months

Colab notebook to reproduce the BRCA2 experiment: gget repo:

GitHub - pachterlab/gget: 🧬 gget enables efficient querying of genomic reference databases

🧬 gget enables efficient querying of genomic reference databases - pachterlab/gget

github.com

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Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold works on Linux and Mac, but unfortunately not on Windows. (Note: all other gget commands do work on Windows.) @GoogleColab notebook demonstrating gget alphafold:

gget_alphafold.ipynb

Colaboratory notebook

colab.research.google.com

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Laura Luebbert

@NeuroLuebbert

3 years

To celebrate my one-year anniversary of moving to the US, here are some of the things I find weird about this country. 🧵

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Laura Luebbert

@NeuroLuebbert

2 years

Applying the same algorithm, gget alphafold produces results identical to AlphaFold Colab. The comparison below of the CASP14 target T1024 was created from the PDBs returned by gget alphafold and AlphaFold Colab using @buildmodels :

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Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold returns the predicted structure (PDB) and alignment error for each amino acid (json). PDB files can be viewed in 3D here: or using PyMOL. When called from Python, gget alphafold automatically generates some cool interactive plots (see above)

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Laura Luebbert

@NeuroLuebbert

4 years

The comments under this tweet by @HiroshiSasak1 leave me speechless. Isn’t this supposed to be the American dream?

Hiroshi Sasaki

@HiroshiSasak1

4 years

Five years ago today, I moved to the US to pursue an academic career and explore new research directions. Today, I'm overwhelmed by deep anxiety about the upcoming Executive Order suspending work visas including H-1B, which I've applied for. Speechless.

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Laura Luebbert

@NeuroLuebbert

8 months

Since the preprint just came out, I finally get to share the recording of this talk with you:

"How to catch a virus" Biology of Genomes 2023

Manuscript preprint: biorxiv.org/content/10.1101/2023.12.11.571168Code and tutorials repository: github.com/pachterlab/LSCHWCP_2023 (the working link to the ...

www.youtube.com

jxtxFoundation

@jxtxFoundation

1 year

A presentation by @jxtxFoundation awardee Laura Luebbert at #BoG23

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Laura Luebbert

@NeuroLuebbert

1 year

@DrRachaelF @arjunrajlab As a PhD student, I can confirm this is why we want to meet

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Laura Luebbert

@NeuroLuebbert

5 years

Although opinions on the exact numbers vary, at least 50% of the cells in your body are not actually human, they’re microbes. We all are more than 50% bacteria. #MyOneScienceTweet

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Laura Luebbert

@NeuroLuebbert

2 years

@razoralign Thank you for sharing! I’m very happy to see so many people finding #gget useful. If anybody is interested, follow me for gget updates

Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold: Predict the 3D structure of a protein from its amino acid sequence using @DeepMind ’s AlphaFold v2.0 from a Python or command-line environment in 3 lines of code. Runs on any laptop and requires only ~4 GB of disk space. Simply ‘pip install gget’ and:

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Laura Luebbert

@NeuroLuebbert

6 months

A quick #gget update for my invertebrate fans: 'gget search' and 'gget ref' now also support fungi, protists, and invertebrate metazoa 🐝🐛🦋🪲🐜🪳🦂🦟🪰🪱🦠🐙🪼🦀🦪🍄🐚🪸

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Laura Luebbert

@NeuroLuebbert

2 years

As a proof of concept, I used gget alphafold to predict the structure of an engineered fluorescent nicotine sensor I worked on in 2018 and compared the result to its crystal structure (PDB 7S7U) ...

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Laura Luebbert

@NeuroLuebbert

11 months

Science truly brings you to unexpected places...

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Laura Luebbert

@NeuroLuebbert

4 years

TIL that there is a species of wasp (Megaphragma mymaripenne) whose adults are smaller than amoebas. Oh and their neurons lack nuclei.

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Laura Luebbert

@NeuroLuebbert

2 years

Finally got around to updating my GitHub banner

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Laura Luebbert

@NeuroLuebbert

2 years

@thesteinegger ’s lab developed the excellent tool ColabFold which can also be run locally (). However, this also requires the download of reference databases (940GB). I highly recommend checking out their ColabFold notebook

AlphaFold2.ipynb

Run, share, and edit Python notebooks

colab.research.google.com

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Laura Luebbert

@NeuroLuebbert

4 years

Thank you all for the helpful responses! Neither of the papers has a DOI, but @MicrobiomDigest helped me get ahold of at least one of them on @PubPeer . Here is the comment for anybody interested:

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Laura Luebbert

@NeuroLuebbert

21 days

MVS has dismissed our findings as "typographical errors and minor oversights," accused Lior and me of being "unprofessional," and called any allegations "totally bizarre." For context, I am showing four examples of duplicated data as described in our arxiv manuscript (Fig 3 & 4).

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Laura Luebbert

@NeuroLuebbert

1 year

At the @Caltech @ChenInstitute , we are currently exploring novel approaches to creating #ai … e.g. by optogenetically stimulating a giant fake brain. Stay tuned!

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Laura Luebbert

@NeuroLuebbert

2 years

My Master of Science work (and first co-first author paper) was published in @eLife ! We developed fluorescent sensors to study the pharmacokinetics of smoking-cessation drugs. 🧵 1/6

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Laura Luebbert

@NeuroLuebbert

2 years

… The prediction is imperfect and illustrates the limitations of AlphaFold2, mainly when predicting residues not found in the reference databases (such as the linker between the GFP and the sensor above). However…

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Laura Luebbert

@NeuroLuebbert

3 months

I'm also very disappointed in @Nature for breaking their own code guidelines. So much about “An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims.”

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Laura Luebbert

@NeuroLuebbert

1 year

New crowd today in Berlin! I got to talk about DNA, RNA, and #gget to a room full of (mostly) software engineers. Thank you, @prototypefund 🦾😊 (Please excuse my double helix…)

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Laura Luebbert

@NeuroLuebbert

1 year

TIL that you can prevent your MacOS from sleeping by simply running 'caffeinate' from the terminal Wish this worked as well on me...

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Laura Luebbert

@NeuroLuebbert

2 years

@PartridgeCG The problem is reproducibility. It is straightforward to reproduce an R, Python, [insert favorite language] script, but it is impossible to trace the exact clicks somebody made in a GUI. Hence mistakes are impossible to catch, and it hinders building on each other's work.

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Laura Luebbert

@NeuroLuebbert

8 months

In line with the ethos of kallisto, the workflow can be executed in a few lines of code, and computational requirements do not exceed those of a standard laptop. The code to reproduce all of the results shown in our manuscript can be found here:

GitHub - pachterlab/LSCHWCP_2023: Identification of viral RNA in single-cell RNA sequencing data

Identification of viral RNA in single-cell RNA sequencing data - pachterlab/LSCHWCP_2023

github.com

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Laura Luebbert

@NeuroLuebbert

5 months

Tune in for my thesis defense this Thursday at 10:30 am PT! 🧬👩‍💻🦠 DM me for a clickable Zoom link.

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Laura Luebbert

@NeuroLuebbert

2 years

@france_soir @raoult_didier Au cas où quelqu'un serait intéressé par des sources plus fiables

Meet this super-spotter of duplicated images in science papers

Nature - Elisabeth Bik quit her job to spot errors in research papers — and has become the public face of image sleuthing.

www.nature.com

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Laura Luebbert

@NeuroLuebbert

2 years

TIL that there is a clippy VSCode extension, and my life will never be the same

˗ˏˋmewtru´ˎ˗

@trunarla

2 years

Downloaded the clippy VSCode extension and my productivity 10x'ed 😂

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Laura Luebbert

@NeuroLuebbert

10 months

I had an excellent time at the Barcelona Supercomputing Center @BSC_CNS ! Thank you so much to the students, PIs and research staff for the wonderful discussions - especially the members of the @mele_lab , @marta_mele_m and @Bioinfo4women for hosting me!

Melé Lab

@mele_lab

10 months

We were so pleased to have @NeuroLuebbert at BSC presenting her strategy to detect known and unknown viruses in single-cell RNA-Seq datasets. This layer of viral information can provide great insights into cell tropism or infecion dynamics. We really enjoyed exchanging ideas!

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Laura Luebbert

@NeuroLuebbert

21 days

For those who missed it, here is our arXiv manuscript describing instances of duplicated figures, indications of data manipulation, and other irregularities in papers on honeybee odometry and navigation:

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Laura Luebbert

@NeuroLuebbert

8 months

The interaction between BRCA2 and PALB2 occurs at the site of a eukaryotic linear motif (ELM). @ChiHoangCaltech and I wrote #gget elm, which can efficiently recognize ELMs in amino acid sequences, and we were able to reproduce the finding by Oliver et al. in a few lines of code:

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Laura Luebbert

@NeuroLuebbert

21 days

Our blog and Twitter posts about the difficulties we faced when we first started documenting these issues have received a lot of attention—thank you all for your support!

The Journal of Scientific Integrity

by Laura Luebbert and Lior Pachter Background (by LL) Four years ago, during the first year of my PhD at Caltech, I participated in a journal club organized by the lab I was rotating in. I was assi…

liorpachter.wordpress.com

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Laura Luebbert

@NeuroLuebbert

4 years

Their lovely golden-colored silk has been used to develop composite nerve grafts of acellularized veins, with Schwann cells completely ensheathing the silk. Spider silk tissue engineering might be used in surgically improving mammalian neuronal regeneration in the future. 2/2

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Laura Luebbert

@NeuroLuebbert

1 year

I got to talk to @prototypefund about the importance of open-source software in academia and how to start contributing. The podcast interview is now finally available across streaming platforms! Don’t speak German? Don’t fret, check the 🧵

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Laura Luebbert

@NeuroLuebbert

4 months

gget elm is now published in Bioinformatics 🎉 So proud of @ChiHoangCaltech who was only a freshman when we started working on this.

Fast and scalable querying of eukaryotic linear motifs with gget elm

AbstractMotivation. Eukaryotic linear motifs (ELMs), or Short Linear Motifs, are protein interaction modules that play an essential role in cellular proces

academic.oup.com

Laura Luebbert

@NeuroLuebbert

8 months

Can you spot the difference between these two BRCA2 protein sequences? They are 3,418 amino acids in length and only differ in a single amino acid. Yet, women expressing the mutant BRCA2 protein have a high likelihood of developing breast cancer. Why is that?

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Laura Luebbert

@NeuroLuebbert

8 months

Feeling very grateful for the amount of support and love gget has received. Thank you all for using and contributing to our software! Here's what the GGETISAWESQMETHANKS protein looks like:

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Laura Luebbert

@NeuroLuebbert

21 days

To quote @lpachter : Careful reading of science articles is crucial to the advancement of science. The same applies to our work; experts (incl MVS) can and should read our preprint carefully, and if they find problems with our technical claims, they can and should report on them.

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Laura Luebbert

@NeuroLuebbert

2 years

… during a previous project, we built new fluorescent sensors by mutating 7S7U to study the subcellular pharmacokinetic properties of various other drugs. Structure predictions could have guided our guesses on which residues to mutate.

Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-ces...

Pharmacokinetics, the venerable science that measures the dynamics and concentrations an administered drug attains in organs, has been extended to the subcellular level – organelles – by a generali...

elifesciences.org

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Laura Luebbert

@NeuroLuebbert

3 years

TIL how to break the matrix using single-cell RNA-seq analysis

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Laura Luebbert

@NeuroLuebbert

8 months

BRCA2 plays an essential role in DNA repair through homologous recombination. The promotion of homologous recombination by BRCA2 requires its interaction with a second protein, the partner and localizer of BRCA2 (PALB2). Schematic from

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Laura Luebbert

@NeuroLuebbert

4 years

Without my 2016 J-1, I would not be in grad school today. I would not have developed a protocol to make brain organoids on chips for personalized medicine; nor contributed to relevant research on how antidepressants work. Non-immigrant visas make all the difference!

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Laura Luebbert

@NeuroLuebbert

8 months

Oliver et al. (EMBO Rep. 2009) found that the mutant BRCA2 cannot interact with PALB2, and hence cannot promote DNA repair.

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Laura Luebbert

@NeuroLuebbert

1 year

Come listen to my brilliant friend Victoria Jorgensen talk about stem cell derived embryo models to study human development 🧫

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Laura Luebbert

@NeuroLuebbert

8 months

Soon in cinemas near you: The gget movie I'm so excited about this short documentary filmed in collaboration with the @prototypefund . Watch for its premiere in early 2024!!

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Laura Luebbert

@NeuroLuebbert

3 years

@lpachter @baym I would like to propose the word Erschöpfungsdepressiondepression. It is a word for being depressed about being depressed due to exhaustion.

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Laura Luebbert

@NeuroLuebbert

2 years

Take 2:

lauraluebbert - Overview

Postdoctoral researcher in the @pachterlab at Caltech · Author of gget - lauraluebbert

github.com

Laura Luebbert

@NeuroLuebbert

2 years

Finally got around to updating my GitHub banner

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Laura Luebbert

@NeuroLuebbert

2 years

gget alphafold is not the only command line option available for running AlphaFold. The full AlphaFold2 can be run using Docker. However, it requires downloading databases (~ 3 TB disk storage) and the computational requirements far transcend a laptop (12 vCPUs, 85 GB RAM).

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Laura Luebbert

@NeuroLuebbert

21 days

Our findings have also gotten some media attention: Science: The Transmitter:

Postdoc’s grad-school sleuthing raises questions about bee waggle-dance data

A journal has flagged two papers with expressions of concern, which note a co-author acknowledged errors.

www.thetransmitter.org

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Laura Luebbert

@NeuroLuebbert

6 months

I’ve discussed this extensively in my podcast and documentary with the @prototypefund . We need to recognize the tremendous societal value of and start compensating developers appropriately for open-source technology so we can retain quality and talent.

Daniel Liu

@daniel_c0deb0t

6 months

I'm going to put out unfinished and unpolished blog posts so I can get more thoughts written down. Here's a post on funding open source bioinformatics:

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Laura Luebbert

@NeuroLuebbert

2 years

Thank you @georgiagkioxari for joining us tonight at our monthly @NeuroTechers fireside AMA! We talked about computer vision and the lack of Greek food in the US 💻👀 Thank you @JieyuZheng3 for co-organizing and to all attendees for a great discussion Stay 🎵 for our next guest

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Laura Luebbert

@NeuroLuebbert

21 days

A huge thank you to reporters @DrShaena ( @_TheTransmitter ) and @SofiQuaglia ( @NewsfromScience ) for writing about our findings and shedding more light on these issues.

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Laura Luebbert

@NeuroLuebbert

5 months

My lab has outdone itself with my thesis posters 🥰 To portray my passion for hiking, they unknowingly used a picture of the first-ever successful ascent of Nanga Parbat by a German team in 1953. Nanga Prabat is nicknamed 'Killer Mountain' - very fitting for a pandemic PhD.

Laura Luebbert

@NeuroLuebbert

5 months

Tune in for my thesis defense this Thursday at 10:30 am PT! 🧬👩‍💻🦠 DM me for a clickable Zoom link.

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Laura Luebbert

@NeuroLuebbert

4 years

I was named Chen Graduate Innovator 2021! 🥳

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Laura Luebbert

@NeuroLuebbert

2 years

To upgrade, run 'pip install --upgrade gget'. We took great care to preserve as much backward compatibility as possible. However, I highly recommend looking at all of the changes listed here . As always, your feedback is highly valued.

GitHub - pachterlab/gget: 🧬 gget enables efficient querying of genomic reference databases

🧬 gget enables efficient querying of genomic reference databases - pachterlab/gget

github.com

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Laura Luebbert

@NeuroLuebbert

8 months

Operating in the amino acid space makes this method robust to nucleotide point mutations.

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Laura Luebbert

@NeuroLuebbert

2 years

Source code and manual:

GitHub - pachterlab/gget: 🧬 gget enables efficient querying of genomic reference databases

🧬 gget enables efficient querying of genomic reference databases - pachterlab/gget

github.com

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Laura Luebbert

@NeuroLuebbert

1 year

@deliprao In case anybody wants to use ChatGPT in their Jupyter notebooks:

Laura Luebbert

@NeuroLuebbert

1 year

💬 gget gpt 💬 (using the ChatCompletion endpoint) is now part of gget v0.27.4 $ pip install -U gget $ gget gpt "How are you today GPT?" your_api_key Python: >>> gget.gpt("How are you today GPT?", your_api_key) You can get your @OpenAI API key here:

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Laura Luebbert

@NeuroLuebbert

8 months

Probably one of the best talks I ever gave. Very excited I finally get to share it with all of you! 😊🦠🦠🦠

Laura Luebbert

@NeuroLuebbert

8 months

Some of you may have seen me present a preliminary version of this work at the Biology of Genomes conference earlier this year. I am happy to finally share the recording of my talk:

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Laura Luebbert

@NeuroLuebbert

21 days

The media articles as well as comments on our blog include responses from Prof. MV Srinivasan, who is the common author across all of the papers we flagged (he is first or last author on most of them).

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Laura Luebbert

@NeuroLuebbert

21 days

Our analysis is described in detail in our manuscript, and we provide immediately executable Google Colab notebooks to maximize its reproducibility:

LP_2024/bee_real_analysis.ipynb at main · pachterlab/LP_2024

Contribute to pachterlab/LP_2024 development by creating an account on GitHub.

github.com

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