robert.bio - Profile | ThreadSky | a Reddit-style client for Bluesky

I also reject the notion that "most biomedical literature is unreliable/untrue." This is simply not the case. The vast majority of biomedical research is so reliable we don't even think about it. And yes, some studies and even subfields have issues, but let's acknowledge all the things that work. 🧵

submitted 6 days ago • 8 comments

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

submitted 6 days ago • 1 comment

Here's why I think there is reason to be bullish on U.S. STEM education. doi.org/10.1093/gene... #STEM #STEMEducation

submitted 13 days ago • 1 comment

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

submitted 18 days ago • 1 comment

We always tell people to create a portfolio to showcase their work, so today we're releasing a template to get you started: github.com/omgenomics/p... It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise

submitted 62 days ago • 0 comments

Thrilled to announce the first release of the "Nanopore for Educators eBook" — nanopore4edu.org/latest/ #genomics #DNA #OxfordNanopore

submitted 73 days ago • 1 comment

In 2024, sandbox.bio had >170,000 tutorial page views! 🥳 The most popular tutorials were: 1. Terminal basics 2. Genomic intervals with bedtools 3. Terminal exercises 4. Data exploration with awk 5. DNA sequencing QC Check them out here: sandbox.bio/tutorials

submitted 104 days ago • 0 comments

We are experiencing an assault on science unparalleled by anything I’ve seen in my life. It’s not one issue or another anymore, the entire institution is under attack by the most powerful individuals in the country. This Friday, where will you be? standupforscience2025.org

submitted 106 days ago • 661 comments

📢 Our first bioinformatics office hours were a lot of fun, so we will be hosting more of them this year! We will also invite special guests to co-host 👀 Join this Google Group to be notified of future office hours: groups.google.com/a/omgenomics... (log in with Google, then "Join Group")

submitted 112 days ago • 0 comments

"I've spent over five decades as a scientist in academia and the federal government," Harold Varmus, the former director of the N.I.H., writes in a guest essay. "Never before have I seen my profession so politicized as it is now under the Trump administration."

submitted 122 days ago • 18 comments

We just released a new video on how to get more out of those “let’s chat” conversations when job hunting, based partly on my past experiences being on the receiving end of requests for advice and job referrals: youtu.be/bpQaIvqqkKw

submitted 124 days ago • 0 comments

🧬🖥️ We are hosting free bioinformatics office hours on Feb 19th at 10am-noon PST. Bring your bioinformatics career or technical questions, and @robert.bio and I will try to answer them. Sign up here: tally.so/r/mOb6dM Please share especially with students and early career scientists!

submitted 126 days ago • 1 comment

Friends are looking for jobs. Collaborators are dropping off papers. Funds are being pulled away. But let’s just pretend everything is normal.

submitted 130 days ago • 5 comments

We now have a tutorial for SKA2 available to run interactively on sandbox.bio, going from genomes to trees: sandbox.bio/tutorials/sk...

submitted 144 days ago • 0 comments

Illumina and NVIDIA Team Up to Remake How to Train Your DRAGEN 🧬🖥️ omicsomics.blogspot.com/2025/01/illu...

submitted 146 days ago • 0 comments

Built a small sequence generator tool 🧬 You can: - constrain to specific bases, specific length - copy as fasta - free to use, all stored locally!

submitted 152 days ago • 1 comment

🌲 New sandbox.bio tutorial: Learn to build phylogenetic trees from closely related genomes using ska (the tool, not the music) 🖥️ 🧬 sandbox.bio/tutorials/sk...

submitted 150 days ago • 1 comment

H/t to Nava for spotting this & posting to ASeq discord First question posted to @nanopore CEO Gordon Sanghera at #JPM25 had 2 parts: 1. Do they have long read technology? 2. Do they see value in long reads?

submitted 153 days ago • 4 comments

Should you learn R or Python first for bioinformatics? 🤔 🧬 🖥️ ➡️ youtu.be/-XU5Jxe4LpE

submitted 157 days ago • 3 comments

Got something interesting cooking up... 👀 @robert.bio

submitted 176 days ago • 6 comments

What does it mean for something to be Turing complete? I answer this question, and more, through a series of fully interactive Turing machine simulations! Play, pause, step forwards and backwards, and even write your own Turing machine programs in my latest blog post. samwho.dev/turing-machi...

submitted 178 days ago • 23 comments

#YIL (Yesterday I learned) this #bioinformatics newbie gotcha: In original CIGAR strings, still widely used, 'M' denotes both matches and mismatches, while in a newer version, mismatches are separated into 'X'es 😳

submitted 179 days ago • 1 comment

Video to audio to transcript to summary using local AI: whisperfile and llama3.3 via Ollama https://doi.org/10.59350/bjvsq-cqg11 1/2 🧵

submitted 181 days ago • 2 comments

🎁 New RNA-Seq tutorial! Learn to run differential expression analysis with DESeq2, and create your own bioinformatics projects using public data and the Expression Atlas 🧬 🖥️ youtu.be/NGbZmlGLG5w

submitted 181 days ago • 1 comment

For anyone interested in PCR enhancers, here’s a new study looking at nine readily accessible compounds that can be used with difficult DNA templates, examining their effects on polymerase thermostability, inhibitors, and amplification of various DNA targets.

submitted 186 days ago • 1 comment

I'm working on a little feature for Circa. It's been over a month since I really coded with all the other startup things like marketing and "strategic thinking" taking up my brain space, so it's really nice just to sit down and code a little algorithm and some SVG paths for overlap-avoiding text.

submitted 188 days ago • 2 comments

I found 80 terabytes of uncompressed genomics files in public S3 buckets on 42basepairs 😯 That's thousands of dollars a month in additional storage and egress costs 💸

submitted 188 days ago • 1 comment

Spread-gl: visualising pathogen dispersal in a high-performance browser application https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae721/7914009 🧬🖥️🧪 https://github.com/GuyBaele/SpreadGL

submitted 189 days ago • 0 comments

“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯 www.statnews.com/sponsor/2024...

submitted 195 days ago • 3 comments

Hi All! I created a new feed for all things Omics! Get your posts on it by including a 🧬 + any other omics related emoji - 🧪🧫🔬☣️🖥️💉💊 (I'll be lightly curating this feed - like to remove porn, etc) bsky.app/profile/did:...

submitted 197 days ago • 3 comments

I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬 42basepairs.com/tools/sequen...

submitted 201 days ago • 1 comment

A great post on "How to generate SAM/BAM records and files for testing with SamBuilder" written by Alison Meynert. It's part of how we rigorously and programmatically test our #bioinformatics #genomics tools @fulcrumgenomics.bsky.social! fulcrumgenomics.com/2024-11-test...

submitted 203 days ago • 1 comment

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included. go.bsky.app/QVPoZXp

submitted 204 days ago • 81 comments

🧬 🖥️ This was a fun one to make: We reviewed 10 CVs sent in by our audience, and here are the 7 common mistakes we kept seeing: youtu.be/qXPJpnrfX_4

submitted 206 days ago • 0 comments

I wrote about the backstory of our recently published metagenomic profiler called sylph (www.nature.com/articles/s41...), partially to celebrate the new migration to bluesky Check out the blog here: jim-shaw-bluenote.github.io/blog/2024/de... -- and I apologize in advance for the lack of brevity :)

submitted 210 days ago • 1 comment