I'm proud to be a part of building this survey. If you're in the life sciences, please help us understand what publicly available tools and datasets are most important for your work! www.surveymonkey.com/r/BioITPubli...

Anybody else going to #ASGCT this year?

Off to BCBB tonight to watch @johnhutchinson.bsky.social give a lightning talk. Hope to see all of you bioinformatics nerds there!

I spent my early career on open-source software for science. Come meet me at BioIT World in Boston's Seaport today for a pop-up meeting about free/open scientific software and data resources.

Is this it? www.ravelry.com/patterns/lib...

I am currently using all of my mental cycles to consider how this applies outside of the arts. Because it clearly does.

Hope to see you all in Seaport on March 20!

Beyond thrilled that @maddow.msnbc.com used my pictures this evening. I hope it helps.

The protest downtown today was well attended. Big thanks to everybody who showed up on a chilly day. 1/?

This excellent interactive tutorial on misleading data visualizations explores the idea of a "counter chart" — the graph you draw in response to refute a misleading claims flowingdata.com/projects/dis...

Just did this to my Senator in as Southern an accent as I could dredge up.

I’m putting together a post on what’s going on in the trenches in various parts of the NIH. Anyone who would like to share experiences (anonymously!) can reach me at Dblowe.18 on Signal

Yes! Folks, spread the word. You can buy ebooks from indie bookstores now at bookshop.org!

Writing the last bit of a new novel and I came up with what I think is an excellent putdown: "he was two birds short of a turducken" #amwriting

Anybody trying to market to me should understand that I am extremely aggressive with the "report spam and block" buttons. The best way to make me never hear from you again is to send me unsolicited email.

It is cold season here in the States, and also the Holiday season. For both reasons, you need to know that there is such a thing as a portable sauna. It's a little one-person pop-up tent with a steamer attachment.

If I can tell that your AI assistant is reading and (incorrectly) responding to my emails, I will supplement future messages with long, derailing passages from The Lord of the Rings or The Stand.

Naomi Kritzer has elevated the snarky gift guide to an art form.

Definitely not just a problem for academics!

It was lovely to catch up with all of my friends and colleagues at the @westorg.bsky.social Women on Wednesdays social. Their Bsky account is new, but you should follow them if you want notification of their excellent programming! Job hunters: there are some great events coming up!

I'm getting lots of inquiries these days about finding a compbio job. This is the worst job market I've seen or heard of, and possibly the worst market since Bioinformatics became a field of its own.

The thing that really solidifies the migration to Bluesky for me is the fact that @rikergoogling.bsky.social is here.

Happy Thanksgiving, everybody. I've got 15 people descending on my house today, and we are going to have a blast.

A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.

People keep talking about how great Bluesky's blocking features are. I haven't even needed them. Maybe if I put my pronouns in my bio...

An excellent post on how biotech companies really work. entrepreneurshipinbiotechnology.substack.com/p/dont-make-... Hat tip to @gilman.bsky.social for the link.

Haters complaining about Bluesky reminds me of the time a random dude in a gym locker room was griping loudly about women refusing to take off their headphones and interact with him, no matter how much he pestered. Eventually another guy was like, ‘bro, shut up, we don’t want to hear it either.’

www.anthropic.com/research/sta... This is an excellent attempt (blog & paper) at bringing more statistical rigor to evaluation of ML models (this is specifically focused on LLM evals). I feel like we need to have similar clear standards for many types of predictive models in biology. 1/

Time to to pick one of three parallel sessions to attend. For now, I'm going with Cancer Targeted Therapies, session II. I'm going to thread all of these together. Before lunch we've got six 15 minute-talks, with 5 minutes for questions.

Now, a sponsored talk from AcroCyte. I do appreciate when the CEO will get up and speak, scientist-to-scientist, with the audience. These folks do three-dimensional cell culture, developed in the CEO's Stanford lab. There are some cool videos of sphereoids growing. www.acrocyte.com

Just a reminder, I'm live-posting talks from the 2024 Cancer R&D conference, ongoing in Newton, MA right now. cancer.unitedscientificgroup.org

William Douglas is asking not to share his presentation, since it's unpublished data, so I'm going to take a break.

Now we have Stanley P Leong from UCSF. Cancer Metastasis Through the Lymphovascular System Leong starts out with a slide about cancer being driven by mutational and epigenetic changes, and an acknowledgement of the chemical changes described by Xu, just now.

Good morning everyone, I'm back to live-posting the Cancer Research Conference, held in Newton, MA. Our first talk is from Ying Xu, of Southern University of Science and Technology, China

Last talk, Hui Shen, Professor at the Van Andel institute. Very excited to hear about single cell methods in ovarian cancer!

Ok, last session of the day opens with Haihui Lu, from NIBR: Empowering T-cell engagers with novel designs. These antibodies can treat cancer by directing T cells to target cancer cells. T cells do this on their own in normal situations, but cancers have several ways to avoid T cells.

Can I just tell you all that the post-covid conference era is so much better than it used to be? I can attend this great conference, while sick, from my house and 1) have as much chicken soup as I want, 2) live-post some fascinating talks, and 2) not be Typhoid Eleanor. Everybody wins.

Eytin Ruppin, from NCI. Classifying tumors and predicting patient response from the pathology slides. He has a super modest goal of putting sequencing companies out of business, by demonstrating that you can use H&E stained slides to stratify patients to treatment and predict response.

Thomas Look, from Dana Farber is up next, talking about epigenetic inhibitors driving differentiation of developmental cancers. Thomas studies neuroblastoma, which is a horrible childhood cancer.

Now, Andreas Califano, from Columbio University, NY. I'm rejoining a little late after relocating my sick self home, so I'm afraid I missed a bit of his talk. We're targeting master tumor regulators with Andreas today!

Now, Raghu Kalluri, from UT MD Anderson Cancer Center. Raghu decided he wanted to study what he describes "cancer without disease". That is, these folks who have what look like cancerous lesions but no malignant progression.

Next up, Sangeeta Bhatia! Sangeeta is at the Whitehead. She's speaking on Nanotechnology for Diagnostic and Therapeutics. Nanotechnology can tell us about the size and shape-dependent localization and cell internalization of materials. These materials can "talk" to biology.

Next up for speakers, JohnQ, aka @johnquackenbush.bsky.social. John was my boss and PhD coadvisor. His talk is focusing on networks and biological complexity.

Shirley Liu, speaker at the Cancer R&D Conference in MA today. Describing using TRUST to scan for novel antibody sequences from RNAseq data. This stuff is normally tossed out early in analysis because it doesn't map to any reference genome!

If you’re making a starter pack, take a quick look at its demographics. Worth a bit of consideration!

Planning to attend the Cancer R&D Conference in Newton, MA next week. Anyone else? @johnquackenbush.bsky.social I know you're speaking! The talks look great, and I'm looking forward to catching up with people in between.

Just got home from the BCBB meetup. I love that community. Thank you to everyone who attended, the BCBB organizers, and Portico Brewing in Somerville!

Hope to see you all at BCBB this evening, 6-8, Portico in Somerville.