Jacob Cram
@cramjaco.bsky.social
Scientist studying marine microbial ecology and biogeochemistry
Reposted by Jacob Cram
Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...
Pull requests · hadley/genzplyr
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 8, 2025 at 12:29 AM
Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...
Reposted by Jacob Cram
What type of #microscopy would allow for watching real time cell division of an anaerobic bacterium (~1 x 0.5 um rod) at resolution high enough to view internal structure? Doubling time of ~2 days.
#MicroSky
#MicroSky
October 17, 2025 at 11:11 PM
What type of #microscopy would allow for watching real time cell division of an anaerobic bacterium (~1 x 0.5 um rod) at resolution high enough to view internal structure? Doubling time of ~2 days.
#MicroSky
#MicroSky
Reposted by Jacob Cram
Big news! We're hiring lots of new faculty here at the University of Virginia School of Data Science @uvadatascience.bsky.social! You can find all our postings here: datascience.virginia.edu/faculty-jobs
October 13, 2025 at 3:28 PM
Big news! We're hiring lots of new faculty here at the University of Virginia School of Data Science @uvadatascience.bsky.social! You can find all our postings here: datascience.virginia.edu/faculty-jobs
Reposted by Jacob Cram
DO NOT GIVE UP!
Our advocacy is working.
A key Senate committee has indicated that it will reject Trump’s proposed cuts to science agencies including NASA and the NSF.
Keep speaking up and calling your electeds 🗣️🗣️🗣️
Our advocacy is working.
A key Senate committee has indicated that it will reject Trump’s proposed cuts to science agencies including NASA and the NSF.
Keep speaking up and calling your electeds 🗣️🗣️🗣️
July 11, 2025 at 7:03 PM
DO NOT GIVE UP!
Our advocacy is working.
A key Senate committee has indicated that it will reject Trump’s proposed cuts to science agencies including NASA and the NSF.
Keep speaking up and calling your electeds 🗣️🗣️🗣️
Our advocacy is working.
A key Senate committee has indicated that it will reject Trump’s proposed cuts to science agencies including NASA and the NSF.
Keep speaking up and calling your electeds 🗣️🗣️🗣️
Reposted by Jacob Cram
Indiana Jones and the Concur Travel Reimbursement System
July 2, 2025 at 10:21 PM
Indiana Jones and the Concur Travel Reimbursement System
Reposted by Jacob Cram
News from the NSF Division of Earth Sciences Informational Webinar: If US scientists want to support NSF EAR, they should continue to submit proposals. The number of proposals is an important metric for quantifying need and therefore influencing the budget
June 17, 2025 at 6:58 PM
News from the NSF Division of Earth Sciences Informational Webinar: If US scientists want to support NSF EAR, they should continue to submit proposals. The number of proposals is an important metric for quantifying need and therefore influencing the budget
Well shoot. This foils my system/hack of having an accessible preprint version of every one of my closed source papers.
Worth reading in full. Many important implications here:
* Wiley can only publish preprinted papers if final version differs substantially from preprint
* After peer review, preprints are no longer preprints (careful with resubmissions!)
* Wiley will change journal policies without consulting EiC
* Wiley can only publish preprinted papers if final version differs substantially from preprint
* After peer review, preprints are no longer preprints (careful with resubmissions!)
* Wiley will change journal policies without consulting EiC
June 17, 2025 at 12:24 PM
Well shoot. This foils my system/hack of having an accessible preprint version of every one of my closed source papers.
Reposted by Jacob Cram
Python for R users blog.stephenturner.us/p/python-for... #rstats
Python for R users
A Google search for “R vs Python” returns thousands of hits across sites like Reddit, IBM, Datacamp, Coursera, Kaggle, and many others.
blog.stephenturner.us
October 21, 2024 at 10:06 AM
Python for R users blog.stephenturner.us/p/python-for... #rstats
Reposted by Jacob Cram
Joining the race to the bottom has never been cooler...
www.biorxiv.org/node/4580343...
www.biorxiv.org/content/10.1...
www.biorxiv.org/node/4580343...
www.biorxiv.org/content/10.1...
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome...
www.biorxiv.org
May 25, 2025 at 2:48 PM
Joining the race to the bottom has never been cooler...
www.biorxiv.org/node/4580343...
www.biorxiv.org/content/10.1...
www.biorxiv.org/node/4580343...
www.biorxiv.org/content/10.1...
Reposted by Jacob Cram
(Longish thread. Apologies)
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
June 8, 2025 at 6:53 PM
(Longish thread. Apologies)
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
Reposted by Jacob Cram
Are all muppets the same species just with wildly different phenotypes like dogs or are there a lot of different species of muppet
June 3, 2025 at 12:20 AM
Are all muppets the same species just with wildly different phenotypes like dogs or are there a lot of different species of muppet
Reposted by Jacob Cram
by carefully mixing 10% cream with 1% skim milk, you can unlock forbidden milk percentages the government doesn't want you to know about, like 7.725%
June 1, 2025 at 12:27 PM
by carefully mixing 10% cream with 1% skim milk, you can unlock forbidden milk percentages the government doesn't want you to know about, like 7.725%
Reposted by Jacob Cram
the INCREDIBLE self-restraint, sustained across DECADES, that's kept anyone from slipping "calendar-makers day, the day when you high-five a maker of calendars" into their calendars
qwantz.com/index.php?co...
qwantz.com/index.php?co...
May 23, 2025 at 1:06 PM
the INCREDIBLE self-restraint, sustained across DECADES, that's kept anyone from slipping "calendar-makers day, the day when you high-five a maker of calendars" into their calendars
qwantz.com/index.php?co...
qwantz.com/index.php?co...
Reposted by Jacob Cram
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...
arxiv.org
May 19, 2025 at 7:40 PM
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Reposted by Jacob Cram
Important piece from a voice outside the biomedical research space amplifying a view in accessible terms into political deal-making corridors that need to raise the alarm...
A Path Forward to Save American Bio-Medical Research talkingpointsmemo.com/edblog/a-pat...
A Path Forward to Save American Bio-Medical Research
Over the past four months I’ve spoken to dozens of biomedical researchers...
talkingpointsmemo.com
May 16, 2025 at 9:08 PM
Important piece from a voice outside the biomedical research space amplifying a view in accessible terms into political deal-making corridors that need to raise the alarm...
Reposted by Jacob Cram
Still struggling with closure here. Trycycler, unicycler, raven all resolve to 2 large linear contigs ~ 3.5 Mbp and 1.3 Mbp. High GC (70%). GC skew does not look like a typical circular chromosome. It's not a streptomyces, but should I be thinking of linear chromosomes? How would I identify this?
We have a hybrid illumina + #nanopore assembly of a culture that resolved into 2 contigs.
We're looking for the best way to close the genome. More long read (the DNA was more fragmented than ideal)? Or develop primers at the contig ends and do PCR? Other options?
We're looking for the best way to close the genome. More long read (the DNA was more fragmented than ideal)? Or develop primers at the contig ends and do PCR? Other options?
May 12, 2025 at 6:23 PM
Still struggling with closure here. Trycycler, unicycler, raven all resolve to 2 large linear contigs ~ 3.5 Mbp and 1.3 Mbp. High GC (70%). GC skew does not look like a typical circular chromosome. It's not a streptomyces, but should I be thinking of linear chromosomes? How would I identify this?
Reposted by Jacob Cram
Exploring themes in {ggplot2}? 🎨 Check out: bit.ly/4d9jtbH
It lets you preview different themes before adding them to your code - so handy for picking the perfect vibe! ✨
It features packages like:
🖌️ {ggthemr}
🌙 {ggdark}
👩🏽🔬 {ggtech}
⚙️ Setting an active theme globally
#RStats #ggplot2 #DataViz
It lets you preview different themes before adding them to your code - so handy for picking the perfect vibe! ✨
It features packages like:
🖌️ {ggthemr}
🌙 {ggdark}
👩🏽🔬 {ggtech}
⚙️ Setting an active theme globally
#RStats #ggplot2 #DataViz
May 9, 2025 at 8:46 AM
Exploring themes in {ggplot2}? 🎨 Check out: bit.ly/4d9jtbH
It lets you preview different themes before adding them to your code - so handy for picking the perfect vibe! ✨
It features packages like:
🖌️ {ggthemr}
🌙 {ggdark}
👩🏽🔬 {ggtech}
⚙️ Setting an active theme globally
#RStats #ggplot2 #DataViz
It lets you preview different themes before adding them to your code - so handy for picking the perfect vibe! ✨
It features packages like:
🖌️ {ggthemr}
🌙 {ggdark}
👩🏽🔬 {ggtech}
⚙️ Setting an active theme globally
#RStats #ggplot2 #DataViz
Reposted by Jacob Cram
Long read sequencing experts: what lysis method would you recommend for skin punch samples? (To be followed by phenol/chloroform extraction) In this case they are whale skin punches but I'll take any recs.
May 8, 2025 at 12:17 AM
Long read sequencing experts: what lysis method would you recommend for skin punch samples? (To be followed by phenol/chloroform extraction) In this case they are whale skin punches but I'll take any recs.
Reposted by Jacob Cram
Excited to share our new mSphere paper describing ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida in mSphere led by Jean Lim - a 🧵(1/10) 🧪🦠🌊 #MicroSky #ProtistsOnSky #USFCMS @asm.org @cmarinescience.bsky.social journals.asm.org/doi/full/10....
April 20, 2025 at 3:52 PM
Excited to share our new mSphere paper describing ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida in mSphere led by Jean Lim - a 🧵(1/10) 🧪🦠🌊 #MicroSky #ProtistsOnSky #USFCMS @asm.org @cmarinescience.bsky.social journals.asm.org/doi/full/10....
Reposted by Jacob Cram
I have learned that some people have still not heard the Good News about Hamiltonian Monte Carlo. My gentle animated interactive explanation: elevanth.org/blog/2017/11...
Markov Chains: Why Walk When You Can Flow?
In 1989, Depeche Mode was popular, the first version of Microsoft Office was released, large demonstrations brought down the wall separating East and West Germany, and a group of statisticians in the ...
elevanth.org
April 18, 2025 at 9:09 AM
I have learned that some people have still not heard the Good News about Hamiltonian Monte Carlo. My gentle animated interactive explanation: elevanth.org/blog/2017/11...
Reposted by Jacob Cram
Alright I need to use this website for something that this website is actually good at: brainstorming examples of things in a category.
The category is: mechanisms of small-scale information delivery.
Examples:
Fortune cookies
Advent Calendars
Jokes on popsicle sticks
What else is there?
The category is: mechanisms of small-scale information delivery.
Examples:
Fortune cookies
Advent Calendars
Jokes on popsicle sticks
What else is there?
April 17, 2025 at 1:15 AM
Alright I need to use this website for something that this website is actually good at: brainstorming examples of things in a category.
The category is: mechanisms of small-scale information delivery.
Examples:
Fortune cookies
Advent Calendars
Jokes on popsicle sticks
What else is there?
The category is: mechanisms of small-scale information delivery.
Examples:
Fortune cookies
Advent Calendars
Jokes on popsicle sticks
What else is there?
I've been enjoying the dire wolf discussion on here but hadn't really seen the pro argument spelled out fully until this video. Apparently, Collosal identified 20 key functional differences between gray- and dire wolves, added those back into gray wolves to make essentially a"functional" direwolf.
A statement from Colossal's Chief Science Officer, my boss, Dr. Beth Shapiro, on the dire wolf project, addressing some of the world's concerns x.com/colossal/sta...
Colossal Biosciences® on X: "A statement from our Chief Science Officer, Dr. Beth Shapiro, on the dire wolf project https://t.co/upl3WPSeUw" / X
A statement from our Chief Science Officer, Dr. Beth Shapiro, on the dire wolf project https://t.co/upl3WPSeUw
x.com
April 11, 2025 at 11:57 AM
I've been enjoying the dire wolf discussion on here but hadn't really seen the pro argument spelled out fully until this video. Apparently, Collosal identified 20 key functional differences between gray- and dire wolves, added those back into gray wolves to make essentially a"functional" direwolf.
Reposted by Jacob Cram
I've been browsing random TV channels and it makes me think of when Rick was channel surfing on inter-dimensional cable on Rick and Morty.
It's so much fun!
It's so much fun!
This is fantastic! This website allows you to watch TV stations from around the world. I just watched 2 minutes of Afghan volleyball. All the small regional TV stations from Germany are here too. Spread the word! Source: tv.garden
March 29, 2025 at 1:02 PM
I've been browsing random TV channels and it makes me think of when Rick was channel surfing on inter-dimensional cable on Rick and Morty.
It's so much fun!
It's so much fun!
Reposted by Jacob Cram
In our latest blog post we discuss why "Shadow Mentors" are important in careers. I've been fortunate to have many—too many to list here.
Check it out below and please share with someone who might find it useful.
uncultured.carinilab.com/p/beyond-off...
Check it out below and please share with someone who might find it useful.
uncultured.carinilab.com/p/beyond-off...
Beyond Official Advisors: The Power of Shadow Mentors
Build a Cabinet of "Shadow Mentors"
uncultured.carinilab.com
March 29, 2025 at 1:24 PM
In our latest blog post we discuss why "Shadow Mentors" are important in careers. I've been fortunate to have many—too many to list here.
Check it out below and please share with someone who might find it useful.
uncultured.carinilab.com/p/beyond-off...
Check it out below and please share with someone who might find it useful.
uncultured.carinilab.com/p/beyond-off...
Reposted by Jacob Cram
Postdoc position available studying the biological carbon pump within Jan Taucher's team at GEOMAR
🌊
www.geomar.de/en/karriere/...
🌊
www.geomar.de/en/karriere/...
Postdoc (m/f/d) position in ocean biogeochemistry
www.geomar.de
March 24, 2025 at 9:58 PM
Postdoc position available studying the biological carbon pump within Jan Taucher's team at GEOMAR
🌊
www.geomar.de/en/karriere/...
🌊
www.geomar.de/en/karriere/...