iiinova — where your digital self keeps evolving

daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 21/02/2025

In the Federal government, almost all new hires (including most promotions) have a “probationary” period. IT HAS NOTHING TO DO WITH POOR PERFORMANCE! Anyone who says otherwise is lying.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 14/02/2025

Aside from the widespread personal misery that cutting probationary employees from the NIH is going to cause, it’s also going to set crucial research back by months or even years. Research/science and health are inextricably linked. Can someone please stop this!?

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 30/01/2025

This week has been the longest year ever 😩

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 22/01/2025

Over half of my tweets deleted now, from nine hundred something down to 450. It’s really a shame what the platform turned into. Some quality content has been lost forever.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 22/01/2025

So I don’t use that other site anymore and haven’t for a long time now, but I’ve finally started purging and deleting all my old tweets. Apparently that’s the best way since if you just delete your account someone can take your old handle.

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Reposted by @daniel-r-roe.bsky.social

Justin Lemkul @justinlemkulvt.bsky.social · 21/01/2025

We have a new #tutorial posted online, this time for Gaussian-accelerated MD as implemented in NAMD. Article has been submitted to LiveCoMS, a great venue for such efforts. We welcome feedback! Yes, it's alanine dipeptide, but you have to start somewhere :) #compchem github.com/Lemkul-Lab/g...

github.com

GitHub - Lemkul-Lab/gamd_livecoms_tutorial

Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 20/01/2025

“This is no time to engage in the luxury of cooling off or to take the tranquilizing drug of gradualism.” MLK’s “I Have a Dream” speech is full of incredible prose and ideas, and is well worth a reread today: www.npr.org/2010/01/18/1...

npr.org

Read Martin Luther King Jr.'s 'I Have a Dream' speech in its entirety

Americans across the U.S. are celebrating King's legacy this weekend. One way to reflect on his life and message is by revisiting his celebrated 1963 speech delivered at the Lincoln Memorial.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 20/01/2025

This is a worrisome time to be a Fed. All that I and my coworkers in the govt. want to do is our jobs to the best of our ability. Hopefully we will be allowed to do that over the next 4 years. 🤞

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Reposted by @daniel-r-roe.bsky.social

Dorothy Bishop @deevybee.bsky.social · 21/12/2024

Are @zbmed.bsky.social aware of the negative reaction on social media to their just-announced contract with MDPI. There's a great many red flags they seem to have missed, e.g. deevybee.blogspot.com/2024/08/gues... deevybee.blogspot.com/2024/02/the-... + @hansonmark@bsky.social's account below

deevybee.blogspot.com

My experience as a reviewer for MDPI

Guest post by René Aquarius, PhD Department of Neurosurgery Radboud University Medical Center, Nijmegen, The Ne...

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Christina Bergonzo 🧬 @cbergonz.bsky.social · 03/12/2024

Using SIRAH to coarse grain my glycosylayed antibody! Hooray for (1) tutorials that work, and (2) my first foray into CG! Can I join the #glycotime club?

A close up of an IgG1 Fc domain glycan (blue) and its attachment point (green)

An IgG1 antibody shown in secondary structure ribbon with coarse grained beads overlapping

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Reposted by @daniel-r-roe.bsky.social

Miranda-Quintana group @groupquintana.bsky.social · 05/12/2024

Tired of how slow hierarchical clustering is? Tired of finding optimum k values for k-means? We present eQual to you: biorxiv.org/content/10.1... the last member of the #MDANCE family, it bridges the gap between k-means and HAC. Thanks to @lexinc.bsky.social and @daniel-r-roe.bsky.social!

biorxiv.org

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 03/12/2024

No matter how experienced with computers I get, BIOS updates will always stress me out.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 01/12/2024

A great thread and an important read. All of the women scientists I know are extremely driven and talented, and often face barriers men simply don’t face. The scientific community as a whole will benefit if we can knock down these barriers and biases.

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Reposted by @daniel-r-roe.bsky.social

Fritz Roth @fritzroth.bsky.social · 20/11/2024

Calling all systems and computational biologists in search of a faculty position: We have Assistant and Associate Professor positions! 🚀 Pittsburgh is beautiful, and we are doing amazing science here. cfopitt.taleo.net/careersectio... cfopitt.taleo.net/careersectio... Please apply by Dec 2!

cfopitt.taleo.net

Faculty.Professor.Assistant - Full-Time

Click the link provided to see the complete job description.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 30/11/2024

The internet is amazing. I wanted to get the original (afaik) periodic boundary conditions paper, which was published in a long-defunct German journal in 1912. After some googling I found it in an archive at Princeton and am using google translate to read it. So awesome!

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Reposted by @daniel-r-roe.bsky.social

Alberto Perez @perezlab.bsky.social · 26/11/2024

We are looking for a #CompChem postdoc to implement MELD (Modeling Employing Limited Data) into the AMBER suite of programs and test new applications in integrative modeling. Work with @adrianroitberg.bsky.social and me at #UFChemistry! Apply here explore.jobs.ufl.edu/en-us/job/53...

explore.jobs.ufl.edu

University of Florida - Details - Post-Doctoral Associate in Computational Chemistry

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 27/11/2024

It feels like the barrier to starting a paper is so high, but once you get started it can be a lot of fun. It sparks lots of questions like “Oh yeah, why did I do that?” and “wait, why did I think this plot made sense?”

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 16/11/2024

Well this doesn’t seem right…#imagingfail

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Christina Bergonzo 🧬 @cbergonz.bsky.social · 15/11/2024

I do molecular dynamics simulations of biopharmaceutical molecules, both protein and nucleic acid (RNA 4ever). Here’s a link to a recent project, modXNA, which parameterizes any combo of base/sugar/bb nucleic acid modification for an MD sim: pubs.acs.org/doi/10.1021/...

pubs.acs.org

modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense olig...

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 15/11/2024

Just made my final post on that _other_ site, downloaded my archived data, and am getting ready to delete the account. Not much but it’s something.

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 14/11/2024

It’s that time of year again when all the hip new cold viruses are going around and your kids make sure that you are among the first to experience them 😩

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 13/11/2024

The Bluesky “starter pack” concept is a really awesome idea!

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 13/11/2024

For anyone else hitting the “Invalid handle” issue, this helped me solve it!

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Reposted by @daniel-r-roe.bsky.social

Justin Lemkul @justinlemkulvt.bsky.social · 12/11/2024

Come be my colleague (pt. 3, yes it's true)! Another non-TT instructional faculty position in our brand new Discovery Space! An amazing opportunity for hands-on, experiential learning with undergrads. #chemsky #academicsky @chemjobber.bsky.social careers.pageuppeople.com/968/cw/en-us...

careers.pageuppeople.com

Details | Collegiate Assistant Professor - Discovery Space | Careers | Division of Human Resources | Virginia Tech

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 10/11/2024

There’s nothing quite like the elation you feel when an idea you’ve coded up appears to work on the first try, followed by the suspicion that it can’t possibly be correct and there must be a bug, followed by worrying about every possible way it could fail. #myscientificprocess

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 09/11/2024

Hi all! I’m Dan, a computational chemist and scientific software dev. I also love music, reading, video/TT gaming, anime, history, and my wife and 2 kiddos. It’s nice to be back on a (so far) positive social media site!

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daniel-r-roe.bsky.social @daniel-r-roe.bsky.social · 09/11/2024

So far Bluesky is basically “Remember when twitter used to be good? Let’s do that again” and I’m here for it.

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