ApostleMatthew

I’ve totally fallen for Directory Opus. Most powerful file manager I’ve ever used, and I’ve only used a fraction of its features.

Statistical mechanics/Biophysics:

Introduction to Modern Statistical Mechanics - David Chandler

Physical Biology of the Cell - Phillips, Kondev, Theriot, & Garcia

Interesting. I, for some reason, was unaware that the benchmarks were user sourced. It appears to mainly be a system for bash scripts to run the program and then automatically format the results, is that correct? There's a benchmark for LAMMPS, but it'd be interesting to get one up for Gromacs or CHARMM.

It’s much the same reason why you wouldn’t go to work wearing a days old, stained shirt and ripped pants — yeah, you’re more than likely going to work just as hard and as well than if you were wearing clean clothes, but that’s not going to stop people from judging you based on your appearance.

Most academics write code to just work. Not work well, or to be generalized, or to be efficient, just work. And while that’s absolutely fine, as your results being reproducible from the code is all that really matters, a lot of people don’t see it that way and will only see code slapped together haphazardly and dismiss you because of it.

Embarrassed by its cobbled-togetherness. Not in whether or not it works.

Oh, I meant making the error in the code fell under the we all make mistakes. Not the refusing to share it.

I wish tech review sites would do a molecular dynamics benchmark for processors like these. It's pretty easy to set up just a simple MD simulation, and there'd be tens of us interested in seeing the results.

I think your first paragraph is a result of you viewing this from the perspective of someone knowledgeable about technology. The vast majority of people using Android phones get their apps exclusively from the Play Store and assume Android is exactly the same as iOS in that way.

In my case, it is very much column A.

My PhD adviser was a good friend of Chandler's, and a lot of my doctoral work was based on previous work done in his lab. I'm honestly really surprised one of his students/post-docs made a mistake of this magnitude -- generating a velocity distribution which does not follow the Boltzmann distribution is not something I'd expect to be a result of code coming from his lab. But we all make mistakes, and this really just lends more weight to the idea that all code used in producing published results should be posted along with the article itself, just like data sets often are (at least from studies with government funding).

Wow. I haven't seen the sequel yet (unfortunately), but the differences is incredibly striking.

In my field (computational biophysics), it's pretty common practice to post published code on a git repository. Code used to produce published results absolutely should be accessible.

It's a (fairly) standardized, robust, and trusted way of peer-reviewing data and results. Without some mechanism like that, there's no easy way to tell if Dr. X's results are as well peer-reviewed as Dr. Y's, at least as it currently stands.