cd4-histone-paper-code
crux
cd4-histone-paper-code | crux | |
---|---|---|
1 | 1 | |
2 | 0 | |
- | - | |
10.0 | 0.0 | |
about 8 years ago | over 2 years ago | |
R | Cython | |
- | - |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
cd4-histone-paper-code
-
Ask HN: Should I publish my research code?
FWIW, this is how I've released the crappy barely-working "academic quality" code for a paper in the past:
https://github.com/DarwinAwardWinner/cd4-histone-paper-code
The main points are that I made only a minimal attempt to organize it, and I made the state of the code clear in the README. I don't recall anyone complaining about the code or even mentioning it during review. (I also don't recall whether I published the code before or after the paper was accepted.)
crux
-
Ask HN: Should I publish my research code?
Been there, done that. I published my doctoral research code [1] so that others could inspect, verify, replicate, extend, etc. YMMV, but the feedback I received from other researchers ranged from neutral to surprisingly positive (e.g. people using it in ways that pleasantly surprised me). But let me expand on my own experiences while developing that software, trying to figure out how to replicate the then-current state of the art.
At the time there were two widely used software packages for phylogenetic inference, PAUP* [2] and MrBayes [3]. The source code for MrBayes was available, and although at the time I had some pretty strong criticisms of the code structure, it was immensely valuable to my research, and I remain very grateful to its author for sharing the code. In contrast the PAUP* source was not available, and I struggled immensely to replicate some of its algorithms. As a case in point, I needed to compute the natural log of the gamma function with similar precision, but there was no documentation for how PAUP* did this. I eventually discovered that the PAUP* author had shared some of the low-level code with another project. Based on comments in that code I pulled the original references from the 60s literature and solved these problems that had plagued me for months in a matter of days. Now, from what I could see in that shared PAUP* code, I suspect that the PAUP* code is of very high quality. But the author significantly reduced his scientific impact by keeping the source to himself.
[1]: https://github.com/canonware/crux
What are some alternatives?
superconductor - A tool to simulate superconducting circuits, comparable to SPICE.
python-qubit-setup - All scripts for controlling the instruments and acquiring data in our qubit setup.
3d-reorganization-prostate-cancer - Code, analysis, and results for Hawley, Zhou, et al., Cancer Research, 2021.
3d-reorganization-prostate-canc
pyview - pyview contains all reusable and generic classes and functions that I used in my qubit data acquisition setup during my PhD thesis.
minion
demystify
vole - A GAP package for backtrack search in permutation groups with graphs