blog.khinsen.net
Composition is the root of all evil
http://blog.khinsen.net/posts/2016/03/04/composition-is-the-root-of-all-evil
Composition is the root of all evil. Composing information is something we all do every day, mostly without thinking of it. A shopping list is the composition of names of things you need to buy. An e-mail message is the composition of the recipients’ addresses, a subject line, and the body of the message. An address book is a composition of addresses, which in turn are compositions of various pieces of information related to some person. When you look at these examples more closely, you might notice that...
blog.khinsen.net
From facts to narratives
http://blog.khinsen.net/posts/2015/12/08/from-facts-to-narratives
From facts to narratives. A computational notebook, as pioneered by Mathematica. And recently popularized by Jupyter. Inverts this relation by embedding the code into a narrative. Computers are good at handling facts but not narratives. Humans are good at handling narratives but not facts in the quantities that typically define a computation. Letting computers intervene in the processing of narratives leads to funny results - try Google Translate. On HDF5 and the future of data management. This blog star...
blog.khinsen.net
A rant about software deployment in 2015
http://blog.khinsen.net/posts/2015/11/06/a-rant-about-software-deployment-in-2015
A rant about software deployment in 2015. The software that I installed is nMOLDYN. An analysis tool for Molecular Dynamics trajectories. From a software engineering point of view, this is a rather standard Python program building on NumPy. For its computations and on Tkinter. For the graphical user interface. There is no need for anything on the bleeding edge, a decent three-year old installation of the scientific Python stack would support this perfectly well. And copy data in and out using. Of all the...
blog.khinsen.net
Posts tagged 'scientific computing'
http://blog.khinsen.net/tags/scientific-computing.html
Composition is the root of all evil. Hellip; more …. On HDF5 and the future of data management. Yesterday a blog post. By Cyrille Rossant entitled “Moving away from HDF5” caught my eye. My own tendency at the moment is to use HDF5 more and more, so I was interested in why someone else would want to do the opposite. Here is my conclusion after reading his post, plus some ideas about where scientific data management is or should be heading in my opinion. Hellip; more …. Hellip; more ….
blog.khinsen.net
The lifecycle of digital scientific knowledge
http://blog.khinsen.net/posts/2015/11/09/the-lifecycle-of-digital-scientific-knowledge
The lifecycle of digital scientific knowledge. For climate research, which takes the form of a software package. Most often, the status of computational models is more fuzzy. As an example, consider force fields for proteins such as AMBER. Which authoring tools are available to support such work? From facts to narratives. A rant about software deployment in 2015. This blog starts in November 2015. For older posts, see my old WordPress blog.
blog.khinsen.net
Posts tagged 'computational science'
http://blog.khinsen.net/tags/computational-science.html
Composition is the root of all evil. Hellip; more …. From facts to narratives. Hellip; more …. The lifecycle of digital scientific knowledge. Hellip; more …. This blog starts in November 2015. For older posts, see my old WordPress blog.
blog.khinsen.net
On HDF5 and the future of data management
http://blog.khinsen.net/posts/2016/01/07/on-hdf5-and-the-future-of-data-management
On HDF5 and the future of data management. Yesterday a blog post. By Cyrille Rossant entitled “Moving away from HDF5” caught my eye. My own tendency at the moment is to use HDF5 more and more, so I was interested in why someone else would want to do the opposite. Here is my conclusion after reading his post, plus some ideas about where scientific data management is or should be heading in my opinion. The peculiar combination of requirements that to the best of my knowledge only HDF5 fulfills is:. For job...
blog.khinsen.net
Konrad Hinsen's Blog
http://blog.khinsen.net/index.html
Reproducibility does not imply reproduction. In discussions about computational reproducibility (or replicability, or repeatability, according to the preference of each author), I often see the argument that reproducing computations may not be worth the investment in terms of human effort and computational resources. I think this argument misses the point of computational reproducibility. Hellip; more …. Sustainable software and reproducible research: dealing with software collapse. Hellip; more …. The l...
blog.khinsen.net
Posts tagged 'python'
http://blog.khinsen.net/tags/python.html
A rant about software deployment in 2015. Hellip; more …. This blog starts in November 2015. For older posts, see my old WordPress blog.
SOCIAL ENGAGEMENT