Fantastic comic / video by Jorge Cham on Open Access over at PhD Comics:
www.phdcomics.com/comics.php?f=1533
The voices behind the video are Jonathan Eisen and Nick Shockey (director of the Right to Research Coalition), and the discussion covers the insanity of the closed-wall access to publicly-funded research as well as the importance of re-use towards discovery.
Adobe released an open source font today called Source Sans Pro. It looks super clean and nearly perfect for user interfaces. Right now it comes in six weights, but a monowidth version is coming soon. (I’m most excited about this, as the sample of the monowidth font on the Adobe blog post is gorgeous). Adobe did this right – they have made all source files used in the production of the fonts available for download at SourceForge.
Maybe we’ll get more scientists using Source Sans Pro instead of releasing their important results in Comic Sans.
Two new collections of tools that may be of interest to the OpenScience community. Not everything on these lists is Open Source, but many of the visualization and research tools look to be very useful. Hat tip to Eric Lease Morgan (@ericleasemorgan) for pointing these out:
Pyofss allows optical component modules to be grouped together into a system. An optical field is propagated through the system and the evolution of the field viewed at each module. Fibre effects include attenuation, dispersion, self-phase modulation, self-steepening, and Raman scattering. There are many examples available demonstrating use of the program. A variety of ODE integration solvers are available along with a range of split-step methods, including the Runge-Kutta in the interaction picture method.
Find pyofss – Python-based optical fibre system simulator at: http://curvedthoughts.com/pyofss/
QuTiP is open-source software for simulating the dynamics of open quantum systems. The QuTiP library depends on the excellent Numpy and Scipy numerical packages. In addition, graphical output is provided by Matplotlib. QuTiP aims to provide user-friendly and efficient numerical simulations of a wide variety of Hamiltonians, including those with arbitrary time-dependence, commonly found in a wide range of physics applications such as quantum optics, trapped ions, superconducting circuits, and quantum nanomechanical resonators. QuTiP is freely available for use and/or modification on all Unix based platforms such as Linux and Mac OSX. Being free of any licensing fees, QuTiP is ideal for exploring quantum mechanics and dynamics in the classroom.
Find QuTiP: Quantum Toolbox in Python at: http://code.google.com/p/qutip/
Molekel is an open-source multi-platform molecular visualization program.
Find Molekel at: http://molekel.cscs.ch/wiki/pmwiki.php
NMR processing software using the Qt framework. Currently only 1D.
Find cuteNMR at: http://cutenmr.sourceforge.net/
rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.
Find rNMR at: http://rnmr.nmrfam.wisc.edu/
XDAT (x-dimensional data analysis tool) reads column-based data in text / csv format and plots it using parallel coordinates. It is written in Java and released under the GPL.
Find XDAT: A Tool to plot Parallel Coordinates at: http://www.xdat.org/
Computational Chemistry Highlights (CCH) is an interesting new overlay journal that identifies important contributions to the field of computational and theoretical chemistry published within the last 1-2 years. I’m involved in this particular overlay journal – I’ll be concentrating on recent developments and papers in molecular dynamics and statistical mechanics. The journal will eventually get to an editorial board of around 50, so it will help us all keep up on advances in the field that are outside our specific areas of expertise.
Overlay journals are a great concept – CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. In addition to highlighting recently-published papers, I’m pretty sure it will also include highlights of non-journal resources like code, publicly available datasets, and papers available on preprint servers (e.g. arXiv, Nature Precedings). It also allows non-anonymous comments on papers and will let authors respond to those comments.
Overlay journals are an interesting experiment. We’ll have to see how important they become, but I’m pretty happy to be included early on this one.
