28

The SIAM Journals, especially SISC (Scientific Computing) and MMS (Multiscale Modeling and Simulation) are obvious established and high-quality choices.


17

Well, I think you have a few options. If you have a stable page—such as one sponsored by a university or other non-profit institution that's unlikely to vanish anytime soon—you could publish there. You could use a service like Github or Bitbucket or SourceForge to distribute the code. If the code is of marginal general value (it's an analysis code for a ...


17

In rough order of importance. Source Code Make the code that implements the key aspects of your algorithm available. Even if the user can't build or run it, they can read exactly what is done. I have several times noticed simple decisions that weren't documented in a paper, but which a couple minutes with the source code answered conclusively. Make it ...


14

I personally have come the way from Gnuplot to Matplotlib with PGFPlots as an intermediate step. I will try to name all aspects of Matplotlib that I like. It is very versatile. You are not limited to line or scatter plots, you can easily do bar plots, images (matrix visualization!), basic 3D plotting and even some animation. You can use Matplotlib as a GUI ...


13

I don't think that the definition of "reproducible research" requires that the author provide for free all of the tools that are needed to reproduce the results obtained. If some of it is proprietary, then it is incumbent on the future user, not the author, to make the arrangements to acquire the needed software. (You wouldn't expect to have to build the ...


11

In no particular order, I'll add more as I think of them. SIAM Journal on Scientific Computing Journal of Scientific Computing Journal of Computational Physics Computer Methods in Applied Mechanics and Engineering International Journal of Numerical Methods in Engineering AIAA conference proceedings Transactions on Mathematical Software Computers and ...


11

The boycott of Elsevier should not be mistaken as a push for open access journals. The phrase "open access" does not appear in any of the reasons given for the boycott at http://thecostofknowledge.com. Rather, the reasons are: High prices Bundling Elsevier's support for SOPA and similar efforts Note that many open access journals run by commercial ...


10

This is not an answer to your question. But if a student came to me asking this question, I would ask him or her to read these articles: You and your research (Hamming) How to choose a good scientific problem (Alon) And a warning: jumping into a "hot" subfield as a student is very dangerous if your advisor is not at the front of that subfield. You're ...


10

The best way to do this to avoid these issues is to publish a paper about what your software package does and the problems it solves and cite your Github repo or website or whatever for access to the software. That way you don't need to give up your copyright on your code, and you can BSD/MIT/GPL it to your heart's content.


9

A listing of all journals that publish papers on numerical solution of PDEs would be quite long, and it would be impossible for any one person to keep up with the entirety of the subject. But if you want to stick to journals that Are highly regarded Include fairly general classes of PDEs (as opposed to only PDEs in some scientific field) then I would ...


9

Physical Review E http://pre.aps.org/about Physical Review E (PRE), interdisciplinary in scope, focuses on many-body phenomena, including recent developments in quantum and classical chaos and soft matter physics. It has sections on statistical physics, equilibrium and transport properties of fluids, liquid crystals, complex fluids, polymers, chaos, fluid ...


9

In addition to all that Bill Barth has already said above, let me mention that people often report the fastest of several runs. The rationale is that the actual run time is the ideal run time plus any number of slow downs resulting from other processes running, OS delays, network delays, etc. Since these are all noise we are not interested in, using the ...


8

Great question and great replies, but I think none addresses the question of persistence adequately, if the goal is to achieve the same standard accorded to the publication itself. (Which may be silly given the chances the code still runs, but may still be at least as useful as the publication all the same). University websites journal supplements aren't ...


8

In an ideal world, you would only consider one thing when choosing where to submit a manuscript: which journal's readership includes the broadest audience that would be interested in this work? In practice, you also consider other factors, perhaps most significantly How much will publishing in this journal help my career? Anyone who can understand ...


8

the planned longevity of TeX comes to mind: “Ever since those beginnings in 1977, the TeX research project that I embarked on was driven by two major goals. The first goal was quality: we wanted to produce documents that were not just nice, but actually the best. (…) The second major goal was archival: to create systems that would be independent of ...


8

You're looking at the wrong metric. In most areas of science, people don't write code at all but still get their papers published. The same is true for more theoretical papers in numerical analysis, proving for example the convergence of a particular scheme. On the other hand, there are papers that discuss particular libraries or implementations. These ...


7

It looks like you're already using some of the concepts from Corwin, Leiserson, Rivest, and Stein, which I've always seen as the "default" introductory text for algorithms, in writing your pseudocode. I don't think there's any more standard reference for pseudocode. However, I would argue that what makes a good pseudocode is to break the problem down into ...


7

A few thoughts on your question: How you report your model fit will depend very much on your audience, and your field. For example, in my field, model fit statistics like R^2 are very rarely reported - regarded as neither impressive nor particularly useful. Instead, some criteria for how you arrived at the model you arrived at tends to be described, and ...


7

I think there are several alternatives, but to some extent, it may depend upon the field. For fluid mechanics, there's obviously J. Fluid Mech.. For many areas in microscopic physics, you could send your work to J. Chem. Phys.


7

I oftem use Matlab and then save the result as an eps file via print -depsc2 -f1 fig. This saves figure 1 as an eps file named fig.eps. There is also the Plot2Svg from matlab file exchange that can save as svg. This is really nice since you can then open the files in Inkscape or other vector graphics software and edit them. If you are willing to learn new ...


7

If you're willing to overcome the learning curve of Gnuplot, you can generate top-quality figures with it (as exemplified in http://www.gnuplotting.org/). In particular, I'd recommend using the epslatex terminal as it allows you to use LaTeX to render all the text in the figure (including any mathematical notation that you may wish to input). If you want ...


7

First, an attempt to just answer the question. My (personal and subjective) feeling is that many jobs and funding opportunities right now are tied to applications in biology and energy, and that the hot research topics are in "multi-scale" and "multi-physics" phenomena, as well as uncertainty quantification. However, in your case you need to know what will ...


6

Most journals aren't set up for this in any formal way, but we've recently founded the Archive of Numerical Software that is specifically intended to have the source code and everything else that's necessary be part of the article. Check it out: http://journals.tdl.org/ans Submissions are welcome!


6

Total running time (wall clock) is the only metric that matters in industry or real life applications: this figure should never be omitted, even if embarrassing. Of course this metric is very dependent on the test environment, so this should be described in detail. All other metrics can (or should be) reported if they provide insight into the problem, or ...


5

What factors determine where I will publish a paper? Will the people I want to read this paper see it? If I'm following up on the work of another group (perhaps to show a different viewpoint, sometimes to show algorithmic improvements or to fix problems with a previous paper), I will want to submit the paper to the same journal, even if there's an impact ...


5

It really depends on how much you believe in journal ratings. The most popular metric I am aware of is the impact factor. This Wikipedia article describes the impact factor, how it is calculated, and how it is susceptible to manipulation, as well as alternative journal rating metrics. The most important thing worth noting is that impact factors for journals ...


5

There are some other application-specific journals to list: such as Journal of Computational Physics or Computer Physics Communications, that accept articles both about algorithms as well as the software used to implement them. If you're in the chemistry field, Journal of Chemical Theory and Computation might be another journal to consider. All of these do ...


5

You're trying to fit a power law to your distribution. Very interesting. These show up all the time in graph theory, social networks, and a slew of other places. There's some tutorials on fitting your data here and here. Also, in reference to question A., how does the probability of a person buying land depend on how much land they already have? You may be ...


5

Along the same lines as aeismail's answer, International Journal of Numerical Methods in Engineering, and International Journal of Numerical Methods in Fluids could be candidate journals for papers that would otherwise go into Journal of Computational Physics. (These journals are both Wiley journals.)


5

The short answer is: it depends. Some journals have a requirement or a guideline to have experimental results that corroborate the numerical simulations. For example, IEEE Transactions on Microwave Theory and Techniques rarely publishes papers that do not have experimental results in one form or another. However, this is very different for IEEE Transactions ...


Only top voted, non community-wiki answers of a minimum length are eligible