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Mozilla Programming Science

Mozilla Plan Seeks To Debug Scientific Code 115

Posted by Soulskill
from the unit-tests-are-for-undergrads dept.
ananyo writes "An offshoot of Mozilla is aiming to discover whether a review process could improve the quality of researcher-built software that is used in myriad fields today, ranging from ecology and biology to social science. In an experiment being run by the Mozilla Science Lab, software engineers have reviewed selected pieces of code from published papers in computational biology. The reviewers looked at snippets of code up to 200 lines long that were included in the papers and written in widely used programming languages, such as R, Python and Perl. The Mozilla engineers have discussed their findings with the papers’ authors, who can now choose what, if anything, to do with the markups — including whether to permit disclosure of the results. But some researchers say that having software reviewers looking over their shoulder might backfire. 'One worry I have is that, with reviews like this, scientists will be even more discouraged from publishing their code,' says biostatistician Roger Peng at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland. 'We need to get more code out there, not improve how it looks.'"
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Mozilla Plan Seeks To Debug Scientific Code

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  • by MrEricSir (398214) on Wednesday September 25, 2013 @12:40AM (#44944713) Homepage

    As we've seen recently, bad decisions can be made from errors in spreadsheets. We need these published so they can be double-checked as well.

  • Re:Wrong objective. (Score:4, Informative)

    by Anonymous Coward on Wednesday September 25, 2013 @12:54AM (#44944775)

    The problem is most papers do not publish the code, only the results. This causes dozens of problems: if you want to run their code on a different instance you can't, if you want to run it on different hardware you can't, if you want to compare it with yours you only sort of can since you have to either reimplement their code or run yours on a different environment than theirs, which makes comparisons difficult. Oh, and it makes verifying the results even more worse, but it isn't like many people try to verify anything.

    On the one hand catching bugs can help find a conclusion was wrong sooner than it would happen otherwise. On the other hand it may make it less likely that authors will put their code out there. Anyhow, I think it's a good idea and worth a shot. Who knows, maybe it'll end up helping a lot.

  • by Anonymous Coward on Wednesday September 25, 2013 @07:09AM (#44946213)

    People doing scientific research and software developers are really doing very different things when they write code. For software developers or software engineers, the code is the end goal. They are building a product that they are going to give to others. It should be intuitive to use, robust, produce clear error messages, and be free of bugs and crashes. The code is the product. For someone doing scientific or engineering research, the end goal is the testing an idea, or running an experiment. The code is a means to an end, not the end itself; it needs only to support the researcher, it only needs to run once, and it only needs to be bug free in the cases that are being explored. The product is a graph or chart or sentence describing the results that is put into a paper that gets published; the code itself is just a tool.

    When I got my Ph.D. in the 1990s, I didn't understand this, and it brought be a lot of grief when I went to a research lab and interacted with software developers and managers, who didn't understand this either. The grief comes about because of the different approaches used during the development of each type of code. Software developers describe their process variously as a waterfall model, agile development model, etc.. These processes describe a roadmap, with milestones, and a set of activities that visualize the project at its end, and lead towards robust software development. The process a researcher uses is related to the scientific method: based on the question, they formulate a hypothesis, create an experiment, test it, observe the results, and then ask more questions. They do not always know how things will turn out, and they build their path as they go along. Very often, the equivalent "roadmap" in a researchers mind is incomplete and is developed during the process, because this is part of what is being explored.

    In my organization, this makes tremendous conflict between software developers, who want a careful, process driven model to produce robust code, and researchers, who are seeking to answer more basic questions and explore unknown territory in a way that has a great deal of uncertainty and cannot always easily deliver specific milestones and clarity into schedule that is often desired.

    It is worse when the research results in a useful algorithm; of course, the researcher often wants to make it available to the world so that others can use it. This is more of a grey area; if the researcher knows how to do software engineering, they may go through the process to create a more robust product, but this takes effort and time. The fact that Mozilla wants to help debug scientific code is a very good thing; it often needs more serious debugging and re-architecting than other software that is openly available.

    I wish more people understood this difference.

  • Re:Wrong objective. (Score:3, Informative)

    by Macchendra (2919537) on Wednesday September 25, 2013 @08:02AM (#44946517)
    It is easier to find bugs in code where all of the objects, variables, methods, etc. are named according to their actual purpose. It is easier for other researchers to integrate their own ideas if the code is self documenting. It is easier to integrate with other software if the interfaces are cleanly defined. It is easier to verify the results of intermediate steps if there is proper encapsulation. Also, proper encapsulation reduces the chances of unintended side-effects when data is modified outside of scope.
  • by umafuckit (2980809) on Wednesday September 25, 2013 @10:53AM (#44948307)

    For example, someone using default settings on a principal component analysis package not understanding that the package expects the user to have pre-processed the data; the output looks fine but it is wrong.

    I'm a biologist who learned enough computational stats to get by and I do see what you mean. Initially I did do stuff like that, but over time I put in the effort to learn what's going on and now I hope I make these sorts of dumb mistakes a lot less often! However this is not so much a coding problem, but a stats problem. People in the "soft sciences" don't just have problems with more advanced stuff such as PCA, ICA, clustering, etc, but even simple stats. For example, it's very common to see ANOVA performed on data that would be much better suited to regression analysis. The concept of fitting a line or curve and extracting meaning from the coefficients is rather foreign to a lot of biologists, who are more comfortable with a table full of p-values. Indeed, there is a general fixation on p-values, despite the fact that these are not well understood. There is a tendency to hide raw data (since biological data are often noisy). There is also a tendency to use analyses such as PCA or hierarchical clustering simply to produce fancy plots to blind reviewers; these plots often add no insight (or the insight they might add is not explored).

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