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Talk presented at the SIAM CSE23 conference MS321 An Update on Software Engineering for Science Abstract: Two important tendencies in scientific research are the increasing importance of computational modelling and the nascent Open Science movement. Together, they force us to revise the way scientists and non-scientists use computational tools and models, as all stakeholders must be able to develop trust in these tools and models at their respective levels of domain knowledge and engagement. Today's software engineering techniques, inherited from an industrial context, focus on small development teams creating computational tools for a large number of users that interact with the tools at a much more abstract level. Software developers thus become gatekeepers of the computational models that are embedded in these tools, which mere users can neither fully understand nor safely modify. Open Science requires reducing this epistemic opacity, allowing all stakeholders to interact with computational models at their level of scientific rather than technical expertise. A strategy that I have been exploring is moving the models out of the tools and into the human-computer interface in the form of specifications. The central user interface of such a future scientific computing environment is an authoring tool for a computational medium that can represent models. Computational tools operate on this medium, reading models and parameters from it and adding back their results. I will conclude my presentation with a demonstration of a prototype implementation.

Guix is described as a package manager and a GNU/Linux distribution. While technically correct, this summary hides the fact that Guix is a valuable support tool for reproducible computational research, as an add-on to any GNU/Linux distribution, much like many of us currently use Docker containers. I will attempt to convince you that Guix is a better choice than Docker, and show you how to get started with integrating Guix into your computational work environment.

Guix-HPC is a collaborative effort to bring reproducible software deployment to scientific workflows and high-performance computing (HPC). Guix-HPC builds upon the GNU Guix software deployment tool and aims to make it a better tool for HPC practitioners and scientists concerned with reproducible research. This report highlights key achievements of Guix-HPC between our previous report a year ago and today, February 2022. This report highlights developments on GNU Guix proper, but also downstream on Guix-Jupyter, the Guix Workflow Language, upstream with Software Heritage integration, as well as experience reports on end-to-end reproducible research article authoring pipelines.

International audience

International audience; Over the last years, the need for better user interfaces in scientific computing has become apparent by the enormous growth in popularity of computational notebooks. However, the user experience provided by these notebooks is very limited compared to the live programming environments of Smalltalk, and first studies on how they are actually used in research studies point out various weaknesses. We present the first steps we have taken towards building a scientific workbench in Pharo, based on the Glamorous Toolkit, and outline future developments towards that goal.

International audience

Editorial

International audience; Using a simple data analysis as an example, the author explores the relative merits of general-purpose library code and code written for a specific narrow application scenario.

Presentation of the ReScience journal given at Loria Laboraty in April 2018.

Correspondence; International audience; As computational scientists who are unsatisfied with the current level of quality control concerning computational work, we applaud Nature's recently announced initiative to encourage the submission of code accompanying an article, and have it checked by reviewers. We hope that more journals will follow Nature's lead. As editors-in-chief of ReScience (http://rescience.github.io/), a journal dedicated to computational replications, we regularly supervise code reviews. Our experience is that they require significant changes to the traditional reviewing process. An effective code review is possible only if reviewers can both run and inspect the software. We therefore consider the submission of source code mandatory. Moreover, inspection of the source code requires that reviewers have experience with software development in addition to scientific domain expertise. ReScience selects reviewers both according to their scientific discipline and according to their familiarity with programming languages. The first step of a code review consists of reproducing the figures and/or tables from the submitted article using the suppled software. This requires that the authors provide all input files and datasets, and clear instructions. Nevertheless, in our experience, technical problems in installing and running scientific software are inevitable. They are resolved most efficiently if authors and reviewers can communicate rapidly and interactively, without the intervention of the editorial staff. ReScience uses an open reviewing approach conducted on the GitHub platform, which has proven to be very effective. A more detailed account of our experience with publishing computational replications in ReScience can be found in PeerJ Computer Science. 2017 Dec 18;3:e142 (doi:10.7717/peerjcs.142). The currently ongoing reviews at ReScience can be viewed at https://github.com/ReScience/ReScience-submission/pulls.

A brief idea

When combined with community specific conventions and application-specific semantics, the Hierarchical Data Format (HDF) provides a robust and reliable foundation that many scientific communities rely on for interoperability and high-performance storage of metadata and data. This foundation addresses many technical obstacles related to sustainable data and software, critical steps towards sustainable science. Building on successes across the communities that are using, or could use, HDF5 successfully, requires significant community engagement and development efforts that are outside of the scope of traditional software development projects in research and non-profit organizations like The HDF Group. Identifying individuals and organizations that are already doing the right things and bringing them together to share best practices for funding and executing these activities is an important step towards our shared goal of sustainable science.

Poster presented at the French conference "Journées Nationales GDR GPL 2014" in Paris.

A method for the flexible docking of high resolution atomic structures into lower resolution densities derived from electron microscopy is presented. The atomic structure is deformed by an iterative process using combinations of normal modes to obtain the best fit of the electron microscopical density. The quality of the computed structures have been evaluated by several techniques borrowed from crystallography. Two atomic structures of the SERCA1 Ca-ATPase correponding to different conformations were used as a starting point to fit the electron density corresponding to a different conformation. The fitted models have been compared to published models obtained by rigid domain docking, and their relation to the known crystallographic structures are explored by normal mode analysis. We find that only a few number of modes contribute significantly to the transition. The associated motions involve almost exclusively rotation and translation of the cytoplamic domains as well as displacement of cytoplasmic loops. We suggest that the movements of the cytoplasmic domains are driven by the conformational change that occurs between non-phosphorylated and phosphorylated intermediate, the latter being mimicked by the presence of vanadate at the phosphorylation site in the electron microscopy structure.

This is the manual for the Numeric software package for array computing with Python. Numeric was the predecessor to NumPy.

International audience; Aspartate transcarbamylase (ATCase) initiates the pyrimidine biosynthetic pathway in Escherichia coli. Binding of aspartate to this allosteric enzyme induces a cooperative transition between the tensed (T) and relaxed (R) states of the enzyme which involves large quaternary and tertiary rearrangements. The mechanisms of the transmission of the regulatory signal to the active site (60 A away) and that of the cooperative transition are not known in detail, although a large number of single, double, and triple site-specific mutants and chimeric forms of ATCase have been obtained and kinetically characterized. A previous analysis of the very low-frequency normal modes of both the T and R state structures of ATCase identified some of the large-amplitude motions mediating the intertrimer elongation and rotation that occur during the cooperative transition (Thomas et al., J. Mol. Biol. 257:1070-1087, 1996; Thomas et al., J. Mol. Biol. 261:490-506, 1996). As a complement to that study, the deformation of the quaternary and tertiary structure of ATCase by normal modes below 5 cm(-1) is investigated in this article. The ability of the modes to reproduce the domain motions occurring during the transition is analyzed, with special attention to the interdomain closure in the catalytic chain, which has been shown to be critical for homotropic cooperativity. The calculations show a coupling between the quaternary motions and more localized motions involving specific residues. The particular dynamic behavior of these residues is examined in the light of biochemical results to obtain insights into their role in the transmission of the allosteric signal.