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Python code to simulate formose reaction in osmotically coupled droplets, and associated data, related to the article "Emergent fitness and ecological dynamics of compartmentalised autocatalytic chemical reactions" by Heng Lu, Alex Blokhuis, Rebecca Turk-MacLeod, Jayaprakash Karuppusamy, Andrea Franconi, Gabrielle Woronoff, Cyrille Jeancolas, Afshin Abrishamkar, Estelle Loire, Fabien Ferrage, Philippe Pelupessy, Ludovic Jullien, Eörs Szathmary, Philippe Nghe and Andrew. D. Griffiths This software is distributed under the Creative Commons International 4.0 License.

ContinuousFlex allows analyzing single particle cryo electron microscopy data and in vitro and in situ cryo electron subtomogram data for continuous conformational variability of biomolecular complexes. It has been developed as a plugin of Scipion 3 software (https://github.com/scipion-em/scipion-em-continuousflex). Currently, ContinuousFlex provides HEMNMA, StructMap, HEMNMA-3D and TomoFlow methods. HEMNMA: Hybrid Electron Microscopy Normal Mode Analysis method to interpret heterogeneity of a set of single particle cryo-EM images in terms of continuous macromolecular conformational transitions [1-3] StructMap: Structural Mapping method to interpret heterogeneity of a set of single particle cryo-EM maps in terms of continuous conformational transitions [4] HEMNMA-3D: Extension of HEMNMA to continuous conformational variability analysis of macromolecules from in situ cryo-ET subtomograms [5,7] TomoFlow: Method for analyzing continuous conformational variability of macromolecules in in vitro and in situ cryogenic subtomograms based on 3D dense optical flow [8-9] Notes: The plugin additionally provides the test data and automated tests of the protocols in Scipion 3. The following two types of tests of HEMNMA and HEMNMA-3D can be produced by running, in the terminal, "scipion3 tests continuousflex.tests.test_workflow_HEMNMA" and “scipion3 tests continuousflex.tests.test_workflow_HEMNMA3D”, respectively: (1) tests of the entire protocol with the flexible references coming from an atomic structure and from an EM map; and (2) test of the alignment module (test run using 5 MPI threads). The automated tests of the TomoFlow method are also available and can be run using "scipion3 tests continuousflex.tests.test_workflow_TomoFlow". HEMNMA additionally provides tools for synthesizing noisy and CTF-affected single particle cryo-EM images with flexible or rigid biomolecular conformations, for several types of conformational distributions, from a given atomic structure or an EM map. One part of the noise is applied on the ideal projections before and the other after the CTF, as described in [6]. HEMNMA-3D additionally provides tools for synthesizing noisy, CTF and missing wedge affected cryo-ET tomograms and single particle subtomograms with flexible or rigid biomolecular conformations, for several types of conformational distributions, from a given atomic structure or an EM map. One part of the noise is applied on the ideal projections before and the other after the CTF, as described in [6]. A reproduction of some utility codes with their corresponding licenses are contained in this plugin for subtomogram averaging, missing wedge correction, denoising and data reading. These codes are not used in the methods above, but they are made optional for data preprocessing and visualization. References: [1] Jin Q, Sorzano CO, de la Rosa-Trevin JM, Bilbao-Castro JR, Nunez-Ramirez R, Llorca O, Tama F, Jonic S: Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes. Structure 2014, 22:496-506. [2] Jonic S: Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images. Curr Opin Struct Biol 2017, 43:114-121. [3] Harastani M, Sorzano CO, Jonic S: Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Protein Sci 2020, 29:223-36. [4] Sanchez Sorzano CO, Alvarez-Cabrera AL, Kazemi M, Carazo JM, Jonic S: StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes. Biophys J 2016, 110:1753-1765. [5] Harastani M, Eltsov M, Leforestier A, Jonic S: HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes. Front Mol Biosci 2021, 8:663121. [6] Jonic S, Sorzano CO, Thevenaz P, El-Bez C, De Carlo S, Unser M: Spline-based image-to-volume registration for three-dimensional electron microscopy. Ultramicroscopy 2005, 103:303-317. [7] Harastani M and Jonic S: Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification. BioRxiv 2021 (https://doi.org/10.1101/2021.10.14.464366) [8] Harastani M, Eltsov M, Leforestier A, Jonic S: TomoFlow: Analysis of continuous conformational variability of macromolecules in cryogenic subtomograms based on 3D dense optical flow. J Mol Biol 2021, 167381. [9] Harastani M and Jonic S: Synthetic cryo electron subtomograms containing biomolecular complexes with continuous conformational variability.[Data set] Zenodo. 2021 (https://doi.org/10.5281/zenodo.5718820).

This repository contains the formalization of a transient stack and its iterator, as described in the CPP'22 paper "Specification and Verification of a Transient Stack".

KINEBEC is a simulation code developed in C dedicated to classical and quantum Boltzmann equations in 2D and 3D in velocity.This code is based on spectral methods in velocity and can uses MPI, OpenMP or CUDA tools for speeding up its execution and for managing large data.More details about the involved numerical methods can be found in the following papers:* Mouhot & Pareschi: *Fast algorithms for computing the Boltzmann collision operator*, Math. Comput. **256**-75 (2006), pp. 1833-1852* Filbet, Hu & Jin: *A numerical scheme for the quantum Boltzmann equation with stiff*, collision terms, Math. Model. Numer. Anal. **46** (2012), pp. 443-463

An Open Source System, Energy and Network Monitoring Tools at the O/S level

Vincent Bouchitté was one of my former professors at Ecole Normale Supérieure de Lyon (France). He taught me deep and excellent fundamental results of graph theory, lattices and orders. Thanks to his courses, we were able to produce fundamental results on code optimisation published in the following article:Sid Touati. Register Saturation in Instruction Level Parallelism. International Journal of Parallel Programming, Springer-Verlag, Volume 33, Issue 4, August 2005. 57 pages.Vincent Bouchitté was member of the LIP laboratory at Ecole Normale Supérieure de Lyon. He died after a long disease. He was 47 years old. Very discrete, he was very appreciated by all his colleagues and students. He leaves major results in graph theory and advised beautiful Ph.D. theses. He was buried at Salindre in France, his birthplace, on March 15th, 2005.In memory of him, I implemented Dilworth decomposition. Vincent Bouchitté taught us beautiful algorithms and formal proofs on the subject.

This is a generic C++ library that handles data dependence graphs (DDG) for optimising compilation. It is built on top of the LEDA graph library (from algorithmic-solutions company). Our graph library is specially though for research purposes where people are willing to make quick, robust and modular implementations of code optimisation techniques for basic blocks and simple innermost loops (modeled by regular mono-dimensional data dependences). We manage directed acyclic graphs (DAGs) for basic blocks and cyclic graphs for innermost loops. The user is able to take advantage of many standard algorithms for graphs. Also, numerous algorithms on data dependence graphs are implemented. It is also possible to configure the library for different instruction set architectures, and multiple register types.