Data and output files for the paper, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome"

The above files contain the output of the model, which we call MDSINE2, developed in the paper titled, "<em>Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome</em>" (See https://github.com/gerberlab/MDSINE2_Paper for implementation details). More specifically, forward_sims.tgz contains the output of forward simulations in .npy format; mixed_prior_fixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for fixed topology; mixed_prior_unfixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for unfixed topology; other_files contains information on eigenvalues and cycles, results for Phylogenetic Neighborhood Analysis, Keystoneness Analysis and the output in .npy format for comparator methods; ASV_OTU_aggregate_and_plylogeneteic trees contains the plots of trajectories (relative abundance) of OTUS and their constituent ASVs, and of phylogenetic trees.上述文件包含某模型的输出结果，我们将该模型命名为MDSINE2，其相关研究成果发表于题为《大规模动力学系统推断揭示失调微生物组的内在不稳定性》（Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome）的论文，实现细节可参见https://github.com/gerberlab/MDSINE2_Paper。具体而言，forward_sims.tgz 包含以.npy格式存储的正向模拟输出结果；mixed_prior_fixed.tgz 包含对应固定拓扑结构下马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）模拟结果的pickle文件；mixed_prior_unfixed.tgz 包含对应非固定拓扑结构下MCMC模拟结果的pickle文件；other_files 包含特征值与循环周期相关信息、系统发育邻域分析（Phylogenetic Neighborhood Analysis）与关键物种分析（Keystoneness Analysis）的结果，以及对比方法的.npy格式输出文件；ASV_OTU_aggregate_and_plylogeneteic trees 包含操作分类单元（Operational Taxonomic Unit, OTU）及其组成的扩增子序列变体（Amplicon Sequence Variant, ASV）的相对丰度轨迹图，以及系统发育树的可视化结果。