These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
7. sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. Angelin-Bonnet O; Biggs PJ; Baldwin S; Thomson S; Vignes M Bioinformatics; 2020 May; 36(9):2938-2940. PubMed ID: 31960894 [TBL] [Abstract][Full Text] [Related]
8. PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Papadopoulos N; Gonzalo PR; Söding J Bioinformatics; 2019 Sep; 35(18):3517-3519. PubMed ID: 30715210 [TBL] [Abstract][Full Text] [Related]
9. RSSALib: a library for stochastic simulation of complex biochemical reactions. Thanh VH Bioinformatics; 2020 Sep; 36(18):4825-4826. PubMed ID: 32614393 [TBL] [Abstract][Full Text] [Related]
10. PSiTE: a Phylogeny guided Simulator for Tumor Evolution. Yang H; Lu B; Lai LH; Lim AH; Alvarez JJS; Zhai W Bioinformatics; 2019 Sep; 35(17):3148-3150. PubMed ID: 30649258 [TBL] [Abstract][Full Text] [Related]
11. POPdemog: visualizing population demographic history from simulation scripts. Zhou Y; Tian X; Browning BL; Browning SR Bioinformatics; 2018 Aug; 34(16):2854-2855. PubMed ID: 29590339 [TBL] [Abstract][Full Text] [Related]
12. MEANS: python package for Moment Expansion Approximation, iNference and Simulation. Fan S; Geissmann Q; Lakatos E; Lukauskas S; Ale A; Babtie AC; Kirk PD; Stumpf MP Bioinformatics; 2016 Sep; 32(18):2863-5. PubMed ID: 27153663 [TBL] [Abstract][Full Text] [Related]
13. J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. Angaroni F; Guidi A; Ascolani G; d'Onofrio A; Antoniotti M; Graudenzi A BMC Bioinformatics; 2022 Jul; 23(1):269. PubMed ID: 35804300 [TBL] [Abstract][Full Text] [Related]
14. Vivarium: an interface and engine for integrative multiscale modeling in computational biology. Agmon E; Spangler RK; Skalnik CJ; Poole W; Peirce SM; Morrison JH; Covert MW Bioinformatics; 2022 Mar; 38(7):1972-1979. PubMed ID: 35134830 [TBL] [Abstract][Full Text] [Related]
15. STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Kierzek AM Bioinformatics; 2002 Mar; 18(3):470-81. PubMed ID: 11934747 [TBL] [Abstract][Full Text] [Related]
16. Axe: rapid, competitive sequence read demultiplexing using a trie. Murray KD; Borevitz JO Bioinformatics; 2018 Nov; 34(22):3924-3925. PubMed ID: 29868827 [TBL] [Abstract][Full Text] [Related]