Computational tools
Computational tools
DDN3.0: An open-source software tool to determine significant rewiring of biological network structures
Complex diseases are often caused and characterized by the misregulation of multiple biological pathways. Differential network analysis enables joint inference of common and rewired biological network structures under different conditions. DDN3.0 provides basic functions to identify a network of significantly rewired molecular players potentially responsible for phenotypic transitions.
Download and installation instructions: https://github.com/cbil-vt/DDN3
Fu Y, Lu Y, Wang Y, Zhang B, Zhang Z, Yu G, Liu C, Clarke R, Herrington DM, Wang Y. DDN3.0: determining significant rewiring of biological network structure with differential dependency networks Bioinformatics. 2024 Jun 3;40(6):btae376. doi: 10.1093/bioinformatics/btae376. PMID: 38902940; PMCID: PMC11199198.
AQuA2: A fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals
AQuA2 (Activity Quantification and Analysis 2) is a fast, accurate, and versatile data analysis platform built upon advanced machine learning techniques. AQuA2 allows for the quantification of spatiotemporal signals across biosensors, cell types, organs, animal models, and imaging modalities. Developed by Axel Nimmerjahn and Guoqiang Yu’s groups, AQuA2 is available for MATLAB and as a Fiji plugin.
Download and installation instructions: https://github.com/yu-lab-vt/AQuA2?tab=readme-ov-file
Mi X, Chen ABY, Duarte D, Carey E, Taylor CR, Braaker PN, Bright M, Almeida RG, Lim JX, Rutten VM, Zheng W, Wang M, Reitman ME, Wang Y, Poskanzer KE, Lyons DA, Nimmerjahn A, Misha Ahrens MB, Yu G. Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals bioRxiv 2024.05.02.592259; doi:https://doi.org/10.1101/2024.05.02.592259.
BILCO: An Efficient Algorithm for Joint Alignment of Time Series
BILCO (BIdirectional pushing with Linear Component Operations) is an efficient algorithm developed by Guoqiang Yu’s group to solve joint alignment problems of time series and min-cut for GTW graphs. BILCO has the same theoretical time complexity as the most popular methods, such as HIPR. However, it provides a significant empirical efficiency boost without sacrificing the accuracy of joint alignment. In thousands of datasets under various simulated scenarios and real application cases, BILCO is around 10 to 50 times faster and only costs 1/10 memory compared to the best peer methods.
Download and installation instructions: https://github.com/yu-lab-vt/BILCO.
Mi X, Wang M, Chen ABY, Lim JX, Wang Y, Ahrens M, Yu G. BILCO: An Efficient Algorithm for Joint Alignment of Time Series. NeurIPS 2022
Synbot: An open-source image analysis software for automated quantification of synapses
Quantifying the number of synaptic contacts from light microscopy images has traditionally been a challenging and time-consuming task, with results varying between experimenters. To overcome these limitations, Cagla Eroglu’s group at Duke University has developed SynBot, a new open-source, ImageJ-based software. SynBot addresses the technical bottlenecks of traditional synapse quantification analysis by automating several stages of the process and incorporates the machine learning algorithm ilastik, which enables accurate thresholding for synaptic puncta identification. Additionally, the software’s code is easily modifiable, allowing users to adapt it to their specific needs.
Download and installation instructions: https://github.com/Eroglu-Lab/Syn_Bot
Savage JT, Ramirez J, Christopher Risher W, Wang Y, Irala D, Eroglu C. SynBot: An open-source image analysis software for automated quantification of synapses. bioRxiv [Preprint]. 2024 Apr 4:2023.06.26.546578. doi: 10.1101/2023.06.26.546578. PMID: 37425715; PMCID: PMC10327002.