• 三维重构体图像去噪软件 冷冻电子断层成像技术(Cryo-ET)适用于原位结构解析这一电镜成像领域研究最前沿的方向,是新冠病毒整体解析的主要技术,可进行大分子、病毒体的原位状态直接观测。受限于成像设备以及电子剂量等因素,冷冻电子断层重构体图像通常会表现出低信噪比以及低衬度的特性,从而会影响到下游任务的分析与计算。此外,不同于单颗粒电镜图像,断层图像的数据量通常是有限的,并且断层图像中缺乏明确的ground truth的定义,依赖大数据集的有监督深度学习算法将很难适配到断层图像去噪问题当中。为了解决以上问题,我们提出了一种稀疏约束的自监督冷冻电子断层图像去噪网络Sparsity Constrained Network (SC-Net)。通过结合盲点替换的自监督数据构造与基于一阶导数的稀疏性约束,SC-Net实现了单样本训练数据下的自监督深度去噪模型。在保证训练效率的同时也保证了相对可靠的结构恢复与噪声抑制。与最先进的Noise2Void方案相比,我们的方法有着更为可靠的结构恢复性能,与大数据驱动的Topaz相比,我们的方法在低数据量情形下取得了相近的性能。

    Categories Structure refinementTool Type: ApplicationTechnologies: Python3Download Count: 1972
  • VP-Detector 三维颗粒定位和分类软件 冷冻电子断层三维重构技术(cryo-ET)允许以分子分辨率对蛋白质或大分子复合物在其原始环境中进行三维可视化,极大地促进了结构生物学的发展。电子断层三维重构是通过旋转生物样品的倾斜系列成像产生的。然而,电子断层三维重构的分辨率受到两个因素的限制:低电子剂量导致的图像低信噪比(SNR)和倾斜角缺失导致的楔形缺失。当一组电子断层图像中出现感兴趣的复合物的众多噪声副本时,子区域平均技术(STA)可以通过提取、分类、对齐和平均在原始生物环境中的子区域来显著提高其分辨率。作为STA过程的前两个步骤,子区域定位和分类对于提高子区域的最终分辨率至关重要。因为低分辨率的电子断层重构和生物大分子形状大小各异,从复杂和拥挤的原始环境中提取和分类大分子是一个挑战。为了解决STA结构测定的瓶颈问题,我们设计了一种基于三维多尺度密集卷积神经网络(3D MSDNet)的生物大分子定位及分类方法VP-Detector,首先,为了检测低信噪比的冷冻电镜图像中的三维颗粒,我们的网络中提出了三维混合膨胀卷积3D HDC技术,避免了缩放操作造成的分辨率损失。其次,为了在数量有限的冷冻电镜图像上进行训练,本方法采用三维稠密连接,以此鼓励重用特征图,减少可训练参数,实现小数据集上的训练。最后,为了缓解了尺寸各异的颗粒造成的类别不平衡,本方法使用加权焦点损失函数进行网络的训练。我们的VP-Detector在模拟数据集和真实世界数据集的实验中都取得了最先进的性能。VP-Detector在三维颗粒挑选方面取得了最高的F1得分,对于形态大小各异的蛋白质均有良好表现,且可代替手动三维颗粒挑选。VP-Detector可以在很少可训练参数的情况下获得较高的粒子检测精度,并支持小数据集上的训练。它还可以缓解形状大小各异的颗粒造成的类不平衡。

    Categories Protein structure refinementTool Type: ApplicationTechnologies: Python3Download Count: 2055
  • PanGraphViewer Show panenome graphs in an easy way

    Categories Variant visualization, Assembly visualizationTool Type: ApplicationTechnologies: Python3Download Count: 1001
  • ARTISTA Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas

    Categories Other toolsTool Type: ToolkitTechnologies: Python3, RDownload Count: 458
  • DeepNoise: Signal and Noise Disentanglement via Deep Learning DeepNoise: Signal and Noise Disentanglement via Deep Learning

    Categories Image analysisTool Type: ApplicationTechnologies: Python3Download Count: 370
  • scEMAIL A source-free and universal cell-type annotation tool

    Tool Type: ApplicationTechnologies: Python3Download Count: 509
  • DGMP Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data

    Categories Driver mutation prioritizationTool Type: Pipeline & ProtocolTechnologies: Python3Download Count: 489
  • SmartGate SmartGate is a spatial metabolomics tool for resolving tissue structures

    Categories Other toolsTool Type: ApplicationTechnologies: Python3Download Count: 232
  • AB-Gen A tool for antibody library design

    Tool Type: ApplicationTechnologies: Python3Download Count: 827
  • DeepETPicker A deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms

    Categories Other toolsTool Type: ToolkitTechnologies: Python3Download Count: 327
  • ART 蛋白质任意分辨率粗粒化模型建立

    Tool Type: ApplicationTechnologies: Python3Download Count: 367
  • DeepAI A deep learning-based isotropic super-resolution method for volume electron microscopy image

    Categories Super-resolution imagingTool Type: ToolkitTechnologies: Python3Download Count: 275
  • SFBMT A fast super-resolution imaging technique based on single-molecule localization and deep learning

    Categories Super-resolution imagingTool Type: ToolkitTechnologies: Python3Download Count: 256
  • HPC-Atlas Computationally Constructing A Comprehensive Atlas of Human Protein Complexes

    Categories Biological network reconstructionTool Type: FrameworkTechnologies: Python2, Python3Download Count: 357
  • GSA_STAT_reads_classification Using STAT in GSA database for short reads classification

    Categories Unclassified toolsTool Type: ApplicationTechnologies: BASH, C++, Python3Download Count: 217
  • SolCuration A tool for aqueous solubility dataset curation

    Tool Type: ApplicationTechnologies: C++, Python3Download Count: 111
  • GraphPolish A tool for molecular optimization

    Tool Type: ApplicationTechnologies: Python3Download Count: 114
  • TraP2 A tool for generates high-fidelity explanations from GNN models

    Tool Type: ApplicationTechnologies: Python3Download Count: 98
  • DeepAAI A tool for identifying antigen-antibody interactions

    Tool Type: ApplicationTechnologies: Python3Download Count: 177
  • AdaPPI A tool for Identifying protein functional modules

    Tool Type: ApplicationTechnologies: Python3Download Count: 115
  • DMA A software for miRNA-disease association network analysis system

    Tool Type: ApplicationTechnologies: Python3Download Count: 97
  • FP-Zernike calculate zernike descriptors for structual analysis

    Categories Other toolsTool Type: ToolkitTechnologies: Python3Download Count: 141
  • DVsc an automated framework for Detecting Viral infection

    Categories Virus detectionTool Type: FrameworkTechnologies: Python3Download Count: 178
  • stMVC Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning

    Categories Other toolsTool Type: ToolkitTechnologies: Python3Download Count: 173
  • scMVAE Deep joint-leaning single-cell multi-omics model

    Tool Type: ToolkitTechnologies: Python3Download Count: 121